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Add from_hdf5() in IncidentPhoton
This commit is contained in:
liangjg
parent
99e5d0ba12
commit
fefb68a866
1 changed files with 308 additions and 120 deletions
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@ -19,13 +19,13 @@ from .endf import Evaluation, get_head_record, get_tab1_record, get_list_record
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from .function import Tabulated1D
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# Electron subshell labels
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_SUBSHELLS = ['K', 'L1', 'L2', 'L3', 'M1', 'M2', 'M3', 'M4', 'M5',
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'N1', 'N2', 'N3', 'N4', 'N5', 'N6', 'N7', 'O1', 'O2',
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'O3', 'O4', 'O5', 'O6', 'O7', 'O8', 'O9', 'P1', 'P2',
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'P3', 'P4', 'P5', 'P6', 'P7', 'P8', 'P9', 'P10', 'P11',
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'Q1', 'Q2', 'Q3']
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# Helper function to map designator to subshell string or None
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def _subshell(i):
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if i == 0:
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@ -33,57 +33,56 @@ def _subshell(i):
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else:
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return _SUBSHELLS[i - 1]
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_REACTION_NAME = {
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501: 'Total photon interaction',
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502: 'Photon coherent scattering',
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504: 'Photon incoherent scattering',
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515: 'Pair production, electron field',
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516: 'Total pair production',
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517: 'Pair production, nuclear field',
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522: 'Photoelectric absorption',
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526: 'Electro-atomic scattering',
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527: 'Electro-atomic bremsstrahlung',
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528: 'Electro-atomic excitation',
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534: 'K (1s1/2) subshell photoelectric',
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535: 'L1 (2s1/2) subshell photoelectric',
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536: 'L2 (2p1/2) subshell photoelectric',
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537: 'L3 (2p3/2) subshell photoelectric',
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538: 'M1 (3s1/2) subshell photoelectric',
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539: 'M2 (3p1/2) subshell photoelectric',
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540: 'M3 (3p3/2) subshell photoelectric',
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541: 'M4 (3d3/2) subshell photoelectric',
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542: 'M5 (3d5/2) subshell photoelectric',
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543: 'N1 (4s1/2) subshell photoelectric',
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544: 'N2 (4p1/2) subshell photoelectric',
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545: 'N3 (4p3/2) subshell photoelectric',
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546: 'N4 (4d3/2) subshell photoelectric',
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547: 'N5 (4d5/2) subshell photoelectric',
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548: 'N6 (4f5/2) subshell photoelectric',
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549: 'N7 (4f7/2) subshell photoelectric',
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550: 'O1 (5s1/2) subshell photoelectric',
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551: 'O2 (5p1/2) subshell photoelectric',
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552: 'O3 (5p3/2) subshell photoelectric',
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553: 'O4 (5d3/2) subshell photoelectric',
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554: 'O5 (5d5/2) subshell photoelectric',
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555: 'O6 (5f5/2) subshell photoelectric',
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556: 'O7 (5f7/2) subshell photoelectric',
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557: 'O8 (5g7/2) subshell photoelectric',
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558: 'O9 (5g9/2) subshell photoelectric',
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559: 'P1 (6s1/2) subshell photoelectric',
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560: 'P2 (6p1/2) subshell photoelectric',
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561: 'P3 (6p3/2) subshell photoelectric',
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562: 'P4 (6d3/2) subshell photoelectric',
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563: 'P5 (6d5/2) subshell photoelectric',
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564: 'P6 (6f5/2) subshell photoelectric',
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565: 'P7 (6f7/2) subshell photoelectric',
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566: 'P8 (6g7/2) subshell photoelectric',
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567: 'P9 (6g9/2) subshell photoelectric',
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568: 'P10 (6h9/2) subshell photoelectric',
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569: 'P11 (6h11/2) subshell photoelectric',
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570: 'Q1 (7s1/2) subshell photoelectric',
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571: 'Q2 (7p1/2) subshell photoelectric',
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572: 'Q3 (7p3/2) subshell photoelectric'
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501: ('Total photon interaction', 'total'),
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502: ('Photon coherent scattering', 'coherent'),
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504: ('Photon incoherent scattering', 'incoherent'),
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515: ('Pair production, electron field', 'pair_production_electron'),
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516: ('Total pair production', 'pair_production_total'),
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517: ('Pair production, nuclear field', 'pair_production_nuclear'),
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522: ('Photoelectric absorption', 'photoelectric'),
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526: ('Electro-atomic scattering', 'electro_atomic_scat'),
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527: ('Electro-atomic bremsstrahlung', 'electro_atomic_brem'),
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528: ('Electro-atomic excitation', 'electro_atomic_excit'),
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534: ('K (1s1/2) subshell photoelectric', 'K'),
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535: ('L1 (2s1/2) subshell photoelectric', 'L1'),
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536: ('L2 (2p1/2) subshell photoelectric', 'L2'),
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537: ('L3 (2p3/2) subshell photoelectric', 'L3'),
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538: ('M1 (3s1/2) subshell photoelectric', 'M1'),
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539: ('M2 (3p1/2) subshell photoelectric', 'M2'),
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540: ('M3 (3p3/2) subshell photoelectric', 'M3'),
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541: ('M4 (3d3/2) subshell photoelectric', 'M4'),
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542: ('M5 (3d5/2) subshell photoelectric', 'M5'),
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543: ('N1 (4s1/2) subshell photoelectric', 'N1'),
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544: ('N2 (4p1/2) subshell photoelectric', 'N2'),
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545: ('N3 (4p3/2) subshell photoelectric', 'N3'),
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546: ('N4 (4d3/2) subshell photoelectric', 'N4'),
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547: ('N5 (4d5/2) subshell photoelectric', 'N5'),
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548: ('N6 (4f5/2) subshell photoelectric', 'N6'),
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549: ('N7 (4f7/2) subshell photoelectric', 'N7'),
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550: ('O1 (5s1/2) subshell photoelectric', 'O1'),
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551: ('O2 (5p1/2) subshell photoelectric', 'O2'),
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552: ('O3 (5p3/2) subshell photoelectric', 'O3'),
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553: ('O4 (5d3/2) subshell photoelectric', 'O4'),
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554: ('O5 (5d5/2) subshell photoelectric', 'O5'),
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555: ('O6 (5f5/2) subshell photoelectric', 'O6'),
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556: ('O7 (5f7/2) subshell photoelectric', 'O7'),
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557: ('O8 (5g7/2) subshell photoelectric', 'O8'),
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558: ('O9 (5g9/2) subshell photoelectric', 'O9'),
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559: ('P1 (6s1/2) subshell photoelectric', 'P1'),
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560: ('P2 (6p1/2) subshell photoelectric', 'P2'),
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561: ('P3 (6p3/2) subshell photoelectric', 'P3'),
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562: ('P4 (6d3/2) subshell photoelectric', 'P4'),
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563: ('P5 (6d5/2) subshell photoelectric', 'P5'),
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564: ('P6 (6f5/2) subshell photoelectric', 'P6'),
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565: ('P7 (6f7/2) subshell photoelectric', 'P7'),
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566: ('P8 (6g7/2) subshell photoelectric', 'P8'),
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567: ('P9 (6g9/2) subshell photoelectric', 'P9'),
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568: ('P10 (6h9/2) subshell photoelectric', 'P10'),
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569: ('P11 (6h11/2) subshell photoelectric', 'P11'),
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570: ('Q1 (7s1/2) subshell photoelectric', 'Q1'),
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571: ('Q2 (7p1/2) subshell photoelectric', 'Q2'),
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572: ('Q3 (7p3/2) subshell photoelectric', 'Q3')
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}
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# Compton profiles are read from a pre-generated HDF5 file when they are first
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@ -323,8 +322,72 @@ class AtomicRelaxation(EqualityMixin):
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# Return instance of class
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return cls(binding_energy, num_electrons, transitions)
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def to_hdf5(self, group):
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raise NotImplementedError
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@classmethod
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def from_hdf5(cls, group):
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"""Generate atomic relaxation data from an HDF5 group
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Parameters
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----------
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group : h5py.Group
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HDF5 group to read from
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Returns
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-------
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openmc.data.AtomicRelaxation
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Atomic relaxation data
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"""
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# Create data dictionaries
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binding_energy = {}
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num_electrons = {}
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transitions = {}
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designators = [s.decode() for s in group.attrs['designators']]
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shell_values = [None] + _SUBSHELLS
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columns = ['secondary', 'tertiary', 'energy (eV)', 'probability']
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for shell in designators:
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# Shell group
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sub_group = group[shell]
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# Read subshell binding energy and number of electrons
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if 'binding_energy' in sub_group.attrs:
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binding_energy[shell] = sub_group.attrs['binding_energy']
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if 'num_electrons' in sub_group.attrs:
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num_electrons[shell] = sub_group.attrs['num_electrons']
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# Read transition data
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if 'transitions' in sub_group:
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df = pd.DataFrame(sub_group['transitions'].value,
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columns=columns)
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# Replace float indexes back to subshell strings
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df[columns[:2]] = df[columns[:2]].replace(
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np.arange(float(len(shell_values))), shell_values)
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transitions[shell] = df
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return cls(binding_energy, num_electrons, transitions)
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def to_hdf5(self, group, shell):
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"""Write atomic relaxation data to an HDF5 group
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Parameters
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----------
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group : h5py.Group
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HDF5 group to write to
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shell : str
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The subshell to write data for
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"""
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# Write subshell binding energy and number of electrons
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group.attrs['binding_energy'] = self.binding_energy[shell]
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group.attrs['num_electrons'] = self.num_electrons[shell]
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# Write transition data with replacements
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if shell in self.transitions:
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shell_values = [None] + _SUBSHELLS
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df = self.transitions[shell].replace(
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shell_values, range(len(shell_values)))
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group.create_dataset('transitions', data=df.values.astype(float))
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class IncidentPhoton(EqualityMixin):
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@ -580,6 +643,89 @@ class IncidentPhoton(EqualityMixin):
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return data
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@classmethod
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def from_hdf5(cls, group_or_filename):
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"""Generate photon reaction from an HDF5 group
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Parameters
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----------
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group_or_filename : h5py.Group or str
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HDF5 group containing interaction data. If given as a string, it is
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assumed to be the filename for the HDF5 file, and the first group is
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used to read from.
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Returns
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-------
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openmc.data.IncidentPhoton
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Photon interaction data
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"""
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if isinstance(group_or_filename, h5py.Group):
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group = group_or_filename
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else:
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h5file = h5py.File(str(group_or_filename), 'r')
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# Make sure version matches
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if 'version' in h5file.attrs:
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major, minor = h5file.attrs['version']
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# For now all versions of HDF5 data can be read
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else:
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raise IOError(
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'HDF5 data does not indicate a version. Your installation '
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'of the OpenMC Python API expects version {}.x data.'
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.format(HDF5_VERSION_MAJOR))
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group = list(h5file.values())[0]
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Z = group.attrs['Z']
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data = cls(Z)
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# Read energy grid
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energy= group['energy'].value
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# Read cross section data
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for mt, (name, key) in _REACTION_NAME.items():
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if key in group:
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rgroup = group[key]
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elif key in group['subshells']:
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rgroup = group['subshells'][key]
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else:
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continue
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data.reactions[mt] = PhotonReaction.from_hdf5(rgroup, mt, energy)
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# Check for necessary reactions
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for mt in [502, 504, 522]:
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assert mt in data, "Reaction {} not found".format(mt)
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# Read atomic relaxation
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data.atomic_relaxation = AtomicRelaxation.from_hdf5(group['subshells'])
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# Read Compton profiles
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if 'compton_profiles' in group:
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rgroup = group['compton_profiles']
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profile = data.compton_profiles
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profile['num_electrons'] = rgroup['num_electrons'].value
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profile['binding_energy'] = rgroup['binding_energy'].value
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# Get electron momentum values
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pz = rgroup['pz'].value
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J = rgroup['J'].value
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if pz.size != J.shape[1]:
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raise ValueError("'J' array shape is not consistent with the "
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"'pz' array shape")
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profile['J'] = [Tabulated1D(pz, Jk) for Jk in J]
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# Read bremsstrahlung
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if 'bremsstrahlung' in group:
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rgroup = group['bremsstrahlung']
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data.bremsstrahlung['I'] = rgroup.attrs['I']
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for key in ('dcs', 'electron_energy', 'ionization_energy',
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'num_electrons', 'photon_energy'):
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data.bremsstrahlung[key] = rgroup[key].value
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return data
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def export_to_hdf5(self, path, mode='a', libver='earliest'):
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"""Export incident photon data to an HDF5 file.
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@ -590,6 +736,9 @@ class IncidentPhoton(EqualityMixin):
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mode : {'r', r+', 'w', 'x', 'a'}
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Mode that is used to open the HDF5 file. This is the second argument
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to the :class:`h5py.File` constructor.
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libver : {'earliest', 'latest'}
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Compatibility mode for the HDF5 file. 'latest' will produce files
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that are less backwards compatible but have performance benefits.
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"""
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# Open file and write version
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@ -607,77 +756,25 @@ class IncidentPhoton(EqualityMixin):
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union_grid = np.union1d(union_grid, rx.xs.x)
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group.create_dataset('energy', data=union_grid)
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# Write coherent scattering cross section
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rx = self.reactions[502]
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coh_group = group.create_group('coherent')
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coh_group.create_dataset('xs', data=rx.xs(union_grid))
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if rx.scattering_factor is not None:
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# Create integrated form factor
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ff = deepcopy(rx.scattering_factor)
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ff.x *= ff.x
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ff.y *= ff.y/Z**2
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int_ff = Tabulated1D(ff.x, ff.integral())
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int_ff.to_hdf5(coh_group, 'integrated_scattering_factor')
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if rx.anomalous_real is not None:
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rx.anomalous_real.to_hdf5(coh_group, 'anomalous_real')
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if rx.anomalous_imag is not None:
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rx.anomalous_imag.to_hdf5(coh_group, 'anomalous_imag')
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# Write incoherent scattering cross section
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rx = self[504]
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incoh_group = group.create_group('incoherent')
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incoh_group.create_dataset('xs', data=rx.xs(union_grid))
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if rx.scattering_factor is not None:
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rx.scattering_factor.to_hdf5(incoh_group, 'scattering_factor')
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# Write electron-field pair production cross section
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if 515 in self:
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pair_group = group.create_group('pair_production_electron')
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pair_group.create_dataset('xs', data=self[515].xs(union_grid))
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# Write nuclear-field pair production cross section
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if 517 in self:
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pair_group = group.create_group('pair_production_nuclear')
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pair_group.create_dataset('xs', data=self[517].xs(union_grid))
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# Write photoelectric cross section
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photoelec_group = group.create_group('photoelectric')
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photoelec_group.create_dataset('xs', data=self[522].xs(union_grid))
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# Write photoionization cross sections
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# Write cross sections
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shell_group = group.create_group('subshells')
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designators = []
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for mt, rx in self.reactions.items():
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if mt >= 534 and mt <= 572:
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# Get name of subshell
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shell = _SUBSHELLS[mt - 534]
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designators.append(shell)
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sub_group = shell_group.create_group(shell)
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name, key = _REACTION_NAME[mt]
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if mt in [502, 504, 515, 517, 522]:
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sub_group = group.create_group(key)
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elif mt >= 534 and mt <= 572:
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# Subshell
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designators.append(key)
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sub_group = shell_group.create_group(key)
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if self.atomic_relaxation is not None:
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relax = self.atomic_relaxation
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# Write subshell binding energy and number of electrons
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sub_group.attrs['binding_energy'] = relax.binding_energy[shell]
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sub_group.attrs['num_electrons'] = relax.num_electrons[shell]
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# Write atomic relaxation
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if key in self.atomic_relaxation.subshells:
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self.atomic_relaxation.to_hdf5(sub_group, key)
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else:
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continue
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# Write transition data with replacements
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if shell in relax.transitions:
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shell_values = _SUBSHELLS.copy()
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shell_values.insert(0, None)
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df = relax.transitions[shell].replace(
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shell_values, range(len(shell_values)))
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sub_group.create_dataset(
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'transitions', data=df.values.astype(float))
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# Determine threshold
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threshold = rx.xs.x[0]
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idx = np.searchsorted(union_grid, threshold, side='right') - 1
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# Interpolate cross section onto union grid and write
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photoionization = rx.xs(union_grid[idx:])
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sub_group.create_dataset('xs', data=photoionization)
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assert len(union_grid) == len(photoionization) + idx
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sub_group['xs'].attrs['threshold_idx'] = idx
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rx.to_hdf5(sub_group, union_grid, Z)
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shell_group.attrs['designators'] = np.array(designators, dtype='S')
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@ -707,6 +804,7 @@ class IncidentPhoton(EqualityMixin):
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else:
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brem_group.create_dataset(key, data=value)
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def _add_bremsstrahlung(self):
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"""Add the data used in the thick-target bremsstrahlung approximation
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@ -805,7 +903,7 @@ class PhotonReaction(EqualityMixin):
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def __repr__(self):
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if self.mt in _REACTION_NAME:
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return "<Photon Reaction: MT={} {}>".format(
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self.mt, _REACTION_NAME[self.mt])
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self.mt, _REACTION_NAME[self.mt][0])
|
||||
else:
|
||||
return "<Photon Reaction: MT={}>".format(self.mt)
|
||||
|
||||
|
|
@ -982,3 +1080,93 @@ class PhotonReaction(EqualityMixin):
|
|||
params, rx.anomalous_imag = get_tab1_record(file_obj)
|
||||
|
||||
return rx
|
||||
|
||||
@classmethod
|
||||
def from_hdf5(cls, group, mt, energy):
|
||||
"""Generate photon reaction from an HDF5 group
|
||||
|
||||
Parameters
|
||||
----------
|
||||
group : h5py.Group
|
||||
HDF5 group to read from
|
||||
mt : int
|
||||
The MT value of the reaction to get data for
|
||||
energy : Iterable of float
|
||||
arrays of energies at which cross sections are tabulated at
|
||||
|
||||
Returns
|
||||
-------
|
||||
openmc.data.PhotonReaction
|
||||
Photon reaction data
|
||||
|
||||
"""
|
||||
# Create instance
|
||||
rx = cls(mt)
|
||||
|
||||
# Cross sections
|
||||
xs = group['xs'].value
|
||||
# Replace zero elements to small non-zero to enable log-log
|
||||
xs[xs == 0.0] = np.exp(-500.0)
|
||||
|
||||
# Threshold
|
||||
threshold_idx = 0
|
||||
if 'threshold_idx' in group['xs'].attrs:
|
||||
threshold_idx = group['xs'].attrs['threshold_idx']
|
||||
|
||||
# Store
|
||||
rx.xs = Tabulated1D(energy[threshold_idx:], xs, [len(xs)], [5])
|
||||
|
||||
# Check for anomalous scattering factor
|
||||
if 'anomalous_real' in group:
|
||||
rx.anomalous_real = Tabulated1D.from_hdf5(group['anomalous_real'])
|
||||
if 'anomalous_imag' in group:
|
||||
rx.anomalous_imag = Tabulated1D.from_hdf5(group['anomalous_imag'])
|
||||
|
||||
# Check for factors / scattering functions
|
||||
if 'scattering_factor' in group:
|
||||
rx.scattering_factor = Tabulated1D.from_hdf5(group['scattering_factor'])
|
||||
|
||||
return rx
|
||||
|
||||
def to_hdf5(self, group, energy, Z):
|
||||
"""Write photon reaction to an HDF5 group
|
||||
|
||||
Parameters
|
||||
----------
|
||||
group : h5py.Group
|
||||
HDF5 group to write to
|
||||
energy : Iterable of float
|
||||
arrays of energies at which cross sections are tabulated at
|
||||
Z : int
|
||||
atomic number
|
||||
|
||||
"""
|
||||
|
||||
# Write cross sections
|
||||
if self.mt >= 534 and self.mt <= 572:
|
||||
# Determine threshold
|
||||
threshold = self.xs.x[0]
|
||||
idx = np.searchsorted(energy, threshold, side='right') - 1
|
||||
|
||||
# Interpolate cross section onto union grid and write
|
||||
photoionization = self.xs(energy[idx:])
|
||||
group.create_dataset('xs', data=photoionization)
|
||||
assert len(energy) == len(photoionization) + idx
|
||||
group['xs'].attrs['threshold_idx'] = idx
|
||||
else:
|
||||
group.create_dataset('xs', data=self.xs(energy))
|
||||
|
||||
# Write scattering factor
|
||||
if self.scattering_factor is not None:
|
||||
if self.mt == 502:
|
||||
# Create integrated form factor
|
||||
ff = deepcopy(self.scattering_factor)
|
||||
ff.x *= ff.x
|
||||
ff.y *= ff.y/Z**2
|
||||
int_ff = Tabulated1D(ff.x, ff.integral())
|
||||
int_ff.to_hdf5(group, 'integrated_scattering_factor')
|
||||
self.scattering_factor.to_hdf5(group, 'scattering_factor')
|
||||
if self.anomalous_real is not None:
|
||||
self.anomalous_real.to_hdf5(group, 'anomalous_real')
|
||||
if self.anomalous_imag is not None:
|
||||
self.anomalous_imag.to_hdf5(group, 'anomalous_imag')
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue