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create from_hdf5 in photon reactions to simplify photon export
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liangjg
parent
0661082337
commit
36641b1029
1 changed files with 112 additions and 110 deletions
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@ -36,56 +36,56 @@ def _subshell(i):
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_SUBSHELL_MT = {s: i + 534 for i, s in enumerate(_SUBSHELLS)}
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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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525: 'Heating',
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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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525: ('Heating', 'heating'),
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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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@ -678,8 +678,8 @@ class IncidentPhoton(EqualityMixin):
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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 of '
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'the OpenMC Python API expects version {}.x data.'
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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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@ -689,69 +689,24 @@ class IncidentPhoton(EqualityMixin):
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# Read energy grid
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energy= group['energy'].value
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n = energy.size
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# Read coherent scattering cross section
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rgroup = group['coherent']
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rx = PhotonReaction(502)
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rx.xs = Tabulated1D(energy, rgroup['xs'].value, [n], [5])
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if 'anomalous_real' in rgroup:
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rx.anomalous_real = Tabulated1D.from_hdf5(rgroup['anomalous_real'])
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if 'anomalous_imag' in rgroup:
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rx.anomalous_imag = Tabulated1D.from_hdf5(rgroup['anomalous_imag'])
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data.reactions[502] = rx
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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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# Read incoherent scattering cross section
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rgroup = group['incoherent']
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rx = PhotonReaction(504)
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rx.xs = Tabulated1D(energy, rgroup['xs'].value, [n], [5])
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if 'scattering_factor' in rgroup:
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dset = rgroup['scattering_factor']
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rx.scattering_factor = Tabulated1D.from_hdf5(dset)
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data.reactions[504] = rx
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data.reactions[mt] = PhotonReaction.from_hdf5(rgroup, mt, energy)
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# Read electron-field pair production cross section
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if 'pair_production_electron' in group:
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rgroup = group['pair_production_electron']
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rx = PhotonReaction(515)
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rx.xs = Tabulated1D(energy, rgroup['xs'].value, [n], [5])
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data.reactions[515] = rx
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# Read nuclear-field pair production cross section
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if 'pair_production_nuclear' in group:
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rgroup = group['pair_production_nuclear']
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rx = PhotonReaction(517)
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rx.xs = Tabulated1D(energy, rgroup['xs'].value, [n], [5])
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data.reactions[517] = rx
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# Read photoelectric cross section
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if 'photoelectric' in group:
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rgroup = group['photoelectric']
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rx = PhotonReaction(522)
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rx.xs = Tabulated1D(energy, rgroup['xs'].value, [n], [5])
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data.reactions[522] = rx
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# Read heating cross section
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if 'heating' in group:
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rgroup = group['heating']
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rx = PhotonReaction(525)
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rx.xs = Tabulated1D(energy, rgroup['xs'].value, [n], [5])
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data.reactions[525] = rx
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rgroup = group['subshells']
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# Read photoionization cross sections
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designators = [i.decode() for i in rgroup.attrs['designators']]
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for shell in designators:
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mt = _SUBSHELL_MT[shell]
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sub_group = rgroup[shell]
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xs = sub_group['xs'].value
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threshold_idx = sub_group['xs'].attrs['threshold_idx']
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rx = PhotonReaction(mt)
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rx.xs = Tabulated1D(energy[threshold_idx:], xs, [len(xs)], [5])
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data.reactions[mt] = rx
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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(rgroup)
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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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@ -1182,3 +1137,50 @@ class PhotonReaction(EqualityMixin):
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params, rx.anomalous_imag = get_tab1_record(file_obj)
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return rx
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@classmethod
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def from_hdf5(cls, group, mt, energy):
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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 : h5py.Group
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HDF5 group to read from
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mt : int
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The MT value of the reaction to get data for
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energy : Iterable of float
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arrays of energies at which cross sections are tabulated at.
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Returns
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-------
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openmc.data.PhotonReaction
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Photon reaction data
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"""
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# Create instance
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rx = cls(mt)
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# Cross sections
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xs = group['xs'].value
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# Replace zero elements to small non-zero to enable log-log
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xs[xs == 0.0] = np.exp(-500.0)
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# Threshold
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threshold_idx = 0
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if 'threshold_idx' in group['xs'].attrs:
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threshold_idx = group['xs'].attrs['threshold_idx']
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# Store
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rx.xs = Tabulated1D(energy[threshold_idx:], xs, [len(xs)], [5])
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# Check for anomalous scattering factor
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if 'anomalous_real' in group:
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rx.anomalous_real = Tabulated1D.from_hdf5(group['anomalous_real'])
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if 'anomalous_imag' in group:
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rx.anomalous_imag = Tabulated1D.from_hdf5(group['anomalous_imag'])
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# Check for factors / scattering functions
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if 'scattering_factor' in group:
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rx.scattering_factor = Tabulated1D.from_hdf5(group['scattering_factor'])
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return rx
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