From 8e295cbadf3b88276465234d669a26c90f8d03ea Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 11 Apr 2019 12:22:16 +0200 Subject: [PATCH 01/13] no need to create type for native data types --- src/HDF5_utilities.f90 | 102 +++++++++++++++++++---------------------- 1 file changed, 47 insertions(+), 55 deletions(-) diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index a2593e1cb..38d3f475f 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -268,10 +268,11 @@ end subroutine HDF5_closeGroup !-------------------------------------------------------------------------------------------------- logical function HDF5_objectExists(loc_id,path) - integer(HID_T), intent(in) :: loc_id + integer(HID_T), intent(in) :: loc_id character(len=*), intent(in), optional :: path - integer :: hdferr - character(len=256) :: p + + integer :: hdferr + character(len=256) :: p if (present(path)) then p = trim(path) @@ -295,13 +296,14 @@ end function HDF5_objectExists !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_str(loc_id,attrLabel,attrValue,path) - integer(HID_T), intent(in) :: loc_id - character(len=*), intent(in) :: attrLabel, attrValue - character(len=*), intent(in), optional :: path - integer :: hdferr - integer(HID_T) :: attr_id, space_id, type_id - logical :: attrExists - character(len=256) :: p + integer(HID_T), intent(in) :: loc_id + character(len=*), intent(in) :: attrLabel, attrValue + character(len=*), intent(in), optional :: path + + integer :: hdferr + integer(HID_T) :: attr_id, space_id, type_id + logical :: attrExists + character(len=256) :: p if (present(path)) then p = trim(path) @@ -340,14 +342,15 @@ end subroutine HDF5_addAttribute_str !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_int(loc_id,attrLabel,attrValue,path) - integer(HID_T), intent(in) :: loc_id - character(len=*), intent(in) :: attrLabel - integer(pInt), intent(in) :: attrValue + integer(HID_T), intent(in) :: loc_id + character(len=*), intent(in) :: attrLabel + integer(pInt), intent(in) :: attrValue character(len=*), intent(in), optional :: path - integer :: hdferr - integer(HID_T) :: attr_id, space_id, type_id - logical :: attrExists - character(len=256) :: p + + integer :: hdferr + integer(HID_T) :: attr_id, space_id + logical :: attrExists + character(len=256) :: p if (present(path)) then p = trim(path) @@ -356,27 +359,21 @@ subroutine HDF5_addAttribute_int(loc_id,attrLabel,attrValue,path) endif call h5screate_f(H5S_SCALAR_F,space_id,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5screate_f') - call h5tcopy_f(H5T_NATIVE_INTEGER, type_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5tcopy_f') - call h5tset_size_f(type_id, 1_HSIZE_T, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5tset_size_f') + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int: h5screate_f') call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5aexists_by_name_f') + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int: h5aexists_by_name_f') if (attrExists) then call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5adelete_by_name_f') + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int: h5adelete_by_name_f') endif - call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),type_id,space_id,attr_id,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5acreate_f') - call h5awrite_f(attr_id, type_id, attrValue, int([1],HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5awrite_f') + call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int: h5acreate_f') + call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, int([1],HSIZE_T), hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int: h5awrite_f') call h5aclose_f(attr_id,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5aclose_f') - call h5tclose_f(type_id,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5tclose_f') + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int: h5tclose_f') call h5sclose_f(space_id,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pInt: h5sclose_f') + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int: h5sclose_f') end subroutine HDF5_addAttribute_int @@ -386,14 +383,15 @@ end subroutine HDF5_addAttribute_int !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path) - integer(HID_T), intent(in) :: loc_id - character(len=*), intent(in) :: attrLabel - real(pReal), intent(in) :: attrValue - character(len=*), intent(in), optional :: path - integer :: hdferr - integer(HID_T) :: attr_id, space_id, type_id - logical :: attrExists - character(len=256) :: p + integer(HID_T), intent(in) :: loc_id + character(len=*), intent(in) :: attrLabel + real(pReal), intent(in) :: attrValue + character(len=*), intent(in), optional :: path + + integer :: hdferr + integer(HID_T) :: attr_id, space_id + logical :: attrExists + character(len=256) :: p if (present(path)) then p = trim(path) @@ -402,27 +400,21 @@ subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path) endif call h5screate_f(H5S_SCALAR_F,space_id,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5screate_f') - call h5tcopy_f(H5T_NATIVE_DOUBLE, type_id, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5tcopy_f') - call h5tset_size_f(type_id, 8_HSIZE_T, hdferr) ! ToDo - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5tset_size_f') + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_real: h5screate_f') call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5aexists_by_name_f') + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_real: h5aexists_by_name_f') if (attrExists) then call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5adelete_by_name_f') + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_real: h5adelete_by_name_f') endif - call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),type_id,space_id,attr_id,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5acreate_f') - call h5awrite_f(attr_id, type_id, attrValue, int([1],HSIZE_T), hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5awrite_f') + call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_real: h5acreate_f') + call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, int([1],HSIZE_T), hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_real: h5awrite_f') call h5aclose_f(attr_id,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5aclose_f') - call h5tclose_f(type_id,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5tclose_f') + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_real: h5tclose_f') call h5sclose_f(space_id,hdferr) - if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_pReal: h5sclose_f') + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_real: h5sclose_f') end subroutine HDF5_addAttribute_real From 3c8d96c54cbe219120108e486fe96cccebe5c111 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 11 Apr 2019 15:44:08 +0200 Subject: [PATCH 02/13] enable more complex attributes --- src/HDF5_utilities.f90 | 90 ++++++++++++++++++++++++++++++++++++++++++ src/results.f90 | 73 +++++++++++++++++++++++++++++++--- 2 files changed, 158 insertions(+), 5 deletions(-) diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index 38d3f475f..731b44f06 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -70,6 +70,8 @@ module HDF5_utilities module procedure HDF5_addAttribute_str module procedure HDF5_addAttribute_int module procedure HDF5_addAttribute_real + module procedure HDF5_addAttribute_int_array + module procedure HDF5_addAttribute_real_array end interface HDF5_addAttribute @@ -419,6 +421,94 @@ subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path) end subroutine HDF5_addAttribute_real +!-------------------------------------------------------------------------------------------------- +!> @brief adds a integer attribute to the path given relative to the location +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_addAttribute_int_array(loc_id,attrLabel,attrValue,path) + + integer(HID_T), intent(in) :: loc_id + character(len=*), intent(in) :: attrLabel + integer(pInt), intent(in), dimension(:) :: attrValue + character(len=*), intent(in), optional :: path + + integer :: hdferr + integer(HID_T) :: attr_id, space_id + integer(HSIZE_T),dimension(1) :: array_size + logical :: attrExists + character(len=256) :: p + + if (present(path)) then + p = trim(path) + else + p = '.' + endif + + array_size = size(attrValue,kind=HSIZE_T) + + call h5screate_simple_f(1, array_size, space_id, hdferr, array_size) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5screate_f') + call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5aexists_by_name_f') + if (attrExists) then + call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5adelete_by_name_f') + endif + call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_INTEGER,space_id,attr_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5acreate_f') + call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, array_size, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5awrite_f') + call h5aclose_f(attr_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5tclose_f') + call h5sclose_f(space_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5sclose_f') + +end subroutine HDF5_addAttribute_int_array + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds a real attribute to the path given relative to the location +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_addAttribute_real_array(loc_id,attrLabel,attrValue,path) + + integer(HID_T), intent(in) :: loc_id + character(len=*), intent(in) :: attrLabel + real(pReal), intent(in), dimension(:) :: attrValue + character(len=*), intent(in), optional :: path + + integer :: hdferr + integer(HID_T) :: attr_id, space_id + integer(HSIZE_T),dimension(1) :: array_size + logical :: attrExists + character(len=256) :: p + + if (present(path)) then + p = trim(path) + else + p = '.' + endif + + array_size = size(attrValue,kind=HSIZE_T) + + call h5screate_simple_f(1, array_size, space_id, hdferr, array_size) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5screate_f') + call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5aexists_by_name_f') + if (attrExists) then + call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5adelete_by_name_f') + endif + call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),H5T_NATIVE_DOUBLE,space_id,attr_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5acreate_f') + call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, array_size, hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5awrite_f') + call h5aclose_f(attr_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5tclose_f') + call h5sclose_f(space_id,hdferr) + if (hdferr < 0) call IO_error(1_pInt,ext_msg='HDF5_addAttribute_int_array: h5sclose_f') + +end subroutine HDF5_addAttribute_real_array + + !-------------------------------------------------------------------------------------------------- !> @brief set link to object in results file !-------------------------------------------------------------------------------------------------- diff --git a/src/results.f90 b/src/results.f90 index 4ed5cc751..20c2aa143 100644 --- a/src/results.f90 +++ b/src/results.f90 @@ -27,6 +27,17 @@ module results module procedure results_writeScalarDataset_rotation end interface results_writeDataset + + interface results_addAttribute + + module procedure results_addAttribute_real + module procedure results_addAttribute_int + module procedure results_addAttribute_str + + module procedure results_addAttribute_int_array + module procedure results_addAttribute_real_array + + end interface results_addAttribute public :: & results_init, & @@ -144,15 +155,67 @@ end subroutine results_setLink !-------------------------------------------------------------------------------------------------- -!> @brief adds an attribute to an object +!> @brief adds a string attribute to an object in the results file !-------------------------------------------------------------------------------------------------- -subroutine results_addAttribute(attrLabel,attrValue,path) +subroutine results_addAttribute_str(attrLabel,attrValue,path) - character(len=*), intent(in) :: attrLabel, attrValue, path + character(len=*), intent(in) :: attrLabel, attrValue, path - call HDF5_addAttribute_str(resultsFile,attrLabel, attrValue, path) + call HDF5_addAttribute(resultsFile,attrLabel, attrValue, path) -end subroutine results_addAttribute +end subroutine results_addAttribute_str + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds an integer attribute an object in the results file +!-------------------------------------------------------------------------------------------------- +subroutine results_addAttribute_int(attrLabel,attrValue,path) + + character(len=*), intent(in) :: attrLabel, path + integer, intent(in) :: attrValue + + call HDF5_addAttribute(resultsFile,attrLabel, attrValue, path) + +end subroutine results_addAttribute_int + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds a real attribute an object in the results file +!-------------------------------------------------------------------------------------------------- +subroutine results_addAttribute_real(attrLabel,attrValue,path) + + character(len=*), intent(in) :: attrLabel, path + real(pReal), intent(in) :: attrValue + + call HDF5_addAttribute(resultsFile,attrLabel, attrValue, path) + +end subroutine results_addAttribute_real + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds an integer array attribute an object in the results file +!-------------------------------------------------------------------------------------------------- +subroutine results_addAttribute_int_array(attrLabel,attrValue,path) + + character(len=*), intent(in) :: attrLabel, path + integer, intent(in), dimension(:) :: attrValue + + call HDF5_addAttribute(resultsFile,attrLabel, attrValue, path) + +end subroutine results_addAttribute_int_array + + +!-------------------------------------------------------------------------------------------------- +!> @brief adds a real array attribute an object in the results file +!-------------------------------------------------------------------------------------------------- +subroutine results_addAttribute_real_array(attrLabel,attrValue,path) + + character(len=*), intent(in) :: attrLabel, path + real(pReal), intent(in), dimension(:) :: attrValue + + call HDF5_addAttribute(resultsFile,attrLabel, attrValue, path) + +end subroutine results_addAttribute_real_array !-------------------------------------------------------------------------------------------------- From 12efa108d6c0bd68fad42e5c3d15ebd6d28dcd07 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 11 Apr 2019 15:44:34 +0200 Subject: [PATCH 03/13] store grid and size store it temporarly at "mappings", later on they will be attached to the (no yet existing) coordinates --- src/DAMASK_grid.f90 | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/DAMASK_grid.f90 b/src/DAMASK_grid.f90 index 29b505d14..f2f52bb2f 100644 --- a/src/DAMASK_grid.f90 +++ b/src/DAMASK_grid.f90 @@ -358,6 +358,11 @@ program DAMASK_spectral enddo close(fileUnit) + call results_openJobFile + call results_addAttribute('grid',grid,'mapping') + call results_addAttribute('size',geomSize,'mapping') + call results_closeJobFile + !-------------------------------------------------------------------------------------------------- ! doing initialization depending on active solvers call Utilities_init() From 89679147e894d27b62c1d3712fb70902dc4942db Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 13 Apr 2019 09:47:56 +0200 Subject: [PATCH 04/13] leaner group structure, centrally handled --- src/constitutive.f90 | 4 +--- src/crystallite.f90 | 6 ++---- src/results.f90 | 15 +++++++++++++++ 3 files changed, 18 insertions(+), 7 deletions(-) diff --git a/src/constitutive.f90 b/src/constitutive.f90 index 1158ddc07..5031616d8 100644 --- a/src/constitutive.f90 +++ b/src/constitutive.f90 @@ -1107,11 +1107,9 @@ subroutine constitutive_results integer :: p character(len=256) :: group - - call HDF5_closeGroup(results_addGroup('current/constitutive')) do p=1,size(config_name_phase) - group = trim('current/constitutive')//'/'//trim(config_name_phase(p)) + group = trim('current/constituent')//'/'//trim(config_name_phase(p)) call HDF5_closeGroup(results_addGroup(group)) group = trim(group)//'/'//'plastic' diff --git a/src/crystallite.f90 b/src/crystallite.f90 index 69c7839c7..c330c8733 100644 --- a/src/crystallite.f90 +++ b/src/crystallite.f90 @@ -1077,7 +1077,7 @@ end function crystallite_postResults !-------------------------------------------------------------------------------------------------- -!> @brief writes constitutive results to HDF5 output file +!> @brief writes crystallite results to HDF5 output file !-------------------------------------------------------------------------------------------------- subroutine crystallite_results #if defined(PETSc) || defined(DAMASK_HDF5) @@ -1096,12 +1096,10 @@ subroutine crystallite_results real(pReal), allocatable, dimension(:,:,:) :: selected_tensors type(rotation), allocatable, dimension(:) :: selected_rotations character(len=256) :: group,lattice_label - - call HDF5_closeGroup(results_addGroup('current/constituent')) do p=1,size(config_name_phase) group = trim('current/constituent')//'/'//trim(config_name_phase(p)) - call HDF5_closeGroup(results_addGroup(group)) + do o = 1, size(output_constituent(p)%label) select case (output_constituent(p)%label(o)) case('f') diff --git a/src/results.f90 b/src/results.f90 index 20c2aa143..a969816d5 100644 --- a/src/results.f90 +++ b/src/results.f90 @@ -115,6 +115,9 @@ subroutine results_addIncrement(inc,time) call HDF5_closeGroup(results_addGroup(trim('inc'//trim(adjustl(incChar))))) call results_setLink(trim('inc'//trim(adjustl(incChar))),'current') call HDF5_addAttribute(resultsFile,'time/s',time,trim('inc'//trim(adjustl(incChar)))) + + call HDF5_closeGroup(results_addGroup('current/constituent')) + call HDF5_closeGroup(results_addGroup('current/materialpoint')) end subroutine results_addIncrement @@ -253,6 +256,8 @@ subroutine results_writeScalarDataset_real(group,dataset,label,description,SIuni call HDF5_addAttribute(groupHandle,'Description',description,label) if (HDF5_objectExists(groupHandle,label) .and. present(SIunit)) & call HDF5_addAttribute(groupHandle,'Unit',SIunit,label) + if (HDF5_objectExists(groupHandle,label)) & + call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label) call HDF5_closeGroup(groupHandle) end subroutine results_writeScalarDataset_real @@ -278,6 +283,8 @@ subroutine results_writeVectorDataset_real(group,dataset,label,description,SIuni call HDF5_addAttribute(groupHandle,'Description',description,label) if (HDF5_objectExists(groupHandle,label) .and. present(SIunit)) & call HDF5_addAttribute(groupHandle,'Unit',SIunit,label) + if (HDF5_objectExists(groupHandle,label)) & + call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label) call HDF5_closeGroup(groupHandle) end subroutine results_writeVectorDataset_real @@ -304,6 +311,8 @@ subroutine results_writeTensorDataset_real(group,dataset,label,description,SIuni call HDF5_addAttribute(groupHandle,'Description',description,label) if (HDF5_objectExists(groupHandle,label) .and. present(SIunit)) & call HDF5_addAttribute(groupHandle,'Unit',SIunit,label) + if (HDF5_objectExists(groupHandle,label)) & + call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label) call HDF5_closeGroup(groupHandle) end subroutine results_writeTensorDataset_real @@ -330,6 +339,8 @@ subroutine results_writeVectorDataset_int(group,dataset,label,description,SIunit call HDF5_addAttribute(groupHandle,'Description',description,label) if (HDF5_objectExists(groupHandle,label) .and. present(SIunit)) & call HDF5_addAttribute(groupHandle,'Unit',SIunit,label) + if (HDF5_objectExists(groupHandle,label)) & + call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label) call HDF5_closeGroup(groupHandle) end subroutine results_writeVectorDataset_int @@ -356,6 +367,8 @@ subroutine results_writeTensorDataset_int(group,dataset,label,description,SIunit call HDF5_addAttribute(groupHandle,'Description',description,label) if (HDF5_objectExists(groupHandle,label) .and. present(SIunit)) & call HDF5_addAttribute(groupHandle,'Unit',SIunit,label) + if (HDF5_objectExists(groupHandle,label)) & + call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label) call HDF5_closeGroup(groupHandle) end subroutine results_writeTensorDataset_int @@ -384,6 +397,8 @@ subroutine results_writeScalarDataset_rotation(group,dataset,label,description,l call HDF5_addAttribute(groupHandle,'Description',description,label) if (HDF5_objectExists(groupHandle,label) .and. present(lattice_structure)) & call HDF5_addAttribute(groupHandle,'Lattice',lattice_structure,label) + if (HDF5_objectExists(groupHandle,label)) & + call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label) call HDF5_closeGroup(groupHandle) end subroutine results_writeScalarDataset_rotation From 8eb1a35dfb649aef6590b03cc04b672cda93ed89 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sat, 13 Apr 2019 11:11:32 +0200 Subject: [PATCH 05/13] first version of a library to parse HDF5 - preliminarly called DADF5 (DAMASK HDF5) - script to write (empty undeformed) geometries is also added --- processing/post/DADF5_vtk_cells.py | 64 ++++++++++++++++++++++++++++++ python/damask/__init__.py | 1 + python/damask/dadf5.py | 38 ++++++++++++++++++ 3 files changed, 103 insertions(+) create mode 100755 processing/post/DADF5_vtk_cells.py create mode 100644 python/damask/dadf5.py diff --git a/processing/post/DADF5_vtk_cells.py b/processing/post/DADF5_vtk_cells.py new file mode 100755 index 000000000..008ac5f66 --- /dev/null +++ b/processing/post/DADF5_vtk_cells.py @@ -0,0 +1,64 @@ +#!/usr/bin/env python3 +# -*- coding: UTF-8 no BOM -*- + +import os,vtk +import numpy as np +import argparse +import damask + +scriptName = os.path.splitext(os.path.basename(__file__))[0] +scriptID = ' '.join([scriptName,damask.version]) + +# -------------------------------------------------------------------- +# MAIN +# -------------------------------------------------------------------- +parser = argparse.ArgumentParser() + +#ToDo: We need to decide on a way of handling arguments of variable lentght +#https://stackoverflow.com/questions/15459997/passing-integer-lists-to-python + +#parser.add_argument('--version', action='version', version='%(prog)s {}'.format(scriptID)) +parser.add_argument('filenames', nargs='+', + help='DADF5 files') + +options = parser.parse_args() + + +# --- loop over input files ------------------------------------------------------------------------ + +for filename in options.filenames: + data = damask.DADF5(filename) + + if data.structured: # for grid solvers use rectilinear grid + rGrid = vtk.vtkRectilinearGrid() + coordArray = [vtk.vtkDoubleArray(), + vtk.vtkDoubleArray(), + vtk.vtkDoubleArray(), + ] + + rGrid.SetDimensions(*data.grid) + for dim in [0,1,2]: + for c in np.linspace(0,data.size[dim],1+data.grid[dim]): + coordArray[dim].InsertNextValue(c) + + rGrid.SetXCoordinates(coordArray[0]) + rGrid.SetYCoordinates(coordArray[1]) + rGrid.SetZCoordinates(coordArray[2]) + + + for i,inc in enumerate(data.increments): + if not inc['active']: pass + + if data.structured: + writer = vtk.vtkXMLRectilinearGridWriter() + + writer.SetCompressorTypeToZLib() + writer.SetDataModeToBinary() + writer.SetFileName(os.path.join(os.path.split(filename)[0], + os.path.splitext(os.path.split(filename)[1])[0] + + '_inc{:04d}'.format(i) + # ToDo: adjust to lenght of increments + '.' + writer.GetDefaultFileExtension())) + if data.structured: + writer.SetInputData(rGrid) + + writer.Write() diff --git a/python/damask/__init__.py b/python/damask/__init__.py index d7ed4a9f9..2dfdac567 100644 --- a/python/damask/__init__.py +++ b/python/damask/__init__.py @@ -14,6 +14,7 @@ from .asciitable import ASCIItable # noqa from .config import Material # noqa from .colormaps import Colormap, Color # noqa from .orientation import Symmetry, Lattice, Rotation, Orientation # noqa +from .dadf5 import DADF5 # noqa #from .block import Block # only one class from .result import Result # noqa diff --git a/python/damask/dadf5.py b/python/damask/dadf5.py new file mode 100644 index 000000000..6342b18e7 --- /dev/null +++ b/python/damask/dadf5.py @@ -0,0 +1,38 @@ +# -*- coding: UTF-8 no BOM -*- +import h5py +import re + +# ------------------------------------------------------------------ +class DADF5(): + """Read and write to DADF5 files""" + +# ------------------------------------------------------------------ + def __init__(self, + filename, + mode = 'r', + ): + + if mode not in ['a','r']: + print('Invalid file access mode') + with h5py.File(filename,mode): + pass + + with h5py.File(filename,'r') as f: + + if f.attrs['DADF5-major'] != 0 or f.attrs['DADF5-minor'] != 1: + print('Unsupported DADF5 version {} '.format(f.attrs['DADF5-version'])) + + self.structured = 'grid' in f['mapping'].attrs.keys() + + if self.structured: + self.grid = f['mapping'].attrs['grid'] + self.size = f['mapping'].attrs['size'] + + r=re.compile('inc[0-9]+') + self.increments = [{'group': u, + 'time': f[u].attrs['time/s'], + 'active': True + } for u in f.keys() if r.match(u)] + + self.filename = filename + self.mode = mode From 7177813710995ae5cb886dc03f01accbd429f6c0 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 17 Apr 2019 19:57:16 +0200 Subject: [PATCH 06/13] adding data to geometry --- processing/post/DADF5_vtk_cells.py | 10 ++++-- python/damask/dadf5.py | 49 +++++++++++++++++++++++++++--- 2 files changed, 52 insertions(+), 7 deletions(-) diff --git a/processing/post/DADF5_vtk_cells.py b/processing/post/DADF5_vtk_cells.py index 008ac5f66..85b999a19 100755 --- a/processing/post/DADF5_vtk_cells.py +++ b/processing/post/DADF5_vtk_cells.py @@ -5,6 +5,7 @@ import os,vtk import numpy as np import argparse import damask +from vtk.util import numpy_support scriptName = os.path.splitext(os.path.basename(__file__))[0] scriptID = ' '.join([scriptName,damask.version]) @@ -36,7 +37,7 @@ for filename in options.filenames: vtk.vtkDoubleArray(), ] - rGrid.SetDimensions(*data.grid) + rGrid.SetDimensions(*(data.grid+1)) for dim in [0,1,2]: for c in np.linspace(0,data.size[dim],1+data.grid[dim]): coordArray[dim].InsertNextValue(c) @@ -47,8 +48,11 @@ for filename in options.filenames: for i,inc in enumerate(data.increments): - if not inc['active']: pass - + data.active['increments'] = [inc] + x = data.get_dataset_location('xi_sl')[0] + VTKarray = numpy_support.numpy_to_vtk(num_array=data.read_dataset(x,0),deep=True,array_type= vtk.VTK_DOUBLE) + VTKarray.SetName('xi_sl') + rGrid.GetCellData().AddArray(VTKarray) if data.structured: writer = vtk.vtkXMLRectilinearGridWriter() diff --git a/python/damask/dadf5.py b/python/damask/dadf5.py index 6342b18e7..043997547 100644 --- a/python/damask/dadf5.py +++ b/python/damask/dadf5.py @@ -1,6 +1,8 @@ # -*- coding: UTF-8 no BOM -*- import h5py import re +import numpy as np +import os # ------------------------------------------------------------------ class DADF5(): @@ -20,7 +22,7 @@ class DADF5(): with h5py.File(filename,'r') as f: if f.attrs['DADF5-major'] != 0 or f.attrs['DADF5-minor'] != 1: - print('Unsupported DADF5 version {} '.format(f.attrs['DADF5-version'])) + raise TypeError('Unsupported DADF5 version {} '.format(f.attrs['DADF5-version'])) self.structured = 'grid' in f['mapping'].attrs.keys() @@ -29,10 +31,49 @@ class DADF5(): self.size = f['mapping'].attrs['size'] r=re.compile('inc[0-9]+') - self.increments = [{'group': u, - 'time': f[u].attrs['time/s'], - 'active': True + self.increments = [{'inc': int(u[3:]), + 'time': round(f[u].attrs['time/s'],12), } for u in f.keys() if r.match(u)] + + self.constituents = np.unique(f['mapping/cellResults/constituent']['Name']).tolist() # ToDo: I am not to happy with the name + self.constituents = [c.decode() for c in self.constituents] + self.materialpoints = np.unique(f['mapping/cellResults/materialpoint']['Name']).tolist() # ToDo: I am not to happy with the name + self.materialpoints = [m.decode() for m in self.materialpoints] + self.Nconstitutents = np.shape(f['mapping/cellResults/constituent'])[1] + self.Nmaterialpoints= np.shape(f['mapping/cellResults/constituent'])[0] + + self.active= {'increments' :self.increments, + 'constituents' :self.constituents, + 'materialpoints':self.materialpoints} self.filename = filename self.mode = mode + + + def get_dataset_location(self,label): + path = [] + with h5py.File(self.filename,'r') as f: + for i in self.active['increments']: + group_inc = 'inc{:05}'.format(i['inc']) + for c in self.active['constituents']: + group_constituent = group_inc+'/constituent/'+c + for t in f[group_constituent].keys(): + try: + f[group_constituent+'/'+t+'/'+label] + path.append(group_constituent+'/'+t+'/'+label) + except: + pass + return path + + + def read_dataset(self,path,c): + with h5py.File(self.filename,'r') as f: + shape = (self.Nmaterialpoints,) + np.shape(f[path])[1:] + dataset = np.full(shape,np.nan) + label = path.split('/')[2] + p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label)) + for s in p: dataset[s,:] = f[path][s,:] + + return dataset + + From 91c200ff8ca855b883fed988c27fb50f7aa6c6e1 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Wed, 17 Apr 2019 20:57:41 +0200 Subject: [PATCH 07/13] correct labels for output (also for DADF5) --- examples/SpectralMethod/Polycrystal/material.config | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/examples/SpectralMethod/Polycrystal/material.config b/examples/SpectralMethod/Polycrystal/material.config index 39e7f1952..71d7e07d7 100644 --- a/examples/SpectralMethod/Polycrystal/material.config +++ b/examples/SpectralMethod/Polycrystal/material.config @@ -30,11 +30,20 @@ plasticity phenopowerlaw (output) resistance_slip (output) shearrate_slip (output) resolvedstress_slip -(output) totalshear +(output) accumulatedshear_slip (output) resistance_twin (output) shearrate_twin (output) resolvedstress_twin -(output) totalvolfrac +(output) accumulatedshear_twin + +# only for HDF5 out +(output) orientation # quaternion +(output) f # deformation gradient tensor; synonyms: "defgrad" +(output) fe # elastic deformation gradient tensor +(output) fp # plastic deformation gradient tensor +(output) p # first Piola-Kichhoff stress tensor; synonyms: "firstpiola", "1stpiola" +(output) lp # plastic velocity gradient tensor + lattice_structure fcc Nslip 12 # per family From 7c771647adfb8222503d099ed41020e497977721 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 18 Apr 2019 11:55:50 +0200 Subject: [PATCH 08/13] adjustments for easier access to output data --- src/constitutive.f90 | 2 +- src/crystallite.f90 | 4 +++- src/results.f90 | 4 ++-- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/src/constitutive.f90 b/src/constitutive.f90 index 5031616d8..6428e19d1 100644 --- a/src/constitutive.f90 +++ b/src/constitutive.f90 @@ -1112,7 +1112,7 @@ subroutine constitutive_results group = trim('current/constituent')//'/'//trim(config_name_phase(p)) call HDF5_closeGroup(results_addGroup(group)) - group = trim(group)//'/'//'plastic' + group = trim(group)//'/plastic' call HDF5_closeGroup(results_addGroup(group)) select case(material_phase_plasticity_type(p)) diff --git a/src/crystallite.f90 b/src/crystallite.f90 index c330c8733..1ba1f7483 100644 --- a/src/crystallite.f90 +++ b/src/crystallite.f90 @@ -1098,7 +1098,9 @@ subroutine crystallite_results character(len=256) :: group,lattice_label do p=1,size(config_name_phase) - group = trim('current/constituent')//'/'//trim(config_name_phase(p)) + group = trim('current/constituent')//'/'//trim(config_name_phase(p))//'/generic' + + call HDF5_closeGroup(results_addGroup(group)) do o = 1, size(output_constituent(p)%label) select case (output_constituent(p)%label(o)) diff --git a/src/results.f90 b/src/results.f90 index a969816d5..516c64552 100644 --- a/src/results.f90 +++ b/src/results.f90 @@ -510,7 +510,7 @@ subroutine results_mapping_constituent(phaseAt,memberAt,label) !--------------------------------------------------------------------------------------------------- ! renumber member from my process to all processes do i = 1, size(label) - where(phaseAt_perIP == i) memberAt_total = memberAt + sum(memberOffset(i,0:worldrank-1)) + where(phaseAt_perIP == i) memberAt_total = memberAt + sum(memberOffset(i,0:worldrank-1)) -1 ! convert to 0-based enddo !-------------------------------------------------------------------------------------------------- @@ -648,7 +648,7 @@ subroutine results_mapping_materialpoint(homogenizationAt,memberAt,label) !--------------------------------------------------------------------------------------------------- ! renumber member from my process to all processes do i = 1, size(label) - where(homogenizationAt_perIP == i) memberAt_total = memberAt + sum(memberOffset(i,0:worldrank-1)) + where(homogenizationAt_perIP == i) memberAt_total = memberAt + sum(memberOffset(i,0:worldrank-1)) - 1 ! convert to 0-based enddo !-------------------------------------------------------------------------------------------------- From 6b7fd6b7ea7eb4c510be011a011025a76c4676d8 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 18 Apr 2019 11:58:17 +0200 Subject: [PATCH 09/13] visualizing data from DADF5: first prototype --- processing/post/DADF5_vtk_cells.py | 50 +++++++++++++++++------ python/damask/dadf5.py | 65 +++++++++++++++++++++++------- 2 files changed, 87 insertions(+), 28 deletions(-) diff --git a/processing/post/DADF5_vtk_cells.py b/processing/post/DADF5_vtk_cells.py index 85b999a19..3bbf9fd45 100755 --- a/processing/post/DADF5_vtk_cells.py +++ b/processing/post/DADF5_vtk_cells.py @@ -24,22 +24,23 @@ parser.add_argument('filenames', nargs='+', options = parser.parse_args() +options.labels = ['Fe','Fp','xi_sl'] # --- loop over input files ------------------------------------------------------------------------ for filename in options.filenames: - data = damask.DADF5(filename) + results = damask.DADF5(filename) - if data.structured: # for grid solvers use rectilinear grid + if results.structured: # for grid solvers use rectilinear grid rGrid = vtk.vtkRectilinearGrid() coordArray = [vtk.vtkDoubleArray(), vtk.vtkDoubleArray(), vtk.vtkDoubleArray(), ] - rGrid.SetDimensions(*(data.grid+1)) + rGrid.SetDimensions(*(results.grid+1)) for dim in [0,1,2]: - for c in np.linspace(0,data.size[dim],1+data.grid[dim]): + for c in np.linspace(0,results.size[dim],1+results.grid[dim]): coordArray[dim].InsertNextValue(c) rGrid.SetXCoordinates(coordArray[0]) @@ -47,22 +48,45 @@ for filename in options.filenames: rGrid.SetZCoordinates(coordArray[2]) - for i,inc in enumerate(data.increments): - data.active['increments'] = [inc] - x = data.get_dataset_location('xi_sl')[0] - VTKarray = numpy_support.numpy_to_vtk(num_array=data.read_dataset(x,0),deep=True,array_type= vtk.VTK_DOUBLE) - VTKarray.SetName('xi_sl') - rGrid.GetCellData().AddArray(VTKarray) - if data.structured: + for i,inc in enumerate(results.increments): + print('Output step {}/{}'.format(i+1,len(results.increments))) + vtk_data = [] + results.active['increments'] = [inc] + for label in options.labels: + for o in results.c_output_types: + results.active['c_output_types'] = [o] + if o != 'generic': + for c in results.constituents: + results.active['constituents'] = [c] + x = results.get_dataset_location(label) + if len(x) == 0: + continue + array = results.read_dataset(x,0) + shape = [array.shape[0],np.product(array.shape[1:])] + vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE)) + vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) + rGrid.GetCellData().AddArray(vtk_data[-1]) + else: + results.active['constituents'] = results.constituents + x = results.get_dataset_location(label) + if len(x) == 0: + continue + array = results.read_dataset(x,0) + shape = [array.shape[0],np.product(array.shape[1:])] + vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE)) + vtk_data[-1].SetName('1_'+x[0].split('/')[1]+'/generic/'+label) + rGrid.GetCellData().AddArray(vtk_data[-1]) + + if results.structured: writer = vtk.vtkXMLRectilinearGridWriter() writer.SetCompressorTypeToZLib() writer.SetDataModeToBinary() writer.SetFileName(os.path.join(os.path.split(filename)[0], os.path.splitext(os.path.split(filename)[1])[0] + - '_inc{:04d}'.format(i) + # ToDo: adjust to lenght of increments + '_inc{:04d}'.format(i) + # ToDo: adjust to length of increments '.' + writer.GetDefaultFileExtension())) - if data.structured: + if results.structured: writer.SetInputData(rGrid) writer.Write() diff --git a/python/damask/dadf5.py b/python/damask/dadf5.py index 043997547..887c32338 100644 --- a/python/damask/dadf5.py +++ b/python/damask/dadf5.py @@ -35,29 +35,56 @@ class DADF5(): 'time': round(f[u].attrs['time/s'],12), } for u in f.keys() if r.match(u)] - self.constituents = np.unique(f['mapping/cellResults/constituent']['Name']).tolist() # ToDo: I am not to happy with the name - self.constituents = [c.decode() for c in self.constituents] - self.materialpoints = np.unique(f['mapping/cellResults/materialpoint']['Name']).tolist() # ToDo: I am not to happy with the name - self.materialpoints = [m.decode() for m in self.materialpoints] - self.Nconstitutents = np.shape(f['mapping/cellResults/constituent'])[1] - self.Nmaterialpoints= np.shape(f['mapping/cellResults/constituent'])[0] + self.constituents = np.unique(f['mapping/cellResults/constituent']['Name']).tolist() # ToDo: I am not to happy with the name + self.constituents = [c.decode() for c in self.constituents] - self.active= {'increments' :self.increments, - 'constituents' :self.constituents, - 'materialpoints':self.materialpoints} + self.materialpoints = np.unique(f['mapping/cellResults/materialpoint']['Name']).tolist() # ToDo: I am not to happy with the name + self.materialpoints = [m.decode() for m in self.materialpoints] + + self.Nconstituents = [i for i in range(np.shape(f['mapping/cellResults/constituent'])[1])] + self.Nmaterialpoints = np.shape(f['mapping/cellResults/constituent'])[0] + + self.c_output_types = [] + for c in self.constituents: + for o in f['inc{:05}/constituent/{}'.format(self.increments[0]['inc'],c)].keys(): + self.c_output_types.append(o) + self.c_output_types = list(set(self.c_output_types)) # make unique + + self.active= {'increments': self.increments, + 'constituents': self.constituents, + 'materialpoints': self.materialpoints, + 'constituent': self.Nconstituents, + 'c_output_types': self.c_output_types} self.filename = filename self.mode = mode - + + def list_data(self): + """Shows information on all datasets in the file""" + with h5py.File(self.filename,'r') as f: + group_inc = 'inc{:05}'.format(self.active['increments'][0]['inc']) + for c in self.active['constituents']: + print('\n'+c) + group_constituent = group_inc+'/constituent/'+c + for t in self.active['c_output_types']: + print(' {}'.format(t)) + group_output_types = group_constituent+'/'+t + try: + for x in f[group_output_types].keys(): + print(' {} ({})'.format(x,f[group_output_types+'/'+x].attrs['Description'].decode())) + except: + pass + def get_dataset_location(self,label): + """Returns the location of all active datasets with given label""" path = [] with h5py.File(self.filename,'r') as f: for i in self.active['increments']: group_inc = 'inc{:05}'.format(i['inc']) for c in self.active['constituents']: group_constituent = group_inc+'/constituent/'+c - for t in f[group_constituent].keys(): + for t in self.active['c_output_types']: try: f[group_constituent+'/'+t+'/'+label] path.append(group_constituent+'/'+t+'/'+label) @@ -67,12 +94,20 @@ class DADF5(): def read_dataset(self,path,c): + """ + Dataset for all points/cells + + + If more than one path is given, the dataset is composed of the individual contributions + """ with h5py.File(self.filename,'r') as f: - shape = (self.Nmaterialpoints,) + np.shape(f[path])[1:] + shape = (self.Nmaterialpoints,) + np.shape(f[path[0]])[1:] dataset = np.full(shape,np.nan) - label = path.split('/')[2] - p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label)) - for s in p: dataset[s,:] = f[path][s,:] + for pa in path: + label = pa.split('/')[2] + p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label))[0] + u = (f['mapping/cellResults/constituent'][p,c]['Position']) + dataset[p,:] = f[pa][u,:] return dataset From ccf13c2c500501e8395aacbde57855abaea7ea7b Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 18 Apr 2019 11:59:27 +0200 Subject: [PATCH 10/13] autodoc does not work for argparse --- .gitlab-ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 1e1b8fe49..0cd8759d9 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -505,7 +505,7 @@ Processing: - rm abq_addUserOutput.py marc_addUserOutput.py - $DAMASKROOT/PRIVATE/documenting/scriptHelpToWiki.py --debug *.py - cd $DAMASKROOT/processing/post - - rm marc_to_vtk.py vtk2ang.py + - rm marc_to_vtk.py vtk2ang.py DAD*.py - $DAMASKROOT/PRIVATE/documenting/scriptHelpToWiki.py --debug *.py except: - master From b746b841f77c4fdd929ee00846db4d5f95ac4a8d Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 18 Apr 2019 12:04:09 +0200 Subject: [PATCH 11/13] not needed --- python/damask/dadf5.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/python/damask/dadf5.py b/python/damask/dadf5.py index 887c32338..4214f4922 100644 --- a/python/damask/dadf5.py +++ b/python/damask/dadf5.py @@ -2,7 +2,6 @@ import h5py import re import numpy as np -import os # ------------------------------------------------------------------ class DADF5(): @@ -97,7 +96,6 @@ class DADF5(): """ Dataset for all points/cells - If more than one path is given, the dataset is composed of the individual contributions """ with h5py.File(self.filename,'r') as f: From f89d318b0309e2536e17996bd400efb9b6f370dc Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Thu, 18 Apr 2019 18:28:22 +0200 Subject: [PATCH 12/13] [skip ci] old output not needed for testing HDF5 --- installation/patch/README.md | 5 +- installation/patch/disable_old_output | 178 ++++++++++++++++++++++++++ 2 files changed, 182 insertions(+), 1 deletion(-) create mode 100644 installation/patch/disable_old_output diff --git a/installation/patch/README.md b/installation/patch/README.md index dd8232758..0b8251510 100644 --- a/installation/patch/README.md +++ b/installation/patch/README.md @@ -12,7 +12,10 @@ patch -p1 < installation/patch/nameOfPatch ## Available patches * **disable_HDF5** disables all HDF5 output. - HDF5 output is an experimental feature. Also, some routines not present in HDF5 1.8.x are remove to allow compilation of DAMASK with HDF5 < 1.10.x + HDF5 output is an experimental feature. Also, some routines not present in HDF5 1.8.x are removed to allow compilation of DAMASK with HDF5 < 1.10.x + + * **disable_old_output** disables all non-HDF5 output. + Saves some memory when using only HDF5 output ## Create patch commit your changes diff --git a/installation/patch/disable_old_output b/installation/patch/disable_old_output new file mode 100644 index 000000000..732dfc83e --- /dev/null +++ b/installation/patch/disable_old_output @@ -0,0 +1,178 @@ +From 6dbd904a4cfc28add3c39bb2a4ec9e2dbb2442b6 Mon Sep 17 00:00:00 2001 +From: Martin Diehl +Date: Thu, 18 Apr 2019 18:25:32 +0200 +Subject: [PATCH] to create patch + +--- + src/DAMASK_grid.f90 | 81 +----------------------------------------- + src/homogenization.f90 | 2 ++ + 2 files changed, 3 insertions(+), 80 deletions(-) + +diff --git a/src/DAMASK_grid.f90 b/src/DAMASK_grid.f90 +index f2f52bb2..a7543f4d 100644 +--- a/src/DAMASK_grid.f90 ++++ b/src/DAMASK_grid.f90 +@@ -18,7 +18,6 @@ program DAMASK_spectral + use DAMASK_interface, only: & + DAMASK_interface_init, & + loadCaseFile, & +- geometryFile, & + getSolverJobName, & + interface_restartInc + use IO, only: & +@@ -49,14 +48,9 @@ program DAMASK_spectral + restartInc + use numerics, only: & + worldrank, & +- worldsize, & + stagItMax, & + maxCutBack, & + continueCalculation +- use homogenization, only: & +- materialpoint_sizeResults, & +- materialpoint_results, & +- materialpoint_postResults + use material, only: & + thermal_type, & + damage_type, & +@@ -131,12 +125,6 @@ program DAMASK_spectral + type(tLoadCase), allocatable, dimension(:) :: loadCases !< array of all load cases + type(tLoadCase) :: newLoadCase + type(tSolutionState), allocatable, dimension(:) :: solres +- integer(MPI_OFFSET_KIND) :: fileOffset +- integer(MPI_OFFSET_KIND), dimension(:), allocatable :: outputSize +- integer(pInt), parameter :: maxByteOut = 2147483647-4096 !< limit of one file output write https://trac.mpich.org/projects/mpich/ticket/1742 +- integer(pInt), parameter :: maxRealOut = maxByteOut/pReal +- integer(pLongInt), dimension(2) :: outputIndex +- PetscErrorCode :: ierr + procedure(grid_mech_spectral_basic_init), pointer :: & + mech_init + procedure(grid_mech_spectral_basic_forward), pointer :: & +@@ -384,22 +372,6 @@ program DAMASK_spectral + ! write header of output file + if (worldrank == 0) then + writeHeader: if (interface_restartInc < 1_pInt) then +- open(newunit=fileUnit,file=trim(getSolverJobName())//& +- '.spectralOut',form='UNFORMATTED',status='REPLACE') +- write(fileUnit) 'load:', trim(loadCaseFile) ! ... and write header +- write(fileUnit) 'workingdir:', 'n/a' +- write(fileUnit) 'geometry:', trim(geometryFile) +- write(fileUnit) 'grid:', grid +- write(fileUnit) 'size:', geomSize +- write(fileUnit) 'materialpoint_sizeResults:', materialpoint_sizeResults +- write(fileUnit) 'loadcases:', size(loadCases) +- write(fileUnit) 'frequencies:', loadCases%outputfrequency ! one entry per LoadCase +- write(fileUnit) 'times:', loadCases%time ! one entry per LoadCase +- write(fileUnit) 'logscales:', loadCases%logscale +- write(fileUnit) 'increments:', loadCases%incs ! one entry per LoadCase +- write(fileUnit) 'startingIncrement:', restartInc ! start with writing out the previous inc +- write(fileUnit) 'eoh' +- close(fileUnit) ! end of header + open(newunit=statUnit,file=trim(getSolverJobName())//& + '.sta',form='FORMATTED',status='REPLACE') + write(statUnit,'(a)') 'Increment Time CutbackLevel Converged IterationsNeeded' ! statistics file +@@ -412,39 +384,6 @@ program DAMASK_spectral + endif writeHeader + endif + +-!-------------------------------------------------------------------------------------------------- +-! prepare MPI parallel out (including opening of file) +- allocate(outputSize(worldsize), source = 0_MPI_OFFSET_KIND) +- outputSize(worldrank+1) = size(materialpoint_results,kind=MPI_OFFSET_KIND)*int(pReal,MPI_OFFSET_KIND) +- call MPI_allreduce(MPI_IN_PLACE,outputSize,worldsize,MPI_LONG,MPI_SUM,PETSC_COMM_WORLD,ierr) ! get total output size over each process +- if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_allreduce') +- call MPI_file_open(PETSC_COMM_WORLD, trim(getSolverJobName())//'.spectralOut', & +- MPI_MODE_WRONLY + MPI_MODE_APPEND, & +- MPI_INFO_NULL, & +- fileUnit, & +- ierr) +- if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_open') +- call MPI_file_get_position(fileUnit,fileOffset,ierr) ! get offset from header +- if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_get_position') +- fileOffset = fileOffset + sum(outputSize(1:worldrank)) ! offset of my process in file (header + processes before me) +- call MPI_file_seek (fileUnit,fileOffset,MPI_SEEK_SET,ierr) +- if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_seek') +- +- writeUndeformed: if (interface_restartInc < 1_pInt) then +- write(6,'(1/,a)') ' ... writing initial configuration to file ........................' +- call CPFEM_results(0_pInt,0.0_pReal) +- do i = 1, size(materialpoint_results,3)/(maxByteOut/(materialpoint_sizeResults*pReal))+1 ! slice the output of my process in chunks not exceeding the limit for one output +- outputIndex = int([(i-1_pInt)*((maxRealOut)/materialpoint_sizeResults)+1_pInt, & ! QUESTION: why not starting i at 0 instead of murky 1? +- min(i*((maxRealOut)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt) +- call MPI_file_write(fileUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)), & +- [(outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)]), & +- int((outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)), & +- MPI_DOUBLE, MPI_STATUS_IGNORE, ierr) +- if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_write') +- enddo +- fileOffset = fileOffset + sum(outputSize) ! forward to current file position +- endif writeUndeformed +- + + loadCaseLooping: do currentLoadCase = 1_pInt, size(loadCases) + time0 = time ! load case start time +@@ -574,7 +513,6 @@ program DAMASK_spectral + write(6,'(/,a)') ' cutting back ' + else ! no more options to continue + call IO_warning(850_pInt) +- call MPI_file_close(fileUnit,ierr) + close(statUnit) + call quit(-1_pInt*(lastRestartWritten+1_pInt)) ! quit and provide information about last restart inc written + endif +@@ -593,24 +531,8 @@ program DAMASK_spectral + ' increment ', totalIncsCounter, ' NOT converged' + endif; flush(6) + +- if (mod(inc,loadCases(currentLoadCase)%outputFrequency) == 0_pInt) then ! at output frequency +- write(6,'(1/,a)') ' ... writing results to file ......................................' +- flush(6) +- call materialpoint_postResults() +- call MPI_file_seek (fileUnit,fileOffset,MPI_SEEK_SET,ierr) +- if (ierr /= 0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_seek') +- do i=1, size(materialpoint_results,3)/(maxByteOut/(materialpoint_sizeResults*pReal))+1 ! slice the output of my process in chunks not exceeding the limit for one output +- outputIndex=int([(i-1_pInt)*((maxRealOut)/materialpoint_sizeResults)+1_pInt, & +- min(i*((maxRealOut)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt) +- call MPI_file_write(fileUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)),& +- [(outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)]), & +- int((outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)),& +- MPI_DOUBLE, MPI_STATUS_IGNORE, ierr) +- if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_write') +- enddo +- fileOffset = fileOffset + sum(outputSize) ! forward to current file position ++ if (mod(inc,loadCases(currentLoadCase)%outputFrequency) == 0_pInt) & ! at output frequency + call CPFEM_results(totalIncsCounter,time) +- endif + if ( loadCases(currentLoadCase)%restartFrequency > 0_pInt & ! writing of restart info requested ... + .and. mod(inc,loadCases(currentLoadCase)%restartFrequency) == 0_pInt) then ! ... and at frequency of writing restart information + restartWrite = .true. ! set restart parameter for FEsolving +@@ -633,7 +555,6 @@ program DAMASK_spectral + real(convergedCounter, pReal)/& + real(notConvergedCounter + convergedCounter,pReal)*100.0_pReal, ' %) increments converged!' + flush(6) +- call MPI_file_close(fileUnit,ierr) + close(statUnit) + + if (notConvergedCounter > 0_pInt) call quit(2_pInt) ! error if some are not converged +diff --git a/src/homogenization.f90 b/src/homogenization.f90 +index 06da6ab2..0743d545 100644 +--- a/src/homogenization.f90 ++++ b/src/homogenization.f90 +@@ -269,6 +269,7 @@ subroutine homogenization_init + + homogenization_maxNgrains * (1 + crystallite_maxSizePostResults & ! crystallite size & crystallite results + + 1 + constitutive_plasticity_maxSizePostResults & ! constitutive size & constitutive results + + constitutive_source_maxSizePostResults) ++ materialpoint_sizeResults = 0 + allocate(materialpoint_results(materialpoint_sizeResults,theMesh%elem%nIPs,theMesh%nElems)) + + write(6,'(/,a)') ' <<<+- homogenization init -+>>>' +@@ -682,6 +683,7 @@ subroutine materialpoint_postResults + i, & !< integration point number + e !< element number + ++ return + !$OMP PARALLEL DO PRIVATE(myNgrains,myCrystallite,thePos,theSize) + elementLooping: do e = FEsolving_execElem(1),FEsolving_execElem(2) + myNgrains = homogenization_Ngrains(mesh_element(3,e)) +-- +2.21.0 + From 55d0c0dad1f80e6ba8c46e65beaf615e9fb5b4fe Mon Sep 17 00:00:00 2001 From: Test User Date: Sat, 27 Apr 2019 20:09:03 +0200 Subject: [PATCH 13/13] [skip ci] updated version information after successful test of v2.0.3-138-g7b04b761 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index a55a6e6d5..4d6205d89 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.3-130-gda034f97 +v2.0.3-138-g7b04b761