Feature/geometric operators

.gitignore

@@ -9,6 +9,7 @@
 
 # General list of files to ignore
 *.mod
+*.smod
 *.o
 *.dirstamp
 *.Po

configure.ac

@@ -9,23 +9,23 @@ AC_PROG_RANLIB
 AC_PROG_INSTALL
 
 AC_ARG_ENABLE(contrib,
-              AS_HELP_STRING([--enable-contrib],[Compile various tools]), 
-              [enable_contrib=${enableval}], [enable_contrib=yes])
+   AS_HELP_STRING([--enable-contrib],[Compile various tools]),
+   [enable_contrib=${enableval}], [enable_contrib=yes])
 
 AC_ARG_ENABLE(real,
-	      AS_HELP_STRING([--enable-real=Xp  Specify working precision of REAL types:
-                    sp -- REAL(kind=4)
-	            dp -- REAL(kind=8) (default)
-	            qp -- REAL(kind=16)]),
-	        [enable_real=${enableval}], [enable_real=dp])
+   AS_HELP_STRING([--enable-real=Xp Specify working precision of REAL types:
+   sp -- REAL(kind=4)
+   dp -- REAL(kind=8) (default)
+   qp -- REAL(kind=16)]),
+   [enable_real=${enableval}], [enable_real=dp])
 
 AC_ARG_ENABLE(blk_size,
-              AS_HELP_STRING([--enable-blk_size=number of values Specify size of fast memory]),
-              [blk_size=${enableval}], [blk_size="10000"])
+   AS_HELP_STRING([--enable-blk_size=number of values Specify size of fast memory]),
+   [blk_size=${enableval}], [blk_size="10000"])
 
 AC_ARG_ENABLE(device-mpi,
-	      AS_HELP_STRING([--enable-device-mpi],[Enable device aware MPI]),
-	      [enable_device_mpi=${enableval}], [enable_device_mpi=no])
+   AS_HELP_STRING([--enable-device-mpi],[Enable device aware MPI]),
+   [enable_device_mpi=${enableval}], [enable_device_mpi=no])
 
 # Test for a sane fortran environment (^-^)
 AC_LANG(Fortran)
@@ -41,50 +41,50 @@ if test "x${have_mpi}" != xno; then
    LIBS="$MPILIBS $LIBS"
    AC_LANG(C)
    AX_MPI([have_mpi=yes],[have_mpi=no])
-   if  test "x${have_mpi}" != xno; then
-       CC="$MPICC"
+   if test "x${have_mpi}" != xno; then
+      CC="$MPICC"
    else
-       AC_MSG_ERROR([Can't find a suitable C MPI compiler])
+      AC_MSG_ERROR([Can't find a suitable C MPI compiler])
    fi
    AC_LANG(C++)
    AX_MPI([have_mpi=yes],[have_mpi=no])
-   if  test "x${have_mpi}" != xno; then
-       CXX="$MPICXX"
+   if test "x${have_mpi}" != xno; then
+      CXX="$MPICXX"
    fi
    AC_LANG(Fortran)
 else
-   AC_MSG_ERROR([Can't find a suitable MPI compiler])   
+   AC_MSG_ERROR([Can't find a suitable MPI compiler])
 fi
 AX_MPIF08
 AX_MPI_DTYPE
 
 AC_FC_PP_SRCEXT([F90])
 AX_COMPILER_VENDOR
 
-        
-              
+
+
 # Checks for platform headers
 AC_LANG_PUSH([C])
 AC_CHECK_HEADERS([cpuid.h])
-AC_LANG_POP([C])  
+AC_LANG_POP([C])
 
 # Set necessary flags to fix issues with various compilers
 if test "x$ax_cv_fc_compiler_vendor" = xportland; then
-   FCFLAGS="$FCFLAGS  -Mbackslash"
+   FCFLAGS="$FCFLAGS -Mbackslash"
 fi
 
 if test "x$ax_cv_fc_compiler_vendor" = xnvhpc; then
-   FCFLAGS="$FCFLAGS  -Mbackslash"
+    FCFLAGS="$FCFLAGS -Mbackslash"
 fi
 
 # Store build information (date, host, FC)
 AC_SUBST(NEKO_BUILD_INFO,
-        ["(build: $(date +%Y-%m-%d) on $host using $ax_cv_fc_compiler_vendor)"], [])
+   ["(build: $(date +%Y-%m-%d) on $host using $ax_cv_fc_compiler_vendor)"], [])
 
 # Checks for Doxygen
 AC_CHECK_PROGS([DOXYGEN], [doxygen])
 if test -n "$DOXYGEN"; then
-  AC_CHECK_PROGS([DOXYGEN_DEPS], [dot])
+   AC_CHECK_PROGS([DOXYGEN_DEPS], [dot])
 fi
 AM_CONDITIONAL([ENABLE_DOXYGEN], [test -n "$DOXYGEN_DEPS"])
 
@@ -106,35 +106,35 @@ AX_PFUNIT
 
 # Check for blas and lapack
 AS_IF([test "x${is_cray}" = xyes || test "x${is_hpe_cray}" = xyes],
-       AX_CRAY_LIBSCI
-       if test "x${have_cray_libsci}" = xyes; then
-         have_blas_lapack="yes"
-       else
-         have_blas_lapack="no"
-       fi, have_blas_lapack="no")
+   AX_CRAY_LIBSCI
+   if test "x${have_cray_libsci}" = xyes; then
+      have_blas_lapack="yes"
+   else
+      have_blas_lapack="no"
+   fi, have_blas_lapack="no")
 
 if test "x${have_blas_lapack}" != xyes; then
-  AX_LAPACK
-  if test "x${ax_lapack_ok}" != xno; then
-     LIBS="$LAPACK_LIBS $BLAS_LIBS $LIBS"
-     have_blas_lapack=yes
-  else
-     have_blas_lapack=no
-  fi
+   AX_LAPACK
+   if test "x${ax_lapack_ok}" != xno; then
+      LIBS="$LAPACK_LIBS $BLAS_LIBS $LIBS"
+      have_blas_lapack=yes
+   else
+      have_blas_lapack=no
+   fi
 fi
 
 if test "x${have_blas_lapack}" != xyes; then
    AC_MSG_ERROR([Can't find a suitable BLAS/LAPACK library])
 fi
 
 if test "x${have_darshan}" != xyes; then
-    AX_DARSHAN
-    if test "x${ax_darshan_ok}" != xno; then
-        LIBS="$DARSHAN_LIBS $LIBS"
-        have_darshan=yes
-    else
-        have_darshan=no
-    fi
+   AX_DARSHAN
+   if test "x${ax_darshan_ok}" != xno; then
+      LIBS="$DARSHAN_LIBS $LIBS"
+      have_darshan=yes
+   else
+      have_darshan=no
+   fi
 fi
 
 found_domain_decomp="no"
@@ -150,8 +150,8 @@ fi
 if test "x${found_domain_decomp}" != xyes; then
    AX_PARMETIS
    if test "${PARMETIS_LIBS}"; then
-       LIBS="$PARMETIS_LIBS $LIBS"
-       found_domain_decomp="yes"
+      LIBS="$PARMETIS_LIBS $LIBS"
+      found_domain_decomp="yes"
    fi
 fi
 
@@ -166,17 +166,17 @@ if test "x$enable_real" = xsp; then
    AC_SUBST(NEKO_REAL_TYPE, "sp")
    AC_SUBST(NEKO_C_REAL_TYPE, "c_float")
    AC_SUBST(NEKO_MPI_REAL_TYPE, "MPI_REAL")
-   AC_SUBST(NEKO_DEV_REAL_TYPE, "float")   				
+   AC_SUBST(NEKO_DEV_REAL_TYPE, "float")
 elif test "x$enable_real" = xdp; then
    AC_SUBST(NEKO_REAL_TYPE, "dp")
    AC_SUBST(NEKO_C_REAL_TYPE, "c_double")
    AC_SUBST(NEKO_MPI_REAL_TYPE, "MPI_DOUBLE_PRECISION")
-   AC_SUBST(NEKO_DEV_REAL_TYPE, "double")   				
+   AC_SUBST(NEKO_DEV_REAL_TYPE, "double")
 elif test "x$enable_real" = xqp; then
    AC_SUBST(NEKO_REAL_TYPE, "qp")
    AC_SUBST(NEKO_C_REAL_TYPE, "c_long_double")
    AC_SUBST(NEKO_MPI_REAL_TYPE, "MPI_REAL16")
-   AC_SUBST(NEKO_DEV_REAL_TYPE, "long double")   				
+   AC_SUBST(NEKO_DEV_REAL_TYPE, "long double")
 else
    AC_MSG_ERROR([Invalid working precision])
 fi
@@ -188,7 +188,7 @@ else
    if test "x$enable_real" = xqp; then
       AC_MSG_ERROR([REAL128 not supported])
    fi
-fi                          
+fi
 
 AC_SUBST(blk_size, ${blk_size})
 
@@ -204,36 +204,36 @@ fi
 
 # Checks for CUDA backend
 if test "x${is_cray}" = xyes; then
-  AX_CRAY_CUDATOOLKIT
+   AX_CRAY_CUDATOOLKIT
 else
-  AX_CUDA
+   AX_CUDA
 fi
 
 # Checks for OpenCL backend
 AX_OPENCL
 
 # Check if device aware MPI is requested
 if (test "x${have_cuda}" = xyes ||
-    test "x${have_hip}" = xyes  ||
-    test "x${have_opencl}" = xyes); then
+   test "x${have_hip}" = xyes  ||
+   test "x${have_opencl}" = xyes); then
    if test "x${enable_device_mpi}" = xyes; then
 
-      # Check that necessary accelerator modules are loaded
-      if (test "x${is_cray}" = xyes || test "x${is_hpe_cray}" = xyes); then    
-      	 AX_CRAY_ACCEL
+     # Check that necessary accelerator modules are loaded
+      if (test "x${is_cray}" = xyes || test "x${is_hpe_cray}" = xyes); then
+         AX_CRAY_ACCEL
       fi
 
       AC_SUBST(device_mpi, .true.)
       AC_DEFINE(HAVE_DEVICE_MPI, 1, [Define if device MPI is requested.])
-      
+
       if test "x${have_cuda}" = xyes; then
          CUDA_CFLAGS="$CUDA_CFLAGS -DHAVE_DEVICE_MPI=1"
 
          # Make sure we have support for atomicAdd
-      	 AS_IF([test "$CUDA_ARCH"],[],[CUDA_ARCH="-arch sm_60"])         
-      fi      
+         AS_IF([test "$CUDA_ARCH"],[],[CUDA_ARCH="-arch sm_60"])
+      fi
 
-      if  test "x${have_hip}" = xyes; then
+      if test "x${have_hip}" = xyes; then
          HIP_HIPCC_FLAGS="$HIP_HIPCC_FLAGS -DHAVE_DEVICE_MPI=1"
       fi
    else
@@ -282,69 +282,70 @@ AC_SUBST(HIP_HIPCC_FLAGS)
 
 # Set device backend if requested (and found)
 if (test "x${have_cuda}" = xyes ||
-    test "x${have_hip}" = xyes  ||
-    test "x${have_opencl}" = xyes); then
-    AC_SUBST(device_bcknd, "1")
+   test "x${have_hip}" = xyes  ||
+   test "x${have_opencl}" = xyes); then
+   AC_SUBST(device_bcknd, "1")
 else
-    AC_SUBST(device_bcknd, "0")
+   AC_SUBST(device_bcknd, "0")
 fi
 
 AC_CONFIG_FILES([Makefile\
-		 src/Makefile\
-		 tests/Makefile\
-		 src/comm/comm.F90\
-	 	 src/config/neko_config.f90\
-		 src/config/num_types.f90\
-		 src/device/device_config.h\
-		 src/scripts/cltostring.sh\
-		 makeneko\
-		 neko.pc])
+   src/Makefile\
+   tests/Makefile\
+   src/comm/comm.F90\
+   src/config/neko_config.f90\
+   src/config/num_types.f90\
+   src/device/device_config.h\
+   src/scripts/cltostring.sh\
+   makeneko\
+   neko.pc])
 
 # Config tests
 AC_CONFIG_FILES([tests/stack/Makefile\
-		 tests/tuple/Makefile\
- 		 tests/point/Makefile\
-		 tests/htable/Makefile\
-		 tests/uset/Makefile\
-		 tests/quad/Makefile\
-		 tests/hex/Makefile\
-		 tests/tet/Makefile\
-		 tests/tri/Makefile\
-		 tests/math/Makefile\
-		 tests/mesh/Makefile\
-		 tests/space/Makefile\
-		 tests/dofmap/Makefile\
-		 tests/field/Makefile\
-		 tests/mean_field/Makefile\
-		 tests/mean_sqr_field/Makefile\
-		 tests/gather_scatter/Makefile\
-		 tests/krylov/Makefile\
-		 tests/bc/Makefile\
-		 tests/signal/Makefile\
-		 tests/jobctrl/Makefile\
-		 tests/device/Makefile\
-		 tests/device_math/Makefile\
-		 tests/mathops/Makefile\
-		 tests/device_mathops/Makefile\
-		 tests/octree/Makefile\
-                 tests/vector/Makefile\
-                 tests/scratch_registry/Makefile\
-                 tests/fast3d/Makefile\
-                 tests/time_scheme/Makefile\
-                 tests/time_scheme_controller/Makefile\
-                 tests/time_based_controller/Makefile\
-                 tests/point_interpolation/Makefile])
+   tests/tuple/Makefile\
+   tests/point/Makefile\
+   tests/htable/Makefile\
+   tests/uset/Makefile\
+   tests/quad/Makefile\
+   tests/hex/Makefile\
+   tests/tet/Makefile\
+   tests/tri/Makefile\
+   tests/math/Makefile\
+   tests/mesh/Makefile\
+   tests/space/Makefile\
+   tests/dofmap/Makefile\
+   tests/field/Makefile\
+   tests/mean_field/Makefile\
+   tests/mean_sqr_field/Makefile\
+   tests/gather_scatter/Makefile\
+   tests/geometric_operators/Makefile\
+   tests/krylov/Makefile\
+   tests/bc/Makefile\
+   tests/signal/Makefile\
+   tests/jobctrl/Makefile\
+   tests/device/Makefile\
+   tests/device_math/Makefile\
+   tests/mathops/Makefile\
+   tests/device_mathops/Makefile\
+   tests/octree/Makefile\
+   tests/vector/Makefile\
+   tests/scratch_registry/Makefile\
+   tests/fast3d/Makefile\
+   tests/time_scheme/Makefile\
+   tests/time_scheme_controller/Makefile\
+   tests/time_based_controller/Makefile\
+   tests/point_interpolation/Makefile])
 
 if test "x${enable_contrib}" = xyes; then
    AC_CONFIG_FILES([contrib/Makefile\
-		    contrib/rea2nbin/Makefile\
-		    contrib/genmeshbox/Makefile\
-		    contrib/average_fields_in_time/Makefile\
-		    contrib/calc_lift_from_field/Makefile\
-		    contrib/postprocess_fluid_stats/Makefile\
-		    contrib/average_field_in_space/Makefile\
-		    contrib/map_to_equidistant_1d/Makefile\
-		    contrib/prepart/Makefile])
+      contrib/rea2nbin/Makefile\
+      contrib/genmeshbox/Makefile\
+      contrib/average_fields_in_time/Makefile\
+      contrib/calc_lift_from_field/Makefile\
+      contrib/postprocess_fluid_stats/Makefile\
+      contrib/average_field_in_space/Makefile\
+      contrib/map_to_equidistant_1d/Makefile\
+      contrib/prepart/Makefile])
 fi
 # Doxygen
 AC_CONFIG_FILES([doc/Doxyfile doc/Makefile])

src/.depends

@@ -85,6 +85,11 @@ math/bcknd/sx/sx_opgrad.o : math/bcknd/sx/sx_opgrad.f90 config/num_types.o
 math/bcknd/sx/sx_cfl.o : math/bcknd/sx/sx_cfl.f90 config/num_types.o 
 math/bcknd/sx/sx_lambda2.o : math/bcknd/sx/sx_lambda2.f90 math/math.o config/num_types.o 
 math/operators.o : math/operators.f90 comm/comm.o field/scratch_registry.o math/bcknd/device/device_math.o device/device.o math/math.o field/field.o sem/coef.o sem/space.o math/bcknd/device/opr_device.o math/bcknd/xsmm/opr_xsmm.o math/bcknd/sx/opr_sx.o math/bcknd/cpu/opr_cpu.o config/num_types.o config/neko_config.o 
+math/geometric_operators.o : math/geometric_operators.f90 mesh/hex.o mesh/quad.o mesh/tet.o mesh/tri.o mesh/point.o config/num_types.o 
+math/bcknd/cpu/distance_primitives.o : math/bcknd/cpu/distance_primitives.f90 config/num_types.o math/geometric_operators.o 
+math/bcknd/cpu/distance_elements.o : math/bcknd/cpu/distance_elements.f90 common/utils.o math/math.o math/geometric_operators.o 
+math/bcknd/cpu/coordinates_linear.o : math/bcknd/cpu/coordinates_linear.f90 mesh/hex.o mesh/quad.o mesh/tet.o mesh/tri.o math/math.o common/utils.o config/num_types.o math/geometric_operators.o 
+math/bcknd/cpu/coordinates_euclidean.o : math/bcknd/cpu/coordinates_euclidean.f90 mesh/hex.o mesh/quad.o mesh/tet.o mesh/tri.o math/math.o common/utils.o config/num_types.o math/geometric_operators.o 
 math/bcknd/cpu/opr_cpu.o : math/bcknd/cpu/opr_cpu.f90 math/mathops.o gs/gather_scatter.o field/field.o math/math.o sem/coef.o sem/space.o config/num_types.o math/bcknd/cpu/conv1.o math/bcknd/cpu/cdtp.o math/bcknd/cpu/opgrad.o math/bcknd/cpu/dudxyz.o 
 math/bcknd/sx/opr_sx.o : math/bcknd/sx/opr_sx.f90 math/mathops.o field/field.o math/math.o sem/coef.o sem/space.o config/num_types.o gs/gather_scatter.o math/bcknd/sx/sx_lambda2.o math/bcknd/sx/sx_cfl.o math/bcknd/sx/sx_cdtp.o math/bcknd/sx/sx_conv1.o math/bcknd/sx/sx_opgrad.o math/bcknd/sx/sx_dudxyz.o 
 math/bcknd/xsmm/opr_xsmm.o : math/bcknd/xsmm/opr_xsmm.F90 math/mathops.o gs/gather_scatter.o field/field.o mesh/mesh.o math/math.o sem/coef.o sem/space.o math/mxm_wrapper.o config/num_types.o 
@@ -100,7 +105,7 @@ math/bcknd/xsmm/fdm_xsmm.o : math/bcknd/xsmm/fdm_xsmm.f90 math/bcknd/xsmm/tensor
 math/schwarz.o : math/schwarz.f90 config/neko_config.o device/device.o math/fdm.o math/bcknd/device/device_math.o math/bcknd/device/device_schwarz.o gs/gather_scatter.o bc/bc.o sem/dofmap.o sem/space.o mesh/mesh.o math/math.o config/num_types.o 
 math/vector.o : math/vector.f90 common/utils.o math/bcknd/device/device_math.o device/device.o config/num_types.o config/neko_config.o 
 math/matrix.o : math/matrix.f90 common/utils.o math/bcknd/device/device_math.o device/device.o config/num_types.o config/neko_config.o 
-math/signed_distance.o : math/signed_distance.f90 adt/stack.o mesh/search_tree/aabb.o mesh/point.o common/utils.o mesh/aabb_tree.o mesh/tri_mesh.o mesh/tri.o field/field.o config/num_types.o 
+math/signed_distance.o : math/signed_distance.f90 common/utils.o adt/stack.o math/math.o mesh/aabb_tree.o mesh/search_tree/aabb.o mesh/tri_mesh.o mesh/tri.o mesh/point.o field/field.o config/num_types.o 
 common/checkpoint.o : common/checkpoint.f90 mesh/mesh.o common/utils.o field/field.o device/device.o sem/space.o field/field_series.o config/num_types.o config/neko_config.o 
 io/generic_file.o : io/generic_file.f90 comm/comm.o common/utils.o config/num_types.o 
 io/map_file.o : io/map_file.f90 io/format/map.o comm/comm.o common/utils.o io/generic_file.o