mirror of
https://github.com/openmc-dev/openmc.git
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Merge pull request #2191 from shimwell/adding_main_to_scripts
added main method to scripts
This commit is contained in:
Paul Romano
GitHub
commit
35f0203000
3 changed files with 226 additions and 195 deletions
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@ -28,102 +28,126 @@ import openmc.data
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from openmc.data.ace import TableType
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class CustomFormatter(argparse.ArgumentDefaultsHelpFormatter,
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argparse.RawDescriptionHelpFormatter):
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pass
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def ace_to_hdf5(destination, xsdir, xsdata, libraries, metastable, libver):
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if not destination.is_dir():
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destination.mkdir(parents=True, exist_ok=True)
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parser = argparse.ArgumentParser(
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description=__doc__,
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formatter_class=CustomFormatter
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)
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parser.add_argument('libraries', nargs='*',
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help='ACE libraries to convert to HDF5')
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parser.add_argument('-d', '--destination', type=Path, default=Path.cwd(),
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help='Directory to create new library in')
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parser.add_argument('-m', '--metastable', choices=['mcnp', 'nndc'],
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default='nndc',
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help='How to interpret ZAIDs for metastable nuclides')
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parser.add_argument('--xsdir', help='MCNP xsdir file that lists '
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'ACE libraries')
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parser.add_argument('--xsdata', help='Serpent xsdata file that lists '
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'ACE libraries')
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parser.add_argument('--libver', choices=['earliest', 'latest'],
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default='earliest', help="Output HDF5 versioning. Use "
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"'earliest' for backwards compatibility or 'latest' for "
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"performance")
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args = parser.parse_args()
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ace_libraries = []
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if xsdir is not None:
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ace_libraries.extend(openmc.data.ace.get_libraries_from_xsdir(xsdir))
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elif xsdata is not None:
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ace_libraries.extend(openmc.data.ace.get_libraries_from_xsdata(xsdata))
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else:
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ace_libraries = [Path(lib) for lib in libraries]
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if not args.destination.is_dir():
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args.destination.mkdir(parents=True, exist_ok=True)
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converted = {}
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library = openmc.data.DataLibrary()
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ace_libraries = []
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if args.xsdir is not None:
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ace_libraries.extend(openmc.data.ace.get_libraries_from_xsdir(args.xsdir))
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elif args.xsdata is not None:
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ace_libraries.extend(openmc.data.ace.get_libraries_from_xsdata(args.xsdata))
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else:
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ace_libraries = [Path(lib) for lib in args.libraries]
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converted = {}
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library = openmc.data.DataLibrary()
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for path in ace_libraries:
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# Check that ACE library exists
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if not os.path.exists(path):
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warnings.warn("ACE library '{}' does not exist.".format(path))
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continue
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lib = openmc.data.ace.Library(path)
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for table in lib.tables:
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# Check type of the ACE table and determine appropriate class /
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# conversion function
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if table.data_type == TableType.NEUTRON_CONTINUOUS:
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name = table.zaid
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cls = openmc.data.IncidentNeutron
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converter = partial(cls.from_ace, metastable_scheme=args.metastable)
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elif table.data_type == TableType.THERMAL_SCATTERING:
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# Adjust name to be the new thermal scattering name
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name = openmc.data.get_thermal_name(table.zaid)
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cls = openmc.data.ThermalScattering
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converter = cls.from_ace
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else:
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print("Can't convert ACE table {}".format(table.name))
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for path in ace_libraries:
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# Check that ACE library exists
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if not os.path.exists(path):
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warnings.warn(f"ACE library '{path}' does not exist.")
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continue
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if name not in converted:
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try:
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data = converter(table)
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except Exception as e:
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print('Failed to convert {}: {}'.format(table.name, e))
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lib = openmc.data.ace.Library(path)
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for table in lib.tables:
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# Check type of the ACE table and determine appropriate class /
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# conversion function
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if table.data_type == TableType.NEUTRON_CONTINUOUS:
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name = table.zaid
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cls = openmc.data.IncidentNeutron
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converter = partial(cls.from_ace, metastable_scheme=metastable)
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elif table.data_type == TableType.THERMAL_SCATTERING:
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# Adjust name to be the new thermal scattering name
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name = openmc.data.get_thermal_name(table.zaid)
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cls = openmc.data.ThermalScattering
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converter = cls.from_ace
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else:
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print(f"Can't convert ACE table {table.name}")
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continue
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print('Converting {} (ACE) to {} (HDF5)'.format(table.name, data.name))
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if name not in converted:
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try:
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data = converter(table)
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except Exception as e:
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print(f"Failed to convert {table.name}: {e}")
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continue
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# Determine output filename
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outfile = args.destination / (data.name.replace('.', '_') + '.h5')
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data.export_to_hdf5(outfile, 'w', libver=args.libver)
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print(f"Converting {table.name} (ACE) to {data.name} (HDF5)")
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# Register with library
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library.register_file(outfile)
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# Determine output filename
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outfile = destination / (data.name.replace(".", "_") + ".h5")
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data.export_to_hdf5(outfile, "w", libver=libver)
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# Add nuclide to list
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converted[name] = outfile
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else:
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# Read existing HDF5 file
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data = cls.from_hdf5(converted[name])
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# Register with library
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library.register_file(outfile)
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# Add data for new temperature
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try:
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print('Converting {} (ACE) to {} (HDF5)'
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.format(table.name, data.name))
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data.add_temperature_from_ace(table, args.metastable)
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except Exception as e:
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print('Failed to convert {}: {}'.format(table.name, e))
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continue
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# Add nuclide to list
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converted[name] = outfile
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else:
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# Read existing HDF5 file
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data = cls.from_hdf5(converted[name])
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# Re-export
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data.export_to_hdf5(converted[name], 'w', libver=args.libver)
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# Add data for new temperature
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try:
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print(f"Converting {table.name} (ACE) to {data.name} (HDF5)")
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data.add_temperature_from_ace(table, metastable)
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except Exception as e:
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print(f"Failed to convert {table.name}: {e}")
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continue
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# Write cross_sections.xml
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library.export_to_xml(args.destination / 'cross_sections.xml')
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# Re-export
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data.export_to_hdf5(converted[name], "w", libver=libver)
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# Write cross_sections.xml
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library.export_to_xml(destination / "cross_sections.xml")
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if __name__ == "__main__":
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class CustomFormatter(
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argparse.ArgumentDefaultsHelpFormatter, argparse.RawDescriptionHelpFormatter
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):
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pass
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parser = argparse.ArgumentParser(
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description=__doc__, formatter_class=CustomFormatter
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)
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parser.add_argument("libraries", nargs="*", help="ACE libraries to convert to HDF5")
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parser.add_argument(
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"-d",
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"--destination",
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type=Path,
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default=Path.cwd(),
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help="Directory to create new library in",
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)
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parser.add_argument(
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"-m",
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"--metastable",
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choices=["mcnp", "nndc"],
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default="nndc",
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help="How to interpret ZAIDs for metastable nuclides",
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)
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parser.add_argument("--xsdir", help="MCNP xsdir file that lists " "ACE libraries")
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parser.add_argument(
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"--xsdata", help="Serpent xsdata file that lists " "ACE libraries"
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)
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parser.add_argument(
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"--libver",
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choices=["earliest", "latest"],
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default="earliest",
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help="Output HDF5 versioning. Use "
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"'earliest' for backwards compatibility or 'latest' "
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"for performance",
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)
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args = parser.parse_args()
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ace_to_hdf5(
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destination=args.destination,
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xsdir=args.xsdir,
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xsdata=args.xsdata,
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libraries=args.libraries,
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metastable=args.metastable,
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libver=args.libver,
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)
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@ -4,96 +4,99 @@ import os
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import sys
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import glob
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import lxml.etree as etree
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from subprocess import call
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from optparse import OptionParser
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# Command line parsing
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parser = OptionParser()
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parser.add_option('-r', '--relaxng-path', dest='relaxng',
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help="Path to RelaxNG files.")
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parser.add_option('-i', '--input-path', dest='inputs', default=os.getcwd(),
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help="Path to OpenMC input files." )
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(options, args) = parser.parse_args()
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def validate_xml(inputs, relaxng):
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# Colored output
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if sys.stdout.isatty():
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OK = '\033[92m'
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FAIL = '\033[91m'
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NOT_FOUND = '\033[93m'
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ENDC = '\033[0m'
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BOLD = '\033[1m'
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else:
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OK = ''
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FAIL = ''
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ENDC = ''
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BOLD = ''
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NOT_FOUND = ''
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# Get absolute paths
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if options.relaxng is not None:
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relaxng_path = os.path.abspath(options.relaxng)
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if options.inputs is not None:
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inputs_path = os.path.abspath(options.inputs)
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# Search for relaxng path if not set
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if options.relaxng is None:
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xml_validate_path = os.path.abspath(os.path.dirname(sys.argv[0]))
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if "bin" in xml_validate_path:
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relaxng_path = os.path.join(xml_validate_path, "..", "share", "relaxng")
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elif os.path.join("src", "utils") in xml_validate_path:
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relaxng_path = os.path.join(xml_validate_path, "..", "relaxng")
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# Colored output
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if sys.stdout.isatty():
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OK = '\033[92m'
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FAIL = '\033[91m'
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NOT_FOUND = '\033[93m'
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ENDC = '\033[0m'
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BOLD = '\033[1m'
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else:
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raise Exception("Set RelaxNG path with -r command line option.")
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if not os.path.exists(relaxng_path):
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raise Exception("RelaxNG path: {0} does not exist, set with -r "
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"command line option.".format(relaxng_path))
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OK = ''
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FAIL = ''
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ENDC = ''
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BOLD = ''
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NOT_FOUND = ''
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# Make sure there are .rng files in RelaxNG path
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rng_files = glob.glob(os.path.join(relaxng_path, "*.rng"))
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if len(rng_files) == 0:
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raise Exception("No .rng files found in RelaxNG "
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"path: {0}.".format(relaxng_path))
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# Get absolute paths
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if relaxng is not None:
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relaxng_path = os.path.abspath(relaxng)
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if inputs is not None:
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inputs_path = os.path.abspath(inputs)
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# Get list of xml input files
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xml_files = glob.glob(os.path.join(inputs_path, "*.xml"))
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if len(xml_files) == 0:
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raise Exception("No .xml files found at input path: {0}"
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".".format(inputs_path))
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# Search for relaxng path if not set
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if relaxng is None:
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xml_validate_path = os.path.abspath(os.path.dirname(sys.argv[0]))
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if "bin" in xml_validate_path:
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relaxng_path = os.path.join(xml_validate_path, "..", "share", "relaxng")
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elif os.path.join("src", "utils") in xml_validate_path:
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relaxng_path = os.path.join(xml_validate_path, "..", "relaxng")
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else:
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raise Exception("Set RelaxNG path with -r command line option.")
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if not os.path.exists(relaxng_path):
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raise Exception(f"RelaxNG path: {relaxng_path} does not exist, set "
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"with -r command line option.")
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# Begin loop around input files
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for xml_file in xml_files:
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# Make sure there are .rng files in RelaxNG path
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rng_files = glob.glob(os.path.join(relaxng_path, "*.rng"))
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if len(rng_files) == 0:
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raise Exception(f"No .rng files found in RelaxNG path: {relaxng_path}.")
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text = "Validating {0}".format(os.path.basename(xml_file))
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print(text + '.'*(30 - len(text)), end="")
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# Get list of xml input files
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xml_files = glob.glob(os.path.join(inputs_path, "*.xml"))
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if len(xml_files) == 0:
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raise Exception(f"No .xml files found at input path: {inputs_path}.")
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# Validate the XML file
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try:
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xml_tree = etree.parse(xml_file)
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except etree.XMLSyntaxError as e:
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print(BOLD + FAIL + '[XML ERROR]' + ENDC)
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print(" {0}".format(e))
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continue
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# Begin loop around input files
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for xml_file in xml_files:
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# Get xml_filename prefix
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xml_prefix = os.path.basename(xml_file)
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xml_prefix = xml_prefix.split(".")[0]
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text = f"Validating {os.path.basename(xml_file)}"
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print(text + '.'*(30 - len(text)), end="")
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# Search for rng file
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rng_file = os.path.join(relaxng_path, xml_prefix + ".rng")
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if rng_file in rng_files:
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# read in RelaxNG
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relaxng_doc = etree.parse(rng_file)
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relaxng = etree.RelaxNG(relaxng_doc)
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# validate xml file again RelaxNG
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# Validate the XML file
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try:
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relaxng.assertValid(xml_tree)
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print(BOLD + OK + '[VALID]' + ENDC)
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except (etree.DocumentInvalid, TypeError) as e:
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print(BOLD + FAIL + '[NOT VALID]' + ENDC)
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print(" {0}".format(e))
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xml_tree = etree.parse(xml_file)
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except etree.XMLSyntaxError as e:
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print(BOLD + FAIL + '[XML ERROR]' + ENDC)
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print(f" {e}")
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continue
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# RNG file does not exist
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else:
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print(BOLD + NOT_FOUND + '[NO RELAXNG FOUND]' + ENDC)
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# Get xml_filename prefix
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xml_prefix = os.path.basename(xml_file)
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xml_prefix = xml_prefix.split(".")[0]
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# Search for rng file
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rng_file = os.path.join(relaxng_path, xml_prefix + ".rng")
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if rng_file in rng_files:
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# read in RelaxNG
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relaxng_doc = etree.parse(rng_file)
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relaxng = etree.RelaxNG(relaxng_doc)
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# validate xml file again RelaxNG
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try:
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relaxng.assertValid(xml_tree)
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print(BOLD + OK + '[VALID]' + ENDC)
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except (etree.DocumentInvalid, TypeError) as e:
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print(BOLD + FAIL + '[NOT VALID]' + ENDC)
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print(f" {e}")
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# RNG file does not exist
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else:
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print(BOLD + NOT_FOUND + '[NO RELAXNG FOUND]' + ENDC)
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if __name__ == "__main__":
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# Command line parsing
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parser = OptionParser()
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parser.add_option('-r', '--relaxng-path', dest='relaxng',
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help="Path to RelaxNG files.")
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parser.add_option('-i', '--input-path', dest='inputs', default=os.getcwd(),
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help="Path to OpenMC input files." )
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(options, args) = parser.parse_args()
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validate_xml(inputs=options.inputs, relaxng=options.relaxng)
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|
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@ -1,54 +1,46 @@
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#!/usr/bin/env python3
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import struct
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import sys
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from argparse import ArgumentParser
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import numpy as np
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import h5py
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import vtk
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_min_version = (2, 0)
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def main():
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# Process command line arguments
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parser = ArgumentParser()
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parser.add_argument('voxel_file', help='Path to voxel file')
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parser.add_argument('-o', '--output', action='store',
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default='plot', help='Path to output VTK file.')
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args = parser.parse_args()
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def voxel_to_vtk(voxel_file: str, output: str):
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# Read data from voxel file
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fh = h5py.File(args.voxel_file, 'r')
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fh = h5py.File(voxel_file, "r")
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# check version
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version = tuple(fh.attrs['version'])
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version = tuple(fh.attrs["version"])
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if version < _min_version:
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old_version = ".".join(map(str,version))
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min_version = ".".join(map(str,_min_version))
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err_msg = "This voxel file's version is {}. This script " \
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"only supports voxel files with version {} or " \
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"higher. Please generate a new voxel file using " \
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"a newer version of OpenMC.".format(old_version, min_version)
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old_version = ".".join(map(str, version))
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min_version = ".".join(map(str, _min_version))
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err_msg = (
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"This voxel file's version is {}. This script "
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"only supports voxel files with version {} or "
|
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"higher. Please generate a new voxel file using "
|
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"a newer version of OpenMC.".format(old_version, min_version)
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)
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raise ValueError(err_msg)
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dimension = fh.attrs['num_voxels']
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width = fh.attrs['voxel_width']
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lower_left = fh.attrs['lower_left']
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||||
dimension = fh.attrs["num_voxels"]
|
||||
width = fh.attrs["voxel_width"]
|
||||
lower_left = fh.attrs["lower_left"]
|
||||
|
||||
nx, ny, nz = dimension
|
||||
upper_right = lower_left + width*dimension
|
||||
|
||||
grid = vtk.vtkImageData()
|
||||
grid.SetDimensions(nx+1, ny+1, nz+1)
|
||||
grid.SetDimensions(nx + 1, ny + 1, nz + 1)
|
||||
grid.SetOrigin(*lower_left)
|
||||
grid.SetSpacing(*width)
|
||||
|
||||
# transpose data from OpenMC ordering (zyx) to VTK ordering (xyz)
|
||||
# and flatten to 1-D array
|
||||
print("Reading and translating data...")
|
||||
h5data = fh['data'][...]
|
||||
h5data = fh["data"][...]
|
||||
|
||||
data = vtk.vtkIntArray()
|
||||
data.SetName("id")
|
||||
|
|
@ -62,11 +54,23 @@ def main():
|
|||
writer.SetInputData(grid)
|
||||
else:
|
||||
writer.SetInput(grid)
|
||||
if not args.output.endswith(".vti"):
|
||||
args.output += ".vti"
|
||||
writer.SetFileName(args.output)
|
||||
print("Writing VTK file {}...".format(args.output))
|
||||
if not output.endswith(".vti"):
|
||||
output += ".vti"
|
||||
writer.SetFileName(output)
|
||||
print("Writing VTK file {}...".format(output))
|
||||
writer.Write()
|
||||
|
||||
if __name__ == '__main__':
|
||||
main()
|
||||
|
||||
if __name__ == "__main__":
|
||||
# Process command line arguments
|
||||
parser = ArgumentParser('Converts a voxel HDF5 file to a VTK file')
|
||||
parser.add_argument("voxel_file", help="Path to voxel h5 file")
|
||||
parser.add_argument(
|
||||
"-o",
|
||||
"--output",
|
||||
action="store",
|
||||
default="plot",
|
||||
help="Path to output VTK file.",
|
||||
)
|
||||
args = parser.parse_args()
|
||||
voxel_to_vtk(args.voxel_file, args.output)
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue