Merge pull request #431 from GiudGiud/PR_merge

Merge 3D MOC into develop

.gitignore

@@ -1,43 +1,137 @@
-# Installation
+# installation
 *.o
 *.cxx
 *.h.gch
 *.so
 *.pyc
-*.o
-*.cxx
-*.h.gch
-*.so
+*/*.o
+*/*.cxx
+*/*.h.gch
+*/*.so
 *~
+*/*~
+*/*.pyc
+build
 build/*
+dist
 dist/*
 openmoc/openmoc.py
-openmoc/openmoc_wrap.cpp
+openmoc/swig/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*
 *.pbs.e*
 *.pbs.o*
 
 # output files
 log
+log/*
+*/log
+*/log/*
 tracks
+tracks/*
+*/tracks
+*/tracks/*
 plots
+plots/*
+*/plots
+*/plots/*
 fission-rates
-simulation-states
+fission-rates/*
+*/fission-rates
+*/fission-rates/*
+simulation-state*
+simulation-state/*
+*/simulation-state*
+*/simulation-state*/*
+
+
 *.data
+*/*.data
 *.png
 *.ppm
+*/*.png
+
 openmoc-*-.log
+*/openmoc-*-.log
 
 Openmp
 */penmp
 penmoc
 penmp-report
 */penmoc
 */penmp-report
-*/*.egg-info/*
+*.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
+
+
+# Tests generated files
+results_error.dat
+tests/test_geometry_dump/geometry_file.geo
+tests/test_geometry_dump/geometry_file_second.geo
+tests/test_geometry_load/geometry_file.geo
+tests/test_geometry_print/geometry.txt
+.pytest_cache/
+
+
+# Built C++ executables
+profile/models/run_time_standard/run_time_standard
+profile/models/c5g7/c5g7-3d-cmfd
+profile/models/c5g7/c5g7-3d
+profile/models/c5g7/c5g7-rodded-B-2x2
+profile/models/c5g7/c5g7-rodded-B
+profile/models/c5g7/c5g7-ws
+profile/models/fixed-source/pin-cell-fixed-3d
+profile/models/homogeneous/homogeneous
+profile/models/pin-cell/pin-cell-3d
+profile/models/simple-lattice/simple-lattice-3d
+profile/models/single-assembly/quarter-c5g7-assembly
+profile/models/single-assembly/single-c5g7-assembly
+profile/models/Takeda/Takeda-unrodded
+
 
 #Documentation
 sphinx/
@@ -46,11 +140,28 @@ docs/build/*
 docs/doxygen/xml
 docs/doxyge/xml/*
 
+# BGQ
+*.lst
+
+*.cobaltlog
+*/*.cobaltlog
+*.error
+*/*.error
+*.output
+*/*.output
+
+*core*
+*/core*
+
 build/*
+*/build/
 */build/*
 
-# PyCharm configuration files
+.idea*
 .idea/*
+.idea/*.xml
+
+sphinx/
 
 *.DS_Store
 */*.DS_Store
@@ -59,19 +170,6 @@ build/*
 # *~
 *.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/
 
@@ -90,3 +188,5 @@ openmoc/
 
 # Doxygen
 docs/doxygen/html/*
+
+

.travis.yml

@@ -1,7 +1,6 @@
 language: python
 python:
-  - "2.7"
-  - "3.4"
+  - "3.6"
 addons:
   apt:
     packages:
@@ -18,11 +17,7 @@ before_install:
   - 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
+  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
   - bash miniconda.sh -b -p $HOME/miniconda
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
@@ -37,12 +32,14 @@ before_install:
 
 install:
   # ================= Get C++11-compatible compiler ==================
-  - sudo apt-get install -qq gcc-4.8 g++-4.8
+  - sudo apt-get install -qq gcc-6 g++-6
   - 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++
+  # - sudo apt install mpich libmpich-dev
+  - sudo ln -s /usr/bin/gcc-6 /usr/bin/gcc
+  - sudo ln -s /usr/bin/g++-6 /usr/bin/g++
+
 
 script:
   - cd tests

Dockerfile

@@ -16,8 +16,9 @@ RUN apt-get install python3.7 -y
 ENV TZ=US
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
 
-RUN apt-get install git swig python-dev python-numpy python-matplotlib python-h5py -y
+RUN apt-get install git swig python3-dev python3-numpy python3-matplotlib python3-h5py -y
 
 #Build OpenMOC
 WORKDIR "/OpenMOC"
-RUN python setup.py install
+RUN python3 setup.py install --user
+RUN python3 setup.py install --user

README.rst

@@ -2,13 +2,16 @@
 OpenMOC
 =======
 
+
 .. image:: https://api.travis-ci.org/mit-crpg/OpenMOC.svg?branch=develop
     :target: https://travis-ci.org/mit-crpg/OpenMOC
 .. image:: https://coveralls.io/repos/github/mit-crpg/OpenMOC/badge.svg?branch=develop
     :target: https://coveralls.io/github/mit-crpg/OpenMOC?branch=develop
 .. 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
+.. image:: https://img.shields.io/badge/pypi-v0.4.0-orange.svg
+    :target: https://pypi.python.org/pypi/openmoc/0.4.0
+.. 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
@@ -72,6 +75,6 @@ OpenMOC is approved for distribution under the MIT/X license_.
 .. _installation instructions: https://mit-crpg.github.io/OpenMOC/usersguide/install.html
 .. _license: https://mit-crpg.github.io/OpenMOC/license.html
 .. _Nuclear Science & Engineering Department: http://web.mit.edu/nse/
-.. _IPython Notebook: https://gist.github.com/wbinventor/8c5d2ffbb86f11735610
+.. _IPython Notebook: http://nbviewer.ipython.org/gist/anonymous/abbce6824bceda49a615
 .. _contact: https://mit-crpg.github.io/OpenMOC/developers.html
 .. _users group: https://groups.google.com/forum/#!forum/openmoc-users