Initial Release

.clang-format

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+---
+Language:        Cpp
+BasedOnStyle:  Google
+# only allow single line functions if they are inlined in class def'n
+AllowShortFunctionsOnASingleLine: Inline
+# do not force new line after template declarations
+AlwaysBreakTemplateDeclarations: false
+# Automatically detect whether a given fuction's arguments are one-per-line
+ExperimentalAutoDetectBinPacking: true
+# Use C++11 standard
+Standard:        Cpp11
+...

.gitignore

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+build
+cmake
+docker
+input
+*.sh

CMakeLists.txt

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+# DO NOT DELETE THIS LINE:: .:tricycle:Reactor
+
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
+# taken from http://geant4.cern.ch/support/source/geant4/CMakeLists.txt
+IF(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
+    message(STATUS "Stub requires an out-of-source build.")
+    message(STATUS "Please remove these files from ${CMAKE_BINARY_DIR} first:")
+    message(STATUS "CMakeCache.txt")
+    message(STATUS "CMakeFiles")
+    message(STATUS "Once these files are removed, create a separate directory")
+    message(STATUS "and run CMake from there")
+    message(FATAL_ERROR "in-source build detected")
+ENDIF()
+
+PROJECT(tricycle)
+
+# check for and enable c++11 support
+INCLUDE(CheckCXXCompilerFlag)
+CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11)
+IF(COMPILER_SUPPORTS_CXX11)
+  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+ELSE()
+  MESSAGE(STATUS "The compiler ${CMAKE_CXX_COMPILER} has no C++11
+  support. Please use a different C++ compiler.")
+ENDIF()
+
+# quiets fortify_source warnings when not compiling with optimizations
+# in linux distros where compilers were compiled with fortify_source enabled by
+# default (e.g. Arch linux).
+MESSAGE("${CMAKE_BUILD_TYPE}")
+STRING(TOLOWER "${CMAKE_BUILD_TYPE}" BUILD_TYPE)
+IF(NOT ${BUILD_TYPE} STREQUAL "release")
+    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=0")
+ENDIF()
+# no overflow warnings because of silly coin-ness
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-overflow")
+
+# Direct any out-of-source builds to this directory
+SET(STUB_SOURCE_DIR ${CMAKE_SOURCE_DIR})
+
+# Direct any binary installation paths to this directory
+SET(STUB_BINARY_DIR ${CMAKE_BINARY_DIR})
+
+# This makes all the libraries build as SHARED
+SET(BUILD_SHARED_LIBS true)
+
+# Setup build locations.
+IF(NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)
+    SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${STUB_BINARY_DIR}/bin)
+endif()
+IF(NOT CMAKE_LIBRARY_OUTPUT_DIRECTORY)
+    SET(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${STUB_BINARY_DIR}/lib)
+endif()
+IF(NOT CMAKE_ARCHIVE_OUTPUT_DIRECTORY)
+    SET(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${STUB_BINARY_DIR}/lib)
+ENDIF()
+
+SET(STUB_EXECUTABLE_DIR ${CMAKE_RUNTIME_OUTPUT_DIRECTORY})
+
+# use, i.e. don't skip the full RPATH for the build tree
+SET(CMAKE_SKIP_BUILD_RPATH  FALSE)
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+
+SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+
+# add the automatically determined parts of the RPATH
+# which point to directories outside the build tree to the install RPATH
+SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+# the RPATH to be used when installing, but only if it's not a system directory
+LIST(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
+IF("${isSystemDir}" STREQUAL "-1")
+    SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/lib/cyclus")
+    GET_FILENAME_COMPONENT(cxxCompilerRoot ${CMAKE_CXX_COMPILER} DIRECTORY)
+    GET_FILENAME_COMPONENT(cxxCompilerRoot ${cxxCompilerRoot} DIRECTORY)
+    IF (NOT "${CMAKE_INSTALL_RPATH}" STREQUAL "${cxxCompilerRoot}")
+        SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_RPATH}:${cxxCompilerRoot}/lib:${cxxCompilerRoot}/lib/cyclus")
+    ENDIF (NOT "${CMAKE_INSTALL_RPATH}" STREQUAL "${cxxCompilerRoot}")
+    SET(CMAKE_BUILD_RPATH "${CMAKE_INSTALL_RPATH}")
+ENDIF("${isSystemDir}" STREQUAL "-1")
+
+# Tell CMake where the modules are
+SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_INSTALL_PREFIX}/share/cyclus/cmake")
+SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${STUB_SOURCE_DIR}/cmake)
+MESSAGE("--CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}")
+
+# Find cyclus
+FIND_PACKAGE(Cyclus REQUIRED)
+SET(STUB_INCLUDE_DIRS ${STUB_INCLUDE_DIRS} ${CYCLUS_CORE_INCLUDE_DIR})
+SET(LIBS ${LIBS} ${CYCLUS_CORE_LIBRARIES})
+
+# Include macros
+INCLUDE(UseCyclus)
+
+MESSAGE("--LD_LIBRARY_PATH: $ENV{LD_LIBRARY_PATH}")
+
+# Include the boost header files, system, and filesystem libraries
+SET(Boost_USE_STATIC_LIBS       OFF)
+SET(Boost_USE_STATIC_RUNTIME    OFF)
+FIND_PACKAGE(Boost COMPONENTS filesystem system REQUIRED)
+SET(STUB_INCLUDE_DIRS ${STUB_INCLUDE_DIRS} ${Boost_INCLUDE_DIR})
+SET(LIBS ${LIBS} ${Boost_FILESYSTEM_LIBRARY})
+SET(LIBS ${LIBS} ${Boost_SYSTEM_LIBRARY})
+
+# Find HDF5
+FIND_PACKAGE(HDF5 REQUIRED)
+ADD_DEFINITIONS(${HDF5_DEFINITIONS})
+SET(STUB_INCLUDE_DIRS ${STUB_INCLUDE_DIRS} ${HDF5_INCLUDE_DIR})
+set(LIBS ${LIBS} ${HDF5_LIBRARIES})
+MESSAGE("--    HDF5 Root: ${HDF5_ROOT}")
+MESSAGE("--    HDF5 Include directory: ${HDF5_INCLUDE_DIR}")
+MESSAGE("--    HDF5 Library directories: ${HDF5_LIBRARY_DIRS}")
+MESSAGE("--    HDF5 Libraries: ${HDF5_LIBRARIES}")
+
+# find Coin
+FIND_PACKAGE(COIN REQUIRED)
+SET(STUB_INCLUDE_DIRS ${STUB_INCLUDE_DIRS} ${COIN_INCLUDE_DIR})
+set(LIBS ${LIBS} ${COIN_LIBRARIES})
+
+
+# include all the directories we just found
+INCLUDE_DIRECTORIES(${STUB_INCLUDE_DIRS})
+
+
+# add the agents
+ADD_SUBDIRECTORY(src)
+
+# uninstall target
+configure_file(
+    "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
+    "${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
+    IMMEDIATE @ONLY)
+
+add_custom_target(uninstall
+    COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake)

README.rst

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+.. code-block:: bash
+
+    ....................................................................................................
+    ....................................................................................................
+    ...........................-@-............%@........................................................
+    ..........................@.@@@-+%.#+=*#%%%%@@@@*...................................................
+    ...........................@@@..-*==%...............................................................
+    ..................................=*................................................................
+    .................................@=#.........................#%.....................................
+    ................................%=*@@@%#=..................#@@%.....................................
+    ................................*=%=======.+%.......@%%%%%@%%@@.....................................
+    ...............................@=%===========:%..........%@%@@......................................
+    ..............................@@++@============-#.........%%........................................
+    .......................-%@@%#@@@%-..+@@:[email protected]%@@@%@@@@+......................
+    .........................@@@%%@=+@+..+=%................:=%%....*@@@%*********#@....................
+    ......................:@%@@@%%--%*:@..%=%...............*@.-*#.@@@#*************#@..................
+    ....................@@@@+..:@#=@%***@+.%=%.............#=...@%%@@****@@@@@@@@@%**=@.................
+    ...................@%*..@%##@-%@@@***@..@=%............+@..%%@@@***%%@..:%%:..@@#*%%................
+    ..................@%..@====@=#%..@@**=@..%=================@%%%%**@@@.======+@.#@#*@................
+    .................@%%.%===@@@%@*%-@@#*+@...%===============@@@@@#**@@.:===%*==*#.@@@@................
+    .............-...@%*.@===@@@#-=%.@@@#%=...........%%%%%@@@@@@@@#@@@%..===@===*%.@@....+.............
+    ..............=..%%@.#+=======%:.@@..=.......................@@@@@%@#.:======%.:@@...#..............
+    ..........-:#....:%@@..@*===%@..@%-...........................@@@@@@%-%:.:=.::=@@[email protected]..#..........
+    .............-+@:%*%@@@......:@@@...............................@@@%@@@@....@@%@#%:+@:##............
+    .............%@%%@@%##@@%@@@%@%.....................................#@@@@@@@@@%@#*@%*@@..:..........
+    ...........:@#********************#%%*=:................=##****************************##:..........
+    .......#************************************************************************************-.......
+    ..*----------------------------------------------------------------------------------------------*..
+    ..|| @@@@@@@@@@+ @@@@@@@@@@.  @@@   @@@@@@@@@  .@@@    :@@@  .@@@@@@@@@  .@@:       .@@@@@@@@@@ ||..
+    ..||    .@@+     @@#     @@@  @@@  @@@     @@@   @@@  *@@=  .@@%    .@@@ .@@:       .@@.        ||..
+    ..||    .@@+     @@#    -@@@  @@@ %@@             @@@%@@.   @@@          .@@:       .@@+======. ||..
+    ..||    .@@+     @@@@@@@@@    @@@ @@@              #@@@.    @@@          .@@:       .@@@@@@@@@. ||..
+    ..||    .@@+     @@#  .@@@    @@@ -@@:     @@.      @@@     @@@      @#  .@@:       .@@.        ||..
+    ..||    .@@+     @@#    @@@.  @@@  @@@@  .@@@*      @@@      @@@:  .@@@. .@@:       .@@.        ||..
+    ..||    .@@+     @@#     @@@+ @@@    @@@@@@@        @@@       :@@@@@@%   .@@@@@@@@@..@@@@@@@@@@ ||..
+    ..*----------------------------------------------------------------------------------------------*..
+    ....................................................................................................
+
+
+Tricycle is a collection of CYCLUS archetypes designed to model the fusion fuel cycle. It is
+currently under development at the University of Wisconsin-Madison, and in its alpha stage.
+Epect more information to come as development continues!

install.py

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+#! /usr/bin/env python
+import os
+import sys
+import subprocess
+import shutil
+
+try:
+    import argparse as ap
+except ImportError:
+    import pyne._argparse as ap
+
+absexpanduser = lambda x: os.path.abspath(os.path.expanduser(x))
+
+
+def check_windows_cmake(cmake_cmd):
+    if os.name == 'nt':
+        files_on_path = set()
+        for p in os.environ['PATH'].split(';')[::-1]:
+            if os.path.exists(p):
+                files_on_path.update(os.listdir(p))
+        if 'cl.exe' in files_on_path:
+            pass
+        elif 'sh.exe' in files_on_path:
+            cmake_cmd += ['-G "MSYS Makefiles"']
+        elif 'gcc.exe' in files_on_path:
+            cmake_cmd += ['-G "MinGW Makefiles"']
+        cmake_cmd = ' '.join(cmake_cmd)
+
+
+def install(args):
+    if not os.path.exists(args.build_dir):
+        os.mkdir(args.build_dir)
+    elif args.clean_build:
+        shutil.rmtree(args.build_dir)
+        os.mkdir(args.build_dir)
+
+    root_dir = os.path.split(__file__)[0]
+    makefile = os.path.join(args.build_dir, 'Makefile')
+
+    if not os.path.exists(makefile):
+        rtn = subprocess.call(['which', 'cmake'], shell=(os.name == 'nt'))
+        if rtn != 0:
+            sys.exit("CMake could not be found, "
+                     "please install CMake before developing Cyclus.")
+        cmake_cmd = ['cmake', os.path.abspath(root_dir)]
+        if args.prefix:
+            cmake_cmd += ['-DCMAKE_INSTALL_PREFIX=' +
+                          absexpanduser(args.prefix)]
+        if args.cmake_prefix_path:
+            cmake_cmd += ['-DCMAKE_PREFIX_PATH=' +
+                          absexpanduser(args.cmake_prefix_path)]
+        if args.coin_root:
+            cmake_cmd += ['-DCOIN_ROOT_DIR=' + absexpanduser(args.coin_root)]
+        if args.cyclus_root:
+            cmake_cmd += ['-DCYCLUS_ROOT_DIR='+absexpanduser(args.cyclus_root)]
+        if args.boost_root:
+            cmake_cmd += ['-DBOOST_ROOT=' + absexpanduser(args.boost_root)]
+        if args.build_type:
+            cmake_cmd += ['-DCMAKE_BUILD_TYPE=' + args.build_type]
+        check_windows_cmake(cmake_cmd)
+        rtn = subprocess.check_call(cmake_cmd, cwd=args.build_dir,
+                                    shell=(os.name == 'nt'))
+
+    make_cmd = ['make']
+    if args.threads:
+        make_cmd += ['-j' + str(args.threads)]
+    rtn = subprocess.check_call(make_cmd, cwd=args.build_dir,
+                                shell=(os.name == 'nt'))
+
+    if args.test:
+        make_cmd += ['test']
+    elif not args.build_only:
+        make_cmd += ['install']
+
+    rtn = subprocess.check_call(make_cmd, cwd=args.build_dir,
+                                shell=(os.name == 'nt'))
+
+def uninstall(args):
+    makefile = os.path.join(args.build_dir, 'Makefile')
+    if not os.path.exists(args.build_dir) or not os.path.exists(makefile):
+        sys.exist("May not uninstall Cyclus since it has not yet been built.")
+    rtn = subprocess.check_call(['make', 'uninstall'], cwd=args.build_dir,
+                                shell=(os.name == 'nt'))
+
+
+def main():
+    localdir = absexpanduser('~/.local')
+
+    description = "An installation helper script. " +\
+        "For more information, please see fuelcycle.org."
+    parser = ap.ArgumentParser(description=description)
+
+    build_dir = 'where to place the build directory'
+    parser.add_argument('--build_dir', help=build_dir, default='build')
+
+    uninst = 'uninstall'
+    parser.add_argument('--uninstall', action='store_true', help=uninst, default=False)
+
+    clean = 'attempt to remove the build directory before building'
+    parser.add_argument('--clean-build', action='store_true', help=clean)
+
+    threads = "the number of threads to use in the make step"
+    parser.add_argument('-j', '--threads', type=int, help=threads)
+
+    prefix = "the relative path to the installation directory"
+    parser.add_argument('--prefix', help=prefix, default=localdir)
+
+    build_only = 'only build the package, do not install'
+    parser.add_argument('--build-only', action='store_true', help=build_only)
+
+    test = 'run tests after building'
+    parser.add_argument('--test', action='store_true', help=test)
+
+    coin = "the relative path to the Coin-OR libraries directory"
+    parser.add_argument('--coin_root', help=coin)
+
+    cyclus = "the relative path to Cyclus installation directory"
+    parser.add_argument('--cyclus_root',help=cyclus, default=localdir)
+
+    boost = "the relative path to the Boost libraries directory"
+    parser.add_argument('--boost_root', help=boost)
+
+    cmake_prefix_path = "the cmake prefix path for use with FIND_PACKAGE, " + \
+        "FIND_PATH, FIND_PROGRAM, or FIND_LIBRARY macros"
+    parser.add_argument('--cmake_prefix_path', help=cmake_prefix_path)
+
+    build_type = "the CMAKE_BUILD_TYPE"
+    parser.add_argument('--build_type', help=build_type)
+
+    args = parser.parse_args()
+    if args.uninstall:
+        uninstall(args)
+    else:
+        install(args)
+
+if __name__ == "__main__":
+    main()

src/CMakeLists.txt

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+### DO NOT DELETE THIS COMMENT: INSERT_ARCHETYPES_HERE ###
+USE_CYCLUS("tricycle" "reactor")
+
+INSTALL_CYCLUS_MODULE("tricycle" "")
+
+# install header files
+FILE(GLOB h_files "${CMAKE_CURRENT_SOURCE_DIR}/*.h")