[skip ci] [skip sc] generic interfaces for HDF5 operations

most existing HDF5 functions are only designed for writing output files
and more general functionality is needed for storing the restart data

src/CPFEM2.f90

@@ -126,7 +126,7 @@ subroutine CPFEM_init
  use HDF5_utilities, only: &
    HDF5_openFile, &
    HDF5_openGroup2, &
-   HDF5_readDataSet
+   HDF5_read
  use DAMASK_interface, only: &
    getSolverJobName
 
@@ -135,10 +135,6 @@ subroutine CPFEM_init
  character(len=1024) :: rankStr
  integer(HID_T) :: fileReadID, groupPlasticID
  integer        :: hdferr
- real(pReal), dimension(:,:,:), allocatable :: dummy3
- real(pReal), dimension(:,:,:,:,:), allocatable :: dummy5
- !dummy = material_phase
- !write(6,*) shape(dummy), flush(6)
 
  mainProcess: if (worldrank == 0) then 
    write(6,'(/,a)')   ' <<<+-  CPFEM init  -+>>>'
@@ -146,11 +142,10 @@ subroutine CPFEM_init
 #include "compilation_info.f90"
    flush(6)
  endif mainProcess
- !restartRead = .true.
+
  ! *** restore the last converged values of each essential variable from the binary file
  if (restartRead) then
    if (iand(debug_level(debug_CPFEM), debug_levelExtensive) /= 0_pInt) then
-     !write(6,'(a)') '<< CPFEM >> restored state variables of last converged step from binary files'
      write(6,'(a)') '<< CPFEM >> restored state variables of last converged step from hdf5 file'
      flush(6)
    endif
@@ -158,22 +153,12 @@ subroutine CPFEM_init
    write(rankStr,'(a1,i0)')'_',worldrank
 
    fileReadID = HDF5_openFile(trim(getSolverJobName())//trim(rankStr)//'.hdf5')
-   
+  
-   allocate(dummy3(size(material_phase,1),size(material_phase,2),size(material_phase,3)))
+   call HDF5_read(crystallite_F0,fileReadID,'convergedF')
-   call HDF5_readDataSet(fileReadID,'recordedPhase',dummy3,int(shape(material_phase),pLongInt))
+   call HDF5_read(crystallite_F0,fileReadID,'convergedFp')
-   material_phase = dummy3
+   call HDF5_read(crystallite_F0,fileReadID,'convergedFi')
-   deallocate(dummy3)
+   call HDF5_read(crystallite_F0,fileReadID,'convergedLp')
-   
+   call HDF5_read(crystallite_F0,fileReadID,'convergedLi')
-   allocate(dummy5(size(crystallite_F0,1),size(crystallite_F0,2),size(crystallite_F0,3), &
-            size(crystallite_F0,4),size(crystallite_F0,5)))
-   call HDF5_readDataSet(fileReadID,'convergedF',dummy5,int(shape(crystallite_F0),pLongInt))
-   crystallite_F0 = dummy5
-   deallocate(dummy5)
-   ! call HDF5_readDataSet(fileReadID,'convergedF')
-   ! call HDF5_readDataSet(fileReadID,'convergedFp')
-   ! call HDF5_readDataSet(fileReadID,'convergedFi')
-   ! call HDF5_readDataSet(fileReadID,'convergedLp')
-   ! call HDF5_readDataSet(fileReadID,'convergedLi')
    ! call HDF5_readDataSet(fileReadID,'convergeddPdF')
    ! call HDF5_readDataSet(fileReadID,'convergedTstar')
    
@@ -285,8 +270,8 @@ subroutine CPFEM_age()
    HDF5_closeFile, &
    HDF5_closeGroup, &
    HDF5_addGroup2, &
-   HDF5_writeScalarDataset3, &
+   HDF5_writeScalarDataset3
-   HDF5_addScalarDataset2
+   !HDF5_addScalarDataset2
  use hdf5
  use DAMASK_interface, only: &
    getSolverJobName

src/HDF5_utilities.f90

@@ -10,6 +10,11 @@ module HDF5_Utilities
  integer(HID_T), private :: resultsFile, currentIncID, plist_id
  integer(pInt),  private :: currentInc
 
+ interface HDF5_read
+   module procedure HDF5_read_double_1
+   module procedure HDF5_read_double_5
+ end interface HDF5_read
+
  public :: &
    HDF5_Utilities_init, &
    HDF5_mappingPhase, &
@@ -31,9 +36,9 @@ module HDF5_Utilities
    HDF5_removeLink, &
    HDF5_createFile, &
    HDF5_closeFile, &
-   HDF5_addGroup2, HDF5_addScalarDataset2, HDF5_writeScalarDataset3, &
+   HDF5_writeScalarDataset3, &
-   HDF5_openFile, &
+   HDF5_addGroup2, HDF5_read, &
-   HDF5_readDataSet
+   HDF5_openFile
 contains
 
 subroutine HDF5_Utilities_init
@@ -1334,7 +1339,7 @@ subroutine HDF5_writeScalarDataset(group,dataset,label,SIunit,dataspace_size,mpi
  integer(HID_T) :: dset_id, space_id, memspace, plist_id
  
  integer(HSIZE_T),  dimension(1) :: counter
- integer(HSSIZE_T), dimension(1) :: fileOffset
+ integer(HSIZE_T), dimension(1) :: fileOffset
  
  nNodes = size(dataset)
  if (nNodes < 1) return
@@ -1452,24 +1457,62 @@ end subroutine HDF5_writeScalarDataset3
  
 ! end subroutine HDF5_writeScalarDatasetLoop
 
+subroutine HDF5_read_double_1(D,ID,label)
+ implicit none
+ real(pReal), dimension(:), intent(out) :: D
+ integer(HID_T),            intent(in)  :: ID
+ character(len=*), intent(in) :: label
+ call  HDF5_read_double_generic(D,ID,label,shape(D))
+end subroutine HDF5_read_double_1
+
+subroutine HDF5_read_double_5(D,ID,label)
+ implicit none
+ real(pReal), dimension(:,:,:,:,:), intent(out) :: D
+ integer(HID_T),                    intent(in)  :: ID
+ character(len=*), intent(in) :: label
+ call  HDF5_read_double_generic(D,ID,label,shape(D))
+end subroutine HDF5_read_double_5
+
+subroutine HDF5_read_double_generic(D,ID,label,myShape)
+ use hdf5
+ implicit none
+ real(pReal), dimension(*), intent(out) :: D
+ integer, dimension(:),intent(in) :: myShape
+ !  real, dimension(:), allocatable :: D1
+ !   real, dimension(:,:), allocatable :: D2
+ !   real, dimension(:,:,:), allocatable :: D3
+ integer(HID_T),                    intent(in) :: ID
+ character(len=*),                  intent(in) :: label
+ 
+ integer(HID_T) :: dset_id
+ integer :: hdferr
+
+ call h5dopen_f(ID,label,dset_id,hdferr)
+ call h5dread_f(dset_id,H5T_NATIVE_DOUBLE,D,int(myshape,HID_T),hdferr)
+ 
+end subroutine
+
 !--------------------------------------------------------------------------------------------------
 !> @brief read datasets from a hdf5 file
 !--------------------------------------------------------------------------------------------------
-subroutine HDF5_readDataSet(FileReadID,NameDataSet,DataSet,myshape)
+!
- use hdf5
+!subroutine HDF5_read_double_2(DataSet,FileReadID,NameDataSet) !,myshape)
- 
+! use hdf5
- implicit none
+! 
- integer(HID_T), intent(in) :: FileReadID
+! implicit none
- character(len=*), intent(in) :: NameDataSet
+! integer(HID_T), intent(in) :: FileReadID
- real(pReal), intent(inout), dimension(*) :: DataSet
+! character(len=*), intent(in) :: NameDataSet
- integer(HSIZE_T), intent(in), dimension(:) :: myshape
+! real(pReal), intent(out), dimension(:,:,:,:,:) :: DataSet
- integer(HID_T) :: dset_id
+! !integer(HSIZE_T), intent(in), dimension(:) :: myshape
- integer :: hdferr
+! integer(HSIZE_T), dimension(:),allocatable :: myshape
- 
+! integer(HID_T) :: dset_id
- call h5dopen_f(FileReadID,NameDataSet,dset_id,hdferr)
+! integer :: hdferr
- call h5dread_f(dset_id,H5T_NATIVE_DOUBLE,DataSet,myshape,hdferr)
+!
- 
+! myShape = int(shape(DataSet),HSIZE_T)
-end subroutine HDF5_readDataSet
+! call h5dopen_f(FileReadID,NameDataSet,dset_id,hdferr)
+! call h5dread_f(dset_id,H5T_NATIVE_DOUBLE,DataSet,myshape,hdferr)
+! 
+!end subroutine
 
 !--------------------------------------------------------------------------------------------------
 !> @brief creates a new scalar dataset in the given group location