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documenting for doxygen

This commit is contained in:
Martin Diehl 2020-03-15 12:46:10 +01:00
parent 7062305ee8
commit ae49e6710d
3 changed files with 157 additions and 156 deletions
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309
src/HDF5_utilities.f90
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@ -30,7 +30,7 @@ module HDF5_utilities
module procedure HDF5_read_real5
module procedure HDF5_read_real6
module procedure HDF5_read_real7
module procedure HDF5_read_int1
module procedure HDF5_read_int2
module procedure HDF5_read_int3
@ -38,7 +38,7 @@ module HDF5_utilities
module procedure HDF5_read_int5
module procedure HDF5_read_int6
module procedure HDF5_read_int7
end interface HDF5_read
!--------------------------------------------------------------------------------------------------
@ -53,7 +53,7 @@ module HDF5_utilities
module procedure HDF5_write_real5
module procedure HDF5_write_real6
module procedure HDF5_write_real7
module procedure HDF5_write_int1
module procedure HDF5_write_int2
module procedure HDF5_write_int3
@ -61,11 +61,11 @@ module HDF5_utilities
module procedure HDF5_write_int5
module procedure HDF5_write_int6
module procedure HDF5_write_int7
module procedure HDF5_write_rotation
end interface HDF5_write
!--------------------------------------------------------------------------------------------------
!> @brief attached attributes of type char, integer or real to a file/dataset/group
!--------------------------------------------------------------------------------------------------
@ -76,7 +76,7 @@ module HDF5_utilities
module procedure HDF5_addAttribute_int_array
module procedure HDF5_addAttribute_real_array
end interface HDF5_addAttribute
contains
@ -116,17 +116,17 @@ integer(HID_T) function HDF5_openFile(fileName,mode,parallel)
character(len=*), intent(in) :: fileName
character, intent(in), optional :: mode
logical, intent(in), optional :: parallel
character :: m
integer(HID_T) :: plist_id
integer :: hdferr
if (present(mode)) then
m = mode
else
m = 'r'
endif
call h5pcreate_f(H5P_FILE_ACCESS_F, plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_openFile: h5pcreate_f')
@ -149,7 +149,7 @@ integer(HID_T) function HDF5_openFile(fileName,mode,parallel)
else
call IO_error(1,ext_msg='HDF5_openFile: h5fopen_f unknown access mode: '//trim(m))
endif
call h5pclose_f(plist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_openFile: h5pclose_f')
@ -162,9 +162,9 @@ end function HDF5_openFile
subroutine HDF5_closeFile(fileHandle)
integer(HID_T), intent(in) :: fileHandle
integer :: hdferr
call h5fclose_f(fileHandle,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_closeFile: h5fclose_f')
@ -178,7 +178,7 @@ integer(HID_T) function HDF5_addGroup(fileHandle,groupName)
integer(HID_T), intent(in) :: fileHandle
character(len=*), intent(in) :: groupName
integer :: hdferr
integer(HID_T) :: aplist_id
@ -193,7 +193,7 @@ integer(HID_T) function HDF5_addGroup(fileHandle,groupName)
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_addGroup: h5pset_all_coll_metadata_ops_f ('//trim(groupName)//')')
#endif
!-------------------------------------------------------------------------------------------------
! Create group
call h5gcreate_f(fileHandle, trim(groupName), HDF5_addGroup, hdferr, OBJECT_NAMELEN_DEFAULT_F,gapl_id = aplist_id)
@ -211,13 +211,13 @@ integer(HID_T) function HDF5_openGroup(fileHandle,groupName)
integer(HID_T), intent(in) :: fileHandle
character(len=*), intent(in) :: groupName
integer :: hdferr
integer(HID_T) :: aplist_id
logical :: is_collective
!-------------------------------------------------------------------------------------------------
! creating a property list for data access properties
call h5pcreate_f(H5P_GROUP_ACCESS_F, aplist_id, hdferr)
@ -229,7 +229,7 @@ integer(HID_T) function HDF5_openGroup(fileHandle,groupName)
call h5pget_all_coll_metadata_ops_f(aplist_id, is_collective, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_openGroup: h5pset_all_coll_metadata_ops_f ('//trim(groupName)//')')
#endif
!-------------------------------------------------------------------------------------------------
! opening the group
call h5gopen_f(fileHandle, trim(groupName), HDF5_openGroup, hdferr, gapl_id = aplist_id)
@ -247,7 +247,7 @@ subroutine HDF5_closeGroup(group_id)
integer(HID_T), intent(in) :: group_id
integer :: hdferr
call h5gclose_f(group_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_closeGroup: h5gclose_f (el is ID)', el = int(group_id))
@ -261,19 +261,19 @@ logical function HDF5_objectExists(loc_id,path)
integer(HID_T), intent(in) :: loc_id
character(len=*), intent(in), optional :: path
integer :: hdferr
character(len=pStringLen) :: p
if (present(path)) then
p = trim(path)
else
p = '.'
endif
call h5lexists_f(loc_id, p, HDF5_objectExists, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_objectExists: h5oexists_by_name_f')
if(HDF5_objectExists) then
call h5oexists_by_name_f(loc_id, p, HDF5_objectExists, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_objectExists: h5oexists_by_name_f')
@ -290,18 +290,18 @@ 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=pStringLen) :: p
if (present(path)) then
p = trim(path)
else
p = '.'
endif
call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_str: h5screate_f')
call h5tcopy_f(H5T_NATIVE_CHARACTER, type_id, hdferr)
@ -337,18 +337,18 @@ subroutine HDF5_addAttribute_int(loc_id,attrLabel,attrValue,path)
character(len=*), intent(in) :: attrLabel
integer, intent(in) :: attrValue
character(len=*), intent(in), optional :: path
integer :: hdferr
integer(HID_T) :: attr_id, space_id
logical :: attrExists
character(len=pStringLen) :: p
if (present(path)) then
p = trim(path)
else
p = '.'
endif
call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_int: h5screate_f')
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
@ -378,18 +378,18 @@ subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path)
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=pStringLen) :: p
if (present(path)) then
p = trim(path)
else
p = '.'
endif
call h5screate_f(H5S_SCALAR_F,space_id,hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_addAttribute_real: h5screate_f')
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
@ -419,21 +419,21 @@ subroutine HDF5_addAttribute_int_array(loc_id,attrLabel,attrValue,path)
character(len=*), intent(in) :: attrLabel
integer, 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=pStringLen) :: 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,ext_msg='HDF5_addAttribute_int_array: h5screate_f')
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
@ -463,21 +463,21 @@ subroutine HDF5_addAttribute_real_array(loc_id,attrLabel,attrValue,path)
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=pStringLen) :: 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,ext_msg='HDF5_addAttribute_int_array: h5screate_f')
call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr)
@ -507,7 +507,7 @@ subroutine HDF5_setLink(loc_id,target_name,link_name)
integer(HID_T), intent(in) :: loc_id
integer :: hdferr
logical :: linkExists
call h5lexists_f(loc_id, link_name,linkExists, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg = 'HDF5_setLink: h5lexists_soft_f ('//trim(link_name)//')')
if (linkExists) then
@ -525,11 +525,11 @@ end subroutine HDF5_setLink
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real1(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:) :: dataset
real(pReal), intent(out), dimension(:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: & ! ToDo: Fortran 2018 size(shape(A)) = rank(A)
myStart, &
@ -551,13 +551,13 @@ subroutine HDF5_read_real1(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real1: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real1
!--------------------------------------------------------------------------------------------------
@ -565,11 +565,11 @@ end subroutine HDF5_read_real1
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real2(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:) :: dataset
real(pReal), intent(out), dimension(:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
@ -591,11 +591,11 @@ subroutine HDF5_read_real2(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real2: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real2
@ -605,11 +605,11 @@ end subroutine HDF5_read_real2
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real3(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:,:) :: dataset
real(pReal), intent(out), dimension(:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
@ -631,7 +631,7 @@ subroutine HDF5_read_real3(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real3: h5dread_f')
@ -645,10 +645,10 @@ end subroutine HDF5_read_real3
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real4(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:,:,:) :: dataset
real(pReal), intent(out), dimension(:,:,:,:) :: dataset !< read data
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
@ -671,11 +671,11 @@ subroutine HDF5_read_real4(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real4: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real4
@ -685,11 +685,11 @@ end subroutine HDF5_read_real4
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real5(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:,:,:,:) :: dataset
real(pReal), intent(out), dimension(:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
@ -711,11 +711,11 @@ subroutine HDF5_read_real5(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real5: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real5
@ -725,11 +725,11 @@ end subroutine HDF5_read_real5
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real6(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:,:,:,:,:) :: dataset
real(pReal), intent(out), dimension(:,:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
@ -765,10 +765,10 @@ end subroutine HDF5_read_real6
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_real7(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset
real(pReal), intent(out), dimension(:,:,:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
@ -791,11 +791,11 @@ subroutine HDF5_read_real7(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_DOUBLE,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_real7: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_real7
@ -806,11 +806,12 @@ end subroutine HDF5_read_real7
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int1(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:) :: dataset
integer, intent(out), dimension(:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
@ -838,7 +839,7 @@ subroutine HDF5_read_int1(loc_id,dataset,datasetName,parallel)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int1: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int1
!--------------------------------------------------------------------------------------------------
@ -846,10 +847,10 @@ end subroutine HDF5_read_int1
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int2(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:) :: dataset
integer, intent(out), dimension(:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
@ -872,11 +873,11 @@ subroutine HDF5_read_int2(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int2: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int2
@ -886,10 +887,10 @@ end subroutine HDF5_read_int2
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int3(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:,:) :: dataset
integer, intent(out), dimension(:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
@ -912,11 +913,11 @@ subroutine HDF5_read_int3(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int3: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int3
@ -926,11 +927,11 @@ end subroutine HDF5_read_int3
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int4(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:,:,:) :: dataset
integer, intent(out), dimension(:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
@ -952,11 +953,11 @@ subroutine HDF5_read_int4(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int4: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int4
@ -966,11 +967,11 @@ end subroutine HDF5_read_int4
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int5(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:,:,:,:) :: dataset
integer, intent(out), dimension(:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
@ -996,7 +997,7 @@ subroutine HDF5_read_int5(loc_id,dataset,datasetName,parallel)
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int5: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int5
@ -1006,10 +1007,10 @@ end subroutine HDF5_read_int5
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int6(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:,:,:,:,:) :: dataset
integer, intent(out), dimension(:,:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
@ -1032,11 +1033,11 @@ subroutine HDF5_read_int6(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int6: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int6
@ -1046,11 +1047,11 @@ end subroutine HDF5_read_int6
!--------------------------------------------------------------------------------------------------
subroutine HDF5_read_int7(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:,:,:,:,:,:) :: dataset
integer, intent(out), dimension(:,:,:,:,:,:,:) :: dataset !< data read from file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer(HSIZE_T), dimension(size(shape(dataset))) :: &
myStart, &
@ -1072,11 +1073,11 @@ subroutine HDF5_read_int7(loc_id,dataset,datasetName,parallel)
call initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id, &
myStart, totalShape, loc_id,myShape,datasetName,.false.)
endif
call h5dread_f(dset_id, H5T_NATIVE_INTEGER,dataset,totalShape, hdferr,&
file_space_id = filespace_id, xfer_prp = plist_id, mem_space_id = memspace_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_read_int7: h5dread_f')
call finalize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_id)
end subroutine HDF5_read_int7
@ -1087,10 +1088,10 @@ end subroutine HDF5_read_int7
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real1(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:) :: dataset
real(pReal), intent(inout), dimension(:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1128,10 +1129,10 @@ end subroutine HDF5_write_real1
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real2(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:) :: dataset
real(pReal), intent(inout), dimension(:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1169,10 +1170,10 @@ end subroutine HDF5_write_real2
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real3(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:,:) :: dataset
real(pReal), intent(inout), dimension(:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1210,10 +1211,10 @@ end subroutine HDF5_write_real3
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real4(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:,:,:) :: dataset
real(pReal), intent(inout), dimension(:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1227,7 +1228,7 @@ subroutine HDF5_write_real4(loc_id,dataset,datasetName,parallel)
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
@ -1235,13 +1236,13 @@ subroutine HDF5_write_real4(loc_id,dataset,datasetName,parallel)
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real4: h5dwrite_f')
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real4
@ -1252,10 +1253,10 @@ end subroutine HDF5_write_real4
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real5(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:,:,:,:) :: dataset
real(pReal), intent(inout), dimension(:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1269,7 +1270,7 @@ subroutine HDF5_write_real5(loc_id,dataset,datasetName,parallel)
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
if (any(myShape(1:size(myShape)-1) == 0)) return !< empty dataset (last dimension can be empty)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,parallel)
@ -1277,13 +1278,13 @@ subroutine HDF5_write_real5(loc_id,dataset,datasetName,parallel)
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,H5T_NATIVE_DOUBLE,.false.)
endif
if (product(totalShape) /= 0) then
call h5dwrite_f(dset_id, H5T_NATIVE_DOUBLE,dataset,int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real5: h5dwrite_f')
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real5
@ -1293,10 +1294,10 @@ end subroutine HDF5_write_real5
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real6(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:,:,:,:,:) :: dataset
real(pReal), intent(inout), dimension(:,:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1324,7 +1325,7 @@ subroutine HDF5_write_real6(loc_id,dataset,datasetName,parallel)
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real6: h5dwrite_f')
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real6
@ -1334,10 +1335,10 @@ end subroutine HDF5_write_real6
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_real7(loc_id,dataset,datasetName,parallel)
real(pReal), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset
real(pReal), intent(inout), dimension(:,:,:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1365,7 +1366,7 @@ subroutine HDF5_write_real7(loc_id,dataset,datasetName,parallel)
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_real7: h5dwrite_f')
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_real7
@ -1376,10 +1377,10 @@ end subroutine HDF5_write_real7
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int1(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:) :: dataset
integer, intent(inout), dimension(:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1407,7 +1408,7 @@ subroutine HDF5_write_int1(loc_id,dataset,datasetName,parallel)
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_int1: h5dwrite_f')
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_int1
@ -1417,10 +1418,10 @@ end subroutine HDF5_write_int1
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int2(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:) :: dataset
integer, intent(inout), dimension(:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1458,10 +1459,10 @@ end subroutine HDF5_write_int2
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int3(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:,:) :: dataset
integer, intent(inout), dimension(:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1489,7 +1490,7 @@ subroutine HDF5_write_int3(loc_id,dataset,datasetName,parallel)
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
if (hdferr < 0) call IO_error(1,ext_msg='HDF5_write_int3: h5dwrite_f')
endif
call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
end subroutine HDF5_write_int3
@ -1499,10 +1500,10 @@ end subroutine HDF5_write_int3
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int4(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:,:,:) :: dataset
integer, intent(inout), dimension(:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1540,10 +1541,10 @@ end subroutine HDF5_write_int4
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int5(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:,:,:,:) :: dataset
integer, intent(inout), dimension(:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1581,10 +1582,10 @@ end subroutine HDF5_write_int5
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int6(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:,:,:,:,:) :: dataset
integer, intent(inout), dimension(:,:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1622,10 +1623,10 @@ end subroutine HDF5_write_int6
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_int7(loc_id,dataset,datasetName,parallel)
integer, intent(inout), dimension(:,:,:,:,:,:,:) :: dataset
integer, intent(inout), dimension(:,:,:,:,:,:,:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
logical, intent(in), optional :: parallel !< dataset is distributed over multiple processes
integer :: hdferr
@ -1666,7 +1667,7 @@ end subroutine HDF5_write_int7
!--------------------------------------------------------------------------------------------------
subroutine HDF5_write_rotation(loc_id,dataset,datasetName,parallel)
type(rotation), intent(in), dimension(:) :: dataset
type(rotation), intent(in), dimension(:) :: dataset !< data written to file
integer(HID_T), intent(in) :: loc_id !< file or group handle
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in), optional :: parallel
@ -1688,17 +1689,17 @@ subroutine HDF5_write_rotation(loc_id,dataset,datasetName,parallel)
!---------------------------------------------------------------------------------------------------
! determine shape of dataset
myShape = int(shape(dataset),HSIZE_T)
!---------------------------------------------------------------------------------------------------
! compound type: name of each quaternion component
call h5tget_size_f(H5T_NATIVE_DOUBLE, type_size_real, hdferr)
call h5tcreate_f(H5T_COMPOUND_F, type_size_real*4_SIZE_T, dtype_id, hdferr)
call h5tinsert_f(dtype_id, "w", type_size_real*0_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
call h5tinsert_f(dtype_id, "x", type_size_real*1_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
call h5tinsert_f(dtype_id, "y", type_size_real*2_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
call h5tinsert_f(dtype_id, "z", type_size_real*3_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
if (present(parallel)) then
call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
myStart, totalShape, loc_id,myShape,datasetName,dtype_id,parallel)
@ -1708,7 +1709,7 @@ subroutine HDF5_write_rotation(loc_id,dataset,datasetName,parallel)
endif
call h5pset_preserve_f(plist_id, .TRUE., hdferr)
if (product(totalShape) /= 0) then
call h5tcreate_f(H5T_COMPOUND_F, type_size_real, x_id, hdferr)
call h5tinsert_f(x_id, "x", 0_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
@ -1718,7 +1719,7 @@ subroutine HDF5_write_rotation(loc_id,dataset,datasetName,parallel)
call h5tinsert_f(y_id, "y", 0_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
call h5tcreate_f(H5T_COMPOUND_F, type_size_real, z_id, hdferr)
call h5tinsert_f(z_id, "z", 0_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
call h5dwrite_f(dset_id, w_id,dataset_asArray(1,:),int(totalShape,HSIZE_T), hdferr,&
file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
call h5dwrite_f(dset_id, x_id,dataset_asArray(2,:),int(totalShape,HSIZE_T), hdferr,&
@ -1746,17 +1747,17 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
character(len=*), intent(in) :: datasetName !< name of the dataset in the file
logical, intent(in) :: parallel
integer(HSIZE_T), intent(in), dimension(:) :: &
localShape
localShape
integer(HSIZE_T), intent(out), dimension(size(localShape,1)):: &
myStart, &
globalShape !< shape of the dataset (all processes)
integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id
integer, dimension(worldsize) :: &
readSize !< contribution of all processes
integer :: ierr
integer :: hdferr
!-------------------------------------------------------------------------------------------------
! creating a property list for transfer properties (is collective for MPI)
call h5pcreate_f(H5P_DATASET_XFER_F, plist_id, hdferr)
@ -1784,7 +1785,7 @@ subroutine initialize_read(dset_id, filespace_id, memspace_id, plist_id, aplist_
!--------------------------------------------------------------------------------------------------
! creating a property list for IO and set it to collective
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
call h5pcreate_f(H5P_DATASET_ACCESS_F, aplist_id, hdferr)
if (hdferr < 0) call IO_error(1,ext_msg='initialize_read: h5pcreate_f')
#ifdef PETSc
call h5pset_all_coll_metadata_ops_f(aplist_id, .true., hdferr)
@ -1840,12 +1841,12 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
logical, intent(in) :: parallel
integer(HID_T), intent(in) :: datatype
integer(HSIZE_T), intent(in), dimension(:) :: &
myShape
myShape
integer(HSIZE_T), intent(out), dimension(size(myShape,1)):: &
myStart, &
totalShape !< shape of the dataset (all processes)
integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id
integer, dimension(worldsize) :: &
writeSize !< contribution of all processes
integer :: ierr

2
src/config.f90
View File

@ -132,7 +132,7 @@ contains
!--------------------------------------------------------------------------------------------------
recursive function read_materialConfig(fileName,cnt) result(fileContent)
character(len=*), intent(in) :: fileName
character(len=*), intent(in) :: fileName !< name of the material configuration file
integer, intent(in), optional :: cnt !< recursion counter
character(len=pStringLen), dimension(:), allocatable :: fileContent !< file content, separated per lines
character(len=pStringLen), dimension(:), allocatable :: includedContent

2
src/crystallite.f90
View File

@ -1522,7 +1522,7 @@ end subroutine integrateStateRKCK45
!--------------------------------------------------------------------------------------------------
!> @brief sets convergence flag for nonlocal calculations
!> @detail one non-converged nonlocal sets all other nonlocals to non-converged to trigger cut back
!> @details one non-converged nonlocal sets all other nonlocals to non-converged to trigger cut back
!--------------------------------------------------------------------------------------------------
subroutine nonlocalConvergenceCheck