Merge branch 'develop' into photon-alund

scripts/openmc-ace-to-hdf5

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 import argparse
 import os
@@ -46,7 +46,8 @@ parser.add_argument('libraries', nargs='*',
                     help='ACE libraries to convert to HDF5')
 parser.add_argument('-d', '--destination', default='.',
                     help='Directory to create new library in')
-parser.add_argument('-m', '--metastable', choices=['mcnp', 'nndc'], default='nndc',
+parser.add_argument('-m', '--metastable', choices=['mcnp', 'nndc'],
+                    default='nndc',
                     help='How to interpret ZAIDs for metastable nuclides')
 parser.add_argument('--xml', help='Old-style cross_sections.xml that '
                     'lists ACE libraries')
@@ -56,6 +57,10 @@ parser.add_argument('--xsdata', help='Serpent xsdata file that lists '
                     'ACE libraries')
 parser.add_argument('--fission_energy_release', help='HDF5 file containing '
                     'fission energy release data')
+parser.add_argument('--libver', choices=['earliest', 'latest'],
+                    default='earliest', help="Output HDF5 versioning. Use "
+                    "'earliest' for backwards compatibility or 'latest' for "
+                    "performance")
 args = parser.parse_args()
 
 if not os.path.isdir(args.destination):
@@ -150,7 +155,7 @@ for filename in ace_libraries:
                 # Determine filename
                 outfile = os.path.join(args.destination,
                                        neutron.name.replace('.', '_') + '.h5')
-                neutron.export_to_hdf5(outfile, 'w')
+                neutron.export_to_hdf5(outfile, 'w', libver=args.libver)
 
                 # Register with library
                 library.register_file(outfile)
@@ -162,10 +167,11 @@ for filename in ace_libraries:
                 try:
                     neutron = \
                         openmc.data.IncidentNeutron.from_hdf5(nuclides[name])
-                    print('Converting {} (ACE) to {} (HDF5)'.format(table.name,
-                                                                    neutron.name))
+                    print('Converting {} (ACE) to {} (HDF5)'
+                          .format(table.name, neutron.name))
                     neutron.add_temperature_from_ace(table, args.metastable)
-                    neutron.export_to_hdf5(nuclides[name] + '_1', 'w')
+                    neutron.export_to_hdf5(nuclides[name] + '_1', 'w',
+                                           libver=args.libver)
                     os.rename(nuclides[name] + '_1', nuclides[name])
                 except Exception as e:
                     print('Failed to convert {}: {}'.format(table.name, e))
@@ -187,7 +193,7 @@ for filename in ace_libraries:
                 # Determine filename
                 outfile = os.path.join(args.destination,
                                        thermal.name.replace('.', '_') + '.h5')
-                thermal.export_to_hdf5(outfile, 'w')
+                thermal.export_to_hdf5(outfile, 'w', libver=args.libver)
 
                 # Register with library
                 library.register_file(outfile)
@@ -198,11 +204,13 @@ for filename in ace_libraries:
             else:
                 # Then we only need to append the data
                 try:
-                    thermal = openmc.data.ThermalScattering.from_hdf5(nuclides[name])
-                    print('Converting {} (ACE) to {} (HDF5)'.format(table.name,
-                                                                    thermal.name))
+                    thermal = openmc.data.ThermalScattering.from_hdf5(
+                                                                 nuclides[name])
+                    print('Converting {} (ACE) to {} (HDF5)'
+                          .format(table.name,thermal.name))
                     thermal.add_temperature_from_ace(table)
-                    thermal.export_to_hdf5(nuclides[name] + '_1', 'w')
+                    thermal.export_to_hdf5(nuclides[name] + '_1', 'w',
+                                           libver=args.libver)
                     os.rename(nuclides[name] + '_1', nuclides[name])
                 except Exception as e:
                     print('Failed to convert {}: {}'.format(table.name, e))

scripts/openmc-convert-mcnp70-data

@@ -1,6 +1,5 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
-from __future__ import print_function
 import argparse
 from collections import defaultdict
 import glob
@@ -26,6 +25,10 @@ parser = argparse.ArgumentParser(
 )
 parser.add_argument('-d', '--destination', default='mcnp_endfb70',
                     help='Directory to create new library in')
+parser.add_argument('--libver', choices=['earliest', 'latest'],
+                    default='earliest', help="Output HDF5 versioning. Use "
+                    "'earliest' for backwards compatibility or 'latest' for "
+                    "performance")
 parser.add_argument('mcnpdata', help='Directory containing endf70[a-k] and endf70sab')
 args = parser.parse_args()
 assert os.path.isdir(args.mcnpdata)
@@ -62,7 +65,7 @@ for path in sorted(endf70):
         # Export HDF5 file
         h5_file = os.path.join(args.destination, data.name + '.h5')
         print('Writing {}...'.format(h5_file))
-        data.export_to_hdf5(h5_file, 'w')
+        data.export_to_hdf5(h5_file, 'w', libver=args.libver)
 
         # Register with library
         library.register_file(h5_file)
@@ -91,7 +94,7 @@ if os.path.exists(endf70sab):
         # Export HDF5 file
         h5_file = os.path.join(args.destination, data.name + '.h5')
         print('Writing {}...'.format(h5_file))
-        data.export_to_hdf5(h5_file, 'w')
+        data.export_to_hdf5(h5_file, 'w', libver=args.libver)
 
         # Register with library
         library.register_file(h5_file)

scripts/openmc-convert-mcnp71-data

@@ -1,6 +1,5 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
-from __future__ import print_function
 import argparse
 from collections import defaultdict
 import glob
@@ -28,6 +27,10 @@ parser.add_argument('-d', '--destination', default='mcnp_endfb71',
                     help='Directory to create new library in')
 parser.add_argument('-f', '--fission_energy_release',
                     help='HDF5 file containing fission energy release data')
+parser.add_argument('--libver', choices=['earliest', 'latest'],
+                    default='earliest', help="Output HDF5 versioning. Use "
+                    "'earliest' for backwards compatibility or 'latest' for "
+                    "performance")
 parser.add_argument('mcnpdata', help='Directory containing endf71x and ENDF71SaB')
 args = parser.parse_args()
 assert os.path.isdir(args.mcnpdata)
@@ -80,7 +83,7 @@ for basename, xs_list in sorted(suffixes.items()):
     # Export HDF5 file
     h5_file = os.path.join(args.destination, data.name + '.h5')
     print('Writing {}...'.format(h5_file))
-    data.export_to_hdf5(h5_file, 'w')
+    data.export_to_hdf5(h5_file, 'w', libver=args.libver)
 
     # Register with library
     library.register_file(h5_file)

scripts/openmc-get-jeff-data

@@ -1,6 +1,5 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
-from __future__ import print_function
 import os
 from collections import defaultdict
 import sys
@@ -9,9 +8,7 @@ import zipfile
 import glob
 import argparse
 from string import digits
-
-from six.moves import input
-from six.moves.urllib.request import urlopen
+from urllib.request import urlopen
 
 import openmc.data
 
@@ -43,6 +40,10 @@ parser.add_argument('-b', '--batch', action='store_true',
                     help='supresses standard in')
 parser.add_argument('-d', '--destination', default='jeff-3.2-hdf5',
                     help='Directory to create new library in')
+parser.add_argument('--libver', choices=['earliest', 'latest'],
+                    default='earliest', help="Output HDF5 versioning. Use "
+                    "'earliest' for backwards compatibility or 'latest' for "
+                    "performance")
 args = parser.parse_args()
 
 response = input(download_warning) if not args.batch else 'y'
@@ -179,7 +180,7 @@ for name, filenames in sorted(tables.items()):
     # Export HDF5 file
     h5_file = os.path.join(args.destination, data.name + '.h5')
     print('Writing {}...'.format(h5_file))
-    data.export_to_hdf5(h5_file, 'w')
+    data.export_to_hdf5(h5_file, 'w', libver=args.libver)
 
     # Register with library
     library.register_file(h5_file)
@@ -222,7 +223,7 @@ for name, filenames in sorted(tables.items()):
     # Export HDF5 file
     h5_file = os.path.join(args.destination, data.name + '.h5')
     print('Writing {}...'.format(h5_file))
-    data.export_to_hdf5(h5_file, 'w')
+    data.export_to_hdf5(h5_file, 'w', libver=args.libver)
 
     # Register with library
     library.register_file(h5_file)

scripts/openmc-get-multipole-data

@@ -1,6 +1,5 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
-from __future__ import print_function
 import os
 import shutil
 import subprocess
@@ -9,9 +8,7 @@ import tarfile
 import glob
 import hashlib
 import argparse
-
-from six.moves import input
-from six.moves.urllib.request import urlopen
+from urllib.request import urlopen
 
 
 description = """

scripts/openmc-get-nndc-data

@@ -6,7 +6,6 @@ from NNDC and convert it to an HDF5 library for use with OpenMC. This data is
 used for OpenMC's regression test suite.
 """
 
-from __future__ import print_function
 import os
 import shutil
 import subprocess
@@ -15,9 +14,7 @@ import tarfile
 import glob
 import hashlib
 import argparse
-
-from six.moves import input
-from six.moves.urllib.request import urlopen
+from urllib.request import urlopen
 
 import openmc.data
 
@@ -34,6 +31,10 @@ parser.add_argument('-b', '--batch', action='store_true',
                     help='supresses standard in')
 parser.add_argument('-n', '--neutron-only', action='store_true',
                     help='Whether to exclude photon interaction/atomic data')
+parser.add_argument('--libver', choices=['earliest', 'latest'],
+                    default='earliest', help="Output HDF5 versioning. Use "
+                    "'earliest' for backwards compatibility or 'latest' for "
+                    "performance")
 args = parser.parse_args()
 
 base_url = 'http://www.nndc.bnl.gov/endf/b7.1/aceFiles/'
@@ -154,10 +155,13 @@ ace_files = sorted(glob.glob(os.path.join('nndc', '**', '*.ace*')))
 data_dir = os.path.dirname(sys.modules['openmc.data'].__file__)
 fer_file = os.path.join(data_dir, 'fission_Q_data_endfb71.h5')
 
+# Call the ace-to-hdf5 conversion script
 pwd = os.path.dirname(os.path.realpath(__file__))
 ace2hdf5 = os.path.join(pwd, 'openmc-ace-to-hdf5')
-subprocess.call([ace2hdf5, '-d', 'nndc_hdf5', '--fission_energy_release',
-                 fer_file] + ace_files)
+subprocess.call([ace2hdf5,
+                 '-d', 'nndc_hdf5',
+                 '--fission_energy_release', fer_file,
+                 '--libver', args.libver] + ace_files)
 
 # Generate photo interaction library files
 if not args.neutron_only:

scripts/openmc-make-depletion-chain

@@ -0,0 +1,33 @@
+#!/usr/bin/env python3
+
+import glob
+import os
+from zipfile import ZipFile
+
+from openmc._utils import download
+import openmc.deplete
+
+
+URLS = [
+    'http://www.nndc.bnl.gov/endf/b7.1/zips/ENDF-B-VII.1-neutrons.zip',
+    'http://www.nndc.bnl.gov/endf/b7.1/zips/ENDF-B-VII.1-decay.zip',
+    'http://www.nndc.bnl.gov/endf/b7.1/zips/ENDF-B-VII.1-nfy.zip'
+]
+
+def main():
+    for url in URLS:
+        basename = download(url)
+        with ZipFile(basename, 'r') as zf:
+            print('Extracting {}...'.format(basename))
+            zf.extractall()
+
+    decay_files = glob.glob(os.path.join('decay', '*.endf'))
+    nfy_files = glob.glob(os.path.join('nfy', '*.endf'))
+    neutron_files = glob.glob(os.path.join('neutrons', '*.endf'))
+
+    chain = openmc.deplete.Chain.from_endf(decay_files, nfy_files, neutron_files)
+    chain.export_to_xml('chain_endfb71.xml')
+
+
+if __name__ == '__main__':
+    main()

scripts/openmc-plot-mesh-tally

@@ -1,16 +1,16 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Python script to plot tally data generated by OpenMC."""
 
 import os
 import sys
 import argparse
+import tkinter as tk
+import tkinter.filedialog as filedialog
+import tkinter.font as font
+import tkinter.messagebox as messagebox
+import tkinter.ttk as ttk
 
-import six.moves.tkinter as tk
-import six.moves.tkinter_filedialog as filedialog
-import six.moves.tkinter_font as font
-import six.moves.tkinter_messagebox as messagebox
-import six.moves.tkinter_ttk as ttk
 from matplotlib.backends.backend_tkagg import FigureCanvasTkAgg
 from matplotlib.backends.backend_tkagg import NavigationToolbar2TkAgg
 from matplotlib.figure import Figure

scripts/openmc-track-to-vtk

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 """Convert HDF5 particle track to VTK poly data.
 

scripts/openmc-update-inputs

@@ -1,10 +1,8 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """Update OpenMC's input XML files to the latest format.
 
 """
 
-from __future__ import print_function
-
 import argparse
 from difflib import get_close_matches
 from itertools import chain

scripts/openmc-update-mgxs

@@ -1,10 +1,9 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 """Update OpenMC's deprecated multi-group cross section XML files to the latest
 HDF5-based format.
 
 """
 
-from __future__ import print_function
 import os
 import warnings
 import xml.etree.ElementTree as ET

scripts/openmc-validate-xml

@@ -1,6 +1,4 @@
-#!/usr/bin/env python
-
-from __future__ import print_function
+#!/usr/bin/env python3
 
 import os
 import sys

scripts/openmc-voxel-to-silovtk

@@ -1,6 +1,5 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
-from __future__ import division, print_function
 import struct
 import sys
 from argparse import ArgumentParser