Merge pull request openmc-dev#944 from paulromano/api-updates

Additions in openmc.capi and elsewhere

.travis.yml

@@ -41,6 +41,7 @@ before_install:
 install:
   - if [[ $OPENMC_CONFIG != "check_source" ]]; then
       pip install numpy cython;
+      pip install --upgrade pytest;
       pip install -e .[test];
     fi
 
@@ -62,6 +63,6 @@ script:
       ./check_source.py;
     else
       ./run_tests.py -C $OPENMC_CONFIG -j 2 &&
-      pytest --cov=../openmc unit_tests/;
+      pytest --cov=../openmc -v unit_tests/;
     fi
   - cd ..

CMakeLists.txt

@@ -46,7 +46,7 @@ add_definitions(-DMAX_COORD=${maxcoord})
 #===============================================================================
 
 set(MPI_ENABLED FALSE)
-if($ENV{FC} MATCHES "mpi[^/]*$")
+if($ENV{FC} MATCHES "(mpi[^/]*|ftn)$")
   message("-- Detected MPI wrapper: $ENV{FC}")
   add_definitions(-DMPI)
   set(MPI_ENABLED TRUE)

docs/source/conf.py

@@ -26,8 +26,9 @@
 
 MOCK_MODULES = ['numpy', 'numpy.polynomial', 'numpy.polynomial.polynomial',
                 'numpy.ctypeslib', 'scipy', 'scipy.sparse', 'scipy.interpolate',
-                'scipy.integrate', 'scipy.optimize', 'scipy.special', 'h5py',
-                'pandas', 'uncertainties', 'openmoc', 'openmc.data.reconstruct']
+                'scipy.integrate', 'scipy.optimize', 'scipy.special',
+                'scipy.stats','h5py', 'pandas', 'uncertainties', 'openmoc',
+                'openmc.data.reconstruct']
 sys.modules.update((mod_name, MagicMock()) for mod_name in MOCK_MODULES)
 
 import numpy as np

docs/source/index.rst

@@ -10,21 +10,25 @@ interaction data is based on a native HDF5 format that can be generated from ACE
 files used by the MCNP and Serpent Monte Carlo codes.
 
 OpenMC was originally developed by members of the `Computational Reactor Physics
-Group`_ at the `Massachusetts Institute of Technology`_ starting
-in 2011. Various universities, laboratories, and other organizations now
-contribute to the development of OpenMC. For more information on OpenMC, feel
-free to send a message to the User's Group `mailing list`_.
+Group <http://crpg.mit.edu>`_ at the `Massachusetts Institute of Technology
+<http://web.mit.edu>`_ starting in 2011. Various universities, laboratories, and
+other organizations now contribute to the development of OpenMC. For more
+information on OpenMC, feel free to send a message to the User's Group `mailing
+list <https://groups.google.com/forum/?fromgroups=#!forum/openmc-users>`_.
 
-.. _Computational Reactor Physics Group: http://crpg.mit.edu
-.. _Massachusetts Institute of Technology: http://web.mit.edu
-.. _mailing list: https://groups.google.com/forum/?fromgroups=#!forum/openmc-users
-.. _Read the Docs: http://openmc.readthedocs.io/en/latest/
+.. admonition:: Recommended publication for citing
+   :class: tip
+
+   Paul K. Romano, Nicholas E. Horelik, Bryan R. Herman, Adam G. Nelson, Benoit
+   Forget, and Kord Smith, "`OpenMC: A State-of-the-Art Monte Carlo Code for
+   Research and Development <https://doi.org/10.1016/j.anucene.2014.07.048>`_,"
+   *Ann. Nucl. Energy*, **82**, 90--97 (2015).
 
 .. only:: html
 
-    --------
-    Contents
-    --------
+   --------
+   Contents
+   --------
 
 .. toctree::
     :maxdepth: 1

docs/source/publications.rst

@@ -10,7 +10,7 @@ Overviews
 
 - Paul K. Romano, Nicholas E. Horelik, Bryan R. Herman, Adam G. Nelson, Benoit
   Forget, and Kord Smith, "`OpenMC: A State-of-the-Art Monte Carlo Code for
-  Research and Development <http://dx.doi.org/10.1016/j.anucene.2014.07.048>`_,"
+  Research and Development <https://doi.org/10.1016/j.anucene.2014.07.048>`_,"
   *Ann. Nucl. Energy*, **82**, 90--97 (2015).
 
 - Paul K. Romano, Bryan R. Herman, Nicholas E. Horelik, Benoit Forget, Kord
@@ -19,16 +19,19 @@ Overviews
   Nuclear Science and Engineering*, Sun Valley, Idaho, May 5--9 (2013).
 
 - Paul K. Romano and Benoit Forget, "`The OpenMC Monte Carlo Particle Transport
-  Code <http://dx.doi.org/10.1016/j.anucene.2012.06.040>`_,"
+  Code <https://doi.org/10.1016/j.anucene.2012.06.040>`_,"
   *Ann. Nucl. Energy*, **51**, 274--281 (2013).
 
 ------------
 Benchmarking
 ------------
 
+- Travis J. Labossiere-Hickman and Benoit Forget, "Selected VERA Core Physics
+  Benchmarks in OpenMC," *Trans. Am. Nucl. Soc.*, **117**, 1520-1523 (2017).
+
 - Khurrum S. Chaudri and Sikander M. Mirza, "`Burnup dependent Monte Carlo
   neutron physics calculations of IAEA MTR benchmark
-  <http://dx.doi.org/10.1016/j.pnucene.2014.12.018>`_," *Prog. Nucl. Energy*,
+  <https://doi.org/10.1016/j.pnucene.2014.12.018>`_," *Prog. Nucl. Energy*,
   **81**, 43-52 (2015).
 
 - Daniel J. Kelly, Brian N. Aviles, Paul K. Romano, Bryan R. Herman,
@@ -54,10 +57,15 @@ Benchmarking
 Coupling and Multi-physics
 --------------------------
 
+- Tianliang Hu, Liangzhu Cao, Hongchun Wu, Xianan Du, and Mingtao He, "`Coupled
+  neutrons and thermal-hydraulics simulation of molten salt reactors based on
+  OpenMC/TANSY <https://doi.org/10.1016/j.anucene.2017.05.002>`_,"
+  *Ann. Nucl. Energy*, **109**, 260-276 (2017).
+
 - Matthew Ellis, Derek Gaston, Benoit Forget, and Kord Smith, "`Preliminary
   Coupling of the Monte Carlo Code OpenMC and the Multiphysics Object-Oriented
   Simulation Environment for Analyzing Doppler Feedback in Monte Carlo
-  Simulations <http://dx.doi.org/10.13182/NSE16-26>`_," *Nucl. Sci. Eng.*,
+  Simulations <https://doi.org/10.13182/NSE16-26>`_," *Nucl. Sci. Eng.*,
   **185**, 184-193 (2017).
 
 - Matthew Ellis, Benoit Forget, Kord Smith, and Derek Gaston, "Continuous
@@ -79,7 +87,7 @@ 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 <http://dx.doi.org/10.1016/j.anucene.2014.10.029>`_,"
+  acceleration methods <https://doi.org/10.1016/j.anucene.2014.10.029>`_,"
   *Ann. Nucl. Energy*, **84**, 63-72 (2015).
 
 - Bryan R. Herman, Benoit Forget, and Kord Smith, "Utilizing CMFD in OpenMC to
@@ -106,6 +114,15 @@ Geometry and Visualization
 Miscellaneous
 -------------
 
+- Adam G. Nelson, Samuel Shaner, William Boyd, and Paul K. Romano,
+  "Incorporation of a Multigroup Transport Capability in the OpenMC Monte Carlo
+  Particle Transport Code," *Trans. Am. Nucl. Soc.*, **117**, 679-681 (2017).
+
+- Youqi Zheng, Yunlong Xiao, and Hongchun Wu, "`Application of the virtual
+  density theory in fast reactor analysis based on the neutron transport
+  calculation <https://doi.org/10.1016/j.nucengdes.2017.05.020>`_,"
+  *Nucl. Eng. Des.*, **320**, 200-206 (2017).
+
 - Amanda L. Lund, Paul K. Romano, and Andrew R. Siegel, "Accelerating Source
   Convergence in Monte Carlo Criticality Calculations Using a Particle Ramp-Up
   Technique," *Proc. Int. Conf. Mathematics & Computational Methods Applied to
@@ -126,7 +143,7 @@ Miscellaneous
 
 - Yunzhao Li, Qingming He, Liangzhi Cao, Hongchun Wu, and Tiejun Zu, "`Resonance
   Elastic Scattering and Interference Effects Treatments in Subgroup Method
-  <http://dx.doi.org/10.1016/j.net.2015.12.015>`_," *Nucl. Eng. Tech.*, **48**,
+  <https://doi.org/10.1016/j.net.2015.12.015>`_," *Nucl. Eng. Tech.*, **48**,
   339-350 (2016).
 
 - William Boyd, Sterling Harper, and Paul K. Romano, "Equipping OpenMC for the
@@ -135,7 +152,7 @@ Miscellaneous
 - Michal Kostal, Vojtech Rypar, Jan Milcak, Vlastimil Juricek, Evzen Losa,
   Benoit Forget, and Sterling Harper, "`Study of graphite reactivity worth on
   well-defined cores assembled on LR-0 reactor
-  <http://dx.doi.org/10.1016/j.anucene.2015.10.010>`_," *Ann. Nucl. Energy*,
+  <https://doi.org/10.1016/j.anucene.2015.10.010>`_," *Ann. Nucl. Energy*,
   **87**, 601-611 (2016).
 
 - Qicang Shen, William Boyd, Benoit Forget, and Kord Smith, "Tally precision
@@ -154,9 +171,25 @@ Miscellaneous
 Multi-group Cross Section Generation
 ------------------------------------
 
+- Zhaoyuan Liu, Kord Smith, Benoit Forget, and Javier Ortensi, "`Cumulative
+  migration method for computing rigorous diffusion coefficients and transport
+  cross sections from Monte Carlo
+  <https://doi.org/10.1016/j.anucene.2017.10.039>`_," *Ann. Nucl. Energy*,
+  **112**, 507-516 (2018).
+
+- Gang Yang, Tongkyu Park, and Won Sik Yang, "Effects of Fuel Salt Velocity
+  Field on Neutronics Performances in Molten Salt Reactors with Open Flow
+  Channels," *Trans. Am. Nucl. Soc.*, **117**, 1339-1342 (2017).
+
+- William Boyd, Nathan Gibson, Benoit Forget, and Kord Smith, "`An analysis of
+  condensation errors in multi-group cross section generation for fine-mesh
+  neutron transport calculations
+  <https://doi.org/10.1016/j.anucene.2017.09.052>`_," *Ann. Nucl. Energy*,
+  **112**, 267-276 (2018).
+
 - Hong Shuang, Yang Yongwei, Zhang Lu, and Gao Yucui, "`Fabrication and
   validation of multigroup cross section library based on the OpenMC code
-  <http://dx.doi.org/10.11889/j.0253-3219.2017.hjs.40.040502>`_,"
+  <https://doi.org/10.11889/j.0253-3219.2017.hjs.40.040502>`_,"
   *Nucl. Techniques* **40** (4), 040504 (2017). (in Mandarin)
 
 - Nicholas E. Stauff, Changho Lee, Paul K. Romano, and Taek K. Kim,
@@ -207,7 +240,7 @@ Doppler Broadening
 
 - Colin Josey, Pablo Ducru, Benoit Forget, and Kord Smith, "`Windowed multipole
   for cross section Doppler broadening
-  <http://dx.doi.org/10.1016/j.jcp.2015.08.013>`_," *J. Comput. Phys.*, **307**,
+  <https://doi.org/10.1016/j.jcp.2015.08.013>`_," *J. Comput. Phys.*, **307**,
   715-727 (2016).
 
 - Jonathan A. Walsh, Benoit Forget, Kord S. Smith, and Forrest B. Brown,
@@ -217,12 +250,12 @@ Doppler Broadening
 
 - Colin Josey, Benoit Forget, and Kord Smith, "`Windowed multipole sensitivity
   to target accuracy of the optimization procedure
-  <http://dx.doi.org/10.1080/00223131.2015.1035353>`_,"
+  <https://doi.org/10.1080/00223131.2015.1035353>`_,"
   *J. Nucl. Sci. Technol.*, **52**, 987-992 (2015).
 
 - Paul K. Romano and Timothy H. Trumbull, "`Comparison of algorithms for Doppler
   broadening pointwise tabulated cross sections
-  <http://dx.doi.org/10.1016/j.anucene.2014.08.046>`_," *Ann. Nucl. Energy*,
+  <https://doi.org/10.1016/j.anucene.2014.08.046>`_," *Ann. Nucl. Energy*,
   **75**, 358--364 (2015).
 
 - Tuomas Viitanen, Jaakko Leppanen, and Benoit Forget, "Target motion sampling
@@ -231,13 +264,17 @@ Doppler Broadening
 
 - Benoit Forget, Sheng Xu, and Kord Smith, "`Direct Doppler broadening in Monte
   Carlo simulations using the multipole representation
-  <http://dx.doi.org/10.1016/j.anucene.2013.09.043>`_," *Ann. Nucl. Energy*,
+  <https://doi.org/10.1016/j.anucene.2013.09.043>`_," *Ann. Nucl. Energy*,
   **64**, 78--85 (2014).
 
 ------------
 Nuclear Data
 ------------
 
+- Jonathan A. Walsh, "Comparison of Unresolved Resonance Region Cross Section
+  Formalisms in Transport Simulations," *Trans. Am. Nucl. Soc.*, **117**,
+  749-752 (2017).
+
 - Jonathan A. Walsh, Benoit Forget, Kord S. Smith, and Forrest B. Brown,
   "`Uncertainty in Fast Reactor-Relevant Critical Benchmark Simulations Due to
   Unresolved Resonance Structure
@@ -255,13 +292,13 @@ Nuclear Data
 - Jonathan A. Walsh, Benoit Froget, Kord S. Smith, and Forrest B. Brown,
   "`Neutron Cross Section Processing Methods for Improved Integral Benchmarking
   of Unresolved Resonance Region Evaluations
-  <http://dx.doi.org/10.1051/epjconf/201611106001>`_," *Eur. Phys. J. Web Conf.*
+  <https://doi.org/10.1051/epjconf/201611106001>`_," *Eur. Phys. J. Web Conf.*
   **111**, 06001 (2016).
 
 - 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
-  <http://dx.doi.org/10.1016/j.cpc.2015.05.025>`_", *Comput. Phys. Commun.*,
+  <https://doi.org/10.1016/j.cpc.2015.05.025>`_", *Comput. Phys. Commun.*,
   **196**, 134-142 (2015).
 
 - Jonathan A. Walsh, Benoit Forget, Kord S. Smith, Brian C. Kiedrowski, and
@@ -280,7 +317,7 @@ Nuclear Data
 
 - Jonathan A. Walsh, Benoit Forget, and Kord S. Smith, "`Accelerated sampling of
   the free gas resonance elastic scattering kernel
-  <http://dx.doi.org/10.1016/j.anucene.2014.01.017>`_," *Ann. Nucl. Energy*,
+  <https://doi.org/10.1016/j.anucene.2014.01.017>`_," *Ann. Nucl. Energy*,
   **69**, 116--124 (2014).
 
 -----------
@@ -325,45 +362,45 @@ Parallelism
 
 - Nicholas Horelik, Andrew Siegel, Benoit Forget, and Kord Smith, "`Monte Carlo
   domain decomposition for robust nuclear reactor analysis
-  <http://dx.doi.org/10.1016/j.parco.2014.10.001>`_," *Parallel Comput.*,
+  <https://doi.org/10.1016/j.parco.2014.10.001>`_," *Parallel Comput.*,
   **40**, 646--660 (2014).
 
 - Andrew Siegel, Kord Smith, Kyle Felker, Paul Romano, Benoit Forget, and Peter
   Beckman, "`Improved cache performance in Monte Carlo transport calculations
-  using energy banding <http://dx.doi.org/10.1016/j.cpc.2013.10.008>`_,"
+  using energy banding <https://doi.org/10.1016/j.cpc.2013.10.008>`_,"
   *Comput. Phys. Commun.*, **185** (4), 1195--1199 (2014).
 
 - Paul K. Romano, Benoit Forget, Kord Smith, and Andrew Siegel, "`On the use of
   tally servers in Monte Carlo simulations of light-water reactors
-  <http://dx.doi.org/10.1051/snamc/201404301>`_," *Proc. Joint International
+  <https://doi.org/10.1051/snamc/201404301>`_," *Proc. Joint International
   Conference on Supercomputing in Nuclear Applications and Monte Carlo*, Paris,
   France, Oct. 27--31 (2013).
 
 - Kyle G. Felker, Andrew R. Siegel, Kord S. Smith, Paul K. Romano, and Benoit
   Forget, "`The energy band memory server algorithm for parallel Monte Carlo
-  calculations <http://dx.doi.org/10.1051/snamc/201404207>`_," *Proc. Joint
+  calculations <https://doi.org/10.1051/snamc/201404207>`_," *Proc. Joint
   International Conference on Supercomputing in Nuclear Applications and Monte
   Carlo*, Paris, France, Oct. 27--31 (2013).
 
 - John R. Tramm and Andrew R. Siegel, "`Memory Bottlenecks and Memory Contention
   in Multi-Core Monte Carlo Transport Codes
-  <http://dx.doi.org/10.1051/snamc/201404208>`_," *Proc. Joint International
+  <https://doi.org/10.1051/snamc/201404208>`_," *Proc. Joint International
   Conference on Supercomputing in Nuclear Applications and Monte Carlo*, Paris,
   France, Oct. 27--31 (2013).
 
 - Andrew R. Siegel, Kord Smith, Paul K. Romano, Benoit Forget, and Kyle Felker,
   "`Multi-core performance studies of a Monte Carlo neutron transport code
-  <http://dx.doi.org/10.1177/1094342013492179>`_," *Int. J. High
+  <https://doi.org/10.1177/1094342013492179>`_," *Int. J. High
   Perform. Comput. Appl.*, **28** (1), 87--96 (2014).
 
 - Paul K. Romano, Andrew R. Siegel, Benoit Forget, and Kord Smith, "`Data
   decomposition of Monte Carlo particle transport simulations via tally servers
-  <http://dx.doi.org/10.1016/j.jcp.2013.06.011>`_," *J. Comput. Phys.*, **252**,
+  <https://doi.org/10.1016/j.jcp.2013.06.011>`_," *J. Comput. Phys.*, **252**,
   20--36 (2013).
 
 - Andrew R. Siegel, Kord Smith, Paul K. Romano, Benoit Forget, and Kyle Felker,
   "`The effect of load imbalances on the performance of Monte Carlo codes in LWR
-  analysis <http://dx.doi.org/10.1016/j.jcp.2012.06.012>`_," *J. Comput. Phys.*,
+  analysis <https://doi.org/10.1016/j.jcp.2012.06.012>`_," *J. Comput. Phys.*,
   **235**, 901--911 (2013).
 
 
@@ -372,21 +409,26 @@ Parallelism
   519--522 (2012).
 
 - Paul K. Romano and Benoit Forget, "`Parallel Fission Bank Algorithms in Monte
-  Carlo Criticality Calculations <http://dx.doi.org/10.13182/NSE10-98>`_,"
+  Carlo Criticality Calculations <https://doi.org/10.13182/NSE10-98>`_,"
   *Nucl. Sci. Eng.*, **170**, 125--135 (2012).
 
 ---------
 Depletion
 ---------
 
+- Colin Josey, Benoit Forget, and Kord Smith, "`High order methods for the
+  integration of the Bateman equations and other problems of the form of y' =
+  F(y,t)y <https://doi.org/10.1016/j.jcp.2017.08.025>`_," *J. Comput. Phys.*,
+  **350**, 296-313 (2017).
+
 - Matthew S. Ellis, Colin Josey, Benoit Forget, and Kord Smith, "`Spatially
   Continuous Depletion Algorithm for Monte Carlo Simulations
   <http://hdl.handle.net/1721.1/107880>`_," *Trans. Am. Nucl. Soc.*, **115**,
   1221-1224 (2016).
 
 - Anas Gul, K. S. Chaudri, R. Khan, and M. Azeen, "`Development and verification
   of LOOP: A Linkage of ORIGEN2.2 and OpenMC
-  <http://dx.doi.org/10.1016/j.anucene.2016.09.016>`_," *Ann. Nucl. Energy*,
+  <https://doi.org/10.1016/j.anucene.2016.09.016>`_," *Ann. Nucl. Energy*,
   **99**, 321--327 (2017).
 
 - Kai Huang, Hongchun Wu, Yunzhao Li, and Liangzhi Cao, "Generalized depletion

docs/source/pythonapi/base.rst

@@ -91,18 +91,6 @@ Many of the above classes are derived from several abstract classes:
    openmc.Region
    openmc.Lattice
 
-Two helper function are also available to create rectangular and hexagonal
-prisms defined by the intersection of four and six surface half-spaces,
-respectively.
-
-.. autosummary::
-   :toctree: generated
-   :nosignatures:
-   :template: myfunction.rst
-
-   openmc.get_hexagonal_prism
-   openmc.get_rectangular_prism
-
 .. _pythonapi_tallies:
 
 Constructing Tallies

docs/source/pythonapi/capi.rst

@@ -18,12 +18,19 @@ Functions
    openmc.capi.find_material
    openmc.capi.hard_reset
    openmc.capi.init
+   openmc.capi.iter_batches
    openmc.capi.keff
    openmc.capi.load_nuclide
+   openmc.capi.next_batch
+   openmc.capi.num_realizations
    openmc.capi.plot_geometry
    openmc.capi.reset
    openmc.capi.run
    openmc.capi.run_in_memory
+   openmc.capi.simulation_init
+   openmc.capi.simulation_finalize
+   openmc.capi.source_bank
+   openmc.capi.statepoint_write
 
 Classes
 -------

docs/source/pythonapi/index.rst

@@ -40,13 +40,13 @@ Modules
 -------
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
 
    base
-   stats
-   mgxs
    model
+   examples
+   mgxs
+   stats
    data
    capi
-   examples
    openmoc