Merge pull request #299 from mit-crpg/develop

Update to v0.2.0

.gitignore

@@ -1,138 +1,56 @@
-# installation
+# Installation
 *.o
 *.cxx
 *.h.gch
 *.so
-*.pbs.e*
-*.pbs.o*
 *.pyc
-*/*.o
-*/*.cxx
-*/*.h.gch
-*/*.so
+*.o
+*.cxx
+*.h.gch
+*.so
 *~
-*/*~
-*/*.pbs.e*
-*/*.pbs.o*
-*/*.pyc
-build
 build/*
-dist
 dist/*
 openmoc/openmoc.py
 openmoc/openmoc_wrap.cpp
-
-openmoc/mic/openmoc_mic.py
-openmoc/mic/openmoc_mic_wrap.cpp
-
-openmoc/intel/single/openmoc_intel_single_wrap.cpp
-openmoc/intel/single/openmoc_intel_single.py
-openmoc/intel/double/openmoc_intel_double_wrap.cpp
-openmoc/intel/double/openmoc_intel_double.py
-
-openmoc/gnu/single/openmoc_gnu_single_wrap.cpp
-openmoc/gnu/single/openmoc_gnu_single.py
-openmoc/gnu/double/openmoc_gnu_double_wrap.cpp
-openmoc/gnu/double/openmoc_gnu_double.py
-
-openmoc/bgq/single/openmoc_bgq_single_wrap.cpp
-openmoc/bgq/single/openmoc_bgq_double.py
-openmoc/bgq/double/openmoc_bgq_double_wrap.cpp
-openmoc/bgq/double/openmoc_bgq_double.py
-
 openmoc/cuda/openmoc_cuda.py
 openmoc/cuda/openmoc_cuda_wrap.cpp
-openmoc/cuda/single/openmoc_cuda_single_wrap.cpp
-openmoc/cuda/single/openmoc_cuda_single.py
-openmoc/cuda/double/openmoc_cuda_double_wrap.cpp
-openmoc/cuda/double/openmoc_cuda_double.py
 
+# TORQUE log files
+*.pbs.e*
+*.pbs.o*
 
 # output files
 log
-log/*
-*/log
-*/log/*
 tracks
-tracks/*
-*/tracks
-*/tracks/*
 plots
-plots/*
-*/plots
-*/plots/*
-pin-powers
-pin-powers/*
-*/pin-powers
-*/pin-powers/*
-simulation-state*
-simulation-state/*
-*/simulation-state*
-*/simulation-state*/*
-
+fission-rates
+simulation-states
 *.data
-*/*.data
 *.png
-*/*.png
-
+*.ppm
 openmoc-*-.log
-*/openmoc-*-.log
 
-penmp
+Openmp
 */penmp
 penmoc
 penmp-report
 */penmoc
 */penmp-report
-*.egg-info/*
-*/*.egg-info/
-
-openmoc/intel/single/openmoc_intel_single.py
-openmoc/intel/single/openmoc_intel_single_wrap.cpp
-openmoc/intel/double/openmoc_intel_double.py
-openmoc/intel/double/openmoc_intel_double_wrap.cpp
-
-openmoc/gnu/single/openmoc_gnu_single.py
-openmoc/gnu/single/openmoc_gnu_single_wrap.cpp
-openmoc/gnu/double/openmoc_gnu_double.py
-openmoc/gnu/doube/openmoc_gnu_double_wrap.cpp
-
-openmoc/cuda/openmoc_cuda.py
-openmoc/cuda/openmoc_cuda_wrap.cpp
-openmoc/cuda/single/openmoc_cuda_single.py
-openmoc/cuda/single/openmoc_cuda_single_wrap.cpp
-openmoc/cuda/double/openmoc_cuda_double.py
-openmoc/cuda/double/openmoc_cuda_double_wrap.cpp
-
+*/*.egg-info/*
 
 #Documentation
+sphinx/
 docs/build
 docs/build/*
 docs/doxygen/xml
 docs/doxyge/xml/*
 
-# BGQ
-*.lst
-
-*.cobaltlog
-*/*.cobaltlog
-*.error
-*/*.error
-*.output
-*/*.output
-
-*core*
-*/core*
-
 build/*
-*/build/
 */build/*
 
-.idea*
+# PyCharm configuration files
 .idea/*
-.idea/*.xml
-
-sphinx/
 
 *.DS_Store
 */*.DS_Store
@@ -141,3 +59,34 @@ sphinx/
 # *~
 *.swp
 
+# C++ Build
+profile/obj/*
+profile/models/c5g7/c5g7-cmfd
+profile/models/c5g7/c5g7-cmfd.o
+profile/models/c5g7/c5g7
+profile/models/c5g7/c5g7.o
+profile/models/gradients/one-directional/one-directional-gradient
+profile/models/gradients/one-directional/one-directional-gradient.o
+profile/models/gradients/two-directional/two-directional-gradient
+profile/models/gradients/two-directional/two-directional-gradient.o
+profile/models/homogeneous/homogeneous-one-group
+profile/models/homogeneous/homogeneous-one-group.o
+
+# IPython Notebook
+.ipynb_checkpoints/
+
+# OpenMC input/output files
+*.xml
+statepoint*
+summary*
+
+# Test results error file
+results_error.dat
+results_test.dat
+
+# Test build files
+openmoc/
+*.log
+
+# Doxygen
+docs/doxygen/html/*

.travis.yml

@@ -0,0 +1,43 @@
+language: python
+python:
+  - "2.7"
+  - "3.4"
+addons:
+  apt:
+    packages:
+    - swig
+cache:
+  directories:
+
+before_install:
+  # ========== Point apt-get to C++11-compatible compiler ==========
+  - sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
+  - sudo apt-get update -qq
+  # ============== Handle Python third-party packages ==============
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
+      wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh;
+    else
+      wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+    fi
+  - bash miniconda.sh -b -p $HOME/miniconda
+  - export PATH="$HOME/miniconda/bin:$PATH"
+  - hash -r
+  - conda config --set always_yes yes --set changeps1 no
+  - conda update -q conda
+  - conda info -a
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy scipy h5py pandas matplotlib pillow
+  - source activate test-environment
+
+install:
+  # ================= Get C++11-compatible compiler ==================
+  - sudo apt-get install -qq gcc-4.8 g++-4.8
+  - sudo apt-get install swig
+  - sudo rm /usr/bin/gcc
+  - sudo rm /usr/bin/g++
+  - sudo ln -s /usr/bin/gcc-4.8 /usr/bin/gcc
+  - sudo ln -s /usr/bin/g++-4.8 /usr/bin/g++
+
+script:
+  - cd tests
+  - ./travis.sh
+  - cd ..

CMakeLists.txt

@@ -0,0 +1,25 @@
+cmake_minimum_required(VERSION 2.8)
+
+#===============================================================================
+# Regression tests
+#===============================================================================
+
+# This allows for dashboard configuration
+include(CTest)
+
+# Get a list of all the tests to run
+file(GLOB_RECURSE TESTS ${CMAKE_CURRENT_SOURCE_DIR}/tests/test_*.py)
+
+# Loop through all the tests
+foreach(test ${TESTS})
+
+  # Get test information
+  get_filename_component(TEST_NAME ${test} NAME)
+  get_filename_component(TEST_PATH ${test} PATH)
+
+  add_test(NAME ${TEST_NAME}
+    WORKING_DIRECTORY ${TEST_PATH}
+    COMMAND ${PYTHON_EXECUTABLE} ${TEST_NAME}
+  )
+
+endforeach(test)

README.rst

@@ -1,38 +1,65 @@
-=================================================================
-OpenMOC Method of Characteristics Neutral Particle Transport Code
-=================================================================
-
-Welcome to the OpenMOC repository! OpenMOC is a simulation tool for 
-solving for the flux, power distribution, and multiplication factor 
-within a nuclear reactor. The code employs the deterministic method 
-of characteristics using source iteration. The OpenMOC project aims 
-to provide a simple-to-use Python package bound to a back-end of source 
-code written in C/C++ and CUDA. It includes support for constructive 
-solid geometry and 2D ray tracing for fully heterogeneous multi-group 
-calculations. Development of OpenMOC began at MIT in 2012 and is 
-spearheaded by several graduate students in the 
+=======
+OpenMOC
+=======
+
+.. image:: https://api.travis-ci.org/mit-crpg/OpenMOC.svg?branch=develop
+    :target: https://travis-ci.org/mit-crpg/OpenMOC
+.. image:: https://img.shields.io/badge/powered%20by-OpenMOC-blue.svg
+    :target: https://mit-crpg.github.io/OpenMOC/
+.. image:: https://img.shields.io/badge/license-MIT%20License-brightgreen.svg
+    :target: https://mit-crpg.github.io/OpenMOC/license.html
+.. image:: https://img.shields.io/badge/anucene-Elsevier-lightgray.svg
+    :target: http://www.sciencedirect.com/science/article/pii/S0306454913006634
+
+Welcome to the OpenMOC repository! OpenMOC is a simulation tool for
+solving for the flux, power distribution, and multiplication factor
+within a nuclear reactor. The code employs the deterministic method
+of characteristics, with support for both fixed source and eigenvalue
+calculations. The OpenMOC project aims to provide a simple-to-use
+Python package bound to a back-end of source code written in C/C++
+and CUDA. It includes support for constructive solid geometry and 2D
+ray tracing for fully heterogeneous multi-group calculations.
+Development of OpenMOC began at MIT in 2012 and is spearheaded by
+several graduate students in the
 `Nuclear Science & Engineering Department`_.
 
-Complete documentation on the usage of OpenMOC is hosted at 
-https://mit-crpg.github.io/OpenMOC/. If you would like to 
-contribute to the OpenMOC project, please `contact`_ the 
+Complete documentation on OpenMOC is hosted at
+https://mit-crpg.github.io/OpenMOC/. If you would like to
+contribute to the OpenMOC project, please `contact`_ the
 development team.
 
+For a guided example, see a demonstration `IPython Notebook`_.
+
 ------------
 Installation
 ------------
 
-Detailed `installation instructions`_ can be found in the 
+Detailed `installation instructions`_ can be found in the
 User's Guide.
 
 ---------------
 Troubleshooting
 ---------------
 
-If you run into problems installing or running OpenMOC, 
-first review the `FAQ`_ in the User's Guide. If you are 
-unable to find a solution to your problem there, please 
-`contact`_ one of the developers.
+Join the OpenMOC `users group`_ to ask questions and discuss
+methods and simulation workflows.
+
+--------------
+Citing OpenMOC
+--------------
+
+Please cite OpenMOC in your publications if it helps your research:
+
+.. code-block:: latex
+
+    @article{openmoc2014,
+      author = {Boyd, William and Shaner, Samuel and Li, Lulu and Forget, Benoit and Smith, Kord},
+      journal = {Annals of Nuclear Energy},
+      title = {The OpenMOC Method of Characteristics Neutral Particle Transport Code},
+      volume = {68},
+      pages = {43--52},
+      year = {2014}
+    }
 
 -------
 License
@@ -41,7 +68,8 @@ License
 OpenMOC is approved for distribution under the MIT/X license_.
 
 .. _installation instructions: https://mit-crpg.github.io/OpenMOC/usersguide/install.html
-.. _FAQ: https://mit-crpg.github.io/OpenMOC/FAQ
 .. _license: https://mit-crpg.github.io/OpenMOC/license.html
-.. _contact: https://mit-crpg.github.io/OpenMOC/developers.html
 .. _Nuclear Science & Engineering Department: http://web.mit.edu/nse/
+.. _IPython Notebook: https://gist.github.com/wbinventor/8c5d2ffbb86f11735610
+.. _contact: https://mit-crpg.github.io/OpenMOC/developers.html
+.. _users group: https://groups.google.com/forum/#!forum/openmoc-users