From 6df80c3396869b7a006c6e2cb1a66096a5c14780 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 7 Nov 2023 17:43:22 +0000 Subject: [PATCH 01/66] extended the geometry transport to cover curved edge and faces case --- .../geometry_transport/packed_geom_2d.hpp | 78 ++++++++++++++----- .../particle_mesh_interface.hpp | 5 -- test/CMakeLists.txt | 1 + 3 files changed, 61 insertions(+), 23 deletions(-) diff --git a/include/nektar_interface/geometry_transport/packed_geom_2d.hpp b/include/nektar_interface/geometry_transport/packed_geom_2d.hpp index 8a299026..8a6d09fe 100644 --- a/include/nektar_interface/geometry_transport/packed_geom_2d.hpp +++ b/include/nektar_interface/geometry_transport/packed_geom_2d.hpp @@ -89,6 +89,31 @@ class PackedGeom2D { push(&id); push(&num_edges); + auto lambda_pack_curve = [&](const auto curve) { + GeomPackSpec gs; + if (curve == nullptr) { + gs.a = 0; + gs.b = 0; + gs.n_points = -1; + } else { + gs.a = curve->m_curveID; + gs.b = static_cast(curve->m_ptype); + gs.n_points = curve->m_points.size(); + } + push(&gs); + if (curve != nullptr) { + const int n_points = curve->m_points.size(); + for (int pointx = 0; pointx < n_points; pointx++) { + auto point = curve->m_points.at(pointx); + PointStruct ps; + ps.coordim = point->GetCoordim(); + ps.vid = point->GetVid(); + point->GetCoords(ps.x, ps.y, ps.z); + push(&ps); + } + } + }; + GeomPackSpec gs; PointStruct ps; @@ -112,22 +137,13 @@ class PackedGeom2D { // curve of the edge auto curve = seg_geom->GetCurve(); - ASSERTL0(curve == nullptr, "Not implemented for curved edges"); // A curve with n_points = -1 will be a taken as non-existant. - gs.a = 0; - gs.b = 0; - gs.n_points = -1; - push(&gs); + lambda_pack_curve(curve); } // curve of geom auto curve = geom.GetCurve(); - ASSERTL0(curve == nullptr, "Not implemented for curved edges"); - // A curve with n_points = -1 will be a taken as non-existant. - gs.a = 0; - gs.b = 0; - gs.n_points = -1; - push(&gs); + lambda_pack_curve(curve); }; // Unpack the data common to both Quads and Triangles. @@ -145,8 +161,33 @@ class PackedGeom2D { ASSERTL0((num_edges == 4) || (num_edges == 3), "Bad number of edges expected 4 or 3"); - GeomPackSpec gs; + // helper lambda to unpack a curve + auto lambda_unpack_curve = + [&](const auto gs) -> SpatialDomains::CurveSharedPtr { + if (gs.n_points < 0) { + return SpatialDomains::CurveSharedPtr(); + } + const int m_curveID = gs.a; + const int m_ptype_int = gs.b; + const LibUtilities::PointsType m_ptype = + static_cast(m_ptype_int); + + const int n_points = gs.n_points; + std::vector m_points; + m_points.reserve(n_points); + for (int pointx = 0; pointx < n_points; pointx++) { + PointStruct ps; + pop(&ps); + m_points.push_back(std::make_shared( + ps.coordim, ps.vid, ps.x, ps.y, ps.z)); + } + auto curve = std::make_shared(m_curveID, m_ptype); + curve->m_points = m_points; + return curve; + }; + PointStruct ps; + GeomPackSpec gs; edges.reserve(num_edges); vertices.reserve(num_edges * 2); @@ -167,20 +208,19 @@ class PackedGeom2D { ps.coordim, ps.vid, ps.x, ps.y, ps.z)); } - // In future the edge might have a corresponding curve pop(&gs); - ASSERTL0(gs.n_points == -1, "unpacking routine did not expect a curve"); + auto curve = lambda_unpack_curve(gs); // actually construct the edge auto edge_tmp = std::make_shared( - edge_id, edge_coordim, vertices.data() + points_offset); + edge_id, edge_coordim, vertices.data() + points_offset, curve); // edge_tmp->Setup(); edges.push_back(edge_tmp); } - // In future the geom might have a curve + // Unpack the curve for the geom if it exists. pop(&gs); - ASSERTL0(gs.n_points == -1, "unpacking routine did not expect a curve"); + this->curve = lambda_unpack_curve(gs); } /* @@ -202,6 +242,7 @@ class PackedGeom2D { std::vector edges; std::vector vertices; + SpatialDomains::CurveSharedPtr curve; public: std::vector buf; @@ -237,7 +278,8 @@ class PackedGeom2D { */ template std::shared_ptr> unpack() { unpack_general(); - std::shared_ptr geom = std::make_shared(this->id, this->edges.data()); + std::shared_ptr geom = + std::make_shared(this->id, this->edges.data(), this->curve); geom->GetGeomFactors(); geom->Setup(); auto remote_geom = std::make_shared>(rank, local_id, geom); diff --git a/include/nektar_interface/particle_mesh_interface.hpp b/include/nektar_interface/particle_mesh_interface.hpp index 00a02772..f9a1d602 100644 --- a/include/nektar_interface/particle_mesh_interface.hpp +++ b/include/nektar_interface/particle_mesh_interface.hpp @@ -858,11 +858,6 @@ class ParticleMeshInterface : public HMesh { MPICHK(MPI_Comm_rank(this->comm, &this->comm_rank)); MPICHK(MPI_Comm_size(this->comm, &this->comm_size)); - NESOASSERT(graph->GetCurvedEdges().size() == 0, - "Curved edge found in graph."); - NESOASSERT(graph->GetCurvedFaces().size() == 0, - "Curved face found in graph."); - auto triangles = graph->GetAllTriGeoms(); auto quads = graph->GetAllQuadGeoms(); std::map> geoms_2d; diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index cb4b2b70..c0214a64 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -46,6 +46,7 @@ set(UNIT_SRC_FILES ${UNIT_SRC}/nektar_interface/test_particle_function_projection_3d.cpp ${UNIT_SRC}/nektar_interface/test_particle_geometry_interface.cpp ${UNIT_SRC}/nektar_interface/test_particle_geometry_interface_3d.cpp + ${UNIT_SRC}/nektar_interface/test_particle_geometry_interface_3d_curved.cpp ${UNIT_SRC}/nektar_interface/test_basis_evaluation.cpp ${UNIT_SRC}/nektar_interface/test_kernel_basis_evaluation.cpp ${UNIT_SRC}/nektar_interface/test_particle_mapping.cpp From 6ad1a54d5c0c4efb58ffaaadb82190c5f03bd86e Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 20 Nov 2023 16:03:29 +0000 Subject: [PATCH 02/66] reimplementation of Bary interpolation in 2D and 3D plus 2D and 3D tests --- CMakeLists.txt | 1 + NESO-Spack | 2 +- .../bary_interpolation/bary_evaluation.hpp | 216 ++++++++++++++++++ .../function_bary_evaluation.hpp | 183 +-------------- .../test_particle_function_evaluation.cpp | 118 ++++++++++ .../test_particle_function_evaluation_3d.cpp | 158 +++++++++++++ ..._particle_geometry_interface_3d_curved.cpp | 166 ++++++++++++++ 7 files changed, 664 insertions(+), 180 deletions(-) create mode 100644 include/nektar_interface/bary_interpolation/bary_evaluation.hpp create mode 100644 test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp diff --git a/CMakeLists.txt b/CMakeLists.txt index 08590c64..c8f794be 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -133,6 +133,7 @@ set(HEADER_FILES ${INC_DIR}/mesh.hpp ${INC_DIR}/nektar_interface/basis_evaluation.hpp ${INC_DIR}/nektar_interface/basis_reference.hpp + ${INC_DIR}/nektar_interface/bary_interpolation/bary_evaluation.hpp ${INC_DIR}/nektar_interface/bounding_box_intersection.hpp ${INC_DIR}/nektar_interface/cell_id_translation.hpp ${INC_DIR}/nektar_interface/coordinate_mapping.hpp diff --git a/NESO-Spack b/NESO-Spack index aacfb840..eb2fab80 160000 --- a/NESO-Spack +++ b/NESO-Spack @@ -1 +1 @@ -Subproject commit aacfb840ac310815a123d4ea385f9e672b26f601 +Subproject commit eb2fab80b23fbf1b55d84169a1f3a528203406f2 diff --git a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp new file mode 100644 index 00000000..69ecb643 --- /dev/null +++ b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp @@ -0,0 +1,216 @@ +#ifndef __BARY_EVALUATION_H__ +#define __BARY_EVALUATION_H__ + +#include +using namespace NESO::Particles; + +namespace NESO::Bary { + +/** + * For quadrature point r_i with weight bw_i compute bw_i / (r - r_i). + * + * @param num_phys The number of quadrature points for the element and + * dimension for which this computation is performed. + * @param[in] coord The evauation point in the dimension of interest. + * @param[in] z_values A length num_phys array containing the quadrature + * points. + * @param[in] z_values A length num_phys array containing the quadrature + * weights. + * @param[in, out] div_values Array of length num_phys which will be + * populated with the bw_i/(r - r_i) values. + */ +inline void preprocess_weights(const int num_phys, const REAL coord, + const REAL *const z_values, + const REAL *const bw_values, REAL *div_values) { + for (int ix = 0; ix < num_phys; ix++) { + div_values[ix] = 0.0; + } + for (int ix = 0; ix < num_phys; ix++) { + const auto xdiff = z_values[ix] - coord; + if (xdiff == 0.0) { + div_values[ix] = 1.0; + return; + } + } + REAL denom = 0.0; + for (int ix = 0; ix < num_phys; ix++) { + const auto xdiff = z_values[ix] - coord; + const auto bw_over_diff = bw_values[ix] / xdiff; + div_values[ix] = bw_over_diff; + denom += bw_over_diff; + } + const REAL factor = 1.0 / denom; + for (int ix = 0; ix < num_phys; ix++) { + div_values[ix] *= factor; + } +} + +/** + * Perform Bary interpolation in the first dimension. This function is + * intended to be called from a function that performs Bary interpolation + * over the second dimension and first dimension. + * + * @param num_phys Number of quadrature points. + * @param physvals Vector of length num_phys plus padding to multiple of the + * vector length which contains the quadrature point values. + * @returns Contribution to Bary interpolation from a dimension 0 evaluation. + */ +inline REAL compute_dir_0(const int num_phys, const REAL *const physvals, + const REAL *const div_space) { + REAL numer = 0.0; + for (int ix = 0; ix < num_phys; ix++) { + const REAL pval = physvals[ix]; + const REAL tmp = div_space[ix]; + numer += tmp * pval; + } + const REAL eval0 = numer; + return eval0; + //} +} + +/** + * Computes Bary interpolation over two dimensions. The inner dimension is + * computed with calls to compute_dir_0. + * + * @param num_phys0 Number of quadrature points in dimension 0. + * @param num_phys1 Number of quadrature points in dimension 1. + * @param physvals Array of function values at quadrature points. + * @param div_space0 The output of preprocess_weights applied to dimension 0. + * @param div_space1 The output of preprocess_weights applied to dimension 1. + * @returns Bary evaluation of a function at a coordinate. + */ +inline REAL compute_dir_10(const int num_phys0, const int num_phys1, + const REAL *const physvals, + const REAL *const div_space0, + const REAL *const div_space1) { + + REAL numer = 0.0; + for (int i1 = 0; i1 < num_phys1; i1++) { + REAL pval = 0.0; + for (int i0 = 0; i0 < num_phys0; i0++) { + pval += physvals[i1 * num_phys0 + i0] * div_space0[i0]; + } + const REAL tmp = div_space1[i1]; + numer += tmp * pval; + } + return numer; +} + +/** + * Computes Bary interpolation over three dimensions. The inner dimensions are + * computed with calls to compute_dir_10. + * + * @param num_phys0 Number of quadrature points in dimension 0. + * @param num_phys1 Number of quadrature points in dimension 1. + * @param num_phys2 Number of quadrature points in dimension 2. + * @param physvals Array of function values at quadrature points. + * @param div_space0 The output of preprocess_weights applied to dimension 0. + * @param div_space1 The output of preprocess_weights applied to dimension 1. + * @param div_space2 The output of preprocess_weights applied to dimension 2. + * @returns Bary evaluation of a function at a coordinate. + */ +inline REAL compute_dir_210(const int num_phys0, const int num_phys1, + const int num_phys2, const REAL *const physvals, + const REAL *const div_space0, + const REAL *const div_space1, + const REAL *const div_space2) { + + const int stride = num_phys0 * num_phys1; + REAL pval2 = 0.0; + for (int i2 = 0; i2 < num_phys2; i2++) { + REAL pval1 = 0.0; + for (int i1 = 0; i1 < num_phys1; i1++) { + REAL pval0 = 0.0; + for (int i0 = 0; i0 < num_phys0; i0++) { + pval0 += physvals[i2 * stride + i1 * num_phys0 + i0] * div_space0[i0]; + } + pval1 += div_space1[i1] * pval0; + } + pval2 += div_space2[i2] * pval1; + } + return pval2; +} + +/** + * Compute a function evaluation at a point using the passed quadrature point + * values, quadrature points and weights. + * + * @param coord0 Evaluation coordinate, x component. + * @param coord1 Evaluation coordinate, y component. + * @param num_phys0 Number of quadrature points in the x direction. + * @param num_phys1 Number of quadrature points in the y direction. + * @param physvals Function evaluations at quadrature points, x runs fastest + * and y slowest. + * @param div_space Space of size num_phys0 + num_phys1 + num_phys2 to use as + * temporary space. + * @param z0 Quadrature points in x direction. + * @param z1 Quadrature points in y direction. + * @param bw0 Weights for each quadrature point in x direction. + * @param bw1 Weights for each quadrature point in y direction. + * @returns Evaluation at passed point using Bary interpolation. + * */ +inline REAL evaluate_2d(const REAL coord0, const REAL coord1, + const int num_phys0, const int num_phys1, + const REAL *const physvals, REAL *div_space, + const REAL *const z0, const REAL *const z1, + const REAL *const bw0, const REAL *const bw1) { + + REAL *div_space0 = div_space; + REAL *div_space1 = div_space0 + num_phys0; + + preprocess_weights(num_phys0, coord0, z0, bw0, div_space0); + preprocess_weights(num_phys1, coord1, z1, bw1, div_space1); + + REAL eval = + compute_dir_10(num_phys0, num_phys1, physvals, div_space0, div_space1); + + return eval; +} + +/** + * Compute a function evaluation at a point using the passed quadrature point + * values, quadrature points and weights. + * + * @param coord0 Evaluation coordinate, x component. + * @param coord1 Evaluation coordinate, y component. + * @param coord2 Evaluation coordinate, z component. + * @param num_phys0 Number of quadrature points in the x direction. + * @param num_phys1 Number of quadrature points in the y direction. + * @param num_phys2 Number of quadrature points in the z direction. + * @param physvals Function evaluations at quadrature points, x runs fastest + * and z slowest. + * @param div_space Space of size num_phys0 + num_phys1 + num_phys2 to use as + * temporary space. + * @param z0 Quadrature points in x direction. + * @param z1 Quadrature points in y direction. + * @param z2 Quadrature points in z direction. + * @param bw0 Weights for each quadrature point in x direction. + * @param bw1 Weights for each quadrature point in y direction. + * @param bw2 Weights for each quadrature point in z direction. + * @returns Evaluation at passed point using Bary interpolation. + */ +inline REAL evaluate_3d(const REAL coord0, const REAL coord1, const REAL coord2, + const int num_phys0, const int num_phys1, + const int num_phys2, const REAL *const physvals, + REAL *div_space, const REAL *const z0, + const REAL *const z1, const REAL *const z2, + const REAL *const bw0, const REAL *const bw1, + const REAL *const bw2) { + + REAL *div_space0 = div_space; + REAL *div_space1 = div_space0 + num_phys0; + REAL *div_space2 = div_space1 + num_phys1; + + preprocess_weights(num_phys0, coord0, z0, bw0, div_space0); + preprocess_weights(num_phys1, coord1, z1, bw1, div_space1); + preprocess_weights(num_phys2, coord2, z2, bw2, div_space2); + + const REAL eval = compute_dir_210(num_phys0, num_phys1, num_phys2, physvals, + div_space0, div_space1, div_space2); + + return eval; +} + +} // namespace NESO::Bary + +#endif diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 97737fc0..b426c090 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -10,6 +10,7 @@ #include #include +#include "bary_interpolation/bary_evaluation.hpp" #include "expansion_looping/geom_to_expansion_builder.hpp" #include "geometry_transport/shape_mapping.hpp" #include "utility_sycl.hpp" @@ -20,172 +21,6 @@ using namespace Nektar::StdRegions; namespace NESO { -namespace Bary { - -/** - * The purpose of these methods is to precompute as much of the Bary - * interpolation algorithm for each coordinate dimension as possible (where - * the cost is O(p)) to minimise the computational work in the O(p^2) double - * loop. - */ -struct Evaluate { - - /** - * For quadrature point r_i with weight bw_i compute bw_i / (r - r_i). - * - * @param[in] stride_base Length of output vector used for temporary storage, - * i.e. the maximum number of quadrature points across all elements plus any - * padding. - * @param num_phys The number of quadrature points for the element and - * dimension for which this computation is performed. - * @param[in] coord The evauation point in the dimension of interest. - * @param[in] z_values A length num_phys array containing the quadrature - * points. - * @param[in] z_values A length num_phys array containing the quadrature - * weights. - * @param[in, out] exact_index If the input coordinate lie exactly on a - * quadrature point then this pointer will be set to the index of that - * quadrature point. Otherwise this memory is untouched. - * @param[in, out] div_values Array of length stride_base which will be - * populated with the bw_i/(r - r_i) values. Entries in the range num_phys to - * stride_base-1 will be zeroed. - */ - static inline void preprocess_weights(const int stride_base, - const int num_phys, const REAL coord, - const REAL *const z_values, - const REAL *const bw_values, - int *exact_index, REAL *div_values) { - const sycl::vec coord_vec{coord}; - - sycl::global_ptr z_ptr{z_values}; - sycl::global_ptr bw_ptr{bw_values}; - sycl::local_ptr div_ptr{div_values}; - - for (int ix = 0; ix * NESO_VECTOR_LENGTH < num_phys; ix++) { - sycl::vec z_vec{}; - z_vec.load(ix, z_ptr); - sycl::vec bw_vec{}; - bw_vec.load(ix, bw_ptr); - const auto xdiff_vec = z_vec - coord_vec; - const auto bw_over_diff = bw_vec / xdiff_vec; - bw_over_diff.store(ix, div_ptr); - - const int max_index = (((ix + 1) * NESO_VECTOR_LENGTH) <= num_phys) - ? ((ix + 1) * NESO_VECTOR_LENGTH) - : num_phys; - - for (int jx = ix * NESO_VECTOR_LENGTH; jx < max_index; jx++) { - if (xdiff_vec[jx % NESO_VECTOR_LENGTH] == 0.0) { - *exact_index = jx; - } - } - } - - // zero the extra padding values so they do not contribute later - // If they contributed a NaN all results would be NaN. - for (int cx = num_phys; cx < stride_base; cx++) { - div_values[cx] = 0.0; - } - }; - - /** - * In each dimension of the Bary interpolation the sum of the weights over - * distances can be precomputed. - * - * @param num_phys Number of quadrature points. - * @param div_space Values to sum. - * @returns Sum of the first num_phys values of div_space. - */ - static inline REAL preprocess_denominator(const int num_phys, - const REAL *const div_space) { - REAL denom = 0.0; - for (int ix = 0; ix < num_phys; ix++) { - const REAL tmp = div_space[ix]; - denom += tmp; - } - return denom; - }; - - /** - * Perform Bary interpolation in the first dimension. This function is - * intended to be called from a function that performs Bary interpolation - * over the second dimension and first dimension. - * - * @param num_phys Number of quadrature points. - * @param physvals Vector of length num_phys plus padding to multiple of the - * vector length which contains the quadrature point values. Padding should - * contain finite values. - * @param exact_i If exact_i is non-negative then exact_i then it is assumed - * that the evaluation point is exactly the quadrature point exact_i. - * @param denom Sum over Bary weights divided by differences, see - * preprocess_denominator. - * @returns Contribution to Bary interpolation from a dimension 0 evaluation. - */ - static inline REAL compute_dir_0(const int num_phys, - const REAL *const physvals, - const REAL *const div_space, - const int exact_i, const REAL denom) { - if ((exact_i > -1) && (exact_i < num_phys)) { - const REAL exact_quadrature_val = physvals[exact_i]; - return exact_quadrature_val; - } else { - REAL numer = 0.0; - - for (int ix = 0; ix < num_phys; ix++) { - const REAL pval = physvals[ix]; - const REAL tmp = div_space[ix]; - numer += tmp * pval; - } - - const REAL eval0 = numer / denom; - return eval0; - } - }; - - /** - * Computes Bary interpolation over two dimensions. The inner dimension is - * computed with calls to compute_dir_0. - * - * @param num_phys0 Number of quadrature points in dimension 0. - * @param num_phys1 Number of quadrature points in dimension 1. - * @param physvals Array of function values at quadrature points. - * @param div_space0 The output of preprocess_weights applied to dimension 0. - * @param div_space1 The output of preprocess_weights applied to dimension 1. - * @param exact_i0 Non-negative value indicates that the coordinate lies on - * quadrature point exact_i0 in dimension 0. - * @param exact_i1 Non-negative value indicates that the coordinate lies on - * quadrature point exact_i1 in dimension 1. - * @returns Bary evaluation of a function at a coordinate. - */ - static inline REAL compute_dir_10(const int num_phys0, const int num_phys1, - const REAL *const physvals, - const REAL *const div_space0, - const REAL *const div_space1, - const int exact_i0, const int exact_i1) { - const REAL denom0 = - Bary::Evaluate::preprocess_denominator(num_phys0, div_space0); - if ((exact_i1 > -1) && (exact_i1 < num_phys1)) { - const REAL bary_eval_0 = Bary::Evaluate::compute_dir_0( - num_phys0, &physvals[exact_i1 * num_phys0], div_space0, exact_i0, - denom0); - return bary_eval_0; - } else { - REAL numer = 0.0; - REAL denom = 0.0; - for (int ix = 0; ix < num_phys1; ix++) { - const REAL pval = Bary::Evaluate::compute_dir_0( - num_phys0, &physvals[ix * num_phys0], div_space0, exact_i0, denom0); - const REAL tmp = div_space1[ix]; - numer += tmp * pval; - denom += tmp; - } - const REAL eval1 = numer / denom; - return eval1; - } - }; -}; -} // namespace Bary - /** * Evaluate 2D expansions at particle locations using Bary Interpolation. * Reimplements the algorithm in Nektar++. @@ -463,19 +298,9 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { // this cell const auto physvals = &k_global_physvals[k_phys_offsets[cellx]]; - int exact_i0 = -1; - int exact_i1 = -1; - - Bary::Evaluate::preprocess_weights(k_stride_base, num_phys0, - coord0, z0, bw0, &exact_i0, - div_space0); - Bary::Evaluate::preprocess_weights(k_stride_base, num_phys1, - coord1, z1, bw1, &exact_i1, - div_space1); - - const REAL evaluation = Bary::Evaluate::compute_dir_10( - num_phys0, num_phys1, physvals, div_space0, div_space1, - exact_i0, exact_i1); + const REAL evaluation = + Bary::evaluate_2d(coord0, coord1, num_phys0, num_phys1, + physvals, div_space0, z0, z1, bw0, bw1); k_output[cellx][k_component][layerx] = evaluation; } diff --git a/test/unit/nektar_interface/test_particle_function_evaluation.cpp b/test/unit/nektar_interface/test_particle_function_evaluation.cpp index 5eb834e3..7b3f5fd4 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation.cpp @@ -604,3 +604,121 @@ TEST(ParticleFunctionEvaluation, ContFieldDerivative) { delete[] argv[1]; delete[] argv[2]; } + +TEST(BaryInterpolation, Evaluation2D) { + + int argc = 3; + char *argv[3]; + + std::filesystem::path source_file = __FILE__; + std::filesystem::path source_dir = source_file.parent_path(); + std::filesystem::path test_resources_dir = + source_dir / "../../test_resources"; + std::filesystem::path mesh_file = + test_resources_dir / "square_triangles_quads_nummodes_6.xml"; + std::filesystem::path conditions_file = + test_resources_dir / "conditions_cg.xml"; + + copy_to_cstring(std::string("test_particle_function_evaluation"), &argv[0]); + copy_to_cstring(std::string(mesh_file), &argv[1]); + copy_to_cstring(std::string(conditions_file), &argv[2]); + + LibUtilities::SessionReaderSharedPtr session; + SpatialDomains::MeshGraphSharedPtr graph; + // Create session reader. + session = LibUtilities::SessionReader::CreateInstance(argc, argv); + graph = SpatialDomains::MeshGraph::Read(session); + + auto cont_field = std::make_shared(session, graph, "u"); + + auto lambda_f = [&](const NekDouble x, const NekDouble y) { + return 2.0 * (x + 0.5) * (x - 0.5) * (y + 0.8) * (y - 0.8); + }; + interpolate_onto_nektar_field_2d(lambda_f, cont_field); + + const auto global_physvals = cont_field->GetPhys(); + + int rank; + MPICHK(MPI_Comm_rank(MPI_COMM_WORLD, &rank)); + std::mt19937 rng(22123234 + rank); + std::uniform_real_distribution uniform_rng(-0.1, 0.1); + + const int num_elts = cont_field->GetNumElmts(); + Array Lcoord(2); + Array coord(2); + for (int ex = 0; ex < num_elts; ex++) { + auto exp = cont_field->GetExp(ex); + auto geom = exp->GetGeom(); + auto base = exp->GetBase(); + const auto &z0 = base[0]->GetZ(); + const auto &bw0 = base[0]->GetBaryWeights(); + const auto &z1 = base[1]->GetZ(); + const auto &bw1 = base[1]->GetBaryWeights(); + const int num_phys0 = z0.size(); + const int num_phys1 = z1.size(); + const int num_phys = std::max(num_phys0, num_phys1); + std::vector div_space(2 * num_phys); + std::vector z0v(num_phys); + std::vector z1v(num_phys); + std::vector bw0v(num_phys); + std::vector bw1v(num_phys); + for (int ix = 0; ix < num_phys0; ix++) { + z0v[ix] = z0[ix]; + bw0v[ix] = bw0[ix]; + } + for (int ix = 0; ix < num_phys1; ix++) { + z1v[ix] = z1[ix]; + bw1v[ix] = bw1[ix]; + } + const auto physvals = global_physvals + cont_field->GetPhys_Offset(ex); + std::vector physvalsv(num_phys0 * num_phys1); + for (int ix = 0; ix < (num_phys0 * num_phys1); ix++) { + physvalsv[ix] = physvals[ix]; + } + + // check bary eval at all the quad points + for (int p0 = 0; p0 < num_phys0; p0++) { + for (int p1 = 0; p1 < num_phys1; p1++) { + const REAL x0 = z0[p0]; + const REAL x1 = z1[p1]; + coord[0] = x0; + coord[1] = x1; + exp->LocCollapsedToLocCoord(coord, Lcoord); + const REAL correct = exp->StdPhysEvaluate(Lcoord, physvals); + const REAL to_test = Bary::evaluate_2d( + x0, x1, num_phys0, num_phys1, physvalsv.data(), div_space.data(), + z0v.data(), z1v.data(), bw0v.data(), bw1v.data()); + + const REAL err_abs = std::abs(correct - to_test); + const REAL abs_correct = std::abs(correct); + const REAL err_rel = + abs_correct > 0 ? err_abs / abs_correct : abs_correct; + EXPECT_TRUE(err_rel < 1.0e-12 || err_abs < 1.0e-12); + } + } + // check bary eval at away from the quad points + for (int p0 = 0; p0 < num_phys0; p0++) { + for (int p1 = 0; p1 < num_phys1; p1++) { + const REAL x0 = z0[p0] + uniform_rng(rng); + const REAL x1 = z1[p1] + uniform_rng(rng); + coord[0] = x0; + coord[1] = x1; + exp->LocCollapsedToLocCoord(coord, Lcoord); + const REAL correct = exp->StdPhysEvaluate(Lcoord, physvals); + const REAL to_test = Bary::evaluate_2d( + x0, x1, num_phys0, num_phys1, physvalsv.data(), div_space.data(), + z0v.data(), z1v.data(), bw0v.data(), bw1v.data()); + + const REAL err_abs = std::abs(correct - to_test); + const REAL abs_correct = std::abs(correct); + const REAL err_rel = + abs_correct > 0 ? err_abs / abs_correct : abs_correct; + EXPECT_TRUE(err_rel < 1.0e-12 || err_abs < 1.0e-12); + } + } + } + + delete[] argv[0]; + delete[] argv[1]; + delete[] argv[2]; +} diff --git a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp index 31969b6c..7a28f768 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp @@ -178,3 +178,161 @@ TEST(ParticleFunctionEvaluation3D, DisContFieldPrismTet) { "reference_prism_tet_cube/conditions.xml", "reference_prism_tet_cube/prism_tet_cube_0.5_perturbed.xml", 1.0e-7); } + +template +static inline void bary_wrapper_3d(std::string condtions_file_s, + std::string mesh_file_s, const double tol) { + + std::filesystem::path source_file = __FILE__; + std::filesystem::path source_dir = source_file.parent_path(); + std::filesystem::path test_resources_dir = + source_dir / "../../test_resources"; + + std::filesystem::path condtions_file_basename{condtions_file_s}; + std::filesystem::path mesh_file_basename{mesh_file_s}; + std::filesystem::path conditions_file = + test_resources_dir / condtions_file_basename; + std::filesystem::path mesh_file = test_resources_dir / mesh_file_basename; + + int argc = 3; + char *argv[3]; + copy_to_cstring(std::string("test_particle_geometry_interface"), &argv[0]); + copy_to_cstring(std::string(conditions_file), &argv[1]); + copy_to_cstring(std::string(mesh_file), &argv[2]); + + LibUtilities::SessionReaderSharedPtr session; + SpatialDomains::MeshGraphSharedPtr graph; + // Create session reader. + session = LibUtilities::SessionReader::CreateInstance(argc, argv); + graph = SpatialDomains::MeshGraph::Read(session); + + auto field = std::make_shared(session, graph, "u"); + + auto lambda_f = [&](const NekDouble x, const NekDouble y, const NekDouble z) { + return 2.0 * (x + 0.5) * (x - 0.5) * (y + 0.8) * (y - 0.8) * (z + 0.2) * + (z - 0.3); + }; + interpolate_onto_nektar_field_3d(lambda_f, field); + + const auto global_physvals = field->GetPhys(); + + int rank; + MPICHK(MPI_Comm_rank(MPI_COMM_WORLD, &rank)); + std::mt19937 rng(22123234 + rank); + std::uniform_real_distribution uniform_rng(-0.1, 0.1); + + const int num_elts = field->GetNumElmts(); + Array Lcoord(3); + Array coord(3); + for (int ex = 0; ex < num_elts; ex++) { + auto exp = field->GetExp(ex); + auto geom = exp->GetGeom(); + auto base = exp->GetBase(); + const auto &z0 = base[0]->GetZ(); + const auto &bw0 = base[0]->GetBaryWeights(); + const auto &z1 = base[1]->GetZ(); + const auto &bw1 = base[1]->GetBaryWeights(); + const auto &z2 = base[2]->GetZ(); + const auto &bw2 = base[2]->GetBaryWeights(); + const int num_phys0 = z0.size(); + const int num_phys1 = z1.size(); + const int num_phys2 = z2.size(); + const int num_phys = std::max(num_phys0, std::max(num_phys1, num_phys2)); + std::vector div_space(3 * num_phys); + std::vector z0v(num_phys); + std::vector z1v(num_phys); + std::vector z2v(num_phys); + std::vector bw0v(num_phys); + std::vector bw1v(num_phys); + std::vector bw2v(num_phys); + for (int ix = 0; ix < num_phys0; ix++) { + z0v[ix] = z0[ix]; + bw0v[ix] = bw0[ix]; + } + for (int ix = 0; ix < num_phys1; ix++) { + z1v[ix] = z1[ix]; + bw1v[ix] = bw1[ix]; + } + for (int ix = 0; ix < num_phys2; ix++) { + z2v[ix] = z2[ix]; + bw2v[ix] = bw2[ix]; + } + const auto physvals = global_physvals + field->GetPhys_Offset(ex); + std::vector physvalsv(num_phys0 * num_phys1 * num_phys2); + for (int ix = 0; ix < (num_phys0 * num_phys1 * num_phys2); ix++) { + physvalsv[ix] = physvals[ix]; + } + + // check bary eval at all the quad points + for (int p0 = 0; p0 < num_phys0; p0++) { + for (int p1 = 0; p1 < num_phys1; p1++) { + for (int p2 = 0; p2 < num_phys2; p2++) { + const REAL x0 = z0[p0]; + const REAL x1 = z1[p1]; + const REAL x2 = z2[p2]; + coord[0] = x0; + coord[1] = x1; + coord[2] = x2; + exp->LocCollapsedToLocCoord(coord, Lcoord); + const REAL correct = exp->StdPhysEvaluate(Lcoord, physvals); + const REAL to_test = Bary::evaluate_3d( + x0, x1, x2, num_phys0, num_phys1, num_phys2, physvalsv.data(), + div_space.data(), z0v.data(), z1v.data(), z2v.data(), bw0v.data(), + bw1v.data(), bw2v.data()); + + const REAL err_abs = std::abs(correct - to_test); + const REAL abs_correct = std::abs(correct); + const REAL err_rel = + abs_correct > 0 ? err_abs / abs_correct : abs_correct; + EXPECT_TRUE(err_rel < 1.0e-12 || err_abs < 1.0e-12); + } + } + } + + // check bary eval at away from the quad points + for (int p0 = 0; p0 < num_phys0; p0++) { + for (int p1 = 0; p1 < num_phys1; p1++) { + for (int p2 = 0; p2 < num_phys2; p2++) { + const REAL x0 = z0[p0] + uniform_rng(rng); + const REAL x1 = z1[p1] + uniform_rng(rng); + const REAL x2 = z2[p2] + uniform_rng(rng); + coord[0] = x0; + coord[1] = x1; + coord[2] = x2; + exp->LocCollapsedToLocCoord(coord, Lcoord); + const REAL correct = exp->StdPhysEvaluate(Lcoord, physvals); + const REAL to_test = Bary::evaluate_3d( + x0, x1, x2, num_phys0, num_phys1, num_phys2, physvalsv.data(), + div_space.data(), z0v.data(), z1v.data(), z2v.data(), bw0v.data(), + bw1v.data(), bw2v.data()); + + const REAL err_abs = std::abs(correct - to_test); + const REAL abs_correct = std::abs(correct); + const REAL err_rel = + abs_correct > 0 ? err_abs / abs_correct : abs_correct; + EXPECT_TRUE(err_rel < 1.0e-12 || err_abs < 1.0e-12); + } + } + } + } + + delete[] argv[0]; + delete[] argv[1]; + delete[] argv[2]; +} + +TEST(BaryInterpolation, Evaluation3DContField) { + evaluation_wrapper_3d( + "reference_all_types_cube/conditions_cg.xml", + "reference_all_types_cube/mixed_ref_cube_0.5_perturbed.xml", 1.0e-7); +} +TEST(BaryInterpolation, Evaluation3DDisContFieldHex) { + evaluation_wrapper_3d( + "reference_hex_cube/conditions.xml", + "reference_hex_cube/hex_cube_0.3_perturbed.xml", 1.0e-7); +} +TEST(BaryInterpolation, Evaluation3DDisContFieldPrismTet) { + evaluation_wrapper_3d( + "reference_prism_tet_cube/conditions.xml", + "reference_prism_tet_cube/prism_tet_cube_0.5_perturbed.xml", 1.0e-7); +} diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp new file mode 100644 index 00000000..183b21c2 --- /dev/null +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -0,0 +1,166 @@ +#include "nektar_interface/coordinate_mapping.hpp" +#include "nektar_interface/geometry_transport/halo_extension.hpp" +#include "nektar_interface/particle_interface.hpp" +#include "nektar_interface/utility_mesh_plotting.hpp" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace std; +using namespace Nektar; +using namespace Nektar::SolverUtils; +using namespace Nektar::LibUtilities; +using namespace Nektar::SpatialDomains; +using namespace NESO::Particles; + +static inline void copy_to_cstring(std::string input, char **output) { + *output = new char[input.length() + 1]; + std::strcpy(*output, input.c_str()); +} + +TEST(ParticleGeometryInterfaceCurved, Init) { + + int size, rank; + MPI_Comm_size(MPI_COMM_WORLD, &size); + MPI_Comm_rank(MPI_COMM_WORLD, &rank); + + LibUtilities::SessionReaderSharedPtr session; + SpatialDomains::MeshGraphSharedPtr graph; + + int argc = 3; + char *argv[3]; + copy_to_cstring(std::string("test_particle_geometry_interface"), &argv[0]); + + std::filesystem::path source_file = __FILE__; + std::filesystem::path source_dir = source_file.parent_path(); + std::filesystem::path test_resources_dir = + source_dir / "../../test_resources"; + std::filesystem::path conditions_file = + test_resources_dir / "reference_all_types_cube/conditions.xml"; + copy_to_cstring(std::string(conditions_file), &argv[1]); + // std::filesystem::path mesh_file = + // test_resources_dir / "reference_all_types_cube/mixed_ref_cube_0.2.xml"; + + std::filesystem::path mesh_file = + "/home/js0259/git-ukaea/NESO-workspace/reference_all_types_cube/" + "mixed_ref_cube_0.5_perturbed_order_2.xml"; + copy_to_cstring(std::string(mesh_file), &argv[2]); + + // Create session reader. + session = LibUtilities::SessionReader::CreateInstance(argc, argv); + + // Create MeshGraph. + graph = SpatialDomains::MeshGraph::Read(session); + + // build map from owned mesh hierarchy cells to geoms that touch that cell + auto particle_mesh_interface = std::make_shared(graph); + + std::map> geoms; + get_all_elements_3d(graph, geoms); + + auto lambda_stype = [](auto s) -> std::string { + switch (s) { + case eTetrahedron: + return "Tet"; + case ePyramid: + return "Pyr"; + case ePrism: + return "Prism"; + case eHexahedron: + return "Hex"; + default: + return "shape unknown"; + } + }; + + auto lambda_btype = [](auto s) -> std::string { + switch (s) { + case eModified_A: + return "eA"; + case eModified_B: + return "eB"; + case eModified_C: + return "eC"; + case eModifiedPyr_C: + return "ePyrC"; + default: + return "basis unknown"; + } + }; + + for (auto gx : geoms) { + auto geom = gx.second; + auto xmap = geom->GetXmap(); + nprint(geom->GetShapeType(), lambda_stype(geom->GetShapeType())); + nprint("Num bases:", xmap->GetNumBases()); + for (int dx = 0; dx < 3; dx++) { + nprint("dx:", dx, "type:", lambda_btype(xmap->GetBasisType(dx)), + xmap->GetBasisNumModes(dx)); + } + + Array Lcoord(3); + Array Lcoord2(3); + Array Gcoord(3); + Array Gcoord2(3); + Lcoord[0] = -0.05; + Lcoord[1] = -0.05; + Lcoord[2] = -0.05; + + for (int dx = 0; dx < 3; dx++) { + // calls phys evaluate which takes a loc coord not a loc collapsed coord + Gcoord[dx] = geom->GetCoord(dx, Lcoord); + } + + geom->GetLocCoords(Gcoord, Lcoord2); + + for (int dx = 0; dx < 3; dx++) { + // calls phys evaluate which takes a loc coord not a loc collapsed coord + Gcoord2[dx] = geom->GetCoord(dx, Lcoord2); + } + nprint(Lcoord[0], Lcoord[1], Lcoord[2], "\n", Lcoord2[0], Lcoord2[1], + Lcoord2[2], "\n", Gcoord[0], Gcoord[1], Gcoord[2], "\n", Gcoord2[0], + Gcoord2[1], Gcoord2[2], "\n------"); + + auto I0 = xmap->GetBasis(0)->GetI(Lcoord); + auto I1 = xmap->GetBasis(1)->GetI(Lcoord); + auto I2 = xmap->GetBasis(2)->GetI(Lcoord); + + for (auto ix = I0->begin(); ix != I0->end(); ix++) { + nprint(*ix); + } + nprint("-----"); + const int npts = xmap->GetTotPoints(); + Array ptsx(npts), ptsy(npts), ptsz(npts); + xmap->BwdTrans(geom->GetCoeffs(0), ptsx); + xmap->BwdTrans(geom->GetCoeffs(1), ptsy); + xmap->BwdTrans(geom->GetCoeffs(2), ptsz); + + Array eta(3); + xmap->LocCoordToLocCollapsed(Lcoord, eta); + Array I(3); + I[0] = xmap->GetBasis(0)->GetI(eta); + I[1] = xmap->GetBasis(1)->GetI(eta + 1); + I[2] = xmap->GetBasis(2)->GetI(eta + 2); + const auto x = xmap->PhysEvaluate(I, ptsx); + const auto y = xmap->PhysEvaluate(I, ptsy); + const auto z = xmap->PhysEvaluate(I, ptsz); + nprint(x, y, z); + } + + particle_mesh_interface->free(); + delete[] argv[0]; + delete[] argv[1]; + delete[] argv[2]; +} From 6cd1f3d68637d7f79d3d75e096c40065ebcf481c Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 20 Nov 2023 18:40:02 +0000 Subject: [PATCH 03/66] simplified Bary interpolation evaluation loops to allow the compiler to reorder how it sees fit --- .../bary_interpolation/bary_evaluation.hpp | 21 +++++++------------ 1 file changed, 8 insertions(+), 13 deletions(-) diff --git a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp index 69ecb643..cc4c5ae7 100644 --- a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp +++ b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp @@ -83,17 +83,14 @@ inline REAL compute_dir_10(const int num_phys0, const int num_phys1, const REAL *const physvals, const REAL *const div_space0, const REAL *const div_space1) { - - REAL numer = 0.0; + REAL pval1 = 0.0; for (int i1 = 0; i1 < num_phys1; i1++) { - REAL pval = 0.0; + const REAL c1 = div_space1[i1]; for (int i0 = 0; i0 < num_phys0; i0++) { - pval += physvals[i1 * num_phys0 + i0] * div_space0[i0]; + pval1 += physvals[i1 * num_phys0 + i0] * div_space0[i0] * c1; } - const REAL tmp = div_space1[i1]; - numer += tmp * pval; } - return numer; + return pval1; } /** @@ -114,19 +111,17 @@ inline REAL compute_dir_210(const int num_phys0, const int num_phys1, const REAL *const div_space0, const REAL *const div_space1, const REAL *const div_space2) { - const int stride = num_phys0 * num_phys1; REAL pval2 = 0.0; for (int i2 = 0; i2 < num_phys2; i2++) { - REAL pval1 = 0.0; + const REAL c2 = div_space2[i2]; for (int i1 = 0; i1 < num_phys1; i1++) { - REAL pval0 = 0.0; + const REAL c1 = c2 * div_space1[i1]; for (int i0 = 0; i0 < num_phys0; i0++) { - pval0 += physvals[i2 * stride + i1 * num_phys0 + i0] * div_space0[i0]; + pval2 += + physvals[i2 * stride + i1 * num_phys0 + i0] * div_space0[i0] * c1; } - pval1 += div_space1[i1] * pval0; } - pval2 += div_space2[i2] * pval1; } return pval2; } From 378c6dab7757b2cf88ea43e0fcf7fc41b8d594d1 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 20 Nov 2023 18:41:18 +0000 Subject: [PATCH 04/66] stray comment --- include/nektar_interface/bary_interpolation/bary_evaluation.hpp | 1 - 1 file changed, 1 deletion(-) diff --git a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp index cc4c5ae7..a0a98963 100644 --- a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp +++ b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp @@ -65,7 +65,6 @@ inline REAL compute_dir_0(const int num_phys, const REAL *const physvals, } const REAL eval0 = numer; return eval0; - //} } /** From b09df365aa52f6225aec92536b16ce6979b6ca7b Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 21 Nov 2023 15:32:49 +0000 Subject: [PATCH 05/66] Bary interpolation of forward X maps passing initial tests --- CMakeLists.txt | 1 + .../map_particles_newton.hpp | 15 +- .../mapping_newton_iteration_base.hpp | 52 +++- .../newton_generic_3d.hpp | 264 ++++++++++++++++++ .../newton_geom_interfaces.hpp | 1 + .../particle_cell_mapping/newton_hex.hpp | 3 +- .../particle_cell_mapping/newton_prism.hpp | 3 +- .../particle_cell_mapping/newton_pyr.hpp | 3 +- .../particle_cell_mapping/newton_quad.hpp | 3 +- .../particle_cell_mapping/newton_tet.hpp | 3 +- .../particle_cell_mapping/x_map_newton.hpp | 64 +++-- ..._particle_geometry_interface_3d_curved.cpp | 150 +++++++++- 12 files changed, 521 insertions(+), 41 deletions(-) create mode 100644 include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp diff --git a/CMakeLists.txt b/CMakeLists.txt index c8f794be..02792b78 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -185,6 +185,7 @@ set(HEADER_FILES ${INC_DIR}/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp ${INC_DIR}/nektar_interface/particle_cell_mapping/nektar_graph_local_mapper.hpp ${INC_DIR}/nektar_interface/particle_cell_mapping/newton_geom_interfaces.hpp + ${INC_DIR}/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp ${INC_DIR}/nektar_interface/particle_cell_mapping/newton_hex.hpp ${INC_DIR}/nektar_interface/particle_cell_mapping/newton_prism.hpp ${INC_DIR}/nektar_interface/particle_cell_mapping/newton_pyr.hpp diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp index abb95334..9793e2a0 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp @@ -78,7 +78,8 @@ class MapParticlesNewton : public CoarseMappersBase { ? this->h_data.data() + index * this->num_bytes_per_map_host : nullptr; - this->newton_type.write_data(geom, h_data_ptr, d_data_ptr); + this->newton_type.write_data(this->sycl_target, geom, h_data_ptr, + d_data_ptr); } public: @@ -342,24 +343,30 @@ class MapParticlesNewton : public CoarseMappersBase { REAL xin0, xin1, xin2; REAL f0, f1, f2; + // TODO REAL residual = k_newton_type.newton_residual( - map_data, xi0, xi1, xi2, p0, p1, p2, &f0, &f1, &f2); + map_data, xi0, xi1, xi2, p0, p1, p2, &f0, &f1, &f2, + nullptr); bool diverged = false; for (int stepx = 0; ((stepx < k_max_iterations) && (residual > k_tol) && (!diverged)); stepx++) { + + // TODO k_newton_type.newton_step(map_data, xi0, xi1, xi2, p0, p1, p2, f0, f1, f2, &xin0, - &xin1, &xin2); + &xin1, &xin2, nullptr); xi0 = xin0; xi1 = xin1; xi2 = xin2; + // TODO residual = k_newton_type.newton_residual( - map_data, xi0, xi1, xi2, p0, p1, p2, &f0, &f1, &f2); + map_data, xi0, xi1, xi2, p0, p1, p2, &f0, &f1, &f2, + nullptr); diverged = (ABS(xi0) > 15.0) || (ABS(xi1) > 15.0) || (ABS(xi2) > 15.0); diff --git a/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp b/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp index aa599519..e524b5a4 100644 --- a/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp +++ b/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp @@ -9,6 +9,10 @@ using namespace Nektar::SpatialDomains; namespace NESO::Newton { +template struct local_memory_required { + static bool const required = false; +}; + /** * Abstract base class for Newton iteration methods for binning particles into * Nektar++ cells. Subclasses must be device copyable. @@ -20,6 +24,8 @@ template struct MappingNewtonIterationBase { * data which will be required to perform a Newton iteration on the SYCL * device. * + * @param sycl_target A SYCLTarget instance which the mapper may use to + * allocate futher device memory. * @param geom A geometry object which particles may be binned into. * @param data_host A host pointer to a buffer which will be kept on the * host. @@ -27,10 +33,11 @@ template struct MappingNewtonIterationBase { * compute device. * */ - inline void write_data(GeometrySharedPtr geom, void *data_host, + inline void write_data(SYCLTargetSharedPtr sycl_target, + GeometrySharedPtr geom, void *data_host, void *data_device) { auto &underlying = static_cast(*this); - underlying.write_data_v(geom, data_host, data_device); + underlying.write_data_v(sycl_target, geom, data_host, data_device); } /** @@ -68,6 +75,22 @@ template struct MappingNewtonIterationBase { return underlying.data_size_device_v(); } + /** + * The number of bytes of kernel local memory required to evaluate the + * mapping or residual. + * + * @param data_host Host data region for mapper. + * @returns Number of bytes required. + */ + inline std::size_t data_size_local(void *data_host) { + if constexpr (local_memory_required::required) { + auto &underlying = static_cast(*this); + return underlying.data_size_local_v(data_host); + } else { + return 0; + } + } + /** * Perform a Newton iteration such that * @@ -97,14 +120,21 @@ template struct MappingNewtonIterationBase { * component. * @param[in, out] xin2 Output new iteration for local coordinate xi, z * component. + * @param[in, out] local_memory Local memory space to use for computation. */ inline void newton_step(const void *d_data, const REAL xi0, const REAL xi1, const REAL xi2, const REAL phys0, const REAL phys1, const REAL phys2, const REAL f0, const REAL f1, - const REAL f2, REAL *xin0, REAL *xin1, REAL *xin2) { + const REAL f2, REAL *xin0, REAL *xin1, REAL *xin2, + void *local_memory) { auto &underlying = static_cast(*this); - underlying.newton_step_v(d_data, xi0, xi1, xi2, phys0, phys1, phys2, f0, f1, - f2, xin0, xin1, xin2); + if constexpr (local_memory_required::required) { + underlying.newton_step_v(d_data, xi0, xi1, xi2, phys0, phys1, phys2, f0, + f1, f2, xin0, xin1, xin2, local_memory); + } else { + underlying.newton_step_v(d_data, xi0, xi1, xi2, phys0, phys1, phys2, f0, + f1, f2, xin0, xin1, xin2); + } } /** @@ -133,15 +163,21 @@ template struct MappingNewtonIterationBase { * @param[in, out] f0 F(xi), x component. * @param[in, out] f1 F(xi), y component. * @param[in, out] f2 F(xi), z component. + * @param[in, out] local_memory Local memory space to use for computation. * @returns Residual. */ inline REAL newton_residual(const void *d_data, const REAL xi0, const REAL xi1, const REAL xi2, const REAL phys0, const REAL phys1, const REAL phys2, REAL *f0, - REAL *f1, REAL *f2) { + REAL *f1, REAL *f2, void *local_memory) { auto &underlying = static_cast(*this); - return underlying.newton_residual_v(d_data, xi0, xi1, xi2, phys0, phys1, - phys2, f0, f1, f2); + if constexpr (local_memory_required::required) { + return underlying.newton_residual_v(d_data, xi0, xi1, xi2, phys0, phys1, + phys2, f0, f1, f2, local_memory); + } else { + return underlying.newton_residual_v(d_data, xi0, xi1, xi2, phys0, phys1, + phys2, f0, f1, f2); + } } /** diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp new file mode 100644 index 00000000..2e2afe2b --- /dev/null +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -0,0 +1,264 @@ +#ifndef ___NESO_PARTICLE_MAPPING_NEWTON_GENERIC_3D_H__ +#define ___NESO_PARTICLE_MAPPING_NEWTON_GENERIC_3D_H__ + +#include "../bary_interpolation/bary_evaluation.hpp" +#include "generated_linear/linear_newton_implementation.hpp" +#include "particle_cell_mapping_newton.hpp" +#include + +using namespace NESO; +using namespace NESO::Particles; + +namespace NESO { +namespace Newton { + +namespace Generic3D { +struct DataDevice { + int shape_type_int; + REAL tol_scaling; + int num_phys0; + int num_phys1; + int num_phys2; + REAL *z0; + REAL *z1; + REAL *z2; + REAL *bw0; + REAL *bw1; + REAL *bw2; + REAL *physvals0; + REAL *physvals1; + REAL *physvals2; +}; +struct DataHost { + std::size_t data_size_local; + std::unique_ptr> d_zbw; + inline void free() { this->d_zbw.reset(); } +}; +} // namespace Generic3D + +struct MappingGeneric3D : MappingNewtonIterationBase { + + inline void write_data_v(SYCLTargetSharedPtr sycl_target, + GeometrySharedPtr geom, void *data_host, + void *data_device) { + Generic3D::DataHost *h_data = static_cast(data_host); + Generic3D::DataDevice *d_data = + static_cast(data_device); + + auto lambda_as_vector = [](const auto &a) -> std::vector { + const std::size_t size = a.size(); + std::vector v(size); + for (int ix = 0; ix < size; ix++) { + v.at(ix) = a[ix]; + } + return v; + }; + + auto exp = geom->GetXmap(); + auto base = exp->GetBase(); + NESOASSERT(base.size() == 3, "Expected base of size 3."); + const auto &z0 = lambda_as_vector(base[0]->GetZ()); + const auto &bw0 = lambda_as_vector(base[0]->GetBaryWeights()); + const auto &z1 = lambda_as_vector(base[1]->GetZ()); + const auto &bw1 = lambda_as_vector(base[1]->GetBaryWeights()); + const auto &z2 = lambda_as_vector(base[2]->GetZ()); + const auto &bw2 = lambda_as_vector(base[2]->GetBaryWeights()); + + const int num_phys0 = z0.size(); + const int num_phys1 = z1.size(); + const int num_phys2 = z2.size(); + const int num_phys_total = num_phys0 + num_phys1 + num_phys2; + const int num_physvals = num_phys0 * num_phys1 * num_phys2; + d_data->num_phys0 = num_phys0; + d_data->num_phys1 = num_phys1; + d_data->num_phys2 = num_phys2; + + // push the quadrature points and weights into a device buffer + std::vector s_zbw; + const int num_elements = 2 * num_phys_total + 3 * num_physvals; + s_zbw.reserve(num_elements); + s_zbw.insert(s_zbw.end(), z0.begin(), z0.end()); + s_zbw.insert(s_zbw.end(), z1.begin(), z1.end()); + s_zbw.insert(s_zbw.end(), z2.begin(), z2.end()); + s_zbw.insert(s_zbw.end(), bw0.begin(), bw0.end()); + s_zbw.insert(s_zbw.end(), bw1.begin(), bw1.end()); + s_zbw.insert(s_zbw.end(), bw2.begin(), bw2.end()); + + NESOASSERT(exp->GetTotPoints() == num_physvals, + "Expected these two evaluations of the number of quadrature " + "points to match."); + + // push the physvals onto the vector + Array tmp(num_physvals); + exp->BwdTrans(geom->GetCoeffs(0), tmp); + const auto physvals0 = lambda_as_vector(tmp); + exp->BwdTrans(geom->GetCoeffs(1), tmp); + const auto physvals1 = lambda_as_vector(tmp); + exp->BwdTrans(geom->GetCoeffs(2), tmp); + const auto physvals2 = lambda_as_vector(tmp); + s_zbw.insert(s_zbw.end(), physvals0.begin(), physvals0.end()); + s_zbw.insert(s_zbw.end(), physvals1.begin(), physvals1.end()); + s_zbw.insert(s_zbw.end(), physvals2.begin(), physvals2.end()); + + // Create a device buffer with the z,bw,physvals + h_data->d_zbw = std::make_unique>(sycl_target, s_zbw); + + // store the pointers into the buffer we just made in the device struct so + // that pointer arithmetric does not have to happen in the kernel but the + // data is all in one contiguous block + d_data->z0 = h_data->d_zbw->ptr; + d_data->z1 = d_data->z0 + num_phys0; + d_data->z2 = d_data->z1 + num_phys1; + d_data->bw0 = d_data->z2 + num_phys2; + d_data->bw1 = d_data->bw0 + num_phys0; + d_data->bw2 = d_data->bw1 + num_phys1; + d_data->physvals0 = d_data->bw2 + num_phys2; + d_data->physvals1 = d_data->physvals0 + num_physvals; + d_data->physvals2 = d_data->physvals1 + num_physvals; + NESOASSERT(d_data->physvals2 + num_physvals == + h_data->d_zbw->ptr + num_elements, + "Error in pointer arithmetic."); + + // Exit tolerance scaling applied by Nektar++ + auto m_xmap = geom->GetXmap(); + auto m_geomFactors = geom->GetGeomFactors(); + Array Jac = + m_geomFactors->GetJac(m_xmap->GetPointsKeys()); + NekDouble tol_scaling = + Vmath::Vsum(Jac.size(), Jac, 1) / ((NekDouble)Jac.size()); + d_data->tol_scaling = ABS(1.0 / tol_scaling); + d_data->shape_type_int = static_cast(geom->GetShapeType()); + } + + inline void free_data_v(void *data_host) { + Generic3D::DataHost *h_data = static_cast(data_host); + h_data->free(); + } + + inline std::size_t data_size_host_v() { return sizeof(Generic3D::DataHost); } + + inline std::size_t data_size_local_v(void *data_host) { + return static_cast(data_host)->data_size_local; + } + + inline std::size_t data_size_device_v() { + return sizeof(Generic3D::DataDevice); + } + + inline void newton_step_v(const void *d_data, const REAL xi0, const REAL xi1, + const REAL xi2, const REAL phys0, const REAL phys1, + const REAL phys2, const REAL f0, const REAL f1, + const REAL f2, REAL *xin0, REAL *xin1, REAL *xin2, + void *local_memory) { + const Generic3D::DataDevice *data = + static_cast(d_data); + } + + inline REAL newton_residual_v(const void *d_data, const REAL xi0, + const REAL xi1, const REAL xi2, + const REAL phys0, const REAL phys1, + const REAL phys2, REAL *f0, REAL *f1, REAL *f2, + void *local_memory) { + + const Generic3D::DataDevice *d = + static_cast(d_data); + const REAL *data_device_real = static_cast(d_data); + + REAL eta0, eta1, eta2; + this->loc_coord_to_loc_collapsed(d_data, xi0, xi1, xi2, &eta0, &eta1, + &eta2); + + // compute X at xi by evaluating the Bary interpolation at eta + REAL *div_space0 = static_cast(local_memory); + REAL *div_space1 = div_space0 + d->num_phys0; + REAL *div_space2 = div_space1 + d->num_phys1; + Bary::preprocess_weights(d->num_phys0, eta0, d->z0, d->bw0, div_space0); + Bary::preprocess_weights(d->num_phys1, eta1, d->z1, d->bw1, div_space1); + Bary::preprocess_weights(d->num_phys2, eta2, d->z2, d->bw2, div_space2); + + const REAL X0 = + Bary::compute_dir_210(d->num_phys0, d->num_phys1, d->num_phys2, + d->physvals0, div_space0, div_space1, div_space2); + const REAL X1 = + Bary::compute_dir_210(d->num_phys0, d->num_phys1, d->num_phys2, + d->physvals1, div_space0, div_space1, div_space2); + const REAL X2 = + Bary::compute_dir_210(d->num_phys0, d->num_phys1, d->num_phys2, + d->physvals2, div_space0, div_space1, div_space2); + + // Residual is defined as F = X(xi) - P + *f0 = X0 - phys0; + *f1 = X1 - phys1; + *f2 = X2 - phys2; + + const REAL norm2 = MAX(MAX(ABS(*f0), ABS(*f1)), ABS(*f2)); + const REAL tol_scaling = d->tol_scaling; + const REAL scaled_norm2 = norm2 * tol_scaling; + return scaled_norm2; + } + + inline int get_ndim_v() { return 3; } + + inline void set_initial_iteration_v(const void *d_data, const REAL phys0, + const REAL phys1, const REAL phys2, + REAL *xi0, REAL *xi1, REAL *xi2) { + *xi0 = 0.0; + *xi1 = 0.0; + *xi2 = 0.0; + } + + inline void loc_coord_to_loc_collapsed_v(const void *d_data, const REAL xi0, + const REAL xi1, const REAL xi2, + REAL *eta0, REAL *eta1, REAL *eta2) { + + const Generic3D::DataDevice *data = + static_cast(d_data); + const int shape_type = data->shape_type_int; + + constexpr int shape_type_tet = + shape_type_to_int(LibUtilities::eTetrahedron); + constexpr int shape_type_pyr = shape_type_to_int(LibUtilities::ePyramid); + constexpr int shape_type_hex = shape_type_to_int(LibUtilities::eHexahedron); + + NekDouble d2 = 1.0 - xi2; + if (fabs(d2) < NekConstants::kNekZeroTol) { + if (d2 >= 0.) { + d2 = NekConstants::kNekZeroTol; + } else { + d2 = -NekConstants::kNekZeroTol; + } + } + NekDouble d12 = -xi1 - xi2; + if (fabs(d12) < NekConstants::kNekZeroTol) { + if (d12 >= 0.) { + d12 = NekConstants::kNekZeroTol; + } else { + d12 = -NekConstants::kNekZeroTol; + } + } + + const REAL id2x2 = 2.0 / d2; + const REAL a = 1.0 + xi0; + const REAL b = (1.0 + xi1) * id2x2 - 1.0; + const REAL c = a * id2x2 - 1.0; + const REAL d = 2.0 * a / d12 - 1.0; + + *eta0 = (shape_type == shape_type_tet) ? d + : (shape_type == shape_type_hex) ? xi0 + : c; + + *eta1 = ((shape_type == shape_type_tet) || (shape_type == shape_type_pyr)) + ? b + : xi1; + *eta2 = xi2; + } +}; + +template <> struct local_memory_required { + static bool const required = true; +}; + +} // namespace Newton +} // namespace NESO + +#endif diff --git a/include/nektar_interface/particle_cell_mapping/newton_geom_interfaces.hpp b/include/nektar_interface/particle_cell_mapping/newton_geom_interfaces.hpp index ff75ad2c..4425b525 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_geom_interfaces.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_geom_interfaces.hpp @@ -1,6 +1,7 @@ #ifndef __NEWTON_GEOM_INTERFACES_H_ #define __NEWTON_GEOM_INTERFACES_H_ +#include "newton_generic_3d.hpp" #include "newton_hex.hpp" #include "newton_prism.hpp" #include "newton_pyr.hpp" diff --git a/include/nektar_interface/particle_cell_mapping/newton_hex.hpp b/include/nektar_interface/particle_cell_mapping/newton_hex.hpp index b98d364b..d6619af6 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_hex.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_hex.hpp @@ -13,7 +13,8 @@ namespace Newton { struct MappingHexLinear3D : MappingNewtonIterationBase { - inline void write_data_v(GeometrySharedPtr geom, void *data_host, + inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, + GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/newton_prism.hpp b/include/nektar_interface/particle_cell_mapping/newton_prism.hpp index bc425567..335306bf 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_prism.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_prism.hpp @@ -13,7 +13,8 @@ namespace Newton { struct MappingPrismLinear3D : MappingNewtonIterationBase { - inline void write_data_v(GeometrySharedPtr geom, void *data_host, + inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, + GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp b/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp index d526d74f..245f8a47 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp @@ -13,7 +13,8 @@ namespace Newton { struct MappingPyrLinear3D : MappingNewtonIterationBase { - inline void write_data_v(GeometrySharedPtr geom, void *data_host, + inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, + GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/newton_quad.hpp b/include/nektar_interface/particle_cell_mapping/newton_quad.hpp index 87c13a66..ee890eea 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_quad.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_quad.hpp @@ -13,7 +13,8 @@ namespace Newton { struct MappingQuadLinear2D : MappingNewtonIterationBase { - inline void write_data_v(GeometrySharedPtr geom, void *data_host, + inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, + GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/newton_tet.hpp b/include/nektar_interface/particle_cell_mapping/newton_tet.hpp index 3142d331..44851b50 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_tet.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_tet.hpp @@ -13,7 +13,8 @@ namespace Newton { struct MappingTetLinear3D : MappingNewtonIterationBase { - inline void write_data_v(GeometrySharedPtr geom, void *data_host, + inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, + GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 9b3a2f8c..46abb95a 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -33,6 +33,7 @@ template class XMapNewton { std::unique_ptr> dh_fdata; /// The data required to perform newton iterations for each geom on the host. std::vector h_data; + std::size_t num_bytes_local; template inline void write_data(U &geom) { if (this->num_bytes_per_map_host) { @@ -48,8 +49,12 @@ template class XMapNewton { auto h_data_ptr = (this->num_bytes_per_map_host) ? this->h_data.data() : nullptr; - this->newton_type.write_data(geom, h_data_ptr, d_data_ptr); + this->newton_type.write_data(this->sycl_target, geom, h_data_ptr, + d_data_ptr); this->dh_data->host_to_device(); + this->num_bytes_local = + std::max(static_cast(1), + this->newton_type.data_size_local(h_data_ptr)); } public: @@ -93,25 +98,33 @@ template class XMapNewton { auto k_map_data = this->dh_data->d_buffer.ptr; auto k_fdata = this->dh_fdata->d_buffer.ptr; + const std::size_t num_bytes_local = this->num_bytes_local; + this->sycl_target->queue .submit([&](sycl::handler &cgh) { - cgh.single_task<>([=]() { - MappingNewtonIterationBase k_newton_type{}; - - REAL f0 = 0.0; - REAL f1 = 0.0; - REAL f2 = 0.0; - const REAL p0 = 0.0; - const REAL p1 = 0.0; - const REAL p2 = 0.0; - - k_newton_type.newton_residual(k_map_data, xi0, xi1, xi2, p0, p1, p2, - &f0, &f1, &f2); - - k_fdata[0] = f0; - k_fdata[1] = f1; - k_fdata[2] = f2; - }); + sycl::accessor + local_mem(sycl::range<1>(num_bytes_local), cgh); + + cgh.parallel_for<>( + sycl::nd_range<1>(sycl::range<1>(1), sycl::range<1>(1)), + [=](auto idx) { + MappingNewtonIterationBase k_newton_type{}; + + REAL f0 = 0.0; + REAL f1 = 0.0; + REAL f2 = 0.0; + const REAL p0 = 0.0; + const REAL p1 = 0.0; + const REAL p2 = 0.0; + + k_newton_type.newton_residual(k_map_data, xi0, xi1, xi2, p0, p1, + p2, &f0, &f1, &f2, &local_mem[0]); + + k_fdata[0] = f0; + k_fdata[1] = f1; + k_fdata[2] = f2; + }); }) .wait_and_throw(); @@ -162,23 +175,30 @@ template class XMapNewton { REAL xin0, xin1, xin2; REAL f0, f1, f2; + // TODO REAL residual = k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, &f2); + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, &f2, + nullptr); bool diverged = false; for (int stepx = 0; ((stepx < k_max_iterations) && (residual > k_tol) && (!diverged)); stepx++) { + + // TODO k_newton_type.newton_step(k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, - p2, f0, f1, f2, &xin0, &xin1, &xin2); + p2, f0, f1, f2, &xin0, &xin1, &xin2, + nullptr); k_xi0 = xin0; k_xi1 = xin1; k_xi2 = xin2; - residual = k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, &f2); + // TODO + residual = k_newton_type.newton_residual(k_map_data, k_xi0, k_xi1, + k_xi2, p0, p1, p2, &f0, + &f1, &f2, nullptr); diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || (ABS(k_xi2) > 15.0); diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 183b21c2..b5657545 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -65,7 +65,7 @@ TEST(ParticleGeometryInterfaceCurved, Init) { graph = SpatialDomains::MeshGraph::Read(session); // build map from owned mesh hierarchy cells to geoms that touch that cell - auto particle_mesh_interface = std::make_shared(graph); + auto mesh = std::make_shared(graph); std::map> geoms; get_all_elements_3d(graph, geoms); @@ -159,7 +159,153 @@ TEST(ParticleGeometryInterfaceCurved, Init) { nprint(x, y, z); } - particle_mesh_interface->free(); + mesh->free(); + delete[] argv[0]; + delete[] argv[1]; + delete[] argv[2]; +} + +TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { + + int size, rank; + MPI_Comm_size(MPI_COMM_WORLD, &size); + MPI_Comm_rank(MPI_COMM_WORLD, &rank); + + LibUtilities::SessionReaderSharedPtr session; + SpatialDomains::MeshGraphSharedPtr graph; + + int argc = 3; + char *argv[3]; + copy_to_cstring(std::string("test_particle_geometry_interface"), &argv[0]); + + std::filesystem::path source_file = __FILE__; + std::filesystem::path source_dir = source_file.parent_path(); + std::filesystem::path test_resources_dir = + source_dir / "../../test_resources"; + std::filesystem::path conditions_file = + test_resources_dir / "reference_all_types_cube/conditions.xml"; + copy_to_cstring(std::string(conditions_file), &argv[1]); + // std::filesystem::path mesh_file = + // test_resources_dir / "reference_all_types_cube/mixed_ref_cube_0.2.xml"; + + std::filesystem::path mesh_file = + "/home/js0259/git-ukaea/NESO-workspace/reference_all_types_cube/" + "mixed_ref_cube_0.5_perturbed_order_2.xml"; + copy_to_cstring(std::string(mesh_file), &argv[2]); + + // Create session reader. + session = LibUtilities::SessionReader::CreateInstance(argc, argv); + + // Create MeshGraph. + graph = SpatialDomains::MeshGraph::Read(session); + + // build map from owned mesh hierarchy cells to geoms that touch that cell + auto mesh = std::make_shared(graph); + auto sycl_target = std::make_shared(0, mesh->get_comm()); + + std::map> geoms; + get_all_elements_3d(graph, geoms); + + auto lambda_stype = [](auto s) -> std::string { + switch (s) { + case eTetrahedron: + return "Tet"; + case ePyramid: + return "Pyr"; + case ePrism: + return "Prism"; + case eHexahedron: + return "Hex"; + default: + return "shape unknown"; + } + }; + + auto lambda_btype = [](auto s) -> std::string { + switch (s) { + case eModified_A: + return "eA"; + case eModified_B: + return "eB"; + case eModified_C: + return "eC"; + case eModifiedPyr_C: + return "ePyrC"; + default: + return "basis unknown"; + } + }; + + for (auto gx : geoms) { + auto geom = gx.second; + auto xmap = geom->GetXmap(); + nprint(geom->GetShapeType(), lambda_stype(geom->GetShapeType())); + nprint("Num bases:", xmap->GetNumBases()); + for (int dx = 0; dx < 3; dx++) { + nprint("dx:", dx, "type:", lambda_btype(xmap->GetBasisType(dx)), + xmap->GetBasisNumModes(dx)); + } + + Array Lcoord(3); + Array Lcoord2(3); + Array Gcoord(3); + Array Gcoord2(3); + Lcoord[0] = -0.05; + Lcoord[1] = -0.05; + Lcoord[2] = -0.05; + + for (int dx = 0; dx < 3; dx++) { + // calls phys evaluate which takes a loc coord not a loc collapsed coord + Gcoord[dx] = geom->GetCoord(dx, Lcoord); + } + + geom->GetLocCoords(Gcoord, Lcoord2); + + for (int dx = 0; dx < 3; dx++) { + // calls phys evaluate which takes a loc coord not a loc collapsed coord + Gcoord2[dx] = geom->GetCoord(dx, Lcoord2); + } + nprint(Lcoord[0], Lcoord[1], Lcoord[2], "\n", Lcoord2[0], Lcoord2[1], + Lcoord2[2], "\n", Gcoord[0], Gcoord[1], Gcoord[2], "\n", Gcoord2[0], + Gcoord2[1], Gcoord2[2], "\n------"); + + auto I0 = xmap->GetBasis(0)->GetI(Lcoord); + auto I1 = xmap->GetBasis(1)->GetI(Lcoord); + auto I2 = xmap->GetBasis(2)->GetI(Lcoord); + + for (auto ix = I0->begin(); ix != I0->end(); ix++) { + nprint(*ix); + } + nprint("-----"); + const int npts = xmap->GetTotPoints(); + Array ptsx(npts), ptsy(npts), ptsz(npts); + xmap->BwdTrans(geom->GetCoeffs(0), ptsx); + xmap->BwdTrans(geom->GetCoeffs(1), ptsy); + xmap->BwdTrans(geom->GetCoeffs(2), ptsz); + + Array eta(3); + xmap->LocCoordToLocCollapsed(Lcoord, eta); + Array I(3); + I[0] = xmap->GetBasis(0)->GetI(eta); + I[1] = xmap->GetBasis(1)->GetI(eta + 1); + I[2] = xmap->GetBasis(2)->GetI(eta + 2); + const auto x = xmap->PhysEvaluate(I, ptsx); + const auto y = xmap->PhysEvaluate(I, ptsy); + const auto z = xmap->PhysEvaluate(I, ptsz); + nprint(x, y, z); + + Newton::XMapNewton mapper(sycl_target, geom); + + REAL phys0, phys1, phys2; + mapper.x(Lcoord[0], Lcoord[1], Lcoord[2], &phys0, &phys1, &phys2); + nprint(phys0, phys1, phys2); + + EXPECT_NEAR(phys0, x, 1.0e-10); + EXPECT_NEAR(phys1, y, 1.0e-10); + EXPECT_NEAR(phys2, z, 1.0e-10); + } + + mesh->free(); delete[] argv[0]; delete[] argv[1]; delete[] argv[2]; From 89bf4d401da606f538f00af4ee5f866e9b709d05 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 21 Nov 2023 16:44:53 +0000 Subject: [PATCH 06/66] interlaced bary evaluation for simultanious evaluation of multiple functions --- .../bary_interpolation/bary_evaluation.hpp | 49 ++++++++++++++++++- .../newton_generic_3d.hpp | 42 ++++++++-------- ..._particle_geometry_interface_3d_curved.cpp | 4 +- 3 files changed, 69 insertions(+), 26 deletions(-) diff --git a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp index a0a98963..99b10334 100644 --- a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp +++ b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp @@ -93,8 +93,7 @@ inline REAL compute_dir_10(const int num_phys0, const int num_phys1, } /** - * Computes Bary interpolation over three dimensions. The inner dimensions are - * computed with calls to compute_dir_10. + * Computes Bary interpolation over three dimensions. * * @param num_phys0 Number of quadrature points in dimension 0. * @param num_phys1 Number of quadrature points in dimension 1. @@ -125,6 +124,52 @@ inline REAL compute_dir_210(const int num_phys0, const int num_phys1, return pval2; } +/** + * Computes Bary interpolation over three dimensions. Evaluates N functions + * with interlaced quadrature point values. + * + * @param[in] num_phys0 Number of quadrature points in dimension 0. + * @param[in] num_phys1 Number of quadrature points in dimension 1. + * @param[in] num_phys2 Number of quadrature points in dimension 2. + * @param[in] physvals Array of function values at quadrature points interlaced + * values for each function to evaluate. + * @param[in] div_space0 The output of preprocess_weights applied to dimension + * 0. + * @param[in] div_space1 The output of preprocess_weights applied to + * dimension 1. + * @param[in] div_space2 The output of preprocess_weights applied to + * dimension 2. + * @param[in, out] output Output function evaluations. + */ +template +inline void compute_dir_210_interlaced( + const int num_phys0, const int num_phys1, const int num_phys2, + const REAL *const physvals, const REAL *const div_space0, + const REAL *const div_space1, const REAL *const div_space2, REAL *output) { + // writes via this tmporary until restrict keyword added TODO. + REAL tmp[N]; + for (int ix = 0; ix < N; ix++) { + tmp[ix] = 0.0; + } + const int stride = num_phys0 * num_phys1; + for (int i2 = 0; i2 < num_phys2; i2++) { + const REAL c2 = div_space2[i2]; + for (int i1 = 0; i1 < num_phys1; i1++) { + const REAL c1 = c2 * div_space1[i1]; + for (int i0 = 0; i0 < num_phys0; i0++) { + const int inner_stride = (i2 * stride + i1 * num_phys0 + i0) * N; + const REAL inner_c = div_space0[i0] * c1; + for (int ix = 0; ix < N; ix++) { + tmp[ix] += physvals[inner_stride + ix] * inner_c; + } + } + } + } + for (int ix = 0; ix < N; ix++) { + output[ix] = tmp[ix]; + } +} + /** * Compute a function evaluation at a point using the passed quadrature point * values, quadrature points and weights. diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index 2e2afe2b..cbdc7321 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -25,9 +25,7 @@ struct DataDevice { REAL *bw0; REAL *bw1; REAL *bw2; - REAL *physvals0; - REAL *physvals1; - REAL *physvals2; + REAL *physvals; }; struct DataHost { std::size_t data_size_local; @@ -96,9 +94,15 @@ struct MappingGeneric3D : MappingNewtonIterationBase { const auto physvals1 = lambda_as_vector(tmp); exp->BwdTrans(geom->GetCoeffs(2), tmp); const auto physvals2 = lambda_as_vector(tmp); - s_zbw.insert(s_zbw.end(), physvals0.begin(), physvals0.end()); - s_zbw.insert(s_zbw.end(), physvals1.begin(), physvals1.end()); - s_zbw.insert(s_zbw.end(), physvals2.begin(), physvals2.end()); + + std::vector interlaced_tmp(3 * num_physvals); + for (int ix = 0; ix < num_physvals; ix++) { + interlaced_tmp.at(3 * ix + 0) = physvals0.at(ix); + interlaced_tmp.at(3 * ix + 1) = physvals1.at(ix); + interlaced_tmp.at(3 * ix + 2) = physvals2.at(ix); + } + + s_zbw.insert(s_zbw.end(), interlaced_tmp.begin(), interlaced_tmp.end()); // Create a device buffer with the z,bw,physvals h_data->d_zbw = std::make_unique>(sycl_target, s_zbw); @@ -112,10 +116,8 @@ struct MappingGeneric3D : MappingNewtonIterationBase { d_data->bw0 = d_data->z2 + num_phys2; d_data->bw1 = d_data->bw0 + num_phys0; d_data->bw2 = d_data->bw1 + num_phys1; - d_data->physvals0 = d_data->bw2 + num_phys2; - d_data->physvals1 = d_data->physvals0 + num_physvals; - d_data->physvals2 = d_data->physvals1 + num_physvals; - NESOASSERT(d_data->physvals2 + num_physvals == + d_data->physvals = d_data->bw2 + num_phys2; + NESOASSERT(d_data->physvals + 3 * num_physvals == h_data->d_zbw->ptr + num_elements, "Error in pointer arithmetic."); @@ -176,20 +178,16 @@ struct MappingGeneric3D : MappingNewtonIterationBase { Bary::preprocess_weights(d->num_phys1, eta1, d->z1, d->bw1, div_space1); Bary::preprocess_weights(d->num_phys2, eta2, d->z2, d->bw2, div_space2); - const REAL X0 = - Bary::compute_dir_210(d->num_phys0, d->num_phys1, d->num_phys2, - d->physvals0, div_space0, div_space1, div_space2); - const REAL X1 = - Bary::compute_dir_210(d->num_phys0, d->num_phys1, d->num_phys2, - d->physvals1, div_space0, div_space1, div_space2); - const REAL X2 = - Bary::compute_dir_210(d->num_phys0, d->num_phys1, d->num_phys2, - d->physvals2, div_space0, div_space1, div_space2); + REAL X[3]; + + Bary::compute_dir_210_interlaced<3>(d->num_phys0, d->num_phys1, + d->num_phys2, d->physvals, div_space0, + div_space1, div_space2, X); // Residual is defined as F = X(xi) - P - *f0 = X0 - phys0; - *f1 = X1 - phys1; - *f2 = X2 - phys2; + *f0 = X[0] - phys0; + *f1 = X[1] - phys1; + *f2 = X[2] - phys2; const REAL norm2 = MAX(MAX(ABS(*f0), ABS(*f1)), ABS(*f2)); const REAL tol_scaling = d->tol_scaling; diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index b5657545..4aabb573 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -292,13 +292,13 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { const auto x = xmap->PhysEvaluate(I, ptsx); const auto y = xmap->PhysEvaluate(I, ptsy); const auto z = xmap->PhysEvaluate(I, ptsz); - nprint(x, y, z); + nprint("P", x, y, z); Newton::XMapNewton mapper(sycl_target, geom); REAL phys0, phys1, phys2; mapper.x(Lcoord[0], Lcoord[1], Lcoord[2], &phys0, &phys1, &phys2); - nprint(phys0, phys1, phys2); + nprint("N", phys0, phys1, phys2); EXPECT_NEAR(phys0, x, 1.0e-10); EXPECT_NEAR(phys1, y, 1.0e-10); From 9bfcf45be77972601e8a93b34a7e065b0ea7c25c Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 21 Nov 2023 17:58:26 +0000 Subject: [PATCH 07/66] bary interpolation X inverse giving sensible values for initial implementation - needs testing --- .../newton_generic_3d.hpp | 96 +++++++++++++--- .../particle_cell_mapping/x_map_newton.hpp | 106 +++++++++--------- ..._particle_geometry_interface_3d_curved.cpp | 4 + 3 files changed, 138 insertions(+), 68 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index cbdc7321..9bc7422a 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -26,6 +26,7 @@ struct DataDevice { REAL *bw1; REAL *bw2; REAL *physvals; + REAL *physvals_deriv; }; struct DataHost { std::size_t data_size_local; @@ -73,7 +74,7 @@ struct MappingGeneric3D : MappingNewtonIterationBase { // push the quadrature points and weights into a device buffer std::vector s_zbw; - const int num_elements = 2 * num_phys_total + 3 * num_physvals; + const int num_elements = 2 * num_phys_total + 12 * num_physvals; s_zbw.reserve(num_elements); s_zbw.insert(s_zbw.end(), z0.begin(), z0.end()); s_zbw.insert(s_zbw.end(), z1.begin(), z1.end()); @@ -86,22 +87,49 @@ struct MappingGeneric3D : MappingNewtonIterationBase { "Expected these two evaluations of the number of quadrature " "points to match."); - // push the physvals onto the vector - Array tmp(num_physvals); - exp->BwdTrans(geom->GetCoeffs(0), tmp); - const auto physvals0 = lambda_as_vector(tmp); - exp->BwdTrans(geom->GetCoeffs(1), tmp); - const auto physvals1 = lambda_as_vector(tmp); - exp->BwdTrans(geom->GetCoeffs(2), tmp); - const auto physvals2 = lambda_as_vector(tmp); - std::vector interlaced_tmp(3 * num_physvals); + // push the function physvals onto the vector + Array physvals0(num_physvals); + Array physvals1(num_physvals); + Array physvals2(num_physvals); + exp->BwdTrans(geom->GetCoeffs(0), physvals0); + exp->BwdTrans(geom->GetCoeffs(1), physvals1); + exp->BwdTrans(geom->GetCoeffs(2), physvals2); for (int ix = 0; ix < num_physvals; ix++) { - interlaced_tmp.at(3 * ix + 0) = physvals0.at(ix); - interlaced_tmp.at(3 * ix + 1) = physvals1.at(ix); - interlaced_tmp.at(3 * ix + 2) = physvals2.at(ix); + interlaced_tmp.at(3 * ix + 0) = physvals0[ix]; + interlaced_tmp.at(3 * ix + 1) = physvals1[ix]; + interlaced_tmp.at(3 * ix + 2) = physvals2[ix]; } + s_zbw.insert(s_zbw.end(), interlaced_tmp.begin(), interlaced_tmp.end()); + // push the function deriv phsvals onto the vector + interlaced_tmp.resize(9 * num_physvals); + + Array D0D0(num_physvals); + Array D0D1(num_physvals); + Array D0D2(num_physvals); + Array D1D0(num_physvals); + Array D1D1(num_physvals); + Array D1D2(num_physvals); + Array D2D0(num_physvals); + Array D2D1(num_physvals); + Array D2D2(num_physvals); + + // get the physvals for the derivatives + exp->PhysDeriv(physvals0, D0D0, D0D1, D0D2); + exp->PhysDeriv(physvals1, D1D0, D1D1, D1D2); + exp->PhysDeriv(physvals2, D2D0, D2D1, D2D2); + for (int ix = 0; ix < num_physvals; ix++) { + interlaced_tmp.at(9 * ix + 0) = D0D0[ix]; + interlaced_tmp.at(9 * ix + 1) = D0D1[ix]; + interlaced_tmp.at(9 * ix + 2) = D0D2[ix]; + interlaced_tmp.at(9 * ix + 3) = D1D0[ix]; + interlaced_tmp.at(9 * ix + 4) = D1D1[ix]; + interlaced_tmp.at(9 * ix + 5) = D1D2[ix]; + interlaced_tmp.at(9 * ix + 6) = D2D0[ix]; + interlaced_tmp.at(9 * ix + 7) = D2D1[ix]; + interlaced_tmp.at(9 * ix + 8) = D2D2[ix]; + } s_zbw.insert(s_zbw.end(), interlaced_tmp.begin(), interlaced_tmp.end()); // Create a device buffer with the z,bw,physvals @@ -117,7 +145,8 @@ struct MappingGeneric3D : MappingNewtonIterationBase { d_data->bw1 = d_data->bw0 + num_phys0; d_data->bw2 = d_data->bw1 + num_phys1; d_data->physvals = d_data->bw2 + num_phys2; - NESOASSERT(d_data->physvals + 3 * num_physvals == + d_data->physvals_deriv = d_data->physvals + 3 * num_physvals; + NESOASSERT(d_data->physvals_deriv + 9 * num_physvals == h_data->d_zbw->ptr + num_elements, "Error in pointer arithmetic."); @@ -152,8 +181,44 @@ struct MappingGeneric3D : MappingNewtonIterationBase { const REAL phys2, const REAL f0, const REAL f1, const REAL f2, REAL *xin0, REAL *xin1, REAL *xin2, void *local_memory) { - const Generic3D::DataDevice *data = + const Generic3D::DataDevice *d = static_cast(d_data); + + REAL eta0, eta1, eta2; + this->loc_coord_to_loc_collapsed(d_data, xi0, xi1, xi2, &eta0, &eta1, + &eta2); + REAL *div_space0 = static_cast(local_memory); + REAL *div_space1 = div_space0 + d->num_phys0; + REAL *div_space2 = div_space1 + d->num_phys1; + Bary::preprocess_weights(d->num_phys0, eta0, d->z0, d->bw0, div_space0); + Bary::preprocess_weights(d->num_phys1, eta1, d->z1, d->bw1, div_space1); + Bary::preprocess_weights(d->num_phys2, eta2, d->z2, d->bw2, div_space2); + + REAL J[9]; + Bary::compute_dir_210_interlaced<9>(d->num_phys0, d->num_phys1, + d->num_phys2, d->physvals_deriv, + div_space0, div_space1, div_space2, J); + REAL *J0 = J; + REAL *J1 = J + 3; + REAL *J2 = J + 6; + const REAL inverse_J = 1.0 / (J0[0] * (J1[1] * J2[2] - J1[2] * J2[1]) - + J0[1] * (J1[0] * J2[2] - J1[2] * J2[0]) + + J0[2] * (J1[0] * J2[1] - J1[1] * J2[0])); + + *xin0 = xi0 + ((J1[1] * J2[2] - J1[2] * J2[1]) * (-f0) - + (J0[1] * J2[2] - J0[2] * J2[1]) * (-f1) + + (J0[1] * J1[2] - J0[2] * J1[1]) * (-f2)) * + inverse_J; + + *xin1 = xi1 - ((J1[0] * J2[2] - J1[2] * J2[0]) * (-f0) - + (J0[0] * J2[2] - J0[2] * J2[0]) * (-f1) + + (J0[0] * J1[2] - J0[2] * J1[0]) * (-f2)) * + inverse_J; + + *xin2 = xi2 + ((J1[0] * J2[1] - J1[1] * J2[0]) * (-f0) - + (J0[0] * J2[1] - J0[1] * J2[0]) * (-f1) + + (J0[0] * J1[1] - J0[1] * J1[0]) * (-f2)) * + inverse_J; } inline REAL newton_residual_v(const void *d_data, const REAL xi0, @@ -164,7 +229,6 @@ struct MappingGeneric3D : MappingNewtonIterationBase { const Generic3D::DataDevice *d = static_cast(d_data); - const REAL *data_device_real = static_cast(d_data); REAL eta0, eta1, eta2; this->loc_coord_to_loc_collapsed(d_data, xi0, xi1, xi2, &eta0, &eta1, diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 46abb95a..65165529 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -97,7 +97,6 @@ template class XMapNewton { auto k_map_data = this->dh_data->d_buffer.ptr; auto k_fdata = this->dh_fdata->d_buffer.ptr; - const std::size_t num_bytes_local = this->num_bytes_local; this->sycl_target->queue @@ -155,60 +154,63 @@ template class XMapNewton { auto k_map_data = this->dh_data->d_buffer.ptr; auto k_fdata = this->dh_fdata->d_buffer.ptr; const REAL k_tol = tol; + const std::size_t num_bytes_local = this->num_bytes_local; this->sycl_target->queue .submit([&](sycl::handler &cgh) { - cgh.single_task<>([=]() { - MappingNewtonIterationBase k_newton_type{}; - - const REAL p0 = phys0; - const REAL p1 = phys1; - const REAL p2 = phys2; - - REAL k_xi0; - REAL k_xi1; - REAL k_xi2; - k_newton_type.set_initial_iteration(k_map_data, p0, p1, p2, &k_xi0, - &k_xi1, &k_xi2); - - // Start of Newton iteration - REAL xin0, xin1, xin2; - REAL f0, f1, f2; - - // TODO - REAL residual = k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, &f2, - nullptr); - - bool diverged = false; - - for (int stepx = 0; ((stepx < k_max_iterations) && - (residual > k_tol) && (!diverged)); - stepx++) { - - // TODO - k_newton_type.newton_step(k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, - p2, f0, f1, f2, &xin0, &xin1, &xin2, - nullptr); - - k_xi0 = xin0; - k_xi1 = xin1; - k_xi2 = xin2; - - // TODO - residual = k_newton_type.newton_residual(k_map_data, k_xi0, k_xi1, - k_xi2, p0, p1, p2, &f0, - &f1, &f2, nullptr); - - diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || - (ABS(k_xi2) > 15.0); - } - - k_fdata[0] = k_xi0; - k_fdata[1] = k_xi1; - k_fdata[2] = k_xi2; - k_fdata[3] = (residual <= tol) ? 1 : -1; - }); + sycl::accessor + local_mem(sycl::range<1>(num_bytes_local), cgh); + cgh.parallel_for<>( + sycl::nd_range<1>(sycl::range<1>(1), sycl::range<1>(1)), + [=](auto idx) { + MappingNewtonIterationBase k_newton_type{}; + + const REAL p0 = phys0; + const REAL p1 = phys1; + const REAL p2 = phys2; + + REAL k_xi0; + REAL k_xi1; + REAL k_xi2; + k_newton_type.set_initial_iteration(k_map_data, p0, p1, p2, + &k_xi0, &k_xi1, &k_xi2); + + // Start of Newton iteration + REAL xin0, xin1, xin2; + REAL f0, f1, f2; + + REAL residual = k_newton_type.newton_residual( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, &f2, + &local_mem[0]); + + bool diverged = false; + + for (int stepx = 0; ((stepx < k_max_iterations) && + (residual > k_tol) && (!diverged)); + stepx++) { + + k_newton_type.newton_step(k_map_data, k_xi0, k_xi1, k_xi2, p0, + p1, p2, f0, f1, f2, &xin0, &xin1, + &xin2, &local_mem[0]); + + k_xi0 = xin0; + k_xi1 = xin1; + k_xi2 = xin2; + + residual = k_newton_type.newton_residual( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, + &f2, &local_mem[0]); + + diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || + (ABS(k_xi2) > 15.0); + } + + k_fdata[0] = k_xi0; + k_fdata[1] = k_xi1; + k_fdata[2] = k_xi2; + k_fdata[3] = (residual <= tol) ? 1 : -1; + }); }) .wait_and_throw(); diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 4aabb573..5911fd7a 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -303,6 +303,10 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { EXPECT_NEAR(phys0, x, 1.0e-10); EXPECT_NEAR(phys1, y, 1.0e-10); EXPECT_NEAR(phys2, z, 1.0e-10); + + REAL xi0, xi1, xi2; + mapper.x_inverse(phys0, phys1, phys2, &xi0, &xi1, &xi2); + nprint("Q", xi0, xi1, xi2); } mesh->free(); From 3b2354a3ad3262489ad90161fb9625879e941c24 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 22 Nov 2023 17:48:44 +0000 Subject: [PATCH 08/66] coordinate mapping for nektar curved elements refactor --- .../nektar_interface/coordinate_mapping.hpp | 53 +++++++++++++ .../mapping_newton_iteration_base.hpp | 4 + .../newton_generic_3d.hpp | 75 ++++++++----------- .../particle_cell_mapping/x_map_newton.hpp | 4 +- ..._particle_geometry_interface_3d_curved.cpp | 58 +++++++++++++- 5 files changed, 146 insertions(+), 48 deletions(-) diff --git a/include/nektar_interface/coordinate_mapping.hpp b/include/nektar_interface/coordinate_mapping.hpp index d55d5110..3a6a18aa 100644 --- a/include/nektar_interface/coordinate_mapping.hpp +++ b/include/nektar_interface/coordinate_mapping.hpp @@ -594,6 +594,59 @@ inline void loc_coord_to_loc_collapsed_3d(const int shape_type, const T &xi, eta[2] = xi2; } +/** + * Map the local coordinate (xi) to the local collapsed coordinate (eta). + * + * @param[in] shape_type Integer denoting shape type found by cast of Nektar++ + * @param[in] xi0 Local coordinate to map to collapsed coordinate, x component. + * @param[in] xi1 Local coordinate to map to collapsed coordinate, y component. + * @param[in] xi2 Local coordinate to map to collapsed coordinate, z component. + * @param[in, out] eta0 Local collapsed coordinate, x component. + * @param[in, out] eta1 Local collapsed coordinate, y component. + * @param[in, out] eta2 Local collapsed coordinate, z component. + */ +template +inline void loc_coord_to_loc_collapsed_3d(const int shape_type, const T xi0, + const T xi1, const T xi2, T *eta0, + T *eta1, T *eta2) { + + constexpr int shape_type_tet = shape_type_to_int(LibUtilities::eTetrahedron); + constexpr int shape_type_pyr = shape_type_to_int(LibUtilities::ePyramid); + constexpr int shape_type_hex = shape_type_to_int(LibUtilities::eHexahedron); + + NekDouble d2 = 1.0 - xi2; + if (fabs(d2) < NekConstants::kNekZeroTol) { + if (d2 >= 0.) { + d2 = NekConstants::kNekZeroTol; + } else { + d2 = -NekConstants::kNekZeroTol; + } + } + NekDouble d12 = -xi1 - xi2; + if (fabs(d12) < NekConstants::kNekZeroTol) { + if (d12 >= 0.) { + d12 = NekConstants::kNekZeroTol; + } else { + d12 = -NekConstants::kNekZeroTol; + } + } + + const REAL id2x2 = 2.0 / d2; + const REAL a = 1.0 + xi0; + const REAL b = (1.0 + xi1) * id2x2 - 1.0; + const REAL c = a * id2x2 - 1.0; + const REAL d = 2.0 * a / d12 - 1.0; + + *eta0 = (shape_type == shape_type_tet) ? d + : (shape_type == shape_type_hex) ? xi0 + : c; + + *eta1 = ((shape_type == shape_type_tet) || (shape_type == shape_type_pyr)) + ? b + : xi1; + *eta2 = xi2; +} + /** * Map the local coordinate (xi) to the local collapsed coordinate (eta). * diff --git a/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp b/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp index e524b5a4..2761fcf8 100644 --- a/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp +++ b/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp @@ -9,6 +9,10 @@ using namespace Nektar::SpatialDomains; namespace NESO::Newton { +/** + * Implementations which require local memory should define a specialisation + * that sets this to true. + */ template struct local_memory_required { static bool const required = false; }; diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index 9bc7422a..0a1e25e4 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -2,6 +2,7 @@ #define ___NESO_PARTICLE_MAPPING_NEWTON_GENERIC_3D_H__ #include "../bary_interpolation/bary_evaluation.hpp" +#include "../coordinate_mapping.hpp" #include "generated_linear/linear_newton_implementation.hpp" #include "particle_cell_mapping_newton.hpp" #include @@ -184,15 +185,11 @@ struct MappingGeneric3D : MappingNewtonIterationBase { const Generic3D::DataDevice *d = static_cast(d_data); - REAL eta0, eta1, eta2; - this->loc_coord_to_loc_collapsed(d_data, xi0, xi1, xi2, &eta0, &eta1, - &eta2); REAL *div_space0 = static_cast(local_memory); REAL *div_space1 = div_space0 + d->num_phys0; REAL *div_space2 = div_space1 + d->num_phys1; - Bary::preprocess_weights(d->num_phys0, eta0, d->z0, d->bw0, div_space0); - Bary::preprocess_weights(d->num_phys1, eta1, d->z1, d->bw1, div_space1); - Bary::preprocess_weights(d->num_phys2, eta2, d->z2, d->bw2, div_space2); + // The call to Newton step always follows a call to the residual + // calculation so we assume that the div_space is already initialised. REAL J[9]; Bary::compute_dir_210_interlaced<9>(d->num_phys0, d->num_phys1, @@ -219,6 +216,7 @@ struct MappingGeneric3D : MappingNewtonIterationBase { (J0[0] * J2[1] - J0[1] * J2[0]) * (-f1) + (J0[0] * J1[1] - J0[1] * J1[0]) * (-f2)) * inverse_J; + nprint("NEW:", *xin0, *xin1, *xin2); } inline REAL newton_residual_v(const void *d_data, const REAL xi0, @@ -234,6 +232,8 @@ struct MappingGeneric3D : MappingNewtonIterationBase { this->loc_coord_to_loc_collapsed(d_data, xi0, xi1, xi2, &eta0, &eta1, &eta2); + nprint("COORDS:", xi0, xi1, xi2, eta0, eta1, eta2); + // compute X at xi by evaluating the Bary interpolation at eta REAL *div_space0 = static_cast(local_memory); REAL *div_space1 = div_space0 + d->num_phys0; @@ -248,6 +248,22 @@ struct MappingGeneric3D : MappingNewtonIterationBase { d->num_phys2, d->physvals, div_space0, div_space1, div_space2, X); + const int n0 = d->num_phys0; + const int n1 = d->num_phys1; + const int n2 = d->num_phys2; + nprint("n:", n0, n1, n2); + for (int ix = 0; ix < n0; ix++) { + nprint(div_space0[ix]); + } + for (int ix = 0; ix < n1; ix++) { + nprint(div_space1[ix]); + } + for (int ix = 0; ix < n2; ix++) { + nprint(div_space2[ix]); + } + + nprint(X[0], X[1], X[2], phys0, phys1, phys2); + // Residual is defined as F = X(xi) - P *f0 = X[0] - phys0; *f1 = X[1] - phys1; @@ -264,9 +280,9 @@ struct MappingGeneric3D : MappingNewtonIterationBase { inline void set_initial_iteration_v(const void *d_data, const REAL phys0, const REAL phys1, const REAL phys2, REAL *xi0, REAL *xi1, REAL *xi2) { - *xi0 = 0.0; - *xi1 = 0.0; - *xi2 = 0.0; + *xi0 = -0.2; + *xi1 = -0.2; + *xi2 = -0.2; } inline void loc_coord_to_loc_collapsed_v(const void *d_data, const REAL xi0, @@ -277,45 +293,14 @@ struct MappingGeneric3D : MappingNewtonIterationBase { static_cast(d_data); const int shape_type = data->shape_type_int; - constexpr int shape_type_tet = - shape_type_to_int(LibUtilities::eTetrahedron); - constexpr int shape_type_pyr = shape_type_to_int(LibUtilities::ePyramid); - constexpr int shape_type_hex = shape_type_to_int(LibUtilities::eHexahedron); - - NekDouble d2 = 1.0 - xi2; - if (fabs(d2) < NekConstants::kNekZeroTol) { - if (d2 >= 0.) { - d2 = NekConstants::kNekZeroTol; - } else { - d2 = -NekConstants::kNekZeroTol; - } - } - NekDouble d12 = -xi1 - xi2; - if (fabs(d12) < NekConstants::kNekZeroTol) { - if (d12 >= 0.) { - d12 = NekConstants::kNekZeroTol; - } else { - d12 = -NekConstants::kNekZeroTol; - } - } - - const REAL id2x2 = 2.0 / d2; - const REAL a = 1.0 + xi0; - const REAL b = (1.0 + xi1) * id2x2 - 1.0; - const REAL c = a * id2x2 - 1.0; - const REAL d = 2.0 * a / d12 - 1.0; - - *eta0 = (shape_type == shape_type_tet) ? d - : (shape_type == shape_type_hex) ? xi0 - : c; - - *eta1 = ((shape_type == shape_type_tet) || (shape_type == shape_type_pyr)) - ? b - : xi1; - *eta2 = xi2; + GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type, xi0, xi1, xi2, + eta0, eta1, eta2); } }; +/** + * This implementation requires local memory. + */ template <> struct local_memory_required { static bool const required = true; }; diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 65165529..0f151452 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -164,6 +164,7 @@ template class XMapNewton { cgh.parallel_for<>( sycl::nd_range<1>(sycl::range<1>(1), sycl::range<1>(1)), [=](auto idx) { + printf("NEWTON:\n"); MappingNewtonIterationBase k_newton_type{}; const REAL p0 = phys0; @@ -185,10 +186,11 @@ template class XMapNewton { &local_mem[0]); bool diverged = false; - + printf("residual: %f\n", residual); for (int stepx = 0; ((stepx < k_max_iterations) && (residual > k_tol) && (!diverged)); stepx++) { + printf("STEPX: %d, RES: %f\n", stepx, residual); k_newton_type.newton_step(k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f0, f1, f2, &xin0, &xin1, diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 5911fd7a..cd25dd53 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -239,6 +239,7 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { for (auto gx : geoms) { auto geom = gx.second; auto xmap = geom->GetXmap(); + const int shape_type_int = static_cast(geom->GetShapeType()); nprint(geom->GetShapeType(), lambda_stype(geom->GetShapeType())); nprint("Num bases:", xmap->GetNumBases()); for (int dx = 0; dx < 3; dx++) { @@ -254,6 +255,7 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { Lcoord[1] = -0.05; Lcoord[2] = -0.05; + for (int dx = 0; dx < 3; dx++) { // calls phys evaluate which takes a loc coord not a loc collapsed coord Gcoord[dx] = geom->GetCoord(dx, Lcoord); @@ -303,10 +305,62 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { EXPECT_NEAR(phys0, x, 1.0e-10); EXPECT_NEAR(phys1, y, 1.0e-10); EXPECT_NEAR(phys2, z, 1.0e-10); + + + const REAL xi00 = Lcoord[0]; + const REAL xi01 = Lcoord[1]; + const REAL xi02 = Lcoord[2]; + REAL eta0, eta1, eta2; + + GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi00, + xi01, xi02, &eta0, + &eta1, &eta2); + EXPECT_NEAR(eta0, eta[0], 1.0e-12); + EXPECT_NEAR(eta1, eta[1], 1.0e-12); + EXPECT_NEAR(eta2, eta[2], 1.0e-12); + nprint("coords:", xi00, xi01, xi02, eta0, eta1, eta2); REAL xi0, xi1, xi2; - mapper.x_inverse(phys0, phys1, phys2, &xi0, &xi1, &xi2); - nprint("Q", xi0, xi1, xi2); + const bool converged = + mapper.x_inverse(phys0, phys1, phys2, &xi0, &xi1, &xi2, 1.0e-10); + nprint("Q", xi0, xi1, xi2, converged); + // these might be quite far depending on the map - the residual is on the X + // map output + EXPECT_NEAR(xi0, Lcoord[0], 1.0e-2); + EXPECT_NEAR(xi1, Lcoord[1], 1.0e-2); + EXPECT_NEAR(xi2, Lcoord[2], 1.0e-2); + + Array Lcoordt(3); + Lcoordt[0] = xi0; + Lcoordt[1] = xi1; + Lcoordt[2] = xi2; + const REAL g0 = geom->GetCoord(0, Lcoordt); + const REAL g1 = geom->GetCoord(1, Lcoordt); + const REAL g2 = geom->GetCoord(2, Lcoordt); + EXPECT_NEAR(g0, Gcoord[0], 1.0e-5); + EXPECT_NEAR(g1, Gcoord[1], 1.0e-5); + EXPECT_NEAR(g2, Gcoord[2], 1.0e-5); + + + + if (static_cast(geom->GetShapeType()) == 5) { + auto z0 = xmap->GetBase()[0]->GetZ(); + auto bw0 = xmap->GetBase()[0]->GetBaryWeights(); + const int N0 = 4; + std::vector div_space0(N0); + Bary::preprocess_weights(N0, eta[0], &z0[0], &bw0[0], div_space0.data()); + for (int ix = 0; ix < N0; ix++) { + nprint("host0:", ix, div_space0[ix]); + } + auto z1 = xmap->GetBase()[1]->GetZ(); + auto bw1 = xmap->GetBase()[1]->GetBaryWeights(); + const int N1 = 3; + std::vector div_space1(N1); + Bary::preprocess_weights(N1, eta[1], &z1[0], &bw1[0], div_space1.data()); + for (int ix = 0; ix < N1; ix++) { + nprint("host1:", ix, div_space1[ix]); + } + } } mesh->free(); From a8542d28b14aff7f53aaf9316c6db15932676fc2 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 8 Jan 2024 17:10:20 +0000 Subject: [PATCH 09/66] higher order x map test refactoring --- .../newton_generic_3d.hpp | 2 + neso-particles | 2 +- ..._particle_geometry_interface_3d_curved.cpp | 231 ++++++++++-------- 3 files changed, 128 insertions(+), 107 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index 0a1e25e4..0101f3a6 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -232,6 +232,7 @@ struct MappingGeneric3D : MappingNewtonIterationBase { this->loc_coord_to_loc_collapsed(d_data, xi0, xi1, xi2, &eta0, &eta1, &eta2); + nprint("PHYS:", phys0, phys1, phys2); nprint("COORDS:", xi0, xi1, xi2, eta0, eta1, eta2); // compute X at xi by evaluating the Bary interpolation at eta @@ -271,6 +272,7 @@ struct MappingGeneric3D : MappingNewtonIterationBase { const REAL norm2 = MAX(MAX(ABS(*f0), ABS(*f1)), ABS(*f2)); const REAL tol_scaling = d->tol_scaling; + nprint("TOL SCALING:", tol_scaling); const REAL scaled_norm2 = norm2 * tol_scaling; return scaled_norm2; } diff --git a/neso-particles b/neso-particles index 9c6b4626..196069f9 160000 --- a/neso-particles +++ b/neso-particles @@ -1 +1 @@ -Subproject commit 9c6b4626645f6aaaca478e4798f2fdee5dd2675b +Subproject commit 196069f90b5d52a09f9260c6f5c17a54d1a46c28 diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index cd25dd53..98e7c5b2 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -236,57 +236,19 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { } }; - for (auto gx : geoms) { - auto geom = gx.second; + auto lambda_forward_map = [&](auto geom, const auto &xi, auto &phys) { + // Evaluate the forward map from xi to physical space using the expansion. auto xmap = geom->GetXmap(); - const int shape_type_int = static_cast(geom->GetShapeType()); - nprint(geom->GetShapeType(), lambda_stype(geom->GetShapeType())); - nprint("Num bases:", xmap->GetNumBases()); - for (int dx = 0; dx < 3; dx++) { - nprint("dx:", dx, "type:", lambda_btype(xmap->GetBasisType(dx)), - xmap->GetBasisNumModes(dx)); - } - - Array Lcoord(3); - Array Lcoord2(3); - Array Gcoord(3); - Array Gcoord2(3); - Lcoord[0] = -0.05; - Lcoord[1] = -0.05; - Lcoord[2] = -0.05; - - - for (int dx = 0; dx < 3; dx++) { - // calls phys evaluate which takes a loc coord not a loc collapsed coord - Gcoord[dx] = geom->GetCoord(dx, Lcoord); - } - - geom->GetLocCoords(Gcoord, Lcoord2); - - for (int dx = 0; dx < 3; dx++) { - // calls phys evaluate which takes a loc coord not a loc collapsed coord - Gcoord2[dx] = geom->GetCoord(dx, Lcoord2); - } - nprint(Lcoord[0], Lcoord[1], Lcoord[2], "\n", Lcoord2[0], Lcoord2[1], - Lcoord2[2], "\n", Gcoord[0], Gcoord[1], Gcoord[2], "\n", Gcoord2[0], - Gcoord2[1], Gcoord2[2], "\n------"); - - auto I0 = xmap->GetBasis(0)->GetI(Lcoord); - auto I1 = xmap->GetBasis(1)->GetI(Lcoord); - auto I2 = xmap->GetBasis(2)->GetI(Lcoord); - - for (auto ix = I0->begin(); ix != I0->end(); ix++) { - nprint(*ix); - } - nprint("-----"); + auto I0 = xmap->GetBasis(0)->GetI(xi); + auto I1 = xmap->GetBasis(1)->GetI(xi); + auto I2 = xmap->GetBasis(2)->GetI(xi); const int npts = xmap->GetTotPoints(); Array ptsx(npts), ptsy(npts), ptsz(npts); xmap->BwdTrans(geom->GetCoeffs(0), ptsx); xmap->BwdTrans(geom->GetCoeffs(1), ptsy); xmap->BwdTrans(geom->GetCoeffs(2), ptsz); - Array eta(3); - xmap->LocCoordToLocCollapsed(Lcoord, eta); + xmap->LocCoordToLocCollapsed(xi, eta); Array I(3); I[0] = xmap->GetBasis(0)->GetI(eta); I[1] = xmap->GetBasis(1)->GetI(eta + 1); @@ -294,73 +256,130 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { const auto x = xmap->PhysEvaluate(I, ptsx); const auto y = xmap->PhysEvaluate(I, ptsy); const auto z = xmap->PhysEvaluate(I, ptsz); - nprint("P", x, y, z); + phys[0] = x; + phys[1] = y; + phys[2] = z; + }; - Newton::XMapNewton mapper(sycl_target, geom); + auto lambda_test_contained_dir = [](const REAL eta) -> REAL { + if ((eta >= -1.0) && (eta <= 1.0)) { + return 0.0; + } else { + if (eta < -1.0) { + return -1.0 - eta; + } else { + return eta - 1.0; + } + } + }; - REAL phys0, phys1, phys2; - mapper.x(Lcoord[0], Lcoord[1], Lcoord[2], &phys0, &phys1, &phys2); - nprint("N", phys0, phys1, phys2); - - EXPECT_NEAR(phys0, x, 1.0e-10); - EXPECT_NEAR(phys1, y, 1.0e-10); - EXPECT_NEAR(phys2, z, 1.0e-10); - - - const REAL xi00 = Lcoord[0]; - const REAL xi01 = Lcoord[1]; - const REAL xi02 = Lcoord[2]; - REAL eta0, eta1, eta2; + auto lambda_test_contained = [&](const auto eta0, const auto eta1, + const auto eta2) -> REAL { + return std::max(lambda_test_contained_dir(eta0), + std::max(lambda_test_contained_dir(eta1), + lambda_test_contained_dir(eta2))); + }; - GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi00, - xi01, xi02, &eta0, - &eta1, &eta2); - EXPECT_NEAR(eta0, eta[0], 1.0e-12); - EXPECT_NEAR(eta1, eta[1], 1.0e-12); - EXPECT_NEAR(eta2, eta[2], 1.0e-12); - nprint("coords:", xi00, xi01, xi02, eta0, eta1, eta2); - - REAL xi0, xi1, xi2; - const bool converged = - mapper.x_inverse(phys0, phys1, phys2, &xi0, &xi1, &xi2, 1.0e-10); - nprint("Q", xi0, xi1, xi2, converged); - // these might be quite far depending on the map - the residual is on the X - // map output - EXPECT_NEAR(xi0, Lcoord[0], 1.0e-2); - EXPECT_NEAR(xi1, Lcoord[1], 1.0e-2); - EXPECT_NEAR(xi2, Lcoord[2], 1.0e-2); - - Array Lcoordt(3); - Lcoordt[0] = xi0; - Lcoordt[1] = xi1; - Lcoordt[2] = xi2; - const REAL g0 = geom->GetCoord(0, Lcoordt); - const REAL g1 = geom->GetCoord(1, Lcoordt); - const REAL g2 = geom->GetCoord(2, Lcoordt); - EXPECT_NEAR(g0, Gcoord[0], 1.0e-5); - EXPECT_NEAR(g1, Gcoord[1], 1.0e-5); - EXPECT_NEAR(g2, Gcoord[2], 1.0e-5); - - - - if (static_cast(geom->GetShapeType()) == 5) { - auto z0 = xmap->GetBase()[0]->GetZ(); - auto bw0 = xmap->GetBase()[0]->GetBaryWeights(); - const int N0 = 4; - std::vector div_space0(N0); - Bary::preprocess_weights(N0, eta[0], &z0[0], &bw0[0], div_space0.data()); - for (int ix = 0; ix < N0; ix++) { - nprint("host0:", ix, div_space0[ix]); - } - auto z1 = xmap->GetBase()[1]->GetZ(); - auto bw1 = xmap->GetBase()[1]->GetBaryWeights(); - const int N1 = 3; - std::vector div_space1(N1); - Bary::preprocess_weights(N1, eta[1], &z1[0], &bw1[0], div_space1.data()); - for (int ix = 0; ix < N1; ix++) { - nprint("host1:", ix, div_space1[ix]); + auto rng = std::mt19937(9457 + rank); + auto lambda_sample_internal_point = [&](auto geom, Array &xi, + Array &phys) { + auto contained = false; + auto bounding_box = geom->GetBoundingBox(); + std::uniform_real_distribution uniform0(bounding_box[0], + bounding_box[3]); + std::uniform_real_distribution uniform1(bounding_box[1], + bounding_box[4]); + std::uniform_real_distribution uniform2(bounding_box[2], + bounding_box[5]); + + INT c = 0; + while (!contained) { + phys[0] = uniform0(rng); + phys[1] = uniform1(rng); + phys[2] = uniform2(rng); + contained = geom->ContainsPoint(phys, xi, 1.0e-12); + if (1e4 < c++) { + nprint( + "Test point sampling is taking an excessive number of iterations."); } } + lambda_forward_map(geom, xi, phys); + }; + + auto lambda_check_x_map = [&](auto geom, Array &xi, + Array &phys) { + nprint("CHECK X MAP START", xi[0], xi[1], xi[2], phys[0], phys[1], phys[2]); + + REAL eta0, eta1, eta2; + const int shape_type_int = static_cast(geom->GetShapeType()); + // The point we sampled was considered contained by Nektar++ + // Check that this alternative reference point is also contained. + const REAL xi00 = xi[0]; + const REAL xi01 = xi[1]; + const REAL xi02 = xi[2]; + GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi00, xi01, + xi02, &eta0, &eta1, &eta2); + const auto dist = lambda_test_contained(eta0, eta1, eta2); + nprint("dist0", dist, eta0, eta1, eta2); + EXPECT_TRUE(dist < 1.0e-8); + + // test the forward x map from reference space to physical space + Newton::XMapNewton mapper(sycl_target, geom); + REAL test_phys0, test_phys1, test_phys2; + mapper.x(xi[0], xi[1], xi[2], &test_phys0, &test_phys1, &test_phys2); + EXPECT_NEAR(phys[0], test_phys0, 1.0e-10); + EXPECT_NEAR(phys[1], test_phys1, 1.0e-10); + EXPECT_NEAR(phys[2], test_phys2, 1.0e-10); + + REAL test_xi0, test_xi1, test_xi2; + const bool converged = mapper.x_inverse( + phys[0], phys[1], phys[2], &test_xi0, &test_xi1, &test_xi2, 1.0e-10); + EXPECT_TRUE(converged); + + const bool same_xi = (std::abs(test_xi0 - xi[0]) < 1.0e-8) && + (std::abs(test_xi1 - xi[1]) < 1.0e-8) && + (std::abs(test_xi2 - xi[2]) < 1.0e-8); + + // If the test_xi is xi then the inverse mapping was good + // Otherwise check test_xi is a reference coordinate that maps to phys + if (!same_xi) { + Array test_phys(3); + lambda_forward_map(geom, xi, test_phys); + const bool equiv_xi = (std::abs(test_phys[0] - phys[0]) < 1.0e-8) && + (std::abs(test_phys[1] - phys[1]) < 1.0e-8) && + (std::abs(test_phys[2] - phys[2]) < 1.0e-8); + + // The point we sampled was considered contained by Nektar++ + // Check that this alternative reference point is also contained. + const REAL xi00 = test_xi0; + const REAL xi01 = test_xi1; + const REAL xi02 = test_xi2; + GeometryInterface::loc_coord_to_loc_collapsed_3d( + shape_type_int, xi00, xi01, xi02, &eta0, &eta1, &eta2); + + const auto dist = lambda_test_contained(eta0, eta1, eta2); + nprint("dist1", dist, eta0, eta1, eta2); + EXPECT_TRUE(dist < 1.0e-8); + } + + nprint("CHECK X MAP END"); + }; + + for (auto gx : geoms) { + auto geom = gx.second; + auto xmap = geom->GetXmap(); + const int shape_type_int = static_cast(geom->GetShapeType()); + nprint(geom->GetShapeType(), lambda_stype(geom->GetShapeType())); + nprint("Num bases:", xmap->GetNumBases()); + for (int dx = 0; dx < 3; dx++) { + nprint("dx:", dx, "type:", lambda_btype(xmap->GetBasisType(dx)), + xmap->GetBasisNumModes(dx)); + } + + Array test_xi(3); + Array test_phys(3); + lambda_sample_internal_point(geom, test_xi, test_phys); + lambda_check_x_map(geom, test_xi, test_phys); } mesh->free(); From ca1410883eb48bd9f6b7674afba4308f8d35e5df Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 21 Oct 2024 12:51:07 +0100 Subject: [PATCH 10/66] updated some of the Newton interfaces which need updating for local memory --- .../particle_cell_mapping/newton_quad_embed_3d.hpp | 2 +- .../particle_cell_mapping/newton_triangle_embed_3d.hpp | 2 +- .../composite_interaction/composite_collections.cpp | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp index 71480933..4877c9b4 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp @@ -14,7 +14,7 @@ namespace Newton { struct MappingQuadLinear2DEmbed3D : MappingNewtonIterationBase { - inline void write_data_v(GeometrySharedPtr geom, void *data_host, + inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp index 6ec3741d..4bb16d0e 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp @@ -19,7 +19,7 @@ namespace Newton { struct MappingTriangleLinear2DEmbed3D : MappingNewtonIterationBase { - inline void write_data_v(GeometrySharedPtr geom, void *data_host, + inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/src/nektar_interface/composite_interaction/composite_collections.cpp b/src/nektar_interface/composite_interaction/composite_collections.cpp index b11fa2ee..4e2673b5 100644 --- a/src/nektar_interface/composite_interaction/composite_collections.cpp +++ b/src/nektar_interface/composite_interaction/composite_collections.cpp @@ -87,7 +87,7 @@ void CompositeCollections::collect_cell(const INT cell) { for (int gx = 0; gx < num_quads; gx++) { auto remote_geom = remote_quads[gx]; auto geom = remote_geom->geom; - mapper_quads.write_data(geom, nullptr, + mapper_quads.write_data(this->sycl_target, geom, nullptr, map_data_quads + gx * stride_quads); LinePlaneIntersection lpi(geom); buf_lpi.push_back(lpi); @@ -106,7 +106,7 @@ void CompositeCollections::collect_cell(const INT cell) { for (int gx = 0; gx < num_tris; gx++) { auto remote_geom = remote_tris[gx]; auto geom = remote_geom->geom; - mapper_tris.write_data(geom, nullptr, map_data_tris + gx * stride_tris); + mapper_tris.write_data(this->sycl_target, geom, nullptr, map_data_tris + gx * stride_tris); LinePlaneIntersection lpi(geom); buf_lpi.push_back(lpi); const auto composite_id = remote_geom->rank; From 5b1031a1d54a82961f74efd10ba7b2d6ffe43588 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 22 Oct 2024 17:11:50 +0100 Subject: [PATCH 11/66] progress updating curved mesh branch to work after mergin in main --- .../map_particles_newton.hpp | 210 ------------------ .../newton_quad_embed_3d.hpp | 3 +- .../newton_triangle_embed_3d.hpp | 3 +- .../x_map_newton_kernel.hpp | 18 +- .../composite_collections.cpp | 5 +- .../composite_intersection.cpp | 14 +- 6 files changed, 31 insertions(+), 222 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp index 48bdd1be..eb45a468 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp @@ -504,216 +504,6 @@ class MapParticlesNewton : public CoarseMappersBase { if (map_cell != -1) { this->map_final(particle_group, map_cell); } - - auto &clm = this->coarse_lookup_map; - // Get kernel pointers to the mesh data. - const auto &mesh = clm->cartesian_mesh; - const auto k_mesh_cell_count = mesh->get_cell_count(); - const auto k_mesh_origin = mesh->dh_origin->d_buffer.ptr; - const auto k_mesh_cell_counts = mesh->dh_cell_counts->d_buffer.ptr; - const auto k_mesh_inverse_cell_widths = - mesh->dh_inverse_cell_widths->d_buffer.ptr; - // Get kernel pointers to the map data. - const auto k_map_cell_ids = this->dh_cell_ids->d_buffer.ptr; - const auto k_map_mpi_ranks = this->dh_mpi_ranks->d_buffer.ptr; - const auto k_map_type = this->dh_type->d_buffer.ptr; - const auto k_map_data = this->dh_data->d_buffer.ptr; - const auto k_map = clm->dh_map->d_buffer.ptr; - const auto k_map_sizes = clm->dh_map_sizes->d_buffer.ptr; - const auto k_map_stride = clm->map_stride; - const double k_tol = this->newton_tol; - const int k_ndim = this->ndim; - const int k_num_bytes_per_map_device = this->num_bytes_per_map_device; - const int k_max_iterations = this->newton_max_iteration; - - // Get kernel pointers to the ParticleDats - const auto position_dat = particle_group.position_dat; - const auto k_part_positions = position_dat->cell_dat.device_ptr(); - auto k_part_cell_ids = particle_group.cell_id_dat->cell_dat.device_ptr(); - auto k_part_mpi_ranks = particle_group.mpi_rank_dat->cell_dat.device_ptr(); - auto k_part_ref_positions = - particle_group[Sym("NESO_REFERENCE_POSITIONS")] - ->cell_dat.device_ptr(); - - // Get iteration set for particles, two cases single cell case or all cells - const int max_cell_occupancy = (map_cell > -1) - ? position_dat->h_npart_cell[map_cell] - : position_dat->cell_dat.get_nrow_max(); - const int k_cell_offset = (map_cell > -1) ? map_cell : 0; - const std::size_t local_size = 256; - const auto div_mod = std::div(max_cell_occupancy, local_size); - const int outer_size = div_mod.quot + (div_mod.rem == 0 ? 0 : 1); - const std::size_t cell_count = - (map_cell > -1) - ? 1 - : static_cast(position_dat->cell_dat.ncells); - sycl::range<2> outer_iterset{local_size * outer_size, cell_count}; - sycl::range<2> local_iterset{local_size, 1}; - const auto k_npart_cell = position_dat->d_npart_cell; - - this->ep->reset(); - auto k_ep = this->ep->device_ptr(); - - this->sycl_target->queue - .submit([&](sycl::handler &cgh) { - cgh.parallel_for<>( - sycl::nd_range<2>(outer_iterset, local_iterset), - [=](sycl::nd_item<2> idx) { - const int cellx = idx.get_global_id(1) + k_cell_offset; - const int layerx = idx.get_global_id(0); - if (layerx < k_npart_cell[cellx]) { - if (k_part_mpi_ranks[cellx][1][layerx] < 0) { - - // read the position of the particle - const REAL p0 = k_part_positions[cellx][0][layerx]; - const REAL p1 = - (k_ndim > 1) ? k_part_positions[cellx][1][layerx] : 0.0; - const REAL p2 = - (k_ndim > 2) ? k_part_positions[cellx][2][layerx] : 0.0; - const REAL shifted_p0 = p0 - k_mesh_origin[0]; - const REAL shifted_p1 = - (k_ndim > 1) ? p1 - k_mesh_origin[1] : 0.0; - const REAL shifted_p2 = - (k_ndim > 2) ? p2 - k_mesh_origin[2] : 0.0; - - // determine the cartesian mesh cell for the position - int c0 = (k_mesh_inverse_cell_widths[0] * shifted_p0); - int c1 = (k_ndim > 1) - ? (k_mesh_inverse_cell_widths[1] * shifted_p1) - : 0; - int c2 = (k_ndim > 2) - ? (k_mesh_inverse_cell_widths[2] * shifted_p2) - : 0; - c0 = (c0 < 0) ? 0 : c0; - c1 = (c1 < 0) ? 0 : c1; - c2 = (c2 < 0) ? 0 : c2; - c0 = (c0 >= k_mesh_cell_counts[0]) - ? k_mesh_cell_counts[0] - 1 - : c0; - if (k_ndim > 1) { - c1 = (c1 >= k_mesh_cell_counts[1]) - ? k_mesh_cell_counts[1] - 1 - : c1; - } - if (k_ndim > 2) { - c2 = (c2 >= k_mesh_cell_counts[2]) - ? k_mesh_cell_counts[2] - 1 - : c2; - } - - const int mcc0 = k_mesh_cell_counts[0]; - const int mcc1 = (k_ndim > 1) ? k_mesh_cell_counts[1] : 0; - const int linear_mesh_cell = - c0 + c1 * mcc0 + c2 * mcc0 * mcc1; - - const bool valid_cell = - (linear_mesh_cell >= 0) && - (linear_mesh_cell < k_mesh_cell_count); - // loop over the candidate geometry objects - bool cell_found = false; - for (int candidate_cell = 0; - (candidate_cell < k_map_sizes[linear_mesh_cell]) && - (valid_cell); - candidate_cell++) { - const int geom_map_index = - k_map[linear_mesh_cell * k_map_stride + - candidate_cell]; - - const char *map_data = - (k_num_bytes_per_map_device) - ? &k_map_data[geom_map_index * - k_num_bytes_per_map_device] - : nullptr; - - REAL xi0; - REAL xi1; - REAL xi2; - MappingNewtonIterationBase k_newton_type{}; - k_newton_type.set_initial_iteration(map_data, p0, p1, p2, - &xi0, &xi1, &xi2); - - // Start of Newton iteration - REAL xin0, xin1, xin2; - REAL f0, f1, f2; - - // TODO - REAL residual = k_newton_type.newton_residual( - map_data, xi0, xi1, xi2, p0, p1, p2, &f0, &f1, &f2, - nullptr); - - bool diverged = false; - - for (int stepx = 0; ((stepx < k_max_iterations) && - (residual > k_tol) && (!diverged)); - stepx++) { - - // TODO - k_newton_type.newton_step(map_data, xi0, xi1, xi2, p0, - p1, p2, f0, f1, f2, &xin0, - &xin1, &xin2, nullptr); - - xi0 = xin0; - xi1 = xin1; - xi2 = xin2; - - // TODO - residual = k_newton_type.newton_residual( - map_data, xi0, xi1, xi2, p0, p1, p2, &f0, &f1, &f2, - nullptr); - - diverged = (ABS(xi0) > 15.0) || (ABS(xi1) > 15.0) || - (ABS(xi2) > 15.0); - } - - bool converged = (residual <= k_tol); - REAL eta0; - REAL eta1; - REAL eta2; - - k_newton_type.loc_coord_to_loc_collapsed( - map_data, xi0, xi1, xi2, &eta0, &eta1, &eta2); - - bool contained = - ((eta0 <= 1.0) && (eta0 >= -1.0) && (eta1 <= 1.0) && - (eta1 >= -1.0) && (eta2 <= 1.0) && (eta2 >= -1.0) && - converged); - - REAL dist = 0.0; - if ((!contained) && converged) { - dist = (eta0 < -1.0) ? (-1.0 - eta0) : 0.0; - dist = - std::max(dist, (eta0 > 1.0) ? (eta0 - 1.0) : 0.0); - dist = - std::max(dist, (eta1 < -1.0) ? (-1.0 - eta1) : 0.0); - dist = - std::max(dist, (eta1 > 1.0) ? (eta1 - 1.0) : 0.0); - dist = - std::max(dist, (eta2 < -1.0) ? (-1.0 - eta2) : 0.0); - dist = - std::max(dist, (eta2 > 1.0) ? (eta2 - 1.0) : 0.0); - } - - cell_found = (dist <= k_tol) && converged; - if (cell_found) { - const int geom_id = k_map_cell_ids[geom_map_index]; - const int mpi_rank = k_map_mpi_ranks[geom_map_index]; - k_part_cell_ids[cellx][0][layerx] = geom_id; - k_part_mpi_ranks[cellx][1][layerx] = mpi_rank; - k_part_ref_positions[cellx][0][layerx] = xi0; - if (k_ndim > 1) { - k_part_ref_positions[cellx][1][layerx] = xi1; - } - if (k_ndim > 2) { - k_part_ref_positions[cellx][2][layerx] = xi2; - } - break; - } - } - } - } - }); - }) - .wait_and_throw(); } }; diff --git a/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp index 71480933..143ea5cd 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp @@ -14,7 +14,8 @@ namespace Newton { struct MappingQuadLinear2DEmbed3D : MappingNewtonIterationBase { - inline void write_data_v(GeometrySharedPtr geom, void *data_host, + inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, + GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp index 6ec3741d..6390ded7 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp @@ -19,7 +19,8 @@ namespace Newton { struct MappingTriangleLinear2DEmbed3D : MappingNewtonIterationBase { - inline void write_data_v(GeometrySharedPtr geom, void *data_host, + inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, + GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp index 598e376d..0d959053 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp @@ -26,9 +26,11 @@ template struct XMapNewtonKernel { * @param[in, out] phys0 Global position X(xi), x component. * @param[in, out] phys1 Global position X(xi), y component. * @param[in, out] phys2 Global position X(xi), z component. + * @param[in, out] local_memory Local memory as required by the Newton + * implementation. May be modified by this function. */ inline void x(const void *map_data, const REAL xi0, const REAL xi1, - const REAL xi2, REAL *phys0, REAL *phys1, REAL *phys2) { + const REAL xi2, REAL *phys0, REAL *phys1, REAL *phys2, void * local_memory) { *phys0 = 0.0; *phys1 = 0.0; @@ -39,7 +41,7 @@ template struct XMapNewtonKernel { MappingNewtonIterationBase k_newton_type{}; k_newton_type.newton_residual(map_data, xi0, xi1, xi2, p0, p1, p2, phys0, - phys1, phys2); + phys1, phys2, local_memory); } /** @@ -53,6 +55,8 @@ template struct XMapNewtonKernel { * @param[in, out] xi0 Reference position, x component. * @param[in, out] xi1 Reference position, y component. * @param[in, out] xi2 Reference position, z component. + * @param[in, out] local_memory Local memory as required by the Newton + * implementation. May be modified by this function. * @param[in] max_iterations Maximum number of Newton iterations. * @param[in] tol Optional exit tolerance for Newton iterations * (default 1.0e-10). @@ -62,7 +66,9 @@ template struct XMapNewtonKernel { */ inline bool x_inverse(const void *map_data, const REAL phys0, const REAL phys1, const REAL phys2, REAL *xi0, - REAL *xi1, REAL *xi2, const INT max_iterations, + REAL *xi1, REAL *xi2, + void * local_memory, + const INT max_iterations, const REAL tol = 1.0e-10, const bool initial_override = false) { @@ -87,7 +93,7 @@ template struct XMapNewtonKernel { REAL f0, f1, f2; REAL residual = k_newton_type.newton_residual(map_data, k_xi0, k_xi1, k_xi2, - p0, p1, p2, &f0, &f1, &f2); + p0, p1, p2, &f0, &f1, &f2, local_memory); bool diverged = false; @@ -95,14 +101,14 @@ template struct XMapNewtonKernel { ((stepx < max_iterations) && (residual > tol) && (!diverged)); stepx++) { k_newton_type.newton_step(map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f0, - f1, f2, &xin0, &xin1, &xin2); + f1, f2, &xin0, &xin1, &xin2, local_memory); k_xi0 = xin0; k_xi1 = xin1; k_xi2 = xin2; residual = k_newton_type.newton_residual(map_data, k_xi0, k_xi1, k_xi2, - p0, p1, p2, &f0, &f1, &f2); + p0, p1, p2, &f0, &f1, &f2, local_memory); diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || (ABS(k_xi2) > 15.0); diff --git a/src/nektar_interface/composite_interaction/composite_collections.cpp b/src/nektar_interface/composite_interaction/composite_collections.cpp index b11fa2ee..3e320b2f 100644 --- a/src/nektar_interface/composite_interaction/composite_collections.cpp +++ b/src/nektar_interface/composite_interaction/composite_collections.cpp @@ -87,7 +87,7 @@ void CompositeCollections::collect_cell(const INT cell) { for (int gx = 0; gx < num_quads; gx++) { auto remote_geom = remote_quads[gx]; auto geom = remote_geom->geom; - mapper_quads.write_data(geom, nullptr, + mapper_quads.write_data(this->sycl_target, geom, nullptr, map_data_quads + gx * stride_quads); LinePlaneIntersection lpi(geom); buf_lpi.push_back(lpi); @@ -106,7 +106,8 @@ void CompositeCollections::collect_cell(const INT cell) { for (int gx = 0; gx < num_tris; gx++) { auto remote_geom = remote_tris[gx]; auto geom = remote_geom->geom; - mapper_tris.write_data(geom, nullptr, map_data_tris + gx * stride_tris); + mapper_tris.write_data(this->sycl_target, geom, nullptr, + map_data_tris + gx * stride_tris); LinePlaneIntersection lpi(geom); buf_lpi.push_back(lpi); const auto composite_id = remote_geom->rank; diff --git a/src/nektar_interface/composite_interaction/composite_intersection.cpp b/src/nektar_interface/composite_interaction/composite_intersection.cpp index e101cb22..70a64624 100644 --- a/src/nektar_interface/composite_interaction/composite_intersection.cpp +++ b/src/nektar_interface/composite_interaction/composite_intersection.cpp @@ -401,6 +401,11 @@ void CompositeIntersection::find_intersections_3d( const int k_grid_size_y = grid_size; const REAL k_grid_width = 2.0 / grid_size; + static_assert( + !Newton::local_memory_required::required, + "Did not expect local memory to be required for this Newton implemenation" + ); + particle_loop( "CompositeIntersection::find_intersections_3d_quads", iteration_set, [=](auto k_P, auto k_PP, auto k_OUT_P, auto k_OUT_C) { @@ -514,7 +519,7 @@ void CompositeIntersection::find_intersections_3d( const bool converged = k_newton_kernel.x_inverse( map_data, i0, i1, i2, &xi[0], &xi[1], &xi[2], - k_max_iterations, k_newton_tol, true); + nullptr, k_max_iterations, k_newton_tol, true); k_newton_type.loc_coord_to_loc_collapsed( map_data, xi[0], xi[1], xi[2], &eta0, &eta1, @@ -558,6 +563,11 @@ void CompositeIntersection::find_intersections_3d( Access::write(dat_positions->sym), Access::write(dat_composite->sym)) ->execute(); + static_assert( + !Newton::local_memory_required::required, + "Did not expect local memory to be required for this Newton implemenation" + ); + particle_loop( "CompositeIntersection::find_intersections_3d_triangles", iteration_set, [=](auto k_P, auto k_PP, auto k_OUT_P, auto k_OUT_C) { @@ -666,7 +676,7 @@ void CompositeIntersection::find_intersections_3d( k_newton_kernel; const bool converged = k_newton_kernel.x_inverse( map_data, i0, i1, i2, &xi0, &xi1, &xi2, - k_max_iterations, k_newton_tol); + nullptr, k_max_iterations, k_newton_tol); k_newton_type.loc_coord_to_loc_collapsed( map_data, xi0, xi1, xi2, &eta0, &eta1, &eta2); From 2e84e5935d401e65e211bbbf282aa7edc6f6f1dc Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 23 Oct 2024 12:16:40 +0100 Subject: [PATCH 12/66] branch compiles again after merging in main --- .../map_particles_newton.hpp | 34 ++++++++++++++----- .../newton_quad_embed_3d.hpp | 4 +-- .../newton_triangle_embed_3d.hpp | 2 +- .../x_map_newton_kernel.hpp | 18 +++++----- .../composite_collections.cpp | 2 +- .../composite_intersection.cpp | 20 +++++------ 6 files changed, 48 insertions(+), 32 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp index eb45a468..fbbc18a6 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp @@ -71,8 +71,10 @@ class MapParticlesNewton : public CoarseMappersBase { MappingNewtonIterationBase newton_type; const std::size_t num_bytes_per_map_device; const std::size_t num_bytes_per_map_host; + std::size_t num_bytes_local_memory; - template inline void write_data(U &geom, const int index) { + template + inline std::size_t write_data(U &geom, const int index) { auto d_data_ptr = (this->num_bytes_per_map_device) ? this->dh_data->h_buffer.ptr + @@ -85,6 +87,8 @@ class MapParticlesNewton : public CoarseMappersBase { this->newton_type.write_data(this->sycl_target, geom, h_data_ptr, d_data_ptr); + // Return the number of bytes of local memory this object requires. + return this->newton_type.data_size_local(h_data_ptr); } inline void map_inital(ParticleGroup &particle_group, const int map_cell) { @@ -120,12 +124,14 @@ class MapParticlesNewton : public CoarseMappersBase { auto mpi_ranks = particle_group.mpi_rank_dat; auto ref_positions = particle_group.get_dat(Sym("NESO_REFERENCE_POSITIONS")); + auto local_memory = LocalMemoryBlock(this->num_bytes_local_memory); auto loop = particle_loop( "MapParticlesNewton::map_inital", position_dat, [=](auto k_part_positions, auto k_part_cell_ids, auto k_part_mpi_ranks, - auto k_part_ref_positions) { + auto k_part_ref_positions, auto k_local_memory) { if (k_part_mpi_ranks.at(1) < 0) { + void *k_local_memory_ptr = k_local_memory.data(); // read the position of the particle const REAL p0 = k_part_positions.at(0); const REAL p1 = (k_ndim > 1) ? k_part_positions.at(1) : 0.0; @@ -182,7 +188,7 @@ class MapParticlesNewton : public CoarseMappersBase { const bool converged = k_newton_kernel.x_inverse( map_data, p0, p1, p2, &xi[0], &xi[1], &xi[2], - k_max_iterations, k_newton_tol); + k_local_memory_ptr, k_max_iterations, k_newton_tol); REAL eta0; REAL eta1; @@ -212,7 +218,8 @@ class MapParticlesNewton : public CoarseMappersBase { } }, Access::read(position_dat), Access::write(cell_ids), - Access::write(mpi_ranks), Access::write(ref_positions)); + Access::write(mpi_ranks), Access::write(ref_positions), + Access::write(local_memory)); if (map_cell > -1) { loop->execute(map_cell); @@ -258,12 +265,14 @@ class MapParticlesNewton : public CoarseMappersBase { auto mpi_ranks = particle_group.mpi_rank_dat; auto ref_positions = particle_group.get_dat(Sym("NESO_REFERENCE_POSITIONS")); + auto local_memory = LocalMemoryBlock(this->num_bytes_local_memory); particle_loop( "MapParticlesNewton::map_final", position_dat, [=](auto k_part_positions, auto k_part_cell_ids, auto k_part_mpi_ranks, - auto k_part_ref_positions) { + auto k_part_ref_positions, auto k_local_memory) { if (k_part_mpi_ranks.at(1) < 0) { + void *k_local_memory_ptr = k_local_memory.data(); // read the position of the particle const REAL p0 = k_part_positions.at(0); const REAL p1 = (k_ndim > 1) ? k_part_positions.at(1) : 0.0; @@ -327,7 +336,8 @@ class MapParticlesNewton : public CoarseMappersBase { const bool converged = k_newton_kernel.x_inverse( map_data, p0, p1, p2, &xi[0], &xi[1], &xi[2], - k_max_iterations, k_newton_tol, true); + k_local_memory_ptr, k_max_iterations, k_newton_tol, + true); REAL eta0; REAL eta1; @@ -361,7 +371,8 @@ class MapParticlesNewton : public CoarseMappersBase { } }, Access::read(position_dat), Access::write(cell_ids), - Access::write(mpi_ranks), Access::write(ref_positions)) + Access::write(mpi_ranks), Access::write(ref_positions), + Access::write(local_memory)) ->execute(map_cell); } @@ -449,6 +460,11 @@ class MapParticlesNewton : public CoarseMappersBase { const int rank = this->sycl_target->comm_pair.rank_parent; int num_modes = 0; + this->num_bytes_local_memory = 0; + auto lambda_update_local_memory = [&](const std::size_t s) { + this->num_bytes_local_memory = + std::max(this->num_bytes_local_memory, s); + }; for (auto &geom : geoms_local) { const int id = geom.second->GetGlobalID(); const int cell_index = this->coarse_lookup_map->gid_to_lookup_id.at(id); @@ -464,7 +480,7 @@ class MapParticlesNewton : public CoarseMappersBase { (geom_type == index_tri) || (geom_type == index_quad), "Unknown shape type."); this->dh_type->h_buffer.ptr[cell_index] = geom_type; - this->write_data(geom.second, cell_index); + lambda_update_local_memory(this->write_data(geom.second, cell_index)); num_modes = std::max(num_modes, geom.second->GetXmap()->EvalBasisNumModesMax()); } @@ -482,7 +498,7 @@ class MapParticlesNewton : public CoarseMappersBase { (geom_type == index_tri) || (geom_type == index_quad), "Unknown shape type."); this->dh_type->h_buffer.ptr[cell_index] = geom_type; - this->write_data(geom->geom, cell_index); + lambda_update_local_memory(this->write_data(geom->geom, cell_index)); num_modes = std::max(num_modes, geom->geom->GetXmap()->EvalBasisNumModesMax()); } diff --git a/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp index 143ea5cd..e2729790 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp @@ -14,8 +14,8 @@ namespace Newton { struct MappingQuadLinear2DEmbed3D : MappingNewtonIterationBase { - inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, - GeometrySharedPtr geom, void *data_host, + inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, + GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp index 6390ded7..89d1a2e7 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp @@ -20,7 +20,7 @@ struct MappingTriangleLinear2DEmbed3D : MappingNewtonIterationBase { inline void write_data_v([[maybe_unused]] SYCLTargetSharedPtr sycl_target, - GeometrySharedPtr geom, void *data_host, + GeometrySharedPtr geom, void *data_host, void *data_device) { REAL *data_device_real = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp index 0d959053..99da0ee7 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp @@ -30,7 +30,8 @@ template struct XMapNewtonKernel { * implementation. May be modified by this function. */ inline void x(const void *map_data, const REAL xi0, const REAL xi1, - const REAL xi2, REAL *phys0, REAL *phys1, REAL *phys2, void * local_memory) { + const REAL xi2, REAL *phys0, REAL *phys1, REAL *phys2, + void *local_memory) { *phys0 = 0.0; *phys1 = 0.0; @@ -66,10 +67,8 @@ template struct XMapNewtonKernel { */ inline bool x_inverse(const void *map_data, const REAL phys0, const REAL phys1, const REAL phys2, REAL *xi0, - REAL *xi1, REAL *xi2, - void * local_memory, - const INT max_iterations, - const REAL tol = 1.0e-10, + REAL *xi1, REAL *xi2, void *local_memory, + const INT max_iterations, const REAL tol = 1.0e-10, const bool initial_override = false) { MappingNewtonIterationBase k_newton_type{}; @@ -92,8 +91,8 @@ template struct XMapNewtonKernel { REAL xin0, xin1, xin2; REAL f0, f1, f2; - REAL residual = k_newton_type.newton_residual(map_data, k_xi0, k_xi1, k_xi2, - p0, p1, p2, &f0, &f1, &f2, local_memory); + REAL residual = k_newton_type.newton_residual( + map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, &f2, local_memory); bool diverged = false; @@ -107,8 +106,9 @@ template struct XMapNewtonKernel { k_xi1 = xin1; k_xi2 = xin2; - residual = k_newton_type.newton_residual(map_data, k_xi0, k_xi1, k_xi2, - p0, p1, p2, &f0, &f1, &f2, local_memory); + residual = + k_newton_type.newton_residual(map_data, k_xi0, k_xi1, k_xi2, p0, p1, + p2, &f0, &f1, &f2, local_memory); diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || (ABS(k_xi2) > 15.0); diff --git a/src/nektar_interface/composite_interaction/composite_collections.cpp b/src/nektar_interface/composite_interaction/composite_collections.cpp index 3e320b2f..c40db14c 100644 --- a/src/nektar_interface/composite_interaction/composite_collections.cpp +++ b/src/nektar_interface/composite_interaction/composite_collections.cpp @@ -106,7 +106,7 @@ void CompositeCollections::collect_cell(const INT cell) { for (int gx = 0; gx < num_tris; gx++) { auto remote_geom = remote_tris[gx]; auto geom = remote_geom->geom; - mapper_tris.write_data(this->sycl_target, geom, nullptr, + mapper_tris.write_data(this->sycl_target, geom, nullptr, map_data_tris + gx * stride_tris); LinePlaneIntersection lpi(geom); buf_lpi.push_back(lpi); diff --git a/src/nektar_interface/composite_interaction/composite_intersection.cpp b/src/nektar_interface/composite_interaction/composite_intersection.cpp index 70a64624..5364897a 100644 --- a/src/nektar_interface/composite_interaction/composite_intersection.cpp +++ b/src/nektar_interface/composite_interaction/composite_intersection.cpp @@ -401,10 +401,10 @@ void CompositeIntersection::find_intersections_3d( const int k_grid_size_y = grid_size; const REAL k_grid_width = 2.0 / grid_size; - static_assert( - !Newton::local_memory_required::required, - "Did not expect local memory to be required for this Newton implemenation" - ); + static_assert(!Newton::local_memory_required< + Newton::MappingQuadLinear2DEmbed3D>::required, + "Did not expect local memory to be required for this Newton " + "implemenation"); particle_loop( "CompositeIntersection::find_intersections_3d_quads", iteration_set, @@ -563,10 +563,10 @@ void CompositeIntersection::find_intersections_3d( Access::write(dat_positions->sym), Access::write(dat_composite->sym)) ->execute(); - static_assert( - !Newton::local_memory_required::required, - "Did not expect local memory to be required for this Newton implemenation" - ); + static_assert(!Newton::local_memory_required< + Newton::MappingTriangleLinear2DEmbed3D>::required, + "Did not expect local memory to be required for this Newton " + "implemenation"); particle_loop( "CompositeIntersection::find_intersections_3d_triangles", iteration_set, @@ -675,8 +675,8 @@ void CompositeIntersection::find_intersections_3d( Newton::MappingTriangleLinear2DEmbed3D> k_newton_kernel; const bool converged = k_newton_kernel.x_inverse( - map_data, i0, i1, i2, &xi0, &xi1, &xi2, - nullptr, k_max_iterations, k_newton_tol); + map_data, i0, i1, i2, &xi0, &xi1, &xi2, nullptr, + k_max_iterations, k_newton_tol); k_newton_type.loc_coord_to_loc_collapsed( map_data, xi0, xi1, xi2, &eta0, &eta1, &eta2); From 85548b62cc89f32482631b21efc9c134fa2b25cb Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 23 Oct 2024 15:06:26 +0100 Subject: [PATCH 13/66] updated NP submodule --- neso-particles | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/neso-particles b/neso-particles index 196069f9..e32da6ce 160000 --- a/neso-particles +++ b/neso-particles @@ -1 +1 @@ -Subproject commit 196069f90b5d52a09f9260c6f5c17a54d1a46c28 +Subproject commit e32da6ceb0e454489ab9172d1c23aba142700ff8 From 0278678f4b78977125eee2bb5725e6cc33d3ac56 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 23 Oct 2024 16:19:07 +0100 Subject: [PATCH 14/66] added reference grid to the X map inverse host helper class --- .../particle_cell_mapping/x_map_newton.hpp | 131 +++++++++++++----- 1 file changed, 93 insertions(+), 38 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 2f474e91..b20fef4e 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -36,6 +36,11 @@ template class XMapNewton { std::vector h_data; std::size_t num_bytes_local; + // variables for higher order grids + int num_modes; + int num_modes_factor; + int ndim; + template inline void write_data(U &geom) { if (this->num_bytes_per_map_host) { this->h_data = std::vector(this->num_bytes_per_map_host); @@ -56,6 +61,9 @@ template class XMapNewton { this->num_bytes_local = std::max(static_cast(1), this->newton_type.data_size_local(h_data_ptr)); + this->num_modes = geom->GetXmap()->EvalBasisNumModesMax(); + MappingNewtonIterationBase newton_type; + this->ndim = newton_type.get_ndim(); } public: @@ -71,13 +79,18 @@ template class XMapNewton { * @param sycl_target SYCLTarget to use for computation. * @param geom Nektar++ geometry type that matches the Newton method * implementation. + * @param num_modes_factor Factor to multiply the number of modes by to + * create the grid in reference space. Default 1, i.e a (num_modes * + * num_modes_factor)^(ndim)). */ template - XMapNewton(SYCLTargetSharedPtr sycl_target, std::shared_ptr geom) + XMapNewton(SYCLTargetSharedPtr sycl_target, std::shared_ptr geom, + const int num_modes_factor = 1) : newton_type(MappingNewtonIterationBase()), sycl_target(sycl_target), num_bytes_per_map_host(newton_type.data_size_host()), - num_bytes_per_map_device(newton_type.data_size_device()) { + num_bytes_per_map_device(newton_type.data_size_device()), + num_modes_factor(num_modes_factor) { this->write_data(geom); this->dh_fdata = std::make_unique>(this->sycl_target, 4); @@ -136,7 +149,8 @@ template class XMapNewton { /** * For a position X(xi) compute the reference position xi via Newton - * iteration. + * iteration. This method will attempt to find a root inside the reference + * element. * * @param[in] phys0 Global position X(xi), x component. * @param[in] phys1 Global position X(xi), y component. @@ -145,18 +159,29 @@ template class XMapNewton { * @param[in, out] xi1 Reference position, y component. * @param[in, out] xi2 Reference position, z component. * @param[in] tol Optional exit tolerance for Newton iterations. + * @param[in] contained_tol Optional tolerance for determining if a point is + * within the reference cell. * @returns True if inverse is found otherwise false. */ inline bool x_inverse(const REAL phys0, const REAL phys1, const REAL phys2, REAL *xi0, REAL *xi1, REAL *xi2, - const REAL tol = 1.0e-10) { + const REAL tol = 1.0e-10, + const REAL contained_tol = 1.0e-10) { const int k_max_iterations = 51; auto k_map_data = this->dh_data->d_buffer.ptr; auto k_fdata = this->dh_fdata->d_buffer.ptr; const REAL k_tol = tol; + const double k_contained_tol = contained_tol; const std::size_t num_bytes_local = this->num_bytes_local; + const int k_ndim = this->ndim; + const int grid_size = this->num_modes_factor * this->num_modes; + const int k_grid_size_x = std::max(grid_size - 1, 1); + const int k_grid_size_y = k_ndim > 1 ? k_grid_size_x : 1; + const int k_grid_size_z = k_ndim > 2 ? k_grid_size_x : 1; + const REAL k_grid_width = 2.0 / (k_grid_size_x); + this->sycl_target->queue .submit([&](sycl::handler &cgh) { sycl::accessor class XMapNewton { const REAL p0 = phys0; const REAL p1 = phys1; const REAL p2 = phys2; - REAL k_xi0; REAL k_xi1; REAL k_xi2; - k_newton_type.set_initial_iteration(k_map_data, p0, p1, p2, - &k_xi0, &k_xi1, &k_xi2); - - // Start of Newton iteration - REAL xin0, xin1, xin2; - REAL f0, f1, f2; - - REAL residual = k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, &f2, - &local_mem[0]); - - bool diverged = false; - printf("residual: %f\n", residual); - for (int stepx = 0; ((stepx < k_max_iterations) && - (residual > k_tol) && (!diverged)); - stepx++) { - printf("STEPX: %d, RES: %f\n", stepx, residual); - - k_newton_type.newton_step(k_map_data, k_xi0, k_xi1, k_xi2, p0, - p1, p2, f0, f1, f2, &xin0, &xin1, - &xin2, &local_mem[0]); - - k_xi0 = xin0; - k_xi1 = xin1; - k_xi2 = xin2; - - residual = k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, - &f2, &local_mem[0]); - - diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || - (ABS(k_xi2) > 15.0); + REAL residual; + bool cell_found = false; + + for (int g2 = 0; (g2 <= k_grid_size_z) && (!cell_found); g2++) { + for (int g1 = 0; (g1 <= k_grid_size_y) && (!cell_found); + g1++) { + for (int g0 = 0; (g0 <= k_grid_size_x) && (!cell_found); + g0++) { + + k_xi0 = -1.0 + g0 * k_grid_width; + k_xi1 = -1.0 + g1 * k_grid_width; + k_xi2 = -1.0 + g2 * k_grid_width; + + // k_newton_type.set_initial_iteration(k_map_data, p0, p1, + // p2, + // &k_xi0, &k_xi1, + // &k_xi2); + + // Start of Newton iteration + REAL xin0, xin1, xin2; + REAL f0, f1, f2; + + residual = k_newton_type.newton_residual( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, + &f2, &local_mem[0]); + + bool diverged = false; + bool converged = false; + printf("residual: %f\n", residual); + for (int stepx = 0; ((stepx < k_max_iterations) && + (!converged) && (!diverged)); + stepx++) { + printf("STEPX: %d, RES: %f\n", stepx, residual); + + k_newton_type.newton_step( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f0, f1, + f2, &xin0, &xin1, &xin2, &local_mem[0]); + + k_xi0 = xin0; + k_xi1 = xin1; + k_xi2 = xin2; + + residual = k_newton_type.newton_residual( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, + &f1, &f2, &local_mem[0]); + + diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || + (ABS(k_xi2) > 15.0); + converged = (residual <= k_tol) && (!diverged); + } + + REAL eta0, eta1, eta2; + k_newton_type.loc_coord_to_loc_collapsed( + k_map_data, k_xi0, k_xi1, k_xi2, &eta0, &eta1, &eta2); + + bool contained = ((-1.0 - k_contained_tol) <= eta0) && + (eta0 <= (1.0 + k_contained_tol)) && + ((-1.0 - k_contained_tol) <= eta1) && + (eta1 <= (1.0 + k_contained_tol)) && + ((-1.0 - k_contained_tol) <= eta2) && + (eta2 <= (1.0 + k_contained_tol)); + cell_found = contained && converged; + } + } } - k_fdata[0] = k_xi0; k_fdata[1] = k_xi1; k_fdata[2] = k_xi2; From 04c28dcdd9c46bd199798dd9112fb38f9dd4a478 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 23 Oct 2024 16:54:50 +0100 Subject: [PATCH 15/66] updated curved X map inverse test to only pass if the inverse finds the original reference position --- .../newton_generic_3d.hpp | 3 ++- .../particle_cell_mapping/x_map_newton.hpp | 2 +- ..._particle_geometry_interface_3d_curved.cpp | 26 ++++--------------- 3 files changed, 8 insertions(+), 23 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index 0101f3a6..82720ee3 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -272,8 +272,9 @@ struct MappingGeneric3D : MappingNewtonIterationBase { const REAL norm2 = MAX(MAX(ABS(*f0), ABS(*f1)), ABS(*f2)); const REAL tol_scaling = d->tol_scaling; - nprint("TOL SCALING:", tol_scaling); const REAL scaled_norm2 = norm2 * tol_scaling; + + nprint("TOL SCALING:", scaled_norm2, tol_scaling); return scaled_norm2; } diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index b20fef4e..9982746c 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -231,7 +231,7 @@ template class XMapNewton { for (int stepx = 0; ((stepx < k_max_iterations) && (!converged) && (!diverged)); stepx++) { - printf("STEPX: %d, RES: %f\n", stepx, residual); + printf("STEPX: %d, RES: %16.8e\n", stepx, residual); k_newton_type.newton_step( k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f0, f1, diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 98e7c5b2..0f05f6b8 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -340,27 +340,11 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { (std::abs(test_xi1 - xi[1]) < 1.0e-8) && (std::abs(test_xi2 - xi[2]) < 1.0e-8); - // If the test_xi is xi then the inverse mapping was good - // Otherwise check test_xi is a reference coordinate that maps to phys - if (!same_xi) { - Array test_phys(3); - lambda_forward_map(geom, xi, test_phys); - const bool equiv_xi = (std::abs(test_phys[0] - phys[0]) < 1.0e-8) && - (std::abs(test_phys[1] - phys[1]) < 1.0e-8) && - (std::abs(test_phys[2] - phys[2]) < 1.0e-8); - - // The point we sampled was considered contained by Nektar++ - // Check that this alternative reference point is also contained. - const REAL xi00 = test_xi0; - const REAL xi01 = test_xi1; - const REAL xi02 = test_xi2; - GeometryInterface::loc_coord_to_loc_collapsed_3d( - shape_type_int, xi00, xi01, xi02, &eta0, &eta1, &eta2); - - const auto dist = lambda_test_contained(eta0, eta1, eta2); - nprint("dist1", dist, eta0, eta1, eta2); - EXPECT_TRUE(dist < 1.0e-8); - } + // If there were multiple points inside the reference element that map to + // the same physical point there there are major problems with the mesh. + // Hence the point inside the reference element that maps to the physical + // point hould be unique. + ASSERT_TRUE(same_xi); nprint("CHECK X MAP END"); }; From 7ccf426a55042cdbbfc741570eec89160b2996d0 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 29 Oct 2024 11:13:06 +0000 Subject: [PATCH 16/66] added more explicit test for 3D coordinate mapping functions --- .../nektar_interface/coordinate_mapping.hpp | 123 ++-- .../mapping_newton_iteration_base.hpp | 23 + .../newton_generic_3d.hpp | 58 +- .../particle_cell_mapping/newton_prism.hpp | 13 +- .../particle_cell_mapping/newton_pyr.hpp | 13 +- .../newton_triangle_embed_3d.hpp | 12 +- .../particle_cell_mapping/x_map_newton.hpp | 10 +- .../test_particle_geometry_interface_3d.cpp | 153 +++-- ..._particle_geometry_interface_3d_curved.cpp | 549 +++++++++++++++++- 9 files changed, 783 insertions(+), 171 deletions(-) diff --git a/include/nektar_interface/coordinate_mapping.hpp b/include/nektar_interface/coordinate_mapping.hpp index 3a6a18aa..109ed65a 100644 --- a/include/nektar_interface/coordinate_mapping.hpp +++ b/include/nektar_interface/coordinate_mapping.hpp @@ -173,14 +173,14 @@ struct Tetrahedron : BaseCoordinateMapping3D { T *eta2) { NekDouble d2 = 1.0 - xi2; NekDouble d12 = -xi1 - xi2; - if (fabs(d2) < NekConstants::kNekZeroTol) { + if (sycl::fabs(d2) < NekConstants::kNekZeroTol) { if (d2 >= 0.) { d2 = NekConstants::kNekZeroTol; } else { d2 = -NekConstants::kNekZeroTol; } } - if (fabs(d12) < NekConstants::kNekZeroTol) { + if (sycl::fabs(d12) < NekConstants::kNekZeroTol) { if (d12 >= 0.) { d12 = NekConstants::kNekZeroTol; } else { @@ -235,7 +235,7 @@ struct Pyramid : BaseCoordinateMapping3D { const T xi2, T *eta0, T *eta1, T *eta2) { NekDouble d2 = 1.0 - xi2; - if (fabs(d2) < NekConstants::kNekZeroTol) { + if (sycl::fabs(d2) < NekConstants::kNekZeroTol) { if (d2 >= 0.) { d2 = NekConstants::kNekZeroTol; } else { @@ -290,7 +290,7 @@ struct Prism : BaseCoordinateMapping3D { const T xi2, T *eta0, T *eta1, T *eta2) { NekDouble d2 = 1.0 - xi2; - if (fabs(d2) < NekConstants::kNekZeroTol) { + if (sycl::fabs(d2) < NekConstants::kNekZeroTol) { if (d2 >= 0.) { d2 = NekConstants::kNekZeroTol; } else { @@ -426,7 +426,7 @@ struct Triangle : BaseCoordinateMapping2D { T *eta1) { const NekDouble d1_original = 1.0 - xi1; const bool mask_small_cond = - (fabs(d1_original) < NekConstants::kNekZeroTol); + (sycl::fabs(d1_original) < NekConstants::kNekZeroTol); NekDouble d1 = d1_original; d1 = (mask_small_cond && (d1 >= 0.0)) ? NekConstants::kNekZeroTol @@ -454,19 +454,30 @@ struct Triangle : BaseCoordinateMapping2D { } }; + + /** * Map the local collapsed coordinate (eta) to the local coordinate (xi). * * @param[in] shape_type Integer denoting shape type found by cast of Nektar++ * shape type enum to int. - * @param[in] eta Local collapsed coordinate to map to local coordinate. Must - * be a subscriptable type for indices 0,1,2. - * @param[in, out] xi Local coordinate. Must be a - * subscriptable type for indices 0,1,2. + * @param[in] eta0 Local collapsed coordinate to map to local coordinate. + * @param[in] eta1 Local collapsed coordinate to map to local coordinate. + * @param[in] eta2 Local collapsed coordinate to map to local coordinate. + * @param[in, out] xi0 Local coordinate. + * @param[in, out] xi1 Local coordinate. + * @param[in, out] xi2 Local coordinate. */ template -inline void loc_collapsed_to_loc_coord(const int shape_type, const T &eta, - T &xi) { +inline void loc_collapsed_to_loc_coord( + const int shape_type, + const T eta0, + const T eta1, + const T eta2, + T * xi0, + T * xi1, + T * xi2 + ) { /* Tet @@ -520,79 +531,39 @@ inline void loc_collapsed_to_loc_coord(const int shape_type, const T &eta, constexpr int shape_type_pyr = shape_type_to_int(LibUtilities::ePyramid); constexpr int shape_type_hex = shape_type_to_int(LibUtilities::eHexahedron); - const REAL eta0 = eta[0]; - const REAL eta1 = eta[1]; - const REAL eta2 = eta[2]; - const REAL a = 1.0 + eta0; const REAL b = 1.0 - eta2; const REAL c = (a) * (b)*0.5 - 1.0; - const REAL xi1 = + *xi1 = (shape_type == shape_type_tet) ? c : ((shape_type == shape_type_pyr) ? (1.0 + eta1) * (b)*0.5 - 1.0 : eta1); - const REAL tet_x = (1.0 + eta0) * (-xi1 - eta2) * 0.5 - 1.0; - xi[0] = (shape_type == shape_type_tet) + const REAL tet_x = (1.0 + eta0) * (-(*xi1) - eta2) * 0.5 - 1.0; + *xi0 = (shape_type == shape_type_tet) ? tet_x : ((shape_type == shape_type_hex) ? eta0 : c); - xi[1] = xi1; - xi[2] = eta2; + *xi2 = eta2; } + /** - * Map the local coordinate (xi) to the local collapsed coordinate (eta). + * Map the local collapsed coordinate (eta) to the local coordinate (xi). * * @param[in] shape_type Integer denoting shape type found by cast of Nektar++ - * @param[in] xi Local coordinate to map to collapsed coordinate. Must be a + * shape type enum to int. + * @param[in] eta Local collapsed coordinate to map to local coordinate. Must + * be a subscriptable type for indices 0,1,2. + * @param[in, out] xi Local coordinate. Must be a * subscriptable type for indices 0,1,2. - * @param[in, out] eta Local collapsed coordinate. Must be a subscriptable - * type for indices 0,1,2. */ template -inline void loc_coord_to_loc_collapsed_3d(const int shape_type, const T &xi, - T &eta) { - - constexpr int shape_type_tet = shape_type_to_int(LibUtilities::eTetrahedron); - constexpr int shape_type_pyr = shape_type_to_int(LibUtilities::ePyramid); - constexpr int shape_type_hex = shape_type_to_int(LibUtilities::eHexahedron); - - const REAL xi0 = xi[0]; - const REAL xi1 = xi[1]; - const REAL xi2 = xi[2]; - - NekDouble d2 = 1.0 - xi2; - if (fabs(d2) < NekConstants::kNekZeroTol) { - if (d2 >= 0.) { - d2 = NekConstants::kNekZeroTol; - } else { - d2 = -NekConstants::kNekZeroTol; - } - } - NekDouble d12 = -xi1 - xi2; - if (fabs(d12) < NekConstants::kNekZeroTol) { - if (d12 >= 0.) { - d12 = NekConstants::kNekZeroTol; - } else { - d12 = -NekConstants::kNekZeroTol; - } - } +inline void loc_collapsed_to_loc_coord(const int shape_type, const T &eta, + T &xi) { + loc_collapsed_to_loc_coord(shape_type, eta[0], eta[1], eta[2], &xi[0], &xi[1], &xi[2]); +} - const REAL id2x2 = 2.0 / d2; - const REAL a = 1.0 + xi0; - const REAL b = (1.0 + xi1) * id2x2 - 1.0; - const REAL c = a * id2x2 - 1.0; - const REAL d = 2.0 * a / d12 - 1.0; - eta[0] = (shape_type == shape_type_tet) ? d - : (shape_type == shape_type_hex) ? xi0 - : c; - - eta[1] = ((shape_type == shape_type_tet) || (shape_type == shape_type_pyr)) - ? b - : xi1; - eta[2] = xi2; -} /** * Map the local coordinate (xi) to the local collapsed coordinate (eta). @@ -615,7 +586,7 @@ inline void loc_coord_to_loc_collapsed_3d(const int shape_type, const T xi0, constexpr int shape_type_hex = shape_type_to_int(LibUtilities::eHexahedron); NekDouble d2 = 1.0 - xi2; - if (fabs(d2) < NekConstants::kNekZeroTol) { + if (sycl::fabs(d2) < NekConstants::kNekZeroTol) { if (d2 >= 0.) { d2 = NekConstants::kNekZeroTol; } else { @@ -623,7 +594,7 @@ inline void loc_coord_to_loc_collapsed_3d(const int shape_type, const T xi0, } } NekDouble d12 = -xi1 - xi2; - if (fabs(d12) < NekConstants::kNekZeroTol) { + if (sycl::fabs(d12) < NekConstants::kNekZeroTol) { if (d12 >= 0.) { d12 = NekConstants::kNekZeroTol; } else { @@ -647,6 +618,22 @@ inline void loc_coord_to_loc_collapsed_3d(const int shape_type, const T xi0, *eta2 = xi2; } + +/** + * Map the local coordinate (xi) to the local collapsed coordinate (eta). + * + * @param[in] shape_type Integer denoting shape type found by cast of Nektar++ + * @param[in] xi Local coordinate to map to collapsed coordinate. Must be a + * subscriptable type for indices 0,1,2. + * @param[in, out] eta Local collapsed coordinate. Must be a subscriptable + * type for indices 0,1,2. + */ +template +inline void loc_coord_to_loc_collapsed_3d(const int shape_type, const T &xi, + T &eta) { + loc_coord_to_loc_collapsed_3d(shape_type, xi[0], xi[1], xi[2], &eta[0], &eta[1], &eta[2]); +} + /** * Map the local coordinate (xi) to the local collapsed coordinate (eta). * @@ -688,7 +675,7 @@ inline bool clamp_loc_coord(T *coord, const T tol = std::numeric_limits::epsilon()) { bool clamp = false; - if (!std::isfinite(*coord)) { + if (!sycl::isfinite(*coord)) { *coord = 0.0; clamp = true; } else if ((*coord) < -(1.0 + tol)) { diff --git a/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp b/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp index 2761fcf8..ea717005 100644 --- a/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp +++ b/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp @@ -237,6 +237,29 @@ template struct MappingNewtonIterationBase { underlying.loc_coord_to_loc_collapsed_v(d_data, xi0, xi1, xi2, eta0, eta1, eta2); } + + /** + * Map from local collapsed coordinate (eta) to local coordinate (xi). + * + * @param[in] d_data Pointer to data required to perform the Newton iteration. + * @param[in] eta0 Local collapsed coordinate (eta), x component. + * @param[in] eta1 Local collapsed coordinate (eta), y component. + * @param[in] eta2 Local collapsed coordinate (eta), z component. + * @param[in, out] xi0 Local coordinate (xi) to be mapped to collapsed coordinate, + * x component. + * @param[in, out] xi1 Local coordinate (xi) to be mapped to collapsed coordinate, + * y component. + * @param[in, out] xi2 Local coordinate (xi) to be mapped to collapsed coordinate, + * z component. + */ + inline void loc_collapsed_to_loc_coord(const void *d_data, const REAL eta0, + const REAL eta1, const REAL eta2, + REAL *xi0, REAL *xi1, REAL *xi2) { + auto &underlying = static_cast(*this); + underlying.loc_collapsed_to_loc_coord_v(d_data, eta0, eta1, eta2, xi0, xi1, + xi2); + // TODO IMPLEMENT FOR NEWTON TYPES + } }; } // namespace NESO::Newton diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index 82720ee3..d9619582 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -232,8 +232,8 @@ struct MappingGeneric3D : MappingNewtonIterationBase { this->loc_coord_to_loc_collapsed(d_data, xi0, xi1, xi2, &eta0, &eta1, &eta2); - nprint("PHYS:", phys0, phys1, phys2); - nprint("COORDS:", xi0, xi1, xi2, eta0, eta1, eta2); + std::cout << std::setprecision(16); + nprint("COORDS: XI", xi0, xi1, xi2, "ETA:", eta0, eta1, eta2); // compute X at xi by evaluating the Bary interpolation at eta REAL *div_space0 = static_cast(local_memory); @@ -249,27 +249,29 @@ struct MappingGeneric3D : MappingNewtonIterationBase { d->num_phys2, d->physvals, div_space0, div_space1, div_space2, X); - const int n0 = d->num_phys0; - const int n1 = d->num_phys1; - const int n2 = d->num_phys2; - nprint("n:", n0, n1, n2); - for (int ix = 0; ix < n0; ix++) { - nprint(div_space0[ix]); - } - for (int ix = 0; ix < n1; ix++) { - nprint(div_space1[ix]); - } - for (int ix = 0; ix < n2; ix++) { - nprint(div_space2[ix]); - } - - nprint(X[0], X[1], X[2], phys0, phys1, phys2); + //const int n0 = d->num_phys0; + //const int n1 = d->num_phys1; + //const int n2 = d->num_phys2; + //nprint("n:", n0, n1, n2); + //for (int ix = 0; ix < n0; ix++) { + // nprint(div_space0[ix]); + //} + //for (int ix = 0; ix < n1; ix++) { + // nprint(div_space1[ix]); + //} + //for (int ix = 0; ix < n2; ix++) { + // nprint(div_space2[ix]); + //} + //nprint(X[0], X[1], X[2], phys0, phys1, phys2); // Residual is defined as F = X(xi) - P *f0 = X[0] - phys0; *f1 = X[1] - phys1; *f2 = X[2] - phys2; + nprint("PHYS:", phys0, phys1, phys2); + nprint(" X:", X[0], X[1], X[2]); + const REAL norm2 = MAX(MAX(ABS(*f0), ABS(*f1)), ABS(*f2)); const REAL tol_scaling = d->tol_scaling; const REAL scaled_norm2 = norm2 * tol_scaling; @@ -283,6 +285,15 @@ struct MappingGeneric3D : MappingNewtonIterationBase { inline void set_initial_iteration_v(const void *d_data, const REAL phys0, const REAL phys1, const REAL phys2, REAL *xi0, REAL *xi1, REAL *xi2) { + + /** + * Implementations that avoid singularities: + * newton_pyr + * + * + */ + + *xi0 = -0.2; *xi1 = -0.2; *xi2 = -0.2; @@ -299,6 +310,19 @@ struct MappingGeneric3D : MappingNewtonIterationBase { GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type, xi0, xi1, xi2, eta0, eta1, eta2); } + + inline void loc_collapsed_to_loc_coord_v(const void *d_data, const REAL eta0, + const REAL eta1, const REAL eta2, + REAL *xi0, REAL *xi1, REAL *xi2) { + + const Generic3D::DataDevice *data = + static_cast(d_data); + const int shape_type = data->shape_type_int; + + GeometryInterface::loc_collapsed_to_loc_coord(shape_type, eta0, eta1, eta2, + xi0, xi1, xi2); + } + }; /** diff --git a/include/nektar_interface/particle_cell_mapping/newton_prism.hpp b/include/nektar_interface/particle_cell_mapping/newton_prism.hpp index 335306bf..c30b2d84 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_prism.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_prism.hpp @@ -104,17 +104,8 @@ struct MappingPrismLinear3D : MappingNewtonIterationBase { inline void loc_coord_to_loc_collapsed_v(const void *d_data, const REAL xi0, const REAL xi1, const REAL xi2, REAL *eta0, REAL *eta1, REAL *eta2) { - NekDouble d2 = 1.0 - xi2; - if (fabs(d2) < NekConstants::kNekZeroTol) { - if (d2 >= 0.) { - d2 = NekConstants::kNekZeroTol; - } else { - d2 = -NekConstants::kNekZeroTol; - } - } - *eta2 = xi2; // eta_z = xi_z - *eta1 = xi1; // eta_y = xi_y - *eta0 = 2.0 * (1.0 + xi0) / d2 - 1.0; + GeometryInterface::Prism{}.loc_coord_to_loc_collapsed( + xi0, xi1, xi2, eta0, eta1, eta2); } }; diff --git a/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp b/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp index 245f8a47..5a510f48 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp @@ -147,17 +147,8 @@ struct MappingPyrLinear3D : MappingNewtonIterationBase { inline void loc_coord_to_loc_collapsed_v(const void *d_data, const REAL xi0, const REAL xi1, const REAL xi2, REAL *eta0, REAL *eta1, REAL *eta2) { - NekDouble d2 = 1.0 - xi2; - if (fabs(d2) < NekConstants::kNekZeroTol) { - if (d2 >= 0.) { - d2 = NekConstants::kNekZeroTol; - } else { - d2 = -NekConstants::kNekZeroTol; - } - } - *eta2 = xi2; // eta_z = xi_z - *eta1 = 2.0 * (1.0 + xi1) / d2 - 1.0; - *eta0 = 2.0 * (1.0 + xi0) / d2 - 1.0; + GeometryInterface::Pyramid{}.loc_coord_to_loc_collapsed( + xi0, xi1, xi2, eta0, eta1, eta2); } }; diff --git a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp index 89d1a2e7..da9cd0af 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp @@ -168,17 +168,9 @@ struct MappingTriangleLinear2DEmbed3D inline void loc_coord_to_loc_collapsed_v(const void *d_data, const REAL xi0, const REAL xi1, const REAL xi2, REAL *eta0, REAL *eta1, REAL *eta2) { - const NekDouble d1_original = 1.0 - xi1; - const bool mask_small_cond = - (fabs(d1_original) < NekConstants::kNekZeroTol); - NekDouble d1 = d1_original; - d1 = (mask_small_cond && (d1 >= 0.0)) - ? NekConstants::kNekZeroTol - : ((mask_small_cond && (d1 < 0.0)) ? -NekConstants::kNekZeroTol - : d1); - *eta0 = 2. * (1. + xi0) / d1 - 1.0; - *eta1 = xi1; *eta2 = 0.0; + GeometryInterface::Triangle{}.loc_coord_to_loc_collapsed( + xi0, xi1, eta0, eta1); } }; diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 9982746c..89cb1cd8 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -180,7 +180,7 @@ template class XMapNewton { const int k_grid_size_x = std::max(grid_size - 1, 1); const int k_grid_size_y = k_ndim > 1 ? k_grid_size_x : 1; const int k_grid_size_z = k_ndim > 2 ? k_grid_size_x : 1; - const REAL k_grid_width = 2.0 / (k_grid_size_x); + const REAL k_grid_width = 1.8 / (k_grid_size_x); this->sycl_target->queue .submit([&](sycl::handler &cgh) { @@ -208,10 +208,11 @@ template class XMapNewton { for (int g0 = 0; (g0 <= k_grid_size_x) && (!cell_found); g0++) { - k_xi0 = -1.0 + g0 * k_grid_width; - k_xi1 = -1.0 + g1 * k_grid_width; - k_xi2 = -1.0 + g2 * k_grid_width; + k_xi0 = -0.9 + g0 * k_grid_width; + k_xi1 = -0.9 + g1 * k_grid_width; + k_xi2 = -0.9 + g2 * k_grid_width; + nprint("~~~~~~~~~~~~~~", g0, g1, g2, ":", k_xi0, k_xi1, k_xi2); // k_newton_type.set_initial_iteration(k_map_data, p0, p1, // p2, // &k_xi0, &k_xi1, @@ -280,6 +281,7 @@ template class XMapNewton { } }; + } // namespace NESO::Newton #endif diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp index 706fc4a2..b36ad2c0 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp @@ -234,10 +234,124 @@ TEST(ParticleGeometryInterface, CoordinateMapping3D) { BufferDeviceHost dh_eta(sycl_target, 3); BufferDeviceHost dh_xi(sycl_target, 3); + std::set> vertices_found; + std::vector> vertices = { + {-1.0, -1.0, -1.0}, + { 1.0, -1.0, -1.0}, + {-1.0, 1.0, -1.0}, + { 1.0, 1.0, -1.0}, + {-1.0, -1.0, 1.0}, + { 1.0, -1.0, 1.0}, + {-1.0, 1.0, 1.0}, + { 1.0, 1.0, 1.0} + }; + for (auto &geom_pair : geoms) { auto geom = geom_pair.second; + auto lambda_test_wrapper = [&]( + auto geom, + auto geom_test + ){ + const int shape_type_int = geom->GetShapeType(); + + Array test_eta(3); + Array test_eta_neso(3); + Array test_xi(3); + Array test_xi_neso(3); + REAL eta0, eta1, eta2, xi0, xi1, xi2; + auto xmap = geom->GetXmap(); + for(auto vx : vertices){ + test_eta[0] = vx.at(0); + test_eta[1] = vx.at(1); + test_eta[2] = vx.at(2); + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + xmap->LocCoordToLocCollapsed(test_xi, test_eta); + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + xmap->LocCoordToLocCollapsed(test_xi, test_eta); + + vertices_found.insert( + { + (int) std::round(test_eta[0]), + (int) std::round(test_eta[1]), + (int) std::round(test_eta[2]) + } + ); + } + + const int num_vertices_expected = geom->GetNumVerts(); + const int num_vertices_found = vertices_found.size(); + + // At the time of writing TetGeom mapping is inconsistent with itself in Nektar++ + const bool nektar_mapping_consistent = num_vertices_found == num_vertices_expected; + + vertices_found.clear(); + + for(auto vx : vertices){ + test_eta[0] = vx.at(0); + test_eta[1] = vx.at(1); + test_eta[2] = vx.at(2); + + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi_neso); + GeometryInterface::loc_collapsed_to_loc_coord( + shape_type_int, test_eta[0], test_eta[1], test_eta[2], &xi0, &xi1, &xi2); + ASSERT_NEAR(test_xi_neso[0], xi0, 1.0e-14); + ASSERT_NEAR(test_xi_neso[1], xi1, 1.0e-14); + ASSERT_NEAR(test_xi_neso[2], xi2, 1.0e-14); + + if (nektar_mapping_consistent) { + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + ASSERT_NEAR(test_xi_neso[0], test_xi[0], 1.0e-14); + ASSERT_NEAR(test_xi_neso[1], test_xi[1], 1.0e-14); + ASSERT_NEAR(test_xi_neso[2], test_xi[2], 1.0e-14); + } + + GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, test_xi_neso, test_eta_neso); + GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi0, xi1, xi2, &eta0, &eta1, &eta2); + ASSERT_NEAR(test_eta_neso[0], eta0, 1.0e-14); + ASSERT_NEAR(test_eta_neso[1], eta1, 1.0e-14); + ASSERT_NEAR(test_eta_neso[2], eta2, 1.0e-14); + + if (nektar_mapping_consistent) { + xmap->LocCoordToLocCollapsed(test_xi_neso, test_eta); + ASSERT_NEAR(test_eta_neso[0], test_eta[0], 1.0e-14); + ASSERT_NEAR(test_eta_neso[1], test_eta[1], 1.0e-14); + ASSERT_NEAR(test_eta_neso[2], test_eta[2], 1.0e-14); + } + + vertices_found.insert( + { + (int) std::round(eta0), + (int) std::round(eta1), + (int) std::round(eta2) + } + ); + + } + + // Our implementations should be consistent. + ASSERT_EQ(vertices_found.size(), num_vertices_expected); + }; + + auto shape_type = geom->GetShapeType(); + if (shape_type == LibUtilities::eTetrahedron) { + GeometryInterface::Tetrahedron geom_test{}; + lambda_test_wrapper(geom, geom_test); + } else if (shape_type == LibUtilities::ePyramid) { + GeometryInterface::Pyramid geom_test{}; + lambda_test_wrapper(geom, geom_test); + } else if (shape_type == LibUtilities::ePrism) { + GeometryInterface::Prism geom_test{}; + lambda_test_wrapper(geom, geom_test); + } else if (shape_type == LibUtilities::eHexahedron) { + GeometryInterface::Hexahedron geom_test{}; + lambda_test_wrapper(geom, geom_test); + } else { + // Unknown shape type + ASSERT_TRUE(false); + } + Array xi0(3); Array eta0(3); double xi1[3] = {0.0, 0.0, 0.0}; @@ -266,44 +380,6 @@ TEST(ParticleGeometryInterface, CoordinateMapping3D) { ASSERT_NEAR(xi0[2], xi1[2], 1.0e-8); }; - auto shape_type = geom->GetShapeType(); - const int k_shape_type_int = shape_type_to_int(shape_type); - if (shape_type == LibUtilities::eTetrahedron) { - GeometryInterface::Tetrahedron geom_test{}; - geom->GetXmap()->LocCollapsedToLocCoord(eta0, xi0); - geom_test.loc_collapsed_to_loc_coord(eta1, xi1); - lambda_test_xi(); - geom->GetXmap()->LocCoordToLocCollapsed(xi0, eta0); - geom_test.loc_coord_to_loc_collapsed(xi1, eta1); - lambda_test_eta(); - } else if (shape_type == LibUtilities::ePyramid) { - GeometryInterface::Pyramid geom_test{}; - geom->GetXmap()->LocCollapsedToLocCoord(eta0, xi0); - geom_test.loc_collapsed_to_loc_coord(eta1, xi1); - lambda_test_xi(); - geom->GetXmap()->LocCoordToLocCollapsed(xi0, eta0); - geom_test.loc_coord_to_loc_collapsed(xi1, eta1); - lambda_test_eta(); - } else if (shape_type == LibUtilities::ePrism) { - GeometryInterface::Prism geom_test{}; - geom->GetXmap()->LocCollapsedToLocCoord(eta0, xi0); - geom_test.loc_collapsed_to_loc_coord(eta1, xi1); - lambda_test_xi(); - geom->GetXmap()->LocCoordToLocCollapsed(xi0, eta0); - geom_test.loc_coord_to_loc_collapsed(xi1, eta1); - lambda_test_eta(); - } else if (shape_type == LibUtilities::eHexahedron) { - GeometryInterface::Hexahedron geom_test{}; - geom->GetXmap()->LocCollapsedToLocCoord(eta0, xi0); - geom_test.loc_collapsed_to_loc_coord(eta1, xi1); - lambda_test_xi(); - geom->GetXmap()->LocCoordToLocCollapsed(xi0, eta0); - geom_test.loc_coord_to_loc_collapsed(xi1, eta1); - lambda_test_eta(); - } else { - // Unknown shape type - ASSERT_TRUE(false); - } // test the function that maps all types dh_eta.h_buffer.ptr[0] = k_eta0; @@ -317,6 +393,7 @@ TEST(ParticleGeometryInterface, CoordinateMapping3D) { auto k_eta = dh_eta.d_buffer.ptr; auto k_xi = dh_xi.d_buffer.ptr; + const int k_shape_type_int = shape_type_to_int(shape_type); sycl_target->queue .submit([&](sycl::handler &cgh) { diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 0f05f6b8..0c721782 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -30,7 +30,179 @@ static inline void copy_to_cstring(std::string input, char **output) { std::strcpy(*output, input.c_str()); } -TEST(ParticleGeometryInterfaceCurved, Init) { +// TODO REMOVE START +namespace NESO::Newton { + +template class XMapNewtonTest : public XMapNewton { +public: + + template + XMapNewtonTest(SYCLTargetSharedPtr sycl_target, std::shared_ptr geom, + const int num_modes_factor = 1) + : XMapNewton(sycl_target, geom, num_modes_factor) + {} + + inline bool x_inverse(const REAL phys0, const REAL phys1, const REAL phys2, + REAL *xi0, REAL *xi1, REAL *xi2, + const REAL tol = 1.0e-10, + const REAL contained_tol = 1.0e-10) { + + const int k_max_iterations = 51; + auto k_map_data = this->dh_data->d_buffer.ptr; + auto k_fdata = this->dh_fdata->d_buffer.ptr; + const REAL k_tol = tol; + const double k_contained_tol = contained_tol; + const std::size_t num_bytes_local = this->num_bytes_local; + + const int k_ndim = this->ndim; + const int grid_size = this->num_modes_factor * this->num_modes; + const int k_grid_size_x = std::max(grid_size - 1, 1); + const int k_grid_size_y = k_ndim > 1 ? k_grid_size_x : 1; + const int k_grid_size_z = k_ndim > 2 ? k_grid_size_x : 1; + const REAL k_grid_width = 2.0 / (k_grid_size_x); + + this->sycl_target->queue + .submit([&](sycl::handler &cgh) { + sycl::accessor + local_mem(sycl::range<1>(num_bytes_local), cgh); + cgh.parallel_for<>( + sycl::nd_range<1>(sycl::range<1>(1), sycl::range<1>(1)), + [=](auto idx) { + printf("NEWTON TEST ETA GRID:\n"); + MappingNewtonIterationBase k_newton_type{}; + + const REAL p0 = phys0; + const REAL p1 = phys1; + const REAL p2 = phys2; + REAL k_xi0; + REAL k_xi1; + REAL k_xi2; + REAL residual; + bool cell_found = false; + + for (int g2 = 0; (g2 <= k_grid_size_z) && (!cell_found); g2++) { + for (int g1 = 0; (g1 <= k_grid_size_y) && (!cell_found); + g1++) { + for (int g0 = 0; (g0 <= k_grid_size_x) && (!cell_found); + g0++) { + + REAL eta0, eta1, eta2; + + eta0 = -1.0 + g0 * k_grid_width; + eta1 = -1.0 + g1 * k_grid_width; + eta2 = -1.0 + g2 * k_grid_width; + + k_newton_type.loc_collapsed_to_loc_coord( + k_map_data, eta0, eta1, eta2, &k_xi0, &k_xi1, &k_xi2); + + nprint("~~~~~~~~~~~ ETA:", eta0, eta1, eta2, "XI:", k_xi0, k_xi1, k_xi2); + + // k_newton_type.set_initial_iteration(k_map_data, p0, p1, + // p2, + // &k_xi0, &k_xi1, + // &k_xi2); + + // Start of Newton iteration + REAL xin0, xin1, xin2; + REAL f0, f1, f2; + + residual = k_newton_type.newton_residual( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, + &f2, &local_mem[0]); + + bool diverged = false; + bool converged = false; + printf("residual: %f\n", residual); + for (int stepx = 0; ((stepx < k_max_iterations) && + (!converged) && (!diverged)); + stepx++) { + printf("STEPX: %d, RES: %16.8e\n", stepx, residual); + + k_newton_type.newton_step( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f0, f1, + f2, &xin0, &xin1, &xin2, &local_mem[0]); + + k_xi0 = xin0; + k_xi1 = xin1; + k_xi2 = xin2; + + residual = k_newton_type.newton_residual( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, + &f1, &f2, &local_mem[0]); + + diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || + (ABS(k_xi2) > 15.0) || (residual != residual); + converged = (residual <= k_tol) && (!diverged); + } + + k_newton_type.loc_coord_to_loc_collapsed( + k_map_data, k_xi0, k_xi1, k_xi2, &eta0, &eta1, &eta2); + + // bool contained = ((-1.0 - k_contained_tol) <= eta0) && + // (eta0 <= (1.0 + k_contained_tol)) && + // ((-1.0 - k_contained_tol) <= eta1) && + // (eta1 <= (1.0 + k_contained_tol)) && + // ((-1.0 - k_contained_tol) <= eta2) && + // (eta2 <= (1.0 + k_contained_tol)); + + nprint("CLAMPED START"); + nprint("BEFORE CLAMP:", eta0, eta1, eta2); + REAL clamped_eta0 = Kernel::min(eta0, 1.0 + k_contained_tol); + REAL clamped_eta1 = Kernel::min(eta1, 1.0 + k_contained_tol); + REAL clamped_eta2 = Kernel::min(eta2, 1.0 + k_contained_tol); + clamped_eta0 = Kernel::max(clamped_eta0, -1.0 - k_contained_tol); + clamped_eta1 = Kernel::max(clamped_eta1, -1.0 - k_contained_tol); + clamped_eta2 = Kernel::max(clamped_eta2, -1.0 - k_contained_tol); + nprint("AFTER CLAMP:", clamped_eta0, clamped_eta1, clamped_eta2); + + REAL clamped_xi0, clamped_xi1, clamped_xi2; + k_newton_type.loc_collapsed_to_loc_coord( + k_map_data, clamped_eta0, clamped_eta1, clamped_eta2, + &clamped_xi0, &clamped_xi1, &clamped_xi2); + + const REAL clamped_residual = k_newton_type.newton_residual( + k_map_data, clamped_xi0, clamped_xi1, clamped_xi2, + p0, p1, p2, &f0, &f1, + &f2, &local_mem[0]); + + const bool contained = clamped_residual <= k_tol; + + nprint("CLAMPED END"); + + + + cell_found = contained && converged; + } + } + } + k_fdata[0] = k_xi0; + k_fdata[1] = k_xi1; + k_fdata[2] = k_xi2; + k_fdata[3] = (residual <= tol) ? 1 : -1; + }); + }) + .wait_and_throw(); + + this->dh_fdata->device_to_host(); + *xi0 = this->dh_fdata->h_buffer.ptr[0]; + *xi1 = this->dh_fdata->h_buffer.ptr[1]; + *xi2 = this->dh_fdata->h_buffer.ptr[2]; + return (this->dh_fdata->h_buffer.ptr[3] > 0); + } + +}; + + + + +} +// TODO REMOVE END + + + + +TEST(ParticleGeometryInterfaceCurved, CoordinateMapping) { int size, rank; MPI_Comm_size(MPI_COMM_WORLD, &size); @@ -53,6 +225,7 @@ TEST(ParticleGeometryInterfaceCurved, Init) { // std::filesystem::path mesh_file = // test_resources_dir / "reference_all_types_cube/mixed_ref_cube_0.2.xml"; + // TODO std::filesystem::path mesh_file = "/home/js0259/git-ukaea/NESO-workspace/reference_all_types_cube/" "mixed_ref_cube_0.5_perturbed_order_2.xml"; @@ -70,6 +243,7 @@ TEST(ParticleGeometryInterfaceCurved, Init) { std::map> geoms; get_all_elements_3d(graph, geoms); + // TODO clenaup auto lambda_stype = [](auto s) -> std::string { switch (s) { case eTetrahedron: @@ -85,6 +259,7 @@ TEST(ParticleGeometryInterfaceCurved, Init) { } }; + // TODO cleanip auto lambda_btype = [](auto s) -> std::string { switch (s) { case eModified_A: @@ -100,9 +275,156 @@ TEST(ParticleGeometryInterfaceCurved, Init) { } }; + auto lambda_to_collapsed_coord = [&]( + auto geom, + auto xi0, + auto xi1, + auto xi2, + auto * eta0, + auto * eta1, + auto * eta2 + ){ + auto s = geom->GetShapeType(); + switch (s) { + case eTetrahedron: + GeometryInterface::Tetrahedron{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, eta1, eta2); + break; + case ePyramid: + GeometryInterface::Pyramid{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, eta1, eta2); + break; + case ePrism: + GeometryInterface::Prism{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, eta1, eta2); + break; + case eHexahedron: + GeometryInterface::Hexahedron{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, eta1, eta2); + break; + default: + return "shape unknown"; + } + }; + auto lambda_to_local_coord = [&]( + auto geom, + auto eta0, + auto eta1, + auto eta2, + auto * xi0, + auto * xi1, + auto * xi2 + ){ + auto s = geom->GetShapeType(); + switch (s) { + case eTetrahedron: + GeometryInterface::Tetrahedron{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, xi0, xi1, xi2); + break; + case ePyramid: + GeometryInterface::Pyramid{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, xi0, xi1, xi2); + break; + case ePrism: + GeometryInterface::Prism{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, xi0, xi1, xi2); + break; + case eHexahedron: + GeometryInterface::Hexahedron{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, xi0, xi1, xi2); + break; + default: + return "shape unknown"; + } + }; + + for (auto gx : geoms) { auto geom = gx.second; auto xmap = geom->GetXmap(); + const int shape_type_int = geom->GetShapeType(); + + std::set> vertices_found; + std::vector> vertices = { + {-1.0, -1.0, -1.0}, + { 1.0, -1.0, -1.0}, + {-1.0, 1.0, -1.0}, + { 1.0, 1.0, -1.0}, + {-1.0, -1.0, 1.0}, + { 1.0, -1.0, 1.0}, + {-1.0, 1.0, 1.0}, + { 1.0, 1.0, 1.0} + }; + + Array test_eta(3); + Array test_eta_neso(3); + Array test_xi(3); + Array test_xi_neso(3); + REAL eta0, eta1, eta2, xi0, xi1, xi2; + for(auto vx : vertices){ + test_eta[0] = vx.at(0); + test_eta[1] = vx.at(1); + test_eta[2] = vx.at(2); + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + xmap->LocCoordToLocCollapsed(test_xi, test_eta); + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + xmap->LocCoordToLocCollapsed(test_xi, test_eta); + + vertices_found.insert( + { + (int) std::round(test_eta[0]), + (int) std::round(test_eta[1]), + (int) std::round(test_eta[2]) + } + ); + } + + const int num_vertices_expected = geom->GetNumVerts(); + const int num_vertices_found = vertices_found.size(); + + // At the time of writing TetGeom mapping is inconsistent with itself in Nektar++ + const bool nektar_mapping_consistent = num_vertices_found == num_vertices_expected; + + vertices_found.clear(); + + for(auto vx : vertices){ + test_eta[0] = vx.at(0); + test_eta[1] = vx.at(1); + test_eta[2] = vx.at(2); + + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi_neso); + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta[0], test_eta[1], test_eta[2], &xi0, &xi1, &xi2); + ASSERT_NEAR(test_xi_neso[0], xi0, 1.0e-14); + ASSERT_NEAR(test_xi_neso[1], xi1, 1.0e-14); + ASSERT_NEAR(test_xi_neso[2], xi2, 1.0e-14); + + if (nektar_mapping_consistent) { + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + ASSERT_NEAR(test_xi_neso[0], test_xi[0], 1.0e-14); + ASSERT_NEAR(test_xi_neso[1], test_xi[1], 1.0e-14); + ASSERT_NEAR(test_xi_neso[2], test_xi[2], 1.0e-14); + } + + GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, test_xi_neso, test_eta_neso); + GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi0, xi1, xi2, &eta0, &eta1, &eta2); + ASSERT_NEAR(test_eta_neso[0], eta0, 1.0e-14); + ASSERT_NEAR(test_eta_neso[1], eta1, 1.0e-14); + ASSERT_NEAR(test_eta_neso[2], eta2, 1.0e-14); + + if (nektar_mapping_consistent) { + xmap->LocCoordToLocCollapsed(test_xi_neso, test_eta); + ASSERT_NEAR(test_eta_neso[0], test_eta[0], 1.0e-14); + ASSERT_NEAR(test_eta_neso[1], test_eta[1], 1.0e-14); + ASSERT_NEAR(test_eta_neso[2], test_eta[2], 1.0e-14); + } + + vertices_found.insert( + { + (int) std::round(eta0), + (int) std::round(eta1), + (int) std::round(eta2) + } + ); + + } + + // Our implementations should be consistent. + ASSERT_EQ(vertices_found.size(), num_vertices_expected); + + /* + nprint(geom->GetShapeType(), lambda_stype(geom->GetShapeType())); nprint("Num bases:", xmap->GetNumBases()); for (int dx = 0; dx < 3; dx++) { @@ -157,6 +479,12 @@ TEST(ParticleGeometryInterfaceCurved, Init) { const auto y = xmap->PhysEvaluate(I, ptsy); const auto z = xmap->PhysEvaluate(I, ptsz); nprint(x, y, z); + + */ + + + + } mesh->free(); @@ -239,20 +567,37 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { auto lambda_forward_map = [&](auto geom, const auto &xi, auto &phys) { // Evaluate the forward map from xi to physical space using the expansion. auto xmap = geom->GetXmap(); - auto I0 = xmap->GetBasis(0)->GetI(xi); - auto I1 = xmap->GetBasis(1)->GetI(xi); - auto I2 = xmap->GetBasis(2)->GetI(xi); const int npts = xmap->GetTotPoints(); Array ptsx(npts), ptsy(npts), ptsz(npts); xmap->BwdTrans(geom->GetCoeffs(0), ptsx); xmap->BwdTrans(geom->GetCoeffs(1), ptsy); xmap->BwdTrans(geom->GetCoeffs(2), ptsz); Array eta(3); + Array test_eta(3); + xmap->LocCoordToLocCollapsed(xi, eta); + const int shape_type_int = static_cast(geom->GetShapeType()); + GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi, test_eta); + + ASSERT_NEAR(eta[0], test_eta[0], 1.0e-8); + ASSERT_NEAR(eta[1], test_eta[1], 1.0e-8); + ASSERT_NEAR(eta[2], test_eta[2], 1.0e-8); + + Array test_xi_neso(3); + Array test_xi_nektar(3); + + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, eta, test_xi_neso); + xmap->LocCollapsedToLocCoord(eta, test_xi_nektar); + ASSERT_NEAR(test_xi_nektar[0], test_xi_neso[0], 1.0e-8); + ASSERT_NEAR(test_xi_nektar[1], test_xi_neso[1], 1.0e-8); + ASSERT_NEAR(test_xi_nektar[2], test_xi_neso[2], 1.0e-8); + Array I(3); + I[0] = xmap->GetBasis(0)->GetI(eta); I[1] = xmap->GetBasis(1)->GetI(eta + 1); I[2] = xmap->GetBasis(2)->GetI(eta + 2); + const auto x = xmap->PhysEvaluate(I, ptsx); const auto y = xmap->PhysEvaluate(I, ptsy); const auto z = xmap->PhysEvaluate(I, ptsz); @@ -324,7 +669,7 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { EXPECT_TRUE(dist < 1.0e-8); // test the forward x map from reference space to physical space - Newton::XMapNewton mapper(sycl_target, geom); + Newton::XMapNewtonTest mapper(sycl_target, geom); REAL test_phys0, test_phys1, test_phys2; mapper.x(xi[0], xi[1], xi[2], &test_phys0, &test_phys1, &test_phys2); EXPECT_NEAR(phys[0], test_phys0, 1.0e-10); @@ -340,17 +685,39 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { (std::abs(test_xi1 - xi[1]) < 1.0e-8) && (std::abs(test_xi2 - xi[2]) < 1.0e-8); - // If there were multiple points inside the reference element that map to - // the same physical point there there are major problems with the mesh. - // Hence the point inside the reference element that maps to the physical - // point hould be unique. - ASSERT_TRUE(same_xi); + mapper.x(test_xi0, test_xi1, test_xi2, &test_phys0, &test_phys1, &test_phys2); + nprint("XI:", test_xi0, test_xi1, test_xi2, "PHYS:", test_phys0, test_phys1, test_phys2); + + // If the test_xi is xi then the inverse mapping was good + // Otherwise check test_xi is a reference coordinate that maps to phys + if (!same_xi) { + Array test_phys(3); + lambda_forward_map(geom, xi, test_phys); + const bool equiv_xi = (std::abs(test_phys[0] - phys[0]) < 1.0e-8) && + (std::abs(test_phys[1] - phys[1]) < 1.0e-8) && + (std::abs(test_phys[2] - phys[2]) < 1.0e-8); + // The point we sampled was considered contained by Nektar++ + // Check that this alternative reference point is also contained. + const REAL xi00 = test_xi0; + const REAL xi01 = test_xi1; + const REAL xi02 = test_xi2; + GeometryInterface::loc_coord_to_loc_collapsed_3d( + shape_type_int, xi00, xi01, xi02, &eta0, &eta1, &eta2); + const auto dist = lambda_test_contained(eta0, eta1, eta2); + nprint("dist1", dist, eta0, eta1, eta2); + EXPECT_TRUE(equiv_xi); + EXPECT_TRUE(dist < 1.0e-8); + } nprint("CHECK X MAP END"); }; for (auto gx : geoms) { auto geom = gx.second; + nprint("GLOBALID:", geom->GetGlobalID()); + if (geom->GetGlobalID() != 45){ + continue; + } auto xmap = geom->GetXmap(); const int shape_type_int = static_cast(geom->GetShapeType()); nprint(geom->GetShapeType(), lambda_stype(geom->GetShapeType())); @@ -359,11 +726,169 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { nprint("dx:", dx, "type:", lambda_btype(xmap->GetBasisType(dx)), xmap->GetBasisNumModes(dx)); } + + { + NekDouble x,y,z; + const auto num_verts = geom->GetNumVerts(); + for(int ix=0 ; ixGetVertex(ix); + vx->GetCoords(x,y,z); + nprint("VX:", ix, x, y, z); + } + } + Array test_eta(3); Array test_xi(3); Array test_phys(3); - lambda_sample_internal_point(geom, test_xi, test_phys); - lambda_check_x_map(geom, test_xi, test_phys); + + test_eta[0] = -1.0; + test_eta[1] = 1.0; + test_eta[2] = -1.0; + + geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); + nprint("ETA to XI"); + nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); + nprint("\t", " XI:", test_xi[0], test_xi[1], test_xi[2]); + geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); + nprint("XI to ETA"); + nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); + geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); + nprint("ETA to XI"); + nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); + nprint("\t", " XI:", test_xi[0], test_xi[1], test_xi[2]); + + nprint("NEKTAR FORWARD"); + lambda_forward_map(geom, test_xi, test_phys); + nprint("\t", "PHYS:", test_phys[0], test_phys[1], test_phys[2]); + + test_eta[0] = 1.0; + test_eta[1] = -1.0; + test_eta[2] = -1.0; + + geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); + nprint("ETA to XI"); + nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); + nprint("\t", " XI:", test_xi[0], test_xi[1], test_xi[2]); + geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); + nprint("XI to ETA"); + nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); + geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); + nprint("ETA to XI"); + nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); + nprint("\t", " XI:", test_xi[0], test_xi[1], test_xi[2]); + + nprint("NEKTAR FORWARD"); + lambda_forward_map(geom, test_xi, test_phys); + nprint("\t", "PHYS:", test_phys[0], test_phys[1], test_phys[2]); + + { + // Test vertices of reference element + std::vector> vertices = { + {-1.0, -1.0, -1.0}, + { 1.0, -1.0, -1.0}, + {-1.0, 1.0, -1.0}, + { 1.0, 1.0, -1.0}, + {-1.0, -1.0, 1.0}, + { 1.0, -1.0, 1.0}, + {-1.0, 1.0, 1.0}, + { 1.0, 1.0, 1.0} + }; + + for(auto &etav : vertices){ + nprint("=============================================="); + test_eta[0] = etav.at(0); + test_eta[1] = etav.at(1); + test_eta[2] = etav.at(2); + + // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi); + + nprint("ETA 0:", test_eta[0], test_eta[1], test_eta[2]); + geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); + // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi); + nprint(" XI 0:", test_xi[0], test_xi[1], test_xi[2]); + geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); + nprint("ETA 1:", test_eta[0], test_eta[1], test_eta[2]); + geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); + // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi); + nprint(" XI 1:", test_xi[0], test_xi[1], test_xi[2]); + geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); + nprint("ETA 2:", test_eta[0], test_eta[1], test_eta[2]); + + + lambda_forward_map(geom, test_xi, test_phys); + nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], "\n ETA O:", test_eta[0], test_eta[1], test_eta[2], "\nPHYS:", test_phys[0], test_phys[1], test_phys[2]); + + // Does nektar sucessfully invert the map? + Array test_xi_nektar(3); + auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); + nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], test_xi_nektar[2], "DIST:", dist); + } + + nprint("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"); + + for(auto &etav : vertices){ + nprint("=============================================="); + test_xi[0] = etav.at(0); + test_xi[1] = etav.at(1); + test_xi[2] = etav.at(2); + + if ((test_xi[0] + test_xi[1] + test_xi[2]) <= -0.9){ + geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); + nprint("ETA::", test_eta[0], test_eta[1], test_eta[2]); + + lambda_forward_map(geom, test_xi, test_phys); + nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], "PHYS:", test_phys[0], test_phys[1], test_phys[2]); + + // Does nektar sucessfully invert the map? + Array test_xi_nektar(3); + auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); + nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], test_xi_nektar[2], "DIST:", dist); + } + } + + + + + } + + + + // Test vertices of reference element + std::vector> vertices = { + //{-1.0, -1.0, -1.0}, + { 1.0, -1.0, -1.0}, + //{-1.0, 1.0, -1.0}, + //{ 1.0, 1.0, -1.0}, + //{-1.0, -1.0, 1.0}, + //{ 1.0, -1.0, 1.0}, + //{-1.0, 1.0, 1.0}, + //{ 1.0, 1.0, 1.0} + }; + + for(auto &etav : vertices){ + nprint("----------------------------------------------"); + test_eta[0] = etav.at(0); + test_eta[1] = etav.at(1); + test_eta[2] = etav.at(2); + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi); + lambda_forward_map(geom, test_xi, test_phys); + nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], "\nETA:", test_eta[0], test_eta[1], test_eta[2], "\nPHYS:", test_phys[0], test_phys[1], test_phys[2]); + + + // Does nektar sucessfully invert the map? + Array test_xi_nektar(3); + auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); + nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], test_xi_nektar[2], "DIST:", dist); + + lambda_check_x_map(geom, test_xi, test_phys); + } + + // test internal points + //for(int testx=0 ; testx<20 ; testx++){ + // nprint("=============================================="); + // lambda_sample_internal_point(geom, test_xi, test_phys); + // lambda_check_x_map(geom, test_xi, test_phys); + //} } mesh->free(); From 9bac47b6ed5bd5a9549eadf2bbf99ac3fb5ccd08 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 29 Oct 2024 11:44:31 +0000 Subject: [PATCH 17/66] added explicit test for 2D coordinate mapping --- .../nektar_interface/coordinate_mapping.hpp | 57 +-- .../mapping_newton_iteration_base.hpp | 12 +- .../newton_generic_3d.hpp | 32 +- .../particle_cell_mapping/newton_prism.hpp | 4 +- .../particle_cell_mapping/newton_pyr.hpp | 4 +- .../newton_triangle_embed_3d.hpp | 4 +- .../particle_cell_mapping/x_map_newton.hpp | 4 +- .../test_particle_geometry_interface.cpp | 108 ++++++ .../test_particle_geometry_interface_3d.cpp | 179 +++++---- ..._particle_geometry_interface_3d_curved.cpp | 350 +++++++++--------- 10 files changed, 422 insertions(+), 332 deletions(-) diff --git a/include/nektar_interface/coordinate_mapping.hpp b/include/nektar_interface/coordinate_mapping.hpp index 109ed65a..6423b858 100644 --- a/include/nektar_interface/coordinate_mapping.hpp +++ b/include/nektar_interface/coordinate_mapping.hpp @@ -454,8 +454,6 @@ struct Triangle : BaseCoordinateMapping2D { } }; - - /** * Map the local collapsed coordinate (eta) to the local coordinate (xi). * @@ -469,15 +467,9 @@ struct Triangle : BaseCoordinateMapping2D { * @param[in, out] xi2 Local coordinate. */ template -inline void loc_collapsed_to_loc_coord( - const int shape_type, - const T eta0, - const T eta1, - const T eta2, - T * xi0, - T * xi1, - T * xi2 - ) { +inline void loc_collapsed_to_loc_coord(const int shape_type, const T eta0, + const T eta1, const T eta2, T *xi0, + T *xi1, T *xi2) { /* Tet @@ -534,19 +526,17 @@ inline void loc_collapsed_to_loc_coord( const REAL a = 1.0 + eta0; const REAL b = 1.0 - eta2; const REAL c = (a) * (b)*0.5 - 1.0; - *xi1 = - (shape_type == shape_type_tet) - ? c - : ((shape_type == shape_type_pyr) ? (1.0 + eta1) * (b)*0.5 - 1.0 - : eta1); + *xi1 = (shape_type == shape_type_tet) + ? c + : ((shape_type == shape_type_pyr) ? (1.0 + eta1) * (b)*0.5 - 1.0 + : eta1); const REAL tet_x = (1.0 + eta0) * (-(*xi1) - eta2) * 0.5 - 1.0; *xi0 = (shape_type == shape_type_tet) - ? tet_x - : ((shape_type == shape_type_hex) ? eta0 : c); + ? tet_x + : ((shape_type == shape_type_hex) ? eta0 : c); *xi2 = eta2; } - /** * Map the local collapsed coordinate (eta) to the local coordinate (xi). * @@ -560,11 +550,10 @@ inline void loc_collapsed_to_loc_coord( template inline void loc_collapsed_to_loc_coord(const int shape_type, const T &eta, T &xi) { - loc_collapsed_to_loc_coord(shape_type, eta[0], eta[1], eta[2], &xi[0], &xi[1], &xi[2]); + loc_collapsed_to_loc_coord(shape_type, eta[0], eta[1], eta[2], &xi[0], &xi[1], + &xi[2]); } - - /** * Map the local coordinate (xi) to the local collapsed coordinate (eta). * @@ -618,7 +607,6 @@ inline void loc_coord_to_loc_collapsed_3d(const int shape_type, const T xi0, *eta2 = xi2; } - /** * Map the local coordinate (xi) to the local collapsed coordinate (eta). * @@ -631,7 +619,8 @@ inline void loc_coord_to_loc_collapsed_3d(const int shape_type, const T xi0, template inline void loc_coord_to_loc_collapsed_3d(const int shape_type, const T &xi, T &eta) { - loc_coord_to_loc_collapsed_3d(shape_type, xi[0], xi[1], xi[2], &eta[0], &eta[1], &eta[2]); + loc_coord_to_loc_collapsed_3d(shape_type, xi[0], xi[1], xi[2], &eta[0], + &eta[1], &eta[2]); } /** @@ -661,6 +650,26 @@ inline void loc_coord_to_loc_collapsed_2d(const int shape_type, const T xi0, *eta1 = xi1; } +/** + * Map the local collapsed coordinate (eta) to the local coordinate (xi). + * + * @param[in] shape_type Integer denoting shape type found by cast of Nektar++ + * shape type enum to int. + * @param[in] eta0 Local collapsed coordinate to map to local coordinate. + * @param[in] eta1 Local collapsed coordinate to map to local coordinate. + * @param[in, out] xi0 Local coordinate. + * @param[in, out] xi1 Local coordinate. + */ +template +inline void loc_collapsed_to_loc_coord_2d(const int shape_type, const T eta0, + const T eta1, T *xi0, T *xi1) { + constexpr int shape_type_tri = shape_type_to_int(LibUtilities::eTriangle); + *xi0 = (shape_type == shape_type_tri) + ? (1.0 + eta0) * (1.0 - eta1) * 0.5 - 1.0 + : eta0; + *xi1 = eta1; +} + /** * Clamp a single coordinate to the interval [-1-tol, 1+tol] for a given * tolerance. diff --git a/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp b/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp index ea717005..b7dc0bb6 100644 --- a/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp +++ b/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp @@ -245,12 +245,12 @@ template struct MappingNewtonIterationBase { * @param[in] eta0 Local collapsed coordinate (eta), x component. * @param[in] eta1 Local collapsed coordinate (eta), y component. * @param[in] eta2 Local collapsed coordinate (eta), z component. - * @param[in, out] xi0 Local coordinate (xi) to be mapped to collapsed coordinate, - * x component. - * @param[in, out] xi1 Local coordinate (xi) to be mapped to collapsed coordinate, - * y component. - * @param[in, out] xi2 Local coordinate (xi) to be mapped to collapsed coordinate, - * z component. + * @param[in, out] xi0 Local coordinate (xi) to be mapped to collapsed + * coordinate, x component. + * @param[in, out] xi1 Local coordinate (xi) to be mapped to collapsed + * coordinate, y component. + * @param[in, out] xi2 Local coordinate (xi) to be mapped to collapsed + * coordinate, z component. */ inline void loc_collapsed_to_loc_coord(const void *d_data, const REAL eta0, const REAL eta1, const REAL eta2, diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index d9619582..645b66ce 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -249,20 +249,20 @@ struct MappingGeneric3D : MappingNewtonIterationBase { d->num_phys2, d->physvals, div_space0, div_space1, div_space2, X); - //const int n0 = d->num_phys0; - //const int n1 = d->num_phys1; - //const int n2 = d->num_phys2; - //nprint("n:", n0, n1, n2); - //for (int ix = 0; ix < n0; ix++) { - // nprint(div_space0[ix]); - //} - //for (int ix = 0; ix < n1; ix++) { - // nprint(div_space1[ix]); - //} - //for (int ix = 0; ix < n2; ix++) { - // nprint(div_space2[ix]); - //} - //nprint(X[0], X[1], X[2], phys0, phys1, phys2); + // const int n0 = d->num_phys0; + // const int n1 = d->num_phys1; + // const int n2 = d->num_phys2; + // nprint("n:", n0, n1, n2); + // for (int ix = 0; ix < n0; ix++) { + // nprint(div_space0[ix]); + // } + // for (int ix = 0; ix < n1; ix++) { + // nprint(div_space1[ix]); + // } + // for (int ix = 0; ix < n2; ix++) { + // nprint(div_space2[ix]); + // } + // nprint(X[0], X[1], X[2], phys0, phys1, phys2); // Residual is defined as F = X(xi) - P *f0 = X[0] - phys0; @@ -285,7 +285,7 @@ struct MappingGeneric3D : MappingNewtonIterationBase { inline void set_initial_iteration_v(const void *d_data, const REAL phys0, const REAL phys1, const REAL phys2, REAL *xi0, REAL *xi1, REAL *xi2) { - + /** * Implementations that avoid singularities: * newton_pyr @@ -293,7 +293,6 @@ struct MappingGeneric3D : MappingNewtonIterationBase { * */ - *xi0 = -0.2; *xi1 = -0.2; *xi2 = -0.2; @@ -322,7 +321,6 @@ struct MappingGeneric3D : MappingNewtonIterationBase { GeometryInterface::loc_collapsed_to_loc_coord(shape_type, eta0, eta1, eta2, xi0, xi1, xi2); } - }; /** diff --git a/include/nektar_interface/particle_cell_mapping/newton_prism.hpp b/include/nektar_interface/particle_cell_mapping/newton_prism.hpp index c30b2d84..ad112989 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_prism.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_prism.hpp @@ -104,8 +104,8 @@ struct MappingPrismLinear3D : MappingNewtonIterationBase { inline void loc_coord_to_loc_collapsed_v(const void *d_data, const REAL xi0, const REAL xi1, const REAL xi2, REAL *eta0, REAL *eta1, REAL *eta2) { - GeometryInterface::Prism{}.loc_coord_to_loc_collapsed( - xi0, xi1, xi2, eta0, eta1, eta2); + GeometryInterface::Prism{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, + eta1, eta2); } }; diff --git a/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp b/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp index 5a510f48..946bbbc9 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp @@ -147,8 +147,8 @@ struct MappingPyrLinear3D : MappingNewtonIterationBase { inline void loc_coord_to_loc_collapsed_v(const void *d_data, const REAL xi0, const REAL xi1, const REAL xi2, REAL *eta0, REAL *eta1, REAL *eta2) { - GeometryInterface::Pyramid{}.loc_coord_to_loc_collapsed( - xi0, xi1, xi2, eta0, eta1, eta2); + GeometryInterface::Pyramid{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, + eta1, eta2); } }; diff --git a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp index da9cd0af..31ef0943 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp @@ -169,8 +169,8 @@ struct MappingTriangleLinear2DEmbed3D const REAL xi1, const REAL xi2, REAL *eta0, REAL *eta1, REAL *eta2) { *eta2 = 0.0; - GeometryInterface::Triangle{}.loc_coord_to_loc_collapsed( - xi0, xi1, eta0, eta1); + GeometryInterface::Triangle{}.loc_coord_to_loc_collapsed(xi0, xi1, eta0, + eta1); } }; diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 89cb1cd8..b6d47307 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -212,7 +212,8 @@ template class XMapNewton { k_xi1 = -0.9 + g1 * k_grid_width; k_xi2 = -0.9 + g2 * k_grid_width; - nprint("~~~~~~~~~~~~~~", g0, g1, g2, ":", k_xi0, k_xi1, k_xi2); + nprint("~~~~~~~~~~~~~~", g0, g1, g2, ":", k_xi0, k_xi1, + k_xi2); // k_newton_type.set_initial_iteration(k_map_data, p0, p1, // p2, // &k_xi0, &k_xi1, @@ -281,7 +282,6 @@ template class XMapNewton { } }; - } // namespace NESO::Newton #endif diff --git a/test/unit/nektar_interface/test_particle_geometry_interface.cpp b/test/unit/nektar_interface/test_particle_geometry_interface.cpp index 505ebbb4..da96d02a 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface.cpp @@ -649,3 +649,111 @@ TEST(ParticleGeometryInterface, PointInSubDomain2D) { delete[] argv[0]; delete[] argv[1]; } + +TEST(ParticleGeometryInterface, CoordinateMapping2D) { + + int argc = 2; + char *argv[2]; + copy_to_cstring(std::string("test_particle_geometry_interface"), &argv[0]); + + std::filesystem::path source_file = __FILE__; + std::filesystem::path source_dir = source_file.parent_path(); + std::filesystem::path test_resources_dir = + source_dir / "../../test_resources"; + std::filesystem::path mesh_file = + test_resources_dir / "square_triangles_quads.xml"; + copy_to_cstring(std::string(mesh_file), &argv[1]); + + // Create session reader. + auto session = LibUtilities::SessionReader::CreateInstance(argc, argv); + + auto graph = SpatialDomains::MeshGraph::Read(session); + auto mesh = std::make_shared(graph); + std::map> geoms; + get_all_elements_2d(graph, geoms); + + std::set> vertices_found; + std::vector> vertices = { + {-1.0, -1.0, 0.0}, + {1.0, -1.0, 0.0}, + {-1.0, 1.0, 0.0}, + {1.0, 1.0, 0.0}, + }; + + auto lambda_test_wrapper = [&](auto geom, auto geom_test) { + const int shape_type_int = geom->GetShapeType(); + + Array test_eta(2); + Array test_xi(2); + REAL eta0, eta1, xi0, xi1, etaa, etab, xia, xib; + auto xmap = geom->GetXmap(); + for (auto vx : vertices) { + test_eta[0] = vx.at(0); + test_eta[1] = vx.at(1); + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + xmap->LocCoordToLocCollapsed(test_xi, test_eta); + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + xmap->LocCoordToLocCollapsed(test_xi, test_eta); + + vertices_found.insert( + {(int)std::round(test_eta[0]), (int)std::round(test_eta[1])}); + } + + const int num_vertices_expected = geom->GetNumVerts(); + const int num_vertices_found = vertices_found.size(); + const bool nektar_mapping_consistent = + num_vertices_found == num_vertices_expected; + vertices_found.clear(); + + for (auto vx : vertices) { + test_eta[0] = vx.at(0); + test_eta[1] = vx.at(1); + GeometryInterface::loc_collapsed_to_loc_coord_2d( + shape_type_int, test_eta[0], test_eta[1], &xi0, &xi1); + geom_test.loc_collapsed_to_loc_coord(test_eta[0], test_eta[1], &xia, + &xib); + ASSERT_NEAR(xia, xi0, 1.0e-14); + ASSERT_NEAR(xib, xi1, 1.0e-14); + + if (nektar_mapping_consistent) { + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + ASSERT_NEAR(test_xi[0], xi0, 1.0e-14); + ASSERT_NEAR(test_xi[1], xi1, 1.0e-14); + } + + GeometryInterface::loc_coord_to_loc_collapsed_2d(shape_type_int, xi0, xi1, + &eta0, &eta1); + geom_test.loc_coord_to_loc_collapsed(xi0, xi1, &etaa, &etab); + ASSERT_NEAR(etaa, eta0, 1.0e-14); + ASSERT_NEAR(etab, eta1, 1.0e-14); + + if (nektar_mapping_consistent) { + xmap->LocCoordToLocCollapsed(test_xi, test_eta); + ASSERT_NEAR(test_eta[0], eta0, 1.0e-14); + ASSERT_NEAR(test_eta[1], eta1, 1.0e-14); + } + vertices_found.insert({(int)std::round(eta0), (int)std::round(eta1)}); + } + + ASSERT_EQ(vertices_found.size(), num_vertices_expected); + }; + + for (auto &geom_pair : geoms) { + + auto geom = geom_pair.second; + auto shape_type = geom->GetShapeType(); + if (shape_type == LibUtilities::eQuadrilateral) { + GeometryInterface::Quadrilateral geom_test{}; + lambda_test_wrapper(geom, geom_test); + } else if (shape_type == LibUtilities::eTriangle) { + GeometryInterface::Triangle geom_test{}; + lambda_test_wrapper(geom, geom_test); + } else { + ASSERT_TRUE(false); + } + } + + mesh->free(); + delete[] argv[0]; + delete[] argv[1]; +} diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp index b36ad2c0..dda62da0 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp @@ -236,103 +236,97 @@ TEST(ParticleGeometryInterface, CoordinateMapping3D) { std::set> vertices_found; std::vector> vertices = { - {-1.0, -1.0, -1.0}, - { 1.0, -1.0, -1.0}, - {-1.0, 1.0, -1.0}, - { 1.0, 1.0, -1.0}, - {-1.0, -1.0, 1.0}, - { 1.0, -1.0, 1.0}, - {-1.0, 1.0, 1.0}, - { 1.0, 1.0, 1.0} - }; - - for (auto &geom_pair : geoms) { - - auto geom = geom_pair.second; + {-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, {-1.0, 1.0, -1.0}, + {1.0, 1.0, -1.0}, {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, + {-1.0, 1.0, 1.0}, {1.0, 1.0, 1.0}}; + + auto lambda_test_wrapper = [&](auto geom, auto geom_test) { + const int shape_type_int = geom->GetShapeType(); + + Array test_eta(3); + Array test_eta_neso(3); + Array test_xi(3); + Array test_xi_neso(3); + REAL eta0, eta1, eta2, xi0, xi1, xi2; + auto xmap = geom->GetXmap(); + for (auto vx : vertices) { + test_eta[0] = vx.at(0); + test_eta[1] = vx.at(1); + test_eta[2] = vx.at(2); + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + xmap->LocCoordToLocCollapsed(test_xi, test_eta); + xmap->LocCollapsedToLocCoord(test_eta, test_xi); + xmap->LocCoordToLocCollapsed(test_xi, test_eta); + + vertices_found.insert({(int)std::round(test_eta[0]), + (int)std::round(test_eta[1]), + (int)std::round(test_eta[2])}); + } - auto lambda_test_wrapper = [&]( - auto geom, - auto geom_test - ){ - const int shape_type_int = geom->GetShapeType(); - - Array test_eta(3); - Array test_eta_neso(3); - Array test_xi(3); - Array test_xi_neso(3); - REAL eta0, eta1, eta2, xi0, xi1, xi2; - auto xmap = geom->GetXmap(); - for(auto vx : vertices){ - test_eta[0] = vx.at(0); - test_eta[1] = vx.at(1); - test_eta[2] = vx.at(2); - xmap->LocCollapsedToLocCoord(test_eta, test_xi); - xmap->LocCoordToLocCollapsed(test_xi, test_eta); + const int num_vertices_expected = geom->GetNumVerts(); + const int num_vertices_found = vertices_found.size(); + + // At the time of writing TetGeom mapping is inconsistent with itself in + // Nektar++ + const bool nektar_mapping_consistent = + num_vertices_found == num_vertices_expected; + + vertices_found.clear(); + + for (auto vx : vertices) { + test_eta[0] = vx.at(0); + test_eta[1] = vx.at(1); + test_eta[2] = vx.at(2); + + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, + test_xi_neso); + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta[0], + test_eta[1], test_eta[2], + &xi0, &xi1, &xi2); + ASSERT_NEAR(test_xi_neso[0], xi0, 1.0e-14); + ASSERT_NEAR(test_xi_neso[1], xi1, 1.0e-14); + ASSERT_NEAR(test_xi_neso[2], xi2, 1.0e-14); + geom_test.loc_collapsed_to_loc_coord(eta0, eta1, eta2, &xi0, &xi1, &xi2); + ASSERT_NEAR(test_xi_neso[0], xi0, 1.0e-14); + ASSERT_NEAR(test_xi_neso[1], xi1, 1.0e-14); + ASSERT_NEAR(test_xi_neso[2], xi2, 1.0e-14); + + if (nektar_mapping_consistent) { xmap->LocCollapsedToLocCoord(test_eta, test_xi); - xmap->LocCoordToLocCollapsed(test_xi, test_eta); - - vertices_found.insert( - { - (int) std::round(test_eta[0]), - (int) std::round(test_eta[1]), - (int) std::round(test_eta[2]) - } - ); + ASSERT_NEAR(test_xi_neso[0], test_xi[0], 1.0e-14); + ASSERT_NEAR(test_xi_neso[1], test_xi[1], 1.0e-14); + ASSERT_NEAR(test_xi_neso[2], test_xi[2], 1.0e-14); } - const int num_vertices_expected = geom->GetNumVerts(); - const int num_vertices_found = vertices_found.size(); - - // At the time of writing TetGeom mapping is inconsistent with itself in Nektar++ - const bool nektar_mapping_consistent = num_vertices_found == num_vertices_expected; - - vertices_found.clear(); - - for(auto vx : vertices){ - test_eta[0] = vx.at(0); - test_eta[1] = vx.at(1); - test_eta[2] = vx.at(2); - - GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi_neso); - GeometryInterface::loc_collapsed_to_loc_coord( - shape_type_int, test_eta[0], test_eta[1], test_eta[2], &xi0, &xi1, &xi2); - ASSERT_NEAR(test_xi_neso[0], xi0, 1.0e-14); - ASSERT_NEAR(test_xi_neso[1], xi1, 1.0e-14); - ASSERT_NEAR(test_xi_neso[2], xi2, 1.0e-14); - - if (nektar_mapping_consistent) { - xmap->LocCollapsedToLocCoord(test_eta, test_xi); - ASSERT_NEAR(test_xi_neso[0], test_xi[0], 1.0e-14); - ASSERT_NEAR(test_xi_neso[1], test_xi[1], 1.0e-14); - ASSERT_NEAR(test_xi_neso[2], test_xi[2], 1.0e-14); - } - - GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, test_xi_neso, test_eta_neso); - GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi0, xi1, xi2, &eta0, &eta1, &eta2); - ASSERT_NEAR(test_eta_neso[0], eta0, 1.0e-14); - ASSERT_NEAR(test_eta_neso[1], eta1, 1.0e-14); - ASSERT_NEAR(test_eta_neso[2], eta2, 1.0e-14); - - if (nektar_mapping_consistent) { - xmap->LocCoordToLocCollapsed(test_xi_neso, test_eta); - ASSERT_NEAR(test_eta_neso[0], test_eta[0], 1.0e-14); - ASSERT_NEAR(test_eta_neso[1], test_eta[1], 1.0e-14); - ASSERT_NEAR(test_eta_neso[2], test_eta[2], 1.0e-14); - } - - vertices_found.insert( - { - (int) std::round(eta0), - (int) std::round(eta1), - (int) std::round(eta2) - } - ); - + GeometryInterface::loc_coord_to_loc_collapsed_3d( + shape_type_int, test_xi_neso, test_eta_neso); + GeometryInterface::loc_coord_to_loc_collapsed_3d( + shape_type_int, xi0, xi1, xi2, &eta0, &eta1, &eta2); + ASSERT_NEAR(test_eta_neso[0], eta0, 1.0e-14); + ASSERT_NEAR(test_eta_neso[1], eta1, 1.0e-14); + ASSERT_NEAR(test_eta_neso[2], eta2, 1.0e-14); + geom_test.loc_coord_to_loc_collapsed(xi0, xi1, xi2, &eta0, &eta1, &eta2); + ASSERT_NEAR(test_eta_neso[0], eta0, 1.0e-14); + ASSERT_NEAR(test_eta_neso[1], eta1, 1.0e-14); + ASSERT_NEAR(test_eta_neso[2], eta2, 1.0e-14); + + if (nektar_mapping_consistent) { + xmap->LocCoordToLocCollapsed(test_xi_neso, test_eta); + ASSERT_NEAR(test_eta_neso[0], test_eta[0], 1.0e-14); + ASSERT_NEAR(test_eta_neso[1], test_eta[1], 1.0e-14); + ASSERT_NEAR(test_eta_neso[2], test_eta[2], 1.0e-14); } - - // Our implementations should be consistent. - ASSERT_EQ(vertices_found.size(), num_vertices_expected); - }; + + vertices_found.insert({(int)std::round(eta0), (int)std::round(eta1), + (int)std::round(eta2)}); + } + + // Our implementations should be consistent. + ASSERT_EQ(vertices_found.size(), num_vertices_expected); + }; + + for (auto &geom_pair : geoms) { + auto geom = geom_pair.second; auto shape_type = geom->GetShapeType(); if (shape_type == LibUtilities::eTetrahedron) { @@ -380,7 +374,6 @@ TEST(ParticleGeometryInterface, CoordinateMapping3D) { ASSERT_NEAR(xi0[2], xi1[2], 1.0e-8); }; - // test the function that maps all types dh_eta.h_buffer.ptr[0] = k_eta0; dh_eta.h_buffer.ptr[1] = k_eta1; diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 0c721782..0f99b65e 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -33,14 +33,14 @@ static inline void copy_to_cstring(std::string input, char **output) { // TODO REMOVE START namespace NESO::Newton { -template class XMapNewtonTest : public XMapNewton { +template +class XMapNewtonTest : public XMapNewton { public: - template - XMapNewtonTest(SYCLTargetSharedPtr sycl_target, std::shared_ptr geom, - const int num_modes_factor = 1) - : XMapNewton(sycl_target, geom, num_modes_factor) - {} + XMapNewtonTest(SYCLTargetSharedPtr sycl_target, + std::shared_ptr geom, + const int num_modes_factor = 1) + : XMapNewton(sycl_target, geom, num_modes_factor) {} inline bool x_inverse(const REAL phys0, const REAL phys1, const REAL phys2, REAL *xi0, REAL *xi1, REAL *xi2, @@ -96,7 +96,8 @@ template class XMapNewtonTest : public XMapNewton class XMapNewtonTest : public XMapNewton 15.0) || (ABS(k_xi1) > 15.0) || - (ABS(k_xi2) > 15.0) || (residual != residual); + (ABS(k_xi2) > 15.0) || + (residual != residual); converged = (residual <= k_tol) && (!diverged); } @@ -148,30 +150,35 @@ template class XMapNewtonTest : public XMapNewton class XMapNewtonTest : public XMapNewtondh_fdata->h_buffer.ptr[2]; return (this->dh_fdata->h_buffer.ptr[3] > 0); } - }; - - - -} +} // namespace NESO::Newton // TODO REMOVE END - - - TEST(ParticleGeometryInterfaceCurved, CoordinateMapping) { int size, rank; @@ -275,62 +275,55 @@ TEST(ParticleGeometryInterfaceCurved, CoordinateMapping) { } }; - auto lambda_to_collapsed_coord = [&]( - auto geom, - auto xi0, - auto xi1, - auto xi2, - auto * eta0, - auto * eta1, - auto * eta2 - ){ + auto lambda_to_collapsed_coord = [&](auto geom, auto xi0, auto xi1, auto xi2, + auto *eta0, auto *eta1, auto *eta2) { auto s = geom->GetShapeType(); switch (s) { case eTetrahedron: - GeometryInterface::Tetrahedron{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, eta1, eta2); + GeometryInterface::Tetrahedron{}.loc_coord_to_loc_collapsed( + xi0, xi1, xi2, eta0, eta1, eta2); break; case ePyramid: - GeometryInterface::Pyramid{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, eta1, eta2); + GeometryInterface::Pyramid{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, + eta0, eta1, eta2); break; case ePrism: - GeometryInterface::Prism{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, eta1, eta2); + GeometryInterface::Prism{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, + eta1, eta2); break; case eHexahedron: - GeometryInterface::Hexahedron{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, eta1, eta2); + GeometryInterface::Hexahedron{}.loc_coord_to_loc_collapsed( + xi0, xi1, xi2, eta0, eta1, eta2); break; default: return "shape unknown"; } }; - auto lambda_to_local_coord = [&]( - auto geom, - auto eta0, - auto eta1, - auto eta2, - auto * xi0, - auto * xi1, - auto * xi2 - ){ + auto lambda_to_local_coord = [&](auto geom, auto eta0, auto eta1, auto eta2, + auto *xi0, auto *xi1, auto *xi2) { auto s = geom->GetShapeType(); switch (s) { case eTetrahedron: - GeometryInterface::Tetrahedron{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, xi0, xi1, xi2); + GeometryInterface::Tetrahedron{}.loc_collapsed_to_loc_coord( + eta0, eta1, eta2, xi0, xi1, xi2); break; case ePyramid: - GeometryInterface::Pyramid{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, xi0, xi1, xi2); + GeometryInterface::Pyramid{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, + xi0, xi1, xi2); break; case ePrism: - GeometryInterface::Prism{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, xi0, xi1, xi2); + GeometryInterface::Prism{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, + xi0, xi1, xi2); break; case eHexahedron: - GeometryInterface::Hexahedron{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, xi0, xi1, xi2); + GeometryInterface::Hexahedron{}.loc_collapsed_to_loc_coord( + eta0, eta1, eta2, xi0, xi1, xi2); break; default: return "shape unknown"; } }; - for (auto gx : geoms) { auto geom = gx.second; auto xmap = geom->GetXmap(); @@ -338,22 +331,16 @@ TEST(ParticleGeometryInterfaceCurved, CoordinateMapping) { std::set> vertices_found; std::vector> vertices = { - {-1.0, -1.0, -1.0}, - { 1.0, -1.0, -1.0}, - {-1.0, 1.0, -1.0}, - { 1.0, 1.0, -1.0}, - {-1.0, -1.0, 1.0}, - { 1.0, -1.0, 1.0}, - {-1.0, 1.0, 1.0}, - { 1.0, 1.0, 1.0} - }; + {-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, {-1.0, 1.0, -1.0}, + {1.0, 1.0, -1.0}, {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, + {-1.0, 1.0, 1.0}, {1.0, 1.0, 1.0}}; Array test_eta(3); Array test_eta_neso(3); Array test_xi(3); Array test_xi_neso(3); REAL eta0, eta1, eta2, xi0, xi1, xi2; - for(auto vx : vertices){ + for (auto vx : vertices) { test_eta[0] = vx.at(0); test_eta[1] = vx.at(1); test_eta[2] = vx.at(2); @@ -361,31 +348,32 @@ TEST(ParticleGeometryInterfaceCurved, CoordinateMapping) { xmap->LocCoordToLocCollapsed(test_xi, test_eta); xmap->LocCollapsedToLocCoord(test_eta, test_xi); xmap->LocCoordToLocCollapsed(test_xi, test_eta); - - vertices_found.insert( - { - (int) std::round(test_eta[0]), - (int) std::round(test_eta[1]), - (int) std::round(test_eta[2]) - } - ); + + vertices_found.insert({(int)std::round(test_eta[0]), + (int)std::round(test_eta[1]), + (int)std::round(test_eta[2])}); } const int num_vertices_expected = geom->GetNumVerts(); const int num_vertices_found = vertices_found.size(); - // At the time of writing TetGeom mapping is inconsistent with itself in Nektar++ - const bool nektar_mapping_consistent = num_vertices_found == num_vertices_expected; + // At the time of writing TetGeom mapping is inconsistent with itself in + // Nektar++ + const bool nektar_mapping_consistent = + num_vertices_found == num_vertices_expected; vertices_found.clear(); - for(auto vx : vertices){ + for (auto vx : vertices) { test_eta[0] = vx.at(0); test_eta[1] = vx.at(1); test_eta[2] = vx.at(2); - - GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi_neso); - GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta[0], test_eta[1], test_eta[2], &xi0, &xi1, &xi2); + + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, + test_xi_neso); + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta[0], + test_eta[1], test_eta[2], + &xi0, &xi1, &xi2); ASSERT_NEAR(test_xi_neso[0], xi0, 1.0e-14); ASSERT_NEAR(test_xi_neso[1], xi1, 1.0e-14); ASSERT_NEAR(test_xi_neso[2], xi2, 1.0e-14); @@ -397,8 +385,10 @@ TEST(ParticleGeometryInterfaceCurved, CoordinateMapping) { ASSERT_NEAR(test_xi_neso[2], test_xi[2], 1.0e-14); } - GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, test_xi_neso, test_eta_neso); - GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi0, xi1, xi2, &eta0, &eta1, &eta2); + GeometryInterface::loc_coord_to_loc_collapsed_3d( + shape_type_int, test_xi_neso, test_eta_neso); + GeometryInterface::loc_coord_to_loc_collapsed_3d( + shape_type_int, xi0, xi1, xi2, &eta0, &eta1, &eta2); ASSERT_NEAR(test_eta_neso[0], eta0, 1.0e-14); ASSERT_NEAR(test_eta_neso[1], eta1, 1.0e-14); ASSERT_NEAR(test_eta_neso[2], eta2, 1.0e-14); @@ -410,16 +400,10 @@ TEST(ParticleGeometryInterfaceCurved, CoordinateMapping) { ASSERT_NEAR(test_eta_neso[2], test_eta[2], 1.0e-14); } - vertices_found.insert( - { - (int) std::round(eta0), - (int) std::round(eta1), - (int) std::round(eta2) - } - ); - + vertices_found.insert({(int)std::round(eta0), (int)std::round(eta1), + (int)std::round(eta2)}); } - + // Our implementations should be consistent. ASSERT_EQ(vertices_found.size(), num_vertices_expected); @@ -481,10 +465,6 @@ TEST(ParticleGeometryInterfaceCurved, CoordinateMapping) { nprint(x, y, z); */ - - - - } mesh->free(); @@ -577,7 +557,8 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { xmap->LocCoordToLocCollapsed(xi, eta); const int shape_type_int = static_cast(geom->GetShapeType()); - GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi, test_eta); + GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi, + test_eta); ASSERT_NEAR(eta[0], test_eta[0], 1.0e-8); ASSERT_NEAR(eta[1], test_eta[1], 1.0e-8); @@ -586,7 +567,8 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { Array test_xi_neso(3); Array test_xi_nektar(3); - GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, eta, test_xi_neso); + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, eta, + test_xi_neso); xmap->LocCollapsedToLocCoord(eta, test_xi_nektar); ASSERT_NEAR(test_xi_nektar[0], test_xi_neso[0], 1.0e-8); ASSERT_NEAR(test_xi_nektar[1], test_xi_neso[1], 1.0e-8); @@ -685,8 +667,10 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { (std::abs(test_xi1 - xi[1]) < 1.0e-8) && (std::abs(test_xi2 - xi[2]) < 1.0e-8); - mapper.x(test_xi0, test_xi1, test_xi2, &test_phys0, &test_phys1, &test_phys2); - nprint("XI:", test_xi0, test_xi1, test_xi2, "PHYS:", test_phys0, test_phys1, test_phys2); + mapper.x(test_xi0, test_xi1, test_xi2, &test_phys0, &test_phys1, + &test_phys2); + nprint("XI:", test_xi0, test_xi1, test_xi2, "PHYS:", test_phys0, test_phys1, + test_phys2); // If the test_xi is xi then the inverse mapping was good // Otherwise check test_xi is a reference coordinate that maps to phys @@ -715,7 +699,7 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { for (auto gx : geoms) { auto geom = gx.second; nprint("GLOBALID:", geom->GetGlobalID()); - if (geom->GetGlobalID() != 45){ + if (geom->GetGlobalID() != 45) { continue; } auto xmap = geom->GetXmap(); @@ -726,13 +710,13 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { nprint("dx:", dx, "type:", lambda_btype(xmap->GetBasisType(dx)), xmap->GetBasisNumModes(dx)); } - + { - NekDouble x,y,z; + NekDouble x, y, z; const auto num_verts = geom->GetNumVerts(); - for(int ix=0 ; ixGetVertex(ix); - vx->GetCoords(x,y,z); + vx->GetCoords(x, y, z); nprint("VX:", ix, x, y, z); } } @@ -782,109 +766,107 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { nprint("\t", "PHYS:", test_phys[0], test_phys[1], test_phys[2]); { - // Test vertices of reference element - std::vector> vertices = { - {-1.0, -1.0, -1.0}, - { 1.0, -1.0, -1.0}, - {-1.0, 1.0, -1.0}, - { 1.0, 1.0, -1.0}, - {-1.0, -1.0, 1.0}, - { 1.0, -1.0, 1.0}, - {-1.0, 1.0, 1.0}, - { 1.0, 1.0, 1.0} - }; - - for(auto &etav : vertices){ - nprint("=============================================="); - test_eta[0] = etav.at(0); - test_eta[1] = etav.at(1); - test_eta[2] = etav.at(2); - - // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi); - - nprint("ETA 0:", test_eta[0], test_eta[1], test_eta[2]); - geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); - // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi); - nprint(" XI 0:", test_xi[0], test_xi[1], test_xi[2]); - geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); - nprint("ETA 1:", test_eta[0], test_eta[1], test_eta[2]); - geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); - // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi); - nprint(" XI 1:", test_xi[0], test_xi[1], test_xi[2]); - geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); - nprint("ETA 2:", test_eta[0], test_eta[1], test_eta[2]); - - - lambda_forward_map(geom, test_xi, test_phys); - nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], "\n ETA O:", test_eta[0], test_eta[1], test_eta[2], "\nPHYS:", test_phys[0], test_phys[1], test_phys[2]); - - // Does nektar sucessfully invert the map? - Array test_xi_nektar(3); - auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); - nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], test_xi_nektar[2], "DIST:", dist); - } + // Test vertices of reference element + std::vector> vertices = { + {-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, {-1.0, 1.0, -1.0}, + {1.0, 1.0, -1.0}, {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, + {-1.0, 1.0, 1.0}, {1.0, 1.0, 1.0}}; + + for (auto &etav : vertices) { + nprint("=============================================="); + test_eta[0] = etav.at(0); + test_eta[1] = etav.at(1); + test_eta[2] = etav.at(2); + + // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, + // test_eta, test_xi); + + nprint("ETA 0:", test_eta[0], test_eta[1], test_eta[2]); + geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); + // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, + // test_eta, test_xi); + nprint(" XI 0:", test_xi[0], test_xi[1], test_xi[2]); + geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); + nprint("ETA 1:", test_eta[0], test_eta[1], test_eta[2]); + geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); + // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, + // test_eta, test_xi); + nprint(" XI 1:", test_xi[0], test_xi[1], test_xi[2]); + geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); + nprint("ETA 2:", test_eta[0], test_eta[1], test_eta[2]); + + lambda_forward_map(geom, test_xi, test_phys); + nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], + "\n ETA O:", test_eta[0], test_eta[1], test_eta[2], + "\nPHYS:", test_phys[0], test_phys[1], test_phys[2]); + + // Does nektar sucessfully invert the map? + Array test_xi_nektar(3); + auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); + nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], + test_xi_nektar[2], "DIST:", dist); + } - nprint("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"); + nprint("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"); - for(auto &etav : vertices){ - nprint("=============================================="); - test_xi[0] = etav.at(0); - test_xi[1] = etav.at(1); - test_xi[2] = etav.at(2); + for (auto &etav : vertices) { + nprint("=============================================="); + test_xi[0] = etav.at(0); + test_xi[1] = etav.at(1); + test_xi[2] = etav.at(2); - if ((test_xi[0] + test_xi[1] + test_xi[2]) <= -0.9){ - geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); - nprint("ETA::", test_eta[0], test_eta[1], test_eta[2]); + if ((test_xi[0] + test_xi[1] + test_xi[2]) <= -0.9) { + geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); + nprint("ETA::", test_eta[0], test_eta[1], test_eta[2]); - lambda_forward_map(geom, test_xi, test_phys); - nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], "PHYS:", test_phys[0], test_phys[1], test_phys[2]); + lambda_forward_map(geom, test_xi, test_phys); + nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], + "PHYS:", test_phys[0], test_phys[1], test_phys[2]); - // Does nektar sucessfully invert the map? - Array test_xi_nektar(3); - auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); - nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], test_xi_nektar[2], "DIST:", dist); + // Does nektar sucessfully invert the map? + Array test_xi_nektar(3); + auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); + nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], + test_xi_nektar[2], "DIST:", dist); + } } } - - - - } - - - // Test vertices of reference element std::vector> vertices = { - //{-1.0, -1.0, -1.0}, - { 1.0, -1.0, -1.0}, - //{-1.0, 1.0, -1.0}, - //{ 1.0, 1.0, -1.0}, - //{-1.0, -1.0, 1.0}, - //{ 1.0, -1.0, 1.0}, - //{-1.0, 1.0, 1.0}, - //{ 1.0, 1.0, 1.0} + //{-1.0, -1.0, -1.0}, + {1.0, -1.0, -1.0}, + //{-1.0, 1.0, -1.0}, + //{ 1.0, 1.0, -1.0}, + //{-1.0, -1.0, 1.0}, + //{ 1.0, -1.0, 1.0}, + //{-1.0, 1.0, 1.0}, + //{ 1.0, 1.0, 1.0} }; - - for(auto &etav : vertices){ + + for (auto &etav : vertices) { nprint("----------------------------------------------"); test_eta[0] = etav.at(0); test_eta[1] = etav.at(1); test_eta[2] = etav.at(2); - GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi); + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, + test_xi); lambda_forward_map(geom, test_xi, test_phys); - nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], "\nETA:", test_eta[0], test_eta[1], test_eta[2], "\nPHYS:", test_phys[0], test_phys[1], test_phys[2]); - + nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], + "\nETA:", test_eta[0], test_eta[1], test_eta[2], + "\nPHYS:", test_phys[0], test_phys[1], test_phys[2]); // Does nektar sucessfully invert the map? Array test_xi_nektar(3); auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); - nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], test_xi_nektar[2], "DIST:", dist); + nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], + test_xi_nektar[2], "DIST:", dist); lambda_check_x_map(geom, test_xi, test_phys); } // test internal points - //for(int testx=0 ; testx<20 ; testx++){ + // for(int testx=0 ; testx<20 ; testx++){ // nprint("=============================================="); // lambda_sample_internal_point(geom, test_xi, test_phys); // lambda_check_x_map(geom, test_xi, test_phys); From c41f27b89d90f810cbb9639908ddc35d1a40d75a Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 29 Oct 2024 11:59:47 +0000 Subject: [PATCH 18/66] NESO tests now expose incorrect Tet coordinate mapping --- .../nektar_interface/test_particle_geometry_interface.cpp | 2 ++ .../test_particle_geometry_interface_3d.cpp | 6 +++++- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/test/unit/nektar_interface/test_particle_geometry_interface.cpp b/test/unit/nektar_interface/test_particle_geometry_interface.cpp index da96d02a..b216f610 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface.cpp @@ -703,6 +703,7 @@ TEST(ParticleGeometryInterface, CoordinateMapping2D) { const int num_vertices_found = vertices_found.size(); const bool nektar_mapping_consistent = num_vertices_found == num_vertices_expected; + ASSERT_TRUE(nektar_mapping_consistent); vertices_found.clear(); for (auto vx : vertices) { @@ -736,6 +737,7 @@ TEST(ParticleGeometryInterface, CoordinateMapping2D) { } ASSERT_EQ(vertices_found.size(), num_vertices_expected); + vertices_found.clear(); }; for (auto &geom_pair : geoms) { diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp index dda62da0..c187b940 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp @@ -270,6 +270,8 @@ TEST(ParticleGeometryInterface, CoordinateMapping3D) { // Nektar++ const bool nektar_mapping_consistent = num_vertices_found == num_vertices_expected; + ASSERT_TRUE(nektar_mapping_consistent || + (geom->GetShapeType() == LibUtilities::eTetrahedron)); vertices_found.clear(); @@ -286,7 +288,8 @@ TEST(ParticleGeometryInterface, CoordinateMapping3D) { ASSERT_NEAR(test_xi_neso[0], xi0, 1.0e-14); ASSERT_NEAR(test_xi_neso[1], xi1, 1.0e-14); ASSERT_NEAR(test_xi_neso[2], xi2, 1.0e-14); - geom_test.loc_collapsed_to_loc_coord(eta0, eta1, eta2, &xi0, &xi1, &xi2); + geom_test.loc_collapsed_to_loc_coord(test_eta[0], test_eta[1], + test_eta[2], &xi0, &xi1, &xi2); ASSERT_NEAR(test_xi_neso[0], xi0, 1.0e-14); ASSERT_NEAR(test_xi_neso[1], xi1, 1.0e-14); ASSERT_NEAR(test_xi_neso[2], xi2, 1.0e-14); @@ -323,6 +326,7 @@ TEST(ParticleGeometryInterface, CoordinateMapping3D) { // Our implementations should be consistent. ASSERT_EQ(vertices_found.size(), num_vertices_expected); + vertices_found.clear(); }; for (auto &geom_pair : geoms) { From 923f1072848882fcbe27d9036b60a9fb5327ed2f Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 29 Oct 2024 12:45:58 +0000 Subject: [PATCH 19/66] updated Tetrahedron collapsed to local coordinate mapping --- include/nektar_interface/coordinate_mapping.hpp | 9 +++++---- .../test_particle_geometry_interface_3d.cpp | 7 +++++-- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/include/nektar_interface/coordinate_mapping.hpp b/include/nektar_interface/coordinate_mapping.hpp index 6423b858..a074cac4 100644 --- a/include/nektar_interface/coordinate_mapping.hpp +++ b/include/nektar_interface/coordinate_mapping.hpp @@ -209,7 +209,7 @@ struct Tetrahedron : BaseCoordinateMapping3D { inline void loc_collapsed_to_loc_coord_v(const T eta0, const T eta1, const T eta2, T *xi0, T *xi1, T *xi2) { - *xi1 = (1.0 + eta0) * (1.0 - eta2) * 0.5 - 1.0; + *xi1 = (1.0 + eta1) * (1.0 - eta2) * 0.5 - 1.0; *xi0 = (1.0 + eta0) * (-(*xi1) - eta2) * 0.5 - 1.0; *xi2 = eta2; } @@ -474,7 +474,7 @@ inline void loc_collapsed_to_loc_coord(const int shape_type, const T eta0, /* Tet - xi[1] = (1.0 + eta[0]) * (1.0 - eta[2]) * 0.5 - 1.0; + xi[1] = (1.0 + eta[1]) * (1.0 - eta[2]) * 0.5 - 1.0; xi[0] = (1.0 + eta[0]) * (-xi[1] - eta[2]) * 0.5 - 1.0; xi[2] = eta[2]; @@ -525,7 +525,8 @@ inline void loc_collapsed_to_loc_coord(const int shape_type, const T eta0, const REAL a = 1.0 + eta0; const REAL b = 1.0 - eta2; - const REAL c = (a) * (b)*0.5 - 1.0; + const REAL c = (1.0 + eta1) * (b)*0.5 - 1.0; + const REAL d = (a) * (b)*0.5 - 1.0; *xi1 = (shape_type == shape_type_tet) ? c : ((shape_type == shape_type_pyr) ? (1.0 + eta1) * (b)*0.5 - 1.0 @@ -533,7 +534,7 @@ inline void loc_collapsed_to_loc_coord(const int shape_type, const T eta0, const REAL tet_x = (1.0 + eta0) * (-(*xi1) - eta2) * 0.5 - 1.0; *xi0 = (shape_type == shape_type_tet) ? tet_x - : ((shape_type == shape_type_hex) ? eta0 : c); + : ((shape_type == shape_type_hex) ? eta0 : d); *xi2 = eta2; } diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp index c187b940..058b1226 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d.cpp @@ -414,7 +414,8 @@ TEST(ParticleGeometryInterface, CoordinateMapping3D) { xi1[dimx] = dh_xi.h_buffer.ptr[dimx]; eta0[dimx] = dh_eta.h_buffer.ptr[dimx]; } - geom->GetXmap()->LocCollapsedToLocCoord(eta0, xi0); + // geom->GetXmap()->LocCollapsedToLocCoord(eta0, xi0); + GeometryInterface::loc_collapsed_to_loc_coord(k_shape_type_int, eta0, xi0); lambda_test_xi(); // test the xi to eta map @@ -440,7 +441,9 @@ TEST(ParticleGeometryInterface, CoordinateMapping3D) { eta1[dimx] = dh_eta.h_buffer.ptr[dimx]; xi0[dimx] = dh_xi.h_buffer.ptr[dimx]; } - geom->GetXmap()->LocCoordToLocCollapsed(xi0, eta0); + // geom->GetXmap()->LocCoordToLocCollapsed(xi0, eta0); + GeometryInterface::loc_coord_to_loc_collapsed_3d(k_shape_type_int, xi0, + eta0); lambda_test_eta(); } From 1fa74886f00eece5e6b2223066b669497939ed0f Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 29 Oct 2024 12:55:21 +0000 Subject: [PATCH 20/66] updated some function names to name a correct namespace --- include/nektar_interface/coordinate_mapping.hpp | 3 ++- .../particle_cell_mapping/particle_cell_mapping_common.hpp | 2 +- src/nektar_interface/particle_boundary_conditions.cpp | 2 +- .../particle_cell_mapping/map_particles_2d_regular.cpp | 2 +- src/species.cpp | 2 +- 5 files changed, 6 insertions(+), 5 deletions(-) diff --git a/include/nektar_interface/coordinate_mapping.hpp b/include/nektar_interface/coordinate_mapping.hpp index a074cac4..99fadace 100644 --- a/include/nektar_interface/coordinate_mapping.hpp +++ b/include/nektar_interface/coordinate_mapping.hpp @@ -641,7 +641,8 @@ inline void loc_coord_to_loc_collapsed_2d(const int shape_type, const T xi0, constexpr int shape_type_tri = shape_type_to_int(LibUtilities::eTriangle); const NekDouble d1_original = 1.0 - xi1; - const bool mask_small_cond = (fabs(d1_original) < NekConstants::kNekZeroTol); + const bool mask_small_cond = + (sycl::fabs(d1_original) < NekConstants::kNekZeroTol); NekDouble d1 = d1_original; d1 = (mask_small_cond && (d1 >= 0.0)) diff --git a/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp b/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp index caba4edd..0620f83c 100644 --- a/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp +++ b/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp @@ -108,7 +108,7 @@ inline double get_local_coords_2d(std::shared_ptr geom, double eta1 = -2; if (geom->GetShapeType() == LibUtilities::eTriangle) { NekDouble d1 = 1. - Lcoords[1]; - if (fabs(d1) < NekConstants::kNekZeroTol) { + if (sycl::fabs(d1) < NekConstants::kNekZeroTol) { if (d1 >= 0.) { d1 = NekConstants::kNekZeroTol; } else { diff --git a/src/nektar_interface/particle_boundary_conditions.cpp b/src/nektar_interface/particle_boundary_conditions.cpp index 5129cc94..fc1ab33e 100644 --- a/src/nektar_interface/particle_boundary_conditions.cpp +++ b/src/nektar_interface/particle_boundary_conditions.cpp @@ -66,7 +66,7 @@ NektarCartesianPeriodic::NektarCartesianPeriodic( const double tmp_extent = k_extents[dimx]; const INT n_extent_offset_int = n_extent_offset_real + 2.0; const double pos_fmod = - fmod(pos + n_extent_offset_int * tmp_extent, tmp_extent); + sycl::fmod(pos + n_extent_offset_int * tmp_extent, tmp_extent); k_positions_dat.at(dimx) = pos_fmod + k_origin[dimx]; } }, diff --git a/src/nektar_interface/particle_cell_mapping/map_particles_2d_regular.cpp b/src/nektar_interface/particle_cell_mapping/map_particles_2d_regular.cpp index 22ce47f7..fc5e0360 100644 --- a/src/nektar_interface/particle_cell_mapping/map_particles_2d_regular.cpp +++ b/src/nektar_interface/particle_cell_mapping/map_particles_2d_regular.cpp @@ -236,7 +236,7 @@ void MapParticles2DRegular::map(ParticleGroup &particle_group, double tmp_eta0; if (geom_type == k_geom_is_triangle) { NekDouble d1 = 1. - xi1; - if (fabs(d1) < NekConstants::kNekZeroTol) { + if (sycl::fabs(d1) < NekConstants::kNekZeroTol) { if (d1 >= 0.) { d1 = NekConstants::kNekZeroTol; } else { diff --git a/src/species.cpp b/src/species.cpp index 92d84162..c694800b 100644 --- a/src/species.cpp +++ b/src/species.cpp @@ -117,7 +117,7 @@ void Species::push(sycl::queue &queue, Mesh *mesh) { while (x_a[idx] < 0) { x_a[idx] += 1.0; } - x_a[idx] = std::fmod(x_a[idx], 1.0); + x_a[idx] = sycl::fmod(x_a[idx], 1.0); const double F1 = Mesh1D::sycl_evaluate_electric_field( mesh_a, k_mesh_size, electric_field_a, x_a[idx]); From 39999dad2bee541fe9ff6d3b56d56dadf9022726 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 29 Oct 2024 14:13:02 +0000 Subject: [PATCH 21/66] cleanup of test for curved cell binning --- ..._particle_geometry_interface_3d_curved.cpp | 190 +----------------- 1 file changed, 7 insertions(+), 183 deletions(-) diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 0f99b65e..82b193ea 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -553,27 +553,8 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { xmap->BwdTrans(geom->GetCoeffs(1), ptsy); xmap->BwdTrans(geom->GetCoeffs(2), ptsz); Array eta(3); - Array test_eta(3); xmap->LocCoordToLocCollapsed(xi, eta); - const int shape_type_int = static_cast(geom->GetShapeType()); - GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi, - test_eta); - - ASSERT_NEAR(eta[0], test_eta[0], 1.0e-8); - ASSERT_NEAR(eta[1], test_eta[1], 1.0e-8); - ASSERT_NEAR(eta[2], test_eta[2], 1.0e-8); - - Array test_xi_neso(3); - Array test_xi_nektar(3); - - GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, eta, - test_xi_neso); - xmap->LocCollapsedToLocCoord(eta, test_xi_nektar); - ASSERT_NEAR(test_xi_nektar[0], test_xi_neso[0], 1.0e-8); - ASSERT_NEAR(test_xi_nektar[1], test_xi_neso[1], 1.0e-8); - ASSERT_NEAR(test_xi_nektar[2], test_xi_neso[2], 1.0e-8); - Array I(3); I[0] = xmap->GetBasis(0)->GetI(eta); @@ -635,8 +616,6 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { auto lambda_check_x_map = [&](auto geom, Array &xi, Array &phys) { - nprint("CHECK X MAP START", xi[0], xi[1], xi[2], phys[0], phys[1], phys[2]); - REAL eta0, eta1, eta2; const int shape_type_int = static_cast(geom->GetShapeType()); // The point we sampled was considered contained by Nektar++ @@ -647,7 +626,6 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { GeometryInterface::loc_coord_to_loc_collapsed_3d(shape_type_int, xi00, xi01, xi02, &eta0, &eta1, &eta2); const auto dist = lambda_test_contained(eta0, eta1, eta2); - nprint("dist0", dist, eta0, eta1, eta2); EXPECT_TRUE(dist < 1.0e-8); // test the forward x map from reference space to physical space @@ -667,11 +645,6 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { (std::abs(test_xi1 - xi[1]) < 1.0e-8) && (std::abs(test_xi2 - xi[2]) < 1.0e-8); - mapper.x(test_xi0, test_xi1, test_xi2, &test_phys0, &test_phys1, - &test_phys2); - nprint("XI:", test_xi0, test_xi1, test_xi2, "PHYS:", test_phys0, test_phys1, - test_phys2); - // If the test_xi is xi then the inverse mapping was good // Otherwise check test_xi is a reference coordinate that maps to phys if (!same_xi) { @@ -688,189 +661,40 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { GeometryInterface::loc_coord_to_loc_collapsed_3d( shape_type_int, xi00, xi01, xi02, &eta0, &eta1, &eta2); const auto dist = lambda_test_contained(eta0, eta1, eta2); - nprint("dist1", dist, eta0, eta1, eta2); EXPECT_TRUE(equiv_xi); EXPECT_TRUE(dist < 1.0e-8); } - - nprint("CHECK X MAP END"); }; for (auto gx : geoms) { auto geom = gx.second; - nprint("GLOBALID:", geom->GetGlobalID()); - if (geom->GetGlobalID() != 45) { - continue; - } - auto xmap = geom->GetXmap(); const int shape_type_int = static_cast(geom->GetShapeType()); - nprint(geom->GetShapeType(), lambda_stype(geom->GetShapeType())); - nprint("Num bases:", xmap->GetNumBases()); - for (int dx = 0; dx < 3; dx++) { - nprint("dx:", dx, "type:", lambda_btype(xmap->GetBasisType(dx)), - xmap->GetBasisNumModes(dx)); - } - - { - NekDouble x, y, z; - const auto num_verts = geom->GetNumVerts(); - for (int ix = 0; ix < num_verts; ix++) { - auto vx = geom->GetVertex(ix); - vx->GetCoords(x, y, z); - nprint("VX:", ix, x, y, z); - } - } Array test_eta(3); Array test_xi(3); Array test_phys(3); - test_eta[0] = -1.0; - test_eta[1] = 1.0; - test_eta[2] = -1.0; - - geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); - nprint("ETA to XI"); - nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); - nprint("\t", " XI:", test_xi[0], test_xi[1], test_xi[2]); - geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); - nprint("XI to ETA"); - nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); - geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); - nprint("ETA to XI"); - nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); - nprint("\t", " XI:", test_xi[0], test_xi[1], test_xi[2]); - - nprint("NEKTAR FORWARD"); - lambda_forward_map(geom, test_xi, test_phys); - nprint("\t", "PHYS:", test_phys[0], test_phys[1], test_phys[2]); - - test_eta[0] = 1.0; - test_eta[1] = -1.0; - test_eta[2] = -1.0; - - geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); - nprint("ETA to XI"); - nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); - nprint("\t", " XI:", test_xi[0], test_xi[1], test_xi[2]); - geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); - nprint("XI to ETA"); - nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); - geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); - nprint("ETA to XI"); - nprint("\t", "ETA:", test_eta[0], test_eta[1], test_eta[2]); - nprint("\t", " XI:", test_xi[0], test_xi[1], test_xi[2]); - - nprint("NEKTAR FORWARD"); - lambda_forward_map(geom, test_xi, test_phys); - nprint("\t", "PHYS:", test_phys[0], test_phys[1], test_phys[2]); - - { - // Test vertices of reference element - std::vector> vertices = { - {-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, {-1.0, 1.0, -1.0}, - {1.0, 1.0, -1.0}, {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, - {-1.0, 1.0, 1.0}, {1.0, 1.0, 1.0}}; - - for (auto &etav : vertices) { - nprint("=============================================="); - test_eta[0] = etav.at(0); - test_eta[1] = etav.at(1); - test_eta[2] = etav.at(2); - - // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, - // test_eta, test_xi); - - nprint("ETA 0:", test_eta[0], test_eta[1], test_eta[2]); - geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); - // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, - // test_eta, test_xi); - nprint(" XI 0:", test_xi[0], test_xi[1], test_xi[2]); - geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); - nprint("ETA 1:", test_eta[0], test_eta[1], test_eta[2]); - geom->GetXmap()->LocCollapsedToLocCoord(test_eta, test_xi); - // GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, - // test_eta, test_xi); - nprint(" XI 1:", test_xi[0], test_xi[1], test_xi[2]); - geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); - nprint("ETA 2:", test_eta[0], test_eta[1], test_eta[2]); - - lambda_forward_map(geom, test_xi, test_phys); - nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], - "\n ETA O:", test_eta[0], test_eta[1], test_eta[2], - "\nPHYS:", test_phys[0], test_phys[1], test_phys[2]); - - // Does nektar sucessfully invert the map? - Array test_xi_nektar(3); - auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); - nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], - test_xi_nektar[2], "DIST:", dist); - } - - nprint("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"); - - for (auto &etav : vertices) { - nprint("=============================================="); - test_xi[0] = etav.at(0); - test_xi[1] = etav.at(1); - test_xi[2] = etav.at(2); - - if ((test_xi[0] + test_xi[1] + test_xi[2]) <= -0.9) { - geom->GetXmap()->LocCoordToLocCollapsed(test_xi, test_eta); - nprint("ETA::", test_eta[0], test_eta[1], test_eta[2]); - - lambda_forward_map(geom, test_xi, test_phys); - nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], - "PHYS:", test_phys[0], test_phys[1], test_phys[2]); - - // Does nektar sucessfully invert the map? - Array test_xi_nektar(3); - auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); - nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], - test_xi_nektar[2], "DIST:", dist); - } - } - } - // Test vertices of reference element std::vector> vertices = { - //{-1.0, -1.0, -1.0}, - {1.0, -1.0, -1.0}, - //{-1.0, 1.0, -1.0}, - //{ 1.0, 1.0, -1.0}, - //{-1.0, -1.0, 1.0}, - //{ 1.0, -1.0, 1.0}, - //{-1.0, 1.0, 1.0}, - //{ 1.0, 1.0, 1.0} - }; + {-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, {-1.0, 1.0, -1.0}, + {1.0, 1.0, -1.0}, {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, + {-1.0, 1.0, 1.0}, {1.0, 1.0, 1.0}}; for (auto &etav : vertices) { - nprint("----------------------------------------------"); test_eta[0] = etav.at(0); test_eta[1] = etav.at(1); test_eta[2] = etav.at(2); GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, test_xi); lambda_forward_map(geom, test_xi, test_phys); - nprint("TEST: XI:", test_xi[0], test_xi[1], test_xi[2], - "\nETA:", test_eta[0], test_eta[1], test_eta[2], - "\nPHYS:", test_phys[0], test_phys[1], test_phys[2]); - - // Does nektar sucessfully invert the map? - Array test_xi_nektar(3); - auto dist = geom->GetLocCoords(test_phys, test_xi_nektar); - nprint("TEST: NK:", test_xi_nektar[0], test_xi_nektar[1], - test_xi_nektar[2], "DIST:", dist); - lambda_check_x_map(geom, test_xi, test_phys); } // test internal points - // for(int testx=0 ; testx<20 ; testx++){ - // nprint("=============================================="); - // lambda_sample_internal_point(geom, test_xi, test_phys); - // lambda_check_x_map(geom, test_xi, test_phys); - //} + for (int testx = 0; testx < 20; testx++) { + lambda_sample_internal_point(geom, test_xi, test_phys); + lambda_check_x_map(geom, test_xi, test_phys); + } } mesh->free(); From 09df508276b3be0bd59906f695437475b27c6768 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 29 Oct 2024 15:09:51 +0000 Subject: [PATCH 22/66] cleanup of newton iterations, XMapNewton test passing with curved cells --- .../map_particles_newton.hpp | 42 +++++++--- .../newton_generic_3d.hpp | 27 +------ .../particle_cell_mapping/newton_hex.hpp | 8 ++ .../particle_cell_mapping/newton_prism.hpp | 7 ++ .../particle_cell_mapping/newton_pyr.hpp | 7 ++ .../particle_cell_mapping/newton_quad.hpp | 8 ++ .../newton_quad_embed_3d.hpp | 8 ++ .../particle_cell_mapping/newton_tet.hpp | 7 ++ .../newton_triangle_embed_3d.hpp | 9 +++ .../particle_cell_mapping/x_map_newton.hpp | 76 ++++++------------- .../x_map_newton_kernel.hpp | 4 +- .../composite_intersection.cpp | 46 +++++++---- ..._particle_geometry_interface_3d_curved.cpp | 4 +- 13 files changed, 147 insertions(+), 106 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp index fbbc18a6..9ed10d63 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp @@ -197,12 +197,21 @@ class MapParticlesNewton : public CoarseMappersBase { k_newton_type.loc_coord_to_loc_collapsed( map_data, xi[0], xi[1], xi[2], &eta0, &eta1, &eta2); - bool contained = ((-1.0 - k_contained_tol) <= eta0) && - (eta0 <= (1.0 + k_contained_tol)) && - ((-1.0 - k_contained_tol) <= eta1) && - (eta1 <= (1.0 + k_contained_tol)) && - ((-1.0 - k_contained_tol) <= eta2) && - (eta2 <= (1.0 + k_contained_tol)); + eta0 = Kernel::min(eta0, 1.0 + k_contained_tol); + eta1 = Kernel::min(eta1, 1.0 + k_contained_tol); + eta2 = Kernel::min(eta2, 1.0 + k_contained_tol); + eta0 = Kernel::max(eta0, -1.0 - k_contained_tol); + eta1 = Kernel::max(eta1, -1.0 - k_contained_tol); + eta2 = Kernel::max(eta2, -1.0 - k_contained_tol); + + k_newton_type.loc_collapsed_to_loc_coord( + map_data, eta0, eta1, eta2, &xi[0], &xi[1], &xi[2]); + + const REAL clamped_residual = k_newton_type.newton_residual( + map_data, xi[0], xi[1], xi[2], p0, p1, p2, &eta0, &eta1, + &eta2, k_local_memory_ptr); + + const bool contained = clamped_residual <= k_newton_tol; cell_found = contained && converged; if (cell_found) { @@ -346,12 +355,21 @@ class MapParticlesNewton : public CoarseMappersBase { k_newton_type.loc_coord_to_loc_collapsed( map_data, xi[0], xi[1], xi[2], &eta0, &eta1, &eta2); - bool contained = ((-1.0 - k_contained_tol) <= eta0) && - (eta0 <= (1.0 + k_contained_tol)) && - ((-1.0 - k_contained_tol) <= eta1) && - (eta1 <= (1.0 + k_contained_tol)) && - ((-1.0 - k_contained_tol) <= eta2) && - (eta2 <= (1.0 + k_contained_tol)); + eta0 = Kernel::min(eta0, 1.0 + k_contained_tol); + eta1 = Kernel::min(eta1, 1.0 + k_contained_tol); + eta2 = Kernel::min(eta2, 1.0 + k_contained_tol); + eta0 = Kernel::max(eta0, -1.0 - k_contained_tol); + eta1 = Kernel::max(eta1, -1.0 - k_contained_tol); + eta2 = Kernel::max(eta2, -1.0 - k_contained_tol); + + k_newton_type.loc_collapsed_to_loc_coord( + map_data, eta0, eta1, eta2, &xi[0], &xi[1], &xi[2]); + + const REAL clamped_residual = k_newton_type.newton_residual( + map_data, xi[0], xi[1], xi[2], p0, p1, p2, &eta0, &eta1, + &eta2, k_local_memory_ptr); + + const bool contained = clamped_residual <= k_newton_tol; cell_found = contained && converged; diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index 645b66ce..cd55ced1 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -216,7 +216,6 @@ struct MappingGeneric3D : MappingNewtonIterationBase { (J0[0] * J2[1] - J0[1] * J2[0]) * (-f1) + (J0[0] * J1[1] - J0[1] * J1[0]) * (-f2)) * inverse_J; - nprint("NEW:", *xin0, *xin1, *xin2); } inline REAL newton_residual_v(const void *d_data, const REAL xi0, @@ -232,9 +231,6 @@ struct MappingGeneric3D : MappingNewtonIterationBase { this->loc_coord_to_loc_collapsed(d_data, xi0, xi1, xi2, &eta0, &eta1, &eta2); - std::cout << std::setprecision(16); - nprint("COORDS: XI", xi0, xi1, xi2, "ETA:", eta0, eta1, eta2); - // compute X at xi by evaluating the Bary interpolation at eta REAL *div_space0 = static_cast(local_memory); REAL *div_space1 = div_space0 + d->num_phys0; @@ -249,34 +245,15 @@ struct MappingGeneric3D : MappingNewtonIterationBase { d->num_phys2, d->physvals, div_space0, div_space1, div_space2, X); - // const int n0 = d->num_phys0; - // const int n1 = d->num_phys1; - // const int n2 = d->num_phys2; - // nprint("n:", n0, n1, n2); - // for (int ix = 0; ix < n0; ix++) { - // nprint(div_space0[ix]); - // } - // for (int ix = 0; ix < n1; ix++) { - // nprint(div_space1[ix]); - // } - // for (int ix = 0; ix < n2; ix++) { - // nprint(div_space2[ix]); - // } - // nprint(X[0], X[1], X[2], phys0, phys1, phys2); - // Residual is defined as F = X(xi) - P *f0 = X[0] - phys0; *f1 = X[1] - phys1; *f2 = X[2] - phys2; - nprint("PHYS:", phys0, phys1, phys2); - nprint(" X:", X[0], X[1], X[2]); - const REAL norm2 = MAX(MAX(ABS(*f0), ABS(*f1)), ABS(*f2)); const REAL tol_scaling = d->tol_scaling; const REAL scaled_norm2 = norm2 * tol_scaling; - nprint("TOL SCALING:", scaled_norm2, tol_scaling); return scaled_norm2; } @@ -288,9 +265,7 @@ struct MappingGeneric3D : MappingNewtonIterationBase { /** * Implementations that avoid singularities: - * newton_pyr - * - * + * newton_pyr? */ *xi0 = -0.2; diff --git a/include/nektar_interface/particle_cell_mapping/newton_hex.hpp b/include/nektar_interface/particle_cell_mapping/newton_hex.hpp index d6619af6..c7ea0588 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_hex.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_hex.hpp @@ -112,6 +112,14 @@ struct MappingHexLinear3D : MappingNewtonIterationBase { *eta1 = xi1; *eta2 = xi2; } + + inline void loc_collapsed_to_loc_coord_v(const void *d_data, const REAL eta0, + const REAL eta1, const REAL eta2, + REAL *xi0, REAL *xi1, REAL *xi2) { + *xi0 = eta0; + *xi1 = eta1; + *xi2 = eta2; + } }; } // namespace Newton diff --git a/include/nektar_interface/particle_cell_mapping/newton_prism.hpp b/include/nektar_interface/particle_cell_mapping/newton_prism.hpp index ad112989..f700a9ac 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_prism.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_prism.hpp @@ -107,6 +107,13 @@ struct MappingPrismLinear3D : MappingNewtonIterationBase { GeometryInterface::Prism{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, eta1, eta2); } + + inline void loc_collapsed_to_loc_coord_v(const void *d_data, const REAL eta0, + const REAL eta1, const REAL eta2, + REAL *xi0, REAL *xi1, REAL *xi2) { + GeometryInterface::Prism{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, xi0, + xi1, xi2); + } }; } // namespace Newton diff --git a/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp b/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp index 946bbbc9..22c66e9c 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_pyr.hpp @@ -150,6 +150,13 @@ struct MappingPyrLinear3D : MappingNewtonIterationBase { GeometryInterface::Pyramid{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, eta1, eta2); } + + inline void loc_collapsed_to_loc_coord_v(const void *d_data, const REAL eta0, + const REAL eta1, const REAL eta2, + REAL *xi0, REAL *xi1, REAL *xi2) { + GeometryInterface::Pyramid{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, + xi0, xi1, xi2); + } }; } // namespace Newton diff --git a/include/nektar_interface/particle_cell_mapping/newton_quad.hpp b/include/nektar_interface/particle_cell_mapping/newton_quad.hpp index ee890eea..7616ef6a 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_quad.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_quad.hpp @@ -122,6 +122,14 @@ struct MappingQuadLinear2D : MappingNewtonIterationBase { *eta1 = xi1; *eta2 = 0.0; } + + inline void loc_collapsed_to_loc_coord_v(const void *d_data, const REAL eta0, + const REAL eta1, const REAL eta2, + REAL *xi0, REAL *xi1, REAL *xi2) { + *xi0 = eta0; + *xi1 = eta1; + *xi2 = 0.0; + } }; } // namespace Newton diff --git a/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp index e2729790..489cbdee 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_quad_embed_3d.hpp @@ -154,6 +154,14 @@ struct MappingQuadLinear2DEmbed3D *eta1 = xi1; *eta2 = 0.0; } + + inline void loc_collapsed_to_loc_coord_v(const void *d_data, const REAL eta0, + const REAL eta1, const REAL eta2, + REAL *xi0, REAL *xi1, REAL *xi2) { + *xi0 = eta0; + *xi1 = eta1; + *xi2 = 0.0; + } }; } // namespace Newton diff --git a/include/nektar_interface/particle_cell_mapping/newton_tet.hpp b/include/nektar_interface/particle_cell_mapping/newton_tet.hpp index 44851b50..77ec3b23 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_tet.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_tet.hpp @@ -104,6 +104,13 @@ struct MappingTetLinear3D : MappingNewtonIterationBase { GeometryInterface::Tetrahedron{}.loc_coord_to_loc_collapsed( xi0, xi1, xi2, eta0, eta1, eta2); } + + inline void loc_collapsed_to_loc_coord_v(const void *d_data, const REAL eta0, + const REAL eta1, const REAL eta2, + REAL *xi0, REAL *xi1, REAL *xi2) { + GeometryInterface::Tetrahedron{}.loc_collapsed_to_loc_coord( + eta0, eta1, eta2, xi0, xi1, xi2); + } }; } // namespace Newton diff --git a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp index 31ef0943..75701a82 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp @@ -172,6 +172,15 @@ struct MappingTriangleLinear2DEmbed3D GeometryInterface::Triangle{}.loc_coord_to_loc_collapsed(xi0, xi1, eta0, eta1); } + + inline void loc_collapsed_to_loc_coord_v(const void *d_data, const REAL eta0, + const REAL eta1, const REAL eta2, + REAL *xi0, REAL *xi1, REAL *xi2) { + + *xi2 = 0.0; + GeometryInterface::Triangle{}.loc_collapsed_to_loc_coord(eta0, eta1, xi0, + xi1); + } }; } // namespace Newton diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index b6d47307..4f80c78e 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -180,7 +180,7 @@ template class XMapNewton { const int k_grid_size_x = std::max(grid_size - 1, 1); const int k_grid_size_y = k_ndim > 1 ? k_grid_size_x : 1; const int k_grid_size_z = k_ndim > 2 ? k_grid_size_x : 1; - const REAL k_grid_width = 1.8 / (k_grid_size_x); + const REAL k_grid_width = 2.0 / (k_grid_size_x); this->sycl_target->queue .submit([&](sycl::handler &cgh) { @@ -190,8 +190,8 @@ template class XMapNewton { cgh.parallel_for<>( sycl::nd_range<1>(sycl::range<1>(1), sycl::range<1>(1)), [=](auto idx) { - printf("NEWTON:\n"); MappingNewtonIterationBase k_newton_type{}; + XMapNewtonKernel k_newton_kernel{}; const REAL p0 = phys0; const REAL p1 = phys1; @@ -208,60 +208,34 @@ template class XMapNewton { for (int g0 = 0; (g0 <= k_grid_size_x) && (!cell_found); g0++) { - k_xi0 = -0.9 + g0 * k_grid_width; - k_xi1 = -0.9 + g1 * k_grid_width; - k_xi2 = -0.9 + g2 * k_grid_width; - - nprint("~~~~~~~~~~~~~~", g0, g1, g2, ":", k_xi0, k_xi1, - k_xi2); - // k_newton_type.set_initial_iteration(k_map_data, p0, p1, - // p2, - // &k_xi0, &k_xi1, - // &k_xi2); - - // Start of Newton iteration - REAL xin0, xin1, xin2; - REAL f0, f1, f2; - - residual = k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, - &f2, &local_mem[0]); - - bool diverged = false; - bool converged = false; - printf("residual: %f\n", residual); - for (int stepx = 0; ((stepx < k_max_iterations) && - (!converged) && (!diverged)); - stepx++) { - printf("STEPX: %d, RES: %16.8e\n", stepx, residual); - - k_newton_type.newton_step( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f0, f1, - f2, &xin0, &xin1, &xin2, &local_mem[0]); - - k_xi0 = xin0; - k_xi1 = xin1; - k_xi2 = xin2; - - residual = k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, - &f1, &f2, &local_mem[0]); - - diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || - (ABS(k_xi2) > 15.0); - converged = (residual <= k_tol) && (!diverged); - } + k_xi0 = -1.0 + g0 * k_grid_width; + k_xi1 = -1.0 + g1 * k_grid_width; + k_xi2 = -1.0 + g2 * k_grid_width; + bool converged = k_newton_kernel.x_inverse( + k_map_data, p0, p1, p2, &k_xi0, &k_xi1, &k_xi2, + &local_mem[0], k_max_iterations, k_tol, true); REAL eta0, eta1, eta2; + k_newton_type.loc_coord_to_loc_collapsed( k_map_data, k_xi0, k_xi1, k_xi2, &eta0, &eta1, &eta2); - bool contained = ((-1.0 - k_contained_tol) <= eta0) && - (eta0 <= (1.0 + k_contained_tol)) && - ((-1.0 - k_contained_tol) <= eta1) && - (eta1 <= (1.0 + k_contained_tol)) && - ((-1.0 - k_contained_tol) <= eta2) && - (eta2 <= (1.0 + k_contained_tol)); + eta0 = Kernel::min(eta0, 1.0 + k_contained_tol); + eta1 = Kernel::min(eta1, 1.0 + k_contained_tol); + eta2 = Kernel::min(eta2, 1.0 + k_contained_tol); + eta0 = Kernel::max(eta0, -1.0 - k_contained_tol); + eta1 = Kernel::max(eta1, -1.0 - k_contained_tol); + eta2 = Kernel::max(eta2, -1.0 - k_contained_tol); + + k_newton_type.loc_collapsed_to_loc_coord( + k_map_data, eta0, eta1, eta2, &k_xi0, &k_xi1, &k_xi2); + + const REAL clamped_residual = + k_newton_type.newton_residual( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, + &eta0, &eta1, &eta2, &local_mem[0]); + + const bool contained = clamped_residual <= k_tol; cell_found = contained && converged; } } diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp index 99da0ee7..73111d06 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp @@ -110,8 +110,8 @@ template struct XMapNewtonKernel { k_newton_type.newton_residual(map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, &f2, local_memory); - diverged = - (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || (ABS(k_xi2) > 15.0); + diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || + (ABS(k_xi2) > 15.0) || (!sycl::isfinite(residual)); } *xi0 = k_xi0; *xi1 = k_xi1; diff --git a/src/nektar_interface/composite_interaction/composite_intersection.cpp b/src/nektar_interface/composite_interaction/composite_intersection.cpp index 5364897a..11dda34e 100644 --- a/src/nektar_interface/composite_interaction/composite_intersection.cpp +++ b/src/nektar_interface/composite_interaction/composite_intersection.cpp @@ -525,13 +525,24 @@ void CompositeIntersection::find_intersections_3d( map_data, xi[0], xi[1], xi[2], &eta0, &eta1, &eta2); + eta0 = Kernel::min(eta0, 1.0 + k_contained_tol); + eta1 = Kernel::min(eta1, 1.0 + k_contained_tol); + eta2 = Kernel::min(eta2, 1.0 + k_contained_tol); + eta0 = Kernel::max(eta0, -1.0 - k_contained_tol); + eta1 = Kernel::max(eta1, -1.0 - k_contained_tol); + eta2 = Kernel::max(eta2, -1.0 - k_contained_tol); + + k_newton_type.loc_collapsed_to_loc_coord( + map_data, eta0, eta1, eta2, &xi[0], &xi[1], + &xi[2]); + + const REAL clamped_residual = + k_newton_type.newton_residual( + map_data, xi[0], xi[1], xi[2], i0, i1, i2, + &eta0, &eta1, &eta2, nullptr); + const bool contained = - ((-1.0 - k_contained_tol) <= eta0) && - (eta0 <= (1.0 + k_contained_tol)) && - ((-1.0 - k_contained_tol) <= eta1) && - (eta1 <= (1.0 + k_contained_tol)) && - ((-1.0 - k_contained_tol) <= eta2) && - (eta2 <= (1.0 + k_contained_tol)); + clamped_residual <= k_newton_tol; cell_found = contained && converged; if (cell_found) { @@ -681,13 +692,22 @@ void CompositeIntersection::find_intersections_3d( k_newton_type.loc_coord_to_loc_collapsed( map_data, xi0, xi1, xi2, &eta0, &eta1, &eta2); - const bool contained = - ((-1.0 - k_contained_tol) <= eta0) && - (eta0 <= (1.0 + k_contained_tol)) && - ((-1.0 - k_contained_tol) <= eta1) && - (eta1 <= (1.0 + k_contained_tol)) && - ((-1.0 - k_contained_tol) <= eta2) && - (eta2 <= (1.0 + k_contained_tol)); + eta0 = Kernel::min(eta0, 1.0 + k_contained_tol); + eta1 = Kernel::min(eta1, 1.0 + k_contained_tol); + eta2 = Kernel::min(eta2, 1.0 + k_contained_tol); + eta0 = Kernel::max(eta0, -1.0 - k_contained_tol); + eta1 = Kernel::max(eta1, -1.0 - k_contained_tol); + eta2 = Kernel::max(eta2, -1.0 - k_contained_tol); + + k_newton_type.loc_collapsed_to_loc_coord( + map_data, eta0, eta1, eta2, &xi0, &xi1, &xi2); + + const REAL clamped_residual = + k_newton_type.newton_residual(map_data, xi0, xi1, xi2, + i0, i1, i2, &eta0, + &eta1, &eta2, nullptr); + + const bool contained = clamped_residual <= k_newton_tol; if (contained && converged) { const REAL r0 = p00 - i0; diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 82b193ea..8096a7a5 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -629,7 +629,7 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { EXPECT_TRUE(dist < 1.0e-8); // test the forward x map from reference space to physical space - Newton::XMapNewtonTest mapper(sycl_target, geom); + Newton::XMapNewton mapper(sycl_target, geom); REAL test_phys0, test_phys1, test_phys2; mapper.x(xi[0], xi[1], xi[2], &test_phys0, &test_phys1, &test_phys2); EXPECT_NEAR(phys[0], test_phys0, 1.0e-10); @@ -691,7 +691,7 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { } // test internal points - for (int testx = 0; testx < 20; testx++) { + for (int testx = 0; testx < 5; testx++) { lambda_sample_internal_point(geom, test_xi, test_phys); lambda_check_x_map(geom, test_xi, test_phys); } From 6dcc6799417834c8c1a9a55b91e0171703099adb Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 29 Oct 2024 15:16:15 +0000 Subject: [PATCH 23/66] removed redundant code from test --- ..._particle_geometry_interface_3d_curved.cpp | 473 ------------------ 1 file changed, 473 deletions(-) diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 8096a7a5..a656e834 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -30,449 +30,6 @@ static inline void copy_to_cstring(std::string input, char **output) { std::strcpy(*output, input.c_str()); } -// TODO REMOVE START -namespace NESO::Newton { - -template -class XMapNewtonTest : public XMapNewton { -public: - template - XMapNewtonTest(SYCLTargetSharedPtr sycl_target, - std::shared_ptr geom, - const int num_modes_factor = 1) - : XMapNewton(sycl_target, geom, num_modes_factor) {} - - inline bool x_inverse(const REAL phys0, const REAL phys1, const REAL phys2, - REAL *xi0, REAL *xi1, REAL *xi2, - const REAL tol = 1.0e-10, - const REAL contained_tol = 1.0e-10) { - - const int k_max_iterations = 51; - auto k_map_data = this->dh_data->d_buffer.ptr; - auto k_fdata = this->dh_fdata->d_buffer.ptr; - const REAL k_tol = tol; - const double k_contained_tol = contained_tol; - const std::size_t num_bytes_local = this->num_bytes_local; - - const int k_ndim = this->ndim; - const int grid_size = this->num_modes_factor * this->num_modes; - const int k_grid_size_x = std::max(grid_size - 1, 1); - const int k_grid_size_y = k_ndim > 1 ? k_grid_size_x : 1; - const int k_grid_size_z = k_ndim > 2 ? k_grid_size_x : 1; - const REAL k_grid_width = 2.0 / (k_grid_size_x); - - this->sycl_target->queue - .submit([&](sycl::handler &cgh) { - sycl::accessor - local_mem(sycl::range<1>(num_bytes_local), cgh); - cgh.parallel_for<>( - sycl::nd_range<1>(sycl::range<1>(1), sycl::range<1>(1)), - [=](auto idx) { - printf("NEWTON TEST ETA GRID:\n"); - MappingNewtonIterationBase k_newton_type{}; - - const REAL p0 = phys0; - const REAL p1 = phys1; - const REAL p2 = phys2; - REAL k_xi0; - REAL k_xi1; - REAL k_xi2; - REAL residual; - bool cell_found = false; - - for (int g2 = 0; (g2 <= k_grid_size_z) && (!cell_found); g2++) { - for (int g1 = 0; (g1 <= k_grid_size_y) && (!cell_found); - g1++) { - for (int g0 = 0; (g0 <= k_grid_size_x) && (!cell_found); - g0++) { - - REAL eta0, eta1, eta2; - - eta0 = -1.0 + g0 * k_grid_width; - eta1 = -1.0 + g1 * k_grid_width; - eta2 = -1.0 + g2 * k_grid_width; - - k_newton_type.loc_collapsed_to_loc_coord( - k_map_data, eta0, eta1, eta2, &k_xi0, &k_xi1, &k_xi2); - - nprint("~~~~~~~~~~~ ETA:", eta0, eta1, eta2, "XI:", k_xi0, - k_xi1, k_xi2); - - // k_newton_type.set_initial_iteration(k_map_data, p0, p1, - // p2, - // &k_xi0, &k_xi1, - // &k_xi2); - - // Start of Newton iteration - REAL xin0, xin1, xin2; - REAL f0, f1, f2; - - residual = k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, &f1, - &f2, &local_mem[0]); - - bool diverged = false; - bool converged = false; - printf("residual: %f\n", residual); - for (int stepx = 0; ((stepx < k_max_iterations) && - (!converged) && (!diverged)); - stepx++) { - printf("STEPX: %d, RES: %16.8e\n", stepx, residual); - - k_newton_type.newton_step( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f0, f1, - f2, &xin0, &xin1, &xin2, &local_mem[0]); - - k_xi0 = xin0; - k_xi1 = xin1; - k_xi2 = xin2; - - residual = k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &f0, - &f1, &f2, &local_mem[0]); - - diverged = (ABS(k_xi0) > 15.0) || (ABS(k_xi1) > 15.0) || - (ABS(k_xi2) > 15.0) || - (residual != residual); - converged = (residual <= k_tol) && (!diverged); - } - - k_newton_type.loc_coord_to_loc_collapsed( - k_map_data, k_xi0, k_xi1, k_xi2, &eta0, &eta1, &eta2); - - // bool contained = ((-1.0 - k_contained_tol) <= eta0) && - // (eta0 <= (1.0 + k_contained_tol)) && - // ((-1.0 - k_contained_tol) <= eta1) && - // (eta1 <= (1.0 + k_contained_tol)) && - // ((-1.0 - k_contained_tol) <= eta2) && - // (eta2 <= (1.0 + k_contained_tol)); - - nprint("CLAMPED START"); - nprint("BEFORE CLAMP:", eta0, eta1, eta2); - REAL clamped_eta0 = - Kernel::min(eta0, 1.0 + k_contained_tol); - REAL clamped_eta1 = - Kernel::min(eta1, 1.0 + k_contained_tol); - REAL clamped_eta2 = - Kernel::min(eta2, 1.0 + k_contained_tol); - clamped_eta0 = - Kernel::max(clamped_eta0, -1.0 - k_contained_tol); - clamped_eta1 = - Kernel::max(clamped_eta1, -1.0 - k_contained_tol); - clamped_eta2 = - Kernel::max(clamped_eta2, -1.0 - k_contained_tol); - nprint("AFTER CLAMP:", clamped_eta0, clamped_eta1, - clamped_eta2); - - REAL clamped_xi0, clamped_xi1, clamped_xi2; - k_newton_type.loc_collapsed_to_loc_coord( - k_map_data, clamped_eta0, clamped_eta1, clamped_eta2, - &clamped_xi0, &clamped_xi1, &clamped_xi2); - - const REAL clamped_residual = - k_newton_type.newton_residual( - k_map_data, clamped_xi0, clamped_xi1, clamped_xi2, - p0, p1, p2, &f0, &f1, &f2, &local_mem[0]); - - const bool contained = clamped_residual <= k_tol; - - nprint("CLAMPED END"); - - cell_found = contained && converged; - } - } - } - k_fdata[0] = k_xi0; - k_fdata[1] = k_xi1; - k_fdata[2] = k_xi2; - k_fdata[3] = (residual <= tol) ? 1 : -1; - }); - }) - .wait_and_throw(); - - this->dh_fdata->device_to_host(); - *xi0 = this->dh_fdata->h_buffer.ptr[0]; - *xi1 = this->dh_fdata->h_buffer.ptr[1]; - *xi2 = this->dh_fdata->h_buffer.ptr[2]; - return (this->dh_fdata->h_buffer.ptr[3] > 0); - } -}; - -} // namespace NESO::Newton -// TODO REMOVE END - -TEST(ParticleGeometryInterfaceCurved, CoordinateMapping) { - - int size, rank; - MPI_Comm_size(MPI_COMM_WORLD, &size); - MPI_Comm_rank(MPI_COMM_WORLD, &rank); - - LibUtilities::SessionReaderSharedPtr session; - SpatialDomains::MeshGraphSharedPtr graph; - - int argc = 3; - char *argv[3]; - copy_to_cstring(std::string("test_particle_geometry_interface"), &argv[0]); - - std::filesystem::path source_file = __FILE__; - std::filesystem::path source_dir = source_file.parent_path(); - std::filesystem::path test_resources_dir = - source_dir / "../../test_resources"; - std::filesystem::path conditions_file = - test_resources_dir / "reference_all_types_cube/conditions.xml"; - copy_to_cstring(std::string(conditions_file), &argv[1]); - // std::filesystem::path mesh_file = - // test_resources_dir / "reference_all_types_cube/mixed_ref_cube_0.2.xml"; - - // TODO - std::filesystem::path mesh_file = - "/home/js0259/git-ukaea/NESO-workspace/reference_all_types_cube/" - "mixed_ref_cube_0.5_perturbed_order_2.xml"; - copy_to_cstring(std::string(mesh_file), &argv[2]); - - // Create session reader. - session = LibUtilities::SessionReader::CreateInstance(argc, argv); - - // Create MeshGraph. - graph = SpatialDomains::MeshGraph::Read(session); - - // build map from owned mesh hierarchy cells to geoms that touch that cell - auto mesh = std::make_shared(graph); - - std::map> geoms; - get_all_elements_3d(graph, geoms); - - // TODO clenaup - auto lambda_stype = [](auto s) -> std::string { - switch (s) { - case eTetrahedron: - return "Tet"; - case ePyramid: - return "Pyr"; - case ePrism: - return "Prism"; - case eHexahedron: - return "Hex"; - default: - return "shape unknown"; - } - }; - - // TODO cleanip - auto lambda_btype = [](auto s) -> std::string { - switch (s) { - case eModified_A: - return "eA"; - case eModified_B: - return "eB"; - case eModified_C: - return "eC"; - case eModifiedPyr_C: - return "ePyrC"; - default: - return "basis unknown"; - } - }; - - auto lambda_to_collapsed_coord = [&](auto geom, auto xi0, auto xi1, auto xi2, - auto *eta0, auto *eta1, auto *eta2) { - auto s = geom->GetShapeType(); - switch (s) { - case eTetrahedron: - GeometryInterface::Tetrahedron{}.loc_coord_to_loc_collapsed( - xi0, xi1, xi2, eta0, eta1, eta2); - break; - case ePyramid: - GeometryInterface::Pyramid{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, - eta0, eta1, eta2); - break; - case ePrism: - GeometryInterface::Prism{}.loc_coord_to_loc_collapsed(xi0, xi1, xi2, eta0, - eta1, eta2); - break; - case eHexahedron: - GeometryInterface::Hexahedron{}.loc_coord_to_loc_collapsed( - xi0, xi1, xi2, eta0, eta1, eta2); - break; - default: - return "shape unknown"; - } - }; - auto lambda_to_local_coord = [&](auto geom, auto eta0, auto eta1, auto eta2, - auto *xi0, auto *xi1, auto *xi2) { - auto s = geom->GetShapeType(); - switch (s) { - case eTetrahedron: - GeometryInterface::Tetrahedron{}.loc_collapsed_to_loc_coord( - eta0, eta1, eta2, xi0, xi1, xi2); - break; - case ePyramid: - GeometryInterface::Pyramid{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, - xi0, xi1, xi2); - break; - case ePrism: - GeometryInterface::Prism{}.loc_collapsed_to_loc_coord(eta0, eta1, eta2, - xi0, xi1, xi2); - break; - case eHexahedron: - GeometryInterface::Hexahedron{}.loc_collapsed_to_loc_coord( - eta0, eta1, eta2, xi0, xi1, xi2); - break; - default: - return "shape unknown"; - } - }; - - for (auto gx : geoms) { - auto geom = gx.second; - auto xmap = geom->GetXmap(); - const int shape_type_int = geom->GetShapeType(); - - std::set> vertices_found; - std::vector> vertices = { - {-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, {-1.0, 1.0, -1.0}, - {1.0, 1.0, -1.0}, {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, - {-1.0, 1.0, 1.0}, {1.0, 1.0, 1.0}}; - - Array test_eta(3); - Array test_eta_neso(3); - Array test_xi(3); - Array test_xi_neso(3); - REAL eta0, eta1, eta2, xi0, xi1, xi2; - for (auto vx : vertices) { - test_eta[0] = vx.at(0); - test_eta[1] = vx.at(1); - test_eta[2] = vx.at(2); - xmap->LocCollapsedToLocCoord(test_eta, test_xi); - xmap->LocCoordToLocCollapsed(test_xi, test_eta); - xmap->LocCollapsedToLocCoord(test_eta, test_xi); - xmap->LocCoordToLocCollapsed(test_xi, test_eta); - - vertices_found.insert({(int)std::round(test_eta[0]), - (int)std::round(test_eta[1]), - (int)std::round(test_eta[2])}); - } - - const int num_vertices_expected = geom->GetNumVerts(); - const int num_vertices_found = vertices_found.size(); - - // At the time of writing TetGeom mapping is inconsistent with itself in - // Nektar++ - const bool nektar_mapping_consistent = - num_vertices_found == num_vertices_expected; - - vertices_found.clear(); - - for (auto vx : vertices) { - test_eta[0] = vx.at(0); - test_eta[1] = vx.at(1); - test_eta[2] = vx.at(2); - - GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta, - test_xi_neso); - GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, test_eta[0], - test_eta[1], test_eta[2], - &xi0, &xi1, &xi2); - ASSERT_NEAR(test_xi_neso[0], xi0, 1.0e-14); - ASSERT_NEAR(test_xi_neso[1], xi1, 1.0e-14); - ASSERT_NEAR(test_xi_neso[2], xi2, 1.0e-14); - - if (nektar_mapping_consistent) { - xmap->LocCollapsedToLocCoord(test_eta, test_xi); - ASSERT_NEAR(test_xi_neso[0], test_xi[0], 1.0e-14); - ASSERT_NEAR(test_xi_neso[1], test_xi[1], 1.0e-14); - ASSERT_NEAR(test_xi_neso[2], test_xi[2], 1.0e-14); - } - - GeometryInterface::loc_coord_to_loc_collapsed_3d( - shape_type_int, test_xi_neso, test_eta_neso); - GeometryInterface::loc_coord_to_loc_collapsed_3d( - shape_type_int, xi0, xi1, xi2, &eta0, &eta1, &eta2); - ASSERT_NEAR(test_eta_neso[0], eta0, 1.0e-14); - ASSERT_NEAR(test_eta_neso[1], eta1, 1.0e-14); - ASSERT_NEAR(test_eta_neso[2], eta2, 1.0e-14); - - if (nektar_mapping_consistent) { - xmap->LocCoordToLocCollapsed(test_xi_neso, test_eta); - ASSERT_NEAR(test_eta_neso[0], test_eta[0], 1.0e-14); - ASSERT_NEAR(test_eta_neso[1], test_eta[1], 1.0e-14); - ASSERT_NEAR(test_eta_neso[2], test_eta[2], 1.0e-14); - } - - vertices_found.insert({(int)std::round(eta0), (int)std::round(eta1), - (int)std::round(eta2)}); - } - - // Our implementations should be consistent. - ASSERT_EQ(vertices_found.size(), num_vertices_expected); - - /* - - nprint(geom->GetShapeType(), lambda_stype(geom->GetShapeType())); - nprint("Num bases:", xmap->GetNumBases()); - for (int dx = 0; dx < 3; dx++) { - nprint("dx:", dx, "type:", lambda_btype(xmap->GetBasisType(dx)), - xmap->GetBasisNumModes(dx)); - } - - Array Lcoord(3); - Array Lcoord2(3); - Array Gcoord(3); - Array Gcoord2(3); - Lcoord[0] = -0.05; - Lcoord[1] = -0.05; - Lcoord[2] = -0.05; - - for (int dx = 0; dx < 3; dx++) { - // calls phys evaluate which takes a loc coord not a loc collapsed coord - Gcoord[dx] = geom->GetCoord(dx, Lcoord); - } - - geom->GetLocCoords(Gcoord, Lcoord2); - - for (int dx = 0; dx < 3; dx++) { - // calls phys evaluate which takes a loc coord not a loc collapsed coord - Gcoord2[dx] = geom->GetCoord(dx, Lcoord2); - } - nprint(Lcoord[0], Lcoord[1], Lcoord[2], "\n", Lcoord2[0], Lcoord2[1], - Lcoord2[2], "\n", Gcoord[0], Gcoord[1], Gcoord[2], "\n", Gcoord2[0], - Gcoord2[1], Gcoord2[2], "\n------"); - - auto I0 = xmap->GetBasis(0)->GetI(Lcoord); - auto I1 = xmap->GetBasis(1)->GetI(Lcoord); - auto I2 = xmap->GetBasis(2)->GetI(Lcoord); - - for (auto ix = I0->begin(); ix != I0->end(); ix++) { - nprint(*ix); - } - nprint("-----"); - const int npts = xmap->GetTotPoints(); - Array ptsx(npts), ptsy(npts), ptsz(npts); - xmap->BwdTrans(geom->GetCoeffs(0), ptsx); - xmap->BwdTrans(geom->GetCoeffs(1), ptsy); - xmap->BwdTrans(geom->GetCoeffs(2), ptsz); - - Array eta(3); - xmap->LocCoordToLocCollapsed(Lcoord, eta); - Array I(3); - I[0] = xmap->GetBasis(0)->GetI(eta); - I[1] = xmap->GetBasis(1)->GetI(eta + 1); - I[2] = xmap->GetBasis(2)->GetI(eta + 2); - const auto x = xmap->PhysEvaluate(I, ptsx); - const auto y = xmap->PhysEvaluate(I, ptsy); - const auto z = xmap->PhysEvaluate(I, ptsz); - nprint(x, y, z); - - */ - } - - mesh->free(); - delete[] argv[0]; - delete[] argv[1]; - delete[] argv[2]; -} - TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { int size, rank; @@ -514,36 +71,6 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { std::map> geoms; get_all_elements_3d(graph, geoms); - auto lambda_stype = [](auto s) -> std::string { - switch (s) { - case eTetrahedron: - return "Tet"; - case ePyramid: - return "Pyr"; - case ePrism: - return "Prism"; - case eHexahedron: - return "Hex"; - default: - return "shape unknown"; - } - }; - - auto lambda_btype = [](auto s) -> std::string { - switch (s) { - case eModified_A: - return "eA"; - case eModified_B: - return "eB"; - case eModified_C: - return "eC"; - case eModifiedPyr_C: - return "ePyrC"; - default: - return "basis unknown"; - } - }; - auto lambda_forward_map = [&](auto geom, const auto &xi, auto &phys) { // Evaluate the forward map from xi to physical space using the expansion. auto xmap = geom->GetXmap(); From 89829a02ce8e659aef528e0105396f235dff9e4a Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 30 Oct 2024 14:18:32 +0000 Subject: [PATCH 24/66] local memory bug fixes and deprecation warnings --- .../function_bary_evaluation.hpp | 5 +- .../function_basis_evaluation.hpp | 5 +- .../function_basis_projection.hpp | 5 +- .../newton_generic_3d.hpp | 3 ++ .../particle_cell_mapping/x_map_newton.hpp | 53 ++++++++++++------- include/nektar_interface/utility_sycl.hpp | 5 +- 6 files changed, 46 insertions(+), 30 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index b426c090..54950cfa 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -256,9 +256,8 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { this->sycl_target->queue .submit([&](sycl::handler &cgh) { // Allocate local memory to compute the divides. - sycl::accessor - local_mem(sycl::range<1>(local_num_reals * local_size), cgh); + sycl::local_accessor local_mem( + sycl::range<1>(local_num_reals * local_size), cgh); cgh.parallel_for<>(pl_iter_range, [=](sycl::nd_item<2> idx) { const INT cellx = idx.get_global_id(0); diff --git a/include/nektar_interface/function_basis_evaluation.hpp b/include/nektar_interface/function_basis_evaluation.hpp index 67d3c6d2..b55b7688 100644 --- a/include/nektar_interface/function_basis_evaluation.hpp +++ b/include/nektar_interface/function_basis_evaluation.hpp @@ -102,9 +102,8 @@ class FunctionEvaluateBasis : public BasisEvaluateBase { sycl::range<2> local_iterset{1, local_size}; auto event_loop = this->sycl_target->queue.submit([&](sycl::handler &cgh) { - sycl::accessor - local_mem(sycl::range<1>(local_mem_num_items), cgh); + sycl::local_accessor local_mem( + sycl::range<1>(local_mem_num_items), cgh); cgh.parallel_for<>( sycl::nd_range<2>(cell_iterset_range, local_iterset), diff --git a/include/nektar_interface/function_basis_projection.hpp b/include/nektar_interface/function_basis_projection.hpp index 2ae3eb1a..29b9a37a 100644 --- a/include/nektar_interface/function_basis_projection.hpp +++ b/include/nektar_interface/function_basis_projection.hpp @@ -102,9 +102,8 @@ template class FunctionProjectBasis : public BasisEvaluateBase { sycl::range<2> local_iterset{1, local_size}; auto event_loop = this->sycl_target->queue.submit([&](sycl::handler &cgh) { - sycl::accessor - local_mem(sycl::range<1>(local_mem_num_items), cgh); + sycl::local_accessor local_mem( + sycl::range<1>(local_mem_num_items), cgh); cgh.parallel_for<>( sycl::nd_range<2>(cell_iterset_range, local_iterset), diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index cd55ced1..808f5f93 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -135,6 +135,9 @@ struct MappingGeneric3D : MappingNewtonIterationBase { // Create a device buffer with the z,bw,physvals h_data->d_zbw = std::make_unique>(sycl_target, s_zbw); + // Number of bytes required for local memory + h_data->data_size_local = + (num_phys0 + num_phys1 + num_phys2) * sizeof(REAL); // store the pointers into the buffer we just made in the device struct so // that pointer arithmetric does not have to happen in the kernel but the diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 4f80c78e..52f4a197 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -57,7 +57,10 @@ template class XMapNewton { this->newton_type.write_data(this->sycl_target, geom, h_data_ptr, d_data_ptr); - this->dh_data->host_to_device(); + + if (this->num_bytes_per_map_device) { + this->dh_data->host_to_device(); + } this->num_bytes_local = std::max(static_cast(1), this->newton_type.data_size_local(h_data_ptr)); @@ -109,15 +112,23 @@ template class XMapNewton { inline void x(const REAL xi0, const REAL xi1, const REAL xi2, REAL *phys0, REAL *phys1, REAL *phys2) { - auto k_map_data = this->dh_data->d_buffer.ptr; + char *k_map_data; + if (this->dh_data) { + k_map_data = this->dh_data->d_buffer.ptr; + } + NESOASSERT(this->dh_fdata != nullptr, "Bad pointer"); auto k_fdata = this->dh_fdata->d_buffer.ptr; + NESOASSERT(k_fdata != nullptr, "Bad pointer"); const std::size_t num_bytes_local = this->num_bytes_local; + const REAL k_xi0 = xi0; + const REAL k_xi1 = xi1; + const REAL k_xi2 = xi2; + this->sycl_target->queue - .submit([&](sycl::handler &cgh) { - sycl::accessor - local_mem(sycl::range<1>(num_bytes_local), cgh); + .submit([=](sycl::handler &cgh) { + sycl::local_accessor local_mem( + sycl::range<1>(num_bytes_local), cgh); cgh.parallel_for<>( sycl::nd_range<1>(sycl::range<1>(1), sycl::range<1>(1)), @@ -131,8 +142,9 @@ template class XMapNewton { const REAL p1 = 0.0; const REAL p2 = 0.0; - k_newton_type.newton_residual(k_map_data, xi0, xi1, xi2, p0, p1, - p2, &f0, &f1, &f2, &local_mem[0]); + k_newton_type.newton_residual(k_map_data, k_xi0, k_xi1, k_xi2, + p0, p1, p2, &f0, &f1, &f2, + &local_mem[0]); k_fdata[0] = f0; k_fdata[1] = f1; @@ -169,8 +181,14 @@ template class XMapNewton { const REAL contained_tol = 1.0e-10) { const int k_max_iterations = 51; - auto k_map_data = this->dh_data->d_buffer.ptr; + char *k_map_data; + if (this->dh_data) { + k_map_data = this->dh_data->d_buffer.ptr; + } + NESOASSERT(this->dh_fdata != nullptr, "Bad pointer"); auto k_fdata = this->dh_fdata->d_buffer.ptr; + NESOASSERT(k_fdata != nullptr, "Bad pointer"); + const REAL k_tol = tol; const double k_contained_tol = contained_tol; const std::size_t num_bytes_local = this->num_bytes_local; @@ -184,9 +202,9 @@ template class XMapNewton { this->sycl_target->queue .submit([&](sycl::handler &cgh) { - sycl::accessor - local_mem(sycl::range<1>(num_bytes_local), cgh); + sycl::local_accessor local_mem( + sycl::range<1>(num_bytes_local), cgh); + cgh.parallel_for<>( sycl::nd_range<1>(sycl::range<1>(1), sycl::range<1>(1)), [=](auto idx) { @@ -230,12 +248,11 @@ template class XMapNewton { k_newton_type.loc_collapsed_to_loc_coord( k_map_data, eta0, eta1, eta2, &k_xi0, &k_xi1, &k_xi2); - const REAL clamped_residual = - k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, - &eta0, &eta1, &eta2, &local_mem[0]); + residual = k_newton_type.newton_residual( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, &eta0, + &eta1, &eta2, &local_mem[0]); - const bool contained = clamped_residual <= k_tol; + const bool contained = residual <= k_tol; cell_found = contained && converged; } } @@ -243,7 +260,7 @@ template class XMapNewton { k_fdata[0] = k_xi0; k_fdata[1] = k_xi1; k_fdata[2] = k_xi2; - k_fdata[3] = (residual <= tol) ? 1 : -1; + k_fdata[3] = (residual <= tol) && cell_found ? 1 : -1; }); }) .wait_and_throw(); diff --git a/include/nektar_interface/utility_sycl.hpp b/include/nektar_interface/utility_sycl.hpp index dc625ad8..a26775bd 100644 --- a/include/nektar_interface/utility_sycl.hpp +++ b/include/nektar_interface/utility_sycl.hpp @@ -25,9 +25,8 @@ inline std::size_t get_num_local_work_items(SYCLTargetSharedPtr sycl_target, const std::size_t default_num) { sycl::device device = sycl_target->device; auto local_mem_exists = - device.is_host() || - (device.get_info() != - sycl::info::local_mem_type::none); + device.get_info() != + sycl::info::local_mem_type::none; auto local_mem_size = device.get_info(); const std::size_t max_num_workitems = local_mem_size / num_bytes; From b571bf2b12a55390a671d36b186d26a16f6fa8cf Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Thu, 31 Oct 2024 11:57:00 +0000 Subject: [PATCH 25/66] loosened regular mapper default tolerance --- .../particle_cell_mapping/map_particles_2d_regular.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/nektar_interface/particle_cell_mapping/map_particles_2d_regular.cpp b/src/nektar_interface/particle_cell_mapping/map_particles_2d_regular.cpp index fc5e0360..1271db29 100644 --- a/src/nektar_interface/particle_cell_mapping/map_particles_2d_regular.cpp +++ b/src/nektar_interface/particle_cell_mapping/map_particles_2d_regular.cpp @@ -9,7 +9,7 @@ MapParticles2DRegular::MapParticles2DRegular( : CoarseMappersBase(sycl_target), particle_mesh_interface(particle_mesh_interface) { - this->tol = config->get("MapParticles2DRegular/tol", 0.0); + this->tol = config->get("MapParticles2DRegular/tol", 1.0e-12); // filter out the non-regular elements // process locally owned elements From edbad59512fddc239faefd5bbab392d8825dc375 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Thu, 31 Oct 2024 12:43:04 +0000 Subject: [PATCH 26/66] cleanup some TODOs --- include/nektar_interface/bary_interpolation/bary_evaluation.hpp | 1 - .../particle_cell_mapping/mapping_newton_iteration_base.hpp | 1 - 2 files changed, 2 deletions(-) diff --git a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp index 99b10334..f2cc1906 100644 --- a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp +++ b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp @@ -146,7 +146,6 @@ inline void compute_dir_210_interlaced( const int num_phys0, const int num_phys1, const int num_phys2, const REAL *const physvals, const REAL *const div_space0, const REAL *const div_space1, const REAL *const div_space2, REAL *output) { - // writes via this tmporary until restrict keyword added TODO. REAL tmp[N]; for (int ix = 0; ix < N; ix++) { tmp[ix] = 0.0; diff --git a/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp b/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp index b7dc0bb6..f0a6a944 100644 --- a/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp +++ b/include/nektar_interface/particle_cell_mapping/mapping_newton_iteration_base.hpp @@ -258,7 +258,6 @@ template struct MappingNewtonIterationBase { auto &underlying = static_cast(*this); underlying.loc_collapsed_to_loc_coord_v(d_data, eta0, eta1, eta2, xi0, xi1, xi2); - // TODO IMPLEMENT FOR NEWTON TYPES } }; From b2e4f03fc854988e6f9726aa0a99c2df689fcc64 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Fri, 1 Nov 2024 14:15:56 +0000 Subject: [PATCH 27/66] moved exising bary interpolation to better particle looping method --- .../function_bary_evaluation.hpp | 135 +++++++++--------- 1 file changed, 66 insertions(+), 69 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 54950cfa..6f7d1000 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -216,22 +216,6 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { } this->dh_global_physvals.host_to_device(); - // iteration set specification for the particle loop - auto mpi_rank_dat = particle_group->mpi_rank_dat; - const auto pl_stride = mpi_rank_dat->get_particle_loop_cell_stride(); - const auto pl_npart_cell = mpi_rank_dat->get_particle_loop_npart_cell(); - - const std::size_t local_num_reals = 2 * this->stride_base; - const std::size_t local_size = get_num_local_work_items( - this->sycl_target, local_num_reals * sizeof(REAL), 32); - const std::size_t cell_global_size = - get_particle_loop_global_size(mpi_rank_dat, local_size); - const std::size_t ncells = mpi_rank_dat->cell_dat.ncells; - - sycl::range<2> global_iter_set{ncells, cell_global_size}; - sycl::range<2> local_iter_set{1, local_size}; - sycl::nd_range<2> pl_iter_range{global_iter_set, local_iter_set}; - // output and particle position dats auto k_output = (*particle_group)[sym]->cell_dat.device_ptr(); const auto k_ref_positions = @@ -253,59 +237,72 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { const auto k_map_to_geom_type = this->cell_id_translation->dh_map_to_geom_type.d_buffer.ptr; - this->sycl_target->queue - .submit([&](sycl::handler &cgh) { - // Allocate local memory to compute the divides. - sycl::local_accessor local_mem( - sycl::range<1>(local_num_reals * local_size), cgh); - - cgh.parallel_for<>(pl_iter_range, [=](sycl::nd_item<2> idx) { - const INT cellx = idx.get_global_id(0); - const int idx_local = idx.get_local_id(1); - const INT layerx = idx.get_global_id(1); - if (layerx < pl_npart_cell[cellx]) { - - REAL *div_space0 = &local_mem[idx_local * 2 * k_stride_base]; - REAL *div_space1 = div_space0 + k_stride_base; - - // query the map from cells to expansion type - const int expansion_type = k_map_to_geom_type[cellx]; - // use the type key to index into the Bary weights and points - const int expansion_type_offset = - (expansion_type == k_index_tri_geom) - ? 0 - : k_stride_expansion_type; - // get the z values and weights for this expansion type - const auto z0 = &k_z[expansion_type_offset]; - const auto z1 = &k_z[expansion_type_offset + k_stride_base]; - const auto bw0 = &k_bw[expansion_type_offset]; - const auto bw1 = &k_bw[expansion_type_offset + k_stride_base]; - - const REAL xi0 = k_ref_positions[cellx][0][layerx]; - const REAL xi1 = k_ref_positions[cellx][1][layerx]; - // If this cell is a triangle then we need to map to the - // collapsed coordinates. - REAL coord0, coord1; - - GeometryInterface::loc_coord_to_loc_collapsed_2d( - expansion_type, xi0, xi1, &coord0, &coord1); - - const int num_phys0 = k_phys_num0[cellx]; - const int num_phys1 = k_phys_num1[cellx]; - - // Get pointer to the start of the quadrature point values for - // this cell - const auto physvals = &k_global_physvals[k_phys_offsets[cellx]]; - - const REAL evaluation = - Bary::evaluate_2d(coord0, coord1, num_phys0, num_phys1, - physvals, div_space0, z0, z1, bw0, bw1); - - k_output[cellx][k_component][layerx] = evaluation; - } - }); - }) - .wait_and_throw(); + // iteration set specification for the particle loop + auto mpi_rank_dat = particle_group->mpi_rank_dat; + ParticleLoopImplementation::ParticleLoopBlockIterationSet ish{mpi_rank_dat, + 16}; + const std::size_t local_size = 256; + const std::size_t local_num_reals = 2 * this->stride_base; + const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); + + EventStack es; + auto is = ish.get_all_cells(local_size, num_bytes_local); + + for (auto &blockx : is) { + const auto block_device = blockx.block_device; + es.push(sycl_target->queue.submit([&](sycl::handler &cgh) { + // Allocate local memory to compute the divides. + sycl::local_accessor local_mem( + sycl::range<1>(local_num_reals * blockx.local_size), cgh); + + cgh.parallel_for<>( + blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { + const int idx_local = idx.get_local_id(1); + std::size_t cell; + std::size_t layer; + block_device.get_cell_layer(idx, &cell, &layer); + if (block_device.work_item_required(cell, layer)) { + REAL *div_space0 = &local_mem[idx_local * 2 * k_stride_base]; + + // query the map from cells to expansion type + const int expansion_type = k_map_to_geom_type[cell]; + // use the type key to index into the Bary weights and points + const int expansion_type_offset = + (expansion_type == k_index_tri_geom) + ? 0 + : k_stride_expansion_type; + // get the z values and weights for this expansion type + const auto z0 = &k_z[expansion_type_offset]; + const auto z1 = &k_z[expansion_type_offset + k_stride_base]; + const auto bw0 = &k_bw[expansion_type_offset]; + const auto bw1 = &k_bw[expansion_type_offset + k_stride_base]; + + const REAL xi0 = k_ref_positions[cell][0][layer]; + const REAL xi1 = k_ref_positions[cell][1][layer]; + // If this cell is a triangle then we need to map to the + // collapsed coordinates. + REAL coord0, coord1; + + GeometryInterface::loc_coord_to_loc_collapsed_2d( + expansion_type, xi0, xi1, &coord0, &coord1); + + const int num_phys0 = k_phys_num0[cell]; + const int num_phys1 = k_phys_num1[cell]; + + // Get pointer to the start of the quadrature point values for + // this cell + const auto physvals = &k_global_physvals[k_phys_offsets[cell]]; + + const REAL evaluation = + Bary::evaluate_2d(coord0, coord1, num_phys0, num_phys1, + physvals, div_space0, z0, z1, bw0, bw1); + + k_output[cell][k_component][layer] = evaluation; + } + }); + })); + } + es.wait(); } }; From 9feb33640e6a72c6b923928babbc132b186a4649 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Fri, 1 Nov 2024 14:49:34 +0000 Subject: [PATCH 28/66] added a stride to the local memory part of bary interpolation --- .../bary_interpolation/bary_evaluation.hpp | 102 ++++++++++-------- .../test_particle_function_evaluation_3d.cpp | 23 +++- 2 files changed, 77 insertions(+), 48 deletions(-) diff --git a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp index f2cc1906..daaa221b 100644 --- a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp +++ b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp @@ -16,19 +16,22 @@ namespace NESO::Bary { * points. * @param[in] z_values A length num_phys array containing the quadrature * weights. - * @param[in, out] div_values Array of length num_phys which will be + * @param[in, out] div_values Array of length num_phys * stride which will be * populated with the bw_i/(r - r_i) values. + * @param[in] stride Stride to use for storing elements in div_values, + * default 1. */ inline void preprocess_weights(const int num_phys, const REAL coord, const REAL *const z_values, - const REAL *const bw_values, REAL *div_values) { + const REAL *const bw_values, REAL *div_values, + const std::size_t stride = 1) { for (int ix = 0; ix < num_phys; ix++) { - div_values[ix] = 0.0; + div_values[ix * stride] = 0.0; } for (int ix = 0; ix < num_phys; ix++) { const auto xdiff = z_values[ix] - coord; if (xdiff == 0.0) { - div_values[ix] = 1.0; + div_values[ix * stride] = 1.0; return; } } @@ -36,31 +39,31 @@ inline void preprocess_weights(const int num_phys, const REAL coord, for (int ix = 0; ix < num_phys; ix++) { const auto xdiff = z_values[ix] - coord; const auto bw_over_diff = bw_values[ix] / xdiff; - div_values[ix] = bw_over_diff; + div_values[ix * stride] = bw_over_diff; denom += bw_over_diff; } const REAL factor = 1.0 / denom; for (int ix = 0; ix < num_phys; ix++) { - div_values[ix] *= factor; + div_values[ix * stride] *= factor; } } /** - * Perform Bary interpolation in the first dimension. This function is - * intended to be called from a function that performs Bary interpolation - * over the second dimension and first dimension. + * Perform Bary interpolation in the first dimension. * * @param num_phys Number of quadrature points. * @param physvals Vector of length num_phys plus padding to multiple of the * vector length which contains the quadrature point values. + * @param stride Stride between elements in div_space, default 1. * @returns Contribution to Bary interpolation from a dimension 0 evaluation. */ inline REAL compute_dir_0(const int num_phys, const REAL *const physvals, - const REAL *const div_space) { + const REAL *const div_space, + const std::size_t stride = 1) { REAL numer = 0.0; for (int ix = 0; ix < num_phys; ix++) { const REAL pval = physvals[ix]; - const REAL tmp = div_space[ix]; + const REAL tmp = div_space[ix * stride]; numer += tmp * pval; } const REAL eval0 = numer; @@ -68,25 +71,26 @@ inline REAL compute_dir_0(const int num_phys, const REAL *const physvals, } /** - * Computes Bary interpolation over two dimensions. The inner dimension is - * computed with calls to compute_dir_0. + * Computes Bary interpolation over two dimensions. * * @param num_phys0 Number of quadrature points in dimension 0. * @param num_phys1 Number of quadrature points in dimension 1. * @param physvals Array of function values at quadrature points. * @param div_space0 The output of preprocess_weights applied to dimension 0. * @param div_space1 The output of preprocess_weights applied to dimension 1. + * @param stride Stride between elements in div_space, default 1. * @returns Bary evaluation of a function at a coordinate. */ inline REAL compute_dir_10(const int num_phys0, const int num_phys1, const REAL *const physvals, const REAL *const div_space0, - const REAL *const div_space1) { + const REAL *const div_space1, + const std::size_t stride = 1) { REAL pval1 = 0.0; for (int i1 = 0; i1 < num_phys1; i1++) { - const REAL c1 = div_space1[i1]; + const REAL c1 = div_space1[i1 * stride]; for (int i0 = 0; i0 < num_phys0; i0++) { - pval1 += physvals[i1 * num_phys0 + i0] * div_space0[i0] * c1; + pval1 += physvals[i1 * num_phys0 + i0] * div_space0[i0 * stride] * c1; } } return pval1; @@ -102,22 +106,25 @@ inline REAL compute_dir_10(const int num_phys0, const int num_phys1, * @param div_space0 The output of preprocess_weights applied to dimension 0. * @param div_space1 The output of preprocess_weights applied to dimension 1. * @param div_space2 The output of preprocess_weights applied to dimension 2. + * @param stride Stride between elements in div_space, default 1. * @returns Bary evaluation of a function at a coordinate. */ inline REAL compute_dir_210(const int num_phys0, const int num_phys1, const int num_phys2, const REAL *const physvals, const REAL *const div_space0, const REAL *const div_space1, - const REAL *const div_space2) { - const int stride = num_phys0 * num_phys1; + const REAL *const div_space2, + const std::size_t stride = 1) { + + const int stride_phys = num_phys0 * num_phys1; REAL pval2 = 0.0; for (int i2 = 0; i2 < num_phys2; i2++) { - const REAL c2 = div_space2[i2]; + const REAL c2 = div_space2[i2 * stride]; for (int i1 = 0; i1 < num_phys1; i1++) { - const REAL c1 = c2 * div_space1[i1]; + const REAL c1 = c2 * div_space1[i1 * stride]; for (int i0 = 0; i0 < num_phys0; i0++) { - pval2 += - physvals[i2 * stride + i1 * num_phys0 + i0] * div_space0[i0] * c1; + pval2 += physvals[i2 * stride_phys + i1 * num_phys0 + i0] * + div_space0[i0 * stride] * c1; } } } @@ -139,25 +146,27 @@ inline REAL compute_dir_210(const int num_phys0, const int num_phys1, * dimension 1. * @param[in] div_space2 The output of preprocess_weights applied to * dimension 2. + * @param stride Stride between elements in div_space, default 1. * @param[in, out] output Output function evaluations. */ template inline void compute_dir_210_interlaced( const int num_phys0, const int num_phys1, const int num_phys2, const REAL *const physvals, const REAL *const div_space0, - const REAL *const div_space1, const REAL *const div_space2, REAL *output) { + const REAL *const div_space1, const REAL *const div_space2, + REAL *RESTRICT output, const std::size_t stride = 1) { REAL tmp[N]; for (int ix = 0; ix < N; ix++) { tmp[ix] = 0.0; } - const int stride = num_phys0 * num_phys1; + const int stride_phys = num_phys0 * num_phys1; for (int i2 = 0; i2 < num_phys2; i2++) { - const REAL c2 = div_space2[i2]; + const REAL c2 = div_space2[i2 * stride]; for (int i1 = 0; i1 < num_phys1; i1++) { - const REAL c1 = c2 * div_space1[i1]; + const REAL c1 = c2 * div_space1[i1 * stride]; for (int i0 = 0; i0 < num_phys0; i0++) { - const int inner_stride = (i2 * stride + i1 * num_phys0 + i0) * N; - const REAL inner_c = div_space0[i0] * c1; + const int inner_stride = (i2 * stride_phys + i1 * num_phys0 + i0) * N; + const REAL inner_c = div_space0[i0 * stride] * c1; for (int ix = 0; ix < N; ix++) { tmp[ix] += physvals[inner_stride + ix] * inner_c; } @@ -179,28 +188,30 @@ inline void compute_dir_210_interlaced( * @param num_phys1 Number of quadrature points in the y direction. * @param physvals Function evaluations at quadrature points, x runs fastest * and y slowest. - * @param div_space Space of size num_phys0 + num_phys1 + num_phys2 to use as - * temporary space. + * @param div_space Space of size (num_phys0 + num_phys1 + num_phys2) * stride + * to use as temporary space. * @param z0 Quadrature points in x direction. * @param z1 Quadrature points in y direction. * @param bw0 Weights for each quadrature point in x direction. * @param bw1 Weights for each quadrature point in y direction. + * @param stride Stride between elements in div_space, default 1. * @returns Evaluation at passed point using Bary interpolation. * */ inline REAL evaluate_2d(const REAL coord0, const REAL coord1, const int num_phys0, const int num_phys1, const REAL *const physvals, REAL *div_space, const REAL *const z0, const REAL *const z1, - const REAL *const bw0, const REAL *const bw1) { + const REAL *const bw0, const REAL *const bw1, + const std::size_t stride = 1) { REAL *div_space0 = div_space; - REAL *div_space1 = div_space0 + num_phys0; + REAL *div_space1 = div_space0 + num_phys0 * stride; - preprocess_weights(num_phys0, coord0, z0, bw0, div_space0); - preprocess_weights(num_phys1, coord1, z1, bw1, div_space1); + preprocess_weights(num_phys0, coord0, z0, bw0, div_space0, stride); + preprocess_weights(num_phys1, coord1, z1, bw1, div_space1, stride); - REAL eval = - compute_dir_10(num_phys0, num_phys1, physvals, div_space0, div_space1); + REAL eval = compute_dir_10(num_phys0, num_phys1, physvals, div_space0, + div_space1, stride); return eval; } @@ -217,14 +228,15 @@ inline REAL evaluate_2d(const REAL coord0, const REAL coord1, * @param num_phys2 Number of quadrature points in the z direction. * @param physvals Function evaluations at quadrature points, x runs fastest * and z slowest. - * @param div_space Space of size num_phys0 + num_phys1 + num_phys2 to use as - * temporary space. + * @param div_space Space of size (num_phys0 + num_phys1 + num_phys2) * stride + * to use as temporary space. * @param z0 Quadrature points in x direction. * @param z1 Quadrature points in y direction. * @param z2 Quadrature points in z direction. * @param bw0 Weights for each quadrature point in x direction. * @param bw1 Weights for each quadrature point in y direction. * @param bw2 Weights for each quadrature point in z direction. + * @param stride Stride between elements in div_space, default 1. * @returns Evaluation at passed point using Bary interpolation. */ inline REAL evaluate_3d(const REAL coord0, const REAL coord1, const REAL coord2, @@ -233,18 +245,18 @@ inline REAL evaluate_3d(const REAL coord0, const REAL coord1, const REAL coord2, REAL *div_space, const REAL *const z0, const REAL *const z1, const REAL *const z2, const REAL *const bw0, const REAL *const bw1, - const REAL *const bw2) { + const REAL *const bw2, const std::size_t stride = 1) { REAL *div_space0 = div_space; - REAL *div_space1 = div_space0 + num_phys0; - REAL *div_space2 = div_space1 + num_phys1; + REAL *div_space1 = div_space0 + num_phys0 * stride; + REAL *div_space2 = div_space1 + num_phys1 * stride; - preprocess_weights(num_phys0, coord0, z0, bw0, div_space0); - preprocess_weights(num_phys1, coord1, z1, bw1, div_space1); - preprocess_weights(num_phys2, coord2, z2, bw2, div_space2); + preprocess_weights(num_phys0, coord0, z0, bw0, div_space0, stride); + preprocess_weights(num_phys1, coord1, z1, bw1, div_space1, stride); + preprocess_weights(num_phys2, coord2, z2, bw2, div_space2, stride); const REAL eval = compute_dir_210(num_phys0, num_phys1, num_phys2, physvals, - div_space0, div_space1, div_space2); + div_space0, div_space1, div_space2, stride); return eval; } diff --git a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp index 35422a7d..49724589 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp @@ -224,6 +224,8 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, const int num_elts = field->GetNumElmts(); Array Lcoord(3); Array coord(3); + const std::size_t stride = 3; + for (int ex = 0; ex < num_elts; ex++) { auto exp = field->GetExp(ex); auto geom = exp->GetGeom(); @@ -238,7 +240,7 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, const int num_phys1 = z1.size(); const int num_phys2 = z2.size(); const int num_phys = std::max(num_phys0, std::max(num_phys1, num_phys2)); - std::vector div_space(3 * num_phys); + std::vector div_space(3 * num_phys * stride); std::vector z0v(num_phys); std::vector z1v(num_phys); std::vector z2v(num_phys); @@ -279,7 +281,11 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, x0, x1, x2, num_phys0, num_phys1, num_phys2, physvalsv.data(), div_space.data(), z0v.data(), z1v.data(), z2v.data(), bw0v.data(), bw1v.data(), bw2v.data()); - + const REAL to_test_stride = Bary::evaluate_3d( + x0, x1, x2, num_phys0, num_phys1, num_phys2, physvalsv.data(), + div_space.data(), z0v.data(), z1v.data(), z2v.data(), bw0v.data(), + bw1v.data(), bw2v.data(), stride); + EXPECT_NEAR(to_test, to_test_stride, 1.0e-15); const REAL err_abs = std::abs(correct - to_test); const REAL abs_correct = std::abs(correct); const REAL err_rel = @@ -305,7 +311,18 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, x0, x1, x2, num_phys0, num_phys1, num_phys2, physvalsv.data(), div_space.data(), z0v.data(), z1v.data(), z2v.data(), bw0v.data(), bw1v.data(), bw2v.data()); - + // Check the values not a multiple of stride are untouched + std::fill(div_space.begin(), div_space.end(), 3.1415); + const REAL to_test_stride = Bary::evaluate_3d( + x0, x1, x2, num_phys0, num_phys1, num_phys2, physvalsv.data(), + div_space.data(), z0v.data(), z1v.data(), z2v.data(), bw0v.data(), + bw1v.data(), bw2v.data(), stride); + EXPECT_NEAR(to_test, to_test_stride, 1.0e-15); + for (int ix = 0; ix < div_space.size(); ix++) { + if (ix % stride != 0) { + EXPECT_EQ(div_space.at(ix), 3.1415); + } + } const REAL err_abs = std::abs(correct - to_test); const REAL abs_correct = std::abs(correct); const REAL err_rel = From 88cf46c25015c5494a1d1e116bea63d6c2dc7931 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Fri, 1 Nov 2024 15:04:10 +0000 Subject: [PATCH 29/66] added stride to function bary evaluation --- .../nektar_interface/function_bary_evaluation.hpp | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 6f7d1000..cf6c68c9 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -250,10 +250,11 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { for (auto &blockx : is) { const auto block_device = blockx.block_device; + const std::size_t local_size = blockx.local_size; es.push(sycl_target->queue.submit([&](sycl::handler &cgh) { // Allocate local memory to compute the divides. sycl::local_accessor local_mem( - sycl::range<1>(local_num_reals * blockx.local_size), cgh); + sycl::range<1>(local_num_reals * local_size), cgh); cgh.parallel_for<>( blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { @@ -262,7 +263,8 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { std::size_t layer; block_device.get_cell_layer(idx, &cell, &layer); if (block_device.work_item_required(cell, layer)) { - REAL *div_space0 = &local_mem[idx_local * 2 * k_stride_base]; + // offset by the local index for the striding to work + REAL *div_space0 = &local_mem[idx_local]; // query the map from cells to expansion type const int expansion_type = k_map_to_geom_type[cell]; @@ -293,9 +295,9 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { // this cell const auto physvals = &k_global_physvals[k_phys_offsets[cell]]; - const REAL evaluation = - Bary::evaluate_2d(coord0, coord1, num_phys0, num_phys1, - physvals, div_space0, z0, z1, bw0, bw1); + const REAL evaluation = Bary::evaluate_2d( + coord0, coord1, num_phys0, num_phys1, physvals, div_space0, + z0, z1, bw0, bw1, local_size); k_output[cell][k_component][layer] = evaluation; } From c5b08574c16737c73549a7efbc0fb9628b858291 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Fri, 1 Nov 2024 16:32:20 +0000 Subject: [PATCH 30/66] reimplemented Bary evaluation to be extendable to 3D/variable p more easily --- .../function_bary_evaluation.hpp | 239 +++++++----------- 1 file changed, 90 insertions(+), 149 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index cf6c68c9..d2712f93 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -27,38 +27,30 @@ namespace NESO { */ template class BaryEvaluateBase : GeomToExpansionBuilder { protected: + int ndim; std::shared_ptr field; ParticleMeshInterfaceSharedPtr mesh; - CellIDTranslationSharedPtr cell_id_translation; SYCLTargetSharedPtr sycl_target; - - BufferDeviceHost dh_phys_offsets; - BufferDeviceHost dh_phys_num0; - BufferDeviceHost dh_phys_num1; BufferDeviceHost dh_global_physvals; - /** - * Helper function to assemble the data required on the device for an - * expansion type. - */ - inline void assemble_data(const int offset, - StdExpansion2DSharedPtr expansion) { - auto base = expansion->GetBase(); - - double *z_ptr = this->dh_z.h_buffer.ptr + offset * stride_expansion_type; - double *bw_ptr = this->dh_bw.h_buffer.ptr + offset * stride_expansion_type; - - for (int dimx = 0; dimx < 2; dimx++) { - const auto &z = base[dimx]->GetZ(); - const auto &bw = base[dimx]->GetBaryWeights(); - NESOASSERT(z.size() == bw.size(), "Expected these two sizes to match."); - const int size = z.size(); - for (int cx = 0; cx < size; cx++) { - z_ptr[dimx * stride_base + cx] = z[cx]; - bw_ptr[dimx * stride_base + cx] = bw[cx]; - } - } - } + struct CellInfo { + int shape_type_int; + std::size_t num_phys[3]; + REAL const *d_z[3]; + REAL const *d_bw[3]; + std::size_t phys_offset; + }; + + using MapKey = std::tuple>; + + std::map map_cells_to_info; + + std::shared_ptr> d_cell_info; + std::stack>> stack_ptrs; + + /// Stride between z and weight values in each dimension for all expansion + /// types. + std::size_t max_num_phys; public: /// Disable (implicit) copies. @@ -66,18 +58,6 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { /// Disable (implicit) copies. BaryEvaluateBase &operator=(BaryEvaluateBase const &a) = delete; - /// Stride between z and weight values in each dimension for all expansion - /// types. - int stride_base; - /// Stride between expansion types for z and weight values. - int stride_expansion_type; - - /// The GetZ values for different expansion types. - BufferDeviceHost dh_z; - - /// The GetBaryWeights for different expansion types. - BufferDeviceHost dh_bw; - /** * Create instance to evaluate a passed field. * @@ -90,104 +70,82 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { BaryEvaluateBase(std::shared_ptr field, ParticleMeshInterfaceSharedPtr mesh, CellIDTranslationSharedPtr cell_id_translation) - : field(field), mesh(mesh), cell_id_translation(cell_id_translation), - sycl_target(cell_id_translation->sycl_target), dh_z(sycl_target, 1), - dh_bw(sycl_target, 1), dh_phys_offsets(sycl_target, 1), - dh_phys_num0(sycl_target, 1), dh_phys_num1(sycl_target, 1), + : ndim(mesh->get_ndim()), field(field), mesh(mesh), + sycl_target(cell_id_translation->sycl_target), dh_global_physvals(sycl_target, 1) { // build the map from geometry ids to expansion ids std::map geom_to_exp; build_geom_to_expansion_map(this->field, geom_to_exp); - - TriExpSharedPtr tri_exp{nullptr}; - QuadExpSharedPtr quad_exp{nullptr}; - auto geom_type_lookup = - this->cell_id_translation->dh_map_to_geom_type.h_buffer.ptr; - - const int index_tri_geom = - shape_type_to_int(LibUtilities::ShapeType::eTriangle); - const int index_quad_geom = - shape_type_to_int(LibUtilities::ShapeType::eQuadrilateral); - const int neso_cell_count = mesh->get_cell_count(); - this->dh_phys_offsets.realloc_no_copy(neso_cell_count); - this->dh_phys_num0.realloc_no_copy(neso_cell_count); - this->dh_phys_num1.realloc_no_copy(neso_cell_count); - // Assume all TriGeoms and QuadGeoms are the same (TODO generalise for - // varying p). Get the offsets to the coefficients for each cell. - for (int neso_cellx = 0; neso_cellx < neso_cell_count; neso_cellx++) { + std::vector v_cell_info; + v_cell_info.reserve(neso_cell_count); + this->max_num_phys = 0; - const int nektar_geom_id = - this->cell_id_translation->map_to_nektar[neso_cellx]; + for (int neso_cellx = 0; neso_cellx < neso_cell_count; neso_cellx++) { + const int nektar_geom_id = cell_id_translation->map_to_nektar[neso_cellx]; const int expansion_id = geom_to_exp[nektar_geom_id]; // get the nektar expansion auto expansion = this->field->GetExp(expansion_id); - // is this a tri expansion? - if ((geom_type_lookup[neso_cellx] == index_tri_geom) && - (tri_exp == nullptr)) { - tri_exp = std::dynamic_pointer_cast(expansion); + MapKey key; + std::get<0>(key) = + shape_type_to_int(expansion->GetGeom()->GetShapeType()); + for (int dimx = 0; dimx < 3; dimx++) { + std::get<1>(key)[dimx] = 0; } - // is this a quad expansion? - if ((geom_type_lookup[neso_cellx] == index_quad_geom) && - (quad_exp == nullptr)) { - quad_exp = std::dynamic_pointer_cast(expansion); + for (int dimx = 0; dimx < this->ndim; dimx++) { + std::get<1>(key)[dimx] = + static_cast(expansion->GetBase()[dimx]->GetZ().size()); } - - // record offsets and number of coefficients - this->dh_phys_offsets.h_buffer.ptr[neso_cellx] = - this->field->GetPhys_Offset(expansion_id); - - // Get the number of quadrature points in both dimensions. - this->dh_phys_num0.h_buffer.ptr[neso_cellx] = - (expansion->GetBase()[0])->GetZ().size(); - this->dh_phys_num1.h_buffer.ptr[neso_cellx] = - (expansion->GetBase()[1])->GetZ().size(); - } - - // stride between basis values across all expansion types - stride_base = 0; - for (int dimx = 0; dimx < 2; dimx++) { - if (tri_exp != nullptr) { - auto base = tri_exp->GetBase(); - stride_base = std::max(stride_base, (int)(base[dimx]->GetZ().size())); + if (this->map_cells_to_info.count(key) == 0) { + CellInfo cell_info; + cell_info.shape_type_int = std::get<0>(key); + for (int dx = 0; dx < 3; dx++) { + cell_info.num_phys[dx] = std::get<1>(key)[dx]; + } + + // Get the z values and bw values for this geom type with this number + // of physvals + for (int dimx = 0; dimx < this->ndim; dimx++) { + auto base = expansion->GetBase(); + const auto &z = base[dimx]->GetZ(); + const auto &bw = base[dimx]->GetBaryWeights(); + NESOASSERT(z.size() == bw.size(), + "Expected these two sizes to match."); + const auto size = z.size(); + this->max_num_phys = std::max(this->max_num_phys, size); + std::vector tmp_reals(2 * size); + for (int cx = 0; cx < size; cx++) { + tmp_reals.at(cx) = z[cx]; + } + for (int cx = 0; cx < size; cx++) { + tmp_reals.at(cx + size) = bw[cx]; + } + auto ptr = std::make_shared>(this->sycl_target, + tmp_reals); + auto d_ptr = ptr->ptr; + this->stack_ptrs.push(ptr); + + cell_info.d_z[dimx] = d_ptr; + cell_info.d_bw[dimx] = d_ptr + size; + } + + this->map_cells_to_info[key] = cell_info; } - if (quad_exp != nullptr) { - auto base = quad_exp->GetBase(); - stride_base = std::max(stride_base, (int)(base[dimx]->GetZ().size())); - } - } - stride_base = pad_to_vector_length(stride_base); - - // stride between expansion types. - stride_expansion_type = 2 * stride_base; - - // malloc space for arrays - const int num_coeffs_all_types = 2 * stride_expansion_type; - this->dh_z.realloc_no_copy(num_coeffs_all_types); - this->dh_bw.realloc_no_copy(num_coeffs_all_types); - for (int cx = 0; cx < num_coeffs_all_types; cx++) { - this->dh_z.h_buffer.ptr[cx] = 0.0; - this->dh_bw.h_buffer.ptr[cx] = 0.0; - } - // TriExp has expansion type 0 - is the first set of data - if (tri_exp != nullptr) { - this->assemble_data(0, std::static_pointer_cast(tri_exp)); - } - // QuadExp has expansion type 1 - is the first set of data - if (quad_exp != nullptr) { - this->assemble_data(1, - std::static_pointer_cast(quad_exp)); + // Get the generic info for this cell type and number of modes + auto cell_info = this->map_cells_to_info.at(key); + // push on the offset for this particular cell + cell_info.phys_offset = + static_cast(this->field->GetPhys_Offset(expansion_id)); + + v_cell_info.push_back(cell_info); } - this->dh_phys_offsets.host_to_device(); - this->dh_phys_num0.host_to_device(); - this->dh_phys_num1.host_to_device(); - this->dh_z.host_to_device(); - this->dh_bw.host_to_device(); + this->d_cell_info = std::make_shared>( + this->sycl_target, v_cell_info); } /** @@ -215,6 +173,7 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { this->dh_global_physvals.h_buffer.ptr[px] = 0.0; } this->dh_global_physvals.host_to_device(); + const auto k_global_physvals = this->dh_global_physvals.d_buffer.ptr; // output and particle position dats auto k_output = (*particle_group)[sym]->cell_dat.device_ptr(); @@ -224,25 +183,15 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { const int k_component = component; // values required to evaluate the field - const int k_index_tri_geom = - shape_type_to_int(LibUtilities::ShapeType::eTriangle); - const auto k_global_physvals = this->dh_global_physvals.d_buffer.ptr; - const auto k_phys_offsets = this->dh_phys_offsets.d_buffer.ptr; - const auto k_phys_num0 = this->dh_phys_num0.d_buffer.ptr; - const auto k_phys_num1 = this->dh_phys_num1.d_buffer.ptr; - const auto k_z = this->dh_z.d_buffer.ptr; - const auto k_bw = this->dh_bw.d_buffer.ptr; - const auto k_stride_base = this->stride_base; - const auto k_stride_expansion_type = this->stride_expansion_type; - const auto k_map_to_geom_type = - this->cell_id_translation->dh_map_to_geom_type.d_buffer.ptr; + auto k_cell_info = this->d_cell_info->ptr; // iteration set specification for the particle loop auto mpi_rank_dat = particle_group->mpi_rank_dat; ParticleLoopImplementation::ParticleLoopBlockIterationSet ish{mpi_rank_dat, 16}; const std::size_t local_size = 256; - const std::size_t local_num_reals = 2 * this->stride_base; + const std::size_t local_num_reals = + static_cast(this->ndim * this->max_num_phys); const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); EventStack es; @@ -265,19 +214,7 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { if (block_device.work_item_required(cell, layer)) { // offset by the local index for the striding to work REAL *div_space0 = &local_mem[idx_local]; - - // query the map from cells to expansion type - const int expansion_type = k_map_to_geom_type[cell]; - // use the type key to index into the Bary weights and points - const int expansion_type_offset = - (expansion_type == k_index_tri_geom) - ? 0 - : k_stride_expansion_type; - // get the z values and weights for this expansion type - const auto z0 = &k_z[expansion_type_offset]; - const auto z1 = &k_z[expansion_type_offset + k_stride_base]; - const auto bw0 = &k_bw[expansion_type_offset]; - const auto bw1 = &k_bw[expansion_type_offset + k_stride_base]; + const auto cell_info = k_cell_info[cell]; const REAL xi0 = k_ref_positions[cell][0][layer]; const REAL xi1 = k_ref_positions[cell][1][layer]; @@ -286,14 +223,18 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { REAL coord0, coord1; GeometryInterface::loc_coord_to_loc_collapsed_2d( - expansion_type, xi0, xi1, &coord0, &coord1); + cell_info.shape_type_int, xi0, xi1, &coord0, &coord1); - const int num_phys0 = k_phys_num0[cell]; - const int num_phys1 = k_phys_num1[cell]; + const auto num_phys0 = cell_info.num_phys[0]; + const auto num_phys1 = cell_info.num_phys[1]; + const auto z0 = cell_info.d_z[0]; + const auto z1 = cell_info.d_z[1]; + const auto bw0 = cell_info.d_bw[0]; + const auto bw1 = cell_info.d_bw[1]; // Get pointer to the start of the quadrature point values for // this cell - const auto physvals = &k_global_physvals[k_phys_offsets[cell]]; + const auto physvals = &k_global_physvals[cell_info.phys_offset]; const REAL evaluation = Bary::evaluate_2d( coord0, coord1, num_phys0, num_phys1, physvals, div_space0, From 07b5439966ef6993f4935a1f57cf87b9b1050268 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Fri, 1 Nov 2024 16:52:24 +0000 Subject: [PATCH 31/66] added profiling information to bary evaluate in 2D --- include/nektar_interface/function_bary_evaluation.hpp | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index d2712f93..a6e20ccc 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -197,6 +197,7 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { EventStack es; auto is = ish.get_all_cells(local_size, num_bytes_local); + ProfileRegion pr("BaryEvaluateBase", "evaluate_2d"); for (auto &blockx : is) { const auto block_device = blockx.block_device; const std::size_t local_size = blockx.local_size; @@ -245,7 +246,14 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { }); })); } + const auto nphys = this->max_num_phys; + const auto npart = particle_group->get_npart_local(); + const auto nflop_prepare = this->ndim * nphys * 5; + const auto nflop_loop = nphys * nphys * 3; + pr.num_flops = (nflop_loop + nflop_prepare) * npart; es.wait(); + pr.end(); + this->sycl_target->profile_map.add_region(pr); } }; From f17287580abdb194950613587e82ef7aa542b751 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Thu, 7 Nov 2024 14:58:24 +0000 Subject: [PATCH 32/66] added low level bary evaluation implementations for runtime numbers of functions --- .../bary_interpolation/bary_evaluation.hpp | 128 +++++++++++ .../function_bary_evaluation.hpp | 99 ++++---- .../function_basis_evaluation.hpp | 6 +- .../function_basis_projection.hpp | 6 +- .../map_particles_3d_regular.cpp | 5 +- .../test_particle_function_evaluation.cpp | 211 ++++++++++++++++++ 6 files changed, 411 insertions(+), 44 deletions(-) diff --git a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp index daaa221b..f90a3627 100644 --- a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp +++ b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp @@ -96,6 +96,85 @@ inline REAL compute_dir_10(const int num_phys0, const int num_phys1, return pval1; } +/** + * Computes Bary interpolation over two dimensions. Evaluates N functions + * with interlaced quadrature point values. + * + * @param[in] num_phys0 Number of quadrature points in dimension 0. + * @param[in] num_phys1 Number of quadrature points in dimension 1. + * @param[in] physvals Array of function values at quadrature points interlaced + * values for each function to evaluate. + * @param[in] div_space0 The output of preprocess_weights applied to dimension + * 0. + * @param[in] div_space1 The output of preprocess_weights applied to + * dimension 1. + * @param stride Stride between elements in div_space, default 1. + * @param[in, out] output Output function evaluations. + */ +template +inline void compute_dir_10_interlaced(const int num_phys0, const int num_phys1, + const REAL *const physvals, + const REAL *const div_space0, + const REAL *const div_space1, + REAL *RESTRICT output, + const std::size_t stride = 1) { + REAL tmp[N]; + for (int ix = 0; ix < N; ix++) { + tmp[ix] = 0.0; + } + for (int i1 = 0; i1 < num_phys1; i1++) { + const REAL c1 = div_space1[i1 * stride]; + for (int i0 = 0; i0 < num_phys0; i0++) { + const int inner_stride = (i1 * num_phys0 + i0) * N; + const REAL inner_c = div_space0[i0 * stride] * c1; + for (int ix = 0; ix < N; ix++) { + tmp[ix] += physvals[inner_stride + ix] * inner_c; + } + } + } + for (int ix = 0; ix < N; ix++) { + output[ix] = tmp[ix]; + } +} + +/** + * Computes Bary interpolation over two dimensions. Evaluates N functions + * with interlaced quadrature point values. + * + * @param[in] num_functions Number of functions to evaluate. + * @param[in] num_phys0 Number of quadrature points in dimension 0. + * @param[in] num_phys1 Number of quadrature points in dimension 1. + * @param[in] physvals Array of function values at quadrature points interlaced + * values for each function to evaluate. + * @param[in] div_space0 The output of preprocess_weights applied to dimension + * 0. + * @param[in] div_space1 The output of preprocess_weights applied to + * dimension 1. + * @param stride Stride between elements in div_space, default 1. + * @param[in, out] output Output function evaluations. + */ +inline void compute_dir_10_interlaced(const int num_functions, + const int num_phys0, const int num_phys1, + const REAL *const physvals, + const REAL *const div_space0, + const REAL *const div_space1, + REAL *RESTRICT output, + const std::size_t stride = 1) { + for (int ix = 0; ix < num_functions; ix++) { + output[ix] = 0.0; + } + for (int i1 = 0; i1 < num_phys1; i1++) { + const REAL c1 = div_space1[i1 * stride]; + for (int i0 = 0; i0 < num_phys0; i0++) { + const int inner_stride = (i1 * num_phys0 + i0) * num_functions; + const REAL inner_c = div_space0[i0 * stride] * c1; + for (int ix = 0; ix < num_functions; ix++) { + output[ix] += physvals[inner_stride + ix] * inner_c; + } + } + } +} + /** * Computes Bary interpolation over three dimensions. * @@ -178,6 +257,55 @@ inline void compute_dir_210_interlaced( } } +/** + * Computes Bary interpolation over three dimensions. Evaluates N functions + * with interlaced quadrature point values. + * + * @param[in] num_functions Number of functions to evaluate. + * @param[in] num_phys0 Number of quadrature points in dimension 0. + * @param[in] num_phys1 Number of quadrature points in dimension 1. + * @param[in] num_phys2 Number of quadrature points in dimension 2. + * @param[in] physvals Array of function values at quadrature points interlaced + * values for each function to evaluate. + * @param[in] div_space0 The output of preprocess_weights applied to dimension + * 0. + * @param[in] div_space1 The output of preprocess_weights applied to + * dimension 1. + * @param[in] div_space2 The output of preprocess_weights applied to + * dimension 2. + * @param stride Stride between elements in div_space, default 1. + * @param[in, out] output Output function evaluations. + */ +inline void compute_dir_210_interlaced(const int num_functions, + const int num_phys0, const int num_phys1, + const int num_phys2, + const REAL *RESTRICT const physvals, + const REAL *RESTRICT const div_space0, + const REAL *RESTRICT const div_space1, + const REAL *RESTRICT const div_space2, + REAL *RESTRICT output, + const std::size_t stride = 1) { + for (int ix = 0; ix < num_functions; ix++) { + output[ix] = 0.0; + } + + const int stride_phys = num_phys0 * num_phys1; + for (int i2 = 0; i2 < num_phys2; i2++) { + const REAL c2 = div_space2[i2 * stride]; + for (int i1 = 0; i1 < num_phys1; i1++) { + const REAL c1 = c2 * div_space1[i1 * stride]; + for (int i0 = 0; i0 < num_phys0; i0++) { + const int inner_stride = + (i2 * stride_phys + i1 * num_phys0 + i0) * num_functions; + const REAL inner_c = div_space0[i0 * stride] * c1; + for (int ix = 0; ix < num_functions; ix++) { + output[ix] += physvals[inner_stride + ix] * inner_c; + } + } + } + } +} + /** * Compute a function evaluation at a point using the passed quadrature point * values, quadrature points and weights. diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index a6e20ccc..0a9808ea 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -187,9 +187,11 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { // iteration set specification for the particle loop auto mpi_rank_dat = particle_group->mpi_rank_dat; - ParticleLoopImplementation::ParticleLoopBlockIterationSet ish{mpi_rank_dat, - 16}; - const std::size_t local_size = 256; + ParticleLoopImplementation::ParticleLoopBlockIterationSet ish{mpi_rank_dat}; + const std::size_t local_size = + this->sycl_target->parameters + ->template get("LOOP_LOCAL_SIZE") + ->value; const std::size_t local_num_reals = static_cast(this->ndim * this->max_num_phys); const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); @@ -206,44 +208,59 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { sycl::local_accessor local_mem( sycl::range<1>(local_num_reals * local_size), cgh); - cgh.parallel_for<>( - blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { - const int idx_local = idx.get_local_id(1); - std::size_t cell; - std::size_t layer; - block_device.get_cell_layer(idx, &cell, &layer); - if (block_device.work_item_required(cell, layer)) { - // offset by the local index for the striding to work - REAL *div_space0 = &local_mem[idx_local]; - const auto cell_info = k_cell_info[cell]; - - const REAL xi0 = k_ref_positions[cell][0][layer]; - const REAL xi1 = k_ref_positions[cell][1][layer]; - // If this cell is a triangle then we need to map to the - // collapsed coordinates. - REAL coord0, coord1; - - GeometryInterface::loc_coord_to_loc_collapsed_2d( - cell_info.shape_type_int, xi0, xi1, &coord0, &coord1); - - const auto num_phys0 = cell_info.num_phys[0]; - const auto num_phys1 = cell_info.num_phys[1]; - const auto z0 = cell_info.d_z[0]; - const auto z1 = cell_info.d_z[1]; - const auto bw0 = cell_info.d_bw[0]; - const auto bw1 = cell_info.d_bw[1]; - - // Get pointer to the start of the quadrature point values for - // this cell - const auto physvals = &k_global_physvals[cell_info.phys_offset]; - - const REAL evaluation = Bary::evaluate_2d( - coord0, coord1, num_phys0, num_phys1, physvals, div_space0, - z0, z1, bw0, bw1, local_size); - - k_output[cell][k_component][layer] = evaluation; - } - }); + auto lambda_inner = [=](auto idx_local, auto cell, auto layer) { + // offset by the local index for the striding to work + REAL *div_space0 = &local_mem[idx_local]; + const auto cell_info = k_cell_info[cell]; + + const REAL xi0 = k_ref_positions[cell][0][layer]; + const REAL xi1 = k_ref_positions[cell][1][layer]; + // If this cell is a triangle then we need to map to the + // collapsed coordinates. + REAL coord0, coord1; + + GeometryInterface::loc_coord_to_loc_collapsed_2d( + cell_info.shape_type_int, xi0, xi1, &coord0, &coord1); + + const auto num_phys0 = cell_info.num_phys[0]; + const auto num_phys1 = cell_info.num_phys[1]; + const auto z0 = cell_info.d_z[0]; + const auto z1 = cell_info.d_z[1]; + const auto bw0 = cell_info.d_bw[0]; + const auto bw1 = cell_info.d_bw[1]; + + // Get pointer to the start of the quadrature point values for + // this cell + const auto physvals = &k_global_physvals[cell_info.phys_offset]; + + const REAL evaluation = + Bary::evaluate_2d(coord0, coord1, num_phys0, num_phys1, physvals, + div_space0, z0, z1, bw0, bw1, local_size); + + k_output[cell][k_component][layer] = evaluation; + }; + + if (blockx.layer_bounds_check_required) { + cgh.parallel_for<>( + blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { + const int idx_local = idx.get_local_id(1); + std::size_t cell; + std::size_t layer; + block_device.get_cell_layer(idx, &cell, &layer); + if (block_device.work_item_required(cell, layer)) { + lambda_inner(idx_local, cell, layer); + } + }); + } else { + cgh.parallel_for<>(blockx.loop_iteration_set, + [=](sycl::nd_item<2> idx) { + const int idx_local = idx.get_local_id(1); + std::size_t cell; + std::size_t layer; + block_device.get_cell_layer(idx, &cell, &layer); + lambda_inner(idx_local, cell, layer); + }); + } })); } const auto nphys = this->max_num_phys; diff --git a/include/nektar_interface/function_basis_evaluation.hpp b/include/nektar_interface/function_basis_evaluation.hpp index b55b7688..0d0b9b1a 100644 --- a/include/nektar_interface/function_basis_evaluation.hpp +++ b/include/nektar_interface/function_basis_evaluation.hpp @@ -81,12 +81,16 @@ class FunctionEvaluateBasis : public BasisEvaluateBase { const int k_max_total_nummodes2 = this->map_total_nummodes.at(shape_type).at(2); + const std::size_t default_local_size = + this->sycl_target->parameters + ->template get("LOOP_LOCAL_SIZE") + ->value; const size_t local_size = get_num_local_work_items( this->sycl_target, static_cast(k_max_total_nummodes0 + k_max_total_nummodes1 + k_max_total_nummodes2) * sizeof(REAL), - 128); + default_local_size); const int local_mem_num_items = (k_max_total_nummodes0 + k_max_total_nummodes1 + diff --git a/include/nektar_interface/function_basis_projection.hpp b/include/nektar_interface/function_basis_projection.hpp index 29b9a37a..98241f3b 100644 --- a/include/nektar_interface/function_basis_projection.hpp +++ b/include/nektar_interface/function_basis_projection.hpp @@ -81,12 +81,16 @@ template class FunctionProjectBasis : public BasisEvaluateBase { const int k_max_total_nummodes2 = this->map_total_nummodes.at(shape_type).at(2); + const std::size_t default_local_size = + this->sycl_target->parameters + ->template get("LOOP_LOCAL_SIZE") + ->value; const size_t local_size = get_num_local_work_items( this->sycl_target, static_cast(k_max_total_nummodes0 + k_max_total_nummodes1 + k_max_total_nummodes2) * sizeof(REAL), - 128); + default_local_size); const int local_mem_num_items = (k_max_total_nummodes0 + k_max_total_nummodes1 + diff --git a/src/nektar_interface/particle_cell_mapping/map_particles_3d_regular.cpp b/src/nektar_interface/particle_cell_mapping/map_particles_3d_regular.cpp index 0eed518b..312d8c59 100644 --- a/src/nektar_interface/particle_cell_mapping/map_particles_3d_regular.cpp +++ b/src/nektar_interface/particle_cell_mapping/map_particles_3d_regular.cpp @@ -147,7 +147,10 @@ void MapParticles3DRegular::map(ParticleGroup &particle_group, ? position_dat->h_npart_cell[map_cell] : position_dat->cell_dat.get_nrow_max(); const int k_cell_offset = (map_cell > -1) ? map_cell : 0; - const size_t local_size = 256; + const std::size_t local_size = + this->sycl_target->parameters + ->template get("LOOP_LOCAL_SIZE") + ->value; const auto div_mod = std::div(max_cell_occupancy, local_size); const int outer_size = div_mod.quot + (div_mod.rem == 0 ? 0 : 1); const size_t cell_count = diff --git a/test/unit/nektar_interface/test_particle_function_evaluation.cpp b/test/unit/nektar_interface/test_particle_function_evaluation.cpp index 7b3f5fd4..5462bdfd 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation.cpp @@ -722,3 +722,214 @@ TEST(BaryInterpolation, Evaluation2D) { delete[] argv[1]; delete[] argv[2]; } + +TEST(BaryInterpolation, Generic) { + + const int stride = 3; + const int num_phys0 = 7; + const int num_phys1 = 5; + const int num_phys2 = 9; + const int num_phys = num_phys0 * num_phys1 * num_phys2; + std::mt19937 rng(22123257); + std::uniform_real_distribution uniform_rng(-2.0, 2.0); + + auto lambda_rng = [&]() -> REAL { return uniform_rng(rng); }; + + auto lambda_make_phys_vals = [&]() -> std::vector { + std::vector data(num_phys); + std::generate(data.begin(), data.end(), lambda_rng); + return data; + }; + + auto lambda_interlace_2 = [](auto p0, auto p1) -> std::vector { + std::vector data(p0.size() + p1.size()); + EXPECT_EQ(p0.size(), p1.size()); + const auto N = p0.size(); + std::size_t index = 0; + for (std::size_t ix = 0; ix < N; ix++) { + data.at(index++) = p0.at(ix); + data.at(index++) = p1.at(ix); + } + return data; + }; + + auto lambda_interlace_3 = [](auto p0, auto p1, auto p2) -> std::vector { + std::vector data(p0.size() + p1.size() + p2.size()); + EXPECT_EQ(p0.size(), p1.size()); + EXPECT_EQ(p0.size(), p2.size()); + const auto N = p0.size(); + std::size_t index = 0; + for (std::size_t ix = 0; ix < N; ix++) { + data.at(index++) = p0.at(ix); + data.at(index++) = p1.at(ix); + data.at(index++) = p2.at(ix); + } + return data; + }; + + auto lambda_rel_error = [](auto a, auto b) { + const auto err_abs = std::abs(a - b); + const auto mag = std::abs(a); + const auto err_rel = mag > 0.0 ? err_abs / mag : err_abs; + const REAL tol = 1.0e-14; + if (err_rel > tol) { + nprint("Error:", a, b); + } + EXPECT_TRUE(err_rel <= tol); + }; + + std::vector div_space0(num_phys0 * stride); + std::vector div_space1(num_phys1 * stride); + std::vector div_space2(num_phys2 * stride); + std::generate(div_space0.begin(), div_space0.end(), lambda_rng); + std::generate(div_space1.begin(), div_space1.end(), lambda_rng); + std::generate(div_space2.begin(), div_space2.end(), lambda_rng); + + REAL output[3]; + + auto func0 = lambda_make_phys_vals(); + auto func1 = lambda_make_phys_vals(); + auto func2 = lambda_make_phys_vals(); + + std::vector strides = {1, stride}; + for (auto test_stride : strides) { + + // 2D, 1 function + { + const REAL correct = Bary::compute_dir_10(num_phys0, num_phys1, + func0.data(), div_space0.data(), + div_space1.data(), test_stride); + + REAL to_test[1]; + Bary::compute_dir_10_interlaced<1>(num_phys0, num_phys1, func0.data(), + div_space0.data(), div_space1.data(), + to_test, test_stride); + lambda_rel_error(correct, to_test[0]); + + Bary::compute_dir_10_interlaced(1, num_phys0, num_phys1, func0.data(), + div_space0.data(), div_space1.data(), + to_test, test_stride); + lambda_rel_error(correct, to_test[0]); + } + + // 2D, 2 functions + { + auto func01 = lambda_interlace_2(func0, func1); + REAL to_test0[2]; + Bary::compute_dir_10_interlaced<2>(num_phys0, num_phys1, func01.data(), + div_space0.data(), div_space1.data(), + to_test0, test_stride); + + REAL *tmp_data[2] = {func0.data(), func1.data()}; + for (int dx = 0; dx < 2; dx++) { + const REAL correct = Bary::compute_dir_10( + num_phys0, num_phys1, tmp_data[dx], div_space0.data(), + div_space1.data(), test_stride); + lambda_rel_error(correct, to_test0[dx]); + } + + REAL to_test1[2]; + Bary::compute_dir_10_interlaced(2, num_phys0, num_phys1, func01.data(), + div_space0.data(), div_space1.data(), + to_test1, test_stride); + + lambda_rel_error(to_test0[0], to_test1[0]); + lambda_rel_error(to_test0[1], to_test1[1]); + } + + // 2D, 3 functions + { + auto func012 = lambda_interlace_3(func0, func1, func2); + REAL to_test0[3]; + Bary::compute_dir_10_interlaced<3>(num_phys0, num_phys1, func012.data(), + div_space0.data(), div_space1.data(), + to_test0, test_stride); + + REAL *tmp_data[3] = {func0.data(), func1.data(), func2.data()}; + for (int dx = 0; dx < 3; dx++) { + const REAL correct = Bary::compute_dir_10( + num_phys0, num_phys1, tmp_data[dx], div_space0.data(), + div_space1.data(), test_stride); + lambda_rel_error(correct, to_test0[dx]); + } + + REAL to_test1[3]; + Bary::compute_dir_10_interlaced(3, num_phys0, num_phys1, func012.data(), + div_space0.data(), div_space1.data(), + to_test1, test_stride); + + lambda_rel_error(to_test0[0], to_test1[0]); + lambda_rel_error(to_test0[1], to_test1[1]); + lambda_rel_error(to_test0[2], to_test1[2]); + } + + // 3D, 1 function + { + const REAL correct = Bary::compute_dir_210( + num_phys0, num_phys1, num_phys2, func0.data(), div_space0.data(), + div_space1.data(), div_space2.data(), test_stride); + + REAL to_test[1]; + Bary::compute_dir_210_interlaced<1>( + num_phys0, num_phys1, num_phys2, func0.data(), div_space0.data(), + div_space1.data(), div_space2.data(), to_test, test_stride); + lambda_rel_error(correct, to_test[0]); + + Bary::compute_dir_210_interlaced( + 1, num_phys0, num_phys1, num_phys2, func0.data(), div_space0.data(), + div_space1.data(), div_space2.data(), to_test, test_stride); + lambda_rel_error(correct, to_test[0]); + } + + // 3D, 2 functions + { + auto func01 = lambda_interlace_2(func0, func1); + REAL to_test0[2]; + Bary::compute_dir_210_interlaced<2>( + num_phys0, num_phys1, num_phys2, func01.data(), div_space0.data(), + div_space1.data(), div_space2.data(), to_test0, test_stride); + + REAL *tmp_data[2] = {func0.data(), func1.data()}; + for (int dx = 0; dx < 2; dx++) { + const REAL correct = Bary::compute_dir_210( + num_phys0, num_phys1, num_phys2, tmp_data[dx], div_space0.data(), + div_space1.data(), div_space2.data(), test_stride); + lambda_rel_error(correct, to_test0[dx]); + } + + REAL to_test1[2]; + Bary::compute_dir_210_interlaced( + 2, num_phys0, num_phys1, num_phys2, func01.data(), div_space0.data(), + div_space1.data(), div_space2.data(), to_test1, test_stride); + + lambda_rel_error(to_test0[0], to_test1[0]); + lambda_rel_error(to_test0[1], to_test1[1]); + } + + // 3D, 3 functions + { + auto func012 = lambda_interlace_3(func0, func1, func2); + REAL to_test0[3]; + Bary::compute_dir_210_interlaced<3>( + num_phys0, num_phys1, num_phys2, func012.data(), div_space0.data(), + div_space1.data(), div_space2.data(), to_test0, test_stride); + + REAL *tmp_data[3] = {func0.data(), func1.data(), func2.data()}; + for (int dx = 0; dx < 3; dx++) { + const REAL correct = Bary::compute_dir_210( + num_phys0, num_phys1, num_phys2, tmp_data[dx], div_space0.data(), + div_space1.data(), div_space2.data(), test_stride); + lambda_rel_error(correct, to_test0[dx]); + } + + REAL to_test1[3]; + Bary::compute_dir_210_interlaced( + 3, num_phys0, num_phys1, num_phys2, func012.data(), div_space0.data(), + div_space1.data(), div_space2.data(), to_test1, test_stride); + + lambda_rel_error(to_test0[0], to_test1[0]); + lambda_rel_error(to_test0[1], to_test1[1]); + lambda_rel_error(to_test0[2], to_test1[2]); + } + } +} From f8a3a758aa073bccbf80c1c573b970ad82f0b4c8 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Thu, 7 Nov 2024 16:41:57 +0000 Subject: [PATCH 33/66] initial implementation of bary evaluation for a generic number of functions --- .../function_bary_evaluation.hpp | 383 +++++++++++++----- .../nektar_interface/function_evaluation.hpp | 28 +- 2 files changed, 293 insertions(+), 118 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 0a9808ea..5e0500cf 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -31,7 +31,7 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { std::shared_ptr field; ParticleMeshInterfaceSharedPtr mesh; SYCLTargetSharedPtr sycl_target; - BufferDeviceHost dh_global_physvals; + BufferDevice d_global_physvals; struct CellInfo { int shape_type_int; @@ -52,6 +52,248 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { /// types. std::size_t max_num_phys; + template + inline void evaluate_inner_2d(ParticleGroupSharedPtr particle_group, + Sym sym, const int component, + Array &global_physvals) { + + // copy the quadrature point values over to the device + const int num_global_physvals = global_physvals.size(); + this->d_global_physvals.realloc_no_copy(num_global_physvals); + NekDouble *k_global_physvals = this->d_global_physvals.ptr; + auto copy_event = this->sycl_target->queue.memcpy( + k_global_physvals, global_physvals.data(), + num_global_physvals * sizeof(NekDouble)); + + // output and particle position dats + auto k_output = (*particle_group)[sym]->cell_dat.device_ptr(); + const auto k_ref_positions = + (*particle_group)[Sym("NESO_REFERENCE_POSITIONS")] + ->cell_dat.device_ptr(); + const int k_component = component; + + // values required to evaluate the field + auto k_cell_info = this->d_cell_info->ptr; + + // iteration set specification for the particle loop + auto mpi_rank_dat = particle_group->mpi_rank_dat; + ParticleLoopImplementation::ParticleLoopBlockIterationSet ish{mpi_rank_dat}; + const std::size_t local_size = + this->sycl_target->parameters + ->template get("LOOP_LOCAL_SIZE") + ->value; + const std::size_t local_num_reals = + static_cast(this->ndim * this->max_num_phys); + const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); + + EventStack es; + auto is = ish.get_all_cells(local_size, num_bytes_local); + copy_event.wait_and_throw(); + ProfileRegion pr("BaryEvaluateBase", "evaluate_2d"); + for (auto &blockx : is) { + const auto block_device = blockx.block_device; + const std::size_t local_size = blockx.local_size; + es.push(sycl_target->queue.submit([&](sycl::handler &cgh) { + // Allocate local memory to compute the divides. + sycl::local_accessor local_mem( + sycl::range<1>(local_num_reals * local_size), cgh); + + cgh.parallel_for<>( + blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { + const int idx_local = idx.get_local_id(1); + std::size_t cell; + std::size_t layer; + block_device.get_cell_layer(idx, &cell, &layer); + if (block_device.work_item_required(cell, layer)) { + // offset by the local index for the striding to work + REAL *div_space0 = &local_mem[idx_local]; + const auto cell_info = k_cell_info[cell]; + + const REAL xi0 = k_ref_positions[cell][0][layer]; + const REAL xi1 = k_ref_positions[cell][1][layer]; + // If this cell is a triangle then we need to map to the + // collapsed coordinates. + REAL eta0, eta1; + + GeometryInterface::loc_coord_to_loc_collapsed_2d( + cell_info.shape_type_int, xi0, xi1, &eta0, &eta1); + + const auto num_phys0 = cell_info.num_phys[0]; + const auto num_phys1 = cell_info.num_phys[1]; + const auto z0 = cell_info.d_z[0]; + const auto z1 = cell_info.d_z[1]; + const auto bw0 = cell_info.d_bw[0]; + const auto bw1 = cell_info.d_bw[1]; + + // Get pointer to the start of the quadrature point values for + // this cell + const auto physvals = &k_global_physvals[cell_info.phys_offset]; + + const REAL evaluation = Bary::evaluate_2d( + eta0, eta1, num_phys0, num_phys1, physvals, div_space0, z0, + z1, bw0, bw1, local_size); + + k_output[cell][k_component][layer] = evaluation; + } + }); + })); + } + const auto nphys = this->max_num_phys; + const auto npart = particle_group->get_npart_local(); + const auto nflop_prepare = this->ndim * nphys * 5; + const auto nflop_loop = nphys * nphys * 3; + pr.num_flops = (nflop_loop + nflop_prepare) * npart; + es.wait(); + pr.end(); + this->sycl_target->profile_map.add_region(pr); + } + + template + inline void + evaluate_inner_2d(ParticleGroupSharedPtr particle_group, + std::vector> syms, const std::vector components, + std::vector> &global_physvals) { + + EventStack es; + NESOASSERT(syms.size() == components.size(), "Input size missmatch"); + NESOASSERT(global_physvals.size() == components.size(), + "Input size missmatch"); + const std::size_t num_functions = static_cast(syms.size()); + const std::size_t num_physvals_per_function = global_physvals.at(0).size(); + + // copy the quadrature point values over to the device + const std::size_t num_global_physvals = + syms.size() * global_physvals.at(0).size(); + this->d_global_physvals.realloc_no_copy(2 * num_global_physvals); + NekDouble *k_global_physvals = this->d_global_physvals.ptr; + NekDouble *k_global_physvals_interlaced = + k_global_physvals + num_global_physvals; + + static_assert( + std::is_same::value == true, + "This implementation assumes that NekDouble and REAL are the same."); + for (std::size_t fx = 0; fx < num_functions; fx++) { + es.push(this->sycl_target->queue.memcpy( + k_global_physvals + fx * num_physvals_per_function, + global_physvals.at(fx).data(), + num_physvals_per_function * sizeof(NekDouble))); + } + // wait for the copies + es.wait(); + + // interlaced the values for the bary evaluation function + matrix_transpose(this->sycl_target, num_functions, + num_physvals_per_function, k_global_physvals, + k_global_physvals_interlaced) + .wait_and_throw(); + + std::vector h_sym_ptrs(num_functions); + for (std::size_t fx = 0; fx < num_functions; fx++) { + h_sym_ptrs.at(fx) = + particle_group->get_dat(syms.at(fx))->cell_dat.device_ptr(); + } + + BufferDevice d_syms_ptrs(this->sycl_target, h_sym_ptrs); + BufferDevice d_components(this->sycl_target, components); + U ****k_syms_ptrs = d_syms_ptrs.ptr; + int *k_components = d_components.ptr; + + const auto k_ref_positions = + particle_group->get_dat(Sym("NESO_REFERENCE_POSITIONS")) + ->cell_dat.device_ptr(); + + // values required to evaluate the field + auto k_cell_info = this->d_cell_info->ptr; + + // iteration set specification for the particle loop + auto mpi_rank_dat = particle_group->mpi_rank_dat; + ParticleLoopImplementation::ParticleLoopBlockIterationSet ish{mpi_rank_dat}; + const std::size_t local_size = + this->sycl_target->parameters + ->template get("LOOP_LOCAL_SIZE") + ->value; + const std::size_t local_num_reals = + static_cast(this->ndim * this->max_num_phys) + + num_functions; + const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); + const auto k_max_num_phys = this->max_num_phys; + + auto is = ish.get_all_cells(local_size, num_bytes_local); + + ProfileRegion pr("BaryEvaluateBase", + "evaluate_2d_" + std::to_string(num_functions)); + for (auto &blockx : is) { + const auto block_device = blockx.block_device; + const std::size_t local_size = blockx.local_size; + es.push(sycl_target->queue.submit([&](sycl::handler &cgh) { + // Allocate local memory to compute the divides. + sycl::local_accessor local_mem( + sycl::range<1>(local_num_reals * local_size), cgh); + + cgh.parallel_for<>( + blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { + const int idx_local = idx.get_local_id(1); + std::size_t cell; + std::size_t layer; + block_device.get_cell_layer(idx, &cell, &layer); + if (block_device.work_item_required(cell, layer)) { + // offset by the local index for the striding to work + REAL *evaluations = &local_mem[0] + idx_local * num_functions; + REAL *div_start = &local_mem[local_size * num_functions]; + REAL *div_space0 = div_start + idx_local; + REAL *div_space1 = div_space0 + k_max_num_phys * local_size; + + const auto cell_info = k_cell_info[cell]; + + const REAL xi0 = k_ref_positions[cell][0][layer]; + const REAL xi1 = k_ref_positions[cell][1][layer]; + // If this cell is a triangle then we need to map to the + // collapsed coordinates. + REAL eta0, eta1; + + GeometryInterface::loc_coord_to_loc_collapsed_2d( + cell_info.shape_type_int, xi0, xi1, &eta0, &eta1); + + const auto num_phys0 = cell_info.num_phys[0]; + const auto num_phys1 = cell_info.num_phys[1]; + const auto z0 = cell_info.d_z[0]; + const auto z1 = cell_info.d_z[1]; + const auto bw0 = cell_info.d_bw[0]; + const auto bw1 = cell_info.d_bw[1]; + + Bary::preprocess_weights(num_phys0, eta0, z0, bw0, div_space0, + local_size); + Bary::preprocess_weights(num_phys1, eta1, z1, bw1, div_space1, + local_size); + + // Get pointer to the start of the quadrature point values for + // this cell + const auto physvals = + &k_global_physvals[cell_info.phys_offset * num_functions]; + + Bary::compute_dir_10_interlaced( + num_functions, num_phys0, num_phys1, physvals, div_space0, + div_space1, evaluations, local_size); + + for (std::size_t fx = 0; fx < num_functions; fx++) { + auto ptr = k_syms_ptrs[fx]; + auto component = k_components[fx]; + ptr[cell][component][layer] = evaluations[fx]; + } + } + }); + })); + } + const auto nphys = this->max_num_phys; + const auto npart = particle_group->get_npart_local(); + const auto nflop_prepare = this->ndim * nphys * 5; + const auto nflop_loop = nphys * nphys * 3; + pr.num_flops = (nflop_loop + nflop_prepare) * npart; + es.wait(); + pr.end(); + this->sycl_target->profile_map.add_region(pr); + } + public: /// Disable (implicit) copies. BaryEvaluateBase(const BaryEvaluateBase &st) = delete; @@ -72,7 +314,7 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { CellIDTranslationSharedPtr cell_id_translation) : ndim(mesh->get_ndim()), field(field), mesh(mesh), sycl_target(cell_id_translation->sycl_target), - dh_global_physvals(sycl_target, 1) { + d_global_physvals(sycl_target, 1) { // build the map from geometry ids to expansion ids std::map geom_to_exp; @@ -158,119 +400,38 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { * output. * @param global_physvals Field values at quadrature points to evaluate. */ - template + template inline void evaluate(ParticleGroupSharedPtr particle_group, Sym sym, - const int component, const V &global_physvals) { - - // copy the quadrature point values over to the device - const int num_global_physvals = global_physvals.size(); - const int device_phys_vals_size = pad_to_vector_length(num_global_physvals); - this->dh_global_physvals.realloc_no_copy(device_phys_vals_size); - for (int px = 0; px < num_global_physvals; px++) { - this->dh_global_physvals.h_buffer.ptr[px] = global_physvals[px]; - } - for (int px = num_global_physvals; px < device_phys_vals_size; px++) { - this->dh_global_physvals.h_buffer.ptr[px] = 0.0; + const int component, + Array &global_physvals) { + if (this->ndim == 2) { + return this->evaluate_inner_2d(particle_group, sym, component, + global_physvals); + } else { + NESOASSERT(false, "Error not implemented"); } - this->dh_global_physvals.host_to_device(); - const auto k_global_physvals = this->dh_global_physvals.d_buffer.ptr; - - // output and particle position dats - auto k_output = (*particle_group)[sym]->cell_dat.device_ptr(); - const auto k_ref_positions = - (*particle_group)[Sym("NESO_REFERENCE_POSITIONS")] - ->cell_dat.device_ptr(); - const int k_component = component; - - // values required to evaluate the field - auto k_cell_info = this->d_cell_info->ptr; - - // iteration set specification for the particle loop - auto mpi_rank_dat = particle_group->mpi_rank_dat; - ParticleLoopImplementation::ParticleLoopBlockIterationSet ish{mpi_rank_dat}; - const std::size_t local_size = - this->sycl_target->parameters - ->template get("LOOP_LOCAL_SIZE") - ->value; - const std::size_t local_num_reals = - static_cast(this->ndim * this->max_num_phys); - const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); - - EventStack es; - auto is = ish.get_all_cells(local_size, num_bytes_local); - - ProfileRegion pr("BaryEvaluateBase", "evaluate_2d"); - for (auto &blockx : is) { - const auto block_device = blockx.block_device; - const std::size_t local_size = blockx.local_size; - es.push(sycl_target->queue.submit([&](sycl::handler &cgh) { - // Allocate local memory to compute the divides. - sycl::local_accessor local_mem( - sycl::range<1>(local_num_reals * local_size), cgh); + } - auto lambda_inner = [=](auto idx_local, auto cell, auto layer) { - // offset by the local index for the striding to work - REAL *div_space0 = &local_mem[idx_local]; - const auto cell_info = k_cell_info[cell]; - - const REAL xi0 = k_ref_positions[cell][0][layer]; - const REAL xi1 = k_ref_positions[cell][1][layer]; - // If this cell is a triangle then we need to map to the - // collapsed coordinates. - REAL coord0, coord1; - - GeometryInterface::loc_coord_to_loc_collapsed_2d( - cell_info.shape_type_int, xi0, xi1, &coord0, &coord1); - - const auto num_phys0 = cell_info.num_phys[0]; - const auto num_phys1 = cell_info.num_phys[1]; - const auto z0 = cell_info.d_z[0]; - const auto z1 = cell_info.d_z[1]; - const auto bw0 = cell_info.d_bw[0]; - const auto bw1 = cell_info.d_bw[1]; - - // Get pointer to the start of the quadrature point values for - // this cell - const auto physvals = &k_global_physvals[cell_info.phys_offset]; - - const REAL evaluation = - Bary::evaluate_2d(coord0, coord1, num_phys0, num_phys1, physvals, - div_space0, z0, z1, bw0, bw1, local_size); - - k_output[cell][k_component][layer] = evaluation; - }; - - if (blockx.layer_bounds_check_required) { - cgh.parallel_for<>( - blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { - const int idx_local = idx.get_local_id(1); - std::size_t cell; - std::size_t layer; - block_device.get_cell_layer(idx, &cell, &layer); - if (block_device.work_item_required(cell, layer)) { - lambda_inner(idx_local, cell, layer); - } - }); - } else { - cgh.parallel_for<>(blockx.loop_iteration_set, - [=](sycl::nd_item<2> idx) { - const int idx_local = idx.get_local_id(1); - std::size_t cell; - std::size_t layer; - block_device.get_cell_layer(idx, &cell, &layer); - lambda_inner(idx_local, cell, layer); - }); - } - })); + /** + * Evaluate Nektar++ fields at particle locations using the provided + * quadrature point values and Bary Interpolation. + * + * @param particle_group ParticleGroup containing the particles. + * @param syms Vector of Syms in which to place evaluations. + * @param components Vector of components in which to place evaluations. + * @param global_physvals Phys values for each function to evaluate. + */ + template + inline void evaluate(ParticleGroupSharedPtr particle_group, + std::vector> syms, + const std::vector components, + std::vector> &global_physvals) { + if (this->ndim == 2) { + return this->evaluate_inner_2d(particle_group, syms, components, + global_physvals); + } else { + NESOASSERT(false, "Error not implemented"); } - const auto nphys = this->max_num_phys; - const auto npart = particle_group->get_npart_local(); - const auto nflop_prepare = this->ndim * nphys * 5; - const auto nflop_loop = nphys * nphys * 3; - pr.num_flops = (nflop_loop + nflop_prepare) * npart; - es.wait(); - pr.end(); - this->sycl_target->profile_map.add_region(pr); } }; diff --git a/include/nektar_interface/function_evaluation.hpp b/include/nektar_interface/function_evaluation.hpp index 89018ac7..85cb2337 100644 --- a/include/nektar_interface/function_evaluation.hpp +++ b/include/nektar_interface/function_evaluation.hpp @@ -93,15 +93,29 @@ template class FieldEvaluate { template inline void evaluate(Sym sym) { if (this->derivative) { + const auto ndim = this->particle_group->domain->mesh->get_ndim(); + auto global_physvals = this->field->GetPhys(); const int num_quadrature_points = this->field->GetTotPoints(); - Array d_global_physvals(num_quadrature_points); - this->field->PhysDeriv(0, global_physvals, d_global_physvals); - this->bary_evaluate_base->evaluate(this->particle_group, sym, 0, - d_global_physvals); - this->field->PhysDeriv(1, global_physvals, d_global_physvals); - this->bary_evaluate_base->evaluate(this->particle_group, sym, 1, - d_global_physvals); + + std::vector> deriv_physvals(ndim); + for (int dx = 0; dx < ndim; dx++) { + deriv_physvals.at(dx) = Array(num_quadrature_points); + } + for (int dx = 0; dx < ndim; dx++) { + this->field->PhysDeriv(dx, global_physvals, deriv_physvals.at(dx)); + } + + std::vector> syms(ndim); + std::vector components(ndim); + for (int dx = 0; dx < ndim; dx++) { + syms.at(dx) = sym; + components.at(dx) = dx; + } + + this->bary_evaluate_base->evaluate(this->particle_group, syms, components, + deriv_physvals); + } else { auto global_coeffs = this->field->GetCoeffs(); this->function_evaluate_basis->evaluate(this->particle_group, sym, 0, From a14a6d8226070292f74ff52518f8cdc658ae991d Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Thu, 7 Nov 2024 16:55:30 +0000 Subject: [PATCH 34/66] multiple function Bary evaluation passes existing derivative test --- include/nektar_interface/function_bary_evaluation.hpp | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 5e0500cf..ab0db5be 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -173,6 +173,9 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { std::is_same::value == true, "This implementation assumes that NekDouble and REAL are the same."); for (std::size_t fx = 0; fx < num_functions; fx++) { + NESOASSERT(num_physvals_per_function == global_physvals.at(fx).size(), + "Missmatch in number of physvals between functions."); + es.push(this->sycl_target->queue.memcpy( k_global_physvals + fx * num_physvals_per_function, global_physvals.at(fx).data(), @@ -269,7 +272,8 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { // Get pointer to the start of the quadrature point values for // this cell const auto physvals = - &k_global_physvals[cell_info.phys_offset * num_functions]; + &k_global_physvals_interlaced[cell_info.phys_offset * + num_functions]; Bary::compute_dir_10_interlaced( num_functions, num_phys0, num_phys1, physvals, div_space0, From c6c95b4693f149f6eb8822c9669b7c7c646f3a50 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Thu, 7 Nov 2024 18:38:19 +0000 Subject: [PATCH 35/66] fixed bad test (calling wrong function) and replaced bad nektar call (tet collapsed to local) --- .../test_particle_function_evaluation_3d.cpp | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp index 49724589..9a0e308a 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp @@ -229,6 +229,7 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, for (int ex = 0; ex < num_elts; ex++) { auto exp = field->GetExp(ex); auto geom = exp->GetGeom(); + const int shape_type_int = static_cast(geom->GetShapeType()); auto base = exp->GetBase(); const auto &z0 = base[0]->GetZ(); const auto &bw0 = base[0]->GetBaryWeights(); @@ -275,7 +276,8 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, coord[0] = x0; coord[1] = x1; coord[2] = x2; - exp->LocCollapsedToLocCoord(coord, Lcoord); + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, coord, + Lcoord); const REAL correct = exp->StdPhysEvaluate(Lcoord, physvals); const REAL to_test = Bary::evaluate_3d( x0, x1, x2, num_phys0, num_phys1, num_phys2, physvalsv.data(), @@ -305,7 +307,8 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, coord[0] = x0; coord[1] = x1; coord[2] = x2; - exp->LocCollapsedToLocCoord(coord, Lcoord); + GeometryInterface::loc_collapsed_to_loc_coord(shape_type_int, coord, + Lcoord); const REAL correct = exp->StdPhysEvaluate(Lcoord, physvals); const REAL to_test = Bary::evaluate_3d( x0, x1, x2, num_phys0, num_phys1, num_phys2, physvalsv.data(), @@ -339,17 +342,17 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, } TEST(BaryInterpolation, Evaluation3DContField) { - evaluation_wrapper_3d( + bary_wrapper_3d( "reference_all_types_cube/conditions_cg.xml", "reference_all_types_cube/mixed_ref_cube_0.5_perturbed.xml", 1.0e-7); } TEST(BaryInterpolation, Evaluation3DDisContFieldHex) { - evaluation_wrapper_3d( + bary_wrapper_3d( "reference_hex_cube/conditions.xml", "reference_hex_cube/hex_cube_0.3_perturbed.xml", 1.0e-7); } TEST(BaryInterpolation, Evaluation3DDisContFieldPrismTet) { - evaluation_wrapper_3d( + bary_wrapper_3d( "reference_prism_tet_cube/conditions.xml", "reference_prism_tet_cube/prism_tet_cube_0.5_perturbed.xml", 1.0e-7); } From cd5cf7233f718590dafbf1dc65b6f4be1df8b811 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Fri, 8 Nov 2024 16:40:00 +0000 Subject: [PATCH 36/66] Derivatives in 3D passing evaluation tests --- .../function_bary_evaluation.hpp | 301 +++++++++--------- .../nektar_interface/function_evaluation.hpp | 12 +- include/nektar_interface/utilities.hpp | 78 +++++ .../test_particle_function_evaluation_3d.cpp | 47 ++- 4 files changed, 274 insertions(+), 164 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index ab0db5be..32a9c0b3 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -52,44 +52,26 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { /// types. std::size_t max_num_phys; - template - inline void evaluate_inner_2d(ParticleGroupSharedPtr particle_group, - Sym sym, const int component, - Array &global_physvals) { - - // copy the quadrature point values over to the device - const int num_global_physvals = global_physvals.size(); - this->d_global_physvals.realloc_no_copy(num_global_physvals); - NekDouble *k_global_physvals = this->d_global_physvals.ptr; - auto copy_event = this->sycl_target->queue.memcpy( - k_global_physvals, global_physvals.data(), - num_global_physvals * sizeof(NekDouble)); - - // output and particle position dats - auto k_output = (*particle_group)[sym]->cell_dat.device_ptr(); - const auto k_ref_positions = - (*particle_group)[Sym("NESO_REFERENCE_POSITIONS")] - ->cell_dat.device_ptr(); - const int k_component = component; - - // values required to evaluate the field - auto k_cell_info = this->d_cell_info->ptr; - - // iteration set specification for the particle loop - auto mpi_rank_dat = particle_group->mpi_rank_dat; + template + static inline void + dispatch_2d(SYCLTargetSharedPtr sycl_target, EventStack &es, + const std::size_t num_functions, const int k_max_num_phys, + const NekDouble *const RESTRICT k_global_physvals_interlaced, + const CellInfo *const RESTRICT k_cell_info, + ParticleDatSharedPtr mpi_rank_dat, + ParticleDatSharedPtr ref_positions_dat, U ****k_syms_ptrs, + int *k_components) { + constexpr int ndim = 2; ParticleLoopImplementation::ParticleLoopBlockIterationSet ish{mpi_rank_dat}; const std::size_t local_size = - this->sycl_target->parameters - ->template get("LOOP_LOCAL_SIZE") + sycl_target->parameters->template get("LOOP_LOCAL_SIZE") ->value; const std::size_t local_num_reals = - static_cast(this->ndim * this->max_num_phys); + static_cast(ndim * k_max_num_phys) + num_functions; const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); - - EventStack es; auto is = ish.get_all_cells(local_size, num_bytes_local); - copy_event.wait_and_throw(); - ProfileRegion pr("BaryEvaluateBase", "evaluate_2d"); + const auto k_ref_positions = ref_positions_dat->cell_dat.device_ptr(); + for (auto &blockx : is) { const auto block_device = blockx.block_device; const std::size_t local_size = blockx.local_size; @@ -106,7 +88,11 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { block_device.get_cell_layer(idx, &cell, &layer); if (block_device.work_item_required(cell, layer)) { // offset by the local index for the striding to work - REAL *div_space0 = &local_mem[idx_local]; + REAL *evaluations = &local_mem[0] + idx_local * num_functions; + REAL *div_start = &local_mem[local_size * num_functions]; + REAL *div_space0 = div_start + idx_local; + REAL *div_space1 = div_space0 + k_max_num_phys * local_size; + const auto cell_info = k_cell_info[cell]; const REAL xi0 = k_ref_positions[cell][0][layer]; @@ -125,106 +111,52 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { const auto bw0 = cell_info.d_bw[0]; const auto bw1 = cell_info.d_bw[1]; + Bary::preprocess_weights(num_phys0, eta0, z0, bw0, div_space0, + local_size); + Bary::preprocess_weights(num_phys1, eta1, z1, bw1, div_space1, + local_size); + // Get pointer to the start of the quadrature point values for // this cell - const auto physvals = &k_global_physvals[cell_info.phys_offset]; + const auto physvals = + &k_global_physvals_interlaced[cell_info.phys_offset * + num_functions]; - const REAL evaluation = Bary::evaluate_2d( - eta0, eta1, num_phys0, num_phys1, physvals, div_space0, z0, - z1, bw0, bw1, local_size); + Bary::compute_dir_10_interlaced( + num_functions, num_phys0, num_phys1, physvals, div_space0, + div_space1, evaluations, local_size); - k_output[cell][k_component][layer] = evaluation; + for (std::size_t fx = 0; fx < num_functions; fx++) { + auto ptr = k_syms_ptrs[fx]; + auto component = k_components[fx]; + ptr[cell][component][layer] = evaluations[fx]; + } } }); })); } - const auto nphys = this->max_num_phys; - const auto npart = particle_group->get_npart_local(); - const auto nflop_prepare = this->ndim * nphys * 5; - const auto nflop_loop = nphys * nphys * 3; - pr.num_flops = (nflop_loop + nflop_prepare) * npart; - es.wait(); - pr.end(); - this->sycl_target->profile_map.add_region(pr); } template - inline void - evaluate_inner_2d(ParticleGroupSharedPtr particle_group, - std::vector> syms, const std::vector components, - std::vector> &global_physvals) { - - EventStack es; - NESOASSERT(syms.size() == components.size(), "Input size missmatch"); - NESOASSERT(global_physvals.size() == components.size(), - "Input size missmatch"); - const std::size_t num_functions = static_cast(syms.size()); - const std::size_t num_physvals_per_function = global_physvals.at(0).size(); - - // copy the quadrature point values over to the device - const std::size_t num_global_physvals = - syms.size() * global_physvals.at(0).size(); - this->d_global_physvals.realloc_no_copy(2 * num_global_physvals); - NekDouble *k_global_physvals = this->d_global_physvals.ptr; - NekDouble *k_global_physvals_interlaced = - k_global_physvals + num_global_physvals; - - static_assert( - std::is_same::value == true, - "This implementation assumes that NekDouble and REAL are the same."); - for (std::size_t fx = 0; fx < num_functions; fx++) { - NESOASSERT(num_physvals_per_function == global_physvals.at(fx).size(), - "Missmatch in number of physvals between functions."); - - es.push(this->sycl_target->queue.memcpy( - k_global_physvals + fx * num_physvals_per_function, - global_physvals.at(fx).data(), - num_physvals_per_function * sizeof(NekDouble))); - } - // wait for the copies - es.wait(); - - // interlaced the values for the bary evaluation function - matrix_transpose(this->sycl_target, num_functions, - num_physvals_per_function, k_global_physvals, - k_global_physvals_interlaced) - .wait_and_throw(); - - std::vector h_sym_ptrs(num_functions); - for (std::size_t fx = 0; fx < num_functions; fx++) { - h_sym_ptrs.at(fx) = - particle_group->get_dat(syms.at(fx))->cell_dat.device_ptr(); - } - - BufferDevice d_syms_ptrs(this->sycl_target, h_sym_ptrs); - BufferDevice d_components(this->sycl_target, components); - U ****k_syms_ptrs = d_syms_ptrs.ptr; - int *k_components = d_components.ptr; - - const auto k_ref_positions = - particle_group->get_dat(Sym("NESO_REFERENCE_POSITIONS")) - ->cell_dat.device_ptr(); - - // values required to evaluate the field - auto k_cell_info = this->d_cell_info->ptr; - - // iteration set specification for the particle loop - auto mpi_rank_dat = particle_group->mpi_rank_dat; + static inline void + dispatch_3d(SYCLTargetSharedPtr sycl_target, EventStack &es, + const std::size_t num_functions, const int k_max_num_phys, + const NekDouble *const RESTRICT k_global_physvals_interlaced, + const CellInfo *const RESTRICT k_cell_info, + ParticleDatSharedPtr mpi_rank_dat, + ParticleDatSharedPtr ref_positions_dat, U ****k_syms_ptrs, + int *k_components) { + constexpr int ndim = 3; ParticleLoopImplementation::ParticleLoopBlockIterationSet ish{mpi_rank_dat}; const std::size_t local_size = - this->sycl_target->parameters - ->template get("LOOP_LOCAL_SIZE") + sycl_target->parameters->template get("LOOP_LOCAL_SIZE") ->value; const std::size_t local_num_reals = - static_cast(this->ndim * this->max_num_phys) + - num_functions; + static_cast(ndim * k_max_num_phys) + num_functions; const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); - const auto k_max_num_phys = this->max_num_phys; - auto is = ish.get_all_cells(local_size, num_bytes_local); + const auto k_ref_positions = ref_positions_dat->cell_dat.device_ptr(); - ProfileRegion pr("BaryEvaluateBase", - "evaluate_2d_" + std::to_string(num_functions)); for (auto &blockx : is) { const auto block_device = blockx.block_device; const std::size_t local_size = blockx.local_size; @@ -245,29 +177,35 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { REAL *div_start = &local_mem[local_size * num_functions]; REAL *div_space0 = div_start + idx_local; REAL *div_space1 = div_space0 + k_max_num_phys * local_size; + REAL *div_space2 = div_space1 + k_max_num_phys * local_size; const auto cell_info = k_cell_info[cell]; const REAL xi0 = k_ref_positions[cell][0][layer]; const REAL xi1 = k_ref_positions[cell][1][layer]; - // If this cell is a triangle then we need to map to the - // collapsed coordinates. - REAL eta0, eta1; + const REAL xi2 = k_ref_positions[cell][2][layer]; + REAL eta0, eta1, eta2; - GeometryInterface::loc_coord_to_loc_collapsed_2d( - cell_info.shape_type_int, xi0, xi1, &eta0, &eta1); + GeometryInterface::loc_coord_to_loc_collapsed_3d( + cell_info.shape_type_int, xi0, xi1, xi2, &eta0, &eta1, + &eta2); const auto num_phys0 = cell_info.num_phys[0]; const auto num_phys1 = cell_info.num_phys[1]; + const auto num_phys2 = cell_info.num_phys[2]; const auto z0 = cell_info.d_z[0]; const auto z1 = cell_info.d_z[1]; + const auto z2 = cell_info.d_z[2]; const auto bw0 = cell_info.d_bw[0]; const auto bw1 = cell_info.d_bw[1]; + const auto bw2 = cell_info.d_bw[2]; Bary::preprocess_weights(num_phys0, eta0, z0, bw0, div_space0, local_size); Bary::preprocess_weights(num_phys1, eta1, z1, bw1, div_space1, local_size); + Bary::preprocess_weights(num_phys2, eta2, z2, bw2, div_space2, + local_size); // Get pointer to the start of the quadrature point values for // this cell @@ -275,9 +213,10 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { &k_global_physvals_interlaced[cell_info.phys_offset * num_functions]; - Bary::compute_dir_10_interlaced( - num_functions, num_phys0, num_phys1, physvals, div_space0, - div_space1, evaluations, local_size); + Bary::compute_dir_210_interlaced( + num_functions, num_phys0, num_phys1, num_phys2, physvals, + div_space0, div_space1, div_space2, evaluations, + local_size); for (std::size_t fx = 0; fx < num_functions; fx++) { auto ptr = k_syms_ptrs[fx]; @@ -288,11 +227,93 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { }); })); } + } + + template + inline void + evaluate_inner(ParticleGroupSharedPtr particle_group, + std::vector> syms, const std::vector components, + std::vector *> &global_physvals) { + + EventStack es; + NESOASSERT(syms.size() == components.size(), "Input size missmatch"); + NESOASSERT(global_physvals.size() == components.size(), + "Input size missmatch"); + const std::size_t num_functions = static_cast(syms.size()); + const std::size_t num_physvals_per_function = global_physvals.at(0)->size(); + + // copy the quadrature point values over to the device + const std::size_t num_global_physvals = + num_functions * num_physvals_per_function; + + const std::size_t factor = (num_functions > 1) ? 2 : 1; + this->d_global_physvals.realloc_no_copy(factor * num_global_physvals); + NekDouble *k_global_physvals = this->d_global_physvals.ptr; + NekDouble *k_global_physvals_interlaced = + (num_functions > 1) ? k_global_physvals + num_global_physvals + : k_global_physvals; + + static_assert( + std::is_same::value == true, + "This implementation assumes that NekDouble and REAL are the same."); + for (std::size_t fx = 0; fx < num_functions; fx++) { + NESOASSERT(num_physvals_per_function == global_physvals.at(fx)->size(), + "Missmatch in number of physvals between functions."); + + es.push(this->sycl_target->queue.memcpy( + k_global_physvals + fx * num_physvals_per_function, + global_physvals.at(fx)->data(), + num_physvals_per_function * sizeof(NekDouble))); + } + // wait for the copies + es.wait(); + + // interlaced the values for the bary evaluation function + if (num_functions > 1) { + matrix_transpose(this->sycl_target, num_functions, + num_physvals_per_function, k_global_physvals, + k_global_physvals_interlaced) + .wait_and_throw(); + } + + std::vector h_sym_ptrs(num_functions); + for (std::size_t fx = 0; fx < num_functions; fx++) { + h_sym_ptrs.at(fx) = + particle_group->get_dat(syms.at(fx))->cell_dat.device_ptr(); + } + BufferDevice d_syms_ptrs(this->sycl_target, h_sym_ptrs); + BufferDevice d_components(this->sycl_target, components); + + ProfileRegion pr("BaryEvaluateBase", "evaluate_" + + std::to_string(this->ndim) + "d_" + + std::to_string(num_functions)); + + if (this->ndim == 2) { + this->dispatch_2d( + this->sycl_target, es, num_functions, this->max_num_phys, + k_global_physvals_interlaced, this->d_cell_info->ptr, + particle_group->mpi_rank_dat, + particle_group->get_dat(Sym("NESO_REFERENCE_POSITIONS")), + d_syms_ptrs.ptr, d_components.ptr); + } else { + this->dispatch_3d( + this->sycl_target, es, num_functions, this->max_num_phys, + k_global_physvals_interlaced, this->d_cell_info->ptr, + particle_group->mpi_rank_dat, + particle_group->get_dat(Sym("NESO_REFERENCE_POSITIONS")), + d_syms_ptrs.ptr, d_components.ptr); + } + const auto nphys = this->max_num_phys; const auto npart = particle_group->get_npart_local(); const auto nflop_prepare = this->ndim * nphys * 5; - const auto nflop_loop = nphys * nphys * 3; + const auto nflop_loop = (this->ndim == 2) + ? nphys * nphys * 3 + : nphys * nphys + nphys * nphys * nphys * 3; pr.num_flops = (nflop_loop + nflop_prepare) * npart; + pr.num_bytes = sizeof(REAL) * (npart * ((this->ndim + num_functions)) + + num_global_physvals); + // wait for the loop to complete es.wait(); pr.end(); this->sycl_target->profile_map.add_region(pr); @@ -394,28 +415,6 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { this->sycl_target, v_cell_info); } - /** - * Evaluate a Nektar++ field at particle locations using the provided - * quadrature point values and Bary Interpolation. - * - * @param particle_group ParticleGroup containing the particles. - * @param sym Symbol that corresponds to a ParticleDat in the ParticleGroup. - * @param component Component in the ParticleDat in which to place the - * output. - * @param global_physvals Field values at quadrature points to evaluate. - */ - template - inline void evaluate(ParticleGroupSharedPtr particle_group, Sym sym, - const int component, - Array &global_physvals) { - if (this->ndim == 2) { - return this->evaluate_inner_2d(particle_group, sym, component, - global_physvals); - } else { - NESOASSERT(false, "Error not implemented"); - } - } - /** * Evaluate Nektar++ fields at particle locations using the provided * quadrature point values and Bary Interpolation. @@ -429,12 +428,12 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { inline void evaluate(ParticleGroupSharedPtr particle_group, std::vector> syms, const std::vector components, - std::vector> &global_physvals) { - if (this->ndim == 2) { - return this->evaluate_inner_2d(particle_group, syms, components, - global_physvals); + std::vector *> &global_physvals) { + if ((this->ndim == 2) || (this->ndim == 3)) { + return this->evaluate_inner(particle_group, syms, components, + global_physvals); } else { - NESOASSERT(false, "Error not implemented"); + NESOASSERT(false, "Not implemented in this number of dimensions."); } } }; diff --git a/include/nektar_interface/function_evaluation.hpp b/include/nektar_interface/function_evaluation.hpp index 85cb2337..49a75415 100644 --- a/include/nektar_interface/function_evaluation.hpp +++ b/include/nektar_interface/function_evaluation.hpp @@ -66,8 +66,9 @@ template class FieldEvaluate { auto particle_mesh_interface = std::dynamic_pointer_cast( particle_group->domain->mesh); - NESOASSERT(particle_mesh_interface->ndim == 2, - "Derivative evaluation supported in 2D only."); + NESOASSERT((particle_mesh_interface->ndim == 2) || + (particle_mesh_interface->ndim == 3), + "Derivative evaluation supported in 2D and 3D only."); this->bary_evaluate_base = std::make_shared>( field, particle_mesh_interface, cell_id_translation); } else { @@ -94,6 +95,9 @@ template class FieldEvaluate { if (this->derivative) { const auto ndim = this->particle_group->domain->mesh->get_ndim(); + const auto ncomp = this->particle_group->get_dat(sym)->ncomp; + NESOASSERT(ncomp >= ndim, "Output ParticleDat does not have a sufficient " + "number of components."); auto global_physvals = this->field->GetPhys(); const int num_quadrature_points = this->field->GetTotPoints(); @@ -108,13 +112,15 @@ template class FieldEvaluate { std::vector> syms(ndim); std::vector components(ndim); + std::vector *> deriv_physvals_ptrs(ndim); for (int dx = 0; dx < ndim; dx++) { syms.at(dx) = sym; components.at(dx) = dx; + deriv_physvals_ptrs.at(dx) = &deriv_physvals.at(dx); } this->bary_evaluate_base->evaluate(this->particle_group, syms, components, - deriv_physvals); + deriv_physvals_ptrs); } else { auto global_coeffs = this->field->GetCoeffs(); diff --git a/include/nektar_interface/utilities.hpp b/include/nektar_interface/utilities.hpp index 8bc2ac7e..5f5109d6 100644 --- a/include/nektar_interface/utilities.hpp +++ b/include/nektar_interface/utilities.hpp @@ -271,6 +271,84 @@ inline double evaluate_scalar_derivative_2d(std::shared_ptr field, return eval; } +/** + * Evaluate the derivative of scalar valued Nektar++ function at a point. + * Avoids assertion issue. + * + * @param field Nektar++ field. + * @param x X coordinate. + * @param y Y coordinate. + * @param z Z coordinate. + * @param direction Direction for derivative. + * @param element_id Optionally specifiy the element ID for the expansion. + * @returns Output du/d(direction). + */ +template +inline double evaluate_scalar_derivative_3d( + std::shared_ptr field, const double x, const double y, const double z, + const int direction, std::optional element_id = std::nullopt) { + Array xi(3); + Array coords(3); + + coords[0] = x; + coords[1] = y; + coords[2] = z; + int elmtIdx; + + if (element_id == std::nullopt) { + elmtIdx = field->GetExpIndex(coords, xi); + } else { + elmtIdx = element_id.value(); + field->GetExp(elmtIdx)->GetGeom()->GetLocCoords(coords, xi); + } + + auto elmtPhys = field->GetPhys() + field->GetPhys_Offset(elmtIdx); + auto expansion = field->GetExp(elmtIdx); + + const int num_quadrature_points = expansion->GetTotPoints(); + auto du = Array(num_quadrature_points); + + expansion->PhysDeriv(direction, elmtPhys, du); + + const double eval = expansion->StdPhysEvaluate(xi, du); + return eval; +} + +/** + * Evaluate the derivative of scalar valued Nektar++ function at a point. + * Avoids assertion issue. Uses local coordinates. + * + * @param field Nektar++ field. + * @param xi0 X local coordinate. + * @param xi1 Y local coordinate. + * @param xi2 Z local coordinate. + * @param direction Direction for derivative. + * @param element_id Specifiy the element ID for the expansion. + * @returns Output du/d(direction). + */ +template +inline double +evaluate_scalar_derivative_local_3d(std::shared_ptr field, const double xi0, + const double xi1, const double xi2, + const int direction, const int element_id) { + + Array xi(3); + xi[0] = xi0; + xi[1] = xi1; + xi[2] = xi2; + + auto elmtPhys = field->GetPhys() + field->GetPhys_Offset(element_id); + auto expansion = field->GetExp(element_id); + + const int num_quadrature_points = expansion->GetTotPoints(); + auto du = Array(num_quadrature_points); + + expansion->PhysDeriv(direction, elmtPhys, du); + + const double eval = expansion->StdPhysEvaluate(xi, du); + return eval; +} + /** * Globally find the nektar++ geometry object that owns a point. * diff --git a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp index 9a0e308a..b1bca673 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp @@ -72,6 +72,7 @@ static inline void evaluation_wrapper_3d(std::string condtions_file_s, ParticleSpec particle_spec{ParticleProp(Sym("P"), ndim, true), ParticleProp(Sym("CELL_ID"), 1, true), ParticleProp(Sym("E"), 1), + ParticleProp(Sym("DEDX"), ndim), ParticleProp(Sym("ID"), 1)}; auto A = std::make_shared(domain, particle_spec, sycl_target); @@ -120,38 +121,64 @@ static inline void evaluation_wrapper_3d(std::string condtions_file_s, (z - 1.0), 4); }; + interpolate_onto_nektar_field_3d(lambda_f, field); NESOCellsToNektarExp map_cells_to_exp(field, cell_id_translation); auto field_evaluate = std::make_shared>( field, A, cell_id_translation); field_evaluate->evaluate(Sym("E")); + auto field_deriv_evaluate = std::make_shared>( + field, A, cell_id_translation, true); + field_deriv_evaluate->evaluate(Sym("DEDX")); - Array local_coord(3); - + Array xi(3); for (int cellx = 0; cellx < cell_count; cellx++) { auto cell_ids = A->cell_id_dat->cell_dat.get_cell(cellx); auto reference_positions = - (*A)[Sym("NESO_REFERENCE_POSITIONS")]->cell_dat.get_cell(cellx); - auto E = (*A)[Sym("E")]->cell_dat.get_cell(cellx); + A->get_cell(Sym("NESO_REFERENCE_POSITIONS"), cellx); + auto E = A->get_cell(Sym("E"), cellx); + auto DEDX = A->get_cell(Sym("DEDX"), cellx); + auto P = A->get_cell(Sym("P"), cellx); const int exp_id = map_cells_to_exp.get_exp_id(cellx); const auto exp = map_cells_to_exp.get_exp(cellx); const auto exp_phys = field->GetPhys() + field->GetPhys_Offset(exp_id); + auto geom = field->GetExp(exp_id)->GetGeom(); for (int rowx = 0; rowx < cell_ids->nrow; rowx++) { + xi[0] = reference_positions->at(rowx, 0); + xi[1] = reference_positions->at(rowx, 1); + xi[2] = reference_positions->at(rowx, 2); - local_coord[0] = (*reference_positions)[0][rowx]; - local_coord[1] = (*reference_positions)[1][rowx]; - local_coord[2] = (*reference_positions)[2][rowx]; - - const REAL to_test = (*E)[0][rowx]; - const REAL correct = exp->StdPhysEvaluate(local_coord, exp_phys); + // Test the scalar function evaluation + const REAL to_test = E->at(rowx, 0); + const REAL correct = exp->StdPhysEvaluate(xi, exp_phys); const double err = relative_error(correct, to_test); const double err_abs = std::abs(correct - to_test); EXPECT_TRUE(err < tol || err_abs < tol); + + // Test the derivative evaluation + for (int dx = 0; dx < ndim; dx++) { + Array eta(3); + field->GetExp(exp_id)->LocCoordToLocCollapsed(xi, eta); + REAL eta0, eta1, eta2; + GeometryInterface::loc_coord_to_loc_collapsed_3d( + geom->GetShapeType(), xi[0], xi[1], xi[2], &eta0, &eta1, &eta2); + + EXPECT_NEAR(eta[0], eta0, 1.0e-14); + EXPECT_NEAR(eta[1], eta1, 1.0e-14); + EXPECT_NEAR(eta[2], eta2, 1.0e-14); + + const auto correctm = evaluate_scalar_derivative_local_3d( + field, xi[0], xi[1], xi[2], dx, exp_id); + const auto to_test = DEDX->at(rowx, dx); + const double err = relative_error(correctm, to_test); + const double err_abs = std::abs(correctm - to_test); + EXPECT_TRUE(err < tol || err_abs < tol); + } } } From 7ac67034de31ef9eb90e2648abaa9ca7db5fbfa8 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 11 Nov 2024 12:09:58 +0000 Subject: [PATCH 37/66] updated NP submodule commit --- neso-particles | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/neso-particles b/neso-particles index e32da6ce..2f097290 160000 --- a/neso-particles +++ b/neso-particles @@ -1 +1 @@ -Subproject commit e32da6ceb0e454489ab9172d1c23aba142700ff8 +Subproject commit 2f097290a46ba8fb4b76579bf8edd8970d55998f From 70a25fad419c936f15de2157316ce0ea2bc7f716 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 11 Nov 2024 13:57:05 +0000 Subject: [PATCH 38/66] added 3D test mesh of order 2 --- .../mixed_ref_cube_0.5_perturbed_order_2.xml | 4771 +++++++++++++++++ ..._particle_geometry_interface_3d_curved.cpp | 64 +- 2 files changed, 4777 insertions(+), 58 deletions(-) create mode 100644 test/test_resources/reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml diff --git a/test/test_resources/reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml b/test/test_resources/reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml new file mode 100644 index 00000000..8219335a --- /dev/null +++ b/test/test_resources/reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml @@ -0,0 +1,4771 @@ + + + + + -1.00000000e+00 -1.00000000e+00 -1.00000000e+00 + -5.00000000e-01 -1.00000000e+00 -1.00000000e+00 + -5.00000000e-01 -5.00000000e-01 -1.00000000e+00 + -1.00000000e+00 -5.00000000e-01 -1.00000000e+00 + -1.00000000e+00 -1.00000000e+00 -8.00000000e-01 + -5.00000000e-01 -1.00000000e+00 -8.00000000e-01 + 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F[1,6,39,43,69,73,99,103,542,409,548,387,128,497,418,309,323,401,330,361,350,370,569,601,604,611,654,660,696,702,738,744,1174,780,1178,1135,1041,1026,1199,957,968,1221,972,1003,996,1012,1060,1035,1240,1245,1274,1278,1300,1304,1326,1330] + F[123,126,93,96,63,66,31,35,545,412,546,384,133,500,422,312,326,393,333,364,347,367,572,600,774,779,730,735,688,693,645,651,1177,785,1180,1133,1050,1029,1145,1202,964,1222,975,1006,993,1009,1057,1039,1347,1350,1321,1324,1295,1298,1267,1271] + F[100,104,108,111,115,118,122,125,549,406,544,390,558,300,415,320,340,395,578,588,353,593,505,494,741,747,752,757,762,767,772,777,1179,868,1176,951,1047,1023,1140,1193,981,1219,989,1210,999,1015,1053,1037,1327,1331,1334,1337,1340,1343,1346,1349] + F[32,36,23,27,14,18,4,9,543,381,547,403,303,217,420,316,336,399,343,377,357,373,584,597,642,648,630,636,618,624,607,614,1175,950,1181,1191,1019,1044,1142,961,978,1128,985,1209,1214,1217,1062,1032,1268,1272,1260,1264,1252,1256,1243,1248] + F[0,11,20,29,38,47,54,61,68,77,84,91,98,107,114,121] + F[1249,1257,1265,1273,1281,1287,1293,1299,1307,1313,1319,1325,1333,1339,1345,1351] + A[32-229,310-507] + P[230-245,508-523] + R[246-309] + + + C[1,601-603] + + + + + L0211-XU + 5.3.0 + 07-Nov-2023 15:14:09 + + -v mixed_ref_cube_0.5_perturbed_order_2.msh mixed_ref_cube_0.5_perturbed_order_2.tmp.xml:xml:uncompress + + diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index a656e834..e6c272bb 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -1,68 +1,19 @@ -#include "nektar_interface/coordinate_mapping.hpp" -#include "nektar_interface/geometry_transport/halo_extension.hpp" -#include "nektar_interface/particle_interface.hpp" -#include "nektar_interface/utility_mesh_plotting.hpp" -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include - -using namespace std; -using namespace Nektar; -using namespace Nektar::SolverUtils; -using namespace Nektar::LibUtilities; -using namespace Nektar::SpatialDomains; -using namespace NESO::Particles; - -static inline void copy_to_cstring(std::string input, char **output) { - *output = new char[input.length() + 1]; - std::strcpy(*output, input.c_str()); -} +#include "test_helper_utilities.hpp" TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { int size, rank; MPI_Comm_size(MPI_COMM_WORLD, &size); MPI_Comm_rank(MPI_COMM_WORLD, &rank); - - LibUtilities::SessionReaderSharedPtr session; - SpatialDomains::MeshGraphSharedPtr graph; - - int argc = 3; - char *argv[3]; - copy_to_cstring(std::string("test_particle_geometry_interface"), &argv[0]); - - std::filesystem::path source_file = __FILE__; - std::filesystem::path source_dir = source_file.parent_path(); - std::filesystem::path test_resources_dir = - source_dir / "../../test_resources"; - std::filesystem::path conditions_file = - test_resources_dir / "reference_all_types_cube/conditions.xml"; - copy_to_cstring(std::string(conditions_file), &argv[1]); - // std::filesystem::path mesh_file = - // test_resources_dir / "reference_all_types_cube/mixed_ref_cube_0.2.xml"; - - std::filesystem::path mesh_file = - "/home/js0259/git-ukaea/NESO-workspace/reference_all_types_cube/" - "mixed_ref_cube_0.5_perturbed_order_2.xml"; - copy_to_cstring(std::string(mesh_file), &argv[2]); + TestUtilities::TestResourceSession resource_session( + "reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml", + "reference_all_types_cube/conditions.xml"); // Create session reader. - session = LibUtilities::SessionReader::CreateInstance(argc, argv); + auto session = resource_session.session; // Create MeshGraph. - graph = SpatialDomains::MeshGraph::Read(session); + auto graph = SpatialDomains::MeshGraph::Read(session); // build map from owned mesh hierarchy cells to geoms that touch that cell auto mesh = std::make_shared(graph); @@ -225,7 +176,4 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { } mesh->free(); - delete[] argv[0]; - delete[] argv[1]; - delete[] argv[2]; } From 109ccbbb080747e4a92a8d434835693e3aea1e4a Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 12 Nov 2024 12:31:00 +0000 Subject: [PATCH 39/66] added curved 3d particle mapper and integration test --- .../geometry_container_3d.hpp | 32 +- .../map_particles_3d.hpp | 20 +- .../map_particles_newton.hpp | 299 +++++++++--------- .../newton_generic_3d.hpp | 1 - .../particle_cell_mapping_common.hpp | 11 + .../map_particles_2d.cpp | 5 +- .../map_particles_3d.cpp | 70 +++- .../test_particle_advection.cpp | 149 +++------ .../test_helper_utilities.hpp | 37 ++- 9 files changed, 350 insertions(+), 274 deletions(-) diff --git a/include/nektar_interface/geometry_transport/geometry_container_3d.hpp b/include/nektar_interface/geometry_transport/geometry_container_3d.hpp index 9a404391..3b36eb9f 100644 --- a/include/nektar_interface/geometry_transport/geometry_container_3d.hpp +++ b/include/nektar_interface/geometry_transport/geometry_container_3d.hpp @@ -27,16 +27,15 @@ namespace NESO { class GeometryContainer3D { protected: inline GeometryTypes3D &classify(std::shared_ptr &geom) { - auto g_type = geom->GetMetricInfo()->GetGtype(); if (g_type == eRegular) { return this->regular; } else { - const std::map expected_num_verts{ - {{eTetrahedron, 4}, {ePyramid, 5}, {ePrism, 6}, {eHexahedron, 8}}}; - const int linear_num_verts = expected_num_verts.at(geom->GetShapeType()); - const int num_verts = geom->GetNumVerts(); - if (num_verts == linear_num_verts) { + auto xmap = geom->GetXmap(); + const bool linear = (xmap->GetBasisNumModes(0) == 2) && + (xmap->GetBasisNumModes(1) == 2) && + (xmap->GetBasisNumModes(2) == 2); + if (linear) { return this->deformed_linear; } else { return this->deformed_non_linear; @@ -70,6 +69,27 @@ class GeometryContainer3D { auto &container = this->classify(geom->geom); container.push_back(geom); } + + /** + * Print information about the number of contained geometry objects. + */ + inline void print() { + nprint("Num regular :", regular.size()); + nprint("\tTetrahedrons:", regular.tet.size()); + nprint("\tPyramid :", regular.pyr.size()); + nprint("\tPrism :", regular.prism.size()); + nprint("\tHexahedrons :", regular.hex.size()); + nprint("Num deformed linear :", deformed_linear.size()); + nprint("\tTetrahedrons:", deformed_linear.tet.size()); + nprint("\tPyramid :", deformed_linear.pyr.size()); + nprint("\tPrism :", deformed_linear.prism.size()); + nprint("\tHexahedrons :", deformed_linear.hex.size()); + nprint("Num deformed non-linear:", deformed_non_linear.size()); + nprint("\tTetrahedrons:", deformed_non_linear.tet.size()); + nprint("\tPyramid :", deformed_non_linear.pyr.size()); + nprint("\tPrism :", deformed_non_linear.prism.size()); + nprint("\tHexahedrons :", deformed_non_linear.hex.size()); + } }; } // namespace NESO diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_3d.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_3d.hpp index 2c9c0a36..e71e1cf1 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_3d.hpp @@ -52,12 +52,24 @@ class MapParticles3D { std::unique_ptr>> map_particles_3d_deformed_linear; + std::unique_ptr> + map_particles_3d_deformed_non_linear; + + template + inline void map_newton_initial(std::unique_ptr &ptr, + ParticleGroup &particle_group, + const int map_cell) { + if (ptr) { + ptr->map_initial(particle_group, map_cell); + } + } + template - inline void map_newton_internal(std::unique_ptr &ptr, - ParticleGroup &particle_group, - const int map_cell) { + inline void map_newton_final(std::unique_ptr &ptr, + ParticleGroup &particle_group, + const int map_cell) { if (ptr) { - ptr->map(particle_group, map_cell); + ptr->map_final(particle_group, map_cell); } } diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp index 9ed10d63..69981c7e 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp @@ -91,7 +91,146 @@ class MapParticlesNewton : public CoarseMappersBase { return this->newton_type.data_size_local(h_data_ptr); } - inline void map_inital(ParticleGroup &particle_group, const int map_cell) { +public: + ~MapParticlesNewton() { + for (int index = 0; index < num_geoms; index++) { + auto h_data_ptr = + (this->num_bytes_per_map_host) + ? this->h_data.data() + index * this->num_bytes_per_map_host + : nullptr; + this->newton_type.free_data(h_data_ptr); + } + } + + /** + * Create new Newton implementation templated on a X(xi) map type and a + * geometry type. + * + * @param newton_type Sub-class of MappingNewtonIterationBase that defines + * the X(xi) map. + * @param sycl_target SYCLTarget That defines where to perform Newton + * iteration. + * @param geoms_local Map of local Nektar++ geometry objects to which + * newton_type is applicable. + * @param geoms_remote Vector of remote Nektar++ geometry objects to which + * newton_type is applicable. + * @param config ParameterStore instance to configure exit tolerance and + * iteration counts. + */ + template + MapParticlesNewton( + MappingNewtonIterationBase newton_type, + SYCLTargetSharedPtr sycl_target, + std::map> &geoms_local, + std::vector> &geoms_remote, + ParameterStoreSharedPtr config = std::make_shared()) + : CoarseMappersBase(sycl_target), newton_type(newton_type), + num_bytes_per_map_device(newton_type.data_size_device()), + num_bytes_per_map_host(newton_type.data_size_host()), + ndim(newton_type.get_ndim()) { + + this->newton_tol = + config->get("MapParticlesNewton/newton_tol", 1.0e-8); + this->newton_max_iteration = + config->get("MapParticlesNewton/newton_max_iteration", 51); + this->contained_tol = + config->get("MapParticlesNewton/contained_tol", this->newton_tol); + const int num_modes_factor = + config->get("MapParticlesNewton/num_modes_factor", 1); + + this->num_geoms = geoms_local.size() + geoms_remote.size(); + if (this->num_geoms > 0) { + + // create the coarse lookup mesh + this->coarse_lookup_map = std::make_unique( + this->ndim, this->sycl_target, geoms_local, geoms_remote); + + // store the information required to evaluate v_GetLocCoords for regular + // Geometry3D objects. + // map from cartesian cells to nektar mesh cells + std::map>> geom_map; + this->dh_cell_ids = + std::make_unique>(this->sycl_target, num_geoms); + this->dh_mpi_ranks = + std::make_unique>(this->sycl_target, num_geoms); + this->dh_type = + std::make_unique>(this->sycl_target, num_geoms); + + if (this->num_bytes_per_map_device) { + this->dh_data = std::make_unique>( + this->sycl_target, num_geoms * this->num_bytes_per_map_device); + } + if (this->num_bytes_per_map_host) { + this->h_data = + std::vector(num_geoms * this->num_bytes_per_map_host); + } + + const int index_tri = shape_type_to_int(eTriangle); + const int index_quad = shape_type_to_int(eQuadrilateral); + const int index_tet = shape_type_to_int(eTetrahedron); + const int index_pyr = shape_type_to_int(ePyramid); + const int index_prism = shape_type_to_int(ePrism); + const int index_hex = shape_type_to_int(eHexahedron); + + const int rank = this->sycl_target->comm_pair.rank_parent; + + int num_modes = 0; + this->num_bytes_local_memory = 0; + auto lambda_update_local_memory = [&](const std::size_t s) { + this->num_bytes_local_memory = + std::max(this->num_bytes_local_memory, s); + }; + for (auto &geom : geoms_local) { + const int id = geom.second->GetGlobalID(); + const int cell_index = this->coarse_lookup_map->gid_to_lookup_id.at(id); + NESOASSERT((cell_index < num_geoms) && (0 <= cell_index), + "Bad cell index from map."); + NESOASSERT(id == geom.first, "ID mismatch"); + + this->dh_cell_ids->h_buffer.ptr[cell_index] = id; + this->dh_mpi_ranks->h_buffer.ptr[cell_index] = rank; + const int geom_type = shape_type_to_int(geom.second->GetShapeType()); + NESOASSERT((geom_type == index_tet) || (geom_type == index_pyr) || + (geom_type == index_prism) || (geom_type == index_hex) || + (geom_type == index_tri) || (geom_type == index_quad), + "Unknown shape type."); + this->dh_type->h_buffer.ptr[cell_index] = geom_type; + lambda_update_local_memory(this->write_data(geom.second, cell_index)); + num_modes = + std::max(num_modes, geom.second->GetXmap()->EvalBasisNumModesMax()); + } + + for (auto &geom : geoms_remote) { + const int id = geom->id; + const int cell_index = this->coarse_lookup_map->gid_to_lookup_id.at(id); + NESOASSERT((cell_index < num_geoms) && (0 <= cell_index), + "Bad cell index from map."); + this->dh_cell_ids->h_buffer.ptr[cell_index] = id; + this->dh_mpi_ranks->h_buffer.ptr[cell_index] = geom->rank; + const int geom_type = shape_type_to_int(geom->geom->GetShapeType()); + NESOASSERT((geom_type == index_tet) || (geom_type == index_pyr) || + (geom_type == index_prism) || (geom_type == index_hex) || + (geom_type == index_tri) || (geom_type == index_quad), + "Unknown shape type."); + this->dh_type->h_buffer.ptr[cell_index] = geom_type; + lambda_update_local_memory(this->write_data(geom->geom, cell_index)); + num_modes = + std::max(num_modes, geom->geom->GetXmap()->EvalBasisNumModesMax()); + } + + this->grid_size = num_modes * num_modes_factor; + this->dh_cell_ids->host_to_device(); + this->dh_mpi_ranks->host_to_device(); + this->dh_type->host_to_device(); + this->dh_data->host_to_device(); + } + } + + /** + * Called internally by NESO to map positions to Nektar++ + * Geometry objects via Newton iteration. + */ + inline void map_initial(ParticleGroup &particle_group, const int map_cell) { if (this->num_geoms == 0) { return; @@ -214,6 +353,7 @@ class MapParticlesNewton : public CoarseMappersBase { const bool contained = clamped_residual <= k_newton_tol; cell_found = contained && converged; + if (cell_found) { const int geom_id = k_map_cell_ids[geom_map_index]; const int mpi_rank = k_map_mpi_ranks[geom_map_index]; @@ -237,6 +377,10 @@ class MapParticlesNewton : public CoarseMappersBase { } } + /** + * Called internally by NESO to map positions to Nektar++ + * Geometry objects via Newton iteration. + */ inline void map_final(ParticleGroup &particle_group, const int map_cell) { if (this->num_geoms == 0) { return; @@ -276,7 +420,7 @@ class MapParticlesNewton : public CoarseMappersBase { particle_group.get_dat(Sym("NESO_REFERENCE_POSITIONS")); auto local_memory = LocalMemoryBlock(this->num_bytes_local_memory); - particle_loop( + auto loop = particle_loop( "MapParticlesNewton::map_final", position_dat, [=](auto k_part_positions, auto k_part_cell_ids, auto k_part_mpi_ranks, auto k_part_ref_positions, auto k_local_memory) { @@ -390,153 +534,12 @@ class MapParticlesNewton : public CoarseMappersBase { }, Access::read(position_dat), Access::write(cell_ids), Access::write(mpi_ranks), Access::write(ref_positions), - Access::write(local_memory)) - ->execute(map_cell); - } - -public: - ~MapParticlesNewton() { - for (int index = 0; index < num_geoms; index++) { - auto h_data_ptr = - (this->num_bytes_per_map_host) - ? this->h_data.data() + index * this->num_bytes_per_map_host - : nullptr; - this->newton_type.free_data(h_data_ptr); - } - } - - /** - * Create new Newton implementation templated on a X(xi) map type and a - * geometry type. - * - * @param newton_type Sub-class of MappingNewtonIterationBase that defines - * the X(xi) map. - * @param sycl_target SYCLTarget That defines where to perform Newton - * iteration. - * @param geoms_local Map of local Nektar++ geometry objects to which - * newton_type is applicable. - * @param geoms_remote Vector of remote Nektar++ geometry objects to which - * newton_type is applicable. - * @param config ParameterStore instance to configure exit tolerance and - * iteration counts. - */ - template - MapParticlesNewton( - MappingNewtonIterationBase newton_type, - SYCLTargetSharedPtr sycl_target, - std::map> &geoms_local, - std::vector> &geoms_remote, - ParameterStoreSharedPtr config = std::make_shared()) - : CoarseMappersBase(sycl_target), newton_type(newton_type), - num_bytes_per_map_device(newton_type.data_size_device()), - num_bytes_per_map_host(newton_type.data_size_host()), - ndim(newton_type.get_ndim()) { - - this->newton_tol = - config->get("MapParticlesNewton/newton_tol", 1.0e-8); - this->newton_max_iteration = - config->get("MapParticlesNewton/newton_max_iteration", 51); - this->contained_tol = - config->get("MapParticlesNewton/contained_tol", this->newton_tol); - const int num_modes_factor = - config->get("MapParticlesNewton/num_modes_factor", 1); - - this->num_geoms = geoms_local.size() + geoms_remote.size(); - if (this->num_geoms > 0) { - - // create the coarse lookup mesh - this->coarse_lookup_map = std::make_unique( - this->ndim, this->sycl_target, geoms_local, geoms_remote); - - // store the information required to evaluate v_GetLocCoords for regular - // Geometry3D objects. - // map from cartesian cells to nektar mesh cells - std::map>> geom_map; - this->dh_cell_ids = - std::make_unique>(this->sycl_target, num_geoms); - this->dh_mpi_ranks = - std::make_unique>(this->sycl_target, num_geoms); - this->dh_type = - std::make_unique>(this->sycl_target, num_geoms); - - if (this->num_bytes_per_map_device) { - this->dh_data = std::make_unique>( - this->sycl_target, num_geoms * this->num_bytes_per_map_device); - } - if (this->num_bytes_per_map_host) { - this->h_data = - std::vector(num_geoms * this->num_bytes_per_map_host); - } - - const int index_tri = shape_type_to_int(eTriangle); - const int index_quad = shape_type_to_int(eQuadrilateral); - const int index_tet = shape_type_to_int(eTetrahedron); - const int index_pyr = shape_type_to_int(ePyramid); - const int index_prism = shape_type_to_int(ePrism); - const int index_hex = shape_type_to_int(eHexahedron); - - const int rank = this->sycl_target->comm_pair.rank_parent; - - int num_modes = 0; - this->num_bytes_local_memory = 0; - auto lambda_update_local_memory = [&](const std::size_t s) { - this->num_bytes_local_memory = - std::max(this->num_bytes_local_memory, s); - }; - for (auto &geom : geoms_local) { - const int id = geom.second->GetGlobalID(); - const int cell_index = this->coarse_lookup_map->gid_to_lookup_id.at(id); - NESOASSERT((cell_index < num_geoms) && (0 <= cell_index), - "Bad cell index from map."); - NESOASSERT(id == geom.first, "ID mismatch"); - - this->dh_cell_ids->h_buffer.ptr[cell_index] = id; - this->dh_mpi_ranks->h_buffer.ptr[cell_index] = rank; - const int geom_type = shape_type_to_int(geom.second->GetShapeType()); - NESOASSERT((geom_type == index_tet) || (geom_type == index_pyr) || - (geom_type == index_prism) || (geom_type == index_hex) || - (geom_type == index_tri) || (geom_type == index_quad), - "Unknown shape type."); - this->dh_type->h_buffer.ptr[cell_index] = geom_type; - lambda_update_local_memory(this->write_data(geom.second, cell_index)); - num_modes = - std::max(num_modes, geom.second->GetXmap()->EvalBasisNumModesMax()); - } - - for (auto &geom : geoms_remote) { - const int id = geom->id; - const int cell_index = this->coarse_lookup_map->gid_to_lookup_id.at(id); - NESOASSERT((cell_index < num_geoms) && (0 <= cell_index), - "Bad cell index from map."); - this->dh_cell_ids->h_buffer.ptr[cell_index] = id; - this->dh_mpi_ranks->h_buffer.ptr[cell_index] = geom->rank; - const int geom_type = shape_type_to_int(geom->geom->GetShapeType()); - NESOASSERT((geom_type == index_tet) || (geom_type == index_pyr) || - (geom_type == index_prism) || (geom_type == index_hex) || - (geom_type == index_tri) || (geom_type == index_quad), - "Unknown shape type."); - this->dh_type->h_buffer.ptr[cell_index] = geom_type; - lambda_update_local_memory(this->write_data(geom->geom, cell_index)); - num_modes = - std::max(num_modes, geom->geom->GetXmap()->EvalBasisNumModesMax()); - } - - this->grid_size = num_modes * num_modes_factor; - this->dh_cell_ids->host_to_device(); - this->dh_mpi_ranks->host_to_device(); - this->dh_type->host_to_device(); - this->dh_data->host_to_device(); - } - } + Access::write(local_memory)); - /** - * Called internally by NESO-Particles to map positions to Nektar++ - * Geometry objects via Newton iteration. - */ - inline void map(ParticleGroup &particle_group, const int map_cell = -1) { - this->map_inital(particle_group, map_cell); - if (map_cell != -1) { - this->map_final(particle_group, map_cell); + if (map_cell > -1) { + loop->execute(map_cell); + } else { + loop->execute(); } } }; diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index 808f5f93..2b95fd2e 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -256,7 +256,6 @@ struct MappingGeneric3D : MappingNewtonIterationBase { const REAL norm2 = MAX(MAX(ABS(*f0), ABS(*f1)), ABS(*f2)); const REAL tol_scaling = d->tol_scaling; const REAL scaled_norm2 = norm2 * tol_scaling; - return scaled_norm2; } diff --git a/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp b/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp index 0620f83c..4045c973 100644 --- a/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp +++ b/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp @@ -172,6 +172,17 @@ inline bool contains_point_3d(std::shared_ptr geom, Array &global_coord, Array &local_coord, const NekDouble tol) { bool contained = geom->ContainsPoint(global_coord, local_coord, tol); + // TODO REMOVE START + if (contained) { + Array test_coord(3); + test_coord[0] = geom->GetCoord(0, local_coord); + test_coord[1] = geom->GetCoord(1, local_coord); + test_coord[2] = geom->GetCoord(2, local_coord); + nprint("P:", global_coord[0], global_coord[1], global_coord[2], + "L:", local_coord[0], local_coord[1], local_coord[2], + "T:", test_coord[0], test_coord[1], test_coord[2]); + } + // TODO REMOVE END return contained; } diff --git a/src/nektar_interface/particle_cell_mapping/map_particles_2d.cpp b/src/nektar_interface/particle_cell_mapping/map_particles_2d.cpp index 59f22952..a15465c2 100644 --- a/src/nektar_interface/particle_cell_mapping/map_particles_2d.cpp +++ b/src/nektar_interface/particle_cell_mapping/map_particles_2d.cpp @@ -73,7 +73,10 @@ void MapParticles2D::map(ParticleGroup &particle_group, const int map_cell) { // attempt to bin the remaining particles into deformed cells if there are // deformed cells. if (particles_not_mapped) { - this->map_particles_newton_linear_quad->map(particle_group, map_cell); + this->map_particles_newton_linear_quad->map_initial(particle_group, + map_cell); + this->map_particles_newton_linear_quad->map_final(particle_group, + map_cell); } } diff --git a/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp b/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp index 7ea446d5..b79e9c5a 100644 --- a/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp +++ b/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp @@ -18,6 +18,7 @@ MapParticles3D::MapParticles3D( std::get<1>(this->map_particles_3d_deformed_linear) = nullptr; std::get<2>(this->map_particles_3d_deformed_linear) = nullptr; std::get<3>(this->map_particles_3d_deformed_linear) = nullptr; + this->map_particles_3d_deformed_non_linear = nullptr; GeometryContainer3D geometry_container_3d; assemble_geometry_container_3d(particle_mesh_interface->graph, @@ -59,13 +60,41 @@ MapParticles3D::MapParticles3D( geometry_container_3d.deformed_linear.pyr.local, geometry_container_3d.deformed_linear.pyr.remote, config); } + if (geometry_container_3d.deformed_non_linear.size()) { + + std::map> local; + std::vector> remote; + remote.reserve( + geometry_container_3d.deformed_non_linear.tet.remote.size() + + geometry_container_3d.deformed_non_linear.pyr.remote.size() + + geometry_container_3d.deformed_non_linear.prism.remote.size() + + geometry_container_3d.deformed_non_linear.hex.remote.size()); + + auto lambda_push = [&](auto &lr) -> void { + for (auto &lx : lr.local) { + local[lx.first] = lx.second; + } + for (auto &rx : lr.remote) { + remote.push_back(rx); + } + }; + lambda_push(geometry_container_3d.deformed_non_linear.tet); + lambda_push(geometry_container_3d.deformed_non_linear.pyr); + lambda_push(geometry_container_3d.deformed_non_linear.prism); + lambda_push(geometry_container_3d.deformed_non_linear.hex); + + this->map_particles_3d_deformed_non_linear = + std::make_unique>( + Newton::MappingGeneric3D{}, this->sycl_target, local, remote, + config); + } // Create a mapper for 3D deformed non-linear geometry objects // as a sycl version is not written yet we reuse the host mapper - if (geometry_container_3d.deformed_non_linear.size()) { - this->map_particles_host = std::make_unique( - sycl_target, particle_mesh_interface, config); - } + // if (geometry_container_3d.deformed_non_linear.size()) { + // this->map_particles_host = std::make_unique( + // sycl_target, particle_mesh_interface, config); + //} } void MapParticles3D::map(ParticleGroup &particle_group, const int map_cell) { @@ -75,16 +104,31 @@ void MapParticles3D::map(ParticleGroup &particle_group, const int map_cell) { this->map_particles_3d_regular->map(particle_group, map_cell); } - map_newton_internal(std::get<0>(this->map_particles_3d_deformed_linear), - particle_group, map_cell); - map_newton_internal(std::get<1>(this->map_particles_3d_deformed_linear), - particle_group, map_cell); - map_newton_internal(std::get<2>(this->map_particles_3d_deformed_linear), - particle_group, map_cell); - map_newton_internal(std::get<3>(this->map_particles_3d_deformed_linear), - particle_group, map_cell); + map_newton_initial(std::get<0>(this->map_particles_3d_deformed_linear), + particle_group, map_cell); + map_newton_initial(std::get<1>(this->map_particles_3d_deformed_linear), + particle_group, map_cell); + map_newton_initial(std::get<2>(this->map_particles_3d_deformed_linear), + particle_group, map_cell); + map_newton_initial(std::get<3>(this->map_particles_3d_deformed_linear), + particle_group, map_cell); + map_newton_initial(this->map_particles_3d_deformed_non_linear, particle_group, + map_cell); + + bool particles_not_mapped = + this->map_particles_common->check_map(particle_group, map_cell); + + map_newton_final(std::get<0>(this->map_particles_3d_deformed_linear), + particle_group, map_cell); + map_newton_final(std::get<1>(this->map_particles_3d_deformed_linear), + particle_group, map_cell); + map_newton_final(std::get<2>(this->map_particles_3d_deformed_linear), + particle_group, map_cell); + map_newton_final(std::get<3>(this->map_particles_3d_deformed_linear), + particle_group, map_cell); + map_newton_final(this->map_particles_3d_deformed_non_linear, particle_group, + map_cell); - bool particles_not_mapped = true; if (this->map_particles_host) { // are there particles whcih are not yet mapped into cells particles_not_mapped = diff --git a/test/integration/nektar_interface/test_particle_advection.cpp b/test/integration/nektar_interface/test_particle_advection.cpp index 9bc98459..2f2c9a70 100644 --- a/test/integration/nektar_interface/test_particle_advection.cpp +++ b/test/integration/nektar_interface/test_particle_advection.cpp @@ -1,51 +1,17 @@ -#include "nektar_interface/particle_interface.hpp" -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include -#include - -using namespace Nektar; -using namespace Nektar::SolverUtils; -using namespace Nektar::SpatialDomains; -using namespace NESO::Particles; - -static inline void copy_to_cstring(std::string input, char **output) { - *output = new char[input.length() + 1]; - std::strcpy(*output, input.c_str()); -} +#include "../../unit/nektar_interface/test_helper_utilities.hpp" // Test advecting particles between ranks TEST(ParticleGeometryInterface, Advection2D) { const int N_total = 1000; const double tol = 1.0e-10; - int argc = 2; - char *argv[2]; - copy_to_cstring(std::string("test_particle_geometry_interface"), &argv[0]); - - std::filesystem::path source_file = __FILE__; - std::filesystem::path source_dir = source_file.parent_path(); - std::filesystem::path test_resources_dir = - source_dir / "../../test_resources"; - std::filesystem::path mesh_file = - test_resources_dir / "square_triangles_quads.xml"; - copy_to_cstring(std::string(mesh_file), &argv[1]); - - LibUtilities::SessionReaderSharedPtr session; - SpatialDomains::MeshGraphSharedPtr graph; + + TestUtilities::TestResourceSession resource_session( + "square_triangles_quads.xml"); + // Create session reader. - session = LibUtilities::SessionReader::CreateInstance(argc, argv); - graph = SpatialDomains::MeshGraph::Read(session); + auto session = resource_session.session; + auto graph = SpatialDomains::MeshGraph::Read(session); auto mesh = std::make_shared(graph); auto sycl_target = std::make_shared(0, mesh->get_comm()); @@ -188,9 +154,6 @@ TEST(ParticleGeometryInterface, Advection2D) { } mesh->free(); - - delete[] argv[0]; - delete[] argv[1]; } class ParticleAdvection3D : public testing::TestWithParam< @@ -201,38 +164,24 @@ TEST_P(ParticleAdvection3D, Advection3D) { std::tuple param = GetParam(); - const int N_total = 1000; + const int N_total = 2000; const double tol = std::get<2>(param); - std::filesystem::path source_file = __FILE__; - std::filesystem::path source_dir = source_file.parent_path(); - std::filesystem::path test_resources_dir = - source_dir / "../../test_resources"; - - std::filesystem::path condtions_file_basename = - static_cast(std::get<0>(param)); - std::filesystem::path mesh_file_basename = - static_cast(std::get<1>(param)); - std::filesystem::path conditions_file = - test_resources_dir / condtions_file_basename; - std::filesystem::path mesh_file = test_resources_dir / mesh_file_basename; - - int argc = 3; - char *argv[3]; - copy_to_cstring(std::string("test_particle_geometry_interface"), &argv[0]); - copy_to_cstring(std::string(conditions_file), &argv[1]); - copy_to_cstring(std::string(mesh_file), &argv[2]); - - LibUtilities::SessionReaderSharedPtr session; - SpatialDomains::MeshGraphSharedPtr graph; + TestUtilities::TestResourceSession resource_session( + static_cast(std::get<1>(param)), + static_cast(std::get<0>(param))); + // Create session reader. - session = LibUtilities::SessionReader::CreateInstance(argc, argv); - graph = SpatialDomains::MeshGraph::Read(session); + auto session = resource_session.session; + auto graph = SpatialDomains::MeshGraph::Read(session); auto mesh = std::make_shared(graph); auto sycl_target = std::make_shared(0, mesh->get_comm()); auto config = std::make_shared(); + config->set("MapParticlesNewton/newton_tol", 1.0e-10); + config->set("MapParticlesNewton/contained_tol", 1.0e-10); + auto nektar_graph_local_mapper = std::make_shared(sycl_target, mesh, config); @@ -266,7 +215,7 @@ TEST_P(ParticleAdvection3D, Advection3D) { MPICHK(MPI_Allreduce(&N, &N_check, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD)); NESOASSERT(N_check == N_total, "Error creating particles"); - const int Nsteps = 2000; + const int Nsteps = 1000; const REAL dt = 0.1; const int cell_count = domain->mesh->get_cell_count(); @@ -319,7 +268,7 @@ TEST_P(ParticleAdvection3D, Advection3D) { auto lambda_check_owning_cell = [&] { Array global_coord(3); - Array local_coord(3); + Array xi(3); Array eta(3); for (int cellx = 0; cellx < cell_count; cellx++) { @@ -328,26 +277,30 @@ TEST_P(ParticleAdvection3D, Advection3D) { auto reference_positions = A->get_cell(Sym("NESO_REFERENCE_POSITIONS"), cellx); - for (int rowx = 0; rowx < cell_ids->nrow; rowx++) { + const int cell_nektar = cell_id_translation.map_to_nektar[cellx]; + auto geom = geoms_3d[cell_nektar]; + + int shape_type = geom->GetShapeType(); + Newton::XMapNewton mapper(sycl_target, geom); + for (int rowx = 0; rowx < cell_ids->nrow; rowx++) { const int cell_neso = (*cell_ids)[0][rowx]; ASSERT_EQ(cell_neso, cellx); - const int cell_nektar = cell_id_translation.map_to_nektar[cell_neso]; - auto geom = geoms_3d[cell_nektar]; - local_coord[0] = reference_positions->at(rowx, 0); - local_coord[1] = reference_positions->at(rowx, 1); - local_coord[2] = reference_positions->at(rowx, 2); - global_coord[0] = geom->GetCoord(0, local_coord); - global_coord[1] = geom->GetCoord(1, local_coord); - global_coord[2] = geom->GetCoord(2, local_coord); - geom->GetXmap()->LocCoordToLocCollapsed(local_coord, eta); + xi[0] = reference_positions->at(rowx, 0); + xi[1] = reference_positions->at(rowx, 1); + xi[2] = reference_positions->at(rowx, 2); + global_coord[0] = geom->GetCoord(0, xi); + global_coord[1] = geom->GetCoord(1, xi); + global_coord[2] = geom->GetCoord(2, xi); // check the global coordinate matches the one on the particle for (int dimx = 0; dimx < ndim; dimx++) { const double err_abs = ABS(positions->at(rowx, dimx) - global_coord[dimx]); - ASSERT_TRUE(err_abs <= tol); + const double err_rel = + err_abs > 0.0 ? err_abs / std::abs(global_coord[dimx]) : err_abs; + ASSERT_TRUE((err_abs <= tol) || (err_rel <= tol)); ASSERT_TRUE(std::fabs((double)eta[dimx]) < (1.0 + tol)); } } @@ -360,7 +313,6 @@ TEST_P(ParticleAdvection3D, Advection3D) { REAL T = 0.0; for (int stepx = 0; stepx < Nsteps; stepx++) { - pbc.execute(); mesh_hierarchy_global_map.execute(); A->hybrid_move(); @@ -375,22 +327,25 @@ TEST_P(ParticleAdvection3D, Advection3D) { // h5part.close(); mesh->free(); - - delete[] argv[0]; - delete[] argv[1]; - delete[] argv[2]; } INSTANTIATE_TEST_SUITE_P( MultipleMeshes, ParticleAdvection3D, - testing::Values(std::tuple( - "reference_all_types_cube/conditions.xml", - "reference_all_types_cube/linear_non_regular_0.5.xml", - 1.0e-4 // The non-linear exit tolerance in Nektar is - // like (err_x * err_x - // + err_y * err_y) < 1.0e-8 - ), - std::tuple( - "reference_all_types_cube/conditions.xml", - "reference_all_types_cube/mixed_ref_cube_0.5.xml", - 1.0e-10))); + testing::Values( + std::tuple( + "reference_all_types_cube/conditions.xml", + "reference_all_types_cube/linear_non_regular_0.5.xml", + 1.0e-4 // The non-linear exit tolerance in Nektar is + // like (err_x * err_x + // + err_y * err_y) < 1.0e-8 + ), + std::tuple( + "reference_all_types_cube/conditions.xml", + "reference_all_types_cube/mixed_ref_cube_0.5.xml", 1.0e-10), + std::tuple( + "reference_all_types_cube/conditions.xml", + "reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml", + 1.0e-4 // The non-linear exit tolerance in Nektar is + // like (err_x * err_x + // + err_y * err_y) < 1.0e-8 + ))); diff --git a/test/unit/nektar_interface/test_helper_utilities.hpp b/test/unit/nektar_interface/test_helper_utilities.hpp index d977f520..aa094809 100644 --- a/test/unit/nektar_interface/test_helper_utilities.hpp +++ b/test/unit/nektar_interface/test_helper_utilities.hpp @@ -40,16 +40,20 @@ namespace NESO::TestUtilities { */ class TestResourceSession { protected: - char *argv[3]; + char *argv[3]{nullptr, nullptr, nullptr}; public: /// The session created from test resources. LibUtilities::SessionReaderSharedPtr session; ~TestResourceSession() { - delete[] this->argv[0]; - delete[] this->argv[1]; - delete[] this->argv[2]; + for (int ix = 0; ix < 3; ix++) { + auto ptr = this->argv[ix]; + if (ptr != nullptr) { + delete[] ptr; + this->argv[ix] = nullptr; + } + } } /** @@ -63,12 +67,14 @@ class TestResourceSession { */ TestResourceSession(const std::string filename_mesh, const std::string filename_conditions) { + copy_to_cstring(std::string("neso_nektar_test"), &this->argv[0]); std::filesystem::path source_file = __FILE__; std::filesystem::path source_dir = source_file.parent_path(); std::filesystem::path test_resources_dir = source_dir / "../../test_resources"; + std::filesystem::path conditions_file = test_resources_dir / filename_conditions; copy_to_cstring(std::string(conditions_file), &this->argv[1]); @@ -78,6 +84,29 @@ class TestResourceSession { // Create session reader. session = LibUtilities::SessionReader::CreateInstance(3, this->argv); } + + /** + * Create a Nektar++ session from a conditions file and mesh file in the + * test_resources directory. + * + * @param filename_mesh Path relative to the test_resources directory for the + * mesh. + */ + TestResourceSession(const std::string filename_mesh) { + + copy_to_cstring(std::string("neso_nektar_test"), &this->argv[0]); + + std::filesystem::path source_file = __FILE__; + std::filesystem::path source_dir = source_file.parent_path(); + std::filesystem::path test_resources_dir = + source_dir / "../../test_resources"; + + std::filesystem::path mesh_file = test_resources_dir / filename_mesh; + copy_to_cstring(std::string(mesh_file), &this->argv[1]); + + // Create session reader. + session = LibUtilities::SessionReader::CreateInstance(2, this->argv); + } }; } // namespace NESO::TestUtilities From 35889039994d25cbd19579ec284eeabb2dd78b53 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 13 Nov 2024 16:35:44 +0000 Subject: [PATCH 40/66] added initial implementation of sycl bounding box estimator --- CMakeLists.txt | 5 + .../coarse_lookup_map.hpp | 2 +- .../map_particles_newton.hpp | 1 - .../particle_cell_mapping/x_map_newton.hpp | 167 +++++++++++++++- .../map_particles_3d.cpp | 27 ++- test/CMakeLists.txt | 8 + .../test_particle_advection.cpp | 181 +++++++++++++++++- 7 files changed, 371 insertions(+), 20 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 14ce7ae7..cfc61529 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -11,6 +11,7 @@ set(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH}) option(ENABLE_NESO_TESTS "Build unit tests for this project and register with ctest" ON) +option(ENABLE_NESO_PROFILING "Enable built in profiling" OFF) # Various sanitizers, including coverage and address sanitizer include(cmake/Sanitizers.cmake) @@ -270,6 +271,10 @@ target_link_libraries( ${NESO_LIBRARY_NAME} PUBLIC Nektar++::nektar++ fft::fft NESO-Particles::NESO-Particles PRIVATE ${TEST_LIBRARIES}) +if(ENABLE_NESO_PROFILING) + target_compile_definitions(${NESO_LIBRARY_NAME} + PUBLIC NESO_PARTICLES_PROFILING_REGION) +endif() add_sycl_to_target(TARGET ${NESO_LIBRARY_NAME} SOURCES ${LIB_SRC_FILES}) # Create executable diff --git a/include/nektar_interface/particle_cell_mapping/coarse_lookup_map.hpp b/include/nektar_interface/particle_cell_mapping/coarse_lookup_map.hpp index e46248af..a2b102ca 100644 --- a/include/nektar_interface/particle_cell_mapping/coarse_lookup_map.hpp +++ b/include/nektar_interface/particle_cell_mapping/coarse_lookup_map.hpp @@ -129,7 +129,7 @@ class CoarseLookupMap { min_extent = std::min(min_extent, dim_extent); } - const int target_cell_count = std::pow(2, ndim) * cell_count; + const int target_cell_count = std::pow(4, ndim) * cell_count; double base_extent = min_extent / 4; std::array grid_cell_counts; int grid_linear_cell_count = 1; diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp index 69981c7e..fc3818c3 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp @@ -1,6 +1,5 @@ #ifndef __MAP_PARTICLES_NEWTON_H_ #define __MAP_PARTICLES_NEWTON_H_ - #include #include #include diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 52f4a197..155c14a1 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -96,7 +96,7 @@ template class XMapNewton { num_modes_factor(num_modes_factor) { this->write_data(geom); this->dh_fdata = - std::make_unique>(this->sycl_target, 4); + std::make_unique>(this->sycl_target, 6); } /** @@ -271,6 +271,171 @@ template class XMapNewton { *xi2 = this->dh_fdata->h_buffer.ptr[2]; return (this->dh_fdata->h_buffer.ptr[3] > 0); } + + /** + * Return a Nektar++ style bounding box for the geometry object. + * + * @param grid_size Resolution of grid to use on each face of the collapsed + * reference space. Default 32. + * @returns Bounding box in format [minx, miny, minz, maxx, maxy, maxz]; + */ + std::array get_bounding_box(std::size_t grid_size = 32) { + char *k_map_data; + if (this->dh_data) { + k_map_data = this->dh_data->d_buffer.ptr; + } + NESOASSERT(this->dh_fdata != nullptr, "Bad pointer"); + auto k_fdata = this->dh_fdata->d_buffer.ptr; + NESOASSERT(k_fdata != nullptr, "Bad pointer"); + const std::size_t num_bytes_local = + std::max(this->num_bytes_local, sizeof(REAL)); + + // Get a local size which is a power of 2. + const std::size_t local_size = + get_prev_power_of_two(static_cast( + std::sqrt(this->sycl_target->get_num_local_work_items( + num_bytes_local, + sycl_target->parameters + ->template get("LOOP_LOCAL_SIZE") + ->value)))); + // make grid_size a multiple of the local size + grid_size = get_next_multiple(grid_size, local_size); + sycl::range<3> range_local(1, local_size, local_size); + const std::size_t local_size_l = local_size * local_size; + // There are 6 faces on the collapsed reference cell + sycl::range<3> range_global(6, grid_size, grid_size); + const REAL k_width = 2.0 / static_cast(grid_size - 1); + + constexpr REAL kc[6][3] = { + {-1.0, 0.0, 0.0}, // x = -1 + {1.0, 0.0, 0.0}, // x = 1 + {0.0, -1.0, 0.0}, // y = -1 + {0.0, 1.0, 0.0}, // y = 1 + {0.0, 0.0, -1.0}, // z = -1 + {0.0, 0.0, 1.0} // z = 1 + }; + + constexpr REAL kcx[6][3] = {{0.0, 1.0, 0.0}, {0.0, 1.0, 0.0}, + {0.0, 0.0, 1.0}, {0.0, 0.0, 1.0}, + {1.0, 0.0, 0.0}, {1.0, 0.0, 0.0}}; + + constexpr REAL kcy[6][3] = {{0.0, 0.0, 1.0}, {0.0, 0.0, 1.0}, + {1.0, 0.0, 0.0}, {1.0, 0.0, 0.0}, + {0.0, 1.0, 0.0}, {0.0, 1.0, 0.0}}; + + static_assert((kc[0][0] + kcx[0][0] + kcy[0][0]) == -1); + static_assert((kc[0][1] + kcx[0][1] + kcy[0][1]) == 1); + static_assert((kc[0][2] + kcx[0][2] + kcy[0][2]) == 1); + static_assert((kc[1][0] + kcx[1][0] + kcy[1][0]) == 1); + static_assert((kc[1][1] + kcx[1][1] + kcy[1][1]) == 1); + static_assert((kc[1][2] + kcx[1][2] + kcy[1][2]) == 1); + static_assert((kc[2][0] + kcx[2][0] + kcy[2][0]) == 1); + static_assert((kc[2][1] + kcx[2][1] + kcy[2][1]) == -1); + static_assert((kc[2][2] + kcx[2][2] + kcy[2][2]) == 1); + static_assert((kc[3][0] + kcx[3][0] + kcy[3][0]) == 1); + static_assert((kc[3][1] + kcx[3][1] + kcy[3][1]) == 1); + static_assert((kc[3][2] + kcx[3][2] + kcy[3][2]) == 1); + static_assert((kc[4][0] + kcx[4][0] + kcy[4][0]) == 1); + static_assert((kc[4][1] + kcx[4][1] + kcy[4][1]) == 1); + static_assert((kc[4][2] + kcx[4][2] + kcy[4][2]) == -1); + static_assert((kc[5][0] + kcx[5][0] + kcy[5][0]) == 1); + static_assert((kc[5][1] + kcx[5][1] + kcy[5][1]) == 1); + static_assert((kc[5][2] + kcx[5][2] + kcy[5][2]) == 1); + + this->dh_fdata->h_buffer.ptr[0] = std::numeric_limits::max(); + this->dh_fdata->h_buffer.ptr[1] = std::numeric_limits::max(); + this->dh_fdata->h_buffer.ptr[2] = std::numeric_limits::max(); + this->dh_fdata->h_buffer.ptr[3] = std::numeric_limits::lowest(); + this->dh_fdata->h_buffer.ptr[4] = std::numeric_limits::lowest(); + this->dh_fdata->h_buffer.ptr[5] = std::numeric_limits::lowest(); + this->dh_fdata->host_to_device(); + + this->sycl_target->queue + .submit([=](sycl::handler &cgh) { + sycl::local_accessor local_mem( + sycl::range<1>(num_bytes_local * local_size_l), cgh); + + cgh.parallel_for<>( + this->sycl_target->device_limits.validate_nd_range( + sycl::nd_range<3>(range_global, range_local)), + [=](auto idx) { + MappingNewtonIterationBase k_newton_type{}; + + const auto local_id = idx.get_local_linear_id(); + const auto iix = idx.get_global_id(2); + const auto iiy = idx.get_global_id(1); + const auto facex = idx.get_global_id(0); + const REAL gx = -1.0 + iix * k_width; + const REAL gy = -1.0 + iiy * k_width; + + const REAL eta0 = + kc[facex][0] + kcx[facex][0] * gx + kcy[facex][0] * gy; + const REAL eta1 = + kc[facex][1] + kcx[facex][1] * gx + kcy[facex][1] * gy; + const REAL eta2 = + kc[facex][2] + kcx[facex][2] * gx + kcy[facex][2] * gy; + + REAL k_xi0, k_xi1, k_xi2; + k_newton_type.loc_collapsed_to_loc_coord( + k_map_data, eta0, eta1, eta2, &k_xi0, &k_xi1, &k_xi2); + + REAL f[3] = {0.0, 0.0, 0.0}; + constexpr REAL p0 = 0.0; + constexpr REAL p1 = 0.0; + constexpr REAL p2 = 0.0; + + k_newton_type.newton_residual( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f, f + 1, + f + 2, &local_mem[local_id * num_bytes_local]); + idx.barrier(sycl::access::fence_space::local_space); + + // Do the reductions, we pessimistically do not use the builtin + // SYCL functions as we have used all the local memory already + // and the SYCL reduction functions also use local memory. + for (int dimx = 0; dimx < 3; dimx++) { + + // Tree reduce the maximum + local_mem[local_id] = f[dimx]; + for (int ix = local_size_l / 2; ix > 0; ix >>= 1) { + idx.barrier(sycl::access::fence_space::local_space); + if (local_id < ix) { + local_mem[local_id] = sycl::max(local_mem[local_id + ix], + local_mem[local_id]); + } + } + if (local_id == 0) { + sycl::atomic_ref + ar(k_fdata[dimx + 3]); + ar.fetch_max(local_mem[0]); + } + // Tree reduce the minimum + local_mem[local_id] = f[dimx]; + for (int ix = local_size_l / 2; ix > 0; ix >>= 1) { + idx.barrier(sycl::access::fence_space::local_space); + if (local_id < ix) { + local_mem[local_id] = sycl::min(local_mem[local_id + ix], + local_mem[local_id]); + } + } + if (local_id == 0) { + sycl::atomic_ref + ar(k_fdata[dimx]); + ar.fetch_min(local_mem[0]); + } + } + }); + }) + .wait_and_throw(); + + this->dh_fdata->device_to_host(); + std::array output; + for (int cx = 0; cx < 6; cx++) { + output[cx] = this->dh_fdata->h_buffer.ptr[cx]; + } + return output; + } }; } // namespace NESO::Newton diff --git a/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp b/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp index b79e9c5a..d2a3c4cb 100644 --- a/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp +++ b/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp @@ -89,12 +89,9 @@ MapParticles3D::MapParticles3D( config); } - // Create a mapper for 3D deformed non-linear geometry objects - // as a sycl version is not written yet we reuse the host mapper - // if (geometry_container_3d.deformed_non_linear.size()) { - // this->map_particles_host = std::make_unique( - // sycl_target, particle_mesh_interface, config); - //} + // Create a host mapper as a last resort mapping attempt. + this->map_particles_host = std::make_unique( + sycl_target, particle_mesh_interface, config); } void MapParticles3D::map(ParticleGroup &particle_group, const int map_cell) { @@ -129,21 +126,19 @@ void MapParticles3D::map(ParticleGroup &particle_group, const int map_cell) { map_newton_final(this->map_particles_3d_deformed_non_linear, particle_group, map_cell); - if (this->map_particles_host) { - // are there particles whcih are not yet mapped into cells + if (map_cell > -1) { + // if there are particles not yet mapped this may be an error depending on + // which stage of NESO-Particles hybrid move we are at. particles_not_mapped = this->map_particles_common->check_map(particle_group, map_cell); - // attempt to bin the remaining particles into deformed cells if there are - // deformed cells. - if (particles_not_mapped) { - this->map_particles_host->map(particle_group, map_cell); + if (this->map_particles_host && particles_not_mapped) { + auto pr = ProfileRegion("MapParticles3D", "host_backup"); + this->map_particles_host->map(particle_group, -1); + pr.end(); + this->sycl_target->profile_map.add_region(pr); } - } - if (map_cell > -1) { - // if there are particles not yet mapped this may be an error depending on - // which stage of NESO-Particles hybrid move we are at. particles_not_mapped = this->map_particles_common->check_map(particle_group, map_cell); diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 6e92cf72..8351a840 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -85,6 +85,10 @@ list(REMOVE_ITEM TEST_LIBRARIES "gcov") set(UNIT_EXE unitTests) add_executable(${UNIT_EXE} ${UNIT_SRC_FILES}) target_link_libraries(${UNIT_EXE} PRIVATE ${NESO_LIBRARY_NAME} GTest::gtest) +if(ENABLE_NESO_PROFILING) + target_compile_definitions(${UNIT_EXE} + PRIVATE NESO_PARTICLES_PROFILING_REGION) +endif() add_sycl_to_target(TARGET ${UNIT_EXE} SOURCES ${UNIT_SRC_FILES}) gtest_add_tests(TARGET ${UNIT_EXE}) @@ -100,6 +104,10 @@ target_link_libraries( PRIVATE ${NESO_LIBRARY_NAME} ${SOLVER_LIBS} ${ELECTROSTATIC_2D3V_LIBRARY_NAME} GTest::gmock_main GTest::gtest Boost::boost) +if(ENABLE_NESO_PROFILING) + target_compile_definitions(${INTEGRATION_EXE} + PRIVATE NESO_PARTICLES_PROFILING_REGION) +endif() # Define the integration test executable as a sycl target add_sycl_to_target(TARGET ${INTEGRATION_EXE} SOURCES ${TEST_MAIN} diff --git a/test/integration/nektar_interface/test_particle_advection.cpp b/test/integration/nektar_interface/test_particle_advection.cpp index 2f2c9a70..f527aef2 100644 --- a/test/integration/nektar_interface/test_particle_advection.cpp +++ b/test/integration/nektar_interface/test_particle_advection.cpp @@ -176,11 +176,14 @@ TEST_P(ParticleAdvection3D, Advection3D) { auto graph = SpatialDomains::MeshGraph::Read(session); auto mesh = std::make_shared(graph); + extend_halos_fixed_offset(1, mesh); auto sycl_target = std::make_shared(0, mesh->get_comm()); auto config = std::make_shared(); config->set("MapParticlesNewton/newton_tol", 1.0e-10); - config->set("MapParticlesNewton/contained_tol", 1.0e-10); + // There are some pyramid corners that are hard to bin into with tighter + // tolerances. + config->set("MapParticlesNewton/contained_tol", 1.0e-2); auto nektar_graph_local_mapper = std::make_shared(sycl_target, mesh, config); @@ -322,6 +325,7 @@ TEST_P(ParticleAdvection3D, Advection3D) { lambda_advect(); T += dt; + // h5part.write(); } @@ -349,3 +353,178 @@ INSTANTIATE_TEST_SUITE_P( // like (err_x * err_x // + err_y * err_y) < 1.0e-8 ))); + +// TODO REMOVE START +class FooBar : public testing::TestWithParam< + std::tuple> {}; +TEST_P(FooBar, Advection3D) { + // Test advecting particles between ranks + + std::tuple param = GetParam(); + + const int N_total = 100000; + const double tol = std::get<2>(param); + + TestUtilities::TestResourceSession resource_session( + static_cast(std::get<1>(param)), + static_cast(std::get<0>(param))); + + // Create session reader. + auto session = resource_session.session; + auto graph = SpatialDomains::MeshGraph::Read(session); + + auto mesh = std::make_shared(graph); + extend_halos_fixed_offset(1, mesh); + auto sycl_target = std::make_shared(0, mesh->get_comm()); + + auto config = std::make_shared(); + config->set("MapParticlesNewton/newton_tol", 1.0e-12); + config->set("MapParticlesNewton/contained_tol", 1.0e-2); + + auto nektar_graph_local_mapper = + std::make_shared(sycl_target, mesh, config); + + auto domain = std::make_shared(mesh, nektar_graph_local_mapper); + + const int ndim = 3; + ParticleSpec particle_spec{ParticleProp(Sym("P"), ndim, true), + ParticleProp(Sym("P_ORIG"), ndim), + ParticleProp(Sym("V"), 3), + ParticleProp(Sym("CELL_ID"), 1, true), + ParticleProp(Sym("ID"), 1)}; + + auto A = std::make_shared(domain, particle_spec, sycl_target); + + NektarCartesianPeriodic pbc(sycl_target, graph, A->position_dat); + + CellIDTranslation cell_id_translation(sycl_target, A->cell_id_dat, mesh); + + const int rank = sycl_target->comm_pair.rank_parent; + const int size = sycl_target->comm_pair.size_parent; + + std::mt19937 rng_pos(52234234 + rank); + std::mt19937 rng_vel(52234231 + rank); + std::mt19937 rng_rank(18241); + + int rstart, rend; + get_decomp_1d(size, N_total, rank, &rstart, &rend); + const int N = rend - rstart; + + int N_check = -1; + MPICHK(MPI_Allreduce(&N, &N_check, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD)); + NESOASSERT(N_check == N_total, "Error creating particles"); + + const int Nsteps = 20; + const REAL dt = 0.1; + const int cell_count = domain->mesh->get_cell_count(); + + if (N > 0) { + auto positions = + uniform_within_extents(N, ndim, pbc.global_extent, rng_pos); + auto velocities = + NESO::Particles::normal_distribution(N, 3, 0.0, 0.5, rng_vel); + std::uniform_int_distribution uniform_dist( + 0, sycl_target->comm_pair.size_parent - 1); + ParticleSet initial_distribution(N, A->get_particle_spec()); + for (int px = 0; px < N; px++) { + for (int dimx = 0; dimx < ndim; dimx++) { + const double pos_orig = positions[dimx][px] + pbc.global_origin[dimx]; + initial_distribution[Sym("P")][px][dimx] = pos_orig; + initial_distribution[Sym("P_ORIG")][px][dimx] = pos_orig; + } + for (int dimx = 0; dimx < 3; dimx++) { + initial_distribution[Sym("V")][px][dimx] = velocities[dimx][px]; + } + initial_distribution[Sym("CELL_ID")][px][0] = 0; + initial_distribution[Sym("ID")][px][0] = px; + const auto px_rank = uniform_dist(rng_rank); + initial_distribution[Sym("NESO_MPI_RANK")][px][0] = px_rank; + } + A->add_particles_local(initial_distribution); + } + reset_mpi_ranks((*A)[Sym("NESO_MPI_RANK")]); + + MeshHierarchyGlobalMap mesh_hierarchy_global_map( + sycl_target, domain->mesh, A->position_dat, A->cell_id_dat, + A->mpi_rank_dat); + + auto lambda_advect = [&] { + auto t0 = profile_timestamp(); + particle_loop( + A, + [=](auto P, auto V) { + for (int dimx = 0; dimx < ndim; dimx++) { + P.at(dimx) += dt * V.at(dimx); + } + }, + Access::write(Sym("P")), Access::read(Sym("V"))) + ->execute(); + sycl_target->profile_map.inc("Advect", "Execute", 1, + profile_elapsed(t0, profile_timestamp())); + }; + + H5Part h5part("trajectory.h5part", A, Sym("P"), + Sym("NESO_MPI_RANK"), + Sym("NESO_REFERENCE_POSITIONS")); + + write_vtk_cells_owned("owned_cells", mesh); + + for (int stepx = 0; stepx < 2; stepx++) { + pbc.execute(); + mesh_hierarchy_global_map.execute(); + A->hybrid_move(); + cell_id_translation.execute(); + A->cell_move(); + lambda_advect(); + h5part.write(); + h5part.close(); + } + sycl_target->profile_map.enable(); + sycl_target->profile_map.reset(); + auto t0 = profile_timestamp(); + REAL T = 0.0; + for (int stepx = 0; stepx < Nsteps; stepx++) { + pbc.execute(); + mesh_hierarchy_global_map.execute(); + A->hybrid_move(); + cell_id_translation.execute(); + A->cell_move(); + + lambda_advect(); + T += dt; + + auto tt = profile_elapsed(t0, profile_timestamp()); + + if (!rank) { + nprint(stepx, tt / (((stepx + 1)) * N_total)); + } + // h5part.write(); + } + sycl_target->profile_map.write_events_json("newton_test_events", rank); + + // h5part.close(); + mesh->free(); +} + +INSTANTIATE_TEST_SUITE_P( + MultipleMeshes, FooBar, + testing::Values( + std::tuple( + "reference_all_types_cube/conditions.xml", + "reference_all_types_cube/linear_non_regular_0.5.xml", + 1.0e-4 // The non-linear exit tolerance in Nektar is + // like (err_x * err_x + // + err_y * err_y) < 1.0e-8 + ), + std::tuple( + "reference_all_types_cube/conditions.xml", + "reference_all_types_cube/mixed_ref_cube_0.5.xml", 1.0e-10), + std::tuple( + "reference_all_types_cube/conditions.xml", + "reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml", + 1.0e-4 // The non-linear exit tolerance in Nektar is + // like (err_x * err_x + // + err_y * err_y) < 1.0e-8 + ))); + +// TODO REMOVE END From 6836d0f258201669939890de2c25e1d42bab87d7 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Fri, 15 Nov 2024 16:46:01 +0000 Subject: [PATCH 41/66] added utility function to create curved HexGeoms on the fly for testing --- .../map_particles_newton.hpp | 11 +- .../particle_cell_mapping/x_map_newton.hpp | 11 +- .../test_helper_utilities.hpp | 2 + ..._particle_geometry_interface_3d_curved.cpp | 417 ++++++++++++++++++ 4 files changed, 433 insertions(+), 8 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp index fc3818c3..77a99da1 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp @@ -134,8 +134,12 @@ class MapParticlesNewton : public CoarseMappersBase { config->get("MapParticlesNewton/newton_max_iteration", 51); this->contained_tol = config->get("MapParticlesNewton/contained_tol", this->newton_tol); - const int num_modes_factor = + const REAL num_modes_factor = config->get("MapParticlesNewton/num_modes_factor", 1); + const auto grid_size_min = + config->get("MapParticlesNewton/grid_size_min", 2); + const auto grid_size_max = + config->get("MapParticlesNewton/grid_size_min", 4); this->num_geoms = geoms_local.size() + geoms_remote.size(); if (this->num_geoms > 0) { @@ -217,7 +221,10 @@ class MapParticlesNewton : public CoarseMappersBase { std::max(num_modes, geom->geom->GetXmap()->EvalBasisNumModesMax()); } - this->grid_size = num_modes * num_modes_factor; + this->grid_size = + std::min(std::max(static_cast(num_modes * num_modes_factor), + static_cast(grid_size_min)), + static_cast(grid_size_max)); this->dh_cell_ids->host_to_device(); this->dh_mpi_ranks->host_to_device(); this->dh_type->host_to_device(); diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 155c14a1..a6bb838b 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -342,12 +342,11 @@ template class XMapNewton { static_assert((kc[5][1] + kcx[5][1] + kcy[5][1]) == 1); static_assert((kc[5][2] + kcx[5][2] + kcy[5][2]) == 1); - this->dh_fdata->h_buffer.ptr[0] = std::numeric_limits::max(); - this->dh_fdata->h_buffer.ptr[1] = std::numeric_limits::max(); - this->dh_fdata->h_buffer.ptr[2] = std::numeric_limits::max(); - this->dh_fdata->h_buffer.ptr[3] = std::numeric_limits::lowest(); - this->dh_fdata->h_buffer.ptr[4] = std::numeric_limits::lowest(); - this->dh_fdata->h_buffer.ptr[5] = std::numeric_limits::lowest(); + for (int dx = 0; dx < 3; dx++) { + this->dh_fdata->h_buffer.ptr[dx] = std::numeric_limits::max(); + this->dh_fdata->h_buffer.ptr[dx + 3] = + std::numeric_limits::lowest(); + } this->dh_fdata->host_to_device(); this->sycl_target->queue diff --git a/test/unit/nektar_interface/test_helper_utilities.hpp b/test/unit/nektar_interface/test_helper_utilities.hpp index aa094809..f482a801 100644 --- a/test/unit/nektar_interface/test_helper_utilities.hpp +++ b/test/unit/nektar_interface/test_helper_utilities.hpp @@ -6,6 +6,8 @@ #include "nektar_interface/utilities.hpp" #include "nektar_interface/utility_mesh_plotting.hpp" #include +#include +#include #include #include #include diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index e6c272bb..5f4a133e 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -175,5 +175,422 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { } } + sycl_target->free(); mesh->free(); } + +template +inline std::shared_ptr make_hex_geom(const int num_modes, T xmapx, + U xmapy, V xmapz) { + + /** + * Vertices: + * + * 7 - 6 + * | | + * 4 - 5 + * + * 3 - 2 + * | | + * 0 - 1 + * + * Edges: + * + * * 10 * + * 11 9 + * * 8 * + * + * 7 - 6 + * | | + * 4 - 5 + * + * * 2 * + * 3 1 + * * 0 * + * + * Faces: + * + * * - * + * | 5 | + * * - * + * + * * 3 * + * 4 2 + * * 1 * + * + * * - * + * | 0 | + * * - * + * + * auto pts = LibUtilities::PointsManager()[*points_key]; + * Triangle is something like trievenlyspaced + * quad will x fastest then y + * Triangles are not the expansion looping ordering - look at nektmesh + * top eta0, eta1, eta2=0 + * eta0 eta1 + * + * make meshgraph, meshgraphio. view -> adavnced "nonlinear subdivisions + * (slider)" + */ + + REAL coords_vertices[8][3] = {{-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, + {1.0, 1.0, -1.0}, {-1.0, 1.0, -1.0}, + {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, + {1.0, 1.0, 1.0}, {-1.0, 1.0, 1.0}}; + + int map_edge_to_vertices[12][2] = { + {0, 1}, {1, 2}, {2, 3}, {3, 0}, + + {0, 4}, {1, 5}, {2, 6}, {3, 7}, + + {4, 5}, {5, 6}, {6, 7}, {7, 4}, + }; + + int map_face_to_edges[6][4] = { + {0, 1, 2, 3}, {0, 5, 8, 4}, {1, 6, 9, 5}, + {2, 7, 10, 6}, {3, 4, 11, 7}, {8, 9, 10, 11}, + }; + + int map_face_to_vertices[6][4] = {{0, 1, 2, 3}, {0, 1, 4, 5}, {1, 2, 6, 5}, + {2, 3, 7, 6}, {1, 3, 7, 4}, {4, 5, 6, 7}}; + + auto points_key = PointsKey(num_modes, ePolyEvenlySpaced); + auto control_points = std::make_shared(points_key); + control_points->Initialize(); + auto Z = control_points->GetZ(); + std::vector Znormalised(Z.size()); + for (int ix = 0; ix < num_modes; ix++) { + Znormalised.at(ix) = (Z[ix] + 1.0) / 2.0; + } + + std::map> v; + std::map> e; + std::map> c; + std::map> q; + + // Create the vertices + int vx_index = 0; + int cx_index = 0; + for (int vx = 0; vx < 8; vx++) { + const REAL px = xmapx(coords_vertices[vx]); + const REAL py = xmapy(coords_vertices[vx]); + const REAL pz = xmapz(coords_vertices[vx]); + v[vx] = std::make_shared(3, vx_index++, px, py, pz); + } + + // Create the edges + auto lambda_get_1D_qpoint = [&](const int point_id, const auto a, + const auto b) -> std::array { + NekDouble ax, ay, az, bx, by, bz; + ax = a[0]; + ay = a[1]; + az = a[2]; + bx = b[0]; + by = b[1]; + bz = b[2]; + const NekDouble dx = bx - ax; + const NekDouble dy = by - ay; + const NekDouble dz = bz - az; + + std::array out; + out[0] = ax + Znormalised[point_id] * dx; + out[1] = ay + Znormalised[point_id] * dy; + out[2] = az + Znormalised[point_id] * dz; + return out; + }; + + for (int ex = 0; ex < 12; ex++) { + auto cx = std::make_shared(cx_index++, ePolyEvenlySpaced); + + for (int mx = 0; mx < num_modes; mx++) { + auto ref_coord = + lambda_get_1D_qpoint(mx, coords_vertices[map_edge_to_vertices[ex][0]], + coords_vertices[map_edge_to_vertices[ex][1]]); + const REAL px = xmapx(ref_coord); + const REAL py = xmapy(ref_coord); + const REAL pz = xmapz(ref_coord); + cx->m_points.push_back( + std::make_shared(3, vx_index++, px, py, pz)); + } + std::shared_ptr vertices_array[2] = { + v.at(map_edge_to_vertices[ex][0]), v.at(map_edge_to_vertices[ex][1])}; + c[ex] = cx; + e[ex] = std::make_shared(ex, 3, vertices_array, cx); + e[ex]->GetGeomFactors(); + e[ex]->Setup(); + } + + // Create the faces + auto lambda_get_2D_qpoint = [&](const int point_id0, const int point_id1, + const auto a, const auto b, + const auto c) -> std::array { + /** + * c + * | + * a - b + */ + + NekDouble ax, ay, az, bx, by, bz, cx, cy, cz; + ax = a[0]; + ay = a[1]; + az = a[2]; + bx = b[0]; + by = b[1]; + bz = b[2]; + cx = c[0]; + cy = c[1]; + cz = c[2]; + const NekDouble d0x = bx - ax; + const NekDouble d0y = by - ay; + const NekDouble d0z = bz - az; + const NekDouble d1x = cx - ax; + const NekDouble d1y = cy - ay; + const NekDouble d1z = cz - az; + + std::array out; + out[0] = ax + Znormalised[point_id0] * d0x + Znormalised[point_id1] * d1x; + out[1] = ay + Znormalised[point_id0] * d0y + Znormalised[point_id1] * d1y; + out[2] = az + Znormalised[point_id0] * d0z + Znormalised[point_id1] * d1z; + return out; + }; + + for (int fx = 0; fx < 6; fx++) { + std::shared_ptr vertices_array[4] = { + v.at(map_face_to_vertices[fx][0]), v.at(map_face_to_vertices[fx][1]), + v.at(map_face_to_vertices[fx][2]), v.at(map_face_to_vertices[fx][3])}; + + auto cx = std::make_shared(cx_index++, ePolyEvenlySpaced); + for (int mx = 0; mx < num_modes; mx++) { + for (int my = 0; my < num_modes; my++) { + auto ref_coord = lambda_get_2D_qpoint( + mx, my, coords_vertices[map_face_to_vertices[fx][0]], + coords_vertices[map_face_to_vertices[fx][1]], + coords_vertices[map_face_to_vertices[fx][3]]); + const REAL px = xmapx(ref_coord); + const REAL py = xmapy(ref_coord); + const REAL pz = xmapz(ref_coord); + cx->m_points.push_back( + std::make_shared(3, vx_index++, px, py, pz)); + } + } + + std::shared_ptr edges_array[4] = { + e.at(map_face_to_edges[fx][0]), e.at(map_face_to_edges[fx][1]), + e.at(map_face_to_edges[fx][2]), e.at(map_face_to_edges[fx][3])}; + q[fx] = std::make_shared(fx, edges_array, cx); + q[fx]->GetGeomFactors(); + q[fx]->Setup(); + } + + std::shared_ptr quads[6] = {q[0], q[1], q[2], q[3], q[4], q[5]}; + + auto hex = std::make_shared(0, quads); + hex->GetGeomFactors(); + hex->Setup(); + + return hex; +} + +TEST(ParticleGeometryInterfaceCurved, MakeCurvedHex) { + + auto lambda_check = [&](auto correct, auto to_test) { + const auto err_abs = std::abs(correct - to_test); + const auto err_rel = + std::abs(correct) > 0.0 ? err_abs / std::abs(correct) : err_abs; + const REAL tol = 1.0e-10; + ASSERT_TRUE(err_abs < tol || err_rel < tol); + }; + + { + auto xmapx = [&](auto eta) { return eta[0] * 2.0; }; + auto xmapy = [&](auto eta) { return eta[1] * 3.0; }; + auto xmapz = [&](auto eta) { return eta[2] * 5.0; }; + + const int num_modes = 3; + auto h = make_hex_geom(num_modes, xmapx, xmapy, xmapz); + + auto points_key = PointsKey(num_modes, ePolyEvenlySpaced); + auto control_points = std::make_shared(points_key); + control_points->Initialize(); + auto Z = control_points->GetZ(); + + Array lcoords(3); + for (int iz = 0; iz < num_modes; iz++) { + for (int iy = 0; iy < num_modes; iy++) { + for (int ix = 0; ix < num_modes; ix++) { + lcoords[0] = Z[ix]; + lcoords[1] = Z[iy]; + lcoords[2] = Z[iz]; + + auto x0 = h->GetCoord(0, lcoords); + auto x1 = h->GetCoord(1, lcoords); + auto x2 = h->GetCoord(2, lcoords); + auto c0 = xmapx(lcoords); + auto c1 = xmapy(lcoords); + auto c2 = xmapz(lcoords); + lambda_check(c0, x0); + lambda_check(c1, x1); + lambda_check(c2, x2); + } + } + } + } + + { + auto xmapx = [&](auto eta) { return eta[0] * 2.0 + 7.0; }; + auto xmapy = [&](auto eta) { return eta[1] * 3.0 + 9.0; }; + auto xmapz = [&](auto eta) { return eta[2] * 5.0 + 11.0; }; + + const int num_modes = 3; + auto h = make_hex_geom(num_modes, xmapx, xmapy, xmapz); + + auto points_key = PointsKey(num_modes, ePolyEvenlySpaced); + auto control_points = std::make_shared(points_key); + control_points->Initialize(); + auto Z = control_points->GetZ(); + + Array lcoords(3); + for (int iz = 0; iz < num_modes; iz++) { + for (int iy = 0; iy < num_modes; iy++) { + for (int ix = 0; ix < num_modes; ix++) { + lcoords[0] = Z[ix]; + lcoords[1] = Z[iy]; + lcoords[2] = Z[iz]; + + auto x0 = h->GetCoord(0, lcoords); + auto x1 = h->GetCoord(1, lcoords); + auto x2 = h->GetCoord(2, lcoords); + auto c0 = xmapx(lcoords); + auto c1 = xmapy(lcoords); + auto c2 = xmapz(lcoords); + lambda_check(c0, x0); + lambda_check(c1, x1); + lambda_check(c2, x2); + } + } + } + } + + { + auto xmapx = [&](auto eta) { return eta[0]; }; + auto xmapy = [&](auto eta) { return eta[1]; }; + auto xmapz = [&](auto eta) { + return eta[2] + 0.2 * eta[0] * eta[0] + 0.2 * eta[1] * eta[1]; + }; + + const int num_modes = 3; + auto h = make_hex_geom(num_modes, xmapx, xmapy, xmapz); + + auto points_key = PointsKey(num_modes, ePolyEvenlySpaced); + auto control_points = std::make_shared(points_key); + control_points->Initialize(); + auto Z = control_points->GetZ(); + + Array lcoords(3); + for (int iz = 0; iz < num_modes; iz++) { + for (int iy = 0; iy < num_modes; iy++) { + for (int ix = 0; ix < num_modes; ix++) { + lcoords[0] = Z[ix]; + lcoords[1] = Z[iy]; + lcoords[2] = Z[iz]; + + auto x0 = h->GetCoord(0, lcoords); + auto x1 = h->GetCoord(1, lcoords); + auto x2 = h->GetCoord(2, lcoords); + auto c0 = xmapx(lcoords); + auto c1 = xmapy(lcoords); + auto c2 = xmapz(lcoords); + lambda_check(c0, x0); + lambda_check(c1, x1); + lambda_check(c2, x2); + } + } + } + } + + { + auto xmapx = [&](auto eta) { return eta[0]; }; + auto xmapy = [&](auto eta) { + return eta[1] + 0.1 * eta[0] + 0.1 * eta[2] * eta[2]; + }; + auto xmapz = [&](auto eta) { + return eta[2] + 0.2 * eta[0] * eta[0] + 0.2 * eta[1] * eta[1]; + }; + + const int num_modes = 3; + auto h = make_hex_geom(num_modes, xmapx, xmapy, xmapz); + + auto points_key = PointsKey(num_modes, ePolyEvenlySpaced); + auto control_points = std::make_shared(points_key); + control_points->Initialize(); + auto Z = control_points->GetZ(); + + Array lcoords(3); + for (int iz = 0; iz < num_modes; iz++) { + for (int iy = 0; iy < num_modes; iy++) { + for (int ix = 0; ix < num_modes; ix++) { + lcoords[0] = Z[ix]; + lcoords[1] = Z[iy]; + lcoords[2] = Z[iz]; + + auto x0 = h->GetCoord(0, lcoords); + auto x1 = h->GetCoord(1, lcoords); + auto x2 = h->GetCoord(2, lcoords); + auto c0 = xmapx(lcoords); + auto c1 = xmapy(lcoords); + auto c2 = xmapz(lcoords); + lambda_check(c0, x0); + lambda_check(c1, x1); + lambda_check(c2, x2); + } + } + } + } + + { + auto xmapx = [&](auto eta) { + return eta[0] + (0.2 - 0.1 * eta[2] * eta[2]) - 2.0; + }; + auto xmapy = [&](auto eta) { + return eta[1] + 0.1 * eta[0] + 0.1 * eta[2] * eta[2]; + }; + auto xmapz = [&](auto eta) { + return eta[2] + 0.2 * eta[0] * eta[0] + 0.2 * eta[1] * eta[1]; + }; + + const int num_modes = 3; + auto h = make_hex_geom(num_modes, xmapx, xmapy, xmapz); + + auto points_key = PointsKey(num_modes, ePolyEvenlySpaced); + auto control_points = std::make_shared(points_key); + control_points->Initialize(); + auto Z = control_points->GetZ(); + + Array lcoords(3); + for (int iz = 0; iz < num_modes; iz++) { + for (int iy = 0; iy < num_modes; iy++) { + for (int ix = 0; ix < num_modes; ix++) { + lcoords[0] = Z[ix]; + lcoords[1] = Z[iy]; + lcoords[2] = Z[iz]; + + auto x0 = h->GetCoord(0, lcoords); + auto x1 = h->GetCoord(1, lcoords); + auto x2 = h->GetCoord(2, lcoords); + auto c0 = xmapx(lcoords); + auto c1 = xmapy(lcoords); + auto c2 = xmapz(lcoords); + lambda_check(c0, x0); + lambda_check(c1, x1); + lambda_check(c2, x2); + } + } + } + } +} + +TEST(ParticleGeometryInterfaceCurved, BoundingBox) { + + auto sycl_target = std::make_shared(0, MPI_COMM_WORLD); + sycl_target->free(); +} From 1bee74c4147752d1725bf9725972e0e7853d14cb Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Fri, 15 Nov 2024 17:23:27 +0000 Subject: [PATCH 42/66] moved hex creation function into neso library --- CMakeLists.txt | 1 + include/nektar_interface/utility_mesh.hpp | 251 ++++++++++++++++++ .../test_helper_utilities.hpp | 1 + ..._particle_geometry_interface_3d_curved.cpp | 212 --------------- 4 files changed, 253 insertions(+), 212 deletions(-) create mode 100644 include/nektar_interface/utility_mesh.hpp diff --git a/CMakeLists.txt b/CMakeLists.txt index cfc61529..17bae3a9 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -238,6 +238,7 @@ set(HEADER_FILES ${INC_DIR}/nektar_interface/solver_base/time_evolved_eqnsys_base.hpp ${INC_DIR}/nektar_interface/typedefs.hpp ${INC_DIR}/nektar_interface/utilities.hpp + ${INC_DIR}/nektar_interface/utility_mesh.hpp ${INC_DIR}/nektar_interface/utility_mesh_cartesian.hpp ${INC_DIR}/nektar_interface/utility_mesh_plotting.hpp ${INC_DIR}/nektar_interface/utility_sycl.hpp diff --git a/include/nektar_interface/utility_mesh.hpp b/include/nektar_interface/utility_mesh.hpp new file mode 100644 index 00000000..7c519658 --- /dev/null +++ b/include/nektar_interface/utility_mesh.hpp @@ -0,0 +1,251 @@ +#ifndef __UTILITY_MESH_H_ +#define __UTILITY_MESH_H_ + +#include +#include +#include + +#include +#include +using namespace Nektar; + +namespace NESO { + +/** + * Create a curved HexGeom from three X maps and a number of modes. Each X map + * should map the reference space [-1,1]^3 to a point in R. + * + * @param num_modes Number of modes in the coordinate mapping for the Xmap, i.e. + * polynomial order plus 1. + * @param xmapx Callable that defines the X map in the x direction with + * signature NekDouble(NekDouble[3]) where the single argument is a + * subscriptable type.; + * @param xmapy Callable that defines the X map in the y direction with + * signature NekDouble(NekDouble[3]) where the single argument is a + * subscriptable type.; + * @param xmapz Callable that defines the X map in the z direction with + * signature NekDouble(NekDouble[3]) where the single argument is a + * subscriptable type.; + * @returns HexGeom constructed from X maps. + */ +template +inline std::shared_ptr +make_hex_geom(const int num_modes, T xmapx, U xmapy, V xmapz) { + + /** + * Vertices: + * + * 7 - 6 + * | | z = 1 + * 4 - 5 + * + * 3 - 2 + * | | z = -1 + * 0 - 1 + * + * Edges: + * + * * 10 * + * 11 9 z = 1 + * * 8 * + * + * 7 - 6 + * | | z = 0 + * 4 - 5 + * + * * 2 * + * 3 1 z = -1 + * * 0 * + * + * Faces: + * + * * - * + * | 5 | Top face, z = 1 + * * - * + * + * * 3 * + * 4 2 Sides, z = 0 + * * 1 * + * + * * - * + * | 0 | Bottom face, z = -1 + * * - * + * + * auto pts = LibUtilities::PointsManager()[*points_key]; + * Triangle is something like trievenlyspaced + * quad will x fastest then y + * Triangles are not the expansion looping ordering - look at nektmesh + * top eta0, eta1, eta2=0 + * eta0 eta1 + * + * make meshgraph, meshgraphio. view -> adavnced "nonlinear subdivisions + * (slider)" + */ + + NekDouble coords_vertices[8][3] = {{-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, + {1.0, 1.0, -1.0}, {-1.0, 1.0, -1.0}, + {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, + {1.0, 1.0, 1.0}, {-1.0, 1.0, 1.0}}; + + int map_edge_to_vertices[12][2] = { + {0, 1}, {1, 2}, {2, 3}, {3, 0}, + + {0, 4}, {1, 5}, {2, 6}, {3, 7}, + + {4, 5}, {5, 6}, {6, 7}, {7, 4}, + }; + + int map_face_to_edges[6][4] = { + {0, 1, 2, 3}, {0, 5, 8, 4}, {1, 6, 9, 5}, + {2, 7, 10, 6}, {3, 4, 11, 7}, {8, 9, 10, 11}, + }; + + int map_face_to_vertices[6][4] = {{0, 1, 2, 3}, {0, 1, 4, 5}, {1, 2, 6, 5}, + {2, 3, 7, 6}, {1, 3, 7, 4}, {4, 5, 6, 7}}; + + auto points_key = + LibUtilities::PointsKey(num_modes, LibUtilities::ePolyEvenlySpaced); + auto control_points = std::make_shared(points_key); + control_points->Initialize(); + auto Z = control_points->GetZ(); + std::vector Znormalised(Z.size()); + for (int ix = 0; ix < num_modes; ix++) { + Znormalised.at(ix) = (Z[ix] + 1.0) / 2.0; + } + + std::map> v; + std::map> e; + std::map> c; + std::map> q; + + // Create the vertices + int vx_index = 0; + int cx_index = 0; + for (int vx = 0; vx < 8; vx++) { + const NekDouble px = xmapx(coords_vertices[vx]); + const NekDouble py = xmapy(coords_vertices[vx]); + const NekDouble pz = xmapz(coords_vertices[vx]); + v[vx] = + std::make_shared(3, vx_index++, px, py, pz); + } + + // Create the edges + auto lambda_get_1D_qpoint = [&](const int point_id, const auto a, + const auto b) -> std::array { + NekDouble ax, ay, az, bx, by, bz; + ax = a[0]; + ay = a[1]; + az = a[2]; + bx = b[0]; + by = b[1]; + bz = b[2]; + const NekDouble dx = bx - ax; + const NekDouble dy = by - ay; + const NekDouble dz = bz - az; + + std::array out; + out[0] = ax + Znormalised[point_id] * dx; + out[1] = ay + Znormalised[point_id] * dy; + out[2] = az + Znormalised[point_id] * dz; + return out; + }; + + for (int ex = 0; ex < 12; ex++) { + auto cx = std::make_shared( + cx_index++, LibUtilities::ePolyEvenlySpaced); + + for (int mx = 0; mx < num_modes; mx++) { + auto ref_coord = + lambda_get_1D_qpoint(mx, coords_vertices[map_edge_to_vertices[ex][0]], + coords_vertices[map_edge_to_vertices[ex][1]]); + const NekDouble px = xmapx(ref_coord); + const NekDouble py = xmapy(ref_coord); + const NekDouble pz = xmapz(ref_coord); + cx->m_points.push_back(std::make_shared( + 3, vx_index++, px, py, pz)); + } + std::shared_ptr vertices_array[2] = { + v.at(map_edge_to_vertices[ex][0]), v.at(map_edge_to_vertices[ex][1])}; + c[ex] = cx; + e[ex] = + std::make_shared(ex, 3, vertices_array, cx); + e[ex]->GetGeomFactors(); + e[ex]->Setup(); + } + + // Create the faces + auto lambda_get_2D_qpoint = [&](const int point_id0, const int point_id1, + const auto a, const auto b, + const auto c) -> std::array { + /** + * c + * | + * a - b + */ + + NekDouble ax, ay, az, bx, by, bz, cx, cy, cz; + ax = a[0]; + ay = a[1]; + az = a[2]; + bx = b[0]; + by = b[1]; + bz = b[2]; + cx = c[0]; + cy = c[1]; + cz = c[2]; + const NekDouble d0x = bx - ax; + const NekDouble d0y = by - ay; + const NekDouble d0z = bz - az; + const NekDouble d1x = cx - ax; + const NekDouble d1y = cy - ay; + const NekDouble d1z = cz - az; + + std::array out; + out[0] = ax + Znormalised[point_id0] * d0x + Znormalised[point_id1] * d1x; + out[1] = ay + Znormalised[point_id0] * d0y + Znormalised[point_id1] * d1y; + out[2] = az + Znormalised[point_id0] * d0z + Znormalised[point_id1] * d1z; + return out; + }; + + for (int fx = 0; fx < 6; fx++) { + std::shared_ptr vertices_array[4] = { + v.at(map_face_to_vertices[fx][0]), v.at(map_face_to_vertices[fx][1]), + v.at(map_face_to_vertices[fx][2]), v.at(map_face_to_vertices[fx][3])}; + + auto cx = std::make_shared( + cx_index++, LibUtilities::ePolyEvenlySpaced); + for (int mx = 0; mx < num_modes; mx++) { + for (int my = 0; my < num_modes; my++) { + auto ref_coord = lambda_get_2D_qpoint( + mx, my, coords_vertices[map_face_to_vertices[fx][0]], + coords_vertices[map_face_to_vertices[fx][1]], + coords_vertices[map_face_to_vertices[fx][3]]); + const NekDouble px = xmapx(ref_coord); + const NekDouble py = xmapy(ref_coord); + const NekDouble pz = xmapz(ref_coord); + cx->m_points.push_back(std::make_shared( + 3, vx_index++, px, py, pz)); + } + } + + std::shared_ptr edges_array[4] = { + e.at(map_face_to_edges[fx][0]), e.at(map_face_to_edges[fx][1]), + e.at(map_face_to_edges[fx][2]), e.at(map_face_to_edges[fx][3])}; + q[fx] = std::make_shared(fx, edges_array, cx); + q[fx]->GetGeomFactors(); + q[fx]->Setup(); + } + + std::shared_ptr quads[6] = {q[0], q[1], q[2], + q[3], q[4], q[5]}; + + auto hex = std::make_shared(0, quads); + hex->GetGeomFactors(); + hex->Setup(); + + return hex; +} + +} // namespace NESO + +#endif diff --git a/test/unit/nektar_interface/test_helper_utilities.hpp b/test/unit/nektar_interface/test_helper_utilities.hpp index f482a801..8104b946 100644 --- a/test/unit/nektar_interface/test_helper_utilities.hpp +++ b/test/unit/nektar_interface/test_helper_utilities.hpp @@ -4,6 +4,7 @@ #include "nektar_interface/composite_interaction/composite_interaction.hpp" #include "nektar_interface/particle_interface.hpp" #include "nektar_interface/utilities.hpp" +#include "nektar_interface/utility_mesh.hpp" #include "nektar_interface/utility_mesh_plotting.hpp" #include #include diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 5f4a133e..d67711d2 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -179,218 +179,6 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { mesh->free(); } -template -inline std::shared_ptr make_hex_geom(const int num_modes, T xmapx, - U xmapy, V xmapz) { - - /** - * Vertices: - * - * 7 - 6 - * | | - * 4 - 5 - * - * 3 - 2 - * | | - * 0 - 1 - * - * Edges: - * - * * 10 * - * 11 9 - * * 8 * - * - * 7 - 6 - * | | - * 4 - 5 - * - * * 2 * - * 3 1 - * * 0 * - * - * Faces: - * - * * - * - * | 5 | - * * - * - * - * * 3 * - * 4 2 - * * 1 * - * - * * - * - * | 0 | - * * - * - * - * auto pts = LibUtilities::PointsManager()[*points_key]; - * Triangle is something like trievenlyspaced - * quad will x fastest then y - * Triangles are not the expansion looping ordering - look at nektmesh - * top eta0, eta1, eta2=0 - * eta0 eta1 - * - * make meshgraph, meshgraphio. view -> adavnced "nonlinear subdivisions - * (slider)" - */ - - REAL coords_vertices[8][3] = {{-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, - {1.0, 1.0, -1.0}, {-1.0, 1.0, -1.0}, - {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, - {1.0, 1.0, 1.0}, {-1.0, 1.0, 1.0}}; - - int map_edge_to_vertices[12][2] = { - {0, 1}, {1, 2}, {2, 3}, {3, 0}, - - {0, 4}, {1, 5}, {2, 6}, {3, 7}, - - {4, 5}, {5, 6}, {6, 7}, {7, 4}, - }; - - int map_face_to_edges[6][4] = { - {0, 1, 2, 3}, {0, 5, 8, 4}, {1, 6, 9, 5}, - {2, 7, 10, 6}, {3, 4, 11, 7}, {8, 9, 10, 11}, - }; - - int map_face_to_vertices[6][4] = {{0, 1, 2, 3}, {0, 1, 4, 5}, {1, 2, 6, 5}, - {2, 3, 7, 6}, {1, 3, 7, 4}, {4, 5, 6, 7}}; - - auto points_key = PointsKey(num_modes, ePolyEvenlySpaced); - auto control_points = std::make_shared(points_key); - control_points->Initialize(); - auto Z = control_points->GetZ(); - std::vector Znormalised(Z.size()); - for (int ix = 0; ix < num_modes; ix++) { - Znormalised.at(ix) = (Z[ix] + 1.0) / 2.0; - } - - std::map> v; - std::map> e; - std::map> c; - std::map> q; - - // Create the vertices - int vx_index = 0; - int cx_index = 0; - for (int vx = 0; vx < 8; vx++) { - const REAL px = xmapx(coords_vertices[vx]); - const REAL py = xmapy(coords_vertices[vx]); - const REAL pz = xmapz(coords_vertices[vx]); - v[vx] = std::make_shared(3, vx_index++, px, py, pz); - } - - // Create the edges - auto lambda_get_1D_qpoint = [&](const int point_id, const auto a, - const auto b) -> std::array { - NekDouble ax, ay, az, bx, by, bz; - ax = a[0]; - ay = a[1]; - az = a[2]; - bx = b[0]; - by = b[1]; - bz = b[2]; - const NekDouble dx = bx - ax; - const NekDouble dy = by - ay; - const NekDouble dz = bz - az; - - std::array out; - out[0] = ax + Znormalised[point_id] * dx; - out[1] = ay + Znormalised[point_id] * dy; - out[2] = az + Znormalised[point_id] * dz; - return out; - }; - - for (int ex = 0; ex < 12; ex++) { - auto cx = std::make_shared(cx_index++, ePolyEvenlySpaced); - - for (int mx = 0; mx < num_modes; mx++) { - auto ref_coord = - lambda_get_1D_qpoint(mx, coords_vertices[map_edge_to_vertices[ex][0]], - coords_vertices[map_edge_to_vertices[ex][1]]); - const REAL px = xmapx(ref_coord); - const REAL py = xmapy(ref_coord); - const REAL pz = xmapz(ref_coord); - cx->m_points.push_back( - std::make_shared(3, vx_index++, px, py, pz)); - } - std::shared_ptr vertices_array[2] = { - v.at(map_edge_to_vertices[ex][0]), v.at(map_edge_to_vertices[ex][1])}; - c[ex] = cx; - e[ex] = std::make_shared(ex, 3, vertices_array, cx); - e[ex]->GetGeomFactors(); - e[ex]->Setup(); - } - - // Create the faces - auto lambda_get_2D_qpoint = [&](const int point_id0, const int point_id1, - const auto a, const auto b, - const auto c) -> std::array { - /** - * c - * | - * a - b - */ - - NekDouble ax, ay, az, bx, by, bz, cx, cy, cz; - ax = a[0]; - ay = a[1]; - az = a[2]; - bx = b[0]; - by = b[1]; - bz = b[2]; - cx = c[0]; - cy = c[1]; - cz = c[2]; - const NekDouble d0x = bx - ax; - const NekDouble d0y = by - ay; - const NekDouble d0z = bz - az; - const NekDouble d1x = cx - ax; - const NekDouble d1y = cy - ay; - const NekDouble d1z = cz - az; - - std::array out; - out[0] = ax + Znormalised[point_id0] * d0x + Znormalised[point_id1] * d1x; - out[1] = ay + Znormalised[point_id0] * d0y + Znormalised[point_id1] * d1y; - out[2] = az + Znormalised[point_id0] * d0z + Znormalised[point_id1] * d1z; - return out; - }; - - for (int fx = 0; fx < 6; fx++) { - std::shared_ptr vertices_array[4] = { - v.at(map_face_to_vertices[fx][0]), v.at(map_face_to_vertices[fx][1]), - v.at(map_face_to_vertices[fx][2]), v.at(map_face_to_vertices[fx][3])}; - - auto cx = std::make_shared(cx_index++, ePolyEvenlySpaced); - for (int mx = 0; mx < num_modes; mx++) { - for (int my = 0; my < num_modes; my++) { - auto ref_coord = lambda_get_2D_qpoint( - mx, my, coords_vertices[map_face_to_vertices[fx][0]], - coords_vertices[map_face_to_vertices[fx][1]], - coords_vertices[map_face_to_vertices[fx][3]]); - const REAL px = xmapx(ref_coord); - const REAL py = xmapy(ref_coord); - const REAL pz = xmapz(ref_coord); - cx->m_points.push_back( - std::make_shared(3, vx_index++, px, py, pz)); - } - } - - std::shared_ptr edges_array[4] = { - e.at(map_face_to_edges[fx][0]), e.at(map_face_to_edges[fx][1]), - e.at(map_face_to_edges[fx][2]), e.at(map_face_to_edges[fx][3])}; - q[fx] = std::make_shared(fx, edges_array, cx); - q[fx]->GetGeomFactors(); - q[fx]->Setup(); - } - - std::shared_ptr quads[6] = {q[0], q[1], q[2], q[3], q[4], q[5]}; - - auto hex = std::make_shared(0, quads); - hex->GetGeomFactors(); - hex->Setup(); - - return hex; -} - TEST(ParticleGeometryInterfaceCurved, MakeCurvedHex) { auto lambda_check = [&](auto correct, auto to_test) { From f2821d0fe614c52fe0d0812add7202679f851f1d Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 19 Nov 2024 19:52:43 +0000 Subject: [PATCH 43/66] blocked Bary cpu evaluation progress --- CMakeLists.txt | 2 + .../bary_interpolation/bary_evaluation.hpp | 105 +++++++++++++ .../function_bary_evaluation.hpp | 140 +++++++++++++++++- include/nektar_interface/utility_sycl.hpp | 2 +- test/CMakeLists.txt | 1 + .../test_particle_function_evaluation_3d.cpp | 123 +++++++++++++++ 6 files changed, 366 insertions(+), 7 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 17bae3a9..3f5bcfcf 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -99,6 +99,8 @@ elseif(BUILD_TYPE STREQUAL "RELEASE") set(BUILD_TYPE_LINK_FLAGS "") set(TEST_LIBRARIES "") endif() +message(STATUS BUILD_TYPE_COMPILE_FLAGS: ${BUILD_TYPE_COMPILE_FLAGS}) +message(STATUS BUILD_TYPE_LINK_FLAGS: ${BUILD_TYPE_LINK_FLAGS}) # ############################################################################## # Set up targets diff --git a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp index f90a3627..1b86d79c 100644 --- a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp +++ b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp @@ -48,6 +48,60 @@ inline void preprocess_weights(const int num_phys, const REAL coord, } } +/** + * TODO + */ +template +inline void +preprocess_weights_block(const int num_phys, const REAL *const coord, + const REAL *const z_values, + const REAL *const bw_values, REAL *div_values) { + + for (int ix = 0; ix < num_phys; ix++) { + for (int blockx = 0; blockx < N; blockx++) { + div_values[ix * N + blockx] = 0.0; + } + } + bool on_point[N]; + for (int blockx = 0; blockx < N; blockx++) { + on_point[blockx] = false; + } + + for (int ix = 0; ix < num_phys; ix++) { + for (int blockx = 0; blockx < N; blockx++) { + const auto xdiff = z_values[ix] - coord[blockx]; + if (xdiff == 0.0) { + div_values[ix * N + blockx] = 1.0; + on_point[blockx] = true; + } + } + } + REAL denom[N]; + for (int blockx = 0; blockx < N; blockx++) { + denom[blockx] = 0.0; + } + + for (int ix = 0; ix < num_phys; ix++) { + for (int blockx = 0; blockx < N; blockx++) { + const auto xdiff = z_values[ix] - coord[blockx]; + const auto bw_over_diff = bw_values[ix] / xdiff; + div_values[ix * N + blockx] = + on_point[blockx] ? div_values[ix * N + blockx] : bw_over_diff; + denom[blockx] += bw_over_diff; + } + } + REAL factor[N]; + for (int blockx = 0; blockx < N; blockx++) { + factor[blockx] = on_point[blockx] ? 1.0 : 1.0 / denom[blockx]; + } + + for (int ix = 0; ix < num_phys; ix++) { + for (int blockx = 0; blockx < N; blockx++) { + div_values[ix * N + blockx] *= factor[blockx]; + } + } +} + /** * Perform Bary interpolation in the first dimension. * @@ -306,6 +360,57 @@ inline void compute_dir_210_interlaced(const int num_functions, } } +/** + * TODO + */ +template +inline void compute_dir_210_interlaced_block( + const int num_functions, const int num_phys0, const int num_phys1, + const int num_phys2, const REAL *RESTRICT const physvals, + const REAL *RESTRICT const div_space0, + const REAL *RESTRICT const div_space1, + const REAL *RESTRICT const div_space2, REAL *RESTRICT output) { + + for (int funcx = 0; funcx < num_functions; funcx++) { + for (int blockx = 0; blockx < N; blockx++) { + output[funcx * N + blockx] = 0.0; + } + } + + const int stride_phys = num_phys0 * num_phys1; + + for (int i2 = 0; i2 < num_phys2; i2++) { + REAL b2[N]; + for (int blockx = 0; blockx < N; blockx++) { + b2[blockx] = div_space2[i2 * N + blockx]; + } + + for (int i1 = 0; i1 < num_phys1; i1++) { + REAL b1[N]; + for (int blockx = 0; blockx < N; blockx++) { + b1[blockx] = div_space1[i1 * N + blockx] * b2[blockx]; + } + + for (int i0 = 0; i0 < num_phys0; i0++) { + REAL basis_eval[N]; + for (int blockx = 0; blockx < N; blockx++) { + const REAL b0 = div_space0[i0 * N + blockx]; + basis_eval[blockx] = b0 * b1[blockx]; + } + + for (int funcx = 0; funcx < num_functions; funcx++) { + const int inner_stride = + (i2 * stride_phys + i1 * num_phys0 + i0) * num_functions; + const REAL func_coeff = physvals[inner_stride + funcx]; + for (int blockx = 0; blockx < N; blockx++) { + output[funcx * N + blockx] += basis_eval[blockx] * func_coeff; + } + } + } + } + } +} + /** * Compute a function evaluation at a point using the passed quadrature point * values, quadrature points and weights. diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 32a9c0b3..64607127 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -229,6 +229,124 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { } } + template + static inline void + dispatch_3d_cpu(SYCLTargetSharedPtr sycl_target, EventStack &es, + const std::size_t num_functions, const int k_max_num_phys, + const NekDouble *const RESTRICT k_global_physvals_interlaced, + const CellInfo *const RESTRICT k_cell_info, + ParticleDatSharedPtr mpi_rank_dat, + ParticleDatSharedPtr ref_positions_dat, + U ****k_syms_ptrs, int *k_components) { + constexpr int ndim = 3; + ParticleLoopImplementation::ParticleLoopBlockIterationSet ish{mpi_rank_dat}; + const std::size_t local_size = + sycl_target->parameters->template get("LOOP_LOCAL_SIZE") + ->value; + const std::size_t local_num_reals = + static_cast(ndim * k_max_num_phys) + num_functions; + const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); + const auto k_ref_positions = ref_positions_dat->cell_dat.device_ptr(); + + for(int cellx=0 ; cellxncell ; cellx++){ + + //auto is = ish.get_all_cells(local_size, num_bytes_local); + auto is = ish.get_single_cell(cellx, local_size, num_bytes_local, NESO_VECTOR_LENGTH); + + for (auto &blockx : is) { + const auto block_device = blockx.block_device; + const std::size_t local_size = blockx.local_size; + es.push(sycl_target->queue.submit([&](sycl::handler &cgh) { + // Allocate local memory to compute the divides. + sycl::local_accessor local_mem( + sycl::range<1>(local_num_reals * local_size * NESO_VECTOR_LENGTH), cgh); + + cgh.parallel_for<>( + blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { + const int idx_local = idx.get_local_id(1); + std::size_t cell; + std::size_t layer; + block_device.stride_get_cell_layer(idx, &cell, &layer); + if (block_device.stride_work_item_required(cell, layer)){ + + const std::size_t particle_start = layer * NESO_VECTOR_LENGTH; + const std::size_t local_bound = particle_start + + block_device.stride_local_index_bound(cell, layer); + + // offset by the local index for the striding to work + REAL *evaluations = &local_mem[0] + idx_local * num_functions * NESO_VECTOR_LENGTH; + REAL *div_start = &local_mem[local_size * num_functions * NESO_VECTOR_LENGTH]; + const std::size_t div_space_per_work_item = NESO_VECTOR_LENGTH * k_max_num_phys; + + REAL *div_space0 = div_start + idx_local * div_space_per_work_item * 3; + REAL *div_space1 = div_space0 + div_space_per_work_item; + REAL *div_space2 = div_space1 + div_space_per_work_item; + + for (std::size_t fx = 0; fx < num_functions; fx++) { + for(std::size_t blockx=0 ; blockx(num_phys0, eta0, z0, bw0, div_space0); + Bary::preprocess_weights_block(num_phys1, eta1, z1, bw1, div_space1); + Bary::preprocess_weights_block(num_phys2, eta2, z2, bw2, div_space2); + + Bary::compute_dir_210_interlaced_block( + num_functions, num_phys0, num_phys1, num_phys2, physvals, + div_space0, div_space1, div_space2, evaluations); + + for (std::size_t fx = 0; fx < num_functions; fx++) { + auto ptr = k_syms_ptrs[fx]; + auto component = k_components[fx]; + ptr[cell][component][layer] = evaluations[fx]; + } + for (std::size_t fx = 0; fx < num_functions; fx++) { + for(std::size_t blockx=0 ; blockx inline void evaluate_inner(ParticleGroupSharedPtr particle_group, @@ -296,12 +414,22 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { particle_group->get_dat(Sym("NESO_REFERENCE_POSITIONS")), d_syms_ptrs.ptr, d_components.ptr); } else { - this->dispatch_3d( - this->sycl_target, es, num_functions, this->max_num_phys, - k_global_physvals_interlaced, this->d_cell_info->ptr, - particle_group->mpi_rank_dat, - particle_group->get_dat(Sym("NESO_REFERENCE_POSITIONS")), - d_syms_ptrs.ptr, d_components.ptr); + + if (this->sycl_target->device.is_gpu()) { + this->dispatch_3d( + this->sycl_target, es, num_functions, this->max_num_phys, + k_global_physvals_interlaced, this->d_cell_info->ptr, + particle_group->mpi_rank_dat, + particle_group->get_dat(Sym("NESO_REFERENCE_POSITIONS")), + d_syms_ptrs.ptr, d_components.ptr); + } else { + this->dispatch_3d_cpu( + this->sycl_target, es, num_functions, this->max_num_phys, + k_global_physvals_interlaced, this->d_cell_info->ptr, + particle_group->mpi_rank_dat, + particle_group->get_dat(Sym("NESO_REFERENCE_POSITIONS")), + d_syms_ptrs.ptr, d_components.ptr); + } } const auto nphys = this->max_num_phys; diff --git a/include/nektar_interface/utility_sycl.hpp b/include/nektar_interface/utility_sycl.hpp index a26775bd..ebb529ba 100644 --- a/include/nektar_interface/utility_sycl.hpp +++ b/include/nektar_interface/utility_sycl.hpp @@ -84,7 +84,7 @@ get_particle_loop_global_size(ParticleDatSharedPtr particle_dat, #ifdef NESO_PARTICLES_VECTOR_LENGTH #define NESO_VECTOR_LENGTH NESO_PARTICLES_VECTOR_LENGTH #else -#define NESO_VECTOR_LENGTH 1 +#define NESO_VECTOR_LENGTH 4 // TODO MAKE THIS CONFIGURATION CMAKE TIME #endif #endif diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index 8351a840..b69869c9 100644 --- a/test/CMakeLists.txt +++ b/test/CMakeLists.txt @@ -84,6 +84,7 @@ list(REMOVE_ITEM TEST_LIBRARIES "gcov") # Build the unit test suite set(UNIT_EXE unitTests) add_executable(${UNIT_EXE} ${UNIT_SRC_FILES}) +target_compile_options(${UNIT_EXE} PRIVATE ${BUILD_TYPE_COMPILE_FLAGS}) target_link_libraries(${UNIT_EXE} PRIVATE ${NESO_LIBRARY_NAME} GTest::gtest) if(ENABLE_NESO_PROFILING) target_compile_definitions(${UNIT_EXE} diff --git a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp index b1bca673..2ea40699 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp @@ -383,3 +383,126 @@ TEST(BaryInterpolation, Evaluation3DDisContFieldPrismTet) { "reference_prism_tet_cube/conditions.xml", "reference_prism_tet_cube/prism_tet_cube_0.5_perturbed.xml", 1.0e-7); } + +// TODO REMOVE START + +template +static inline void evaluation_marco(std::string condtions_file_s, + std::string mesh_file_s, const double tol) { + + const int N_total = 1200000; + + std::filesystem::path source_file = __FILE__; + std::filesystem::path source_dir = source_file.parent_path(); + std::filesystem::path test_resources_dir = + source_dir / "../../test_resources"; + + std::filesystem::path condtions_file_basename{condtions_file_s}; + std::filesystem::path mesh_file_basename{mesh_file_s}; + std::filesystem::path conditions_file = + test_resources_dir / condtions_file_basename; + std::filesystem::path mesh_file = test_resources_dir / mesh_file_basename; + + int argc = 3; + char *argv[3]; + copy_to_cstring(std::string("test_particle_geometry_interface"), &argv[0]); + copy_to_cstring(std::string(conditions_file), &argv[1]); + copy_to_cstring(std::string(mesh_file), &argv[2]); + + LibUtilities::SessionReaderSharedPtr session; + SpatialDomains::MeshGraphSharedPtr graph; + // Create session reader. + session = LibUtilities::SessionReader::CreateInstance(argc, argv); + graph = SpatialDomains::MeshGraph::Read(session); + + auto mesh = std::make_shared(graph); + auto sycl_target = std::make_shared(0, mesh->get_comm()); + + std::mt19937 rng{182348}; + + auto nektar_graph_local_mapper = + std::make_shared(sycl_target, mesh); + auto domain = std::make_shared(mesh, nektar_graph_local_mapper); + + const int ndim = 3; + ParticleSpec particle_spec{ParticleProp(Sym("P"), ndim, true), + ParticleProp(Sym("CELL_ID"), 1, true), + ParticleProp(Sym("E"), 1), + ParticleProp(Sym("DEDX"), ndim), + ParticleProp(Sym("ID"), 1)}; + + auto A = std::make_shared(domain, particle_spec, sycl_target); + + NektarCartesianPeriodic pbc(sycl_target, graph, A->position_dat); + auto cell_id_translation = + std::make_shared(sycl_target, A->cell_id_dat, mesh); + const int rank = sycl_target->comm_pair.rank_parent; + const int size = sycl_target->comm_pair.size_parent; + + std::mt19937 rng_pos(52234234 + rank); + int rstart, rend; + get_decomp_1d(size, N_total, rank, &rstart, &rend); + const int N = rend - rstart; + int N_check = -1; + MPICHK(MPI_Allreduce(&N, &N_check, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD)); + NESOASSERT(N_check == N_total, "Error creating particles"); + const int cell_count = domain->mesh->get_cell_count(); + if (N > 0) { + auto positions = + uniform_within_extents(N, ndim, pbc.global_extent, rng_pos); + + ParticleSet initial_distribution(N, A->get_particle_spec()); + for (int px = 0; px < N; px++) { + for (int dimx = 0; dimx < ndim; dimx++) { + const double pos_orig = positions[dimx][px] + pbc.global_origin[dimx]; + initial_distribution[Sym("P")][px][dimx] = pos_orig; + } + + initial_distribution[Sym("CELL_ID")][px][0] = 0; + initial_distribution[Sym("ID")][px][0] = px; + } + A->add_particles_local(initial_distribution); + } + reset_mpi_ranks((*A)[Sym("NESO_MPI_RANK")]); + + pbc.execute(); + A->hybrid_move(); + cell_id_translation->execute(); + A->cell_move(); + + auto field = std::make_shared(session, graph, "u"); + + auto lambda_f = [&](const NekDouble x, const NekDouble y, const NekDouble z) { + return std::pow((x + 1.0) * (x - 1.0) * (y + 1.0) * (y - 1.0) * (z + 1.0) * + (z - 1.0), + 4); + }; + + interpolate_onto_nektar_field_3d(lambda_f, field); + NESOCellsToNektarExp map_cells_to_exp(field, cell_id_translation); + + // auto field_evaluate = std::make_shared>( + // field, A, cell_id_translation); + // field_evaluate->evaluate(Sym("E")); + auto field_deriv_evaluate = std::make_shared>( + field, A, cell_id_translation, true); + + for (int cellx = 0; cellx < 10; cellx++) { + field_deriv_evaluate->evaluate(Sym("DEDX")); + } + + A->free(); + mesh->free(); + + delete[] argv[0]; + delete[] argv[1]; + delete[] argv[2]; +} + +TEST(Marco, Polo) { + evaluation_marco( + "reference_hex_cube/conditions.xml", + "reference_hex_cube/hex_cube_0.5.xml", 1.0e-7); +} + +// TODO REMOVE END From 77f07c3276c31990b725f5510f36b2313734d33c Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 20 Nov 2024 11:07:51 +0000 Subject: [PATCH 44/66] fixed indexing bugs in blocked bary cpu evaluation --- .../function_bary_evaluation.hpp | 85 ++++++++++--------- 1 file changed, 44 insertions(+), 41 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 64607127..cd6b76a7 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -248,46 +248,42 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); const auto k_ref_positions = ref_positions_dat->cell_dat.device_ptr(); - for(int cellx=0 ; cellxncell ; cellx++){ + for (int cellx = 0; cellx < mpi_rank_dat->ncell; cellx++) { - //auto is = ish.get_all_cells(local_size, num_bytes_local); - auto is = ish.get_single_cell(cellx, local_size, num_bytes_local, NESO_VECTOR_LENGTH); + // auto is = ish.get_all_cells(local_size, num_bytes_local); + auto is = ish.get_single_cell(cellx, local_size, num_bytes_local, + NESO_VECTOR_LENGTH); for (auto &blockx : is) { const auto block_device = blockx.block_device; const std::size_t local_size = blockx.local_size; es.push(sycl_target->queue.submit([&](sycl::handler &cgh) { + const std::size_t local_mem_stride = + local_num_reals * NESO_VECTOR_LENGTH; // Allocate local memory to compute the divides. sycl::local_accessor local_mem( - sycl::range<1>(local_num_reals * local_size * NESO_VECTOR_LENGTH), cgh); + sycl::range<1>(local_size * local_mem_stride), cgh); cgh.parallel_for<>( blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { const int idx_local = idx.get_local_id(1); std::size_t cell; - std::size_t layer; - block_device.stride_get_cell_layer(idx, &cell, &layer); - if (block_device.stride_work_item_required(cell, layer)){ - - const std::size_t particle_start = layer * NESO_VECTOR_LENGTH; - const std::size_t local_bound = particle_start + - block_device.stride_local_index_bound(cell, layer); - - // offset by the local index for the striding to work - REAL *evaluations = &local_mem[0] + idx_local * num_functions * NESO_VECTOR_LENGTH; - REAL *div_start = &local_mem[local_size * num_functions * NESO_VECTOR_LENGTH]; - const std::size_t div_space_per_work_item = NESO_VECTOR_LENGTH * k_max_num_phys; - - REAL *div_space0 = div_start + idx_local * div_space_per_work_item * 3; + std::size_t block; + block_device.stride_get_cell_block(idx, &cell, &block); + if (block_device.stride_work_item_required(cell, block)) { + const std::size_t particle_start = block * NESO_VECTOR_LENGTH; + const std::size_t local_bound = + block_device.stride_local_index_bound(cell, block); + + REAL *evaluations = + &local_mem[0] + idx_local * local_mem_stride; + const std::size_t div_space_per_work_item = + NESO_VECTOR_LENGTH * k_max_num_phys; + REAL *div_space0 = + evaluations + NESO_VECTOR_LENGTH * num_functions; REAL *div_space1 = div_space0 + div_space_per_work_item; REAL *div_space2 = div_space1 + div_space_per_work_item; - for (std::size_t fx = 0; fx < num_functions; fx++) { - for(std::size_t blockx=0 ; blockx class BaryEvaluateBase : GeomToExpansionBuilder { const auto physvals = &k_global_physvals_interlaced[cell_info.phys_offset * num_functions]; - + + REAL xi0[NESO_VECTOR_LENGTH]; + REAL xi1[NESO_VECTOR_LENGTH]; + REAL xi2[NESO_VECTOR_LENGTH]; REAL eta0[NESO_VECTOR_LENGTH]; REAL eta1[NESO_VECTOR_LENGTH]; REAL eta2[NESO_VECTOR_LENGTH]; - for(std::size_t blockx=0 ; blockx(num_phys0, eta0, z0, bw0, div_space0); - Bary::preprocess_weights_block(num_phys1, eta1, z1, bw1, div_space1); - Bary::preprocess_weights_block(num_phys2, eta2, z2, bw2, div_space2); + Bary::preprocess_weights_block( + num_phys0, eta0, z0, bw0, div_space0); + Bary::preprocess_weights_block( + num_phys1, eta1, z1, bw1, div_space1); + Bary::preprocess_weights_block( + num_phys2, eta2, z2, bw2, div_space2); Bary::compute_dir_210_interlaced_block( num_functions, num_phys0, num_phys1, num_phys2, physvals, div_space0, div_space1, div_space2, evaluations); for (std::size_t fx = 0; fx < num_functions; fx++) { - auto ptr = k_syms_ptrs[fx]; - auto component = k_components[fx]; - ptr[cell][component][layer] = evaluations[fx]; - } - for (std::size_t fx = 0; fx < num_functions; fx++) { - for(std::size_t blockx=0 ; blockx From a794dd8faf919c0be51ba9bb2acfdca9bba093b6 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 20 Nov 2024 16:30:49 +0000 Subject: [PATCH 45/66] moved 3D bary eval CPU variant to all cells loop construct --- .../function_bary_evaluation.hpp | 187 +++++++++--------- include/nektar_interface/utility_sycl.hpp | 6 + .../test_particle_function_evaluation_3d.cpp | 2 +- 3 files changed, 100 insertions(+), 95 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index cd6b76a7..73f6e266 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -243,110 +243,109 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { const std::size_t local_size = sycl_target->parameters->template get("LOOP_LOCAL_SIZE") ->value; + const std::size_t nbin = + sycl_target->parameters->template get("LOOP_NBIN") + ->value; const std::size_t local_num_reals = static_cast(ndim * k_max_num_phys) + num_functions; const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); const auto k_ref_positions = ref_positions_dat->cell_dat.device_ptr(); - for (int cellx = 0; cellx < mpi_rank_dat->ncell; cellx++) { - - // auto is = ish.get_all_cells(local_size, num_bytes_local); - auto is = ish.get_single_cell(cellx, local_size, num_bytes_local, - NESO_VECTOR_LENGTH); - - for (auto &blockx : is) { - const auto block_device = blockx.block_device; - const std::size_t local_size = blockx.local_size; - es.push(sycl_target->queue.submit([&](sycl::handler &cgh) { - const std::size_t local_mem_stride = - local_num_reals * NESO_VECTOR_LENGTH; - // Allocate local memory to compute the divides. - sycl::local_accessor local_mem( - sycl::range<1>(local_size * local_mem_stride), cgh); - - cgh.parallel_for<>( - blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { - const int idx_local = idx.get_local_id(1); - std::size_t cell; - std::size_t block; - block_device.stride_get_cell_block(idx, &cell, &block); - if (block_device.stride_work_item_required(cell, block)) { - const std::size_t particle_start = block * NESO_VECTOR_LENGTH; - const std::size_t local_bound = - block_device.stride_local_index_bound(cell, block); - - REAL *evaluations = - &local_mem[0] + idx_local * local_mem_stride; - const std::size_t div_space_per_work_item = - NESO_VECTOR_LENGTH * k_max_num_phys; - REAL *div_space0 = - evaluations + NESO_VECTOR_LENGTH * num_functions; - REAL *div_space1 = div_space0 + div_space_per_work_item; - REAL *div_space2 = div_space1 + div_space_per_work_item; - - const auto cell_info = k_cell_info[cell]; - const auto num_phys0 = cell_info.num_phys[0]; - const auto num_phys1 = cell_info.num_phys[1]; - const auto num_phys2 = cell_info.num_phys[2]; - const auto z0 = cell_info.d_z[0]; - const auto z1 = cell_info.d_z[1]; - const auto z2 = cell_info.d_z[2]; - const auto bw0 = cell_info.d_bw[0]; - const auto bw1 = cell_info.d_bw[1]; - const auto bw2 = cell_info.d_bw[2]; - // Get pointer to the start of the quadrature point values for - // this cell - const auto physvals = - &k_global_physvals_interlaced[cell_info.phys_offset * - num_functions]; - - REAL xi0[NESO_VECTOR_LENGTH]; - REAL xi1[NESO_VECTOR_LENGTH]; - REAL xi2[NESO_VECTOR_LENGTH]; - REAL eta0[NESO_VECTOR_LENGTH]; - REAL eta1[NESO_VECTOR_LENGTH]; - REAL eta2[NESO_VECTOR_LENGTH]; + // auto is = ish.get_all_cells(local_size, num_bytes_local); + auto is = ish.get_all_cells(nbin, local_size, num_bytes_local, + NESO_VECTOR_BLOCK_SIZE); - for (std::size_t blockx = 0; blockx < local_bound; blockx++) { - const std::size_t px = particle_start + blockx; - xi0[blockx] = k_ref_positions[cell][0][px]; - xi1[blockx] = k_ref_positions[cell][1][px]; - xi2[blockx] = k_ref_positions[cell][2][px]; - } + for (auto &blockx : is) { + const auto block_device = blockx.block_device; + const std::size_t local_size = blockx.local_size; + es.push(sycl_target->queue.submit([&](sycl::handler &cgh) { + const std::size_t local_mem_stride = + local_num_reals * NESO_VECTOR_BLOCK_SIZE; + // Allocate local memory to compute the divides. + sycl::local_accessor local_mem( + sycl::range<1>(local_size * local_mem_stride), cgh); - for (std::size_t blockx = 0; blockx < NESO_VECTOR_LENGTH; - blockx++) { - GeometryInterface::loc_coord_to_loc_collapsed_3d( - cell_info.shape_type_int, xi0[blockx], xi1[blockx], - xi2[blockx], eta0 + blockx, eta1 + blockx, - eta2 + blockx); - } + cgh.parallel_for<>( + blockx.loop_iteration_set, [=](sycl::nd_item<2> idx) { + const int idx_local = idx.get_local_id(1); + std::size_t cell; + std::size_t block; + block_device.stride_get_cell_block(idx, &cell, &block); + if (block_device.stride_work_item_required(cell, block)) { + const std::size_t particle_start = + block * NESO_VECTOR_BLOCK_SIZE; + const std::size_t local_bound = + block_device.stride_local_index_bound(cell, block); + + REAL *evaluations = + &local_mem[0] + idx_local * local_mem_stride; + const std::size_t div_space_per_work_item = + NESO_VECTOR_BLOCK_SIZE * k_max_num_phys; + REAL *div_space0 = + evaluations + NESO_VECTOR_BLOCK_SIZE * num_functions; + REAL *div_space1 = div_space0 + div_space_per_work_item; + REAL *div_space2 = div_space1 + div_space_per_work_item; - Bary::preprocess_weights_block( - num_phys0, eta0, z0, bw0, div_space0); - Bary::preprocess_weights_block( - num_phys1, eta1, z1, bw1, div_space1); - Bary::preprocess_weights_block( - num_phys2, eta2, z2, bw2, div_space2); - - Bary::compute_dir_210_interlaced_block( - num_functions, num_phys0, num_phys1, num_phys2, physvals, - div_space0, div_space1, div_space2, evaluations); - - for (std::size_t fx = 0; fx < num_functions; fx++) { - for (std::size_t blockx = 0; blockx < local_bound; - blockx++) { - const std::size_t px = particle_start + blockx; - auto ptr = k_syms_ptrs[fx]; - auto component = k_components[fx]; - ptr[cell][component][px] = - evaluations[fx * NESO_VECTOR_LENGTH + blockx]; - } + const auto cell_info = k_cell_info[cell]; + const auto num_phys0 = cell_info.num_phys[0]; + const auto num_phys1 = cell_info.num_phys[1]; + const auto num_phys2 = cell_info.num_phys[2]; + const auto z0 = cell_info.d_z[0]; + const auto z1 = cell_info.d_z[1]; + const auto z2 = cell_info.d_z[2]; + const auto bw0 = cell_info.d_bw[0]; + const auto bw1 = cell_info.d_bw[1]; + const auto bw2 = cell_info.d_bw[2]; + // Get pointer to the start of the quadrature point values for + // this cell + const auto physvals = + &k_global_physvals_interlaced[cell_info.phys_offset * + num_functions]; + + REAL xi0[NESO_VECTOR_BLOCK_SIZE]; + REAL xi1[NESO_VECTOR_BLOCK_SIZE]; + REAL xi2[NESO_VECTOR_BLOCK_SIZE]; + REAL eta0[NESO_VECTOR_BLOCK_SIZE]; + REAL eta1[NESO_VECTOR_BLOCK_SIZE]; + REAL eta2[NESO_VECTOR_BLOCK_SIZE]; + + for (std::size_t blockx = 0; blockx < local_bound; blockx++) { + const std::size_t px = particle_start + blockx; + xi0[blockx] = k_ref_positions[cell][0][px]; + xi1[blockx] = k_ref_positions[cell][1][px]; + xi2[blockx] = k_ref_positions[cell][2][px]; + } + + for (std::size_t blockx = 0; blockx < NESO_VECTOR_BLOCK_SIZE; + blockx++) { + GeometryInterface::loc_coord_to_loc_collapsed_3d( + cell_info.shape_type_int, xi0[blockx], xi1[blockx], + xi2[blockx], eta0 + blockx, eta1 + blockx, eta2 + blockx); + } + + Bary::preprocess_weights_block( + num_phys0, eta0, z0, bw0, div_space0); + Bary::preprocess_weights_block( + num_phys1, eta1, z1, bw1, div_space1); + Bary::preprocess_weights_block( + num_phys2, eta2, z2, bw2, div_space2); + + Bary::compute_dir_210_interlaced_block( + num_functions, num_phys0, num_phys1, num_phys2, physvals, + div_space0, div_space1, div_space2, evaluations); + + for (std::size_t fx = 0; fx < num_functions; fx++) { + for (std::size_t blockx = 0; blockx < local_bound; blockx++) { + const std::size_t px = particle_start + blockx; + auto ptr = k_syms_ptrs[fx]; + auto component = k_components[fx]; + ptr[cell][component][px] = + evaluations[fx * NESO_VECTOR_BLOCK_SIZE + blockx]; } } - }); - })); - } + } + }); + })); } } diff --git a/include/nektar_interface/utility_sycl.hpp b/include/nektar_interface/utility_sycl.hpp index ebb529ba..fcfc6756 100644 --- a/include/nektar_interface/utility_sycl.hpp +++ b/include/nektar_interface/utility_sycl.hpp @@ -88,6 +88,12 @@ get_particle_loop_global_size(ParticleDatSharedPtr particle_dat, #endif #endif +#ifndef NESO_VECTOR_BLOCK_FACTOR +#define NESO_VECTOR_BLOCK_FACTOR 8 // TODO MAKE THIS CONFIGURATION CMAKE TIME +#endif + +#define NESO_VECTOR_BLOCK_SIZE (NESO_VECTOR_LENGTH * NESO_VECTOR_BLOCK_FACTOR) + /** * For an input integer L >= 0 return smallest M such that M >= L and M % * NESO_VECTOR_LENGTH == 0. diff --git a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp index 2ea40699..1845fe7f 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp @@ -487,7 +487,7 @@ static inline void evaluation_marco(std::string condtions_file_s, auto field_deriv_evaluate = std::make_shared>( field, A, cell_id_translation, true); - for (int cellx = 0; cellx < 10; cellx++) { + for (int cellx = 0; cellx < 40; cellx++) { field_deriv_evaluate->evaluate(Sym("DEDX")); } From 909908848d6ccb93d6e2b739dfb0c1ec6229550d Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 20 Nov 2024 18:02:00 +0000 Subject: [PATCH 46/66] updated flop estimation --- .../function_bary_evaluation.hpp | 16 +++++++++++----- src/nektar_interface/function_evaluation.cpp | 1 + .../test_particle_function_evaluation_3d.cpp | 9 ++++++++- 3 files changed, 20 insertions(+), 6 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 73f6e266..72ad8297 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -407,6 +407,12 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { ProfileRegion pr("BaryEvaluateBase", "evaluate_" + std::to_string(this->ndim) + "d_" + std::to_string(num_functions)); +// TODO GET THIS INTO CMAKE +#ifdef __INTEL_LLVM_COMPILER + constexpr bool always_gpu = true; +#else + constexpr bool always_gpu = false; +#endif if (this->ndim == 2) { this->dispatch_2d( @@ -416,8 +422,7 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { particle_group->get_dat(Sym("NESO_REFERENCE_POSITIONS")), d_syms_ptrs.ptr, d_components.ptr); } else { - - if (this->sycl_target->device.is_gpu()) { + if (this->sycl_target->device.is_gpu() || always_gpu) { this->dispatch_3d( this->sycl_target, es, num_functions, this->max_num_phys, k_global_physvals_interlaced, this->d_cell_info->ptr, @@ -437,9 +442,10 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { const auto nphys = this->max_num_phys; const auto npart = particle_group->get_npart_local(); const auto nflop_prepare = this->ndim * nphys * 5; - const auto nflop_loop = (this->ndim == 2) - ? nphys * nphys * 3 - : nphys * nphys + nphys * nphys * nphys * 3; + const auto nflop_loop = + (this->ndim == 2) + ? nphys * nphys * (1 + num_functions * 2) + : nphys * nphys + nphys * nphys * nphys * (1 + num_functions * 2); pr.num_flops = (nflop_loop + nflop_prepare) * npart; pr.num_bytes = sizeof(REAL) * (npart * ((this->ndim + num_functions)) + num_global_physvals); diff --git a/src/nektar_interface/function_evaluation.cpp b/src/nektar_interface/function_evaluation.cpp index 4010915f..8ed52725 100644 --- a/src/nektar_interface/function_evaluation.cpp +++ b/src/nektar_interface/function_evaluation.cpp @@ -1,3 +1,4 @@ +#define NESO_PARTICLES_PROFILING_REGION // TODO REMOVE #include namespace NESO { diff --git a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp index 1845fe7f..0e58b5a0 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp @@ -1,3 +1,4 @@ +#define NESO_PARTICLES_PROFILING_REGION // TODO REMOVE #include "nektar_interface/function_evaluation.hpp" #include "nektar_interface/particle_interface.hpp" #include "nektar_interface/utilities.hpp" @@ -390,7 +391,7 @@ template static inline void evaluation_marco(std::string condtions_file_s, std::string mesh_file_s, const double tol) { - const int N_total = 1200000; + const int N_total = 12000000; std::filesystem::path source_file = __FILE__; std::filesystem::path source_dir = source_file.parent_path(); @@ -487,9 +488,15 @@ static inline void evaluation_marco(std::string condtions_file_s, auto field_deriv_evaluate = std::make_shared>( field, A, cell_id_translation, true); + for (int cellx = 0; cellx < 2; cellx++) { + field_deriv_evaluate->evaluate(Sym("DEDX")); + } + + sycl_target->profile_map.enable(); for (int cellx = 0; cellx < 40; cellx++) { field_deriv_evaluate->evaluate(Sym("DEDX")); } + sycl_target->profile_map.write_events_json("bary_evaluation", rank); A->free(); mesh->free(); From a2decff50274f78543af9e92b70853a6135ff77b Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Thu, 21 Nov 2024 12:38:42 +0000 Subject: [PATCH 47/66] added missing number of bins argument to get_all_cells --- .../nektar_interface/function_bary_evaluation.hpp | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 72ad8297..8a3f4659 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -66,10 +66,14 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { const std::size_t local_size = sycl_target->parameters->template get("LOOP_LOCAL_SIZE") ->value; + const std::size_t nbin = + sycl_target->parameters->template get("LOOP_NBIN") + ->value; + const std::size_t local_num_reals = static_cast(ndim * k_max_num_phys) + num_functions; const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); - auto is = ish.get_all_cells(local_size, num_bytes_local); + auto is = ish.get_all_cells(nbin, local_size, num_bytes_local); const auto k_ref_positions = ref_positions_dat->cell_dat.device_ptr(); for (auto &blockx : is) { @@ -151,10 +155,13 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { const std::size_t local_size = sycl_target->parameters->template get("LOOP_LOCAL_SIZE") ->value; + const std::size_t nbin = + sycl_target->parameters->template get("LOOP_NBIN") + ->value; const std::size_t local_num_reals = static_cast(ndim * k_max_num_phys) + num_functions; const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); - auto is = ish.get_all_cells(local_size, num_bytes_local); + auto is = ish.get_all_cells(nbin, local_size, num_bytes_local); const auto k_ref_positions = ref_positions_dat->cell_dat.device_ptr(); for (auto &blockx : is) { @@ -251,10 +258,8 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { const std::size_t num_bytes_local = local_num_reals * sizeof(REAL); const auto k_ref_positions = ref_positions_dat->cell_dat.device_ptr(); - // auto is = ish.get_all_cells(local_size, num_bytes_local); auto is = ish.get_all_cells(nbin, local_size, num_bytes_local, NESO_VECTOR_BLOCK_SIZE); - for (auto &blockx : is) { const auto block_device = blockx.block_device; const std::size_t local_size = blockx.local_size; From 6dae47e76c4b39ebe8ce6f48582a3ad640204f88 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Thu, 21 Nov 2024 15:21:05 +0000 Subject: [PATCH 48/66] removed always gpu for intel backends as it is not benefitial --- include/nektar_interface/function_bary_evaluation.hpp | 9 +-------- .../test_particle_function_evaluation_3d.cpp | 6 +++--- 2 files changed, 4 insertions(+), 11 deletions(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 8a3f4659..5b6693ae 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -412,13 +412,6 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { ProfileRegion pr("BaryEvaluateBase", "evaluate_" + std::to_string(this->ndim) + "d_" + std::to_string(num_functions)); -// TODO GET THIS INTO CMAKE -#ifdef __INTEL_LLVM_COMPILER - constexpr bool always_gpu = true; -#else - constexpr bool always_gpu = false; -#endif - if (this->ndim == 2) { this->dispatch_2d( this->sycl_target, es, num_functions, this->max_num_phys, @@ -427,7 +420,7 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { particle_group->get_dat(Sym("NESO_REFERENCE_POSITIONS")), d_syms_ptrs.ptr, d_components.ptr); } else { - if (this->sycl_target->device.is_gpu() || always_gpu) { + if (this->sycl_target->device.is_gpu()) { this->dispatch_3d( this->sycl_target, es, num_functions, this->max_num_phys, k_global_physvals_interlaced, this->d_cell_info->ptr, diff --git a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp index 0e58b5a0..48184382 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp @@ -315,7 +315,7 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, x0, x1, x2, num_phys0, num_phys1, num_phys2, physvalsv.data(), div_space.data(), z0v.data(), z1v.data(), z2v.data(), bw0v.data(), bw1v.data(), bw2v.data(), stride); - EXPECT_NEAR(to_test, to_test_stride, 1.0e-15); + EXPECT_NEAR(to_test, to_test_stride, 1.0e-14); const REAL err_abs = std::abs(correct - to_test); const REAL abs_correct = std::abs(correct); const REAL err_rel = @@ -348,7 +348,7 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, x0, x1, x2, num_phys0, num_phys1, num_phys2, physvalsv.data(), div_space.data(), z0v.data(), z1v.data(), z2v.data(), bw0v.data(), bw1v.data(), bw2v.data(), stride); - EXPECT_NEAR(to_test, to_test_stride, 1.0e-15); + EXPECT_NEAR(to_test, to_test_stride, 1.0e-14); for (int ix = 0; ix < div_space.size(); ix++) { if (ix % stride != 0) { EXPECT_EQ(div_space.at(ix), 3.1415); @@ -391,7 +391,7 @@ template static inline void evaluation_marco(std::string condtions_file_s, std::string mesh_file_s, const double tol) { - const int N_total = 12000000; + const int N_total = 1200000; std::filesystem::path source_file = __FILE__; std::filesystem::path source_dir = source_file.parent_path(); From f80caebcd59e179b5e48cfa78b653baac763dd28 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 9 Dec 2024 14:20:49 +0000 Subject: [PATCH 49/66] MeshGraph::Read -> MeshGraphIO::Read --- test/integration/nektar_interface/test_particle_advection.cpp | 2 +- .../nektar_interface/test_particle_function_evaluation.cpp | 2 +- .../nektar_interface/test_particle_function_evaluation_3d.cpp | 4 ++-- .../nektar_interface/test_particle_geometry_interface.cpp | 2 +- .../test_particle_geometry_interface_3d_curved.cpp | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/test/integration/nektar_interface/test_particle_advection.cpp b/test/integration/nektar_interface/test_particle_advection.cpp index 56b68ab7..e1d36947 100644 --- a/test/integration/nektar_interface/test_particle_advection.cpp +++ b/test/integration/nektar_interface/test_particle_advection.cpp @@ -371,7 +371,7 @@ TEST_P(FooBar, Advection3D) { // Create session reader. auto session = resource_session.session; - auto graph = SpatialDomains::MeshGraph::Read(session); + auto graph = SpatialDomains::MeshGraphIO::Read(session); auto mesh = std::make_shared(graph); extend_halos_fixed_offset(1, mesh); diff --git a/test/unit/nektar_interface/test_particle_function_evaluation.cpp b/test/unit/nektar_interface/test_particle_function_evaluation.cpp index ba2f5379..3a554e3d 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation.cpp @@ -628,7 +628,7 @@ TEST(BaryInterpolation, Evaluation2D) { SpatialDomains::MeshGraphSharedPtr graph; // Create session reader. session = LibUtilities::SessionReader::CreateInstance(argc, argv); - graph = SpatialDomains::MeshGraph::Read(session); + graph = SpatialDomains::MeshGraphIO::Read(session); auto cont_field = std::make_shared(session, graph, "u"); diff --git a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp index 85b4dc2a..f8d3e317 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp @@ -233,7 +233,7 @@ static inline void bary_wrapper_3d(std::string condtions_file_s, SpatialDomains::MeshGraphSharedPtr graph; // Create session reader. session = LibUtilities::SessionReader::CreateInstance(argc, argv); - graph = SpatialDomains::MeshGraph::Read(session); + graph = SpatialDomains::MeshGraphIO::Read(session); auto field = std::make_shared(session, graph, "u"); @@ -415,7 +415,7 @@ static inline void evaluation_marco(std::string condtions_file_s, SpatialDomains::MeshGraphSharedPtr graph; // Create session reader. session = LibUtilities::SessionReader::CreateInstance(argc, argv); - graph = SpatialDomains::MeshGraph::Read(session); + graph = SpatialDomains::MeshGraphIO::Read(session); auto mesh = std::make_shared(graph); auto sycl_target = std::make_shared(0, mesh->get_comm()); diff --git a/test/unit/nektar_interface/test_particle_geometry_interface.cpp b/test/unit/nektar_interface/test_particle_geometry_interface.cpp index 7c1fc1d6..266b536d 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface.cpp @@ -668,7 +668,7 @@ TEST(ParticleGeometryInterface, CoordinateMapping2D) { // Create session reader. auto session = LibUtilities::SessionReader::CreateInstance(argc, argv); - auto graph = SpatialDomains::MeshGraph::Read(session); + auto graph = SpatialDomains::MeshGraphIO::Read(session); auto mesh = std::make_shared(graph); std::map> geoms; get_all_elements_2d(graph, geoms); diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index d67711d2..82ba32f2 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -13,7 +13,7 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { auto session = resource_session.session; // Create MeshGraph. - auto graph = SpatialDomains::MeshGraph::Read(session); + auto graph = SpatialDomains::MeshGraphIO::Read(session); // build map from owned mesh hierarchy cells to geoms that touch that cell auto mesh = std::make_shared(graph); From 47c69d746080aa2cf25d2e472820676d44b18648 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 9 Dec 2024 15:45:02 +0000 Subject: [PATCH 50/66] added bounding box wrapper function for xmap variant --- CMakeLists.txt | 2 ++ .../coarse_lookup_map.hpp | 1 + .../newton_geom_interfaces.hpp | 1 - .../x_map_bounding_box.hpp | 36 +++++++++++++++++++ .../particle_cell_mapping/x_map_newton.hpp | 24 ++++++++++--- .../x_map_bounding_box.cpp | 18 ++++++++++ ..._particle_geometry_interface_3d_curved.cpp | 19 +++++++++- 7 files changed, 95 insertions(+), 6 deletions(-) create mode 100644 include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp create mode 100644 src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp diff --git a/CMakeLists.txt b/CMakeLists.txt index 4239c88c..adc1053c 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -120,6 +120,7 @@ set(LIB_SRC_FILES ${SRC_DIR}/nektar_interface/particle_cell_mapping/map_particles_common.cpp ${SRC_DIR}/nektar_interface/particle_cell_mapping/map_particles_host.cpp ${SRC_DIR}/nektar_interface/particle_cell_mapping/nektar_graph_local_mapper.cpp + ${SRC_DIR}/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp ${SRC_DIR}/nektar_interface/utilities.cpp ${SRC_DIR}/nektar_interface/solver_base/partsys_base.cpp) @@ -208,6 +209,7 @@ set(HEADER_FILES ${INC_DIR}/nektar_interface/particle_cell_mapping/particle_cell_mapping_3d.hpp ${INC_DIR}/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp ${INC_DIR}/nektar_interface/particle_cell_mapping/particle_cell_mapping_newton.hpp + ${INC_DIR}/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp ${INC_DIR}/nektar_interface/particle_cell_mapping/x_map_newton.hpp ${INC_DIR}/nektar_interface/particle_cell_mapping/x_map_newton_kernel.hpp ${INC_DIR}/nektar_interface/particle_interface.hpp diff --git a/include/nektar_interface/particle_cell_mapping/coarse_lookup_map.hpp b/include/nektar_interface/particle_cell_mapping/coarse_lookup_map.hpp index a2b102ca..f5c0b8a2 100644 --- a/include/nektar_interface/particle_cell_mapping/coarse_lookup_map.hpp +++ b/include/nektar_interface/particle_cell_mapping/coarse_lookup_map.hpp @@ -3,6 +3,7 @@ #include "../bounding_box_intersection.hpp" #include "../utility_mesh_cartesian.hpp" +#include "x_map_bounding_box.hpp" #include #include diff --git a/include/nektar_interface/particle_cell_mapping/newton_geom_interfaces.hpp b/include/nektar_interface/particle_cell_mapping/newton_geom_interfaces.hpp index 541cdbf1..eb7a640d 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_geom_interfaces.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_geom_interfaces.hpp @@ -9,6 +9,5 @@ #include "newton_quad_embed_3d.hpp" #include "newton_tet.hpp" #include "newton_triangle_embed_3d.hpp" -#include "particle_cell_mapping_newton.hpp" #endif diff --git a/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp b/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp new file mode 100644 index 00000000..0d0a3ec9 --- /dev/null +++ b/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp @@ -0,0 +1,36 @@ +#ifndef __NESO_PARTICLE_CELL_MAPPING_X_MAP_BOUNDING_BOX_HPP__ +#define __NESO_PARTICLE_CELL_MAPPING_X_MAP_BOUNDING_BOX_HPP__ + +#include +#include + +namespace { +namespace SD = Nektar::SpatialDomains; +} + +namespace NESO::BoundingBox { + +/** + * Return a Nektar++ style bounding box for the geometry object. Padding is + * added to each end of each dimension. i.e. a padding of 5% (pad_rel = 0.05) + * at each end is 10% globally. + * + * @param sycl_target Compute device to compute bounding box on. + * @param geom Geometry object to get bounding box for. + * @param grid_size Resolution of grid to use on each face of the collapsed + * reference space. Default 32. + * @param pad_rel Relative padding to add to computed bounding box, default + * 0.05, i.e. 5%. + * @param pad_abs Absolute padding to add to computed bounding box, default + * 0.0. + * @returns Bounding box in format [minx, miny, minz, maxx, maxy, maxz]; + */ +std::array +get_bounding_box(Particles::SYCLTargetSharedPtr sycl_target, + SD::Geometry3DSharedPtr geom, std::size_t grid_size = 32, + const Particles::REAL pad_rel = 0.05, + const Particles::REAL pad_abs = 0.0); + +} // namespace NESO::BoundingBox + +#endif diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index a6bb838b..b6b5aba4 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -273,13 +273,21 @@ template class XMapNewton { } /** - * Return a Nektar++ style bounding box for the geometry object. + * Return a Nektar++ style bounding box for the geometry object. Padding is + * added to each end of each dimension. i.e. a padding of 5% (pad_rel = 0.05) + * at each end is 10% globally. * * @param grid_size Resolution of grid to use on each face of the collapsed * reference space. Default 32. + * @param pad_rel Relative padding to add to computed bounding box, default + * 0.05, i.e. 5%. + * @param pad_abs Absolute padding to add to computed bounding box, default + * 0.0. * @returns Bounding box in format [minx, miny, minz, maxx, maxy, maxz]; */ - std::array get_bounding_box(std::size_t grid_size = 32) { + std::array get_bounding_box(std::size_t grid_size = 32, + const REAL pad_rel = 0.05, + const REAL pad_abs = 0.0) { char *k_map_data; if (this->dh_data) { k_map_data = this->dh_data->d_buffer.ptr; @@ -289,6 +297,7 @@ template class XMapNewton { NESOASSERT(k_fdata != nullptr, "Bad pointer"); const std::size_t num_bytes_local = std::max(this->num_bytes_local, sizeof(REAL)); + NESOASSERT(this->ndim == 3, "Only implemented in 3D"); // Get a local size which is a power of 2. const std::size_t local_size = @@ -406,7 +415,7 @@ template class XMapNewton { sycl::atomic_ref ar(k_fdata[dimx + 3]); - ar.fetch_max(local_mem[0]); + ar.fetch_max(static_cast(local_mem[0])); } // Tree reduce the minimum local_mem[local_id] = f[dimx]; @@ -421,7 +430,7 @@ template class XMapNewton { sycl::atomic_ref ar(k_fdata[dimx]); - ar.fetch_min(local_mem[0]); + ar.fetch_min(static_cast(local_mem[0])); } } }); @@ -433,6 +442,13 @@ template class XMapNewton { for (int cx = 0; cx < 6; cx++) { output[cx] = this->dh_fdata->h_buffer.ptr[cx]; } + + for (int dx = 0; dx < this->ndim; dx++) { + const REAL width = output.at(dx + 3) - output.at(dx); + const REAL padding = pad_rel * width + pad_abs; + output.at(dx) -= padding; + output.at(dx + 3) += padding; + } return output; } }; diff --git a/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp b/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp new file mode 100644 index 00000000..b547e281 --- /dev/null +++ b/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp @@ -0,0 +1,18 @@ +#include +#include +#include + +namespace NESO::BoundingBox { + +std::array get_bounding_box(SYCLTargetSharedPtr sycl_target, + SD::Geometry3DSharedPtr geom, + std::size_t grid_size, + const REAL pad_rel, const REAL pad_abs) { + + NESOASSERT(geom != nullptr, "Bad geometry object passed."); + + Newton::XMapNewton x_map(sycl_target, geom); + return x_map.get_bounding_box(grid_size, pad_rel, pad_abs); +} + +} // namespace NESO::BoundingBox diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 82ba32f2..ce3adbe9 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -378,7 +378,24 @@ TEST(ParticleGeometryInterfaceCurved, MakeCurvedHex) { } TEST(ParticleGeometryInterfaceCurved, BoundingBox) { - auto sycl_target = std::make_shared(0, MPI_COMM_WORLD); + + { + auto xmapx = [&](auto eta) { + return eta[0] + (0.2 - 0.1 * eta[2] * eta[2]) - 2.0; + }; + auto xmapy = [&](auto eta) { + return eta[1] + 0.1 * eta[0] + 0.1 * eta[2] * eta[2]; + }; + auto xmapz = [&](auto eta) { + return eta[2] + 0.2 * eta[0] * eta[0] + 0.2 * eta[1] * eta[1]; + }; + + const int num_modes = 3; + auto h = make_hex_geom(num_modes, xmapx, xmapy, xmapz); + + auto bb = BoundingBox::get_bounding_box(sycl_target, h, 32, 0.05, 0.0); + } + sycl_target->free(); } From 9c54c973e80d678b1ae5c87c32f749a862d90409 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 9 Dec 2024 17:44:56 +0000 Subject: [PATCH 51/66] fixed local memory type issue --- .../particle_cell_mapping/x_map_newton.hpp | 22 ++++++++++++------- ..._particle_geometry_interface_3d_curved.cpp | 20 +++++++++-------- 2 files changed, 25 insertions(+), 17 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index b6b5aba4..8b754270 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -395,42 +395,48 @@ template class XMapNewton { k_newton_type.newton_residual( k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f, f + 1, f + 2, &local_mem[local_id * num_bytes_local]); + idx.barrier(sycl::access::fence_space::local_space); + REAL *local_mem_real = + static_cast(static_cast(&local_mem[0])); + // Do the reductions, we pessimistically do not use the builtin // SYCL functions as we have used all the local memory already // and the SYCL reduction functions also use local memory. for (int dimx = 0; dimx < 3; dimx++) { // Tree reduce the maximum - local_mem[local_id] = f[dimx]; + local_mem_real[local_id] = f[dimx]; for (int ix = local_size_l / 2; ix > 0; ix >>= 1) { idx.barrier(sycl::access::fence_space::local_space); if (local_id < ix) { - local_mem[local_id] = sycl::max(local_mem[local_id + ix], - local_mem[local_id]); + local_mem_real[local_id] = + sycl::max(local_mem_real[local_id + ix], + local_mem_real[local_id]); } } if (local_id == 0) { sycl::atomic_ref ar(k_fdata[dimx + 3]); - ar.fetch_max(static_cast(local_mem[0])); + auto check = ar.fetch_max(local_mem_real[0]); } // Tree reduce the minimum - local_mem[local_id] = f[dimx]; + local_mem_real[local_id] = f[dimx]; for (int ix = local_size_l / 2; ix > 0; ix >>= 1) { idx.barrier(sycl::access::fence_space::local_space); if (local_id < ix) { - local_mem[local_id] = sycl::min(local_mem[local_id + ix], - local_mem[local_id]); + local_mem_real[local_id] = + sycl::min(local_mem_real[local_id + ix], + local_mem_real[local_id]); } } if (local_id == 0) { sycl::atomic_ref ar(k_fdata[dimx]); - ar.fetch_min(static_cast(local_mem[0])); + auto check = ar.fetch_min(local_mem_real[0]); } } }); diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index ce3adbe9..cca4d59e 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -380,21 +380,23 @@ TEST(ParticleGeometryInterfaceCurved, MakeCurvedHex) { TEST(ParticleGeometryInterfaceCurved, BoundingBox) { auto sycl_target = std::make_shared(0, MPI_COMM_WORLD); + // Test a linear mapped box { - auto xmapx = [&](auto eta) { - return eta[0] + (0.2 - 0.1 * eta[2] * eta[2]) - 2.0; - }; - auto xmapy = [&](auto eta) { - return eta[1] + 0.1 * eta[0] + 0.1 * eta[2] * eta[2]; - }; - auto xmapz = [&](auto eta) { - return eta[2] + 0.2 * eta[0] * eta[0] + 0.2 * eta[1] * eta[1]; - }; + auto xmapx = [&](auto eta) { return eta[0] + 1; }; + auto xmapy = [&](auto eta) { return eta[1] * 2 - 4; }; + auto xmapz = [&](auto eta) { return eta[2] * 0.5 + 7; }; const int num_modes = 3; auto h = make_hex_geom(num_modes, xmapx, xmapy, xmapz); auto bb = BoundingBox::get_bounding_box(sycl_target, h, 32, 0.05, 0.0); + + nprint_variable(bb[0]); + nprint_variable(bb[1]); + nprint_variable(bb[2]); + nprint_variable(bb[3]); + nprint_variable(bb[4]); + nprint_variable(bb[5]); } sycl_target->free(); From f65918a32cb34eed0d984f8f282becd41020e85f Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 10 Dec 2024 14:56:23 +0000 Subject: [PATCH 52/66] added linear tests for bounding box computation --- CMakeLists.txt | 1 + .../geometry_transport/utility_geometry.hpp | 25 ++++++++ .../x_map_bounding_box.hpp | 21 ++++--- .../x_map_bounding_box.cpp | 37 +++++++++-- ..._particle_geometry_interface_3d_curved.cpp | 62 ++++++++++++++++--- 5 files changed, 124 insertions(+), 22 deletions(-) create mode 100644 include/nektar_interface/geometry_transport/utility_geometry.hpp diff --git a/CMakeLists.txt b/CMakeLists.txt index adc1053c..62a7f100 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -167,6 +167,7 @@ set(HEADER_FILES ${INC_DIR}/nektar_interface/geometry_transport/geometry_transport_2d.hpp ${INC_DIR}/nektar_interface/geometry_transport/geometry_transport_3d.hpp ${INC_DIR}/nektar_interface/geometry_transport/geometry_types_3d.hpp + ${INC_DIR}/nektar_interface/geometry_transport/utility_geometry.hpp ${INC_DIR}/nektar_interface/geometry_transport/halo_extension.hpp ${INC_DIR}/nektar_interface/geometry_transport/packed_geom_2d.hpp ${INC_DIR}/nektar_interface/geometry_transport/packed_geoms_2d.hpp diff --git a/include/nektar_interface/geometry_transport/utility_geometry.hpp b/include/nektar_interface/geometry_transport/utility_geometry.hpp new file mode 100644 index 00000000..3c82fc91 --- /dev/null +++ b/include/nektar_interface/geometry_transport/utility_geometry.hpp @@ -0,0 +1,25 @@ +#ifndef _NESO_GEOMETRY_TRANSPORT_UTILITY_GEOMETRY_HPP_ +#define _NESO_GEOMETRY_TRANSPORT_UTILITY_GEOMETRY_HPP_ + +#include + +namespace NESO { + +/** + * @returns True if the geometry object is linear. + */ +template +inline bool geometry_is_linear(std::shared_ptr geom) { + const int ndim = geom->GetCoordim(); + const auto xmap = geom->GetXmap(); + for (int dimx = 0; dimx < ndim; dimx++) { + if (xmap->GetBasisNumModes(dimx) != 2) { + return false; + } + } + return true; +} + +} // namespace NESO + +#endif diff --git a/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp b/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp index 0d0a3ec9..16644d51 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp @@ -1,6 +1,8 @@ #ifndef __NESO_PARTICLE_CELL_MAPPING_X_MAP_BOUNDING_BOX_HPP__ #define __NESO_PARTICLE_CELL_MAPPING_X_MAP_BOUNDING_BOX_HPP__ +#include "../geometry_transport/utility_geometry.hpp" +#include "../parameter_store.hpp" #include #include @@ -15,21 +17,22 @@ namespace NESO::BoundingBox { * added to each end of each dimension. i.e. a padding of 5% (pad_rel = 0.05) * at each end is 10% globally. * + * Parameters: + * get_bounding_box/linear_pad_rel + * get_bounding_box/linear_pad_abs + * get_bounding_box/nonlinear_pad_rel + * get_bounding_box/nonlinear_pad_abs + * get_bounding_box/nonlinear_grid_size_factor + * * @param sycl_target Compute device to compute bounding box on. * @param geom Geometry object to get bounding box for. - * @param grid_size Resolution of grid to use on each face of the collapsed - * reference space. Default 32. - * @param pad_rel Relative padding to add to computed bounding box, default - * 0.05, i.e. 5%. - * @param pad_abs Absolute padding to add to computed bounding box, default - * 0.0. + * @param parameter_store ParameterStore containing parameters. * @returns Bounding box in format [minx, miny, minz, maxx, maxy, maxz]; */ std::array get_bounding_box(Particles::SYCLTargetSharedPtr sycl_target, - SD::Geometry3DSharedPtr geom, std::size_t grid_size = 32, - const Particles::REAL pad_rel = 0.05, - const Particles::REAL pad_abs = 0.0); + SD::Geometry3DSharedPtr geom, + ParameterStoreSharedPtr parameter_store); } // namespace NESO::BoundingBox diff --git a/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp b/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp index b547e281..7c25537f 100644 --- a/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp +++ b/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp @@ -4,14 +4,41 @@ namespace NESO::BoundingBox { -std::array get_bounding_box(SYCLTargetSharedPtr sycl_target, - SD::Geometry3DSharedPtr geom, - std::size_t grid_size, - const REAL pad_rel, const REAL pad_abs) { +std::array +get_bounding_box(Particles::SYCLTargetSharedPtr sycl_target, + SD::Geometry3DSharedPtr geom, + ParameterStoreSharedPtr parameter_store) { NESOASSERT(geom != nullptr, "Bad geometry object passed."); - + const bool is_linear = geometry_is_linear(geom); + const std::size_t max_num_modes = + static_cast(geom->GetXmap()->EvalBasisNumModesMax()); Newton::XMapNewton x_map(sycl_target, geom); + + REAL pad_rel = 0.0; + REAL pad_abs = 0.0; + std::size_t grid_size = 2; + + if (is_linear) { + pad_rel = + parameter_store->get("get_bounding_box/linear_pad_rel", 0.0); + pad_abs = + parameter_store->get("get_bounding_box/linear_pad_abs", 0.0); + grid_size = 2; + } else { + pad_rel = + parameter_store->get("get_bounding_box/nonlinear_pad_rel", 0.05); + pad_abs = + parameter_store->get("get_bounding_box/nonlinear_pad_abs", 0.0); + const auto grid_size_factor = parameter_store->get( + "get_bounding_box/nonlinear_grid_size_factor", 4); + grid_size = static_cast(grid_size_factor) * max_num_modes; + } + + NESOASSERT(grid_size >= 2, "Bad bounding box grid size (< 2)."); + NESOASSERT(pad_rel >= 0.0, "Bad bounding box pad_rel (< 0.0)"); + NESOASSERT(pad_abs >= 0.0, "Bad bounding box pad_abs (< 0.0)"); + return x_map.get_bounding_box(grid_size, pad_rel, pad_abs); } diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index cca4d59e..67d6e648 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -379,6 +379,39 @@ TEST(ParticleGeometryInterfaceCurved, MakeCurvedHex) { TEST(ParticleGeometryInterfaceCurved, BoundingBox) { auto sycl_target = std::make_shared(0, MPI_COMM_WORLD); + const REAL k_tol = 1.0e-12; + auto lambda_test = [&](const std::array &bb, + const std::array correct) { + ASSERT_NEAR(bb[0], correct[0], k_tol); + ASSERT_NEAR(bb[3], correct[3], k_tol); + ASSERT_NEAR(bb[1], correct[1], k_tol); + ASSERT_NEAR(bb[4], correct[4], k_tol); + ASSERT_NEAR(bb[2], correct[2], k_tol); + ASSERT_NEAR(bb[5], correct[5], k_tol); + }; + + auto lambda_get_linear_bb = [&](auto geom) -> std::array { + const int num_verts = geom->GetNumVerts(); + const int ndim = geom->GetCoordim(); + Array coords(3); + std::array bb; + std::fill(bb.begin(), bb.end(), 0.0); + std::fill(bb.begin(), bb.begin() + ndim, + std::numeric_limits::max()); + std::fill(bb.begin() + 3, bb.begin() + 3 + ndim, + std::numeric_limits::lowest()); + + for (int vx = 0; vx < num_verts; vx++) { + auto point = geom->GetVertex(vx); + point->GetCoords(coords); + for (int dx = 0; dx < ndim; dx++) { + bb.at(dx) = std::min(bb.at(dx), coords[dx]); + bb.at(dx + 3) = std::max(bb.at(dx + 3), coords[dx]); + } + } + + return bb; + }; // Test a linear mapped box { @@ -386,17 +419,30 @@ TEST(ParticleGeometryInterfaceCurved, BoundingBox) { auto xmapy = [&](auto eta) { return eta[1] * 2 - 4; }; auto xmapz = [&](auto eta) { return eta[2] * 0.5 + 7; }; - const int num_modes = 3; + const int num_modes = 2; auto h = make_hex_geom(num_modes, xmapx, xmapy, xmapz); - auto bb = BoundingBox::get_bounding_box(sycl_target, h, 32, 0.05, 0.0); + auto config = std::make_shared(); + auto bb = BoundingBox::get_bounding_box(sycl_target, h, config); + + lambda_test(bb, {0.0, -6.0, 6.5, 2.0, -2.0, 7.5}); + lambda_test(bb, lambda_get_linear_bb(h)); + } + + // Test a bilinear mapped box + { + auto xmapx = [&](auto eta) { return eta[0] + 0.1 * eta[1] + 1; }; + auto xmapy = [&](auto eta) { return eta[1] * 2 - 4 + eta[2] * 0.2; }; + auto xmapz = [&](auto eta) { + return eta[2] * 0.5 + 7 + eta[0] * 0.1 + eta[1] * 0.2; + }; + + const int num_modes = 2; + auto h = make_hex_geom(num_modes, xmapx, xmapy, xmapz); - nprint_variable(bb[0]); - nprint_variable(bb[1]); - nprint_variable(bb[2]); - nprint_variable(bb[3]); - nprint_variable(bb[4]); - nprint_variable(bb[5]); + auto config = std::make_shared(); + auto bb = BoundingBox::get_bounding_box(sycl_target, h, config); + lambda_test(bb, lambda_get_linear_bb(h)); } sycl_target->free(); From bdd4f9153d32834d3a955c263ae8978a02b90ccf Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 10 Dec 2024 16:02:49 +0000 Subject: [PATCH 53/66] added a set of quadratic xmaps for bounding box computation tests --- include/nektar_interface/utility_mesh.hpp | 14 +++---- ..._particle_geometry_interface_3d_curved.cpp | 41 ++++++++++++++++++- 2 files changed, 47 insertions(+), 8 deletions(-) diff --git a/include/nektar_interface/utility_mesh.hpp b/include/nektar_interface/utility_mesh.hpp index 7c519658..dc8b86a2 100644 --- a/include/nektar_interface/utility_mesh.hpp +++ b/include/nektar_interface/utility_mesh.hpp @@ -18,13 +18,13 @@ namespace NESO { * @param num_modes Number of modes in the coordinate mapping for the Xmap, i.e. * polynomial order plus 1. * @param xmapx Callable that defines the X map in the x direction with - * signature NekDouble(NekDouble[3]) where the single argument is a + * signature NekDouble(std::array) where the single argument is a * subscriptable type.; * @param xmapy Callable that defines the X map in the y direction with - * signature NekDouble(NekDouble[3]) where the single argument is a + * signature NekDouble(std::array) where the single argument is a * subscriptable type.; * @param xmapz Callable that defines the X map in the z direction with - * signature NekDouble(NekDouble[3]) where the single argument is a + * signature NekDouble(std::array) where the single argument is a * subscriptable type.; * @returns HexGeom constructed from X maps. */ @@ -82,10 +82,10 @@ make_hex_geom(const int num_modes, T xmapx, U xmapy, V xmapz) { * (slider)" */ - NekDouble coords_vertices[8][3] = {{-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, - {1.0, 1.0, -1.0}, {-1.0, 1.0, -1.0}, - {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, - {1.0, 1.0, 1.0}, {-1.0, 1.0, 1.0}}; + std::array coords_vertices[8] = { + {-1.0, -1.0, -1.0}, {1.0, -1.0, -1.0}, {1.0, 1.0, -1.0}, + {-1.0, 1.0, -1.0}, {-1.0, -1.0, 1.0}, {1.0, -1.0, 1.0}, + {1.0, 1.0, 1.0}, {-1.0, 1.0, 1.0}}; int map_edge_to_vertices[12][2] = { {0, 1}, {1, 2}, {2, 3}, {3, 0}, diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 67d6e648..981f8e35 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -379,7 +379,7 @@ TEST(ParticleGeometryInterfaceCurved, MakeCurvedHex) { TEST(ParticleGeometryInterfaceCurved, BoundingBox) { auto sycl_target = std::make_shared(0, MPI_COMM_WORLD); - const REAL k_tol = 1.0e-12; + REAL k_tol = 1.0e-12; auto lambda_test = [&](const std::array &bb, const std::array correct) { ASSERT_NEAR(bb[0], correct[0], k_tol); @@ -445,5 +445,44 @@ TEST(ParticleGeometryInterfaceCurved, BoundingBox) { lambda_test(bb, lambda_get_linear_bb(h)); } + // quadratic maps + k_tol = 1.0e-2; + { + auto lambda_id0 = [](auto eta) { return eta[0]; }; + auto lambda_id1 = [](auto eta) { return eta[1]; }; + auto lambda_id2 = [](auto eta) { return eta[2]; }; + + auto config = std::make_shared(); + config->set("get_bounding_box/nonlinear_pad_rel", 0.0); + config->set("get_bounding_box/nonlinear_pad_abs", 0.0); + config->set("get_bounding_box/nonlinear_grid_size_factor", 5); + + for (int dx : {0, 1, 2}) { + + std::function)> xmap[3] = { + lambda_id0, lambda_id1, lambda_id2}; + + for (auto a : {-0.4, 0.4}) { + const int dy = (dx + 1) % 3; + auto xmapdx = [&](auto eta) { + return eta[dx] + a * (1.0 - eta[dy] * eta[dy]); + }; + xmap[dx] = xmapdx; + + const int num_modes = 3; + auto h = make_hex_geom(num_modes, xmap[0], xmap[1], xmap[2]); + auto ll = lambda_get_linear_bb(h); + auto bb = BoundingBox::get_bounding_box(sycl_target, h, config); + + if (a > 0.0) { + ll[dx + 3] += a; + } else { + ll[dx] += a; + } + lambda_test(bb, ll); + } + } + } + sycl_target->free(); } From 8a9e8082dbaf50cc9af21b297d8bd97d5f1e0bc2 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 10 Dec 2024 16:35:44 +0000 Subject: [PATCH 54/66] made utility bounding box function accept 2D geoms such that it can be a drop in replacement --- .../geometry_transport/utility_geometry.hpp | 2 +- .../particle_cell_mapping/x_map_bounding_box.hpp | 2 +- .../particle_cell_mapping/x_map_newton.hpp | 1 - .../particle_cell_mapping/x_map_bounding_box.cpp | 11 +++++++++-- .../test_particle_geometry_interface_3d_curved.cpp | 6 +++--- 5 files changed, 14 insertions(+), 8 deletions(-) diff --git a/include/nektar_interface/geometry_transport/utility_geometry.hpp b/include/nektar_interface/geometry_transport/utility_geometry.hpp index 3c82fc91..979e9a48 100644 --- a/include/nektar_interface/geometry_transport/utility_geometry.hpp +++ b/include/nektar_interface/geometry_transport/utility_geometry.hpp @@ -10,8 +10,8 @@ namespace NESO { */ template inline bool geometry_is_linear(std::shared_ptr geom) { - const int ndim = geom->GetCoordim(); const auto xmap = geom->GetXmap(); + const int ndim = xmap->GetBase().size(); for (int dimx = 0; dimx < ndim; dimx++) { if (xmap->GetBasisNumModes(dimx) != 2) { return false; diff --git a/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp b/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp index 16644d51..b44ab8cc 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp @@ -31,7 +31,7 @@ namespace NESO::BoundingBox { */ std::array get_bounding_box(Particles::SYCLTargetSharedPtr sycl_target, - SD::Geometry3DSharedPtr geom, + SD::GeometrySharedPtr geom, ParameterStoreSharedPtr parameter_store); } // namespace NESO::BoundingBox diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 8b754270..c9a92890 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -297,7 +297,6 @@ template class XMapNewton { NESOASSERT(k_fdata != nullptr, "Bad pointer"); const std::size_t num_bytes_local = std::max(this->num_bytes_local, sizeof(REAL)); - NESOASSERT(this->ndim == 3, "Only implemented in 3D"); // Get a local size which is a power of 2. const std::size_t local_size = diff --git a/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp b/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp index 7c25537f..c49e79ff 100644 --- a/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp +++ b/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp @@ -6,13 +6,20 @@ namespace NESO::BoundingBox { std::array get_bounding_box(Particles::SYCLTargetSharedPtr sycl_target, - SD::Geometry3DSharedPtr geom, + SD::GeometrySharedPtr geom, ParameterStoreSharedPtr parameter_store) { NESOASSERT(geom != nullptr, "Bad geometry object passed."); + + auto xmap = geom->GetXmap(); + const int ndim = xmap->GetBase().size(); + if (ndim < 3) { + return geom->GetBoundingBox(); + } + const bool is_linear = geometry_is_linear(geom); const std::size_t max_num_modes = - static_cast(geom->GetXmap()->EvalBasisNumModesMax()); + static_cast(xmap->EvalBasisNumModesMax()); Newton::XMapNewton x_map(sycl_target, geom); REAL pad_rel = 0.0; diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 981f8e35..5abbadaf 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -413,7 +413,7 @@ TEST(ParticleGeometryInterfaceCurved, BoundingBox) { return bb; }; - // Test a linear mapped box + // Test a linear mapped hex { auto xmapx = [&](auto eta) { return eta[0] + 1; }; auto xmapy = [&](auto eta) { return eta[1] * 2 - 4; }; @@ -429,7 +429,7 @@ TEST(ParticleGeometryInterfaceCurved, BoundingBox) { lambda_test(bb, lambda_get_linear_bb(h)); } - // Test a bilinear mapped box + // Test a bilinear mapped hex { auto xmapx = [&](auto eta) { return eta[0] + 0.1 * eta[1] + 1; }; auto xmapy = [&](auto eta) { return eta[1] * 2 - 4 + eta[2] * 0.2; }; @@ -445,7 +445,7 @@ TEST(ParticleGeometryInterfaceCurved, BoundingBox) { lambda_test(bb, lambda_get_linear_bb(h)); } - // quadratic maps + // quadratic mapped hex k_tol = 1.0e-2; { auto lambda_id0 = [](auto eta) { return eta[0]; }; From b0e52c2213d3bcdb3e6ca89ed1b277547d01a4a5 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 10 Dec 2024 16:49:57 +0000 Subject: [PATCH 55/66] reordered head files to make slightly more sense --- .../particle_cell_mapping/map_particles_3d.hpp | 2 +- .../particle_cell_mapping/map_particles_newton.hpp | 1 + .../particle_cell_mapping/newton_generic_3d.hpp | 3 +-- .../nektar_interface/particle_cell_mapping/newton_hex.hpp | 3 ++- .../particle_cell_mapping/newton_triangle_embed_3d.hpp | 6 ++++-- 5 files changed, 9 insertions(+), 6 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_3d.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_3d.hpp index e71e1cf1..ed146f7b 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_3d.hpp @@ -20,7 +20,7 @@ #include #include -#include "newton_geom_interfaces.hpp" +#include "particle_cell_mapping_newton.hpp" using namespace Nektar::SpatialDomains; using namespace NESO; diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp index 77a99da1..d1b4cf72 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp @@ -10,6 +10,7 @@ #include "coarse_mappers_base.hpp" #include "mapping_newton_iteration_base.hpp" #include "nektar_interface/parameter_store.hpp" +#include "newton_geom_interfaces.hpp" #include "particle_cell_mapping_common.hpp" #include "x_map_newton_kernel.hpp" diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index 2b95fd2e..a3ee2e3c 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -3,8 +3,7 @@ #include "../bary_interpolation/bary_evaluation.hpp" #include "../coordinate_mapping.hpp" -#include "generated_linear/linear_newton_implementation.hpp" -#include "particle_cell_mapping_newton.hpp" +#include "mapping_newton_iteration_base.hpp" #include using namespace NESO; diff --git a/include/nektar_interface/particle_cell_mapping/newton_hex.hpp b/include/nektar_interface/particle_cell_mapping/newton_hex.hpp index c7ea0588..061d71aa 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_hex.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_hex.hpp @@ -2,9 +2,10 @@ #define ___NESO_PARTICLE_MAPPING_NEWTON_HEX_H__ #include "generated_linear/linear_newton_implementation.hpp" -#include "particle_cell_mapping_newton.hpp" #include +#include "mapping_newton_iteration_base.hpp" +using namespace Nektar; using namespace NESO; using namespace NESO::Particles; diff --git a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp index 75701a82..da4aae53 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp @@ -1,11 +1,13 @@ #ifndef ___NESO_PARTICLE_MAPPING_NEWTON_TRIANGLE_EMBED_3D_H__ #define ___NESO_PARTICLE_MAPPING_NEWTON_TRIANGLE_EMBED_3D_H__ -#include "generated_linear/linear_newton_implementation.hpp" #include "nektar_interface/special_functions.hpp" -#include "particle_cell_mapping_newton.hpp" + +#include "generated_linear/linear_newton_implementation.hpp" #include +#include "mapping_newton_iteration_base.hpp" +using namespace Nektar; using namespace NESO; using namespace NESO::Particles; From a7c725daefb6bfa3e3ad0aeccd616a3ee06ba944 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 16 Dec 2024 12:02:04 +0000 Subject: [PATCH 56/66] helper interfaces for BoundingBox::get_bounding_box --- .../bounding_box_intersection.hpp | 3 +- .../x_map_bounding_box.hpp | 22 +++++++++++- .../x_map_bounding_box.cpp | 35 +++++++++++++------ 3 files changed, 48 insertions(+), 12 deletions(-) diff --git a/include/nektar_interface/bounding_box_intersection.hpp b/include/nektar_interface/bounding_box_intersection.hpp index e8c431d1..678bd04e 100644 --- a/include/nektar_interface/bounding_box_intersection.hpp +++ b/include/nektar_interface/bounding_box_intersection.hpp @@ -100,7 +100,8 @@ expand_bounding_box_array(std::array &bounding_box_in, /** * Extend the bounds of a bounding box to include the given element. * - * @param element Nektar++ element that includes a GetBoundingBox method. + * @param element Nektar++ element for which BoundingBox::get_bounding_box can + * be called. * @param bounding_box Bounding box to extend using element. */ template diff --git a/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp b/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp index b44ab8cc..8bb22c03 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_bounding_box.hpp @@ -32,7 +32,27 @@ namespace NESO::BoundingBox { std::array get_bounding_box(Particles::SYCLTargetSharedPtr sycl_target, SD::GeometrySharedPtr geom, - ParameterStoreSharedPtr parameter_store); + ParameterStoreSharedPtr parameter_store = nullptr); + +/** + * Return a Nektar++ style bounding box for the geometry object. Padding is + * added to each end of each dimension. i.e. a padding of 5% (pad_rel = 0.05) + * at each end is 10% globally. + * + * Parameters: + * get_bounding_box/linear_pad_rel + * get_bounding_box/linear_pad_abs + * get_bounding_box/nonlinear_pad_rel + * get_bounding_box/nonlinear_pad_abs + * get_bounding_box/nonlinear_grid_size_factor + * + * @param geom Geometry object to get bounding box for. + * @param parameter_store ParameterStore containing parameters. + * @returns Bounding box in format [minx, miny, minz, maxx, maxy, maxz]; + */ +std::array +get_bounding_box(SD::GeometrySharedPtr geom, + ParameterStoreSharedPtr parameter_store = nullptr); } // namespace NESO::BoundingBox diff --git a/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp b/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp index c49e79ff..ee52e0c2 100644 --- a/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp +++ b/src/nektar_interface/particle_cell_mapping/x_map_bounding_box.cpp @@ -27,18 +27,24 @@ get_bounding_box(Particles::SYCLTargetSharedPtr sycl_target, std::size_t grid_size = 2; if (is_linear) { - pad_rel = - parameter_store->get("get_bounding_box/linear_pad_rel", 0.0); - pad_abs = - parameter_store->get("get_bounding_box/linear_pad_abs", 0.0); + if (parameter_store != nullptr) { + pad_rel = + parameter_store->get("get_bounding_box/linear_pad_rel", 0.0); + pad_abs = + parameter_store->get("get_bounding_box/linear_pad_abs", 0.0); + } grid_size = 2; } else { - pad_rel = - parameter_store->get("get_bounding_box/nonlinear_pad_rel", 0.05); - pad_abs = - parameter_store->get("get_bounding_box/nonlinear_pad_abs", 0.0); - const auto grid_size_factor = parameter_store->get( - "get_bounding_box/nonlinear_grid_size_factor", 4); + pad_rel = 0.0; + INT grid_size_factor = 4; + if (parameter_store != nullptr) { + pad_rel = parameter_store->get("get_bounding_box/nonlinear_pad_rel", + 0.05); + pad_abs = + parameter_store->get("get_bounding_box/nonlinear_pad_abs", 0.0); + grid_size_factor = parameter_store->get( + "get_bounding_box/nonlinear_grid_size_factor", 4); + } grid_size = static_cast(grid_size_factor) * max_num_modes; } @@ -49,4 +55,13 @@ get_bounding_box(Particles::SYCLTargetSharedPtr sycl_target, return x_map.get_bounding_box(grid_size, pad_rel, pad_abs); } +std::array +get_bounding_box(SD::GeometrySharedPtr geom, + ParameterStoreSharedPtr parameter_store) { + auto sycl_target = std::make_shared(0, MPI_COMM_SELF, 0); + auto bb = get_bounding_box(sycl_target, geom, parameter_store); + sycl_target->free(); + return bb; +} + } // namespace NESO::BoundingBox From 87d9c6018368e5a9cc4415495c1c4aa2ddbd4993 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 16 Dec 2024 12:04:14 +0000 Subject: [PATCH 57/66] removed some dead code marked as to-remove --- src/nektar_interface/function_evaluation.cpp | 1 - .../test_particle_advection.cpp | 175 ------------------ .../test_particle_function_evaluation_3d.cpp | 130 ------------- 3 files changed, 306 deletions(-) diff --git a/src/nektar_interface/function_evaluation.cpp b/src/nektar_interface/function_evaluation.cpp index 8ed52725..4010915f 100644 --- a/src/nektar_interface/function_evaluation.cpp +++ b/src/nektar_interface/function_evaluation.cpp @@ -1,4 +1,3 @@ -#define NESO_PARTICLES_PROFILING_REGION // TODO REMOVE #include namespace NESO { diff --git a/test/integration/nektar_interface/test_particle_advection.cpp b/test/integration/nektar_interface/test_particle_advection.cpp index e1d36947..515d2ba2 100644 --- a/test/integration/nektar_interface/test_particle_advection.cpp +++ b/test/integration/nektar_interface/test_particle_advection.cpp @@ -353,178 +353,3 @@ INSTANTIATE_TEST_SUITE_P( // like (err_x * err_x // + err_y * err_y) < 1.0e-8 ))); - -// TODO REMOVE START -class FooBar : public testing::TestWithParam< - std::tuple> {}; -TEST_P(FooBar, Advection3D) { - // Test advecting particles between ranks - - std::tuple param = GetParam(); - - const int N_total = 100000; - const double tol = std::get<2>(param); - - TestUtilities::TestResourceSession resource_session( - static_cast(std::get<1>(param)), - static_cast(std::get<0>(param))); - - // Create session reader. - auto session = resource_session.session; - auto graph = SpatialDomains::MeshGraphIO::Read(session); - - auto mesh = std::make_shared(graph); - extend_halos_fixed_offset(1, mesh); - auto sycl_target = std::make_shared(0, mesh->get_comm()); - - auto config = std::make_shared(); - config->set("MapParticlesNewton/newton_tol", 1.0e-12); - config->set("MapParticlesNewton/contained_tol", 1.0e-2); - - auto nektar_graph_local_mapper = - std::make_shared(sycl_target, mesh, config); - - auto domain = std::make_shared(mesh, nektar_graph_local_mapper); - - const int ndim = 3; - ParticleSpec particle_spec{ParticleProp(Sym("P"), ndim, true), - ParticleProp(Sym("P_ORIG"), ndim), - ParticleProp(Sym("V"), 3), - ParticleProp(Sym("CELL_ID"), 1, true), - ParticleProp(Sym("ID"), 1)}; - - auto A = std::make_shared(domain, particle_spec, sycl_target); - - NektarCartesianPeriodic pbc(sycl_target, graph, A->position_dat); - - CellIDTranslation cell_id_translation(sycl_target, A->cell_id_dat, mesh); - - const int rank = sycl_target->comm_pair.rank_parent; - const int size = sycl_target->comm_pair.size_parent; - - std::mt19937 rng_pos(52234234 + rank); - std::mt19937 rng_vel(52234231 + rank); - std::mt19937 rng_rank(18241); - - int rstart, rend; - get_decomp_1d(size, N_total, rank, &rstart, &rend); - const int N = rend - rstart; - - int N_check = -1; - MPICHK(MPI_Allreduce(&N, &N_check, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD)); - NESOASSERT(N_check == N_total, "Error creating particles"); - - const int Nsteps = 20; - const REAL dt = 0.1; - const int cell_count = domain->mesh->get_cell_count(); - - if (N > 0) { - auto positions = - uniform_within_extents(N, ndim, pbc.global_extent, rng_pos); - auto velocities = - NESO::Particles::normal_distribution(N, 3, 0.0, 0.5, rng_vel); - std::uniform_int_distribution uniform_dist( - 0, sycl_target->comm_pair.size_parent - 1); - ParticleSet initial_distribution(N, A->get_particle_spec()); - for (int px = 0; px < N; px++) { - for (int dimx = 0; dimx < ndim; dimx++) { - const double pos_orig = positions[dimx][px] + pbc.global_origin[dimx]; - initial_distribution[Sym("P")][px][dimx] = pos_orig; - initial_distribution[Sym("P_ORIG")][px][dimx] = pos_orig; - } - for (int dimx = 0; dimx < 3; dimx++) { - initial_distribution[Sym("V")][px][dimx] = velocities[dimx][px]; - } - initial_distribution[Sym("CELL_ID")][px][0] = 0; - initial_distribution[Sym("ID")][px][0] = px; - const auto px_rank = uniform_dist(rng_rank); - initial_distribution[Sym("NESO_MPI_RANK")][px][0] = px_rank; - } - A->add_particles_local(initial_distribution); - } - reset_mpi_ranks((*A)[Sym("NESO_MPI_RANK")]); - - MeshHierarchyGlobalMap mesh_hierarchy_global_map( - sycl_target, domain->mesh, A->position_dat, A->cell_id_dat, - A->mpi_rank_dat); - - auto lambda_advect = [&] { - auto t0 = profile_timestamp(); - particle_loop( - A, - [=](auto P, auto V) { - for (int dimx = 0; dimx < ndim; dimx++) { - P.at(dimx) += dt * V.at(dimx); - } - }, - Access::write(Sym("P")), Access::read(Sym("V"))) - ->execute(); - sycl_target->profile_map.inc("Advect", "Execute", 1, - profile_elapsed(t0, profile_timestamp())); - }; - - H5Part h5part("trajectory.h5part", A, Sym("P"), - Sym("NESO_MPI_RANK"), - Sym("NESO_REFERENCE_POSITIONS")); - - write_vtk_cells_owned("owned_cells", mesh); - - for (int stepx = 0; stepx < 2; stepx++) { - pbc.execute(); - mesh_hierarchy_global_map.execute(); - A->hybrid_move(); - cell_id_translation.execute(); - A->cell_move(); - lambda_advect(); - h5part.write(); - h5part.close(); - } - sycl_target->profile_map.enable(); - sycl_target->profile_map.reset(); - auto t0 = profile_timestamp(); - REAL T = 0.0; - for (int stepx = 0; stepx < Nsteps; stepx++) { - pbc.execute(); - mesh_hierarchy_global_map.execute(); - A->hybrid_move(); - cell_id_translation.execute(); - A->cell_move(); - - lambda_advect(); - T += dt; - - auto tt = profile_elapsed(t0, profile_timestamp()); - - if (!rank) { - nprint(stepx, tt / (((stepx + 1)) * N_total)); - } - // h5part.write(); - } - sycl_target->profile_map.write_events_json("newton_test_events", rank); - - // h5part.close(); - mesh->free(); -} - -INSTANTIATE_TEST_SUITE_P( - MultipleMeshes, FooBar, - testing::Values( - std::tuple( - "reference_all_types_cube/conditions.xml", - "reference_all_types_cube/linear_non_regular_0.5.xml", - 1.0e-4 // The non-linear exit tolerance in Nektar is - // like (err_x * err_x - // + err_y * err_y) < 1.0e-8 - ), - std::tuple( - "reference_all_types_cube/conditions.xml", - "reference_all_types_cube/mixed_ref_cube_0.5.xml", 1.0e-10), - std::tuple( - "reference_all_types_cube/conditions.xml", - "reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml", - 1.0e-4 // The non-linear exit tolerance in Nektar is - // like (err_x * err_x - // + err_y * err_y) < 1.0e-8 - ))); - -// TODO REMOVE END diff --git a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp index f8d3e317..2e109bb9 100644 --- a/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp +++ b/test/unit/nektar_interface/test_particle_function_evaluation_3d.cpp @@ -1,4 +1,3 @@ -#define NESO_PARTICLES_PROFILING_REGION // TODO REMOVE #include "nektar_interface/function_evaluation.hpp" #include "nektar_interface/particle_interface.hpp" #include "nektar_interface/utilities.hpp" @@ -385,132 +384,3 @@ TEST(BaryInterpolation, Evaluation3DDisContFieldPrismTet) { "reference_prism_tet_cube/conditions.xml", "reference_prism_tet_cube/prism_tet_cube_0.5_perturbed.xml", 1.0e-7); } - -// TODO REMOVE START - -template -static inline void evaluation_marco(std::string condtions_file_s, - std::string mesh_file_s, const double tol) { - - const int N_total = 1200000; - - std::filesystem::path source_file = __FILE__; - std::filesystem::path source_dir = source_file.parent_path(); - std::filesystem::path test_resources_dir = - source_dir / "../../test_resources"; - - std::filesystem::path condtions_file_basename{condtions_file_s}; - std::filesystem::path mesh_file_basename{mesh_file_s}; - std::filesystem::path conditions_file = - test_resources_dir / condtions_file_basename; - std::filesystem::path mesh_file = test_resources_dir / mesh_file_basename; - - int argc = 3; - char *argv[3]; - copy_to_cstring(std::string("test_particle_geometry_interface"), &argv[0]); - copy_to_cstring(std::string(conditions_file), &argv[1]); - copy_to_cstring(std::string(mesh_file), &argv[2]); - - LibUtilities::SessionReaderSharedPtr session; - SpatialDomains::MeshGraphSharedPtr graph; - // Create session reader. - session = LibUtilities::SessionReader::CreateInstance(argc, argv); - graph = SpatialDomains::MeshGraphIO::Read(session); - - auto mesh = std::make_shared(graph); - auto sycl_target = std::make_shared(0, mesh->get_comm()); - - std::mt19937 rng{182348}; - - auto nektar_graph_local_mapper = - std::make_shared(sycl_target, mesh); - auto domain = std::make_shared(mesh, nektar_graph_local_mapper); - - const int ndim = 3; - ParticleSpec particle_spec{ParticleProp(Sym("P"), ndim, true), - ParticleProp(Sym("CELL_ID"), 1, true), - ParticleProp(Sym("E"), 1), - ParticleProp(Sym("DEDX"), ndim), - ParticleProp(Sym("ID"), 1)}; - - auto A = std::make_shared(domain, particle_spec, sycl_target); - - NektarCartesianPeriodic pbc(sycl_target, graph, A->position_dat); - auto cell_id_translation = - std::make_shared(sycl_target, A->cell_id_dat, mesh); - const int rank = sycl_target->comm_pair.rank_parent; - const int size = sycl_target->comm_pair.size_parent; - - std::mt19937 rng_pos(52234234 + rank); - int rstart, rend; - get_decomp_1d(size, N_total, rank, &rstart, &rend); - const int N = rend - rstart; - int N_check = -1; - MPICHK(MPI_Allreduce(&N, &N_check, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD)); - NESOASSERT(N_check == N_total, "Error creating particles"); - const int cell_count = domain->mesh->get_cell_count(); - if (N > 0) { - auto positions = - uniform_within_extents(N, ndim, pbc.global_extent, rng_pos); - - ParticleSet initial_distribution(N, A->get_particle_spec()); - for (int px = 0; px < N; px++) { - for (int dimx = 0; dimx < ndim; dimx++) { - const double pos_orig = positions[dimx][px] + pbc.global_origin[dimx]; - initial_distribution[Sym("P")][px][dimx] = pos_orig; - } - - initial_distribution[Sym("CELL_ID")][px][0] = 0; - initial_distribution[Sym("ID")][px][0] = px; - } - A->add_particles_local(initial_distribution); - } - reset_mpi_ranks((*A)[Sym("NESO_MPI_RANK")]); - - pbc.execute(); - A->hybrid_move(); - cell_id_translation->execute(); - A->cell_move(); - - auto field = std::make_shared(session, graph, "u"); - - auto lambda_f = [&](const NekDouble x, const NekDouble y, const NekDouble z) { - return std::pow((x + 1.0) * (x - 1.0) * (y + 1.0) * (y - 1.0) * (z + 1.0) * - (z - 1.0), - 4); - }; - - interpolate_onto_nektar_field_3d(lambda_f, field); - NESOCellsToNektarExp map_cells_to_exp(field, cell_id_translation); - - // auto field_evaluate = std::make_shared>( - // field, A, cell_id_translation); - // field_evaluate->evaluate(Sym("E")); - auto field_deriv_evaluate = std::make_shared>( - field, A, cell_id_translation, true); - - for (int cellx = 0; cellx < 2; cellx++) { - field_deriv_evaluate->evaluate(Sym("DEDX")); - } - - sycl_target->profile_map.enable(); - for (int cellx = 0; cellx < 40; cellx++) { - field_deriv_evaluate->evaluate(Sym("DEDX")); - } - sycl_target->profile_map.write_events_json("bary_evaluation", rank); - - A->free(); - mesh->free(); - - delete[] argv[0]; - delete[] argv[1]; - delete[] argv[2]; -} - -TEST(Marco, Polo) { - evaluation_marco( - "reference_hex_cube/conditions.xml", - "reference_hex_cube/hex_cube_0.5.xml", 1.0e-7); -} - -// TODO REMOVE END From d6d62aabfb3726b94c6560cb14ded26ad1532747 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 16 Dec 2024 12:11:00 +0000 Subject: [PATCH 58/66] populated some API docstrings which were TODOs --- .../bary_interpolation/bary_evaluation.hpp | 31 +++++++++++++++++-- 1 file changed, 29 insertions(+), 2 deletions(-) diff --git a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp index 1b86d79c..b485678f 100644 --- a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp +++ b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp @@ -49,7 +49,18 @@ inline void preprocess_weights(const int num_phys, const REAL coord, } /** - * TODO + * For quadrature point r_i with weight bw_i compute bw_i / (r - r_i). + * + * @param num_phys The number of quadrature points for the element and + * dimension for which this computation is performed. + * @param[in] coord The evauation points, size N, in the dimension of interest. + * @param[in] z_values A length num_phys array containing the quadrature + * points. + * @param[in] z_values A length num_phys array containing the quadrature + * weights. + * @param[in, out] div_values Array of length num_phys * N which will be + * populated with the bw_i/(r - r_i) values. Ordering is particle then + * component. */ template inline void @@ -361,7 +372,23 @@ inline void compute_dir_210_interlaced(const int num_functions, } /** - * TODO + * Computes Bary interpolation over three dimensions. Evaluates N functions + * with interlaced quadrature point values. See function + * preprocess_weights_block. + * + * @param[in] num_functions Number of functions to evaluate. + * @param[in] num_phys0 Number of quadrature points in dimension 0. + * @param[in] num_phys1 Number of quadrature points in dimension 1. + * @param[in] num_phys2 Number of quadrature points in dimension 2. + * @param[in] physvals Array of function values at quadrature points interlaced + * values for each function to evaluate. + * @param[in] div_space0 The output of preprocess_weights applied to dimension + * 0. + * @param[in] div_space1 The output of preprocess_weights applied to + * dimension 1. + * @param[in] div_space2 The output of preprocess_weights applied to + * dimension 2. + * @param[in, out] output Output function evaluations. */ template inline void compute_dir_210_interlaced_block( From fd18d3ad6b1c3bcfcc6734590a7440307cec2d04 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 17 Dec 2024 10:58:33 +0000 Subject: [PATCH 59/66] Added more robust self checking for new Bary interpolation. --- .../function_bary_evaluation.hpp | 46 ++++++++++++++++++- .../geometry_transport/utility_geometry.hpp | 34 ++++++++++++++ 2 files changed, 79 insertions(+), 1 deletion(-) diff --git a/include/nektar_interface/function_bary_evaluation.hpp b/include/nektar_interface/function_bary_evaluation.hpp index 5b6693ae..b33e59cf 100644 --- a/include/nektar_interface/function_bary_evaluation.hpp +++ b/include/nektar_interface/function_bary_evaluation.hpp @@ -484,6 +484,9 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { v_cell_info.reserve(neso_cell_count); this->max_num_phys = 0; + // Temporary map for testing values are consistent between cells. + std::map> map_test_coeffs; + for (int neso_cellx = 0; neso_cellx < neso_cell_count; neso_cellx++) { const int nektar_geom_id = cell_id_translation->map_to_nektar[neso_cellx]; const int expansion_id = geom_to_exp[nektar_geom_id]; @@ -496,11 +499,16 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { for (int dimx = 0; dimx < 3; dimx++) { std::get<1>(key)[dimx] = 0; } + std::size_t size_sum = 0; for (int dimx = 0; dimx < this->ndim; dimx++) { - std::get<1>(key)[dimx] = + const std::size_t tmp_size = static_cast(expansion->GetBase()[dimx]->GetZ().size()); + std::get<1>(key)[dimx] = tmp_size; + size_sum += tmp_size; } if (this->map_cells_to_info.count(key) == 0) { + map_test_coeffs[key].reserve(2 * size_sum); + CellInfo cell_info; cell_info.shape_type_int = std::get<0>(key); for (int dx = 0; dx < 3; dx++) { @@ -520,9 +528,11 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { std::vector tmp_reals(2 * size); for (int cx = 0; cx < size; cx++) { tmp_reals.at(cx) = z[cx]; + map_test_coeffs.at(key).push_back(z[cx]); } for (int cx = 0; cx < size; cx++) { tmp_reals.at(cx + size) = bw[cx]; + map_test_coeffs.at(key).push_back(bw[cx]); } auto ptr = std::make_shared>(this->sycl_target, tmp_reals); @@ -534,6 +544,40 @@ template class BaryEvaluateBase : GeomToExpansionBuilder { } this->map_cells_to_info[key] = cell_info; + } else { + // Test that the held values that we reuse are actually the same. + std::vector to_test; + to_test.reserve(2 * size_sum); + for (int dimx = 0; dimx < this->ndim; dimx++) { + auto base = expansion->GetBase(); + const auto &z = base[dimx]->GetZ(); + const auto &bw = base[dimx]->GetBaryWeights(); + NESOASSERT(z.size() == bw.size(), + "Expected these two sizes to match."); + const auto size = z.size(); + for (int cx = 0; cx < size; cx++) { + to_test.push_back(z[cx]); + } + for (int cx = 0; cx < size; cx++) { + to_test.push_back(bw[cx]); + } + } + NESOASSERT(to_test.size() == map_test_coeffs.at(key).size(), + "Size missmatch in coeff checking."); + const std::size_t size = to_test.size(); + auto lambda_rel_err = [](const REAL a, const REAL b) { + const REAL err_abs = std::abs(a - b); + const REAL abs_a = std::abs(a); + const REAL err_rel = abs_a > 0.0 ? err_abs / abs_a : err_abs; + return std::min(err_rel, err_abs); + }; + + for (std::size_t ix = 0; ix < size; ix++) { + NESOASSERT(lambda_rel_err(to_test.at(ix), + map_test_coeffs.at(key).at(ix)) < 1.0e-10, + "Big missmatch in coefficients detected. Please raise an " + "issue on the git repository."); + } } // Get the generic info for this cell type and number of modes diff --git a/include/nektar_interface/geometry_transport/utility_geometry.hpp b/include/nektar_interface/geometry_transport/utility_geometry.hpp index 979e9a48..bcc23999 100644 --- a/include/nektar_interface/geometry_transport/utility_geometry.hpp +++ b/include/nektar_interface/geometry_transport/utility_geometry.hpp @@ -1,7 +1,9 @@ #ifndef _NESO_GEOMETRY_TRANSPORT_UTILITY_GEOMETRY_HPP_ #define _NESO_GEOMETRY_TRANSPORT_UTILITY_GEOMETRY_HPP_ +#include #include +#include namespace NESO { @@ -20,6 +22,38 @@ inline bool geometry_is_linear(std::shared_ptr geom) { return true; } +/** + * @param geom Geometry object. + * @returns String describing geometry. + */ +template +inline std::string get_geometry_name(GEOM_TYPE geom) { + using namespace Nektar::LibUtilities; + + const auto shape_type = geom->GetShapeType(); + + if (shape_type == ShapeType::eTriangle) { + return "Triangle"; + } + if (shape_type == ShapeType::eQuadrilateral) { + return "Quadrilateral"; + } + if (shape_type == ShapeType::eHexahedron) { + return "Hexahedron"; + } + if (shape_type == ShapeType::ePrism) { + return "Prism"; + } + if (shape_type == ShapeType::eTetrahedron) { + return "Tetrahedron"; + } + if (shape_type == ShapeType::ePyramid) { + return "Pyramid"; + } + + return "Unknown ShapeType"; +} + } // namespace NESO #endif From d72602a6958cc69a124395d38b5e990f573ce87d Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 17 Dec 2024 14:47:26 +0000 Subject: [PATCH 60/66] removed bad test mesh and added an initial torus mesh in its place --- .../bary_interpolation/bary_evaluation.hpp | 2 +- .../particle_cell_mapping_common.hpp | 11 - include/nektar_interface/utility_mesh.hpp | 3 +- .../map_particles_3d.cpp | 8 +- .../map_particles_common.cpp | 3 +- .../map_particles_host.cpp | 9 + .../test_particle_advection.cpp | 57 +- .../mixed_ref_cube_0.5_perturbed_order_2.xml | 4771 ----------------- test/test_resources/torus/conditions.xml | 46 + .../torus/quarter_torus_tets_order_2.xml | 4082 ++++++++++++++ ..._particle_geometry_interface_3d_curved.cpp | 3 +- 11 files changed, 4166 insertions(+), 4829 deletions(-) delete mode 100644 test/test_resources/reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml create mode 100644 test/test_resources/torus/conditions.xml create mode 100644 test/test_resources/torus/quarter_torus_tets_order_2.xml diff --git a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp index b485678f..08f37983 100644 --- a/include/nektar_interface/bary_interpolation/bary_evaluation.hpp +++ b/include/nektar_interface/bary_interpolation/bary_evaluation.hpp @@ -372,7 +372,7 @@ inline void compute_dir_210_interlaced(const int num_functions, } /** - * Computes Bary interpolation over three dimensions. Evaluates N functions + * Computes Bary interpolation over three dimensions. Evaluates N particles * with interlaced quadrature point values. See function * preprocess_weights_block. * diff --git a/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp b/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp index 4045c973..0620f83c 100644 --- a/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp +++ b/include/nektar_interface/particle_cell_mapping/particle_cell_mapping_common.hpp @@ -172,17 +172,6 @@ inline bool contains_point_3d(std::shared_ptr geom, Array &global_coord, Array &local_coord, const NekDouble tol) { bool contained = geom->ContainsPoint(global_coord, local_coord, tol); - // TODO REMOVE START - if (contained) { - Array test_coord(3); - test_coord[0] = geom->GetCoord(0, local_coord); - test_coord[1] = geom->GetCoord(1, local_coord); - test_coord[2] = geom->GetCoord(2, local_coord); - nprint("P:", global_coord[0], global_coord[1], global_coord[2], - "L:", local_coord[0], local_coord[1], local_coord[2], - "T:", test_coord[0], test_coord[1], test_coord[2]); - } - // TODO REMOVE END return contained; } diff --git a/include/nektar_interface/utility_mesh.hpp b/include/nektar_interface/utility_mesh.hpp index dc8b86a2..156824cf 100644 --- a/include/nektar_interface/utility_mesh.hpp +++ b/include/nektar_interface/utility_mesh.hpp @@ -242,7 +242,8 @@ make_hex_geom(const int num_modes, T xmapx, U xmapy, V xmapz) { auto hex = std::make_shared(0, quads); hex->GetGeomFactors(); hex->Setup(); - + NESOWARN(hex->GetMetricInfo()->IsValid(), + "Created HexGeom has a negative Jacobian."); return hex; } diff --git a/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp b/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp index d2a3c4cb..0aa6dc4e 100644 --- a/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp +++ b/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp @@ -112,9 +112,6 @@ void MapParticles3D::map(ParticleGroup &particle_group, const int map_cell) { map_newton_initial(this->map_particles_3d_deformed_non_linear, particle_group, map_cell); - bool particles_not_mapped = - this->map_particles_common->check_map(particle_group, map_cell); - map_newton_final(std::get<0>(this->map_particles_3d_deformed_linear), particle_group, map_cell); map_newton_final(std::get<1>(this->map_particles_3d_deformed_linear), @@ -129,7 +126,7 @@ void MapParticles3D::map(ParticleGroup &particle_group, const int map_cell) { if (map_cell > -1) { // if there are particles not yet mapped this may be an error depending on // which stage of NESO-Particles hybrid move we are at. - particles_not_mapped = + bool particles_not_mapped = this->map_particles_common->check_map(particle_group, map_cell); if (this->map_particles_host && particles_not_mapped) { @@ -140,7 +137,7 @@ void MapParticles3D::map(ParticleGroup &particle_group, const int map_cell) { } particles_not_mapped = - this->map_particles_common->check_map(particle_group, map_cell); + this->map_particles_common->check_map(particle_group); if (particles_not_mapped) { nprint( @@ -154,6 +151,7 @@ void MapParticles3D::map(ParticleGroup &particle_group, const int map_cell) { auto sym_cell = cell_id_dat->sym; auto sym_positions = positions_dat->sym; const auto ndim = particle_group.domain->mesh->get_ndim(); + nprint("rank:", this->sycl_target->comm_pair.rank_parent); for (int cx = 0; cx < cell_count; cx++) { auto P = particle_group.get_cell(sym_positions, cx); auto C = particle_group.get_cell(sym_cell, cx); diff --git a/src/nektar_interface/particle_cell_mapping/map_particles_common.cpp b/src/nektar_interface/particle_cell_mapping/map_particles_common.cpp index 9539e19d..92053f0d 100644 --- a/src/nektar_interface/particle_cell_mapping/map_particles_common.cpp +++ b/src/nektar_interface/particle_cell_mapping/map_particles_common.cpp @@ -28,7 +28,8 @@ bool MapParticlesCommon::check_map(ParticleGroup &particle_group, // If the return flag is true there are particles which were not binned into // cells. If the return flag is false all particles were binned into cells. - return this->ep->get_flag(); + const bool flag = this->ep->get_flag(); + return flag; } } // namespace NESO diff --git a/src/nektar_interface/particle_cell_mapping/map_particles_host.cpp b/src/nektar_interface/particle_cell_mapping/map_particles_host.cpp index d39e6893..63a4dcce 100644 --- a/src/nektar_interface/particle_cell_mapping/map_particles_host.cpp +++ b/src/nektar_interface/particle_cell_mapping/map_particles_host.cpp @@ -82,6 +82,10 @@ void MapParticlesHost::map(ParticleGroup &particle_group, const int map_cell) { // Is this particle already binned into a cell? if ((mpi_ranks)[1][rowx] < 0) { + if (Debug::enabled(Debug::MOVEMENT_LEVEL)) { + nprint("MapParticlesHost::map"); + nprint("\tcell:", cellx, "layer:", rowx); + } // copy the particle position into a nektar++ point format for (int dimx = 0; dimx < ndim; dimx++) { @@ -89,6 +93,11 @@ void MapParticlesHost::map(ParticleGroup &particle_group, const int map_cell) { local_coord[dimx] = ref_particle_positions[dimx][rowx]; } + if (Debug::enabled(Debug::MOVEMENT_LEVEL)) { + nprint("\tglobal_coord:", global_coord[0], global_coord[1], + global_coord[2]); + } + // update the PointGeom point->UpdatePosition(global_coord[0], global_coord[1], global_coord[2]); diff --git a/test/integration/nektar_interface/test_particle_advection.cpp b/test/integration/nektar_interface/test_particle_advection.cpp index 515d2ba2..f038b32d 100644 --- a/test/integration/nektar_interface/test_particle_advection.cpp +++ b/test/integration/nektar_interface/test_particle_advection.cpp @@ -80,10 +80,6 @@ TEST(ParticleGeometryInterface, Advection2D) { } reset_mpi_ranks((*A)[Sym("NESO_MPI_RANK")]); - MeshHierarchyGlobalMap mesh_hierarchy_global_map( - sycl_target, domain->mesh, A->position_dat, A->cell_id_dat, - A->mpi_rank_dat); - auto lambda_advect = [&] { auto t0 = profile_timestamp(); particle_loop( @@ -139,7 +135,6 @@ TEST(ParticleGeometryInterface, Advection2D) { for (int stepx = 0; stepx < Nsteps; stepx++) { pbc.execute(); - mesh_hierarchy_global_map.execute(); A->hybrid_move(); cell_id_translation.execute(); A->cell_move(); @@ -175,6 +170,9 @@ TEST_P(ParticleAdvection3D, Advection3D) { auto session = resource_session.session; auto graph = SpatialDomains::MeshGraphIO::Read(session); + std::map> geoms_3d; + get_all_elements_3d(graph, geoms_3d); + auto mesh = std::make_shared(graph); extend_halos_fixed_offset(1, mesh); auto sycl_target = std::make_shared(0, mesh->get_comm()); @@ -248,10 +246,6 @@ TEST_P(ParticleAdvection3D, Advection3D) { } reset_mpi_ranks((*A)[Sym("NESO_MPI_RANK")]); - MeshHierarchyGlobalMap mesh_hierarchy_global_map( - sycl_target, domain->mesh, A->position_dat, A->cell_id_dat, - A->mpi_rank_dat); - auto lambda_advect = [&] { auto t0 = profile_timestamp(); particle_loop( @@ -266,8 +260,6 @@ TEST_P(ParticleAdvection3D, Advection3D) { sycl_target->profile_map.inc("Advect", "Execute", 1, profile_elapsed(t0, profile_timestamp())); }; - std::map> geoms_3d; - get_all_elements_3d(graph, geoms_3d); auto lambda_check_owning_cell = [&] { Array global_coord(3); @@ -310,14 +302,9 @@ TEST_P(ParticleAdvection3D, Advection3D) { } }; - // H5Part h5part("trajectory.h5part", A, Sym("P"), - // Sym("NESO_MPI_RANK"), - // Sym("NESO_REFERENCE_POSITIONS")); - REAL T = 0.0; for (int stepx = 0; stepx < Nsteps; stepx++) { pbc.execute(); - mesh_hierarchy_global_map.execute(); A->hybrid_move(); cell_id_translation.execute(); A->cell_move(); @@ -325,31 +312,27 @@ TEST_P(ParticleAdvection3D, Advection3D) { lambda_advect(); T += dt; - - // h5part.write(); } - // h5part.close(); mesh->free(); } INSTANTIATE_TEST_SUITE_P( MultipleMeshes, ParticleAdvection3D, - testing::Values( - std::tuple( - "reference_all_types_cube/conditions.xml", - "reference_all_types_cube/linear_non_regular_0.5.xml", - 1.0e-4 // The non-linear exit tolerance in Nektar is - // like (err_x * err_x - // + err_y * err_y) < 1.0e-8 - ), - std::tuple( - "reference_all_types_cube/conditions.xml", - "reference_all_types_cube/mixed_ref_cube_0.5.xml", 1.0e-10), - std::tuple( - "reference_all_types_cube/conditions.xml", - "reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml", - 1.0e-4 // The non-linear exit tolerance in Nektar is - // like (err_x * err_x - // + err_y * err_y) < 1.0e-8 - ))); + testing::Values(std::tuple( + "reference_all_types_cube/conditions.xml", + "reference_all_types_cube/linear_non_regular_0.5.xml", + 1.0e-4 // The non-linear exit tolerance in Nektar is + // like (err_x * err_x + // + err_y * err_y) < 1.0e-8 + ), + std::tuple( + "reference_all_types_cube/conditions.xml", + "reference_all_types_cube/mixed_ref_cube_0.5.xml", + 1.0e-10), + std::tuple( + "reference_all_types_cube/conditions.xml", "foo.xml", + 1.0e-4 // The non-linear exit tolerance in Nektar is + // like (err_x * err_x + // + err_y * err_y) < 1.0e-8 + ))); diff --git a/test/test_resources/reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml b/test/test_resources/reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml deleted file mode 100644 index 8219335a..00000000 --- a/test/test_resources/reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml +++ /dev/null @@ -1,4771 +0,0 @@ - - - - - -1.00000000e+00 -1.00000000e+00 -1.00000000e+00 - -5.00000000e-01 -1.00000000e+00 -1.00000000e+00 - -5.00000000e-01 -5.00000000e-01 -1.00000000e+00 - -1.00000000e+00 -5.00000000e-01 -1.00000000e+00 - -1.00000000e+00 -1.00000000e+00 -8.00000000e-01 - -5.00000000e-01 -1.00000000e+00 -8.00000000e-01 - -4.50759435e-01 -5.07516091e-01 -7.91771330e-01 - -1.00000000e+00 -5.00000000e-01 -8.00000000e-01 - -1.00000000e+00 -1.00000000e+00 -6.00000000e-01 - -5.00000000e-01 -1.00000000e+00 -6.00000000e-01 - -4.90951945e-01 -4.63804978e-01 -5.84100454e-01 - -1.00000000e+00 -5.00000000e-01 -6.00000000e-01 - -5.00000000e-01 1.37639899e-12 -1.00000000e+00 - -1.00000000e+00 2.75279799e-12 -1.00000000e+00 - -4.96695706e-01 -7.34886487e-03 -7.54764538e-01 - -1.00000000e+00 2.75279799e-12 -8.00000000e-01 - -5.00312350e-01 3.13724879e-02 -5.99415152e-01 - -1.00000000e+00 2.75279799e-12 -6.00000000e-01 - -5.00000000e-01 5.00000000e-01 -1.00000000e+00 - -1.00000000e+00 5.00000000e-01 -1.00000000e+00 - 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- - H[0-31,524-555] - F[1,6,39,43,69,73,99,103,542,409,548,387,128,497,418,309,323,401,330,361,350,370,569,601,604,611,654,660,696,702,738,744,1174,780,1178,1135,1041,1026,1199,957,968,1221,972,1003,996,1012,1060,1035,1240,1245,1274,1278,1300,1304,1326,1330] - F[123,126,93,96,63,66,31,35,545,412,546,384,133,500,422,312,326,393,333,364,347,367,572,600,774,779,730,735,688,693,645,651,1177,785,1180,1133,1050,1029,1145,1202,964,1222,975,1006,993,1009,1057,1039,1347,1350,1321,1324,1295,1298,1267,1271] - F[100,104,108,111,115,118,122,125,549,406,544,390,558,300,415,320,340,395,578,588,353,593,505,494,741,747,752,757,762,767,772,777,1179,868,1176,951,1047,1023,1140,1193,981,1219,989,1210,999,1015,1053,1037,1327,1331,1334,1337,1340,1343,1346,1349] - F[32,36,23,27,14,18,4,9,543,381,547,403,303,217,420,316,336,399,343,377,357,373,584,597,642,648,630,636,618,624,607,614,1175,950,1181,1191,1019,1044,1142,961,978,1128,985,1209,1214,1217,1062,1032,1268,1272,1260,1264,1252,1256,1243,1248] - F[0,11,20,29,38,47,54,61,68,77,84,91,98,107,114,121] - F[1249,1257,1265,1273,1281,1287,1293,1299,1307,1313,1319,1325,1333,1339,1345,1351] - A[32-229,310-507] - P[230-245,508-523] - R[246-309] - - - C[1,601-603] - - - - - L0211-XU - 5.3.0 - 07-Nov-2023 15:14:09 - - -v mixed_ref_cube_0.5_perturbed_order_2.msh mixed_ref_cube_0.5_perturbed_order_2.tmp.xml:xml:uncompress - - diff --git a/test/test_resources/torus/conditions.xml b/test/test_resources/torus/conditions.xml new file mode 100644 index 00000000..76c872bf --- /dev/null +++ b/test/test_resources/torus/conditions.xml @@ -0,0 +1,46 @@ + + + + + + + + + + + + + + + + + +

Lambda = 0.0

+ + + + u + + + + C[100] + C[200] + C[300] + + + + + + + + + + + + + + + + + diff --git a/test/test_resources/torus/quarter_torus_tets_order_2.xml b/test/test_resources/torus/quarter_torus_tets_order_2.xml new file mode 100644 index 00000000..659b4ae3 --- /dev/null +++ b/test/test_resources/torus/quarter_torus_tets_order_2.xml @@ -0,0 +1,4082 @@ + + + + + 1.96316234e+00 4.67346532e+00 -1.68911610e-02 + 1.54860554e+00 3.54808542e+00 -1.65108235e+00 + 2.68895544e+00 3.70210606e+00 -5.87199511e-01 + 9.59140167e-01 4.07341982e+00 -5.67357895e-01 + 1.76701972e+00 4.45263593e+00 -1.98899096e+00 + 2.92502923e+00 5.02069415e+00 -4.56159172e-01 + 6.91202058e-01 6.84908918e+00 -6.71566734e-01 + 9.96203868e-01 6.92875009e+00 -4.89858720e-16 + 1.12146756e+00 5.55164805e+00 5.56236736e-01 + 1.20153714e+00 5.25120069e+00 -7.90659956e-01 + 4.83769328e+00 1.79640676e+00 -1.84951288e-01 + 5.55517653e+00 1.10950218e+00 5.53521335e-01 + 4.69391929e+00 2.68789105e+00 6.89739971e-01 + 4.82274819e+00 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-6.71566734e-01 9.48976276e-01 6.05930912e+00 -7.37472356e-01 1.20153714e+00 5.25120069e+00 -7.90659956e-01 + 5.55517653e+00 1.10950218e+00 5.53521335e-01 5.12774395e+00 1.90025804e+00 6.27183586e-01 4.69391929e+00 2.68789105e+00 6.89739971e-01 + 4.83769328e+00 1.79640676e+00 -1.84951288e-01 4.76735292e+00 2.24396265e+00 2.53765496e-01 4.69391929e+00 2.68789105e+00 6.89739971e-01 + 4.83769328e+00 1.79640676e+00 -1.84951288e-01 4.83122351e+00 1.30930802e+00 4.25026606e-01 4.82274819e+00 8.19003004e-01 1.02744998e+00 + + + A[0-591] + F[1323,1291,1275,1311,1325,1315,1293,1272,1280,1239,1286,1334,1289,1111,1297,1215,1305,1008,1317,1138,1319,1060,1219,873,1309,1065,1307,1283,1295,1156,1242,592,232,800,337,108,63,579,166,471,735,381,362,426,112,1340,1082,1313,1267,770,266,1023,1330,283,308,605,854,1261,1162,960,445,1104,391,1300,1118,1238,1194,716,1006,1229,1130,1331,238,1120,848,1263,918,767,89,1251,876,1278,984,1227,1182,1257,884,1303,1270,1321,1175,1265,1184,798,1079,1206,1347,514,1014,725,1063,1256,916,1171,1199,923,1218,364,952,1110,910,1080,786,1188,1144,324,1164,1170,791,788,301,643,622,373,784,1154,978,1150,1146,1015,900,1137,1012,1070,1166,1196,1253,1131,1161,1133,944,1093,1051,925,1179,1021,529,1207,908,524,1029,450,840,1038,1249,1204,678,1152,1222,1254,1260,624,938,1042,833,1202,582,393,1068,1345,517,640,878,869,721,348,175,1191,733,1017,982,970,250,1148,576,684,762,1040,1198,353,608,871,1349,966,478,610,915,741,852,595,676,764,1209,1189,645,236,204,1221,1019,370,1087,1269,1234,828,739,590,781,927,1211,83,689,661,207,727,1001,455,376,988,996,895,1058,757,147,424,556,1236,1250,637,863,480,814,842,897,1031,1192,772,980,1213,241,150,839,1135] + F[1326,1316,1281,1245,1287,1336,1290,977,1298,1187,1306,937,1318,1178,1320,1101,1220,907,1310,1129,1308,1296,1174,1233,959,544,822,948,987,616,569,850,1201,436,1074,1151,1126,1302,342,663,1049] + F[1324,1312,1314,1248,1262,1117,1301,868,1230,887,1264,951,1252,862,1279,998,1228,902,1258,892,1304,1322,1143,1226,865,461,747,1180,1217,913,653,416,991,1328,1077,1155,1102,1299,246,571,1047] + + + C[1] + + + + + P0818 + 5.7.0 + 17-Dec-2024 14:26:59 + + -f -v quarter_torus.msh quarter_torus.xml:xml:uncompress + + diff --git a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp index 5abbadaf..d4b8c017 100644 --- a/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp +++ b/test/unit/nektar_interface/test_particle_geometry_interface_3d_curved.cpp @@ -6,8 +6,7 @@ TEST(ParticleGeometryInterfaceCurved, XMapNewtonBase) { MPI_Comm_size(MPI_COMM_WORLD, &size); MPI_Comm_rank(MPI_COMM_WORLD, &rank); TestUtilities::TestResourceSession resource_session( - "reference_all_types_cube/mixed_ref_cube_0.5_perturbed_order_2.xml", - "reference_all_types_cube/conditions.xml"); + "torus/quarter_torus_tets_order_2.xml", "torus/conditions.xml"); // Create session reader. auto session = resource_session.session; From f8fc3cbd255e31545dfa39a9adbb3e55e287ca7e Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 17 Dec 2024 15:35:32 +0000 Subject: [PATCH 61/66] use generic 3D mapper for non-regular mesh in integration test --- .../map_particles_3d.cpp | 29 +++++++++++++-- .../test_particle_advection.cpp | 37 +++++++++++-------- 2 files changed, 47 insertions(+), 19 deletions(-) diff --git a/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp b/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp index 0aa6dc4e..730506b1 100644 --- a/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp +++ b/src/nektar_interface/particle_cell_mapping/map_particles_3d.cpp @@ -21,9 +21,32 @@ MapParticles3D::MapParticles3D( this->map_particles_3d_deformed_non_linear = nullptr; GeometryContainer3D geometry_container_3d; - assemble_geometry_container_3d(particle_mesh_interface->graph, - particle_mesh_interface->remote_geoms_3d, - geometry_container_3d); + const bool all_generic_newton = static_cast( + config->get("MapParticles3D/all_generic_newton", 0)); + + if (!all_generic_newton) { + // Get the geometry objects in their different categories. + assemble_geometry_container_3d(particle_mesh_interface->graph, + particle_mesh_interface->remote_geoms_3d, + geometry_container_3d); + } else { + // If we are putting all geoms through the generic 3D mapper then only + // populate the deformed_non_linear container. + { + std::map> geoms; + get_all_elements_3d(particle_mesh_interface->graph, geoms); + for (auto gx : geoms) { + std::pair> + tmp = {gx.first, gx.second}; + geometry_container_3d.deformed_non_linear.push_back(tmp); + } + } + { + for (auto gx : particle_mesh_interface->remote_geoms_3d) { + geometry_container_3d.deformed_non_linear.push_back(gx); + } + } + } // Create a mapper for 3D regular geometry objects if (geometry_container_3d.regular.size()) { diff --git a/test/integration/nektar_interface/test_particle_advection.cpp b/test/integration/nektar_interface/test_particle_advection.cpp index f038b32d..f40a9e86 100644 --- a/test/integration/nektar_interface/test_particle_advection.cpp +++ b/test/integration/nektar_interface/test_particle_advection.cpp @@ -151,13 +151,13 @@ TEST(ParticleGeometryInterface, Advection2D) { mesh->free(); } -class ParticleAdvection3D : public testing::TestWithParam< - std::tuple> { -}; +class ParticleAdvection3D + : public testing::TestWithParam< + std::tuple> {}; TEST_P(ParticleAdvection3D, Advection3D) { // Test advecting particles between ranks - std::tuple param = GetParam(); + std::tuple param = GetParam(); const int N_total = 2000; const double tol = std::get<2>(param); @@ -178,10 +178,13 @@ TEST_P(ParticleAdvection3D, Advection3D) { auto sycl_target = std::make_shared(0, mesh->get_comm()); auto config = std::make_shared(); + config->set("MapParticlesNewton/newton_tol", 1.0e-10); // There are some pyramid corners that are hard to bin into with tighter // tolerances. config->set("MapParticlesNewton/contained_tol", 1.0e-2); + // Use the non-linear mapper for all geoms + config->set("MapParticles3D/all_generic_newton", std::get<3>(param)); auto nektar_graph_local_mapper = std::make_shared(sycl_target, mesh, config); @@ -319,20 +322,22 @@ TEST_P(ParticleAdvection3D, Advection3D) { INSTANTIATE_TEST_SUITE_P( MultipleMeshes, ParticleAdvection3D, - testing::Values(std::tuple( + testing::Values(std::tuple( "reference_all_types_cube/conditions.xml", "reference_all_types_cube/linear_non_regular_0.5.xml", - 1.0e-4 // The non-linear exit tolerance in Nektar is - // like (err_x * err_x - // + err_y * err_y) < 1.0e-8 - ), - std::tuple( + 1.0e-4, // The non-linear exit tolerance in Nektar is + // like (err_x * err_x + // + err_y * err_y) < 1.0e-8 + 0), + std::tuple( "reference_all_types_cube/conditions.xml", "reference_all_types_cube/mixed_ref_cube_0.5.xml", - 1.0e-10), - std::tuple( - "reference_all_types_cube/conditions.xml", "foo.xml", - 1.0e-4 // The non-linear exit tolerance in Nektar is - // like (err_x * err_x - // + err_y * err_y) < 1.0e-8 + 1.0e-10, 0), + std::tuple( + "reference_all_types_cube/conditions.xml", + "reference_all_types_cube/linear_non_regular_0.5.xml", + 1.0e-4, // The non-linear exit tolerance in Nektar is + // like (err_x * err_x + // + err_y * err_y) < 1.0e-8 + 1 // Use the Generic3D mapper for the linear geoms. ))); From 4d652a0300550b9b8350ac4a4e377479ff1ba73d Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 17 Dec 2024 19:33:15 +0000 Subject: [PATCH 62/66] made Generic3D mapper robust to unaligned memory --- .../newton_generic_3d.hpp | 17 +- .../particle_cell_mapping/x_map_newton.hpp | 161 ++++++++---------- include/nektar_interface/utility_sycl.hpp | 14 ++ 3 files changed, 95 insertions(+), 97 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index a3ee2e3c..9caa8542 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -3,6 +3,7 @@ #include "../bary_interpolation/bary_evaluation.hpp" #include "../coordinate_mapping.hpp" +#include "../utility_sycl.hpp" #include "mapping_newton_iteration_base.hpp" #include @@ -136,7 +137,8 @@ struct MappingGeneric3D : MappingNewtonIterationBase { h_data->d_zbw = std::make_unique>(sycl_target, s_zbw); // Number of bytes required for local memory h_data->data_size_local = - (num_phys0 + num_phys1 + num_phys2) * sizeof(REAL); + (num_phys0 + num_phys1 + num_phys2) * sizeof(REAL) + + std::alignment_of::value; // store the pointers into the buffer we just made in the device struct so // that pointer arithmetric does not have to happen in the kernel but the @@ -187,7 +189,8 @@ struct MappingGeneric3D : MappingNewtonIterationBase { const Generic3D::DataDevice *d = static_cast(d_data); - REAL *div_space0 = static_cast(local_memory); + REAL *div_space0 = neso_cast_align_pointer( + local_memory, std::alignment_of::value); REAL *div_space1 = div_space0 + d->num_phys0; REAL *div_space2 = div_space1 + d->num_phys1; // The call to Newton step always follows a call to the residual @@ -234,12 +237,14 @@ struct MappingGeneric3D : MappingNewtonIterationBase { &eta2); // compute X at xi by evaluating the Bary interpolation at eta - REAL *div_space0 = static_cast(local_memory); + REAL *div_space0 = neso_cast_align_pointer( + local_memory, std::alignment_of::value); REAL *div_space1 = div_space0 + d->num_phys0; REAL *div_space2 = div_space1 + d->num_phys1; - Bary::preprocess_weights(d->num_phys0, eta0, d->z0, d->bw0, div_space0); - Bary::preprocess_weights(d->num_phys1, eta1, d->z1, d->bw1, div_space1); - Bary::preprocess_weights(d->num_phys2, eta2, d->z2, d->bw2, div_space2); + + Bary::preprocess_weights(d->num_phys0, eta0, d->z0, d->bw0, div_space0, 1); + Bary::preprocess_weights(d->num_phys1, eta1, d->z1, d->bw1, div_space1, 1); + Bary::preprocess_weights(d->num_phys2, eta2, d->z2, d->bw2, div_space2, 1); REAL X[3]; diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index c9a92890..a97b2d8c 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -1,6 +1,7 @@ #ifndef __X_MAP_NEWTON_H__ #define __X_MAP_NEWTON_H__ +#include "../utility_sycl.hpp" #include "x_map_newton_kernel.hpp" #include #include @@ -112,7 +113,7 @@ template class XMapNewton { inline void x(const REAL xi0, const REAL xi1, const REAL xi2, REAL *phys0, REAL *phys1, REAL *phys2) { - char *k_map_data; + char *k_map_data = nullptr; if (this->dh_data) { k_map_data = this->dh_data->d_buffer.ptr; } @@ -181,7 +182,7 @@ template class XMapNewton { const REAL contained_tol = 1.0e-10) { const int k_max_iterations = 51; - char *k_map_data; + char *k_map_data = nullptr; if (this->dh_data) { k_map_data = this->dh_data->d_buffer.ptr; } @@ -288,15 +289,15 @@ template class XMapNewton { std::array get_bounding_box(std::size_t grid_size = 32, const REAL pad_rel = 0.05, const REAL pad_abs = 0.0) { - char *k_map_data; + char *k_map_data = nullptr; if (this->dh_data) { k_map_data = this->dh_data->d_buffer.ptr; } NESOASSERT(this->dh_fdata != nullptr, "Bad pointer"); auto k_fdata = this->dh_fdata->d_buffer.ptr; NESOASSERT(k_fdata != nullptr, "Bad pointer"); - const std::size_t num_bytes_local = - std::max(this->num_bytes_local, sizeof(REAL)); + const std::size_t num_bytes_local = std::max( + this->num_bytes_local, sizeof(REAL) + std::alignment_of::value); // Get a local size which is a power of 2. const std::size_t local_size = @@ -308,10 +309,9 @@ template class XMapNewton { ->value)))); // make grid_size a multiple of the local size grid_size = get_next_multiple(grid_size, local_size); - sycl::range<3> range_local(1, local_size, local_size); - const std::size_t local_size_l = local_size * local_size; + sycl::range<1> range_local(local_size); // There are 6 faces on the collapsed reference cell - sycl::range<3> range_global(6, grid_size, grid_size); + sycl::range<1> range_global(grid_size * grid_size); const REAL k_width = 2.0 / static_cast(grid_size - 1); constexpr REAL kc[6][3] = { @@ -357,90 +357,69 @@ template class XMapNewton { } this->dh_fdata->host_to_device(); - this->sycl_target->queue - .submit([=](sycl::handler &cgh) { - sycl::local_accessor local_mem( - sycl::range<1>(num_bytes_local * local_size_l), cgh); - - cgh.parallel_for<>( - this->sycl_target->device_limits.validate_nd_range( - sycl::nd_range<3>(range_global, range_local)), - [=](auto idx) { - MappingNewtonIterationBase k_newton_type{}; - - const auto local_id = idx.get_local_linear_id(); - const auto iix = idx.get_global_id(2); - const auto iiy = idx.get_global_id(1); - const auto facex = idx.get_global_id(0); - const REAL gx = -1.0 + iix * k_width; - const REAL gy = -1.0 + iiy * k_width; - - const REAL eta0 = - kc[facex][0] + kcx[facex][0] * gx + kcy[facex][0] * gy; - const REAL eta1 = - kc[facex][1] + kcx[facex][1] * gx + kcy[facex][1] * gy; - const REAL eta2 = - kc[facex][2] + kcx[facex][2] * gx + kcy[facex][2] * gy; - - REAL k_xi0, k_xi1, k_xi2; - k_newton_type.loc_collapsed_to_loc_coord( - k_map_data, eta0, eta1, eta2, &k_xi0, &k_xi1, &k_xi2); - - REAL f[3] = {0.0, 0.0, 0.0}; - constexpr REAL p0 = 0.0; - constexpr REAL p1 = 0.0; - constexpr REAL p2 = 0.0; - - k_newton_type.newton_residual( - k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f, f + 1, - f + 2, &local_mem[local_id * num_bytes_local]); - - idx.barrier(sycl::access::fence_space::local_space); - - REAL *local_mem_real = - static_cast(static_cast(&local_mem[0])); - - // Do the reductions, we pessimistically do not use the builtin - // SYCL functions as we have used all the local memory already - // and the SYCL reduction functions also use local memory. - for (int dimx = 0; dimx < 3; dimx++) { - - // Tree reduce the maximum - local_mem_real[local_id] = f[dimx]; - for (int ix = local_size_l / 2; ix > 0; ix >>= 1) { - idx.barrier(sycl::access::fence_space::local_space); - if (local_id < ix) { - local_mem_real[local_id] = - sycl::max(local_mem_real[local_id + ix], - local_mem_real[local_id]); - } - } - if (local_id == 0) { - sycl::atomic_ref - ar(k_fdata[dimx + 3]); - auto check = ar.fetch_max(local_mem_real[0]); - } - // Tree reduce the minimum - local_mem_real[local_id] = f[dimx]; - for (int ix = local_size_l / 2; ix > 0; ix >>= 1) { - idx.barrier(sycl::access::fence_space::local_space); - if (local_id < ix) { - local_mem_real[local_id] = - sycl::min(local_mem_real[local_id + ix], - local_mem_real[local_id]); - } - } - if (local_id == 0) { - sycl::atomic_ref - ar(k_fdata[dimx]); - auto check = ar.fetch_min(local_mem_real[0]); - } + EventStack event_stack; + + for (std::size_t facex = 0; facex < 6; facex++) { + + event_stack.push(this->sycl_target->queue.submit([=](sycl::handler &cgh) { + sycl::local_accessor local_mem( + sycl::range<1>(num_bytes_local * local_size), cgh); + + cgh.parallel_for<>( + this->sycl_target->device_limits.validate_nd_range( + sycl::nd_range<1>(range_global, range_local)), + [=](auto idx) { + MappingNewtonIterationBase k_newton_type{}; + + const auto local_id = idx.get_local_linear_id(); + const std::size_t gid = idx.get_global_linear_id(); + + const auto iix = gid % grid_size; + const auto iiy = gid / grid_size; + const REAL gx = -1.0 + iix * k_width; + const REAL gy = -1.0 + iiy * k_width; + + const REAL eta0 = + kc[facex][0] + kcx[facex][0] * gx + kcy[facex][0] * gy; + const REAL eta1 = + kc[facex][1] + kcx[facex][1] * gx + kcy[facex][1] * gy; + const REAL eta2 = + kc[facex][2] + kcx[facex][2] * gx + kcy[facex][2] * gy; + + REAL k_xi0, k_xi1, k_xi2; + k_newton_type.loc_collapsed_to_loc_coord( + k_map_data, eta0, eta1, eta2, &k_xi0, &k_xi1, &k_xi2); + + REAL f[3] = {0.0, 0.0, 0.0}; + constexpr REAL p0 = 0.0; + constexpr REAL p1 = 0.0; + constexpr REAL p2 = 0.0; + + k_newton_type.newton_residual( + k_map_data, k_xi0, k_xi1, k_xi2, p0, p1, p2, f, f + 1, f + 2, + &local_mem[local_id * num_bytes_local]); + + //// Do the reductions, we pessimistically do not use the builtin + //// SYCL functions as we have used all the local memory already + //// and the SYCL reduction functions also use local memory. + for (int dimx = 0; dimx < 3; dimx++) { + { + sycl::atomic_ref + ar(k_fdata[dimx + 3]); + ar.fetch_max(f[dimx]); } - }); - }) - .wait_and_throw(); + { + sycl::atomic_ref + ar(k_fdata[dimx]); + ar.fetch_min(f[dimx]); + } + } + }); + })); + } + event_stack.wait(); this->dh_fdata->device_to_host(); std::array output; diff --git a/include/nektar_interface/utility_sycl.hpp b/include/nektar_interface/utility_sycl.hpp index fcfc6756..087fe0d5 100644 --- a/include/nektar_interface/utility_sycl.hpp +++ b/include/nektar_interface/utility_sycl.hpp @@ -5,6 +5,7 @@ #include #include #include +#include #include using namespace NESO::Particles; @@ -110,6 +111,19 @@ template inline T pad_to_vector_length(const T L) { } } +/** + * @param ptr Pointer to align to alignment. + * @param alignment Power of two to align to. + * @returns Aligned pointer. + */ +template +constexpr inline T *neso_cast_align_pointer(void *ptr, + const std::size_t alignment) { + std::size_t ptr_int = reinterpret_cast(ptr); + ptr_int = (ptr_int + (alignment - 1)) & -alignment; + return reinterpret_cast(ptr_int); +} + } // namespace NESO #endif From 134d31b8138d102ee363880b3fedc9a5d5906e61 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 18 Dec 2024 15:42:35 +0000 Subject: [PATCH 63/66] made mallocs for newton interfaces robust by using aligned mallocs --- .../map_particles_newton.hpp | 30 +++++++++++-------- .../newton_triangle_embed_3d.hpp | 1 + .../particle_cell_mapping/x_map_newton.hpp | 26 +++++++++------- neso-particles | 2 +- .../composite_collections.cpp | 26 +++++++++++----- 5 files changed, 54 insertions(+), 31 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp index d1b4cf72..fb6a5c45 100644 --- a/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/map_particles_newton.hpp @@ -64,9 +64,9 @@ class MapParticlesNewton : public CoarseMappersBase { const int ndim; /// The data required to perform newton iterations for each geom on the /// device. - std::unique_ptr> dh_data; + std::unique_ptr> dh_data; /// The data required to perform newton iterations for each geom on the host. - std::vector h_data; + std::unique_ptr> h_data; /// The Newton iteration class. MappingNewtonIterationBase newton_type; const std::size_t num_bytes_per_map_device; @@ -82,7 +82,7 @@ class MapParticlesNewton : public CoarseMappersBase { : nullptr; auto h_data_ptr = (this->num_bytes_per_map_host) - ? this->h_data.data() + index * this->num_bytes_per_map_host + ? this->h_data->ptr + index * this->num_bytes_per_map_host : nullptr; this->newton_type.write_data(this->sycl_target, geom, h_data_ptr, @@ -96,7 +96,7 @@ class MapParticlesNewton : public CoarseMappersBase { for (int index = 0; index < num_geoms; index++) { auto h_data_ptr = (this->num_bytes_per_map_host) - ? this->h_data.data() + index * this->num_bytes_per_map_host + ? this->h_data->ptr + index * this->num_bytes_per_map_host : nullptr; this->newton_type.free_data(h_data_ptr); } @@ -125,8 +125,12 @@ class MapParticlesNewton : public CoarseMappersBase { std::vector> &geoms_remote, ParameterStoreSharedPtr config = std::make_shared()) : CoarseMappersBase(sycl_target), newton_type(newton_type), - num_bytes_per_map_device(newton_type.data_size_device()), - num_bytes_per_map_host(newton_type.data_size_host()), + num_bytes_per_map_device( + get_next_multiple(newton_type.data_size_device(), + std::alignment_of::value)), + num_bytes_per_map_host( + get_next_multiple(newton_type.data_size_host(), + std::alignment_of::value)), ndim(newton_type.get_ndim()) { this->newton_tol = @@ -161,12 +165,14 @@ class MapParticlesNewton : public CoarseMappersBase { std::make_unique>(this->sycl_target, num_geoms); if (this->num_bytes_per_map_device) { - this->dh_data = std::make_unique>( - this->sycl_target, num_geoms * this->num_bytes_per_map_device); + this->dh_data = std::make_unique>( + this->sycl_target, num_geoms * this->num_bytes_per_map_device, + std::alignment_of::value); } if (this->num_bytes_per_map_host) { - this->h_data = - std::vector(num_geoms * this->num_bytes_per_map_host); + this->h_data = std::make_unique>( + this->sycl_target, num_geoms * this->num_bytes_per_map_host, + std::alignment_of::value); } const int index_tri = shape_type_to_int(eTriangle); @@ -322,7 +328,7 @@ class MapParticlesNewton : public CoarseMappersBase { const int geom_map_index = k_map[linear_mesh_cell * k_map_stride + candidate_cell]; - const char *map_data = + const std::byte *map_data = (k_num_bytes_per_map_device) ? &k_map_data[geom_map_index * k_num_bytes_per_map_device] : nullptr; @@ -477,7 +483,7 @@ class MapParticlesNewton : public CoarseMappersBase { const int geom_map_index = k_map[linear_mesh_cell * k_map_stride + candidate_cell]; - const char *map_data = + const std::byte *map_data = (k_num_bytes_per_map_device) ? &k_map_data[geom_map_index * k_num_bytes_per_map_device] : nullptr; diff --git a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp index da4aae53..a997e4c5 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_triangle_embed_3d.hpp @@ -1,6 +1,7 @@ #ifndef ___NESO_PARTICLE_MAPPING_NEWTON_TRIANGLE_EMBED_3D_H__ #define ___NESO_PARTICLE_MAPPING_NEWTON_TRIANGLE_EMBED_3D_H__ +#include "../coordinate_mapping.hpp" #include "nektar_interface/special_functions.hpp" #include "generated_linear/linear_newton_implementation.hpp" diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index a97b2d8c..907412a6 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -30,11 +30,12 @@ template class XMapNewton { /// The data required to perform newton iterations for each geom on the /// device. - std::unique_ptr> dh_data; + std::unique_ptr> dh_data; + /// The data required to perform newton iterations for each geom on the host. + std::unique_ptr> h_data; std::unique_ptr> dh_fdata; - /// The data required to perform newton iterations for each geom on the host. - std::vector h_data; + std::size_t num_bytes_local; // variables for higher order grids @@ -44,17 +45,20 @@ template class XMapNewton { template inline void write_data(U &geom) { if (this->num_bytes_per_map_host) { - this->h_data = std::vector(this->num_bytes_per_map_host); + this->h_data = std::make_unique>( + this->sycl_target, this->num_bytes_per_map_host, + std::alignment_of::value); } if (this->num_bytes_per_map_device) { - this->dh_data = std::make_unique>( - this->sycl_target, this->num_bytes_per_map_device); + this->dh_data = std::make_unique>( + this->sycl_target, this->num_bytes_per_map_device, + std::alignment_of::value); } auto d_data_ptr = (this->num_bytes_per_map_device) ? this->dh_data->h_buffer.ptr : nullptr; auto h_data_ptr = - (this->num_bytes_per_map_host) ? this->h_data.data() : nullptr; + (this->num_bytes_per_map_host) ? this->h_data->ptr : nullptr; this->newton_type.write_data(this->sycl_target, geom, h_data_ptr, d_data_ptr); @@ -73,7 +77,7 @@ template class XMapNewton { public: ~XMapNewton() { auto h_data_ptr = - (this->num_bytes_per_map_host) ? this->h_data.data() : nullptr; + (this->num_bytes_per_map_host) ? this->h_data->ptr : nullptr; this->newton_type.free_data(h_data_ptr); } @@ -113,7 +117,7 @@ template class XMapNewton { inline void x(const REAL xi0, const REAL xi1, const REAL xi2, REAL *phys0, REAL *phys1, REAL *phys2) { - char *k_map_data = nullptr; + std::byte *k_map_data = nullptr; if (this->dh_data) { k_map_data = this->dh_data->d_buffer.ptr; } @@ -182,7 +186,7 @@ template class XMapNewton { const REAL contained_tol = 1.0e-10) { const int k_max_iterations = 51; - char *k_map_data = nullptr; + std::byte *k_map_data = nullptr; if (this->dh_data) { k_map_data = this->dh_data->d_buffer.ptr; } @@ -289,7 +293,7 @@ template class XMapNewton { std::array get_bounding_box(std::size_t grid_size = 32, const REAL pad_rel = 0.05, const REAL pad_abs = 0.0) { - char *k_map_data = nullptr; + std::byte *k_map_data = nullptr; if (this->dh_data) { k_map_data = this->dh_data->d_buffer.ptr; } diff --git a/neso-particles b/neso-particles index 9097d541..dc5cb6d5 160000 --- a/neso-particles +++ b/neso-particles @@ -1 +1 @@ -Subproject commit 9097d541e64760c67f5f717b04502299f7c3b264 +Subproject commit dc5cb6d5d570ce6cd54bfc94cec29e0a54c200e1 diff --git a/src/nektar_interface/composite_interaction/composite_collections.cpp b/src/nektar_interface/composite_interaction/composite_collections.cpp index c40db14c..71bc7adf 100644 --- a/src/nektar_interface/composite_interaction/composite_collections.cpp +++ b/src/nektar_interface/composite_interaction/composite_collections.cpp @@ -57,8 +57,12 @@ void CompositeCollections::collect_cell(const INT cell) { Newton::MappingQuadLinear2DEmbed3D mapper_quads{}; Newton::MappingTriangleLinear2DEmbed3D mapper_tris{}; - const int stride_quads = mapper_quads.data_size_device(); - const int stride_tris = mapper_tris.data_size_device(); + const int stride_quads = + get_next_multiple(mapper_quads.data_size_device(), + std::alignment_of::value); + const int stride_tris = + get_next_multiple(mapper_tris.data_size_device(), + std::alignment_of::value); NESOASSERT(mapper_quads.data_size_host() == 0, "Expected 0 host bytes required for this mapper."); NESOASSERT(mapper_tris.data_size_host() == 0, @@ -69,12 +73,16 @@ void CompositeCollections::collect_cell(const INT cell) { const int num_bytes = stride_quads * num_quads + stride_tris * num_tris; const int offset_tris = stride_quads * num_quads; - std::vector buf(num_bytes); + auto h_buf = std::make_shared>( + this->sycl_target, num_bytes, + std::alignment_of::value); + std::vector buf_lpi{}; buf_lpi.reserve(num_quads + num_tris); - unsigned char *map_data_quads = buf.data(); - unsigned char *map_data_tris = buf.data() + offset_tris; + unsigned char *map_data_quads = h_buf->ptr; + unsigned char *map_data_tris = h_buf->ptr + offset_tris; + std::vector composite_ids(num_quads + num_tris); std::vector geom_ids(num_quads + num_tris); @@ -122,8 +130,12 @@ void CompositeCollections::collect_cell(const INT cell) { } // create a device buffer from the vector - auto d_buf = - std::make_shared>(this->sycl_target, buf); + auto d_buf = std::make_shared>( + this->sycl_target, num_bytes, + std::alignment_of::value); + + buffer_memcpy(*d_buf, *h_buf).wait_and_throw(); + this->stack_geometry_data.push(d_buf); unsigned char *d_ptr = d_buf->ptr; From a873d721c3198f6e7730c13277d5c4c86f6c5a69 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Wed, 18 Dec 2024 17:00:45 +0000 Subject: [PATCH 64/66] fixed uninitialised memory usage in Generic3D geometry mapper --- .../particle_cell_mapping/newton_generic_3d.hpp | 5 ++++- .../nektar_interface/particle_cell_mapping/x_map_newton.hpp | 1 - 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp index 9caa8542..0a6fedde 100644 --- a/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp +++ b/include/nektar_interface/particle_cell_mapping/newton_generic_3d.hpp @@ -41,7 +41,10 @@ struct MappingGeneric3D : MappingNewtonIterationBase { inline void write_data_v(SYCLTargetSharedPtr sycl_target, GeometrySharedPtr geom, void *data_host, void *data_device) { - Generic3D::DataHost *h_data = static_cast(data_host); + + // We need to actually construct a DataHost at this pointer + Generic3D::DataHost *h_data = new (data_host) Generic3D::DataHost; + Generic3D::DataDevice *d_data = static_cast(data_device); diff --git a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp index 907412a6..4df0988b 100644 --- a/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp +++ b/include/nektar_interface/particle_cell_mapping/x_map_newton.hpp @@ -59,7 +59,6 @@ template class XMapNewton { : nullptr; auto h_data_ptr = (this->num_bytes_per_map_host) ? this->h_data->ptr : nullptr; - this->newton_type.write_data(this->sycl_target, geom, h_data_ptr, d_data_ptr); From 3d40aaa272648c1d23de72072a0c6ea363fb598e Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Mon, 6 Jan 2025 17:20:49 +0000 Subject: [PATCH 65/66] added integration test for particle advection on second order mesh --- .../test_particle_advection.cpp | 178 ++++++++++++++++++ 1 file changed, 178 insertions(+) diff --git a/test/integration/nektar_interface/test_particle_advection.cpp b/test/integration/nektar_interface/test_particle_advection.cpp index f40a9e86..1300d2c3 100644 --- a/test/integration/nektar_interface/test_particle_advection.cpp +++ b/test/integration/nektar_interface/test_particle_advection.cpp @@ -341,3 +341,181 @@ INSTANTIATE_TEST_SUITE_P( // + err_y * err_y) < 1.0e-8 1 // Use the Generic3D mapper for the linear geoms. ))); + +TEST(ParticleAdvection3D, Torus) { + // Test advecting particles between ranks + + const int N_per_element = 10; + const double tol = 1.0e-4; + + TestUtilities::TestResourceSession resource_session( + "torus/quarter_torus_tets_order_2.xml", "torus/conditions.xml"); + const REAL torus_radius_major = 5.0; + const REAL torus_radius_minor = 1.9; + + // Create session reader. + auto session = resource_session.session; + auto graph = SpatialDomains::MeshGraphIO::Read(session); + + std::map> geoms_3d; + get_all_elements_3d(graph, geoms_3d); + + auto mesh = std::make_shared(graph); + extend_halos_fixed_offset(1, mesh); + auto sycl_target = std::make_shared(0, mesh->get_comm()); + + auto config = std::make_shared(); + + config->set("MapParticlesNewton/newton_tol", 1.0e-10); + // There are some pyramid corners that are hard to bin into with tighter + // tolerances. + config->set("MapParticlesNewton/contained_tol", 1.0e-2); + // Use the non-linear mapper for all geoms + config->set("MapParticles3D/all_generic_newton", 1); + + auto nektar_graph_local_mapper = + std::make_shared(sycl_target, mesh, config); + + auto domain = std::make_shared(mesh, nektar_graph_local_mapper); + + const int ndim = 3; + ParticleSpec particle_spec{ParticleProp(Sym("P"), ndim, true), + ParticleProp(Sym("V"), 3), + ParticleProp(Sym("CELL_ID"), 1, true), + ParticleProp(Sym("ID"), 2)}; + + auto A = std::make_shared(domain, particle_spec, sycl_target); + CellIDTranslation cell_id_translation(sycl_target, A->cell_id_dat, mesh); + + const int rank = sycl_target->comm_pair.rank_parent; + const int size = sycl_target->comm_pair.size_parent; + + std::mt19937 rng_pos(52234234 + rank); + std::mt19937 rng_vel(52234231 + rank); + + const int Nsteps = 400; + const REAL dt = 0.1; + const int cell_count = domain->mesh->get_cell_count(); + + std::vector> positions; + std::vector cells; + + rng_pos = uniform_within_elements(graph, N_per_element, positions, cells, + 1.0e-4, rng_pos); + + const int N = cells.size(); + + auto velocities = + NESO::Particles::normal_distribution(N, 3, 0.0, 0.5, rng_vel); + std::uniform_int_distribution uniform_dist( + 0, sycl_target->comm_pair.size_parent - 1); + ParticleSet initial_distribution(N, A->get_particle_spec()); + for (int px = 0; px < N; px++) { + for (int dimx = 0; dimx < ndim; dimx++) { + const double pos_orig = positions.at(dimx).at(px); + initial_distribution[Sym("P")][px][dimx] = pos_orig; + } + for (int dimx = 0; dimx < 3; dimx++) { + initial_distribution[Sym("V")][px][dimx] = + velocities.at(dimx).at(px); + } + initial_distribution[Sym("CELL_ID")][px][0] = cells.at(px); + initial_distribution[Sym("ID")][px][0] = rank; + initial_distribution[Sym("ID")][px][1] = px; + initial_distribution[Sym("NESO_MPI_RANK")][px][0] = rank; + } + A->add_particles_local(initial_distribution); + + reset_mpi_ranks((*A)[Sym("NESO_MPI_RANK")]); + + auto lambda_advect = [&] { + auto t0 = profile_timestamp(); + particle_loop( + A, + [=](auto P, auto V) { + for (int dimx = 0; dimx < ndim; dimx++) { + P.at(dimx) += dt * V.at(dimx); + } + }, + Access::write(Sym("P")), Access::read(Sym("V"))) + ->execute(); + sycl_target->profile_map.inc("Advect", "Execute", 1, + profile_elapsed(t0, profile_timestamp())); + }; + + auto lambda_check_owning_cell = [&] { + Array global_coord(3); + Array xi(3); + Array eta(3); + for (int cellx = 0; cellx < cell_count; cellx++) { + + auto positions = A->position_dat->cell_dat.get_cell(cellx); + auto cell_ids = A->cell_id_dat->cell_dat.get_cell(cellx); + auto reference_positions = + A->get_cell(Sym("NESO_REFERENCE_POSITIONS"), cellx); + + const int cell_nektar = cell_id_translation.map_to_nektar[cellx]; + auto geom = geoms_3d[cell_nektar]; + + int shape_type = geom->GetShapeType(); + Newton::XMapNewton mapper(sycl_target, geom); + + for (int rowx = 0; rowx < cell_ids->nrow; rowx++) { + const int cell_neso = (*cell_ids)[0][rowx]; + ASSERT_EQ(cell_neso, cellx); + + xi[0] = reference_positions->at(rowx, 0); + xi[1] = reference_positions->at(rowx, 1); + xi[2] = reference_positions->at(rowx, 2); + global_coord[0] = geom->GetCoord(0, xi); + global_coord[1] = geom->GetCoord(1, xi); + global_coord[2] = geom->GetCoord(2, xi); + + // check the global coordinate matches the one on the particle + for (int dimx = 0; dimx < ndim; dimx++) { + const double err_abs = + ABS(positions->at(rowx, dimx) - global_coord[dimx]); + const double err_rel = + err_abs > 0.0 ? err_abs / std::abs(global_coord[dimx]) : err_abs; + ASSERT_TRUE((err_abs <= tol) || (err_rel <= tol)); + ASSERT_TRUE(std::fabs((double)eta[dimx]) < (1.0 + tol)); + } + } + } + }; + + auto boundary_loop = particle_loop( + "boundary_loop", A, + [=](auto P) { + REAL x = P.at(0); + REAL y = P.at(1); + REAL z = P.at(2); + REAL r, phi, theta; + ExternalCommon::cartesian_to_torus_cylindrical(torus_radius_major, x, y, + z, &r, &phi, &theta); + + const REAL test_pi = 3.14159265358979323846; + phi = Kernel::fmod(phi + 2.0 * test_pi, 0.5 * test_pi); + r = Kernel::fmod(r, torus_radius_minor); + + ExternalCommon::torus_cylindrical_to_cartesian(torus_radius_major, r, + phi, theta, &x, &y, &z); + P.at(0) = x; + P.at(1) = y; + P.at(2) = z; + }, + Access::write(Sym("P"))); + + REAL T = 0.0; + for (int stepx = 0; stepx < Nsteps; stepx++) { + boundary_loop->execute(); + A->hybrid_move(); + cell_id_translation.execute(); + A->cell_move(); + lambda_check_owning_cell(); + lambda_advect(); + T += dt; + } + + mesh->free(); +} From fe4052fad844d79260dde9143767ec7624e00f26 Mon Sep 17 00:00:00 2001 From: Will Saunders Date: Tue, 7 Jan 2025 14:44:33 +0000 Subject: [PATCH 66/66] updated NP submodule --- neso-particles | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/neso-particles b/neso-particles index dc5cb6d5..ddedc7fa 160000 --- a/neso-particles +++ b/neso-particles @@ -1 +1 @@ -Subproject commit dc5cb6d5d570ce6cd54bfc94cec29e0a54c200e1 +Subproject commit ddedc7fae3e0c96595fcc831c2fe73984fb69a70