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Merge branch 'release-0.7.1' into develop

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Paul Romano 2015-12-23 15:40:51 -06:00
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2
docs/source/conf.py
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@ -55,7 +55,7 @@ copyright = u'2011-2015, Massachusetts Institute of Technology'
# The short X.Y version.
version = "0.7"
# The full version, including alpha/beta/rc tags.
release = "0.7.0"
release = "0.7.1"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.

63
docs/source/publications.rst
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@ -26,6 +26,10 @@ Overviews
Benchmarking
------------
- Khurrum S. Chaudri and Sikander M. Mirza, "Burnup dependent Monte Carlo
neutron physics calculations of IAEA MTR benchmark," *Prog. Nucl. Energy*,
**81**, 43-52 (2015). `<http://dx.doi.org/j.pnucene.2014.12.018>`_
- Daniel J. Kelly, Brian N. Aviles, Paul K. Romano, Bryan R. Herman,
Nicholas E. Horelik, and Benoit Forget, "Analysis of select BEAVRS PWR
benchmark cycle 1 results using MC21 and OpenMC," *Proc. PHYSOR*, Kyoto,
@ -57,13 +61,8 @@ Coupling and Multi-physics
- Bryan R. Herman, Benoit Forget, and Kord Smith, "Progress toward Monte
Carlo-thermal hydraulic coupling using low-order nonlinear diffusion
acceleration methods." In press, *Ann. Nucl. Energy*,
(2014). `<http://dx.doi.org/10.1016/j.anucene/2014.10.029>`_
- Adam G. Nelson and William R. Martin, "Improved Convergence of Monte Carlo
Generated Multi-Group Scattering Moments," *Proc. Int. Conf. Mathematics and
Computational Methods Applied to Nuclear Science and Engineering*, Sun Valley,
Idaho, May 5--9 (2013).
acceleration methods." *Ann. Nucl. Energy*, **84**, 63-72
(2015). `<http://dx.doi.org/10.1016/j.anucene.2014.10.029>`_
- Bryan R. Herman, Benoit Forget, and Kord Smith, "Utilizing CMFD in OpenMC to
Estimate Dominance Ratio and Adjoint," *Trans. Am. Nucl. Soc.*, **109**,
@ -81,19 +80,65 @@ Geometry
Miscellaneous
-------------
- William Boyd, Sterling Harper, and Paul K. Romano, "Equipping OpenMC for the
big data era," Accepted, *PHYSOR 2016*, Sun Valley, Idaho, May 1-5, 2016.
- Qicang Shen, William Boyd, Benoit Forget, and Kord Smith, "Tally precision
triggers for the OpenMC Monte Carlo code," *Trans. Am. Nucl. Soc.*, **112**,
637-640 (2015).
- Timothy P. Burke, Brian C. Kiedrowski, and William R. Martin, "Flux and
Reaction Rate Kernel Density Estimators in OpenMC," *Trans. Am. Nucl. Soc.*,
**109**, 683-686 (2013).
------------------------------------
Multi-group Cross Section Generation
------------------------------------
- Adam G. Nelson and William R. Martin, "Improved Monte Carlo tallying of
multi-group scattering moments using the NDPP code," *Trans. Am. Nucl. Soc.*,
**113**, 645-648 (2015)
- Adam G. Nelson and William R. Martin, "Improved Monte Carlo tallying of
multi-group scattering moment matrices," *Trans. Am. Nucl. Soc.*, **110**,
217-220 (2014).
- Adam G. Nelson and William R. Martin, "Improved Convergence of Monte Carlo
Generated Multi-Group Scattering Moments," *Proc. Int. Conf. Mathematics and
Computational Methods Applied to Nuclear Science and Engineering*, Sun Valley,
Idaho, May 5--9 (2013).
------------
Nuclear Data
------------
- Colin Josey, Pablo Ducru, Benoit Forget, and Kord Smith, "Windowed multipole
for cross section Doppler broadening," *J. Comput. Phys.*, In Press
(2016). `<http://dx.doi.org/10.1016/jcp.2015.08.013>`_
- Colin Josey, Benoit Forget, and Kord Smith, "Windowed multipole sensitivity to
target accuracy of the optimization procedure," *J. Nucl. Sci. Technol.*,
**52**, 987-992 (2015). `<http://dx.doi.org/10.1080/00223131.2015.1035353>`_
- Jonathan A. Walsh, Paul K. Romano, Benoit Forget, and Kord S. Smith,
"Optimizations of the energy grid search algorithm in continuous-energy Monte
Carlo particle transport codes", *Comput. Phys. Commun.*, **196**, 134-142
(2015). `<http://dx.doi.org/10.1016/j.cpc.2015.05.025>`_
- Jonathan A. Walsh, Benoit Forget, Kord S. Smith, Brian C. Kiedrowski, and
Forrest B. Brown, "Direct, on-the-fly calculation of unresolved resonance
region cross sections in Monte Carlo simulations," *Proc. Joint
Int. Conf. M&C+SNA+MC*, Nashville, Tennessee, Apr. 19--23 (2015).
- Amanda L. Lund, Andrew R. Siegel, Benoit Forget, Colin Josey, and
Paul K. Romano, "Using fractional cascading to accelerate cross section
lookups in Monte Carlo particle transport calculations," *Proc. Joint
Int. Conf. M&C+SNA+MC*, Nashville, Tennessee, Apr. 19--23 (2015).
- Ronald O. Rahaman, Andrew R. Siegel, and Paul K. Romano, "Monte Carlo
performance analysis for varying cross section parameter regimes,"
*Proc. Joint Int. Conf. M&C+SNA+MC*, Nashville, Tennessee, Apr. 19--23 (2015).
- Paul K. Romano and Timothy H. Trumbull, "Comparison of algorithms for Doppler
broadening pointwise tabulated cross sections," *Ann. Nucl. Energy*, **75**,
358--364 (2015). `<http://dx.doi.org/10.1016/j.anucene.2014.08.046>`_
@ -114,6 +159,10 @@ Nuclear Data
Parallelism
-----------
- Paul K. Romano, John R. Tramm, and Andrew R. Siegel, "Efficacy of hardware
threading for Monte Carlo particle transport calculations on multi- and
many-core systems," Accepted, *PHYSOR 2016*, Sun Valley, Idaho, May 1-5, 2016.
- David Ozog, Allen D. Malony, and Andrew R. Siegel, "A performance analysis of
SIMD algorithms for Monte Carlo simulations of nuclear reactor cores,"
*Proc. IEEE Int. Parallel and Distributed Processing Symposium*, Hyderabad,

84
docs/source/releasenotes.rst
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@ -1,9 +1,30 @@
.. _releasenotes:
==============================
Release Notes for OpenMC 0.7.0
Release Notes for OpenMC 0.7.1
==============================
This release of OpenMC provides some substantial improvements over version
0.7.0. Non-simple cell regions can now be defined through the ``|`` (union) and
``~`` (complement) operators. Similar changes in the Python API also allow
complex cell regions to be defined. A true secondary particle bank now exists;
this is crucial for photon transport (to be added in the next minor release). A
rich API for multi-group cross section generation has been added via the
``openmc.mgxs`` Python module.
Various improvements to tallies have also been made. It is now possible to
explicitly specify that a collision estimator be used in a tally. A new
``delayedgroup`` filter and ``delayed-nu-fission`` score allow a user to obtain
delayed fission neutron production rates filtered by delayed group. Finally, the
new ``inverse-velocity`` score may be useful for calculating kinetics
parameters.
.. caution:: In previous versions, depending on how OpenMC was compiled binary
output was either given in HDF5 or a flat binary format. With this
version, all binary output is now HDF5 which means you **must**
have HDF5 in order to install OpenMC. Please consult the user's
guide for instructions on how to compile with HDF5.
-------------------
System Requirements
-------------------
@ -17,36 +38,41 @@ the problem at hand (mostly on the number of nuclides in the problem).
New Features
------------
- Complete Python API
- Python 3 compatability for all scripts
- All scripts consistently named openmc-* and installed together
- New 'distribcell' tally filter for repeated cells
- Ability to specify outer lattice universe
- XML input validation utility (openmc-validate-xml)
- Support for hexagonal lattices
- Material union energy grid method
- Tally triggers
- Remove dependence on PETSc
- Significant OpenMP performance improvements
- Support for Fortran 2008 MPI interface
- Use of Travis CI for continuous integration
- Simplifications and improvements to test suite
- Support for complex cell regions (union and complement operators)
- Generic quadric surface type
- Improved handling of secondary particles
- Binary output is now solely HDF5
- ``openmc.mgxs`` Python module enabling multi-group cross section generation
- Collision estimator for tallies
- Delayed fission neutron production tallies with ability to filter by delayed
group
- Inverse velocity tally score
- Performance improvements for binary search
- Performance improvements for reaction rate tallies
---------
Bug Fixes
---------
- b5f712_: Fix bug in spherical harmonics tallies
- e6675b_: Ensure all constants are double precision
- 04e2c1_: Fix potential bug in sample_nuclide routine
- 6121d9_: Fix bugs related to particle track files
- 2f0e89_: Fixes for nuclide specification in tallies
- 299322_: Bug with material filter when void material present
- d74840_: Fix triggers on tallies with multiple filters
- c29a81_: Correctly handle maximum transport energy
- 3edc23_: Fixes in the nu-scatter score
- 629e3b_: Assume unspecified surface coefficients are zero in Python API
- 5dbe8b_: Fix energy filters for openmc-plot-mesh-tally
- ff66f4_: Fixes in the openmc-plot-mesh-tally script
- 441fd4_: Fix bug in kappa-fission score
- 7e5974_: Allow fixed source simulations from Python API
.. _b5f712: https://github.com/mit-crpg/openmc/commit/b5f712
.. _e6675b: https://github.com/mit-crpg/openmc/commit/e6675b
.. _04e2c1: https://github.com/mit-crpg/openmc/commit/04e2c1
.. _6121d9: https://github.com/mit-crpg/openmc/commit/6121d9
.. _2f0e89: https://github.com/mit-crpg/openmc/commit/2f0e89
.. _299322: https://github.com/mit-crpg/openmc/commit/299322
.. _d74840: https://github.com/mit-crpg/openmc/commit/d74840
.. _c29a81: https://github.com/mit-crpg/openmc/commit/c29a81
.. _3edc23: https://github.com/mit-crpg/openmc/commit/3edc23
.. _629e3b: https://github.com/mit-crpg/openmc/commit/629e3b
.. _5dbe8b: https://github.com/mit-crpg/openmc/commit/5dbe8b
.. _ff66f4: https://github.com/mit-crpg/openmc/commit/ff66f4
.. _441fd4: https://github.com/mit-crpg/openmc/commit/441fd4
.. _7e5974: https://github.com/mit-crpg/openmc/commit/7e5974
------------
Contributors
@ -55,13 +81,11 @@ Contributors
This release contains new contributions from the following people:
- `Will Boyd <wbinventor@gmail.com>`_
- `Matt Ellis <mellis13@mit.edu>`_
- `Sterling Harper <sterlingmharper@mit.edu>`_
- `Bryan Herman <bherman@mit.edu>`_
- `Nicholas Horelik <nicholas.horelik@gmail.com>`_
- `Bryan Herman <hermab53@gmail.com>`_
- `Colin Josey <cjosey@mit.edu>`_
- `William Lyu <PaleNeutron@users.noreply.github.com>`_
- `Adam Nelson <nelsonag@umich.edu>`_
- `Paul Romano <paul.k.romano@gmail.com>`_
- `Anthony Scopatz <scopatz@gmail.com>`_
- `Kelly Rowland <kellylynnerowland@gmail.com>`_
- `Sam Shaner <samuelshaner@gmail.com>`_
- `Jon Walsh <walshjon@mit.edu>`_

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docs/source/usersguide/install.rst
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@ -8,7 +8,7 @@ Installation and Configuration
Installing on Ubuntu with PPA
-----------------------------
For users with Ubuntu 11.10 or later, a binary package for OpenMC is available
For users with Ubuntu 15.04 or later, a binary package for OpenMC is available
through a Personal Package Archive (PPA) and can be installed through the APT
package manager. First, add the following PPA to the repository sources:
@ -28,6 +28,9 @@ Now OpenMC should be recognized within the repository and can be installed:
sudo apt-get install openmc
Binary packages from this PPA may exist for earlier versions of Ubuntu, but they
are no longer supported.
--------------------
Building from Source
--------------------
@ -74,6 +77,12 @@ Prerequisites
You may omit ``--enable-parallel`` if you want to compile HDF5_ in serial.
.. important::
OpenMC uses various parts of the HDF5 Fortran 2003 API; as such you
must include ``--enable-fortran2003`` or else OpenMC will not be able
to compile.
On Debian derivatives, HDF5 and/or parallel HDF5 can be installed through
the APT package manager:

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openmc/clean_xml.py
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@ -1,7 +1,7 @@
def sort_xml_elements(tree):
# Retrieve all children of the root XML node in the tree
elements = tree.getchildren()
elements = list(tree)
# Initialize empty lists for the sorted and comment elements
sorted_elements = []

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openmc/region.py
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@ -355,6 +355,8 @@ class Complement(Region):
temp_region = Intersection(*[~n for n in self.node.nodes])
elif isinstance(self.node, Intersection):
temp_region = Union(*[~n for n in self.node.nodes])
elif isinstance(self.node, Complement):
temp_region = self.node.node
else:
temp_region = ~n
temp_region = ~self.node
return temp_region.bounding_box

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setup.py
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@ -10,7 +10,7 @@ except ImportError:
have_setuptools = False
kwargs = {'name': 'openmc',
'version': '0.7.0',
'version': '0.7.1',
'packages': ['openmc', 'openmc.mgxs'],
'scripts': glob.glob('scripts/openmc-*'),

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src/constants.F90
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@ -8,7 +8,7 @@ module constants
! OpenMC major, minor, and release numbers
integer, parameter :: VERSION_MAJOR = 0
integer, parameter :: VERSION_MINOR = 7
integer, parameter :: VERSION_RELEASE = 0
integer, parameter :: VERSION_RELEASE = 1
! Revision numbers for binary files
integer, parameter :: REVISION_STATEPOINT = 14

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src/state_point.F90
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@ -870,7 +870,6 @@ contains
integer(HSIZE_T) :: dims(1)
type(c_ptr) :: f_ptr
#ifdef PHDF5
integer :: data_xfer_mode
integer(HID_T) :: plist ! property list
#else
integer :: i
@ -989,7 +988,6 @@ contains
integer(HSIZE_T) :: offset(1) ! offset of data
type(c_ptr) :: f_ptr
#ifdef PHDF5
integer :: data_xfer_mode
integer(HID_T) :: plist ! property list
#endif