From fd2d4d856bdca634111370c9537eed4ae8e19643 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 12 Dec 2018 07:45:20 +0100 Subject: [PATCH] cleaned + suggested structure to write data --- src/CPFEM2.f90 | 3 +- src/HDF5_utilities.f90 | 26 +++- src/constitutive.f90 | 19 ++- src/plastic_phenopowerlaw.f90 | 23 ++- src/results.f90 | 267 ++-------------------------------- 5 files changed, 78 insertions(+), 260 deletions(-) diff --git a/src/CPFEM2.f90 b/src/CPFEM2.f90 index 731fcf231..e22909231 100644 --- a/src/CPFEM2.f90 +++ b/src/CPFEM2.f90 @@ -331,7 +331,8 @@ subroutine CPFEM_results(inc) call results_openJobFile 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 results_closeJobFile diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index 144bc9098..32747218c 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -13,7 +13,7 @@ module HDF5_utilities #endif implicit none - private + public integer(pInt), parameter, private :: & HDF5_ERR_TYPE = 4_pInt !< kind of the integer return in the HDF5 library @@ -71,7 +71,8 @@ module HDF5_utilities HDF5_openGroup, & HDF5_addGroup, & HDF5_read, & - HDF5_write + HDF5_write, & + HDF5_setLink contains subroutine HDF5_utilities_init @@ -304,7 +305,28 @@ subroutine HDF5_addIntegerAttribute(entity,attrLabel,attrValue) 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 diff --git a/src/constitutive.f90 b/src/constitutive.f90 index 61bb55542..db90bfc20 100644 --- a/src/constitutive.f90 +++ b/src/constitutive.f90 @@ -1193,10 +1193,25 @@ subroutine constitutive_results() PLASTICITY_DISLOUCLA_ID, & PLASTICITY_NONLOCAL_ID #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: & 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 diff --git a/src/plastic_phenopowerlaw.f90 b/src/plastic_phenopowerlaw.f90 index ebfab0560..677d2872c 100644 --- a/src/plastic_phenopowerlaw.f90 +++ b/src/plastic_phenopowerlaw.f90 @@ -749,8 +749,29 @@ end function plastic_phenopowerlaw_postResults !-------------------------------------------------------------------------------------------------- !> @brief writes results to HDF5 output file !-------------------------------------------------------------------------------------------------- -subroutine plastic_phenopowerlaw_results() +subroutine plastic_phenopowerlaw_results(instance,group) #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 end subroutine plastic_phenopowerlaw_results diff --git a/src/results.f90 b/src/results.f90 index aff53b1ba..5fe35f0ee 100644 --- a/src/results.f90 +++ b/src/results.f90 @@ -34,8 +34,7 @@ module results results_addGroup, & results_openGroup, & results_writeVectorDataset, & - HDF5_writeScalarDataset, & - HDF5_writeTensorDataset, & + results_setLink, & HDF5_removeLink contains @@ -116,24 +115,16 @@ end function results_addGroup !-------------------------------------------------------------------------------------------------- !> @brief set link to object in results file !-------------------------------------------------------------------------------------------------- -subroutine HDF5_setLink(path,link) - use hdf5 +subroutine results_setLink(path,link) + use hdf5_utilities, only: & + HDF5_setLink 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)//')') + call HDF5_setLink(resultsFile,path,link) -end subroutine HDF5_setLink +end subroutine results_setLink !-------------------------------------------------------------------------------------------------- !> @brief remove link to an object @@ -952,253 +943,21 @@ subroutine HDF5_mappingCells(mapping) 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 !-------------------------------------------------------------------------------------------------- subroutine results_writeVectorDataset(group,dataset,label,SIunit) - use hdf5 implicit none - integer(HID_T), intent(in) :: group - character(len=*), intent(in) :: SIunit,label - 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 h5dopen_f(group, label, dset_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_writeVectorDataset: h5dopen_f') - + character(len=*), intent(in) :: SIunit,label,group + real(pReal), intent(inout), dimension(:,:) :: dataset + integer(HID_T) :: groupHandle + + groupHandle = results_openGroup(group) + call HDF5_write(dataset,groupHandle,label) + call HDF5_closeGroup(groupHandle) 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