Ejemplo n.º 1
0
def photon_sampling_setup(mesh, phtn_src, tags):
    """This function reads in an ALARA photon source file and creates and tags
    photon source densities onto a Mesh object for the second R2S transport
    step.

    Parameters
    ----------
    mesh : PyNE Mesh
       The object containing the iMesh instance to be tagged.
    phtn_src : str
        The path of the ALARA phtn_file.
    tags: dict
        A dictionary were the keys are tuples with two values. The first is a
        string denoting an nuclide in any form that is understood by
        pyne.nucname (e.g. '1001', 'U-235', '242Am') or 'TOTAL' for all
        nuclides. The second is a string denoting the decay time as it appears
        in the phtn_src file (e.g. 'shutdown', '1 h' '3 d'). The values of the
        dictionary are the requested tag names for the combination of nuclide
        and decay time. These tag names should be the tag names that are read
        by the sampling subroutine. For example:

        tags = {('U-235', 'shutdown'): 'tag1', ('TOTAL', '1 h'): 'tag2'}
    """
    photon_source_to_hdf5(phtn_src)
    h5_file = phtn_src + ".h5"
    photon_source_hdf5_to_mesh(mesh, h5_file, tags)
Ejemplo n.º 2
0
def test_photon_source_hdf5_to_mesh():
    """Tests the function photon source_h5_to_mesh."""

    if not HAVE_PYTAPS:
        raise SkipTest

    filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
    photon_source_to_hdf5(filename, chunkshape=(10, ))
    assert_true(os.path.exists(filename + '.h5'))

    mesh = Mesh(structured=True,
                structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])

    tags = {('1001', 'shutdown'): 'tag1', ('TOTAL', '1 h'): 'tag2'}
    photon_source_hdf5_to_mesh(mesh, filename + '.h5', tags)

    # create lists of lists of expected results
    tag1_answers = [[1] + [0] * 41, [2] + [0] * 41, [3] + [0] * 41,
                    [4] + [0] * 41]
    tag2_answers = [[5] + [0] * 41, [6] + [0] * 41, [7] + [0] * 41,
                    [8] + [0] * 41]

    ves = list(mesh.structured_iterate_hex("xyz"))
    for i, ve in enumerate(ves):
        assert_array_equal(mesh.mesh.getTagHandle("tag1")[ve], tag1_answers[i])
        assert_array_equal(mesh.mesh.getTagHandle("tag2")[ve], tag2_answers[i])

    if os.path.isfile(filename + '.h5'):
        os.remove(filename + '.h5')
Ejemplo n.º 3
0
Archivo: r2s.py Proyecto: gonuke/pyne
def photon_sampling_setup(mesh, phtn_src, tags):
    """This function reads in an ALARA photon source file and creates and tags
    photon source densities onto a Mesh object for the second R2S transport
    step.

    Parameters
    ----------
    mesh : PyNE Mesh
        The object containing the mesh instance to be tagged.
    phtn_src : str
        The path of the ALARA phtn_file.
    tags: dict
        A dictionary were the keys are tuples with two values. The first is a
        string denoting an nuclide in any form that is understood by
        pyne.nucname (e.g. '1001', 'U-235', '242Am') or 'TOTAL' for all
        nuclides. The second is a string denoting the decay time as it appears
        in the phtn_src file (e.g. 'shutdown', '1 h' '3 d'). The values of the
        dictionary are the requested tag names for the combination of nuclide
        and decay time. These tag names should be the tag names that are read
        by the sampling subroutine. For example:

        tags = {('U-235', 'shutdown'): 'tag1', ('TOTAL', '1 h'): 'tag2'}
    """
    photon_source_to_hdf5(phtn_src)
    h5_file = phtn_src + ".h5"
    photon_source_hdf5_to_mesh(mesh, h5_file, tags)
Ejemplo n.º 4
0
def test_photon_source_hdf5_to_mesh():
    """Tests the function photon source_h5_to_mesh."""

    if not HAVE_PYTAPS:
        raise SkipTest

    filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
    photon_source_to_hdf5(filename, chunkshape=(10,))
    assert_true(os.path.exists(filename + ".h5"))

    mesh = Mesh(structured=True, structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])

    tags = {("1001", "shutdown"): "tag1", ("TOTAL", "1 h"): "tag2"}
    photon_source_hdf5_to_mesh(mesh, filename + ".h5", tags)

    # create lists of lists of expected results
    tag1_answers = [[1] + [0] * 41, [2] + [0] * 41, [3] + [0] * 41, [4] + [0] * 41]
    tag2_answers = [[5] + [0] * 41, [6] + [0] * 41, [7] + [0] * 41, [8] + [0] * 41]

    ves = list(mesh.structured_iterate_hex("xyz"))
    for i, ve in enumerate(ves):
        assert_array_equal(mesh.mesh.getTagHandle("tag1")[ve], tag1_answers[i])
        assert_array_equal(mesh.mesh.getTagHandle("tag2")[ve], tag2_answers[i])

    if os.path.isfile(filename + ".h5"):
        os.remove(filename + ".h5")
Ejemplo n.º 5
0
def step2():
    config = ConfigParser.ConfigParser()
    config.read(config_filename)
    structured = config.getboolean("general", "structured")
    sub_voxel = config.getboolean("general", "sub_voxel")
    decay_times = config.get("step2", "decay_times").split(",")
    output = config.get("step2", "output")
    tot_phtn_src_intensities = config.get("step2", "tot_phtn_src_intensities")
    tag_name = "source_density"

    if sub_voxel:
        geom = config.get("step1", "geom")
        load(geom)
        cell_mats = cell_materials(geom)
    else:
        cell_mats = None
    h5_file = "phtn_src.h5"
    if not isfile(h5_file):
        photon_source_to_hdf5(filename="phtn_src", nucs="total")
    intensities = "Total photon source intensities (p/s)\n"
    e_bounds = phtn_src_energy_bounds("alara_inp")
    for i in range(len(e_bounds)):
        e_bounds[i] /= 1.0e6  # convert unit from eV to MeV
    for i, dt in enumerate(decay_times):
        print("Writing source for decay time: {0} to mesh".format(dt))
        mesh = Mesh(structured=structured, mesh="blank_mesh.h5m")
        tags = {("TOTAL", dt): tag_name}
        photon_source_hdf5_to_mesh(mesh,
                                   h5_file,
                                   tags,
                                   sub_voxel=sub_voxel,
                                   cell_mats=cell_mats)
        p_src_filename = "{0}_{1}.h5m".format(output, i + 1)
        intensity = total_photon_source_intensity(mesh,
                                                  tag_name,
                                                  sub_voxel=sub_voxel)
        mesh = tag_e_bounds(mesh, e_bounds)
        mesh = tag_source_intensity(mesh, intensity)
        # get and tag decay time
        decay_time = to_sec(float(dt.split()[0]), dt.split()[1])
        mesh = tag_decay_time(mesh, decay_time)
        # set version manually when changing the information of source.h5m
        mesh = tag_version(mesh)
        mesh.write_hdf5("{0}_{1}.h5m".format(output, i + 1))
        intensities += "{0}: {1}\n".format(dt, intensity)

    with open(tot_phtn_src_intensities, "w") as f:
        f.write(intensities)

    print("R2S step2 complete.")
Ejemplo n.º 6
0
def test_photon_source_hdf5_to_mesh_subvoxel():
    """Tests the function photon source_h5_to_mesh
    under sub-voxel r2s condition."""

    if not HAVE_PYMOAB:
        raise SkipTest

    filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
    photon_source_to_hdf5(filename, chunkshape=(10, ))
    assert_true(os.path.exists(filename + '.h5'))
    sub_voxel = True
    mesh = Mesh(structured=True,
                structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])
    cell_fracs = np.zeros(6,
                          dtype=[('idx', np.int64), ('cell', np.int64),
                                 ('vol_frac', np.float64),
                                 ('rel_error', np.float64)])

    cell_fracs[:] = [(0, 11, 1.0, 0.0), (1, 11, 0.5, 0.0), (1, 12, 0.5, 0.0),
                     (2, 11, 0.5, 0.0), (2, 13, 0.5, 0.0), (3, 13, 1.0, 0.0)]

    cell_mats = {
        11: Material({'H': 1.0}, density=1.0),
        12: Material({'He': 1.0}, density=1.0),
        13: Material({}, density=0.0, metadata={'name': 'void'})
    }
    mesh.tag_cell_fracs(cell_fracs)
    tags = {('1001', 'shutdown'): 'tag1', ('TOTAL', '1 h'): 'tag2'}

    photon_source_hdf5_to_mesh(mesh,
                               filename + '.h5',
                               tags,
                               sub_voxel=sub_voxel,
                               cell_mats=cell_mats)

    # create lists of lists of expected results
    tag1_answers = [[1.0] + [0.0] * 41 + [0.0] * 42,
                    [2.0] + [0.0] * 41 + [3.0] + [0.0] * 41,
                    [4.0] + [0.0] * 41 + [0.0] * 42, [0.0] * 42 * 2]
    tag2_answers = [[5.0] + [0.0] * 41 + [0.0] * 42,
                    [6.0] + [0.0] * 41 + [7.0] + [0.0] * 41,
                    [8.0] + [0.0] * 41 + [0.0] * 42, [0.0] * 42 * 2]

    for i, _, ve in mesh:
        assert_array_equal(mesh.tag1[ve], tag1_answers[i])
        assert_array_equal(mesh.tag2[ve], tag2_answers[i])

    if os.path.isfile(filename + '.h5'):
        os.remove(filename + '.h5')
Ejemplo n.º 7
0
def step2():
    config = ConfigParser.ConfigParser()
    config.read(config_filename)
    structured = config.getboolean('general', 'structured')
    sub_voxel = config.getboolean('general', 'sub_voxel')
    decay_times = config.get('step2', 'decay_times').split(',')
    output = config.get('step2', 'output')
    tot_phtn_src_intensities = config.get('step2', 'tot_phtn_src_intensities')
    tag_name = "source_density"

    if sub_voxel:
        geom = config.get('step1', 'geom')
        load(geom)
        cell_mats = cell_materials(geom)
    else:
        cell_mats = None
    h5_file = 'phtn_src.h5'
    if not isfile(h5_file):
        photon_source_to_hdf5('phtn_src')
    intensities = "Total photon source intensities (p/s)\n"
    for i, dc in enumerate(decay_times):
        print('Writing source for decay time: {0}'.format(dc))
        mesh = Mesh(structured=structured, mesh='blank_mesh.h5m')
        tags = {('TOTAL', dc): tag_name}
        photon_source_hdf5_to_mesh(mesh,
                                   h5_file,
                                   tags,
                                   sub_voxel=sub_voxel,
                                   cell_mats=cell_mats)
        mesh.write_hdf5('{0}_{1}.h5m'.format(output, i + 1))
        intensity = total_photon_source_intensity(mesh,
                                                  tag_name,
                                                  sub_voxel=sub_voxel)
        intensities += "{0}: {1}\n".format(dc, intensity)

    with open(tot_phtn_src_intensities, 'w') as f:
        f.write(intensities)

    e_bounds = phtn_src_energy_bounds("alara_inp")
    e_bounds_str = ""
    for e in e_bounds:
        e = e / 1e6  # convert unit to MeV
        e_bounds_str += "{0}\n".format(e)
    with open("e_bounds", 'w') as f:
        f.write(e_bounds_str)

    print('R2S step2 complete.')
Ejemplo n.º 8
0
def step2():
    config = ConfigParser.ConfigParser()
    config.read(config_filename)
    structured = config.getboolean('general', 'structured')
    sub_voxel = config.getboolean('general', 'sub_voxel')
    decay_times = config.get('step2', 'decay_times').split(',')
    output = config.get('step2', 'output')
    tot_phtn_src_intensities = config.get('step2', 'tot_phtn_src_intensities')
    tag_name = "source_density"

    if sub_voxel:
        geom = config.get('step1', 'geom')
        load(geom)
        cell_mats = cell_materials(geom)
    else:
        cell_mats = None
    h5_file = 'phtn_src.h5'
    if not isfile(h5_file):
        photon_source_to_hdf5(filename='phtn_src', nucs='total')
    intensities = "Total photon source intensities (p/s)\n"
    e_bounds = phtn_src_energy_bounds("alara_inp")
    for i in range(len(e_bounds)):
        e_bounds[i] /= 1.0e6 # convert unit from eV to MeV
    for i, dt in enumerate(decay_times):
        print('Writing source for decay time: {0} to mesh'.format(dt))
        mesh = Mesh(structured=structured, mesh='blank_mesh.h5m')
        tags = {('TOTAL', dt): tag_name}
        photon_source_hdf5_to_mesh(mesh, h5_file, tags, sub_voxel=sub_voxel,
                                   cell_mats=cell_mats)
        intensity = total_photon_source_intensity(mesh, tag_name,
                                                  sub_voxel=sub_voxel)
        mesh = tag_e_bounds(mesh, e_bounds)
        mesh = tag_source_intensity(mesh, intensity)
        # get and tag decay time
        decay_time = to_sec(float(dt.split()[0]), dt.split()[1])
        mesh = tag_decay_time(mesh, decay_time)
        # set version manually when changing the information of source.h5m
        mesh = tag_version(mesh)
        mesh.write_hdf5('{0}_{1}.h5m'.format(output, i+1))
        intensities += "{0}: {1}\n".format(dt, intensity)

    with open(tot_phtn_src_intensities, 'w') as f:
        f.write(intensities)

    print('R2S step2 complete.')
Ejemplo n.º 9
0
def test_photon_source_hdf5_to_mesh_subvoxel_size1():
    """Tests the function photon source_h5_to_mesh
    under sub-voxel r2s condition."""

    if not HAVE_PYMOAB:
        raise SkipTest

    filename = os.path.join(thisdir, "files_test_alara", "phtn_src")
    photon_source_to_hdf5(filename, chunkshape=(10, ))
    assert_true(os.path.exists(filename + ".h5"))
    sub_voxel = True
    mesh = Mesh(structured=True,
                structured_coords=[[0, 1, 2], [0, 1, 2], [0, 1]])
    cell_fracs = np.zeros(
        4,
        dtype=[
            ("idx", np.int64),
            ("cell", np.int64),
            ("vol_frac", np.float64),
            ("rel_error", np.float64),
        ],
    )

    cell_fracs[:] = [
        (0, 11, 1.0, 0.0),
        (1, 12, 1.0, 0.0),
        (2, 13, 1.0, 0.0),
        (3, 14, 1.0, 0.0),
    ]

    cell_mats = {
        11: Material({"H": 1.0}, density=1.0),
        12: Material({"He": 1.0}, density=1.0),
        13: Material({"He": 1.0}, density=1.0),
        14: Material({}, density=0.0, metadata={"name": "void"}),
    }
    mesh.tag_cell_fracs(cell_fracs)
    tags = {("1001", "shutdown"): "tag1", ("TOTAL", "1 h"): "tag2"}

    photon_source_hdf5_to_mesh(mesh,
                               filename + ".h5",
                               tags,
                               sub_voxel=sub_voxel,
                               cell_mats=cell_mats)

    # create lists of lists of expected results
    tag1_answers = [
        [1.0] + [0.0] * 41,
        [2.0] + [0.0] * 41,
        [3.0] + [0.0] * 41,
        [0.0] * 42,
    ]
    tag2_answers = [
        [5.0] + [0.0] * 41,
        [6.0] + [0.0] * 41,
        [7.0] + [0.0] * 41,
        [0.0] * 42,
    ]

    for i, _, ve in mesh:
        assert_array_equal(mesh.tag1[ve], tag1_answers[i])
        assert_array_equal(mesh.tag2[ve], tag2_answers[i])

    if os.path.isfile(filename + ".h5"):
        os.remove(filename + ".h5")