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DAMASK_EICMD/src/HDF5_utilities.f90

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number of helper functions for HDF5
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module HDF5_Utilities
use prec
use IO
use HDF5
MPI write only in case that PETSc is used
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#ifdef PETSc
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use PETSC
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#endif
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integer(HID_T), public, protected :: tempCoordinates, tempResults
integer(HID_T), private :: resultsFile, currentIncID, plist_id
integer(pInt), private :: currentInc
[skip ci] [skip sc] generic interfaces for HDF5 operations most existing HDF5 functions are only designed for writing output files and more general functionality is needed for storing the restart data
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interface HDF5_read
module procedure HDF5_read_double_1
module procedure HDF5_read_double_5
end interface HDF5_read
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public :: &
HDF5_Utilities_init, &
HDF5_mappingPhase, &
HDF5_mappingHomog, &
HDF5_mappingCrystallite, &
HDF5_backwardMappingPhase, &
HDF5_backwardMappingHomog, &
HDF5_backwardMappingCrystallite, &
HDF5_mappingCells, &
HDF5_addGroup ,&
HDF5_closeGroup ,&
HDF5_openGroup, &
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HDF5_openGroup2, &
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HDF5_forwardResults, &
HDF5_writeVectorDataset, &
HDF5_writeScalarDataset, &
HDF5_writeTensorDataset, &
HDF5_closeJobFile, &
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HDF5_removeLink, &
HDF5_createFile, &
HDF5_closeFile, &
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HDF5_writeScalarDataset3, &
HDF5_addGroup2, HDF5_read, &
HDF5_openFile
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contains
subroutine HDF5_Utilities_init
use, intrinsic :: &
iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
implicit none
integer :: hdferr
integer(SIZE_T) :: typeSize
write(6,'(/,a)') ' <<<+- HDF5_Utilities init -+>>>'
#include "compilation_info.f90"
currentInc = -1_pInt
call HDF5_createJobFile
end subroutine HDF5_Utilities_init
!--------------------------------------------------------------------------------------------------
!> @brief creates and initializes HDF5 output files
!--------------------------------------------------------------------------------------------------
subroutine HDF5_createJobFile
use hdf5
use DAMASK_interface, only: &
getSolverJobName
implicit none
integer :: hdferr
integer(SIZE_T) :: typeSize
character(len=1024) :: path
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#ifdef PETSc
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#include <petsc/finclude/petscsys.h>
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#endif
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!--------------------------------------------------------------------------------------------------
! initialize HDF5 library and check if integer and float type size match
call h5open_f(hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5open_f')
call h5tget_size_f(H5T_NATIVE_INTEGER,typeSize, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5tget_size_f (int)')
if (int(pInt,SIZE_T)/=typeSize) call IO_error(0_pInt,ext_msg='pInt does not match H5T_NATIVE_INTEGER')
call h5tget_size_f(H5T_NATIVE_DOUBLE,typeSize, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5tget_size_f (double)')
if (int(pReal,SIZE_T)/=typeSize) call IO_error(0_pInt,ext_msg='pReal does not match H5T_NATIVE_DOUBLE')
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#ifdef PETSC
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call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5pcreate_f')
call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5pset_fapl_mpio_f')
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#endif
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!--------------------------------------------------------------------------------------------------
! open file
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path = trim(getSolverJobName())//'.'//'hdf5'
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!call h5fcreate_f(path,H5F_ACC_TRUNC_F,resultsFile,hdferr)
call h5fcreate_f(path,H5F_ACC_TRUNC_F,resultsFile,hdferr,access_prp = plist_id)
if (hdferr < 0) call IO_error(100_pInt,ext_msg=path)
call HDF5_addStringAttribute(resultsFile,'createdBy',DAMASKVERSION)
call h5pclose_f(plist_id, hdferr) !neu
end subroutine HDF5_createJobFile
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!--------------------------------------------------------------------------------------------------
!> @brief creates and initializes HDF5 output files
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_createFile(path)
use hdf5
use DAMASK_interface, only: &
getSolverJobName
implicit none
integer :: hdferr
integer(SIZE_T) :: typeSize
character(len=*), intent(in) :: path
#ifdef PETSc
#include <petsc/finclude/petscsys.h>
#endif
call h5open_f(hdferr) !############################################################ DANGEROUS
#ifdef PETSC
call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5pcreate_f')
call h5pset_fapl_mpio_f(plist_id, PETSC_COMM_WORLD, MPI_INFO_NULL, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_Utilities_init: h5pset_fapl_mpio_f')
#endif
!--------------------------------------------------------------------------------------------------
! open file
!call h5fcreate_f(path,H5F_ACC_TRUNC_F,resultsFile,hdferr)
call h5fcreate_f(path,H5F_ACC_TRUNC_F,HDF5_createFile,hdferr,access_prp = plist_id)
if (hdferr < 0) call IO_error(100_pInt,ext_msg=path)
!call HDF5_addStringAttribute(HDF5_createFile,'createdBy',DAMASKVERSION)
call h5pclose_f(plist_id, hdferr) !neu
end function HDF5_createFile
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!--------------------------------------------------------------------------------------------------
!> @brief creates and initializes HDF5 output file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_closeJobFile()
use hdf5
implicit none
integer :: hdferr
call HDF5_removeLink('current')
call h5fclose_f(resultsFile,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_closeJobFile: h5fclose_f',el=hdferr)
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call h5close_f(hdferr)
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end subroutine HDF5_closeJobFile
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!--------------------------------------------------------------------------------------------------
!> @brief open and initializes HDF5 output file
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_openFile(filePath)
use hdf5
implicit none
integer :: hdferr
character(len=*), intent(in) :: filePath
call h5open_f(hdferr)!############################################################ DANGEROUS
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5open_f',el=hdferr)
call h5fopen_f(filePath,H5F_ACC_RDONLY_F,HDF5_openFile,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_openFile: h5fopen_f',el=hdferr)
end function HDF5_openFile
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!--------------------------------------------------------------------------------------------------
!> @brief creates and initializes HDF5 output file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_closeFile(fileHandle)
use hdf5
implicit none
integer :: hdferr
integer(HID_T), intent(in) :: fileHandle
call h5fclose_f(fileHandle,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_closeFile: h5fclose_f',el=hdferr)
call h5close_f(hdferr)!############################################################ DANGEROUS
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_closeFile: h5close_f',el=hdferr)
end subroutine HDF5_closeFile
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!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the results file, or if loc is present at the given location
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_addGroup(path)
use hdf5
implicit none
character(len=*), intent(in) :: path
integer :: hdferr
call h5gcreate_f(resultsFile, trim(path), HDF5_addGroup, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_addGroup: h5gcreate_f ('//trim(path)//')')
end function HDF5_addGroup
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!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the results file, or if loc is present at the given location
!--------------------------------------------------------------------------------------------------
Combined the dataset creation and writing dataset in single subroutine. Created group for looped writing.
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integer(HID_T) function HDF5_addGroup2(fileHandle,groupName)
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use hdf5
implicit none
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character(len=*), intent(in) :: groupName
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integer(HID_T), intent(in) :: fileHandle
integer :: hdferr
Combined the dataset creation and writing dataset in single subroutine. Created group for looped writing.
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call h5gcreate_f(fileHandle, trim(groupName), HDF5_addGroup2, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_addGroup2: h5gcreate_f ('//trim(groupName)//')')
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end function HDF5_addGroup2
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!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the results file
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_openGroup(path)
use hdf5
implicit none
character(len=*), intent(in) :: path
integer :: hdferr
call h5gopen_f(resultsFile, trim(path), HDF5_openGroup, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_openGroup: h5gopen_f ('//trim(path)//')')
end function HDF5_openGroup
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!--------------------------------------------------------------------------------------------------
!> @brief open a existing group of the results file
!--------------------------------------------------------------------------------------------------
integer(HID_T) function HDF5_openGroup2(FileReadID,path)
use hdf5
implicit none
character(len=*), intent(in) :: path
integer :: hdferr
integer(HID_T), intent(in) :: FileReadID
write(6,*) FileReadID,'hello';flush(6)
call h5gopen_f(FileReadID, trim(path), HDF5_openGroup2, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_openGroup2: h5gopen_f ('//trim(path)//')')
end function HDF5_openGroup2
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!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_setLink(path,link)
use hdf5
implicit none
character(len=*), intent(in) :: path, link
integer :: hdferr
logical :: linkExists
call h5lexists_f(resultsFile, link,linkExists, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_setLink: h5lexists_soft_f ('//trim(link)//')')
if (linkExists) then
call h5ldelete_f(resultsFile,link, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_setLink: h5ldelete_soft_f ('//trim(link)//')')
endif
call h5lcreate_soft_f(path, resultsFile, link, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_setLink: h5lcreate_soft_f ('//trim(path)//' '//trim(link)//')')
end subroutine HDF5_setLink
!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_removeLink(link)
use hdf5
implicit none
character(len=*), intent(in) :: link
integer :: hdferr
call h5ldelete_f(resultsFile,link, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_removeLink: h5ldelete_soft_f ('//trim(link)//')')
end subroutine HDF5_removeLink
!--------------------------------------------------------------------------------------------------
!> @brief closes a group
!--------------------------------------------------------------------------------------------------
subroutine HDF5_closeGroup(ID)
use hdf5
implicit none
integer(HID_T), intent(in) :: ID
integer :: hdferr
call h5gclose_f(ID, hdferr)
type mismatch
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if (hdferr < 0) call IO_error(1_pInt,ext_msg = 'HDF5_closeGroup: h5gclose_f (el is ID)', el = int(ID,pInt))
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end subroutine HDF5_closeGroup
!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addStringAttribute(entity,attrLabel,attrValue)
use hdf5
implicit none
integer(HID_T), intent(in) :: entity
character(len=*), intent(in) :: attrLabel, attrValue
integer :: hdferr
integer(HID_T) :: attr_id, space_id, type_id
call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5screate_f')
call h5tcopy_f(H5T_NATIVE_CHARACTER, type_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5tcopy_f')
call h5tset_size_f(type_id, int(len(trim(attrValue)),HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5tset_size_f')
call h5acreate_f(entity, trim(attrLabel),type_id,space_id,attr_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5acreate_f')
call h5awrite_f(attr_id, type_id, trim(attrValue), int([1],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5awrite_f')
call h5aclose_f(attr_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5aclose_f')
call h5sclose_f(space_id,hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_addStringAttribute: h5sclose_f')
end subroutine HDF5_addStringAttribute
!--------------------------------------------------------------------------------------------------
!> @brief adds the unique mapping from spatial position and constituent ID to results
!--------------------------------------------------------------------------------------------------
subroutine HDF5_mappingPhase(mapping,mapping2,Nconstituents,material_phase,phase_name,dataspace_size,mpiOffset,mpiOffset_phase)
use hdf5
implicit none
integer(pInt), intent(in) :: Nconstituents, dataspace_size, mpiOffset
integer(pInt), intent(in), dimension(:) :: mapping, mapping2
character(len=*), intent(in), dimension(:) :: phase_name
integer(pInt), intent(in), dimension(:) :: mpiOffset_phase
integer(pInt), intent(in), dimension(:,:,:) :: material_phase
character(len=len(phase_name(1))), dimension(:), allocatable :: namesNA
character(len=len(phase_name(1))) :: a
character(len=*),parameter :: n = "NULL"
integer(pInt) :: hdferr, NmatPoints, i, j, k
integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, name_id, position_id, plist_id, memspace
integer(HID_T) :: dt5_id ! Memory datatype identifier
integer(SIZE_T) :: typesize, type_sizec, type_sizei, type_size
integer(HSIZE_T), dimension(2) :: counter
integer(HSSIZE_T), dimension(2) :: fileOffset
integer(pInt), dimension(:,:), allocatable :: arrOffset
a = n
allocate(namesNA(0:size(phase_name)),source=[a,phase_name])
NmatPoints = size(mapping,1)/Nconstituents
mapping_ID = HDF5_openGroup("current/mapGeometry")
allocate(arrOffset(Nconstituents,NmatPoints))
do i=1_pInt, NmatPoints
do k=1_pInt, Nconstituents
do j=1_pInt, size(phase_name)
if(material_phase(k,1,i) == j) &
arrOffset(k,i) = mpiOffset_phase(j)
enddo
enddo
enddo
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(2, int([Nconstituents,dataspace_size],HSIZE_T), space_id, hdferr, &
int([Nconstituents,dataspace_size],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping')
!--------------------------------------------------------------------------------------------------
! compound type
! First calculate total size by calculating sizes of each member
!
CALL h5tcopy_f(H5T_NATIVE_CHARACTER, dt5_id, hdferr)
typesize = len(phase_name(1))
CALL h5tset_size_f(dt5_id, typesize, hdferr)
CALL h5tget_size_f(dt5_id, type_sizec, hdferr)
CALL h5tget_size_f(H5T_STD_I32LE,type_sizei, hdferr)
type_size = type_sizec + type_sizei
call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping: h5tcreate_f dtype_id')
call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt5_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tinsert_f 0')
call h5tinsert_f(dtype_id, "Position", type_sizec, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tinsert_f 2')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, 'constitutive', dtype_id, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase')
!--------------------------------------------------------------------------------------------------
! Create memory types (one compound datatype for each member)
call h5tcreate_f(H5T_COMPOUND_F, int(type_sizec,SIZE_T), name_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tcreate_f instance_id')
call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt5_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tinsert_f instance_id')
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tcreate_f position_id')
call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tinsert_f position_id')
!--------------------------------------------------------------------------------------------------
! Define and select hyperslabs
counter(1) = Nconstituents ! how big i am
counter(2) = NmatPoints
fileOffset(1) = 0 ! where i start to write my data
fileOffset(2) = mpiOffset
call h5screate_simple_f(2, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5dget_space_f')
call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! Create property list for collective dataset write
MPI write only in case that PETSc is used
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#ifdef PETSC
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5pset_dxpl_mpio_f')
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#endif
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!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, name_id, reshape(namesNA(mapping),[Nconstituents,NmatPoints]), &
int([Nconstituents, dataspace_size],HSIZE_T), hdferr, &
file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5dwrite_f position_id')
call h5dwrite_f(dset_id, position_id, reshape(mapping2-1_pInt,[Nconstituents,NmatPoints])+arrOffset, &
int([Nconstituents, dataspace_size],HSIZE_T), hdferr, &
file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5dwrite_f instance_id')
!--------------------------------------------------------------------------------------------------
! close types, dataspaces
call h5tclose_f(dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tclose_f dtype_id')
call h5tclose_f(position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tclose_f position_id')
call h5tclose_f(name_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tclose_f instance_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5sclose_f')
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5pclose_f')
call HDF5_closeGroup(mapping_ID)
end subroutine HDF5_mappingPhase
!--------------------------------------------------------------------------------------------------
!> @brief adds the backward mapping from spatial position and constituent ID to results
!--------------------------------------------------------------------------------------------------
subroutine HDF5_backwardMappingPhase(material_phase,phasememberat,phase_name,dataspace_size,mpiOffset,mpiOffset_phase)
use hdf5
implicit none
integer(pInt), intent(in), dimension(:,:,:) :: material_phase, phasememberat
character(len=*), intent(in), dimension(:) :: phase_name
integer(pInt), intent(in), dimension(:) :: dataspace_size, mpiOffset_phase
integer(pInt), intent(in) :: mpiOffset
integer(pInt) :: hdferr, NmatPoints, Nconstituents, i, j
integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, position_id, plist_id, memspace
integer(SIZE_T) :: type_size
integer(pInt), dimension(:,:), allocatable :: arr
integer(HSIZE_T), dimension(1) :: counter
integer(HSSIZE_T), dimension(1) :: fileOffset
character(len=64) :: phaseID
Nconstituents = size(phasememberat,1)
NmatPoints = count(material_phase /=0_pInt)/Nconstituents
allocate(arr(2,NmatPoints*Nconstituents))
do i=1_pInt, NmatPoints
do j=Nconstituents-1_pInt, 0_pInt, -1_pInt
arr(1,Nconstituents*i-j) = i-1_pInt
enddo
enddo
arr(2,:) = pack(material_phase,material_phase/=0_pInt)
do i=1_pInt, size(phase_name)
write(phaseID, '(i0)') i
mapping_ID = HDF5_openGroup('/current/constitutive/'//trim(phaseID)//'_'//phase_name(i))
NmatPoints = count(material_phase == i)
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(1, int([dataspace_size(i)],HSIZE_T), space_id, hdferr, &
int([dataspace_size(i)],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping')
!--------------------------------------------------------------------------------------------------
! compound type
call h5tget_size_f(H5T_STD_I32LE, type_size, hdferr)
call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping: h5tcreate_f dtype_id')
call h5tinsert_f(dtype_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5tinsert_f 0')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, 'mapGeometry', dtype_id, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase')
!--------------------------------------------------------------------------------------------------
! Create memory types (one compound datatype for each member)
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5tcreate_f position_id')
call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5tinsert_f position_id')
!--------------------------------------------------------------------------------------------------
! Define and select hyperslabs
counter = NmatPoints ! how big i am
fileOffset = mpiOffset_phase(i) ! where i start to write my data
call h5screate_simple_f(1, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5dget_space_f')
call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! Create property list for collective dataset write
MPI write only in case that PETSc is used
2018-08-05 10:11:35 +05:30
#ifdef PETSC
number of helper functions for HDF5
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5pset_dxpl_mpio_f')
copy and paste error
2018-08-19 01:00:57 +05:30
#endif
number of helper functions for HDF5
2018-08-03 12:23:37 +05:30
!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, position_id, pack(arr(1,:),arr(2,:)==i)+mpiOffset, int([dataspace_size(i)],HSIZE_T),&
hdferr, file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5dwrite_f instance_id')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5tclose_f(dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5tclose_f dtype_id')
call h5tclose_f(position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5tclose_f position_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5sclose_f')
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5pclose_f')
call HDF5_closeGroup(mapping_ID)
enddo
end subroutine HDF5_backwardMappingPhase
!--------------------------------------------------------------------------------------------------
!> @brief adds the unique mapping from spatial position and constituent ID to results
!--------------------------------------------------------------------------------------------------
subroutine HDF5_mappingHomog(material_homog,homogmemberat,homogenization_name,dataspace_size,mpiOffset,mpiOffset_homog)
use hdf5
implicit none
integer(pInt), intent(in), dimension(:,:) :: material_homog, homogmemberat
character(len=*), intent(in), dimension(:) :: homogenization_name
integer(pInt), intent(in), dimension(:) :: mpiOffset_homog
integer(pInt), intent(in) :: dataspace_size, mpiOffset
integer(pInt) :: hdferr, NmatPoints, i, j
integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, name_id, position_id, plist_id, memspace
integer(HID_T) :: dt5_id ! Memory datatype identifier
integer(SIZE_T) :: typesize, type_sizec, type_sizei, type_size
integer(HSIZE_T), dimension(1) :: counter
integer(HSSIZE_T), dimension(1) :: fileOffset
integer(pInt), dimension(:), allocatable :: arrOffset
NmatPoints = count(material_homog /=0_pInt)
mapping_ID = HDF5_openGroup("current/mapGeometry")
allocate(arrOffset(NmatPoints))
do i=1_pInt, NmatPoints
do j=1_pInt, size(homogenization_name)
if(material_homog(1,i) == j) &
arrOffset(i) = mpiOffset_homog(j)
enddo
enddo
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(1, int([dataspace_size],HSIZE_T), space_id, hdferr, &
int([dataspace_size],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping')
!--------------------------------------------------------------------------------------------------
! compound type
! First calculate total size by calculating sizes of each member
!
CALL h5tcopy_f(H5T_NATIVE_CHARACTER, dt5_id, hdferr)
typesize = len(homogenization_name(1))
CALL h5tset_size_f(dt5_id, typesize, hdferr)
CALL h5tget_size_f(dt5_id, type_sizec, hdferr)
CALL h5tget_size_f(H5T_STD_I32LE,type_sizei, hdferr)
type_size = type_sizec + type_sizei
call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping: h5tcreate_f dtype_id')
call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt5_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tinsert_f 0')
call h5tinsert_f(dtype_id, "Position", type_sizec, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tinsert_f 2')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, 'homogenization', dtype_id, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog')
!--------------------------------------------------------------------------------------------------
! Create memory types (one compound datatype for each member)
call h5tcreate_f(H5T_COMPOUND_F, int(type_sizec,SIZE_T), name_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tcreate_f instance_id')
call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt5_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tinsert_f instance_id')
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tcreate_f position_id')
call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tinsert_f position_id')
!--------------------------------------------------------------------------------------------------
! Define and select hyperslabs
counter = NmatPoints ! how big i am
fileOffset = mpiOffset ! where i start to write my data
call h5screate_simple_f(1, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5dget_space_f')
call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! Create property list for collective dataset write
MPI write only in case that PETSc is used
2018-08-05 10:11:35 +05:30
#ifdef PETSC
number of helper functions for HDF5
2018-08-03 12:23:37 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5pset_dxpl_mpio_f')
copy and paste error
2018-08-19 01:00:57 +05:30
#endif
number of helper functions for HDF5
2018-08-03 12:23:37 +05:30
!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, name_id, homogenization_name(pack(material_homog,material_homog/=0_pInt)), &
int([dataspace_size],HSIZE_T), hdferr, file_space_id = space_id, &
mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5dwrite_f position_id')
call h5dwrite_f(dset_id, position_id, pack(homogmemberat-1_pInt,homogmemberat/=0_pInt) + arrOffset, &
int([dataspace_size],HSIZE_T), hdferr, file_space_id = space_id, &
mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5dwrite_f instance_id')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5tclose_f(dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tclose_f dtype_id')
call h5tclose_f(position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tclose_f position_id')
call h5tclose_f(name_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tclose_f instance_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5sclose_f')
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5pclose_f')
call HDF5_closeGroup(mapping_ID)
end subroutine HDF5_mappingHomog
!--------------------------------------------------------------------------------------------------
!> @brief adds the backward mapping from spatial position and constituent ID to results
!--------------------------------------------------------------------------------------------------
subroutine HDF5_backwardMappingHomog(material_homog,homogmemberat,homogenization_name,dataspace_size,mpiOffset,mpiOffset_homog)
use hdf5
implicit none
integer(pInt), intent(in), dimension(:,:) :: material_homog, homogmemberat
character(len=*), intent(in), dimension(:) :: homogenization_name
integer(pInt), intent(in), dimension(:) :: dataspace_size, mpiOffset_homog
integer(pInt), intent(in) :: mpiOffset
integer(pInt) :: hdferr, NmatPoints, i
integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, position_id, plist_id, memspace
integer(SIZE_T) :: type_size
integer(pInt), dimension(:,:), allocatable :: arr
integer(HSIZE_T), dimension(1) :: counter
integer(HSSIZE_T), dimension(1) :: fileOffset
character(len=64) :: homogID
NmatPoints = count(material_homog /=0_pInt)
allocate(arr(2,NmatPoints))
arr(1,:) = (/(i, i=0_pint,NmatPoints-1_pInt)/)
arr(2,:) = pack(material_homog,material_homog/=0_pInt)
do i=1_pInt, size(homogenization_name)
write(homogID, '(i0)') i
mapping_ID = HDF5_openGroup('/current/homogenization/'//trim(homogID)//'_'//homogenization_name(i))
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(1, int([dataspace_size(i)],HSIZE_T), space_id, hdferr, &
int([dataspace_size(i)],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping')
!--------------------------------------------------------------------------------------------------
! compound type
call h5tget_size_f(H5T_STD_I32LE, type_size, hdferr)
call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping: h5tcreate_f dtype_id')
call h5tinsert_f(dtype_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5tinsert_f 0')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, 'mapGeometry', dtype_id, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog')
!--------------------------------------------------------------------------------------------------
! Create memory types (one compound datatype for each member)
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5tcreate_f position_id')
call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5tinsert_f position_id')
!--------------------------------------------------------------------------------------------------
! Define and select hyperslabs
counter = NmatPoints ! how big i am
fileOffset = mpiOffset_homog(i) ! where i start to write my data
call h5screate_simple_f(1, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5dget_space_f')
call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! Create property list for collective dataset write
MPI write only in case that PETSc is used
2018-08-05 10:11:35 +05:30
#ifdef PETSC
number of helper functions for HDF5
2018-08-03 12:23:37 +05:30
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5pset_dxpl_mpio_f')
copy and paste error
2018-08-19 01:00:57 +05:30
#endif
number of helper functions for HDF5
2018-08-03 12:23:37 +05:30
!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, position_id, pack(arr(1,:),arr(2,:)==i)+mpiOffset,int([dataspace_size(i)],HSIZE_T),&
hdferr, file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5dwrite_f instance_id')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5tclose_f(dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5tclose_f dtype_id')
call h5tclose_f(position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5tclose_f position_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5sclose_f')
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5pclose_f')
call HDF5_closeGroup(mapping_ID)
enddo
end subroutine HDF5_backwardMappingHomog
!--------------------------------------------------------------------------------------------------
!> @brief adds the unique mapping from spatial position and constituent ID to results
!--------------------------------------------------------------------------------------------------
subroutine HDF5_mappingCrystallite(crystalliteAt,crystmemberAt,crystallite_name,dataspace_size,mpiOffset,mpiOffset_cryst)
use hdf5
implicit none
integer(pInt), intent(in), dimension(:,:) :: crystalliteAt
integer(pInt), intent(in), dimension(:,:,:) :: crystmemberAt
character(len=*), intent(in), dimension(:) :: crystallite_name
integer(pInt), intent(in), dimension(:) :: mpiOffset_cryst
integer(pInt), intent(in) :: dataspace_size, mpiOffset
integer :: hdferr
integer(pInt) :: NmatPoints, Nconstituents, i, j
integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, name_id, plist_id, memspace
integer(HID_T), dimension(:), allocatable :: position_id
integer(HID_T) :: dt5_id ! Memory datatype identifier
integer(SIZE_T) :: typesize, type_sizec, type_sizei, type_size
integer(HSIZE_T), dimension(1) :: counter
integer(HSSIZE_T), dimension(1) :: fileOffset
integer(pInt), dimension(:), allocatable :: arrOffset
character(len=64) :: m
Nconstituents = size(crystmemberAt,1)
NmatPoints = count(crystalliteAt /=0_pInt)
mapping_ID = HDF5_openGroup("current/mapGeometry")
allocate(position_id(Nconstituents))
allocate(arrOffset(NmatPoints))
do i=1_pInt, NmatPoints
do j=1_pInt, size(crystallite_name)
if(crystalliteAt(1,i) == j) &
arrOffset(i) = Nconstituents*mpiOffset_cryst(j)
enddo
enddo
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(1, int([dataspace_size],HSIZE_T), space_id, hdferr, &
int([dataspace_size],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping')
!--------------------------------------------------------------------------------------------------
! compound type
! First calculate total size by calculating sizes of each member
!
CALL h5tcopy_f(H5T_NATIVE_CHARACTER, dt5_id, hdferr)
typesize = len(crystallite_name(1))
CALL h5tset_size_f(dt5_id, typesize, hdferr)
CALL h5tget_size_f(dt5_id, type_sizec, hdferr)
CALL h5tget_size_f(H5T_STD_I32LE, type_sizei, hdferr)
type_size = type_sizec + type_sizei*Nconstituents
call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeMapping: h5tcreate_f dtype_id')
call h5tinsert_f(dtype_id, "Name", 0_SIZE_T, dt5_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f 0')
do i=1_pInt, Nconstituents
write(m, '(i0)') i
call h5tinsert_f(dtype_id, "Position "//trim(m), type_sizec+(i-1)*type_sizei, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f 2 '//trim(m))
enddo
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, 'crystallite', dtype_id, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite')
!--------------------------------------------------------------------------------------------------
! Create memory types (one compound datatype for each member)
call h5tcreate_f(H5T_COMPOUND_F, int(type_sizec,SIZE_T), name_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tcreate_f instance_id')
call h5tinsert_f(name_id, "Name", 0_SIZE_T, dt5_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f instance_id')
do i=1_pInt, Nconstituents
write(m, '(i0)') i
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id(i), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tcreate_f position_id')
call h5tinsert_f(position_id(i), "Position "//trim(m), 0_SIZE_T, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tinsert_f position_id')
enddo
!--------------------------------------------------------------------------------------------------
! Define and select hyperslabs
counter = NmatPoints ! how big i am
fileOffset = mpiOffset ! where i start to write my data
call h5screate_simple_f(1, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dget_space_f')
call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! Create property list for collective dataset write
MPI write only in case that PETSc is used
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#ifdef PETSC
number of helper functions for HDF5
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5pset_dxpl_mpio_f')
copy and paste error
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#endif
number of helper functions for HDF5
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!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, name_id, crystallite_name(pack(crystalliteAt,crystalliteAt/=0_pInt)), &
int([dataspace_size],HSIZE_T), hdferr, file_space_id = space_id, &
mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dwrite_f position_id')
do i=1_pInt, Nconstituents
call h5dwrite_f(dset_id, position_id(i), pack(crystmemberAt(i,:,:)-1_pInt,crystmemberAt(i,:,:)/=0_pInt)+arrOffset,&
int([dataspace_size],HSIZE_T), hdferr, file_space_id = space_id, &
mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dwrite_f instance_id')
enddo
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5tclose_f(dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tclose_f dtype_id')
do i=1_pInt, Nconstituents
call h5tclose_f(position_id(i), hdferr)
enddo
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tclose_f position_id')
call h5tclose_f(name_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tclose_f instance_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5sclose_f')
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5pclose_f')
call HDF5_closeGroup(mapping_ID)
end subroutine HDF5_mappingCrystallite
!--------------------------------------------------------------------------------------------------
!> @brief adds the backward mapping from spatial position and constituent ID to results
!--------------------------------------------------------------------------------------------------
subroutine HDF5_backwardMappingCrystallite(crystalliteAt,crystmemberAt,crystallite_name,dataspace_size,mpiOffset,mpiOffset_cryst)
use hdf5
implicit none
integer(pInt), intent(in), dimension(:,:) :: crystalliteAt
integer(pInt), intent(in), dimension(:,:,:) :: crystmemberAt
character(len=*), intent(in), dimension(:) :: crystallite_name
integer(pInt), intent(in), dimension(:) :: dataspace_size, mpiOffset_cryst
integer(pInt), intent(in) :: mpiOffset
integer :: hdferr
integer(pInt) :: NmatPoints, Nconstituents, i, j
integer(HID_T) :: mapping_id, dtype_id, dset_id, space_id, position_id, plist_id, memspace
integer(SIZE_T) :: type_size
integer(pInt), dimension(:,:), allocatable :: h_arr, arr
integer(HSIZE_T), dimension(1) :: counter
integer(HSSIZE_T), dimension(1) :: fileOffset
character(len=64) :: crystallID
Nconstituents = size(crystmemberAt,1)
NmatPoints = count(crystalliteAt /=0_pInt)
allocate(h_arr(2,NmatPoints))
allocate(arr(2,Nconstituents*NmatPoints))
h_arr(1,:) = (/(i, i=0_pInt,NmatPoints-1_pInt)/)
h_arr(2,:) = pack(crystalliteAt,crystalliteAt/=0_pInt)
do i=1_pInt, NmatPoints
do j=Nconstituents-1_pInt, 0_pInt, -1_pInt
arr(1,Nconstituents*i-j) = h_arr(1,i)
arr(2,Nconstituents*i-j) = h_arr(2,i)
enddo
enddo
do i=1_pInt, size(crystallite_name)
if (crystallite_name(i) == 'none') cycle
write(crystallID, '(i0)') i
mapping_ID = HDF5_openGroup('/current/crystallite/'//trim(crystallID)//'_'//crystallite_name(i))
NmatPoints = count(crystalliteAt == i)
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(1, int([Nconstituents*dataspace_size(i)],HSIZE_T), space_id, hdferr, &
int([Nconstituents*dataspace_size(i)],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping')
!--------------------------------------------------------------------------------------------------
! compound type
call h5tget_size_f(H5T_STD_I32LE, type_size, hdferr)
call h5tcreate_f(H5T_COMPOUND_F, type_size, dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeBackwardMapping: h5tcreate_f dtype_id')
call h5tinsert_f(dtype_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5tinsert_f 0')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, 'mapGeometry', dtype_id, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite')
!--------------------------------------------------------------------------------------------------
! Create memory types
call h5tcreate_f(H5T_COMPOUND_F, int(pInt,SIZE_T), position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5tcreate_f position_id')
call h5tinsert_f(position_id, "Position", 0_SIZE_T, H5T_STD_I32LE, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5tinsert_f position_id')
!--------------------------------------------------------------------------------------------------
! Define and select hyperslabs
counter = Nconstituents*NmatPoints ! how big i am
fileOffset = Nconstituents*mpiOffset_cryst(i) ! where i start to write my data
call h5screate_simple_f(1, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5dget_space_f')
call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5sselect_hyperslab_f')
!--------------------------------------------------------------------------------------------------
! Create property list for collective dataset write
MPI write only in case that PETSc is used
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#ifdef PETSC
number of helper functions for HDF5
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5pset_dxpl_mpio_f')
copy and paste error
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#endif
number of helper functions for HDF5
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!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, position_id, pack(arr(1,:),arr(2,:)==i) + mpiOffset,&
int([Nconstituents*dataspace_size(i)],HSIZE_T), hdferr, file_space_id = space_id, &
mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5dwrite_f instance_id')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5tclose_f(dtype_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5tclose_f dtype_id')
call h5tclose_f(position_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5tclose_f position_id')
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5sclose_f')
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5pclose_f')
call HDF5_closeGroup(mapping_ID)
enddo
end subroutine HDF5_backwardMappingCrystallite
writing of multidimensional dataset into hdf5 does not appear as multiple pages in hdfviewer
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!--------------------------------------------------------------------------------------------------
!> @brief adds the unique cell to node mapping
!--------------------------------------------------------------------------------------------------
subroutine HDF5_mappingCells(mapping)
use hdf5
implicit none
integer(pInt), intent(in), dimension(:) :: mapping
integer :: hdferr, Nnodes
integer(HID_T) :: mapping_id, dset_id, space_id
Nnodes=size(mapping)
mapping_ID = HDF5_openGroup("mapping")
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(1, int([Nnodes],HSIZE_T), space_id, hdferr, &
int([Nnodes],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCells: h5screate_simple_f')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(mapping_id, "Cell",H5T_NATIVE_INTEGER, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCells')
!--------------------------------------------------------------------------------------------------
! write data by fields in the datatype. Fields order is not important.
call h5dwrite_f(dset_id, H5T_NATIVE_INTEGER, mapping, int([Nnodes],HSIZE_T), hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCells: h5dwrite_f instance_id')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingConstitutive: h5sclose_f')
call HDF5_closeGroup(mapping_ID)
end subroutine HDF5_mappingCells
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addTensor3DDataset(group,Nnodes,tensorSize,label,SIunit)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
integer(pInt), intent(in) :: Nnodes, tensorSize
character(len=*), intent(in) :: SIunit, label
integer :: hdferr
integer(HID_T) :: space_id, dset_id
integer(HSIZE_T), dimension(3) :: dataShape
dataShape = int([tensorSize,tensorSize,Nnodes], HSIZE_T)
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(3, dataShape, space_id, hdferr, dataShape)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addTensor3DDataset: h5screate_simple_f')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(group, trim(label),H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addTensor3DDataset: h5dcreate_f')
call HDF5_addStringAttribute(dset_id,'unit',trim(SIunit))
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addTensor3DDataset: h5dclose_f')
call h5sclose_f(space_id, hdferr)
end subroutine HDF5_addTensor3DDataset
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_writeVectorDataset(group,dataset,label,SIunit,dataspace_size,mpiOffset)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
character(len=*), intent(in) :: SIunit,label
integer(pInt), intent(in) :: dataspace_size, mpiOffset
real(pReal), intent(in), dimension(:,:) :: dataset
integer :: hdferr, vectorSize
integer(HID_T) :: dset_id, space_id, memspace, plist_id
integer(HSIZE_T), dimension(2) :: counter
integer(HSSIZE_T), dimension(2) :: fileOffset
if(any(shape(dataset) == 0)) return
vectorSize = size(dataset,1)
call HDF5_addVectorDataset(group,dataspace_size,vectorSize,label,SIunit) ! here nNodes need to be global
call h5dopen_f(group, label, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5dopen_f')
! Define and select hyperslabs
counter(1) = vectorSize ! how big i am
counter(2) = size(dataset,2)
fileOffset(1) = 0 ! where i start to write my data
fileOffset(2) = mpiOffset
call h5screate_simple_f(2, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5dget_space_f')
call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5sselect_hyperslab_f')
! Create property list for collective dataset write
MPI write only in case that PETSc is used
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#ifdef PETSC
number of helper functions for HDF5
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5pset_dxpl_mpio_f')
copy and paste error
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#endif
number of helper functions for HDF5
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! Write the dataset collectively
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([vectorSize, dataspace_size],HSIZE_T), hdferr, &
file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5dwrite_f')
call h5sclose_f(space_id, hdferr)
call h5sclose_f(memspace, hdferr)
call h5dclose_f(dset_id, hdferr)
call h5pclose_f(plist_id, hdferr)
end subroutine HDF5_writeVectorDataset
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
! by default, a 3x3 tensor is assumed
!--------------------------------------------------------------------------------------------------
subroutine HDF5_writeTensorDataset(group,dataset,label,SIunit,dataspace_size,mpiOffset)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
character(len=*), intent(in) :: SIunit,label
integer(pInt), intent(in) :: dataspace_size, mpiOffset
real(pReal), intent(in), dimension(:,:,:) :: dataset
integer :: hdferr, tensorSize
integer(HID_T) :: dset_id, space_id, memspace, plist_id
integer(HSIZE_T), dimension(3) :: counter
integer(HSSIZE_T), dimension(3) :: fileOffset
if(any(shape(dataset) == 0)) return
tensorSize = size(dataset,1)
call HDF5_addTensor3DDataset(group,dataspace_size,tensorSize,label,SIunit)
call h5dopen_f(group, label, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5dopen_f')
! Define and select hyperslabs
counter(1) = tensorSize ! how big i am
counter(2) = tensorSize
counter(3) = size(dataset,3)
fileOffset(1) = 0 ! where i start to write my data
fileOffset(2) = 0
fileOffset(3) = mpiOffset
call h5screate_simple_f(3, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5dget_space_f')
call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5sselect_hyperslab_f')
! Create property list for collective dataset write
MPI write only in case that PETSc is used
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#ifdef PETSC
number of helper functions for HDF5
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5pset_dxpl_mpio_f')
copy and paste error
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#endif
number of helper functions for HDF5
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! Write the dataset collectively
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([tensorSize, dataspace_size],HSIZE_T), hdferr, &
file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeTensorDataset: h5dwrite_f')
call h5sclose_f(space_id, hdferr)
call h5sclose_f(memspace, hdferr)
call h5dclose_f(dset_id, hdferr)
call h5pclose_f(plist_id, hdferr)
end subroutine HDF5_writeTensorDataset
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addVectorDataset(group,nnodes,vectorSize,label,SIunit)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
integer(pInt), intent(in) :: nnodes,vectorSize
character(len=*), intent(in) :: SIunit,label
integer :: hdferr
integer(HID_T) :: space_id, dset_id
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(2, int([vectorSize,Nnodes],HSIZE_T), space_id, hdferr, &
int([vectorSize,Nnodes],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addVectorDataset: h5screate_simple_f')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(group, trim(label), H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addVectorDataset: h5dcreate_f')
call HDF5_addStringAttribute(dset_id,'unit',trim(SIunit))
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addVectorDataset: h5dclose_f')
call h5sclose_f(space_id, hdferr)
end subroutine HDF5_addVectorDataset
!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_writeScalarDataset(group,dataset,label,SIunit,dataspace_size,mpiOffset)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
character(len=*), intent(in) :: SIunit,label
integer(pInt), intent(in) :: dataspace_size, mpiOffset
real(pReal), intent(in), dimension(:) :: dataset
integer :: hdferr, nNodes
integer(HID_T) :: dset_id, space_id, memspace, plist_id
integer(HSIZE_T), dimension(1) :: counter
[skip ci] [skip sc] generic interfaces for HDF5 operations most existing HDF5 functions are only designed for writing output files and more general functionality is needed for storing the restart data
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integer(HSIZE_T), dimension(1) :: fileOffset
number of helper functions for HDF5
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nNodes = size(dataset)
if (nNodes < 1) return
call HDF5_addScalarDataset(group,dataspace_size,label,SIunit)
call h5dopen_f(group, label, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dopen_f')
! Define and select hyperslabs
counter = size(dataset) ! how big i am
fileOffset = mpiOffset ! where i start to write my data
call h5screate_simple_f(1, counter, memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5screate_simple_f')
call h5dget_space_f(dset_id, space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dget_space_f')
call h5sselect_hyperslab_f(space_id, H5S_SELECT_SET_F, fileOffset, counter, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5sselect_hyperslab_f')
! Create property list for collective dataset write
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#ifdef PETSC
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call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pcreate_f')
call h5pset_dxpl_mpio_f(plist_id, H5FD_MPIO_COLLECTIVE_F, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5pset_dxpl_mpio_f')
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#endif
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! Write the dataset collectively
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE, dataset, int([dataspace_size],HSIZE_T), hdferr, &
file_space_id = space_id, mem_space_id = memspace, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset: h5dwrite_f')
call h5sclose_f(space_id, hdferr)
call h5sclose_f(memspace, hdferr)
call h5dclose_f(dset_id, hdferr)
call h5pclose_f(plist_id, hdferr)
end subroutine HDF5_writeScalarDataset
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!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
Combined the dataset creation and writing dataset in single subroutine. Created group for looped writing.
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subroutine HDF5_writeScalarDataset3(group,dataset,label,myShape)
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use hdf5
implicit none
integer(HID_T), intent(in) :: group
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integer(pInt), intent(in), dimension(:) :: myShape
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character(len=*), intent(in) :: label
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real(pReal), intent(in), dimension(*) :: dataset
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integer :: hdferr
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integer(HID_T) :: dset_id, space_id
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!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(size(myShape), int(myShape,HSIZE_T), space_id, hdferr, &
int(myShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset3: h5screate_simple_f')
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!--------------------------------------------------------------------------------------------------
Combined the dataset creation and writing dataset in single subroutine. Created group for looped writing.
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! create Dataset
call h5dcreate_f(group, trim(label), H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset3: h5dcreate_f')
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CALL h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(myShape,HSIZE_T), hdferr)
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!--------------------------------------------------------------------------------------------------
!close types, dataspaces
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call h5dclose_f(dset_id, hdferr)
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if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset3: h5dclose_f')
call h5sclose_f(space_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset3: h5sclose_f')
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end subroutine HDF5_writeScalarDataset3
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!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
Combined the dataset creation and writing dataset in single subroutine. Created group for looped writing.
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! subroutine HDF5_writeScalarDatasetLoop(group,dataset,label,myShape)
! use hdf5
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! implicit none
! integer(HID_T), intent(in) :: group
! integer(pInt), intent(in), dimension(:) :: myShape
! character(len=*), intent(in) :: label
! real(pReal), intent(in), dimension(*) :: dataset
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! integer :: hdferr
! integer(HID_T) :: dset_id, space_id
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! !--------------------------------------------------------------------------------------------------
! ! create dataspace
! call h5screate_simple_f(size(myShape), int(myShape,HSIZE_T), space_id, hdferr, &
! int(myShape,HSIZE_T))
! if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset3: h5screate_simple_f')
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! !--------------------------------------------------------------------------------------------------
! ! create Dataset
! call h5dcreate_f(group, trim(label), H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr)
! if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset3: h5dcreate_f')
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! CALL h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(myShape,HSIZE_T), hdferr)
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! !--------------------------------------------------------------------------------------------------
! !close types, dataspaces
! call h5dclose_f(dset_id, hdferr)
! if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset3: h5dclose_f')
! call h5sclose_f(space_id, hdferr)
! if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeScalarDataset3: h5sclose_f')
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! end subroutine HDF5_writeScalarDatasetLoop
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[skip ci] [skip sc] generic interfaces for HDF5 operations most existing HDF5 functions are only designed for writing output files and more general functionality is needed for storing the restart data
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subroutine HDF5_read_double_1(D,ID,label)
implicit none
real(pReal), dimension(:), intent(out) :: D
integer(HID_T), intent(in) :: ID
character(len=*), intent(in) :: label
call HDF5_read_double_generic(D,ID,label,shape(D))
end subroutine HDF5_read_double_1
subroutine HDF5_read_double_5(D,ID,label)
implicit none
real(pReal), dimension(:,:,:,:,:), intent(out) :: D
integer(HID_T), intent(in) :: ID
character(len=*), intent(in) :: label
call HDF5_read_double_generic(D,ID,label,shape(D))
end subroutine HDF5_read_double_5
subroutine HDF5_read_double_generic(D,ID,label,myShape)
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use hdf5
implicit none
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real(pReal), dimension(*), intent(out) :: D
integer, dimension(:),intent(in) :: myShape
! real, dimension(:), allocatable :: D1
! real, dimension(:,:), allocatable :: D2
! real, dimension(:,:,:), allocatable :: D3
integer(HID_T), intent(in) :: ID
character(len=*), intent(in) :: label
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integer(HID_T) :: dset_id
integer :: hdferr
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call h5dopen_f(ID,label,dset_id,hdferr)
call h5dread_f(dset_id,H5T_NATIVE_DOUBLE,D,int(myshape,HID_T),hdferr)
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end subroutine
!--------------------------------------------------------------------------------------------------
!> @brief read datasets from a hdf5 file
!--------------------------------------------------------------------------------------------------
!
!subroutine HDF5_read_double_2(DataSet,FileReadID,NameDataSet) !,myshape)
! use hdf5
!
! implicit none
! integer(HID_T), intent(in) :: FileReadID
! character(len=*), intent(in) :: NameDataSet
! real(pReal), intent(out), dimension(:,:,:,:,:) :: DataSet
! !integer(HSIZE_T), intent(in), dimension(:) :: myshape
! integer(HSIZE_T), dimension(:),allocatable :: myshape
! integer(HID_T) :: dset_id
! integer :: hdferr
!
! myShape = int(shape(DataSet),HSIZE_T)
! call h5dopen_f(FileReadID,NameDataSet,dset_id,hdferr)
! call h5dread_f(dset_id,H5T_NATIVE_DOUBLE,DataSet,myshape,hdferr)
!
!end subroutine
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!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addScalarDataset(group,nnodes,label,SIunit)
use hdf5
implicit none
integer(HID_T), intent(in) :: group
integer(pInt), intent(in) :: nnodes
character(len=*), intent(in) :: SIunit,label
integer :: hdferr
integer(HID_T) :: space_id, dset_id
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(1, int([Nnodes],HSIZE_T), space_id, hdferr, &
int([Nnodes],HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5screate_simple_f')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(group, trim(label),H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5dcreate_f')
call HDF5_addStringAttribute(dset_id,'unit',trim(SIunit))
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5dclose_f')
call h5sclose_f(space_id, hdferr)
end subroutine HDF5_addScalarDataset
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!--------------------------------------------------------------------------------------------------
!> @brief creates a new scalar dataset in the given group location
!--------------------------------------------------------------------------------------------------
subroutine HDF5_addScalarDataset2(fileHandle,dataShape,label)
use hdf5
implicit none
integer(HID_T), intent(in) :: fileHandle
integer(pInt), dimension(:), intent(in) :: dataShape
character(len=*), intent(in) :: label
integer :: hdferr
integer(HID_T) :: space_id, dset_id
!--------------------------------------------------------------------------------------------------
! create dataspace
call h5screate_simple_f(size(dataShape), int(dataShape,HSIZE_T), space_id, hdferr, &
int(dataShape,HSIZE_T))
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5screate_simple_f')
!--------------------------------------------------------------------------------------------------
! create Dataset
call h5dcreate_f(fileHandle, trim(label),H5T_NATIVE_DOUBLE, space_id, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5dcreate_f')
!--------------------------------------------------------------------------------------------------
!close types, dataspaces
call h5dclose_f(dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addScalarDataset: h5dclose_f')
call h5sclose_f(space_id, hdferr)
end subroutine HDF5_addScalarDataset2
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!--------------------------------------------------------------------------------------------------
!> @brief copies the current temp results to the actual results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_forwardResults(time)
use hdf5
use IO, only: &
IO_intOut
implicit none
integer :: hdferr
real(pReal), intent(in) :: time
character(len=1024) :: myName
currentInc = currentInc +1_pInt
write(6,*) 'forward results';flush(6)
write(myName,'(a,'//IO_intOut(currentInc)//')') 'inc',currentInc
currentIncID = HDF5_addGroup(myName)
call HDF5_setLink(myName,'current')
! call HDF5_flush(resultsFile)
call HDF5_closeGroup(currentIncID)
end subroutine HDF5_forwardResults
end module HDF5_Utilities