Start moving surface->summary.h5 to C++

CMakeLists.txt

@@ -48,14 +48,14 @@ add_definitions(-DMAX_COORD=${maxcoord})
 set(MPI_ENABLED FALSE)
 if($ENV{FC} MATCHES "(mpi[^/]*|ftn)$")
   message("-- Detected MPI wrapper: $ENV{FC}")
-  add_definitions(-DMPI)
+  add_definitions(-DOPENMC_MPI)
   set(MPI_ENABLED TRUE)
 endif()
 
 # Check for Fortran 2008 MPI interface
 if(MPI_ENABLED AND mpif08)
   message("-- Using Fortran 2008 MPI bindings")
-  add_definitions(-DMPIF08)
+  add_definitions(-DOPENMC_MPIF08)
 endif()
 
 #===============================================================================
@@ -435,6 +435,7 @@ set(LIBOPENMC_FORTRAN_SRC
   src/tallies/trigger_header.F90
 )
 set(LIBOPENMC_CXX_SRC
+  src/hdf5_interface.h
   src/random_lcg.h
   src/random_lcg.cpp
   src/surface_header.C

src/api.F90

@@ -171,7 +171,7 @@ subroutine openmc_finalize() bind(C)
     ! Close FORTRAN interface.
     call h5close_f(err)
 
-#ifdef MPI
+#ifdef OPENMC_MPI
     ! Free all MPI types
     call MPI_TYPE_FREE(MPI_BANK, err)
 #endif

src/cmfd_execute.F90

@@ -105,7 +105,7 @@ subroutine calc_fission_source()
     real(8) :: hxyz(3) ! cell dimensions of current ijk cell
     real(8) :: vol     ! volume of cell
     real(8),allocatable :: source(:,:,:,:)  ! tmp source array for entropy
-#ifdef MPI
+#ifdef OPENMC_MPI
     integer :: mpi_err ! MPI error code
 #endif
 
@@ -197,7 +197,7 @@ subroutine calc_fission_source()
 
     end if
 
-#ifdef MPI
+#ifdef OPENMC_MPI
     ! Broadcast full source to all procs
     call MPI_BCAST(cmfd % cmfd_src, n, MPI_REAL8, 0, mpi_intracomm, mpi_err)
 #endif
@@ -234,7 +234,7 @@ subroutine cmfd_reweight(new_weights)
     real(8) :: norm     ! normalization factor
     logical :: outside  ! any source sites outside mesh
     logical :: in_mesh  ! source site is inside mesh
-#ifdef MPI
+#ifdef OPENMC_MPI
     integer :: mpi_err
 #endif
 
@@ -291,7 +291,7 @@ subroutine cmfd_reweight(new_weights)
       if (.not. cmfd_feedback) return
 
       ! Broadcast weight factors to all procs
-#ifdef MPI
+#ifdef OPENMC_MPI
       call MPI_BCAST(cmfd % weightfactors, ng*nx*ny*nz, MPI_REAL8, 0, &
            mpi_intracomm, mpi_err)
 #endif

src/eigenvalue.F90

@@ -42,11 +42,11 @@ subroutine synchronize_bank()
     type(Bank), save, allocatable :: &
          & temp_sites(:)       ! local array of extra sites on each node
 
-#ifdef MPI
+#ifdef OPENMC_MPI
     integer    :: mpi_err      ! MPI error code
     integer(8) :: n            ! number of sites to send/recv
     integer    :: neighbor     ! processor to send/recv data from
-#ifdef MPIF08
+#ifdef OPENMC_MPIF08
     type(MPI_Request) :: request(20)
 #else
     integer    :: request(20)  ! communication request for send/recving sites
@@ -66,7 +66,7 @@ subroutine synchronize_bank()
     ! fission bank its own sites starts in order to ensure reproducibility by
     ! skipping ahead to the proper seed.
 
-#ifdef MPI
+#ifdef OPENMC_MPI
     start = 0_8
     call MPI_EXSCAN(n_bank, start, 1, MPI_INTEGER8, MPI_SUM, &
          mpi_intracomm, mpi_err)
@@ -148,7 +148,7 @@ subroutine synchronize_bank()
     ! neighboring processors, we have to perform an ALLGATHER to determine the
     ! indices for all processors
 
-#ifdef MPI
+#ifdef OPENMC_MPI
     ! First do an exclusive scan to get the starting indices for
     start = 0_8
     call MPI_EXSCAN(index_temp, start, 1, MPI_INTEGER8, MPI_SUM, &
@@ -191,7 +191,7 @@ subroutine synchronize_bank()
     call time_bank_sample % stop()
     call time_bank_sendrecv % start()
 
-#ifdef MPI
+#ifdef OPENMC_MPI
     ! ==========================================================================
     ! SEND BANK SITES TO NEIGHBORS
 
@@ -343,14 +343,14 @@ end subroutine shannon_entropy
   subroutine calculate_generation_keff()
 
     real(8) :: keff_reduced
-#ifdef MPI
+#ifdef OPENMC_MPI
     integer :: mpi_err ! MPI error code
 #endif
 
     ! Get keff for this generation by subtracting off the starting value
     keff_generation = global_tallies(RESULT_VALUE, K_TRACKLENGTH) - keff_generation
 
-#ifdef MPI
+#ifdef OPENMC_MPI
     ! Combine values across all processors
     call MPI_ALLREDUCE(keff_generation, keff_reduced, 1, MPI_REAL8, &
          MPI_SUM, mpi_intracomm, mpi_err)
@@ -584,7 +584,7 @@ subroutine count_source_for_ufs()
 
     real(8) :: total         ! total weight in source bank
     logical :: sites_outside ! were there sites outside the ufs mesh?
-#ifdef MPI
+#ifdef OPENMC_MPI
     integer :: n             ! total number of ufs mesh cells
     integer :: mpi_err       ! MPI error code
 #endif
@@ -608,7 +608,7 @@ subroutine count_source_for_ufs()
         call fatal_error("Source sites outside of the UFS mesh!")
       end if
 
-#ifdef MPI
+#ifdef OPENMC_MPI
       ! Send source fraction to all processors
       n = product(m % dimension)
       call MPI_BCAST(source_frac, n, MPI_REAL8, 0, mpi_intracomm, mpi_err)

src/error.F90

@@ -128,7 +128,7 @@ subroutine fatal_error(message, error_code)
     integer :: line_wrap ! length of line
     integer :: length    ! length of message
     integer :: indent    ! length of indentation
-#ifdef MPI
+#ifdef OPENMC_MPI
     integer :: mpi_err
 #endif
 
@@ -180,7 +180,7 @@ subroutine fatal_error(message, error_code)
       end if
     end do
 
-#ifdef MPI
+#ifdef OPENMC_MPI
     ! Abort MPI
     call MPI_ABORT(mpi_intracomm, code, mpi_err)
 #endif

src/geometry.F90

@@ -537,7 +537,6 @@ subroutine distance_to_boundary(p, dist, surface_crossed, lattice_translation, &
     real(8) :: surf_uvw(3)        ! surface normal direction
     logical :: coincident         ! is particle on surface?
     type(Cell),       pointer :: c
-    class(Surface),   pointer :: surf
     class(Lattice),   pointer :: lat
 
     ! inialize distance to infinity (huge)

src/hdf5_interface.F90

@@ -124,7 +124,7 @@ function file_create(filename, parallel) result(file_id)
       ! Setup file access property list with parallel I/O access
       call h5pcreate_f(H5P_FILE_ACCESS_F, plist, hdf5_err)
 #ifdef PHDF5
-#ifdef MPIF08
+#ifdef OPENMC_MPIF08
       call h5pset_fapl_mpio_f(plist, mpi_intracomm%MPI_VAL, &
            MPI_INFO_NULL%MPI_VAL, hdf5_err)
 #else
@@ -174,7 +174,7 @@ function file_open(filename, mode, parallel) result(file_id)
       ! Setup file access property list with parallel I/O access
       call h5pcreate_f(H5P_FILE_ACCESS_F, plist, hdf5_err)
 #ifdef PHDF5
-#ifdef MPIF08
+#ifdef OPENMC_MPIF08
       call h5pset_fapl_mpio_f(plist, mpi_intracomm%MPI_VAL, &
            MPI_INFO_NULL%MPI_VAL, hdf5_err)
 #else

src/hdf5_interface.h

@@ -0,0 +1,47 @@
+#ifndef HDF5_INTERFACE_H
+#define HDF5_INTERFACE_H
+
+#include <array>  // For std::array
+#include <string.h>  // For strlen
+
+#include "hdf5.h"
+
+
+template<std::size_t array_len> void
+write_double_1D(hid_t group_id, char const *name,
+                std::array<double, array_len> &buffer)
+{
+  hsize_t dims[1]{array_len};
+  hid_t dataspace = H5Screate_simple(1, dims, NULL);
+
+  hid_t dataset = H5Dcreate(group_id, name, H5T_NATIVE_DOUBLE, dataspace,
+                            H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+  H5Dwrite(dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT,
+           &buffer[0]);
+
+  H5Sclose(dataspace);
+  H5Dclose(dataset);
+}
+
+
+void
+write_string(hid_t group_id, char const *name, char const *buffer)
+{
+  size_t buffer_len = strlen(buffer);
+  hid_t datatype = H5Tcopy(H5T_C_S1);
+  H5Tset_size(datatype, buffer_len);
+
+  hid_t dataspace = H5Screate(H5S_SCALAR);
+
+  hid_t dataset = H5Dcreate(group_id, name, datatype, dataspace,
+                            H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+
+  H5Dwrite(dataset, datatype, H5S_ALL, H5S_ALL, H5P_DEFAULT, buffer);
+
+  H5Tclose(datatype);
+  H5Sclose(dataspace);
+  H5Dclose(dataset);
+}
+
+#endif //HDF5_INTERFACE_H

src/initialize.F90

@@ -52,8 +52,8 @@ subroutine openmc_init(intracomm) bind(C)
     ! Copy the communicator to a new variable. This is done to avoid changing
     ! the signature of this subroutine. If MPI is being used but no communicator
     ! was passed, assume MPI_COMM_WORLD.
-#ifdef MPI
-#ifdef MPIF08
+#ifdef OPENMC_MPI
+#ifdef OPENMC_MPIF08
     type(MPI_Comm), intent(in) :: comm     ! MPI intracommunicator
     if (present(intracomm)) then
       comm % MPI_VAL = intracomm
@@ -74,7 +74,7 @@ subroutine openmc_init(intracomm) bind(C)
     call time_total%start()
     call time_initialize%start()
 
-#ifdef MPI
+#ifdef OPENMC_MPI
     ! Setup MPI
     call initialize_mpi(comm)
 #endif
@@ -108,23 +108,23 @@ subroutine openmc_init(intracomm) bind(C)
 
   end subroutine openmc_init
 
-#ifdef MPI
+#ifdef OPENMC_MPI
 !===============================================================================
 ! INITIALIZE_MPI starts up the Message Passing Interface (MPI) and determines
 ! the number of processors the problem is being run with as well as the rank of
 ! each processor.
 !===============================================================================
 
   subroutine initialize_mpi(intracomm)
-#ifdef MPIF08
+#ifdef OPENMC_MPIF08
     type(MPI_Comm), intent(in) :: intracomm  ! MPI intracommunicator
 #else
     integer, intent(in) :: intracomm         ! MPI intracommunicator
 #endif
 
     integer                   :: mpi_err          ! MPI error code
     integer                   :: bank_blocks(5)   ! Count for each datatype
-#ifdef MPIF08
+#ifdef OPENMC_MPIF08
     type(MPI_Datatype)        :: bank_types(5)
 #else
     integer                   :: bank_types(5)    ! Datatypes

src/input_xml.F90

@@ -54,7 +54,7 @@ subroutine read_surfaces(node_ptr) bind(C, name='read_surfaces')
       implicit none
       type(C_PTR) :: node_ptr
     end subroutine read_surfaces
-  end interface 
+  end interface
 
 contains
 
@@ -1081,77 +1081,23 @@ subroutine read_geometry_xml()
 
       select type(s)
       type is (SurfaceXPlane)
-        s%x0 = coeffs(1)
-
         ! Determine outer surfaces
-        xmin = min(xmin, s % x0)
-        xmax = max(xmax, s % x0)
-        if (xmin == s % x0) i_xmin = i
-        if (xmax == s % x0) i_xmax = i
+        xmin = min(xmin, coeffs(1))
+        xmax = max(xmax, coeffs(1))
+        if (xmin == coeffs(1)) i_xmin = i
+        if (xmax == coeffs(1)) i_xmax = i
       type is (SurfaceYPlane)
-        s%y0 = coeffs(1)
-
         ! Determine outer surfaces
-        ymin = min(ymin, s % y0)
-        ymax = max(ymax, s % y0)
-        if (ymin == s % y0) i_ymin = i
-        if (ymax == s % y0) i_ymax = i
+        ymin = min(ymin, coeffs(1))
+        ymax = max(ymax, coeffs(1))
+        if (ymin == coeffs(1)) i_ymin = i
+        if (ymax == coeffs(1)) i_ymax = i
       type is (SurfaceZPlane)
-        s%z0 = coeffs(1)
-
         ! Determine outer surfaces
-        zmin = min(zmin, s % z0)
-        zmax = max(zmax, s % z0)
-        if (zmin == s % z0) i_zmin = i
-        if (zmax == s % z0) i_zmax = i
-      type is (SurfacePlane)
-        s%A = coeffs(1)
-        s%B = coeffs(2)
-        s%C = coeffs(3)
-        s%D = coeffs(4)
-      type is (SurfaceXCylinder)
-        s%y0 = coeffs(1)
-        s%z0 = coeffs(2)
-        s%r = coeffs(3)
-      type is (SurfaceYCylinder)
-        s%x0 = coeffs(1)
-        s%z0 = coeffs(2)
-        s%r = coeffs(3)
-      type is (SurfaceZCylinder)
-        s%x0 = coeffs(1)
-        s%y0 = coeffs(2)
-        s%r = coeffs(3)
-      type is (SurfaceSphere)
-        s%x0 = coeffs(1)
-        s%y0 = coeffs(2)
-        s%z0 = coeffs(3)
-        s%r = coeffs(4)
-      type is (SurfaceXCone)
-        s%x0 = coeffs(1)
-        s%y0 = coeffs(2)
-        s%z0 = coeffs(3)
-        s%r2 = coeffs(4)
-      type is (SurfaceYCone)
-        s%x0 = coeffs(1)
-        s%y0 = coeffs(2)
-        s%z0 = coeffs(3)
-        s%r2 = coeffs(4)
-      type is (SurfaceZCone)
-        s%x0 = coeffs(1)
-        s%y0 = coeffs(2)
-        s%z0 = coeffs(3)
-        s%r2 = coeffs(4)
-      type is (SurfaceQuadric)
-        s%A = coeffs(1)
-        s%B = coeffs(2)
-        s%C = coeffs(3)
-        s%D = coeffs(4)
-        s%E = coeffs(5)
-        s%F = coeffs(6)
-        s%G = coeffs(7)
-        s%H = coeffs(8)
-        s%J = coeffs(9)
-        s%K = coeffs(10)
+        zmin = min(zmin, coeffs(1))
+        zmax = max(zmax, coeffs(1))
+        if (zmin == coeffs(1)) i_zmin = i
+        if (zmax == coeffs(1)) i_zmax = i
       end select
 
       ! No longer need coefficients