cleaned + suggested structure to write data

This commit is contained in:
Martin Diehl 2018-12-12 07:45:20 +01:00
parent cb28d10d79
commit fd2d4d856b
5 changed files with 78 additions and 260 deletions

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@ -332,6 +332,7 @@ subroutine CPFEM_results(inc)
call results_openJobFile call results_openJobFile
write(incChar,*) inc write(incChar,*) inc
call HDF5_closeGroup(results_addGroup(trim('inc'//trim(adjustl(incChar))))) call HDF5_closeGroup(results_addGroup(trim('inc'//trim(adjustl(incChar)))))
call results_setLink(trim('inc'//trim(adjustl(incChar))),'current')
call constitutive_results() call constitutive_results()
call results_closeJobFile call results_closeJobFile

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@ -13,7 +13,7 @@ module HDF5_utilities
#endif #endif
implicit none implicit none
private public
integer(pInt), parameter, private :: & integer(pInt), parameter, private :: &
HDF5_ERR_TYPE = 4_pInt !< kind of the integer return in the HDF5 library HDF5_ERR_TYPE = 4_pInt !< kind of the integer return in the HDF5 library
@ -71,7 +71,8 @@ module HDF5_utilities
HDF5_openGroup, & HDF5_openGroup, &
HDF5_addGroup, & HDF5_addGroup, &
HDF5_read, & HDF5_read, &
HDF5_write HDF5_write, &
HDF5_setLink
contains contains
subroutine HDF5_utilities_init subroutine HDF5_utilities_init
@ -304,7 +305,28 @@ subroutine HDF5_addIntegerAttribute(entity,attrLabel,attrValue)
end subroutine HDF5_addIntegerAttribute end subroutine HDF5_addIntegerAttribute
!--------------------------------------------------------------------------------------------------
!> @brief set link to object in results file
!--------------------------------------------------------------------------------------------------
subroutine HDF5_setLink(fileHandle,path,link)
use hdf5
implicit none
character(len=*), intent(in) :: path, link
integer(HID_T), intent(in) :: fileHandle
integer(HDF5_ERR_TYPE) :: hdferr
logical :: linkExists
call h5lexists_f(fileHandle, 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(fileHandle,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, fileHandle, 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 subroutine for reading dataset of type pReal with 1 dimensions !> @brief subroutine for reading dataset of type pReal with 1 dimensions

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@ -1193,10 +1193,25 @@ subroutine constitutive_results()
PLASTICITY_DISLOUCLA_ID, & PLASTICITY_DISLOUCLA_ID, &
PLASTICITY_NONLOCAL_ID PLASTICITY_NONLOCAL_ID
#if defined(PETSc) || defined(DAMASKHDF5) #if defined(PETSc) || defined(DAMASKHDF5)
use results
use HDF5_utilities
use config, only: &
config_name_phase => phase_name ! anticipate logical name
use material, only: &
material_phase_plasticity_type => phase_plasticity
use plastic_phenopowerlaw, only: & use plastic_phenopowerlaw, only: &
plastic_phenopowerlaw_results plastic_phenopowerlaw_results
call plastic_phenopowerlaw_results implicit none
integer(pInt) :: p
call HDF5_closeGroup(results_addGroup('current/phase'))
do p=1,size(config_name_phase)
call HDF5_closeGroup(results_addGroup('current/phase/'//trim(config_name_phase(p))))
if (material_phase_plasticity_type(p) == PLASTICITY_PHENOPOWERLAW_ID) then
call plastic_phenopowerlaw_results(p,'current/phase/'//trim(config_name_phase(p)))
endif
enddo
#endif #endif

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@ -749,8 +749,29 @@ end function plastic_phenopowerlaw_postResults
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief writes results to HDF5 output file !> @brief writes results to HDF5 output file
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
subroutine plastic_phenopowerlaw_results() subroutine plastic_phenopowerlaw_results(instance,group)
#if defined(PETSc) || defined(DAMASKHDF5) #if defined(PETSc) || defined(DAMASKHDF5)
use results
implicit none
integer(pInt), intent(in) :: instance
character(len=*) :: group
integer(pInt) :: o
associate(prm => param(instance), stt => state(instance))
outputsLoop: do o = 1_pInt,size(prm%outputID)
select case(prm%outputID(o))
case (resistance_slip_ID)
call results_writeVectorDataset(group,stt%xi_slip,'xi_slip','Pa')
case (accumulatedshear_slip_ID)
call results_writeVectorDataset(group,stt%gamma_slip,'gamma_slip','1/s')
end select
enddo outputsLoop
end associate
!results_writeVectorDataset
#else
integer(pInt), intent(in) :: instance
character(len=*) :: group
#endif #endif
end subroutine plastic_phenopowerlaw_results end subroutine plastic_phenopowerlaw_results

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@ -34,8 +34,7 @@ module results
results_addGroup, & results_addGroup, &
results_openGroup, & results_openGroup, &
results_writeVectorDataset, & results_writeVectorDataset, &
HDF5_writeScalarDataset, & results_setLink, &
HDF5_writeTensorDataset, &
HDF5_removeLink HDF5_removeLink
contains contains
@ -116,24 +115,16 @@ end function results_addGroup
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief set link to object in results file !> @brief set link to object in results file
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
subroutine HDF5_setLink(path,link) subroutine results_setLink(path,link)
use hdf5 use hdf5_utilities, only: &
HDF5_setLink
implicit none implicit none
character(len=*), intent(in) :: path, link character(len=*), intent(in) :: path, link
integer :: hdferr
logical :: linkExists
call h5lexists_f(resultsFile, link,linkExists, hdferr) call HDF5_setLink(resultsFile,path,link)
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 end subroutine results_setLink
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
!> @brief remove link to an object !> @brief remove link to an object
@ -952,253 +943,21 @@ subroutine HDF5_mappingCells(mapping)
end subroutine HDF5_mappingCells 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 !> @brief creates a new vector dataset in the given group location
!-------------------------------------------------------------------------------------------------- !--------------------------------------------------------------------------------------------------
subroutine results_writeVectorDataset(group,dataset,label,SIunit) subroutine results_writeVectorDataset(group,dataset,label,SIunit)
use hdf5
implicit none implicit none
integer(HID_T), intent(in) :: group character(len=*), intent(in) :: SIunit,label,group
character(len=*), intent(in) :: SIunit,label real(pReal), intent(inout), dimension(:,:) :: dataset
real(pReal), intent(in), dimension(:,:) :: dataset integer(HID_T) :: groupHandle
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 h5dopen_f(group, label, dset_id, hdferr)
if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5dopen_f')
groupHandle = results_openGroup(group)
call HDF5_write(dataset,groupHandle,label)
call HDF5_closeGroup(groupHandle)
end subroutine results_writeVectorDataset end subroutine results_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
end module results end module results