From ae49e6710ddc834d9c82a81d743e82133a99931d Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Sun, 15 Mar 2020 12:46:10 +0100 Subject: [PATCH] documenting for doxygen --- src/HDF5_utilities.f90 | 309 +++++++++++++++++++++-------------------- src/config.f90 | 2 +- src/crystallite.f90 | 2 +- 3 files changed, 157 insertions(+), 156 deletions(-) diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index aa75d9c87..66705cc3f 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -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 diff --git a/src/config.f90 b/src/config.f90 index 58b0d69a1..187c4880f 100644 --- a/src/config.f90 +++ b/src/config.f90 @@ -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 diff --git a/src/crystallite.f90 b/src/crystallite.f90 index 41a8c3891..5852f6f38 100644 --- a/src/crystallite.f90 +++ b/src/crystallite.f90 @@ -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