Collect common solver functionality in base classes (#228)

* Skeleton for EqnSysBase. Only templates on Nektar eqsys, not particle sys yet. * Add TimeEvoEqnSysBase class. * Move equation sys base classes to nektar_interface dir. * m_field_to_index, m_required_flds, validate_fields, m_int_fld_names. * Remove virtual inheritance. * Move load_params to EqnSysBase. * Add v_InitObject to check required fields, load parameters, set time-integrated fields. * Missing utils header. * Add a base particle system, and a template parameter of TimeEvoEqnSysBase that must inherit from it. * Add missing v_InitObject() pass-through in TimeEvoEqnSysBase. * Convert SimpleSOL to use TimeEvoEqnSysBase, PartSysBase. * Use SolverRunner for SimpleSOL entrypoint. * Remove debug output. * Move cell indices map into PartSysBase. * Move num_parts_tot to PartSysBase and set its value from session file params at construction. * Correct a param string. * Correct order of calls in PartSysBase::free(). * Init particle_sys in EqnSysBase. * Free particle sys memory after fluid solver loop has finished, rather than in destructor. * Cope with particles being turned off. * Move solver base classes to nektar_interface subdir. * Consistent use of this-> in base classes. * Remove some variables and functions in SimpleSOL/NeutralParticleSystem that duplicate base class members. * Remove some variables and functions in SOLSystem that duplicate base class members. * m_ => this-> in SimpleSOL * Report some parameters commont to all particle systems. * Add [] operator to NektarFieldIndexMap. * Add write() functionality to PartSysBase. * Remove superfluous destructor definition. * Parameter name tweaks and further docstrings. * Add zero_array_of_arrays util function to EqnSysBase. * missing 'virtual' * Correct v_DoInitialise signature for [email protected]. * Missing 'override'. * Add an options struct for PartSysBase. * Call extend_halos_fixed_offset in PartSysBase after constructing the particle-mesh interface.
ExCALIBUR-NEPTUNE · May 8, 2024 · c03be8d · c03be8d
1 parent db278a4
commit c03be8d
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Showing 13 changed files with 557 additions and 237 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -147,6 +147,7 @@ set(HEADER_FILES
     ${INC_DIR}/nektar_interface/bounding_box_intersection.hpp
     ${INC_DIR}/nektar_interface/cell_id_translation.hpp
     ${INC_DIR}/nektar_interface/coordinate_mapping.hpp
+    ${INC_DIR}/nektar_interface/solver_base/eqnsys_base.hpp
     ${INC_DIR}/nektar_interface/expansion_looping/basis_evaluate_base.hpp
     ${INC_DIR}/nektar_interface/expansion_looping/expansion_looping.hpp
     ${INC_DIR}/nektar_interface/expansion_looping/geom_to_expansion_builder.hpp
@@ -176,6 +177,7 @@ set(HEADER_FILES
     ${INC_DIR}/nektar_interface/geometry_transport/remote_geom_3d.hpp
     ${INC_DIR}/nektar_interface/geometry_transport/shape_mapping.hpp
     ${INC_DIR}/nektar_interface/parameter_store.hpp
+    ${INC_DIR}/nektar_interface/solver_base/partsys_base.hpp
     ${INC_DIR}/nektar_interface/particle_boundary_conditions.hpp
     ${INC_DIR}/nektar_interface/particle_cell_mapping/coarse_lookup_map.hpp
     ${INC_DIR}/nektar_interface/particle_cell_mapping/coarse_mappers_base.hpp
@@ -209,6 +211,7 @@ set(HEADER_FILES
     ${INC_DIR}/nektar_interface/particle_interface.hpp
     ${INC_DIR}/nektar_interface/particle_mesh_interface.hpp
     ${INC_DIR}/nektar_interface/special_functions.hpp
+    ${INC_DIR}/nektar_interface/solver_base/time_evolved_eqnsys_base.hpp
     ${INC_DIR}/nektar_interface/utilities.hpp
     ${INC_DIR}/nektar_interface/utility_mesh_cartesian.hpp
     ${INC_DIR}/nektar_interface/utility_mesh_plotting.hpp

diff --git a/include/nektar_interface/solver_base/eqnsys_base.hpp b/include/nektar_interface/solver_base/eqnsys_base.hpp
@@ -0,0 +1,142 @@
+#ifndef __EQNSYS_BASE_H_
+#define __EQNSYS_BASE_H_
+
+#include <SolverUtils/EquationSystem.h>
+
+#include <type_traits>
+
+#include "nektar_interface/solver_base/partsys_base.hpp"
+#include "nektar_interface/utilities.hpp"
+
+namespace LU = Nektar::LibUtilities;
+namespace SD = Nektar::SpatialDomains;
+namespace SU = Nektar::SolverUtils;
+
+namespace NESO::Solvers {
+
+// Fwd declare NEKEQNSYS, PARTSYS as classes
+class NEKEQNSYS;
+class PARTSYS;
+
+/**
+ * @brief Base class for Nektar++ equation systems, coupled to a NESO-Particles
+ * particle system derived from NESO::Solvers::PartSysBase.
+ */
+template <typename NEKEQNSYS, typename PARTSYS>
+class EqnSysBase : public NEKEQNSYS {
+  // Template param must derive from Nektar's EquationSystem base class
+  static_assert(std::is_base_of<SU::EquationSystem, NEKEQNSYS>(),
+                "Template arg to EqnSysBase must derive from "
+                "Nektar::SolverUtils::EquationSystem");
+  // Particle system must derive from PartSysBase
+  static_assert(
+      std::is_base_of<PartSysBase, PARTSYS>(),
+      "PARTSYS template arg to EqnSysBase must derive from PartSysBase");
+
+protected:
+  EqnSysBase(const LU::SessionReaderSharedPtr &session,
+             const SD::MeshGraphSharedPtr &graph)
+      : NEKEQNSYS(session, graph), field_to_index(session->GetVariables()),
+        required_fld_names() {
+
+    // If number of particles / number per cell was set in config; construct the
+    // particle system
+    int num_parts_per_cell, num_parts_tot;
+    session->LoadParameter(PartSysBase::NUM_PARTS_TOT_STR, num_parts_tot, -1);
+    session->LoadParameter(PartSysBase::NUM_PARTS_PER_CELL_STR,
+                           num_parts_per_cell, -1);
+    this->particles_enabled = num_parts_tot > 0 || num_parts_per_cell > 0;
+    if (this->particles_enabled) {
+      this->particle_sys = std::make_shared<PARTSYS>(session, graph);
+    }
+  }
+
+  /// Field name => index mapper
+  NESO::NektarFieldIndexMap field_to_index;
+
+  /// Particle system
+  std::shared_ptr<PARTSYS> particle_sys;
+
+  /// Flag identifying whether particles were enabled in the config file
+  bool particles_enabled;
+
+  /// List of field names required by the solver
+  std::vector<std::string> required_fld_names;
+
+  /// Placeholder for subclasses to override; called in v_InitObject()
+  virtual void load_params(){};
+
+  /**
+   * @brief Check that all required fields are defined. All fields must have the
+   * same number of quad points for now.
+   */
+  void validate_fields() {
+    int npts_exp = NEKEQNSYS::GetNpoints();
+    for (auto &fld_name : this->required_fld_names) {
+      int idx = this->field_to_index.get_idx(fld_name);
+      // Check field exists
+
+      std::string err_msg = "Required field [" + fld_name + "] is not defined.";
+      NESOASSERT(idx >= 0, err_msg.c_str());
+
+      // Check fields all have the same number of quad points
+      int npts = this->m_fields[idx]->GetNpoints();
+      err_msg = "Expecting " + std::to_string(npts_exp) +
+                " quad points, but field '" + fld_name + "' has " +
+                std::to_string(npts) +
+                ". Check NUMMODES is the same for all required fields.";
+      NESOASSERT(npts == npts_exp, err_msg.c_str());
+    }
+  }
+
+  /** @brief Write particle params to stdout on task 0. Ensures they appear just
+   * after fluid params are written by nektar.
+   *
+   * */
+  virtual void v_DoInitialise() override {
+    if (this->m_session->GetComm()->TreatAsRankZero() &&
+        this->particles_enabled) {
+      particle_sys->add_params_report();
+    }
+    NEKEQNSYS::v_DoInitialise();
+  }
+
+  /**
+   * @brief Free particle system memory after solver loop has finished.
+   * Prevent further overrides to guarantee that subclasses do the same.
+   */
+  virtual void v_DoSolve() override final {
+    NEKEQNSYS::v_DoSolve();
+    if (this->particle_sys) {
+      this->particle_sys->free();
+    }
+  }
+
+  /**
+   * @brief Initialise the equation system, then check required fields are set
+   * and load parameters.
+   */
+  virtual void v_InitObject(bool create_fields) override {
+    NEKEQNSYS::v_InitObject(create_fields);
+
+    // Ensure that the session file defines all required variables
+    validate_fields();
+
+    // Load parameters
+    load_params();
+  }
+
+  /**
+   * @brief Utility function to zero a Nektar++ array of arrays
+   *
+   * @param arr Array-of-arrays to zero
+   */
+  void zero_array_of_arrays(Array<OneD, Array<OneD, NekDouble>> &arr) {
+    for (auto ii = 0; ii < arr.size(); ii++) {
+      Vmath::Zero(arr[ii].size(), arr[ii], 1);
+    }
+  }
+};
+
+} // namespace NESO::Solvers
+#endif