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https://github.com/openmc-dev/openmc.git
synced 2026-07-28 06:05:58 -04:00
Correctly write deferred-length character to HDF5 datasets
This commit is contained in:
Paul Romano
parent
f92cf9eac5
commit
f97154c6c0
6 changed files with 53 additions and 53 deletions
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@ -129,7 +129,7 @@ class Lattice(object):
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"""
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lattice_id = int(group.name.split('/')[-1].lstrip('lattice '))
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name = group['name'].value.decode()
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name = group['name'].value.decode() if 'name' in group else ''
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lattice_type = group['type'].value.decode()
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if 'offsets' in group:
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@ -292,7 +292,7 @@ class Material(object):
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"""
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mat_id = int(group.name.split('/')[-1].lstrip('material '))
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name = group['name'].value.decode()
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name = group['name'].value.decode() if 'name' in group else ''
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density = group['atom_density'].value
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nuc_densities = group['nuclide_densities'][...]
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nuclides = group['nuclides'].value
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@ -342,7 +342,7 @@ class StatePoint(object):
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# Create Tally object and assign basic properties
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tally = openmc.Tally(tally_id)
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tally._sp_filename = self._f.filename
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tally.name = group['name'].value.decode()
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tally.name = group['name'].value.decode() if 'name' in group else ''
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tally.estimator = group['estimator'].value.decode()
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tally.num_realizations = n_realizations
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@ -105,7 +105,7 @@ class Summary(object):
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for key, group in self._f['geometry/cells'].items():
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cell_id = int(key.lstrip('cell '))
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name = group['name'].value.decode()
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name = group['name'].value.decode() if 'name' in group else ''
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fill_type = group['fill_type'].value.decode()
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if fill_type == 'material':
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@ -115,10 +115,7 @@ class Summary(object):
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else:
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fill = group['lattice'].value
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if 'region' in group.keys():
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region = group['region'].value.decode()
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else:
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region = []
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region = group['region'].value.decode() if 'region' in group else ''
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# Create this Cell
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cell = openmc.Cell(cell_id=cell_id, name=name)
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@ -210,7 +210,7 @@ class Surface(object):
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"""
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surface_id = int(group.name.split('/')[-1].lstrip('surface '))
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name = group['name'].value.decode()
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name = group['name'].value.decode() if 'name' in group else ''
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surf_type = group['type'].value.decode()
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bc = group['boundary_type'].value.decode()
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coeffs = group['coefficients'][...]
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@ -1758,8 +1758,8 @@ contains
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integer(HID_T) :: dset ! data set handle
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integer(HID_T) :: dspace ! data or file space handle
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integer(HID_T) :: filetype
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integer(HID_T) :: memtype
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integer(SIZE_T) :: n
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integer(SIZE_T) :: i, n
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character(kind=C_CHAR), allocatable, target :: temp_buffer(:)
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type(c_ptr) :: f_ptr
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! Set up collective vs. independent I/O
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@ -1770,35 +1770,38 @@ contains
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! Create datatype for HDF5 file based on C char
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n = len_trim(buffer)
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call h5tcopy_f(H5T_C_S1, filetype, hdf5_err)
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call h5tset_size_f(filetype, n + 1, hdf5_err)
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if (n > 0) then
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call h5tcopy_f(H5T_C_S1, filetype, hdf5_err)
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call h5tset_size_f(filetype, n, hdf5_err)
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! Create datatype in memory based on Fortran character
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call h5tcopy_f(H5T_FORTRAN_S1, memtype, hdf5_err)
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if (n > 0) call h5tset_size_f(memtype, n, hdf5_err)
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! Create dataspace/dataset
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call h5screate_f(H5S_SCALAR_F, dspace, hdf5_err)
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call h5dcreate_f(group_id, trim(name), filetype, dspace, dset, hdf5_err)
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! Create dataspace/dataset
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call h5screate_f(H5S_SCALAR_F, dspace, hdf5_err)
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call h5dcreate_f(group_id, trim(name), filetype, dspace, dset, hdf5_err)
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! Copy string to temporary buffer
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allocate(temp_buffer(n))
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do i = 1, n
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temp_buffer(i) = buffer(i:i)
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end do
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! Get pointer to start of string
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f_ptr = c_loc(buffer(1:1))
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! Get pointer to start of string
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f_ptr = c_loc(temp_buffer(1))
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if (using_mpio_device(group_id)) then
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if (using_mpio_device(group_id)) then
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#ifdef PHDF5
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call h5pcreate_f(H5P_DATASET_XFER_F, plist, hdf5_err)
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call h5pset_dxpl_mpio_f(plist, data_xfer_mode, hdf5_err)
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if (n > 0) call h5dwrite_f(dset, memtype, f_ptr, hdf5_err, xfer_prp=plist)
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call h5pclose_f(plist, hdf5_err)
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call h5pcreate_f(H5P_DATASET_XFER_F, plist, hdf5_err)
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call h5pset_dxpl_mpio_f(plist, data_xfer_mode, hdf5_err)
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call h5dwrite_f(dset, filetype, f_ptr, hdf5_err, xfer_prp=plist)
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call h5pclose_f(plist, hdf5_err)
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#endif
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else
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if (n > 0) call h5dwrite_f(dset, memtype, f_ptr, hdf5_err)
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end if
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else
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call h5dwrite_f(dset, filetype, f_ptr, hdf5_err)
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end if
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call h5dclose_f(dset, hdf5_err)
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call h5sclose_f(dspace, hdf5_err)
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call h5tclose_f(memtype, hdf5_err)
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call h5tclose_f(filetype, hdf5_err)
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call h5dclose_f(dset, hdf5_err)
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call h5sclose_f(dspace, hdf5_err)
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call h5tclose_f(filetype, hdf5_err)
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end if
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end subroutine write_string
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!===============================================================================
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@ -1817,11 +1820,10 @@ contains
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integer(HID_T) :: plist ! property list
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#endif
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integer(HID_T) :: dset_id
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integer(HID_T) :: space_id
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integer(HID_T) :: filetype
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integer(HID_T) :: memtype
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integer(SIZE_T) :: size
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integer(SIZE_T) :: n
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integer(SIZE_T) :: i, n
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character(kind=C_CHAR), allocatable, target :: temp_buffer(:)
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type(c_ptr) :: f_ptr
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if (present(name)) then
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@ -1836,40 +1838,41 @@ contains
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if (indep) data_xfer_mode = H5FD_MPIO_INDEPENDENT_F
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end if
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! Get dataspace
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call h5dget_space_f(dset_id, space_id, hdf5_err)
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! Make sure buffer is large enough
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call h5dget_type_f(dset_id, filetype, hdf5_err)
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call h5tget_size_f(filetype, size, hdf5_err)
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if (size > len(buffer) + 1) then
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call h5tget_size_f(filetype, n, hdf5_err)
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if (n > len(buffer)) then
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call fatal_error("Character buffer is not long enough to &
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&read HDF5 string.")
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end if
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! Get datatype in memory based on Fortran character
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n = len(buffer)
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call h5tcopy_f(H5T_FORTRAN_S1, memtype, hdf5_err)
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call h5tset_size_f(memtype, n, hdf5_err)
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call h5tcopy_f(H5T_C_S1, memtype, hdf5_err)
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call h5tset_size_f(memtype, n + 1, hdf5_err)
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! Get pointer to start of string
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f_ptr = c_loc(buffer(1:1))
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allocate(temp_buffer(n))
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f_ptr = c_loc(temp_buffer(1))
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if (using_mpio_device(dset_id)) then
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#ifdef PHDF5
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call h5pcreate_f(H5P_DATASET_XFER_F, plist, hdf5_err)
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call h5pset_dxpl_mpio_f(plist, data_xfer_mode, hdf5_err)
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call h5dread_f(dset_id, memtype, f_ptr, hdf5_err, &
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mem_space_id=space_id, xfer_prp=plist)
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call h5dread_f(dset_id, memtype, f_ptr, hdf5_err, xfer_prp=plist)
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call h5pclose_f(plist, hdf5_err)
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#endif
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else
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call h5dread_f(dset_id, memtype, f_ptr, hdf5_err, mem_space_id=space_id)
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call h5dread_f(dset_id, memtype, f_ptr, hdf5_err)
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end if
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buffer = ''
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do i = 1, n
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if (temp_buffer(i) == C_NULL_CHAR) cycle
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buffer(i:i) = temp_buffer(i)
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end do
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if (present(name)) call h5dclose_f(dset_id, hdf5_err)
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call h5sclose_f(space_id, hdf5_err)
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call h5tclose_f(filetype, hdf5_err)
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call h5tclose_f(memtype, hdf5_err)
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end subroutine read_string
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@ -2372,9 +2375,9 @@ contains
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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), target :: buffer ! read data to here
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integer(HID_T), intent(in) :: obj_id
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character(*), intent(in) :: name ! name for data
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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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character(*), intent(in) :: name ! name for data
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integer :: hdf5_err
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integer(HID_T) :: attr_id ! data set handle
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@ -2407,9 +2410,9 @@ contains
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call h5aread_f(attr_id, memtype, f_ptr, hdf5_err)
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buffer = ''
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do i = 1, size
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if (temp_buffer(i) == C_NULL_CHAR) cycle
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buffer(i:i) = temp_buffer(i)
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end do
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deallocate(temp_buffer)
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call h5aclose_f(attr_id, hdf5_err)
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call h5tclose_f(filetype, hdf5_err)
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