diff --git a/src/HDF5_utilities.f90 b/src/HDF5_utilities.f90 index 638b74c0e..c981fad53 100644 --- a/src/HDF5_utilities.f90 +++ b/src/HDF5_utilities.f90 @@ -71,6 +71,7 @@ module HDF5_utilities module procedure HDF5_addAttribute_str module procedure HDF5_addAttribute_int module procedure HDF5_addAttribute_real + module procedure HDF5_addAttribute_str_array module procedure HDF5_addAttribute_int_array module procedure HDF5_addAttribute_real_array end interface HDF5_addAttribute @@ -270,7 +271,7 @@ end subroutine HDF5_closeGroup !-------------------------------------------------------------------------------------------------- -!> @brief check whether a group or a dataset exists +!> @brief Check whether a group or a dataset exists. !-------------------------------------------------------------------------------------------------- logical function HDF5_objectExists(loc_id,path) @@ -280,6 +281,7 @@ logical function HDF5_objectExists(loc_id,path) integer :: hdferr character(len=:), allocatable :: p + if (present(path)) then p = trim(path) else @@ -298,7 +300,7 @@ end function HDF5_objectExists !-------------------------------------------------------------------------------------------------- -!> @brief adds a string attribute to the path given relative to the location +!> @brief Add a string attribute to the path given relative to the location. !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_str(loc_id,attrLabel,attrValue,path) @@ -313,6 +315,7 @@ subroutine HDF5_addAttribute_str(loc_id,attrLabel,attrValue,path) character(len=:,kind=C_CHAR), allocatable,target :: attrValue_ type(c_ptr), target, dimension(1) :: ptr + if (present(path)) then p = trim(path) else @@ -326,6 +329,7 @@ subroutine HDF5_addAttribute_str(loc_id,attrLabel,attrValue,path) if(hdferr < 0) error stop 'HDF5 error' call h5tcopy_f(H5T_STRING, type_id, hdferr) if(hdferr < 0) error stop 'HDF5 error' + call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if(hdferr < 0) error stop 'HDF5 error' if (attrExists) then @@ -336,6 +340,7 @@ subroutine HDF5_addAttribute_str(loc_id,attrLabel,attrValue,path) if(hdferr < 0) error stop 'HDF5 error' call h5awrite_f(attr_id, type_id, c_loc(ptr(1)), hdferr) if(hdferr < 0) error stop 'HDF5 error' + call h5aclose_f(attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5tclose_f(type_id,hdferr) @@ -347,7 +352,7 @@ end subroutine HDF5_addAttribute_str !-------------------------------------------------------------------------------------------------- -!> @brief adds a integer attribute to the path given relative to the location +!> @brief Add an integer attribute to the path given relative to the location. !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_int(loc_id,attrLabel,attrValue,path) @@ -361,6 +366,7 @@ subroutine HDF5_addAttribute_int(loc_id,attrLabel,attrValue,path) logical :: attrExists character(len=:), allocatable :: p + if (present(path)) then p = trim(path) else @@ -369,6 +375,7 @@ subroutine HDF5_addAttribute_int(loc_id,attrLabel,attrValue,path) call h5screate_f(H5S_SCALAR_F,space_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' + call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if(hdferr < 0) error stop 'HDF5 error' if (attrExists) then @@ -379,6 +386,7 @@ subroutine HDF5_addAttribute_int(loc_id,attrLabel,attrValue,path) if(hdferr < 0) error stop 'HDF5 error' call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, int([1],HSIZE_T), hdferr) if(hdferr < 0) error stop 'HDF5 error' + call h5aclose_f(attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(space_id,hdferr) @@ -388,7 +396,7 @@ end subroutine HDF5_addAttribute_int !-------------------------------------------------------------------------------------------------- -!> @brief adds a integer attribute to the path given relative to the location +!> @brief Add a real attribute to the path given relative to the location. !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path) @@ -402,6 +410,7 @@ subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path) logical :: attrExists character(len=:), allocatable :: p + if (present(path)) then p = trim(path) else @@ -410,6 +419,7 @@ subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path) call h5screate_f(H5S_SCALAR_F,space_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' + call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if(hdferr < 0) error stop 'HDF5 error' if (attrExists) then @@ -420,6 +430,7 @@ subroutine HDF5_addAttribute_real(loc_id,attrLabel,attrValue,path) if(hdferr < 0) error stop 'HDF5 error' call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, int([1],HSIZE_T), hdferr) if(hdferr < 0) error stop 'HDF5 error' + call h5aclose_f(attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(space_id,hdferr) @@ -429,7 +440,67 @@ end subroutine HDF5_addAttribute_real !-------------------------------------------------------------------------------------------------- -!> @brief adds a integer attribute to the path given relative to the location +!> @brief Add a string array attribute to the path given relative to the location. +!-------------------------------------------------------------------------------------------------- +subroutine HDF5_addAttribute_str_array(loc_id,attrLabel,attrValue,path) + + integer(HID_T), intent(in) :: loc_id + character(len=*), intent(in) :: attrLabel + character(len=*), intent(in), dimension(:) :: attrValue + character(len=*), intent(in), optional :: path + + integer(HID_T) :: attr_id, space_id, filetype_id, memtype_id + integer :: hdferr + logical :: attrExists + character(len=:), allocatable :: p + type(C_PTR) :: f_ptr + character(len=:), allocatable, dimension(:), target :: attrValue_ + + + if (present(path)) then + p = trim(path) + else + p = '.' + endif + + attrValue_ = attrValue + + call h5tcopy_f(H5T_C_S1,filetype_id,hdferr) + if(hdferr < 0) error stop 'HDF5 error' + call h5tset_size_f(filetype_id, int(len(attrValue_)+1,C_SIZE_T),hdferr) + if(hdferr < 0) error stop 'HDF5 error' + call h5tcopy_f(H5T_FORTRAN_S1, memtype_id, hdferr) + if(hdferr < 0) error stop 'HDF5 error' + call h5tset_size_f(memtype_id, int(len(attrValue_),C_SIZE_T), hdferr) + if(hdferr < 0) error stop 'HDF5 error' + call h5screate_simple_f(1,shape(attrValue_,kind=HSIZE_T),space_id, hdferr) + if(hdferr < 0) error stop 'HDF5 error' + + call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) + if (attrExists) then + call h5adelete_by_name_f(loc_id, trim(p), attrLabel, hdferr) + if(hdferr < 0) error stop 'HDF5 error' + endif + call h5acreate_by_name_f(loc_id,trim(p),trim(attrLabel),filetype_id,space_id,attr_id,hdferr) + if(hdferr < 0) error stop 'HDF5 error' + f_ptr = c_loc(attrValue_) + call h5awrite_f(attr_id, memtype_id, f_ptr, hdferr) + if(hdferr < 0) error stop 'HDF5 error' + + call h5tclose_f(memtype_id,hdferr) + if(hdferr < 0) error stop 'HDF5 error' + call h5tclose_f(filetype_id,hdferr) + if(hdferr < 0) error stop 'HDF5 error' + call h5aclose_f(attr_id,hdferr) + if(hdferr < 0) error stop 'HDF5 error' + call h5sclose_f(space_id,hdferr) + if(hdferr < 0) error stop 'HDF5 error' + +end subroutine HDF5_addAttribute_str_array + + +!-------------------------------------------------------------------------------------------------- +!> @brief Add an integer array attribute to the path given relative to the location. !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_int_array(loc_id,attrLabel,attrValue,path) @@ -444,6 +515,7 @@ subroutine HDF5_addAttribute_int_array(loc_id,attrLabel,attrValue,path) logical :: attrExists character(len=:), allocatable :: p + if (present(path)) then p = trim(path) else @@ -454,6 +526,7 @@ subroutine HDF5_addAttribute_int_array(loc_id,attrLabel,attrValue,path) call h5screate_simple_f(1, array_size, space_id, hdferr, array_size) if(hdferr < 0) error stop 'HDF5 error' + call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if(hdferr < 0) error stop 'HDF5 error' if (attrExists) then @@ -464,6 +537,7 @@ subroutine HDF5_addAttribute_int_array(loc_id,attrLabel,attrValue,path) if(hdferr < 0) error stop 'HDF5 error' call h5awrite_f(attr_id, H5T_NATIVE_INTEGER, attrValue, array_size, hdferr) if(hdferr < 0) error stop 'HDF5 error' + call h5aclose_f(attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(space_id,hdferr) @@ -473,7 +547,7 @@ end subroutine HDF5_addAttribute_int_array !-------------------------------------------------------------------------------------------------- -!> @brief adds a real attribute to the path given relative to the location +!> @brief Add a real array attribute to the path given relative to the location. !-------------------------------------------------------------------------------------------------- subroutine HDF5_addAttribute_real_array(loc_id,attrLabel,attrValue,path) @@ -488,6 +562,7 @@ subroutine HDF5_addAttribute_real_array(loc_id,attrLabel,attrValue,path) logical :: attrExists character(len=:), allocatable :: p + if (present(path)) then p = trim(path) else @@ -498,6 +573,7 @@ subroutine HDF5_addAttribute_real_array(loc_id,attrLabel,attrValue,path) call h5screate_simple_f(1, array_size, space_id, hdferr, array_size) if(hdferr < 0) error stop 'HDF5 error' + call h5aexists_by_name_f(loc_id,trim(p),attrLabel,attrExists,hdferr) if(hdferr < 0) error stop 'HDF5 error' if (attrExists) then @@ -508,6 +584,7 @@ subroutine HDF5_addAttribute_real_array(loc_id,attrLabel,attrValue,path) if(hdferr < 0) error stop 'HDF5 error' call h5awrite_f(attr_id, H5T_NATIVE_DOUBLE, attrValue, array_size, hdferr) if(hdferr < 0) error stop 'HDF5 error' + call h5aclose_f(attr_id,hdferr) if(hdferr < 0) error stop 'HDF5 error' call h5sclose_f(space_id,hdferr) @@ -517,7 +594,7 @@ end subroutine HDF5_addAttribute_real_array !-------------------------------------------------------------------------------------------------- -!> @brief set link to object in results file +!> @brief Set link to object in results file. !-------------------------------------------------------------------------------------------------- subroutine HDF5_setLink(loc_id,target_name,link_name) @@ -549,7 +626,7 @@ subroutine HDF5_read_real1(dataset,loc_id,datasetName,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) + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -589,7 +666,7 @@ subroutine HDF5_read_real2(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -629,7 +706,7 @@ subroutine HDF5_read_real3(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -669,7 +746,7 @@ subroutine HDF5_read_real4(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -709,7 +786,7 @@ subroutine HDF5_read_real5(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -749,7 +826,7 @@ subroutine HDF5_read_real6(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -789,7 +866,7 @@ subroutine HDF5_read_real7(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -831,7 +908,7 @@ subroutine HDF5_read_int1(dataset,loc_id,datasetName,parallel) integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id, aplist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -871,7 +948,7 @@ subroutine HDF5_read_int2(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -911,7 +988,7 @@ subroutine HDF5_read_int3(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -951,7 +1028,7 @@ subroutine HDF5_read_int4(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -991,7 +1068,7 @@ subroutine HDF5_read_int5(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1031,7 +1108,7 @@ subroutine HDF5_read_int6(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1071,7 +1148,7 @@ subroutine HDF5_read_int7(dataset,loc_id,datasetName,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))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1114,7 +1191,7 @@ subroutine HDF5_write_real1(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1155,7 +1232,7 @@ subroutine HDF5_write_real2(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1196,7 +1273,7 @@ subroutine HDF5_write_real3(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1237,7 +1314,7 @@ subroutine HDF5_write_real4(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1279,7 +1356,7 @@ subroutine HDF5_write_real5(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1320,7 +1397,7 @@ subroutine HDF5_write_real6(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1361,7 +1438,7 @@ subroutine HDF5_write_real7(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1403,7 +1480,7 @@ subroutine HDF5_write_int1(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1444,7 +1521,7 @@ subroutine HDF5_write_int2(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1485,7 +1562,7 @@ subroutine HDF5_write_int3(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1526,7 +1603,7 @@ subroutine HDF5_write_int4(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1567,7 +1644,7 @@ subroutine HDF5_write_int5(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1608,7 +1685,7 @@ subroutine HDF5_write_int6(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) @@ -1649,7 +1726,7 @@ subroutine HDF5_write_int7(dataset,loc_id,datasetName,parallel) integer :: hdferr integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id - integer(HSIZE_T), dimension(size(shape(dataset))) :: & + integer(HSIZE_T), dimension(rank(dataset)) :: & myStart, & myShape, & !< shape of the dataset (this process) totalShape !< shape of the dataset (all processes) diff --git a/src/material.f90 b/src/material.f90 index cd8a320fa..652cc30fb 100644 --- a/src/material.f90 +++ b/src/material.f90 @@ -8,6 +8,7 @@ module material use prec use config use results + use math use IO use rotations use discretization @@ -19,8 +20,12 @@ module material type :: tRotationContainer type(Rotation), dimension(:), allocatable :: data end type + type :: tTensorContainer + real(pReal), dimension(:,:,:), allocatable :: data + end type - type(tRotationContainer), dimension(:), allocatable :: material_orientation0 + + type(tRotationContainer), dimension(:), allocatable :: material_O_0 integer, dimension(:), allocatable, public, protected :: & homogenization_Nconstituents !< number of grains in each homogenization @@ -41,8 +46,9 @@ module material integer, dimension(:,:,:), allocatable, public, protected :: & ! (constituent,IP,elem) material_phaseMemberAt !TODO: remove public :: & + tTensorContainer, & tRotationContainer, & - material_orientation0, & + material_O_0, & material_init contains @@ -152,15 +158,15 @@ subroutine parse() enddo - allocate(material_orientation0(materials%length)) + allocate(material_O_0(materials%length)) do ma = 1, materials%length material => materials%get(ma) constituents => material%get('constituents') - allocate(material_orientation0(ma)%data(constituents%length)) + allocate(material_O_0(ma)%data(constituents%length)) do co = 1, constituents%length constituent => constituents%get(co) - call material_orientation0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4)) + call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4)) enddo enddo diff --git a/src/math.f90 b/src/math.f90 index 36fe91bac..a48f44b93 100644 --- a/src/math.f90 +++ b/src/math.f90 @@ -545,19 +545,6 @@ pure function math_symmetric33(m) end function math_symmetric33 -!-------------------------------------------------------------------------------------------------- -!> @brief symmetrize a 6x6 matrix -!-------------------------------------------------------------------------------------------------- -pure function math_symmetric66(m) - - real(pReal), dimension(6,6) :: math_symmetric66 - real(pReal), dimension(6,6), intent(in) :: m - - math_symmetric66 = 0.5_pReal * (m + transpose(m)) - -end function math_symmetric66 - - !-------------------------------------------------------------------------------------------------- !> @brief skew part of a 3x3 matrix !-------------------------------------------------------------------------------------------------- diff --git a/src/phase.f90 b/src/phase.f90 index d90f41ccc..effe189d3 100644 --- a/src/phase.f90 +++ b/src/phase.f90 @@ -26,12 +26,8 @@ module phase real(pReal), allocatable, dimension(:) :: phase_rho type(tRotationContainer), dimension(:), allocatable :: & - phase_orientation0, & - phase_orientation - - type :: tTensorContainer - real(pReal), dimension(:,:,:), allocatable :: data - end type + phase_O_0, & + phase_O type :: tNumerics integer :: & @@ -364,7 +360,7 @@ subroutine phase_init allocate(phase_lattice(phases%length)) allocate(phase_cOverA(phases%length),source=-1.0_pReal) allocate(phase_rho(phases%length)) - allocate(phase_orientation0(phases%length)) + allocate(phase_O_0(phases%length)) do ph = 1,phases%length phase => phases%get(ph) @@ -374,20 +370,20 @@ subroutine phase_init if (any(phase_lattice(ph) == ['hP','tI'])) & phase_cOverA(ph) = phase%get_asFloat('c/a') phase_rho(ph) = phase%get_asFloat('rho',defaultVal=0.0_pReal) - allocate(phase_orientation0(ph)%data(count(material_phaseID==ph))) + allocate(phase_O_0(ph)%data(count(material_phaseID==ph))) enddo do ce = 1, size(material_phaseID,2) ma = discretization_materialAt((ce-1)/discretization_nIPs+1) do co = 1,homogenization_Nconstituents(material_homogenizationID(ce)) ph = material_phaseID(co,ce) - phase_orientation0(ph)%data(material_phaseEntry(co,ce)) = material_orientation0(ma)%data(co) + phase_O_0(ph)%data(material_phaseEntry(co,ce)) = material_O_0(ma)%data(co) enddo enddo - allocate(phase_orientation(phases%length)) + allocate(phase_O(phases%length)) do ph = 1,phases%length - phase_orientation(ph)%data = phase_orientation0(ph)%data + phase_O(ph)%data = phase_O_0(ph)%data enddo call mechanical_init(materials,phases) @@ -577,10 +573,10 @@ subroutine crystallite_orientations(co,ip,el) ph = material_phaseID(co,(el-1)*discretization_nIPs + ip) en = material_phaseEntry(co,(el-1)*discretization_nIPs + ip) - call phase_orientation(ph)%data(en)%fromMatrix(transpose(math_rotationalPart(mechanical_F_e(ph,en)))) + call phase_O(ph)%data(en)%fromMatrix(transpose(math_rotationalPart(mechanical_F_e(ph,en)))) if (plasticState(material_phaseAt(1,el))%nonlocal) & - call plastic_nonlocal_updateCompatibility(phase_orientation,material_phaseAt(1,el),ip,el) + call plastic_nonlocal_updateCompatibility(phase_O,material_phaseAt(1,el),ip,el) end subroutine crystallite_orientations @@ -602,7 +598,7 @@ function crystallite_push33ToRef(co,ce, tensor33) ph = material_phaseID(co,ce) en = material_phaseEntry(co,ce) - T = matmul(phase_orientation0(ph)%data(en)%asMatrix(),transpose(math_inv33(phase_F(co,ce)))) ! ToDo: initial orientation correct? + T = matmul(phase_O_0(ph)%data(en)%asMatrix(),transpose(math_inv33(phase_F(co,ce)))) ! ToDo: initial orientation correct? crystallite_push33ToRef = matmul(transpose(T),matmul(tensor33,T)) diff --git a/src/phase_mechanical.f90 b/src/phase_mechanical.f90 index ac75e870c..52ce43c84 100644 --- a/src/phase_mechanical.f90 +++ b/src/phase_mechanical.f90 @@ -265,7 +265,7 @@ module subroutine mechanical_init(materials,phases) do ph = 1, phases%length do en = 1, count(material_phaseID == ph) - phase_mechanical_Fp0(ph)%data(1:3,1:3,en) = phase_orientation0(ph)%data(en)%asMatrix() ! Fp reflects initial orientation (see 10.1016/j.actamat.2006.01.005) + phase_mechanical_Fp0(ph)%data(1:3,1:3,en) = phase_O_0(ph)%data(en)%asMatrix() ! Fp reflects initial orientation (see 10.1016/j.actamat.2006.01.005) phase_mechanical_Fp0(ph)%data(1:3,1:3,en) = phase_mechanical_Fp0(ph)%data(1:3,1:3,en) & / math_det33(phase_mechanical_Fp0(ph)%data(1:3,1:3,en))**(1.0_pReal/3.0_pReal) phase_mechanical_Fi0(ph)%data(1:3,1:3,en) = math_I3 @@ -902,7 +902,6 @@ subroutine crystallite_results(group,ph) integer, intent(in) :: ph integer :: ou - real(pReal), allocatable, dimension(:,:) :: selected_rotations call results_closeGroup(results_addGroup(group//'/mechanical')) @@ -935,8 +934,7 @@ subroutine crystallite_results(group,ph) call results_writeDataset(phase_mechanical_S(ph)%data,group//'/mechanical/','S', & 'second Piola-Kirchhoff stress','Pa') case('O') - selected_rotations = select_rotations(phase_orientation(ph)%data) - call results_writeDataset(selected_rotations,group//'/mechanical',output_constituent(ph)%label(ou),& + call results_writeDataset(to_quaternion(phase_O(ph)%data),group//'/mechanical',output_constituent(ph)%label(ou),& 'crystal orientation as quaternion','q_0 (q_1 q_2 q_3)') call results_addAttribute('lattice',phase_lattice(ph),group//'/mechanical/'//output_constituent(ph)%label(ou)) if (any(phase_lattice(ph) == ['hP', 'tI'])) & @@ -948,19 +946,21 @@ subroutine crystallite_results(group,ph) contains !-------------------------------------------------------------------------------------------------- -!> @brief Convert orientation for output: ToDo: implement in HDF5/results +!> @brief Convert orientation array to quaternion array !-------------------------------------------------------------------------------------------------- - function select_rotations(dataset) + function to_quaternion(dataset) type(rotation), dimension(:), intent(in) :: dataset - real(pReal), dimension(4,size(dataset,1)) :: select_rotations - integer :: en + real(pReal), dimension(4,size(dataset,1)) :: to_quaternion - do en = 1, size(dataset,1) - select_rotations(:,en) = dataset(en)%asQuaternion() - enddo + integer :: i - end function select_rotations + + do i = 1, size(dataset,1) + to_quaternion(:,i) = dataset(i)%asQuaternion() + enddo + + end function to_quaternion end subroutine crystallite_results diff --git a/src/phase_mechanical_plastic_nonlocal.f90 b/src/phase_mechanical_plastic_nonlocal.f90 index 9510d0b81..f7941c7e5 100644 --- a/src/phase_mechanical_plastic_nonlocal.f90 +++ b/src/phase_mechanical_plastic_nonlocal.f90 @@ -1402,8 +1402,8 @@ module subroutine plastic_nonlocal_updateCompatibility(orientation,ph,i,e) forall(s1 = 1:ns) my_compatibility(:,s1,s1,n) = 0.0_pReal elseif (prm%chi_GB >= 0.0_pReal) then !* GRAIN BOUNDARY - if (any(dNeq(phase_orientation0(ph)%data(en)%asQuaternion(), & - phase_orientation0(neighbor_phase)%data(neighbor_me)%asQuaternion())) .and. & + if (any(dNeq(phase_O_0(ph)%data(en)%asQuaternion(), & + phase_O_0(neighbor_phase)%data(neighbor_me)%asQuaternion())) .and. & plasticState(neighbor_phase)%nonlocal) & forall(s1 = 1:ns) my_compatibility(:,s1,s1,n) = sqrt(prm%chi_GB) else