Merge remote-tracking branch 'origin/development' into misc-improvements
This commit is contained in:
Martin Diehl
commit
a881e6e57a
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@ -46,7 +46,7 @@ class Result:
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self.version_major = f.attrs['DADF5_version_major']
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self.version_minor = f.attrs['DADF5_version_minor']
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if self.version_major != 0 or not 7 <= self.version_minor <= 10:
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if self.version_major != 0 or not 7 <= self.version_minor <= 11:
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raise TypeError(f'Unsupported DADF5 version {self.version_major}.{self.version_minor}')
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self.structured = 'grid' in f['geometry'].attrs.keys() or \
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@ -790,7 +790,10 @@ class Result:
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lattice = {'fcc':'cF','bcc':'cI','hex':'hP'}[q['meta']['Lattice']]
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except KeyError:
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lattice = q['meta']['Lattice']
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try:
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o = Orientation(rotation = (rfn.structured_to_unstructured(q['data'])),lattice=lattice)
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except ValueError:
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o = Orientation(rotation = q['data'],lattice=lattice)
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return {
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'data': np.uint8(o.IPF_color(l)*255),
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@ -1130,6 +1133,7 @@ class Result:
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Arguments parsed to func.
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"""
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chunk_size = 1024**2//8
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num_threads = damask.environment.options['DAMASK_NUM_THREADS']
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pool = mp.Pool(int(num_threads) if num_threads is not None else None)
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lock = mp.Manager().Lock()
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@ -1152,6 +1156,14 @@ class Result:
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dataset[...] = result[1]['data']
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dataset.attrs['Overwritten'] = 'Yes' if h5py3 else \
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'Yes'.encode()
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else:
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if result[1]['data'].size >= chunk_size*2:
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shape = result[1]['data'].shape
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chunks = (chunk_size//np.prod(shape[1:]),)+shape[1:]
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dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data'],
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maxshape=shape, chunks=chunks,
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compression='gzip', compression_opts=6,
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shuffle=True,fletcher32=True)
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else:
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dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data'])
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@ -12,7 +12,6 @@ module HDF5_utilities
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use prec
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use parallelization
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use rotations
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implicit none
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public
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@ -37,7 +36,6 @@ module HDF5_utilities
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module procedure HDF5_read_int5
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module procedure HDF5_read_int6
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module procedure HDF5_read_int7
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end interface HDF5_read
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!--------------------------------------------------------------------------------------------------
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@ -60,9 +58,6 @@ module HDF5_utilities
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module procedure HDF5_write_int5
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module procedure HDF5_write_int6
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module procedure HDF5_write_int7
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module procedure HDF5_write_rotation
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end interface HDF5_write
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!--------------------------------------------------------------------------------------------------
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@ -1663,82 +1658,6 @@ subroutine HDF5_write_int7(loc_id,dataset,datasetName,parallel)
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end subroutine HDF5_write_int7
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!--------------------------------------------------------------------------------------------------
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!> @brief writes a scalar orientation dataset
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! ToDo: It might be possible to write the dataset as a whole
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! ToDo: We could optionally write out other representations (axis angle, euler, ...)
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!--------------------------------------------------------------------------------------------------
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subroutine HDF5_write_rotation(loc_id,dataset,datasetName,parallel)
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type(rotation), intent(in), dimension(:) :: dataset !< data written to file
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integer(HID_T), intent(in) :: loc_id !< file or group handle
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character(len=*), intent(in) :: datasetName !< name of the dataset in the file
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logical, intent(in), optional :: parallel
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integer :: hdferr
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real(pReal), dimension(4,size(dataset)) :: dataset_asArray
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integer(HID_T) :: dset_id, filespace_id, memspace_id, plist_id,dtype_id,w_id,x_id,y_id,z_id
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integer(HSIZE_T), dimension(size(shape(dataset))) :: &
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myStart, &
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myShape, & !< shape of the dataset (this process)
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totalShape !< shape of the dataset (all processes)
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integer(SIZE_T) :: type_size_real
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integer :: i
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do i = 1, size(dataset)
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dataset_asArray(1:4,i) = dataset(i)%asQuaternion()
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enddo
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!---------------------------------------------------------------------------------------------------
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! determine shape of dataset
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myShape = int(shape(dataset),HSIZE_T)
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!---------------------------------------------------------------------------------------------------
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! compound type: name of each quaternion component
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call h5tget_size_f(H5T_NATIVE_DOUBLE, type_size_real, hdferr)
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call h5tcreate_f(H5T_COMPOUND_F, type_size_real*4_SIZE_T, dtype_id, hdferr)
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call h5tinsert_f(dtype_id, "w", type_size_real*0_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
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call h5tinsert_f(dtype_id, "x", type_size_real*1_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
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call h5tinsert_f(dtype_id, "y", type_size_real*2_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
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call h5tinsert_f(dtype_id, "z", type_size_real*3_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
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if (present(parallel)) then
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call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
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myStart, totalShape, loc_id,myShape,datasetName,dtype_id,parallel)
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else
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call initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
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myStart, totalShape, loc_id,myShape,datasetName,dtype_id,.false.)
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endif
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call h5pset_preserve_f(plist_id, .TRUE., hdferr)
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if (product(totalShape) /= 0) then
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call h5tcreate_f(H5T_COMPOUND_F, type_size_real, x_id, hdferr)
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call h5tinsert_f(x_id, "x", 0_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
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call h5tcreate_f(H5T_COMPOUND_F, type_size_real, w_id, hdferr)
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call h5tinsert_f(w_id, "w", 0_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
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call h5tcreate_f(H5T_COMPOUND_F, type_size_real, y_id, hdferr)
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call h5tinsert_f(y_id, "y", 0_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
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call h5tcreate_f(H5T_COMPOUND_F, type_size_real, z_id, hdferr)
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call h5tinsert_f(z_id, "z", 0_SIZE_T, H5T_NATIVE_DOUBLE, hdferr)
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call h5dwrite_f(dset_id, w_id,dataset_asArray(1,:),int(totalShape,HSIZE_T), hdferr,&
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file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
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call h5dwrite_f(dset_id, x_id,dataset_asArray(2,:),int(totalShape,HSIZE_T), hdferr,&
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file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
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call h5dwrite_f(dset_id, y_id,dataset_asArray(3,:),int(totalShape,HSIZE_T), hdferr,&
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file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
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call h5dwrite_f(dset_id, z_id,dataset_asArray(4,:),int(totalShape,HSIZE_T), hdferr,&
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file_space_id = filespace_id, mem_space_id = memspace_id, xfer_prp = plist_id)
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if(hdferr < 0) error stop 'HDF5 error'
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endif
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call finalize_write(plist_id, dset_id, filespace_id, memspace_id)
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end subroutine HDF5_write_rotation
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!--------------------------------------------------------------------------------------------------
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!> @brief initialize HDF5 handles, determines global shape and start for parallel read
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!--------------------------------------------------------------------------------------------------
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@ -1850,10 +1769,10 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
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totalShape !< shape of the dataset (all processes)
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integer(HID_T), intent(out) :: dset_id, filespace_id, memspace_id, plist_id
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integer, dimension(worldsize) :: &
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writeSize !< contribution of all processes
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integer :: ierr
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integer :: hdferr
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integer, dimension(worldsize) :: writeSize !< contribution of all processes
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integer(HID_T) :: dcpl
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integer :: ierr, hdferr
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integer(HSIZE_T), parameter :: chunkSize = 1024_HSIZE_T**2/8_HSIZE_T
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!-------------------------------------------------------------------------------------------------
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! creating a property list for transfer properties (is collective when reading in parallel)
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@ -1880,6 +1799,21 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
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myStart(ubound(myStart)) = int(sum(writeSize(1:worldrank)),HSIZE_T)
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totalShape = [myShape(1:ubound(myShape,1)-1),int(sum(writeSize),HSIZE_T)]
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!--------------------------------------------------------------------------------------------------
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! compress (and chunk) larger datasets
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call h5pcreate_f(H5P_DATASET_CREATE_F, dcpl, hdferr)
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if(hdferr < 0) error stop 'HDF5 error'
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if(product(totalShape) >= chunkSize*2_HSIZE_T) then
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call h5pset_chunk_f(dcpl, size(totalShape), getChunks(totalShape,chunkSize), hdferr)
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if(hdferr < 0) error stop 'HDF5 error'
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call h5pset_shuffle_f(dcpl, hdferr)
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if(hdferr < 0) error stop 'HDF5 error'
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call h5pset_deflate_f(dcpl, 6, hdferr)
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if(hdferr < 0) error stop 'HDF5 error'
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call h5pset_Fletcher32_f(dcpl,hdferr)
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if(hdferr < 0) error stop 'HDF5 error'
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endif
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!--------------------------------------------------------------------------------------------------
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! create dataspace in memory (local shape) and in file (global shape)
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call h5screate_simple_f(size(myShape), myShape, memspace_id, hdferr, myShape)
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@ -1889,11 +1823,29 @@ subroutine initialize_write(dset_id, filespace_id, memspace_id, plist_id, &
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!--------------------------------------------------------------------------------------------------
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! create dataset in the file and select a hyperslab from it (the portion of the current process)
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call h5dcreate_f(loc_id, trim(datasetName), datatype, filespace_id, dset_id, hdferr)
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call h5dcreate_f(loc_id, trim(datasetName), datatype, filespace_id, dset_id, hdferr, dcpl)
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if(hdferr < 0) error stop 'HDF5 error'
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call h5sselect_hyperslab_f(filespace_id, H5S_SELECT_SET_F, myStart, myShape, hdferr)
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if(hdferr < 0) error stop 'HDF5 error'
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call h5pclose_f(dcpl , hdferr)
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if(hdferr < 0) error stop 'HDF5 error'
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contains
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!------------------------------------------------------------------------------------------------
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!> @brief determine chunk layout
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!------------------------------------------------------------------------------------------------
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pure function getChunks(totalShape,chunkSize)
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integer(HSIZE_T), dimension(:), intent(in) :: totalShape
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integer(HSIZE_T), intent(in) :: chunkSize
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integer(HSIZE_T), dimension(size(totalShape)) :: getChunks
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getChunks = [totalShape(1:size(totalShape)-1),&
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chunkSize/product(totalShape(1:size(totalShape)-1))]
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end function getChunks
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end subroutine initialize_write
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@ -1916,4 +1868,5 @@ subroutine finalize_write(plist_id, dset_id, filespace_id, memspace_id)
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end subroutine finalize_write
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end module HDF5_Utilities
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|
|
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@ -454,10 +454,10 @@ end subroutine constitutive_plastic_LpAndItsTangents
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module subroutine plastic_results
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integer :: p
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character(len=pStringLen) :: group
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character(len=:), allocatable :: group
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plasticityLoop: do p=1,size(material_name_phase)
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group = trim('current/phase')//'/'//trim(material_name_phase(p))
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group = '/current/phase/'//trim(material_name_phase(p))
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call results_closeGroup(results_addGroup(group))
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group = trim(group)//'/plastic'
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|
|
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@ -735,7 +735,7 @@ subroutine crystallite_results
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|
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integer :: p,o
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real(pReal), allocatable, dimension(:,:,:) :: selected_tensors
|
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type(rotation), allocatable, dimension(:) :: selected_rotations
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real(pReal), allocatable, dimension(:,:) :: selected_rotations
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character(len=:), allocatable :: group,structureLabel
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do p=1,size(material_name_phase)
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@ -794,7 +794,8 @@ subroutine crystallite_results
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|||
end select
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selected_rotations = select_rotations(crystallite_orientation,p)
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call results_writeDataset(group,selected_rotations,output_constituent(p)%label(o),&
|
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'crystal orientation as quaternion',structureLabel)
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'crystal orientation as quaternion','q_0 <q_1 q_2 q_3>')
|
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call results_addAttribute('Lattice',structureLabel,group//'/'//output_constituent(p)%label(o))
|
||||
end select
|
||||
enddo
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||||
enddo
|
||||
|
|
@ -835,10 +836,10 @@ subroutine crystallite_results
|
|||
|
||||
integer, intent(in) :: instance
|
||||
type(rotation), dimension(:,:,:), intent(in) :: dataset
|
||||
type(rotation), allocatable, dimension(:) :: select_rotations
|
||||
real(pReal), allocatable, dimension(:,:) :: select_rotations
|
||||
integer :: e,i,c,j
|
||||
|
||||
allocate(select_rotations(count(material_phaseAt==instance)*homogenization_maxNconstituents*discretization_nIPs))
|
||||
allocate(select_rotations(4,count(material_phaseAt==instance)*homogenization_maxNconstituents*discretization_nIPs))
|
||||
|
||||
j=0
|
||||
do e = 1, size(material_phaseAt,2)
|
||||
|
|
@ -846,7 +847,7 @@ subroutine crystallite_results
|
|||
do c = 1, size(material_phaseAt,1) !ToDo: this needs to be changed for varying Ngrains
|
||||
if (material_phaseAt(c,e) == instance) then
|
||||
j = j + 1
|
||||
select_rotations(j) = dataset(c,i,e)
|
||||
select_rotations(1:4,j) = dataset(c,i,e)%asQuaternion()
|
||||
endif
|
||||
enddo
|
||||
enddo
|
||||
|
|
|
|||
|
|
@ -16,6 +16,7 @@ module grid_mech_FEM
|
|||
use IO
|
||||
use HDF5_utilities
|
||||
use math
|
||||
use rotations
|
||||
use spectral_utilities
|
||||
use FEsolving
|
||||
use config
|
||||
|
|
|
|||
|
|
@ -16,6 +16,7 @@ module grid_mech_spectral_basic
|
|||
use IO
|
||||
use HDF5_utilities
|
||||
use math
|
||||
use rotations
|
||||
use spectral_utilities
|
||||
use FEsolving
|
||||
use config
|
||||
|
|
|
|||
|
|
@ -16,6 +16,7 @@ module grid_mech_spectral_polarisation
|
|||
use IO
|
||||
use HDF5_utilities
|
||||
use math
|
||||
use rotations
|
||||
use spectral_utilities
|
||||
use FEsolving
|
||||
use config
|
||||
|
|
|
|||
|
|
@ -52,7 +52,7 @@ module material
|
|||
HOMOGENIZATION_RGC_ID
|
||||
end enum
|
||||
|
||||
character(len=pStringLen), public, protected, allocatable, dimension(:) :: &
|
||||
character(len=:), public, protected, allocatable, dimension(:) :: &
|
||||
material_name_phase, & !< name of each phase
|
||||
material_name_homogenization !< name of each homogenization
|
||||
|
||||
|
|
@ -392,13 +392,21 @@ end subroutine sanityCheck
|
|||
function getKeys(dict)
|
||||
|
||||
class(tNode), intent(in) :: dict
|
||||
character(len=pStringLen), dimension(:), allocatable :: getKeys
|
||||
character(len=:), dimension(:), allocatable :: getKeys
|
||||
character(len=pStringLen), dimension(:), allocatable :: temp
|
||||
|
||||
integer :: i
|
||||
integer :: i,l
|
||||
|
||||
allocate(getKeys(dict%length))
|
||||
allocate(temp(dict%length))
|
||||
l = 0
|
||||
do i=1, dict%length
|
||||
getKeys(i) = dict%getKey(i)
|
||||
temp(i) = dict%getKey(i)
|
||||
l = max(len_trim(temp(i)),l)
|
||||
enddo
|
||||
|
||||
allocate(character(l)::getKeys(dict%length))
|
||||
do i=1, dict%length
|
||||
getKeys(i) = trim(temp(i))
|
||||
enddo
|
||||
|
||||
end function getKeys
|
||||
|
|
|
|||
|
|
@ -8,7 +8,6 @@ module results
|
|||
use DAMASK_interface
|
||||
use parallelization
|
||||
use IO
|
||||
use rotations
|
||||
use HDF5_utilities
|
||||
#ifdef PETSc
|
||||
use PETSC
|
||||
|
|
@ -20,27 +19,21 @@ module results
|
|||
integer(HID_T) :: resultsFile
|
||||
|
||||
interface results_writeDataset
|
||||
|
||||
module procedure results_writeTensorDataset_real
|
||||
module procedure results_writeVectorDataset_real
|
||||
module procedure results_writeScalarDataset_real
|
||||
|
||||
module procedure results_writeTensorDataset_int
|
||||
module procedure results_writeVectorDataset_int
|
||||
|
||||
module procedure results_writeScalarDataset_rotation
|
||||
|
||||
end interface results_writeDataset
|
||||
|
||||
interface results_addAttribute
|
||||
|
||||
module procedure results_addAttribute_real
|
||||
module procedure results_addAttribute_int
|
||||
module procedure results_addAttribute_str
|
||||
|
||||
module procedure results_addAttribute_int_array
|
||||
module procedure results_addAttribute_real_array
|
||||
|
||||
end interface results_addAttribute
|
||||
|
||||
public :: &
|
||||
|
|
@ -74,7 +67,7 @@ subroutine results_init(restart)
|
|||
if(.not. restart) then
|
||||
resultsFile = HDF5_openFile(trim(getSolverJobName())//'.hdf5','w',.true.)
|
||||
call results_addAttribute('DADF5_version_major',0)
|
||||
call results_addAttribute('DADF5_version_minor',10)
|
||||
call results_addAttribute('DADF5_version_minor',11)
|
||||
call results_addAttribute('DAMASK_version',DAMASKVERSION)
|
||||
call get_command(commandLine)
|
||||
call results_addAttribute('Call',trim(commandLine))
|
||||
|
|
@ -465,38 +458,6 @@ subroutine results_writeTensorDataset_int(group,dataset,label,description,SIunit
|
|||
end subroutine results_writeTensorDataset_int
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief stores a scalar dataset in a group
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine results_writeScalarDataset_rotation(group,dataset,label,description,lattice_structure)
|
||||
|
||||
character(len=*), intent(in) :: label,group,description
|
||||
character(len=*), intent(in), optional :: lattice_structure
|
||||
type(rotation), intent(inout), dimension(:) :: dataset
|
||||
|
||||
integer(HID_T) :: groupHandle
|
||||
|
||||
groupHandle = results_openGroup(group)
|
||||
|
||||
#ifdef PETSc
|
||||
call HDF5_write(groupHandle,dataset,label,.true.)
|
||||
#else
|
||||
call HDF5_write(groupHandle,dataset,label,.false.)
|
||||
#endif
|
||||
|
||||
if (HDF5_objectExists(groupHandle,label)) &
|
||||
call HDF5_addAttribute(groupHandle,'Description',description,label)
|
||||
if (HDF5_objectExists(groupHandle,label) .and. present(lattice_structure)) &
|
||||
call HDF5_addAttribute(groupHandle,'Lattice',lattice_structure,label)
|
||||
if (HDF5_objectExists(groupHandle,label)) &
|
||||
call HDF5_addAttribute(groupHandle,'Creator','DAMASK '//DAMASKVERSION,label)
|
||||
if (HDF5_objectExists(groupHandle,label)) &
|
||||
call HDF5_addAttribute(groupHandle,'Created',now(),label)
|
||||
call HDF5_closeGroup(groupHandle)
|
||||
|
||||
end subroutine results_writeScalarDataset_rotation
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief adds the unique mapping from spatial position and constituent ID to results
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
|
|
@ -504,7 +465,7 @@ subroutine results_mapping_constituent(phaseAt,memberAtLocal,label)
|
|||
|
||||
integer, dimension(:,:), intent(in) :: phaseAt !< phase section at (constituent,element)
|
||||
integer, dimension(:,:,:), intent(in) :: memberAtLocal !< phase member at (constituent,IP,element)
|
||||
character(len=pStringLen), dimension(:), intent(in) :: label !< label of each phase section
|
||||
character(len=*), dimension(:), intent(in) :: label !< label of each phase section
|
||||
|
||||
integer, dimension(size(memberAtLocal,1),size(memberAtLocal,2),size(memberAtLocal,3)) :: &
|
||||
phaseAtMaterialpoint, &
|
||||
|
|
@ -527,7 +488,6 @@ subroutine results_mapping_constituent(phaseAt,memberAtLocal,label)
|
|||
plist_id, &
|
||||
dt_id
|
||||
|
||||
|
||||
integer(SIZE_T) :: type_size_string, type_size_int
|
||||
integer :: hdferr, ierr, i
|
||||
|
||||
|
|
@ -659,7 +619,7 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
|
|||
|
||||
integer, dimension(:), intent(in) :: homogenizationAt !< homogenization section at (element)
|
||||
integer, dimension(:,:), intent(in) :: memberAtLocal !< homogenization member at (IP,element)
|
||||
character(len=pStringLen), dimension(:), intent(in) :: label !< label of each homogenization section
|
||||
character(len=*), dimension(:), intent(in) :: label !< label of each homogenization section
|
||||
|
||||
integer, dimension(size(memberAtLocal,1),size(memberAtLocal,2)) :: &
|
||||
homogenizationAtMaterialpoint, &
|
||||
|
|
@ -682,7 +642,6 @@ subroutine results_mapping_homogenization(homogenizationAt,memberAtLocal,label)
|
|||
plist_id, &
|
||||
dt_id
|
||||
|
||||
|
||||
integer(SIZE_T) :: type_size_string, type_size_int
|
||||
integer :: hdferr, ierr, i
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue