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Merge pull request #1613 from paulromano/release-prep

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Preparation for 0.12.0 release
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Amanda Lund 2020-07-21 22:42:19 -05:00 • committed by GitHub
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18
MANIFEST.in
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@ -1,15 +1,17 @@
include CMakeLists.txt
include LICENSE
include CODE_OF_CONDUCT.md
include CODEOWNERS
include CONTRIBUTING.md
include Dockerfile
include schemas.xml
include pyproject.toml
include pytest.ini
include openmc/data/reconstruct.pyx
include docs/source/_templates/layout.html
include docs/sphinxext/LICENSE
recursive-include . *.rst
recursive-include cmake *.cmake
global-include *.cmake
global-include *.cmake.in
global-include *.rst
recursive-include docs *.css
recursive-include docs *.dia
recursive-include docs *.png
@ -23,8 +25,10 @@ recursive-include examples *.ipynb
recursive-include examples *.png
recursive-include examples *.py
recursive-include examples *.xml
recursive-include include *.h
recursive-include man *.1
recursive-include src *.F90
recursive-inlcude openmc *.pyx
recursive-include openmc *.c
recursive-include src *.c
recursive-include src *.cc
recursive-include src *.cpp
@ -34,13 +38,17 @@ recursive-include src *.rnc
recursive-include src *.rng
recursive-include tests *.dat
recursive-include tests *.h5
recursive-inlcude tests *.h5m
recursive-include tests *.py
recursive-include tests *.xml
recursive-include vendor CMakeLists.txt
recursive-include vendor *.cmake.in
recursive-include vendor *.cc
recursive-include vendor *.cpp
recursive-include vendor *.h
recursive-include vendor *.hh
recursive-include vendor *.hpp
recursive-include vendor *.pc.in
recursive-include vendor *.natvis
include vendor/gsl-lite/include/gsl/gsl
prune docs/build
prune docs/source/pythonapi/generated/

149
docs/source/releasenotes/0.12.0.rst Normal file
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@ -0,0 +1,149 @@
====================
What's New in 0.12.0
====================
.. currentmodule:: openmc
-------
Summary
-------
This release of OpenMC includes an assortment of new features and many bug fixes.
In particular, the :mod:`openmc.deplete` module has been heavily tested which
has resulted in a number of usability improvements, bug fixes, and other
enhancements. Energy deposition calculations, particularly for coupled
neutron-photon simulations, have been improved as well.
Improvements in modeling capabilities continue to be added to the code,
including the ability to rotate surfaces in the Python API, several new
"composite" surfaces, a variety of new methods on :class:`openmc.Material`,
unstructured mesh tallies that leverage the existing DAGMC infrastructure,
effective dose coefficients from ICRP-116, and a new cell instance tally
filter.
------------
New Features
------------
- All surfaces now have a `rotate` method that allows them to be rotated.
- Several "composite" surfaces, which are actually composed of multiple surfaces
but can be treated as a normal surface through the -/+ unary operators, have
been added. These include:
- :class:`openmc.model.RightCircularCylinder`
- :class:`openmc.model.RectangularParallelepiped`
- :class:`openmc.model.XConeOneSided` (and equivalent versions for y- and z-axes)
- Various improvements related to depletion:
- The matrix exponential solver can now be configured through the `solver`
argument on depletion integrator classes.
- The :meth:`openmc.deplete.Chain.reduce` method can automatically reduce the
number of nuclides in a depletion chain.
- Depletion integrator classes now allow a user to specify timesteps in several
units (s, min, h, d, MWd/kg).
- :meth:`openmc.deplete.ResultsList.get_atoms` now allows a user to obtain
depleted material compositions in atom/b-cm.
- Several new methods on :class:`openmc.Material`:
- The :meth:`openmc.Material.add_elements_from_formula` method allows a user
to create a material based on a chemical formula.
- :meth:`openmc.Material.add_element` now supports the `enrichment` argument for
non-uranium elements when only two isotopes are naturally occurring.
- :meth:`openmc.Material.add_element` now supports adding elements by name
rather than by symbol.
- The :meth:`openmc.Material.get_elements` method returns a list of elements
within a material.
- The :meth:`openmc.Material.mix_materials` method allows multiple materials to
be mixed together based on atom, weight, or volume fractions.
- The acceptable number of lost particles can now be configured through
:attr:`openmc.Settings.max_lost_particles` and
:attr:`openmc.Settings.rel_max_lost_particles`.
- Delayed photons produced from fission are now accounted for by default by
scaling the yield of prompt fission photons. This behavior can be modified
through the :attr:`openmc.Settings.delayed_photon_scaling` attribute.
- A trigger can now be specified for a volume calculation via the
:meth:`openmc.VolumeCalculation.set_trigger` method.
- The :class:`openmc.stats.SphericalIndependent` and
:class:`openmc.stats.CylindricalIndependent` classes allow a user to
specify source distributions based on spherical or cylindrical coordinates.
- Custom external source distributions can be used via the
:attr:`openmc.Source.library` attribute.
- Unstructured mesh class, :class:`openmc.UnstructuredMesh`, that can be used in
tallies.
- The :class:`openmc.CellInstanceFilter` class allows one or more instances of a
repeated cell to be tallied. This is effectively a more flexible version of
the existing :class:`openmc.DistribcellFilter` class.
- The :func:`openmc.data.dose_coefficients` function provides effective dose
coefficients from ICRP-116 and can be used in conjunction with
:class:`openmc.EnergyFunctionFilter` in a tally.
---------
Bug Fixes
---------
- `Keep user-supplied prev_results on operator <https://github.com/openmc-dev/openmc/pull/1605>`_
- `Fix bug when S(a,b) tables appear in depletable material <https://github.com/openmc-dev/openmc/pull/1605>`_
- `DAGMC fix for implicit complement material assignment <https://github.com/openmc-dev/openmc/pull/1604>`_
- `Bug fix for tallying reaction rates in coupled n-p runs <https://github.com/openmc-dev/openmc/pull/1603>`_
- `Corrected issue with multiplicity matrix <https://github.com/openmc-dev/openmc/pull/1598>`_
- `Fix depletion with photon transport <https://github.com/openmc-dev/openmc/pull/1595>`_
- `Fix secondary photon creation <https://github.com/openmc-dev/openmc/pull/1591>`_
- `Bug fix for total xs plotting <https://github.com/openmc-dev/openmc/pull/1563>`_
- `Account for light nuclide production in depletion <https://github.com/openmc-dev/openmc/pull/1555>`_
- `Reset timer in depletion calculations <https://github.com/openmc-dev/openmc/pull/1539>`_
- `Fix for Model.run <https://github.com/openmc-dev/openmc/pull/1536>`_
- `Ensure NJOY output goes to specified directory <https://github.com/openmc-dev/openmc/pull/1522>`_
- `Fix bug preventing creating photon data <https://github.com/openmc-dev/openmc/pull/1489>`_
- `Fix bug when surface ID > 999999 <https://github.com/openmc-dev/openmc/pull/1486>`_
- `Fix bug for reading output settings in Settings.from_xml <https://github.com/openmc-dev/openmc/pull/1478>`_
- `Fix improve energy deposition for coupled neutron-photon <https://github.com/openmc-dev/openmc/pull/1449>`_
- `Use number of particles for tally normalization <https://github.com/openmc-dev/openmc/pull/1442>`_
- `Fix a number of problems related to photoatomic data <https://github.com/openmc-dev/openmc/pull/1425>`_
- `Fix cosine smearing for S(a,b) <https://github.com/openmc-dev/openmc/pull/1420>`_
- `Use relative distances for coincidence test in hex lattice <https://github.com/openmc-dev/openmc/pull/1414>`_
- `Fix RPATH for non-Debian linux systems <https://github.com/openmc-dev/openmc/pull/1411>`_
- `Fix mesh plotter energy filter bins <https://github.com/openmc-dev/openmc/pull/1409>`_
- `Fix memory leak <https://github.com/openmc-dev/openmc/pull/1395>`_
- `Fix volume allocation related to burnable materials <https://github.com/openmc-dev/openmc/pull/1392>`_
- `Fix tally mesh bug for short tracks <https://github.com/openmc-dev/openmc/pull/1387>`_
- `DAGMC void material assignment fix <https://github.com/openmc-dev/openmc/pull/1375>`_
- `Fix for Mesh __repr__ methods <https://github.com/openmc-dev/openmc/pull/1385>`_
------------
Contributors
------------
This release contains new contributions from the following people:
- `Paul Cosgrove <https://github.com/ChasingNeutrons>`_
- `Steven Dargaville <https://github.com/stevendargaville>`_
- `Andrew Davis <https://github.com/makeclean>`_
- `Iurii Drobyshev <https://github.com/dryuri92>`_
- `Guillaume Giudicelli <https://github.com/GiudGiud>`_
- `Alec Golas <https://github.com/awgolas>`_
- `Avery Grieve <https://github.com/NuclearEngideer>`_
- `Sterling Harper <https://github.com/smharper>`_
- `Yuan Hu <https://github.com/YuanHu-PKU-KIT>`_
- `Yue Jin <https://github.com/kingyue737>`_
- `Andrew Johnson <https://github.com/drewejohnson>`_
- `Mikolaj Kowalski <https://github.com/Mikolaj-A-Kowalski>`_
- `Shikhar Kumar <https://github.com/shikhar413>`_
- `Jingang Liang <https://github.com/liangjg>`_
- `David Long <https://github.com/davidjohnlong>`_
- `Amanda Lund <https://github.com/amandalund>`_
- `Alex Lyons <https://github.com/alex-lyons>`_
- `Adam Nelson <https://github.com/nelsonag>`_
- `Ethan Peterson <https://github.com/eepeterson>`_
- `Sam Powell-Gill <https://github.com/sampug>`_
- `Ariful Islam Pranto <https://github.com/AI-Pranto>`_
- `Simon Richards <https://github.com/simondrichards>`_
- `Gavin Ridley <https://github.com/gridley>`_
- `Paul Romano <https://github.com/paulromano>`_
- `Jonathan Shimwell <https://github.com/Shimwell>`_
- `Patrick Shriwise <https://github.com/pshriwise>`_
- `John Tramm <https://github.com/jtramm>`_
- `Paul P.H. Wilson <https://github.com/gonuke>`_
- `Jiankai Yu <https://github.com/rockfool>`_

1
docs/source/releasenotes/index.rst
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@ -7,6 +7,7 @@ Release Notes
.. toctree::
:maxdepth: 1
0.12.0
0.11.0
0.10.0
0.9.0

77
scripts/openmc-get-photon-data
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#!/usr/bin/env python3
"""
Download ENDF/B-VII.1 ENDF data from NNDC for photo-atomic and atomic
relaxation data and convert it to an HDF5 library for use with OpenMC.
This data is used for photon transport in OpenMC.
"""
import argparse
import os
from pathlib import Path
import zipfile
import openmc.data
from openmc._utils import download
class CustomFormatter(argparse.ArgumentDefaultsHelpFormatter,
argparse.RawDescriptionHelpFormatter):
pass
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=CustomFormatter
)
parser.add_argument('-c', '--cross-sections',
help='cross_sections.xml file to append libraries to')
args = parser.parse_args()
base_url = 'https://www.nndc.bnl.gov/endf/b7.1/zips/'
files = ['ENDF-B-VII.1-photoat.zip', 'ENDF-B-VII.1-atomic_relax.zip']
block_size = 16384
# ==============================================================================
# DOWNLOAD FILES FROM NNDC SITE
output = Path('photon_hdf5')
output.mkdir(exist_ok=True)
for f in files:
download(base_url + f)
# ==============================================================================
# EXTRACT FILES
for f in files:
print('Extracting {}...'.format(f))
zipfile.ZipFile(f).extractall()
# ==============================================================================
# GENERATE HDF5 DATA LIBRARY
# If previous cross_sections.xml was specified, load it in
if args.cross_sections is not None:
lib_path = args.cross_sections
library = openmc.data.DataLibrary.from_xml(lib_path)
else:
lib_path = output / 'cross_sections.xml'
library = openmc.data.DataLibrary()
# Iterate over each natural element from Z=1 to Z=100
for z in range(1, 101):
element = openmc.data.ATOMIC_SYMBOL[z]
print('Generating HDF5 file for Z={} ({})...'.format(z, element))
# Generate instance of IncidentPhoton
photo_file = os.path.join('photoat', 'photoat-{:03}_{}_000.endf'.format(z, element))
atom_file = os.path.join('atomic_relax', 'atom-{:03}_{}_000.endf'.format(z, element))
data = openmc.data.IncidentPhoton.from_endf(photo_file, atom_file)
# Write HDF5 file and register it
hdf5_file = output / (element + '.h5')
data.export_to_hdf5(hdf5_file, 'w')
library.register_file(hdf5_file)
library.export_to_xml(lib_path)

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scripts/openmc-make-compton
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@ -1,69 +0,0 @@
#!/usr/bin/env python
import os
import tarfile
import numpy as np
import h5py
from openmc._utils import download
base_url = 'http://geant4.cern.ch/support/source/'
filename = 'G4EMLOW.6.48.tar.gz'
# ==============================================================================
# DOWNLOAD FILES FROM GEANT4 SITE
download(base_url + filename)
# ==============================================================================
# EXTRACT FILES FROM TGZ
if not os.path.isdir('G4EMLOW6.48'):
with tarfile.open(filename, 'r') as tgz:
print('Extracting {}...'.format(filename))
tgz.extractall()
# ==============================================================================
# GENERATE COMPTON PROFILE HDF5 FILE
print('Generating compton_profiles.h5...')
shell_file = os.path.join('G4EMLOW6.48', 'doppler', 'shell-doppler.dat')
with open(shell_file, 'r') as shell, h5py.File('compton_profiles.h5', 'w') as f:
# Read/write electron momentum values
pz = np.loadtxt(os.path.join('G4EMLOW6.48', 'doppler', 'p-biggs.dat'))
f.create_dataset('pz', data=pz)
for z in range(1, 101):
# Create group for this element
group = f.create_group('{:03}'.format(z))
# Read data into one long array
path = os.path.join('G4EMLOW6.48', 'doppler', 'profile-{}.dat'.format(z))
with open(path, 'r') as profile:
j = np.fromstring(profile.read(), sep=' ')
# Determine number of electron shells and reshape. Profiles are
# tabulated against a grid of 31 momentum values.
n_shells = j.size // 31
j.shape = (n_shells, 31)
# Write Compton profile for this Z
group.create_dataset('J', data=j)
# Determine binding energies and number of electrons for each shell
num_electrons = []
binding_energy = []
while True:
words = shell.readline().split()
if words[0] == '-1':
break
num_electrons.append(float(words[0]))
binding_energy.append(float(words[1]))
# Write binding energies and number of electrons
group.create_dataset('num_electrons', data=num_electrons)
group.create_dataset('binding_energy', data=binding_energy)

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scripts/openmc-make-stopping-powers
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@ -1,53 +0,0 @@
#!/usr/bin/env python
from urllib.parse import urlencode
from urllib.request import urlopen
from lxml import html
import numpy as np
import h5py
from openmc.data import ATOMIC_SYMBOL
base_url = 'https://physics.nist.gov/cgi-bin/Star/e_table-t.pl'
energies = np.logspace(-3, 3, 200)
data = {'matno': '', 'Energies': '\n'.join(str(x) for x in energies)}
columns = {1: 's_collision', 2: 's_radiative'}
# ==============================================================================
# SCRAPE DATA FROM ESTAR SITE AND GENERATE STOPPING POWER HDF5 FILE
print('Generating stopping_powers.h5...')
with h5py.File('stopping_powers.h5', 'w') as f:
# Write energies
f.create_dataset('energy', data=energies)
# Look over atomic number; ESTAR only goes up to Z=98 (Californium)
for Z in range(1, 99):
print('Processing {} data...'.format(ATOMIC_SYMBOL[Z]))
# Update form-encoded data to send in POST request for this element
data['matno'] = '{:03}'.format(Z)
payload = urlencode(data).encode("utf-8")
# Retrieve data from ESTAR site
with urlopen(url=base_url, data=payload) as response:
r = response.read()
# Remove text and reformat data -- omit first 12 and last 5 lines to get
# only data in table
r = html.fromstring(r).xpath('//pre//text()')
values = np.fromstring(' '.join(r[12:-5]), sep=' ').reshape((-1, 5)).T
# Create group for this element
group = f.create_group('{:03}'.format(Z))
# Write the mean excitation energy
attributes = np.fromstring(r[3], sep=' ')
group.attrs['I'] = attributes[2]
# Write collision and radiative stopping powers
for i in columns:
group.create_dataset(columns[i], data=values[i])