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DAMASK_EICMD
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DAMASK_EICMD/src/results.f90

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clearer separation of tasks 1) general HDF5_utilities (for results, restart, ...) 2) results related helpers (based on HDF5_utilities)
2018-11-15 11:19:31 +05:30
!--------------------------------------------------------------------------------------------------
!> @author Vitesh Shah, Max-Planck-Institut für Eisenforschung GmbH
!> @author Yi-Chin Yang, Max-Planck-Institut für Eisenforschung GmbH
!> @author Jennifer Nastola, Max-Planck-Institut für Eisenforschung GmbH
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!--------------------------------------------------------------------------------------------------
compile results module
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module results
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use prec
use IO
use HDF5
create results file
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use HDF5_utilities
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#ifdef PETSc
use PETSC
#endif
implicit none
private
integer(HID_T), public, protected :: tempCoordinates, tempResults
integer(HID_T), private :: resultsFile, currentIncID, plist_id
public :: &
compile results module
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results_init, &
planning the forwarding of the results
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results_openJobFile, &
results_closeJobFile, &
results_addIncrement, &
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HDF5_mappingPhase, &
HDF5_mappingHomog, &
HDF5_mappingCrystallite, &
HDF5_backwardMappingPhase, &
HDF5_backwardMappingHomog, &
HDF5_backwardMappingCrystallite, &
HDF5_mappingCells, &
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results_addGroup, &
results_openGroup, &
clearer separation of tasks 1) general HDF5_utilities (for results, restart, ...) 2) results related helpers (based on HDF5_utilities)
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HDF5_writeVectorDataset, &
HDF5_writeScalarDataset, &
HDF5_writeTensorDataset, &
create results file
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HDF5_removeLink
clearer separation of tasks 1) general HDF5_utilities (for results, restart, ...) 2) results related helpers (based on HDF5_utilities)
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contains
compile results module
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subroutine results_init
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use, intrinsic :: &
iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
create results file
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use DAMASK_interface, only: &
getSolverJobName
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implicit none
create results file
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write(6,'(/,a)') ' <<<+- results init -+>>>'
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#include "compilation_info.f90"
create results file
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call HDF5_closeFile(HDF5_openFile(trim(getSolverJobName())//'.hdf5','w',.true.))
clearer separation of tasks 1) general HDF5_utilities (for results, restart, ...) 2) results related helpers (based on HDF5_utilities)
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compile results module
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end subroutine results_init
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planning the forwarding of the results
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!--------------------------------------------------------------------------------------------------
!> @brief opens the results file to append data
!--------------------------------------------------------------------------------------------------
subroutine results_openJobFile()
use DAMASK_interface, only: &
getSolverJobName
implicit none
resultsFile = HDF5_openFile(trim(getSolverJobName())//'.hdf5','a',.true.)
end subroutine results_openJobFile
!--------------------------------------------------------------------------------------------------
!> @brief closes the results file
!--------------------------------------------------------------------------------------------------
subroutine results_closeJobFile()
implicit none
call HDF5_closeFile(resultsFile)
end subroutine results_closeJobFile
!--------------------------------------------------------------------------------------------------
!> @brief closes the results file
!--------------------------------------------------------------------------------------------------
subroutine results_addIncrement()
implicit none
call HDF5_addIntegerAttribute(resultsFile,'test',1)
end subroutine results_addIncrement
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!--------------------------------------------------------------------------------------------------
create results file
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!> @brief open a group from the results file
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!--------------------------------------------------------------------------------------------------
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integer(HID_T) function results_openGroup(groupName)
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implicit none
create results file
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character(len=*), intent(in) :: groupName
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results_openGroup = HDF5_openGroup(resultsFile,groupName)
create results file
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end function results_openGroup
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!--------------------------------------------------------------------------------------------------
!> @brief adds a new group to the results file
!--------------------------------------------------------------------------------------------------
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integer(HID_T) function results_addGroup(groupName)
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implicit none
character(len=*), intent(in) :: groupName
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results_addGroup = HDF5_addGroup(resultsFile,groupName)
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end function results_addGroup
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!--------------------------------------------------------------------------------------------------
!> @brief set link to object in 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 remove link to an object
!--------------------------------------------------------------------------------------------------
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 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
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mapping_ID = results_openGroup("current/mapGeometry")
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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
#ifdef PETSc
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')
#endif
!--------------------------------------------------------------------------------------------------
! 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 name_id ')
call h5tclose_f(dt5_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5tclose_f dt5_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 space_id')
call h5sclose_f(memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingPhase: h5sclose_f memspace')
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
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mapping_ID = results_openGroup('/current/constitutive/'//trim(phaseID)//'_'//phase_name(i))
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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
#ifdef PETSc
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')
#endif
!--------------------------------------------------------------------------------------------------
! 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 space_id')
call h5sclose_f(memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingPhase: h5sclose_f memspace')
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)
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mapping_ID = results_openGroup("current/mapGeometry")
clearer separation of tasks 1) general HDF5_utilities (for results, restart, ...) 2) results related helpers (based on HDF5_utilities)
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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
#ifdef PETSc
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')
#endif
!--------------------------------------------------------------------------------------------------
! 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 name_id ')
call h5tclose_f(dt5_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5tclose_f dt5_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 space_id')
call h5sclose_f(memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingHomog: h5sclose_f memspace')
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
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mapping_ID = results_openGroup('/current/homogenization/'//trim(homogID)//'_'//homogenization_name(i))
clearer separation of tasks 1) general HDF5_utilities (for results, restart, ...) 2) results related helpers (based on HDF5_utilities)
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!--------------------------------------------------------------------------------------------------
! 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
#ifdef PETSc
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')
#endif
!--------------------------------------------------------------------------------------------------
! 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 space_id')
call h5sclose_f(memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingHomog: h5sclose_f memspace')
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)
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mapping_ID = results_openGroup("current/mapGeometry")
clearer separation of tasks 1) general HDF5_utilities (for results, restart, ...) 2) results related helpers (based on HDF5_utilities)
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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
#ifdef PETSc
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')
#endif
!--------------------------------------------------------------------------------------------------
! 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 name_id')
call h5tclose_f(dt5_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5tclose_f dt5_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 space_id')
call h5sclose_f(memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_mappingCrystallite: h5sclose_f memspace')
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
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mapping_ID = results_openGroup('/current/crystallite/'//trim(crystallID)//'_'//crystallite_name(i))
clearer separation of tasks 1) general HDF5_utilities (for results, restart, ...) 2) results related helpers (based on HDF5_utilities)
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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
#ifdef PETSc
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')
#endif
!--------------------------------------------------------------------------------------------------
! 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 space_id')
call h5sclose_f(memspace, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='IO_backwardMappingCrystallite: h5sclose_f memspace')
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
!--------------------------------------------------------------------------------------------------
!> @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)
cleaning and separating functions
2018-12-05 03:39:25 +05:30
mapping_ID = results_openGroup("mapping")
clearer separation of tasks 1) general HDF5_utilities (for results, restart, ...) 2) results related helpers (based on HDF5_utilities)
2018-11-15 11:19:31 +05:30
!--------------------------------------------------------------------------------------------------
! 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 3D Tensor dataset in the given group location !!!TODO: really necessary?
!--------------------------------------------------------------------------------------------------
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 vector dataset in the given group location !!!TODO: really necessary?
!--------------------------------------------------------------------------------------------------
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
#ifdef PETSc
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')
#endif
! 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 tensor dataset in the given group location
! by default, a 3x3 tensor is assumed !!!TODO: really necessary?
!--------------------------------------------------------------------------------------------------
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
#ifdef PETSc
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')
#endif
! 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 adds a new vector dataset to 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 writes to 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
integer(HSIZE_T), dimension(1) :: fileOffset
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
#ifdef PETSc
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')
#endif
! 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
!--------------------------------------------------------------------------------------------------
!> @brief adds a new scalar dataset to 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
compile results module
2018-11-18 16:02:53 +05:30
end module results