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https://github.com/openmc-dev/openmc.git
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Handle most writing of attributes in C++
This commit is contained in:
Paul Romano
parent
342d207fc4
commit
ad3bb0b43a
3 changed files with 115 additions and 139 deletions
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@ -105,6 +105,19 @@ module hdf5_interface
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integer(HID_T), value :: file_id
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end subroutine file_close
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subroutine get_shape_c(obj_id, dims) bind(C, name='get_shape')
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import HID_T, HSIZE_T
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integer(HID_T), value :: obj_id
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integer(HSIZE_T), intent(out) :: dims(*)
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end subroutine get_shape_c
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subroutine get_shape_attr(obj_id, name, dims) bind(C)
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import HID_T, HSIZE_T, C_CHAR
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integer(HID_T), value :: obj_id
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character(kind=C_CHAR), intent(in) :: name(*)
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integer(HSIZE_T), intent(out) :: dims(*)
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end subroutine get_shape_attr
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subroutine read_double_c(obj_id, name, buffer, indep) &
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bind(C, name='read_double')
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import HID_T, C_DOUBLE, C_BOOL, C_PTR
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@ -114,6 +127,22 @@ module hdf5_interface
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logical(C_BOOL), intent(in) :: indep
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end subroutine read_double_c
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subroutine read_attr_int_c(obj_id, name, buffer) &
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bind(C, name='read_attr_int')
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import HID_T, C_CHAR, C_INT
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integer(HID_T), value :: obj_id
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character(kind=C_CHAR), intent(in) :: name(*)
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integer(C_INT), intent(in) :: buffer(*)
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end subroutine read_attr_int_c
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subroutine read_attr_double_c(obj_id, name, buffer) &
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bind(C, name='read_attr_double')
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import HID_T, C_CHAR, C_DOUBLE
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integer(HID_T), value :: obj_id
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character(kind=C_CHAR), intent(in) :: name(*)
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real(C_DOUBLE), intent(in) :: buffer(*)
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end subroutine read_attr_double_c
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subroutine read_int_c(obj_id, name, buffer, indep) &
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bind(C, name='read_int')
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import HID_T, C_INT, C_BOOL, C_PTR
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@ -1178,14 +1207,10 @@ contains
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name
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integer :: hdf5_err
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integer(HID_T) :: attr_id
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type(c_ptr) :: f_ptr
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real(C_DOUBLE) :: buffer_(1)
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call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err)
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f_ptr = c_loc(buffer)
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call h5aread_f(attr_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err)
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call h5aclose_f(attr_id, hdf5_err)
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call read_attr_double_c(obj_id, to_c_string(name), buffer_)
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buffer = buffer_(1)
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end subroutine read_attribute_double
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subroutine write_attribute_double(obj_id, name, buffer)
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@ -1205,39 +1230,16 @@ contains
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name
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integer :: hdf5_err
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integer(HID_T) :: space_id
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integer(HID_T) :: attr_id
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integer(HSIZE_T) :: dims(1)
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integer(HSIZE_T) :: maxdims(1)
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call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err)
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if (allocated(buffer)) then
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dims(:) = shape(buffer)
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else
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call h5aget_space_f(attr_id, space_id, hdf5_err)
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call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err)
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if (.not. allocated(buffer)) then
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call get_shape_attr(obj_id, to_c_string(name), dims)
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allocate(buffer(dims(1)))
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call h5sclose_f(space_id, hdf5_err)
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end if
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call read_attribute_double_1D_explicit(attr_id, dims, buffer)
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call h5aclose_f(attr_id, hdf5_err)
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call read_attr_double_c(obj_id, to_c_string(name), buffer)
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end subroutine read_attribute_double_1D
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subroutine read_attribute_double_1D_explicit(attr_id, dims, buffer)
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integer(HID_T), intent(in) :: attr_id
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integer(HSIZE_T), intent(in) :: dims(1)
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real(8), target, intent(inout) :: buffer(dims(1))
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integer :: hdf5_err
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type(c_ptr) :: f_ptr
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f_ptr = c_loc(buffer)
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call h5aread_f(attr_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err)
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end subroutine read_attribute_double_1D_explicit
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subroutine write_attribute_double_1D(obj_id, name, buffer)
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name
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@ -1254,52 +1256,25 @@ contains
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name
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integer :: hdf5_err
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integer(HID_T) :: space_id
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integer(HID_T) :: attr_id
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integer(HSIZE_T) :: dims(2)
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integer(HSIZE_T) :: maxdims(2)
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call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err)
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if (allocated(buffer)) then
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dims(:) = shape(buffer)
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else
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call h5aget_space_f(attr_id, space_id, hdf5_err)
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call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err)
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allocate(buffer(dims(1), dims(2)))
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call h5sclose_f(space_id, hdf5_err)
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if (.not. allocated(buffer)) then
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call get_shape_attr(obj_id, to_c_string(name), dims)
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allocate(buffer(dims(2), dims(1)))
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end if
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call read_attribute_double_2D_explicit(attr_id, dims, buffer)
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call h5aclose_f(attr_id, hdf5_err)
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call read_attr_double_c(obj_id, to_c_string(name), buffer)
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end subroutine read_attribute_double_2D
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subroutine read_attribute_double_2D_explicit(attr_id, dims, buffer)
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integer(HID_T), intent(in) :: attr_id
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integer(HSIZE_T), intent(in) :: dims(2)
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real(8), target, intent(inout) :: buffer(dims(1),dims(2))
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integer :: hdf5_err
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type(c_ptr) :: f_ptr
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f_ptr = c_loc(buffer)
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call h5aread_f(attr_id, H5T_NATIVE_DOUBLE, f_ptr, hdf5_err)
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end subroutine read_attribute_double_2D_explicit
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subroutine read_attribute_integer(buffer, obj_id, name)
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integer, intent(inout), target :: buffer
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name
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integer :: hdf5_err
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integer(HID_T) :: attr_id
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type(c_ptr) :: f_ptr
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integer(C_INT) :: buffer_(1)
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call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err)
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f_ptr = c_loc(buffer)
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call h5aread_f(attr_id, H5T_NATIVE_INTEGER, f_ptr, hdf5_err)
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call h5aclose_f(attr_id, hdf5_err)
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call read_attr_int_c(obj_id, to_c_string(name), buffer_)
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buffer = buffer_(1)
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end subroutine read_attribute_integer
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subroutine write_attribute_integer(obj_id, name, buffer)
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@ -1319,39 +1294,16 @@ contains
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name
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integer :: hdf5_err
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integer(HID_T) :: space_id
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integer(HID_T) :: attr_id
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integer(HSIZE_T) :: dims(1)
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integer(HSIZE_T) :: maxdims(1)
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call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err)
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if (allocated(buffer)) then
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dims(:) = shape(buffer)
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else
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call h5aget_space_f(attr_id, space_id, hdf5_err)
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call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err)
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if (.not. allocated(buffer)) then
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call get_shape_attr(obj_id, to_c_string(name), dims)
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allocate(buffer(dims(1)))
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call h5sclose_f(space_id, hdf5_err)
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end if
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call read_attribute_integer_1D_explicit(attr_id, dims, buffer)
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call h5aclose_f(attr_id, hdf5_err)
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call read_attr_int_c(obj_id, to_c_string(name), buffer)
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end subroutine read_attribute_integer_1D
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subroutine read_attribute_integer_1D_explicit(attr_id, dims, buffer)
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integer(HID_T), intent(in) :: attr_id
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integer(HSIZE_T), intent(in) :: dims(1)
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integer, target, intent(inout) :: buffer(dims(1))
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integer :: hdf5_err
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type(c_ptr) :: f_ptr
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f_ptr = c_loc(buffer)
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call h5aread_f(attr_id, H5T_NATIVE_INTEGER, f_ptr, hdf5_err)
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end subroutine read_attribute_integer_1D_explicit
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subroutine write_attribute_integer_1D(obj_id, name, buffer)
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name
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@ -1368,39 +1320,16 @@ contains
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name
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integer :: hdf5_err
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integer(HID_T) :: space_id
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integer(HID_T) :: attr_id
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integer(HSIZE_T) :: dims(2)
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integer(HSIZE_T) :: maxdims(2)
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call h5aopen_f(obj_id, trim(name), attr_id, hdf5_err)
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if (allocated(buffer)) then
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dims(:) = shape(buffer)
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else
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call h5aget_space_f(attr_id, space_id, hdf5_err)
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call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err)
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allocate(buffer(dims(1), dims(2)))
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call h5sclose_f(space_id, hdf5_err)
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if (.not. allocated(buffer)) then
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call get_shape_attr(obj_id, to_c_string(name), dims)
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allocate(buffer(dims(2), dims(1)))
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end if
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call read_attribute_integer_2D_explicit(attr_id, dims, buffer)
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call h5aclose_f(attr_id, hdf5_err)
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call read_attr_int_C(obj_id, to_c_string(name), buffer)
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end subroutine read_attribute_integer_2D
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subroutine read_attribute_integer_2D_explicit(attr_id, dims, buffer)
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integer(HID_T), intent(in) :: attr_id
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integer(HSIZE_T), intent(in) :: dims(2)
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integer, target, intent(inout) :: buffer(dims(1),dims(2))
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integer :: hdf5_err
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type(c_ptr) :: f_ptr
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f_ptr = c_loc(buffer)
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call h5aread_f(attr_id, H5T_NATIVE_INTEGER, f_ptr, hdf5_err)
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end subroutine read_attribute_integer_2D_explicit
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subroutine read_attribute_string(buffer, obj_id, name)
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character(*), intent(inout) :: buffer ! read data to here
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integer(HID_T), intent(in) :: obj_id
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@ -1533,21 +1462,13 @@ contains
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integer(HID_T), intent(in) :: obj_id
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integer(HSIZE_T), intent(out) :: dims(:)
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integer :: hdf5_err
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integer :: type
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integer(HID_T) :: space_id
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integer(HSIZE_T) :: maxdims(size(dims))
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integer :: i
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integer(HSIZE_T) :: dims_c(size(dims))
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call h5iget_type_f(obj_id, type, hdf5_err)
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if (type == H5I_DATASET_F) then
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call h5dget_space_f(obj_id, space_id, hdf5_err)
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call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err)
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call h5sclose_f(space_id, hdf5_err)
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elseif (type == H5I_ATTR_F) then
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call h5aget_space_f(obj_id, space_id, hdf5_err)
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call h5sget_simple_extent_dims_f(space_id, dims, maxdims, hdf5_err)
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call h5sclose_f(space_id, hdf5_err)
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end if
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call get_shape_c(obj_id, dims_c)
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do i = 1, size(dims)
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dims(i) = dims_c(size(dims) - i + 1)
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end do
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end subroutine get_shape
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subroutine get_ndims(obj_id, ndims)
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@ -31,6 +31,32 @@ using_mpio_device(hid_t obj_id)
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}
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void
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get_shape(hid_t obj_id, hsize_t* dims)
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{
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auto type = H5Iget_type(obj_id);
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hid_t dspace;
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if (type == H5I_DATASET) {
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dspace = H5Dget_space(obj_id);
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} else if (type == H5I_ATTR) {
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dspace = H5Aget_space(obj_id);
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}
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H5Sget_simple_extent_dims(dspace, dims, nullptr);
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H5Sclose(dspace);
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}
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void
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get_shape_attr(hid_t obj_id, const char* name, hsize_t* dims)
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{
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hid_t attr = H5Aopen(obj_id, name, H5P_DEFAULT);
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hid_t dspace = H5Aget_space(attr);
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H5Sget_simple_extent_dims(dspace, dims, nullptr);
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H5Sclose(dspace);
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H5Aclose(attr);
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}
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hid_t
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create_group(hid_t parent_id, char const *name)
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{
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@ -159,10 +185,32 @@ open_group(hid_t group_id, const char* name)
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}
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}
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void
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read_attr(hid_t obj_id, const char* name, hid_t mem_type_id, void* buffer)
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{
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hid_t attr = H5Aopen(obj_id, name, H5P_DEFAULT);
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H5Aread(attr, mem_type_id, buffer);
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H5Aclose(attr);
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}
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void
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read_attr_double(hid_t obj_id, const char* name, double* buffer)
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{
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read_attr(obj_id, name, H5T_NATIVE_DOUBLE, buffer);
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}
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void
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read_attr_int(hid_t obj_id, const char* name, int* buffer)
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{
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read_attr(obj_id, name, H5T_NATIVE_INT, buffer);
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}
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void
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read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id,
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void* buffer, bool indep)
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void* buffer, bool indep)
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{
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hid_t dset = obj_id;
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if (name) dset = H5Dopen(obj_id, name, H5P_DEFAULT);
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@ -176,7 +224,7 @@ read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id,
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hid_t plist = H5Pcreate(H5P_DATASET_XFER);
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H5Pset_dxpl_mpio(plist, data_xfer_mode);
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// Write data
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// Read data
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H5Dread(dset, mem_type_id, H5S_ALL, H5S_ALL, plist, buffer);
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H5Pclose(plist);
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#endif
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@ -11,7 +11,6 @@
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namespace openmc {
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bool using_mpio_device(hid_t obj_id);
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hid_t create_group(hid_t parent_id, const char* name);
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hid_t create_group(hid_t parent_id, const std::string& name);
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void close_dataset(hid_t dataset_id);
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@ -19,9 +18,12 @@ void close_group(hid_t group_id);
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extern "C" hid_t file_open(const char* filename, char mode, bool parallel);
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hid_t file_open(const std::string& filename, char mode, bool parallel);
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extern "C" void file_close(hid_t file_id);
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extern "C" void get_shape(hid_t obj_if, hsize_t* dims);
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extern "C" void get_shape_attr(hid_t obj_if, const char* name, hsize_t* dims);
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bool object_exists(hid_t object_id, const char* name);
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hid_t open_dataset(hid_t group_id, const char* name);
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hid_t open_group(hid_t group_id, const char* name);
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bool using_mpio_device(hid_t obj_id);
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template<std::size_t array_len> void
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@ -41,8 +43,13 @@ write_double_1D(hid_t group_id, char const *name,
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H5Dclose(dataset);
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}
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void read_dataset(hid_t obj_id, const char* name, double* buffer,
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hid_t mem_type_id, bool indep);
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void read_attr(hid_t obj_id, const char* name, hid_t mem_type_id,
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const void* buffer);
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extern "C" void read_attr_double(hid_t obj_id, const char* name, double* buffer);
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extern "C" void read_attr_int(hid_t obj_id, const char* name, int* buffer);
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void read_dataset(hid_t obj_id, const char* name, hid_t mem_type_id,
|
||||
void* buffer, bool indep);
|
||||
extern "C" void read_double(hid_t obj_id, const char* name, double* buffer,
|
||||
bool indep);
|
||||
extern "C" void read_int(hid_t obj_id, const char* name, int* buffer,
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue