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embecosm · Sep 29, 2022 · ce8b512 · ce8b512
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diff --git a/.clang-format b/.clang-format
@@ -0,0 +1,117 @@
+---
+Language:        Cpp
+# BasedOnStyle:  Google
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+AlignAfterOpenBracket: Align
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+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Left
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
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+AlwaysBreakTemplateDeclarations: true
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+BinPackParameters: true
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+BreakBeforeBraces: Attach
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+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
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+CommentPragmas:  '^ IWYU pragma:'
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+ConstructorInitializerAllOnOneLineOrOnePerLine: true
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+Cpp11BracedListStyle: true
+DerivePointerAlignment: true
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:   
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Preserve
+IncludeCategories: 
+  - Regex:           '^<ext/.*\.h>'
+    Priority:        2
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: true
+IndentPPDirectives: None
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
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+ObjCBlockIndentWidth: 2
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+...
+
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,7 @@
+src/obj/*
+src/all
+src/out_test
+src/out_*
+src/Octave/*
+*.vscode
+build/*
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,10 @@
+[submodule "lib/googletest"]
+	path = lib/googletest
+	url = https://github.com/google/googletest/
+[submodule "lib/eigen"]
+	path = lib/eigen
+	url = https://gitlab.com/libeigen/eigen.git
+	branch = 3.4
+[submodule "lib/cereal"]
+	path = lib/cereal
+	url = https://github.com/USCiLab/cereal.git
diff --git a/AUTHORS b/AUTHORS
@@ -0,0 +1,9 @@
+# This is the list of the Embecosm DCM (dcEmb)'s significant contributors.
+#
+# This does not necessarily list everyone who has contributed code,
+# especially since many employees of one corporation may be contributing.
+# To see the full list of contributors, see the revision history in
+# source control.
+Embecosm Limited
+William Jones
+Elliot Stein
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0 +1,142 @@
+# 
+# Copyright (C) 2022 Embecosm Limited
+# 
+# Contributor William Jones <[email protected]>
+# Contributor Elliot Stein <[email protected]>
+# 
+# SPDX-License-Identifier: GPL-3.0-or-later 
+# 
+
+cmake_minimum_required(VERSION 3.16)
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+project(dcm_demo LANGUAGES CXX)
+
+add_subdirectory(${CMAKE_SOURCE_DIR}/lib/googletest)
+add_subdirectory(${CMAKE_SOURCE_DIR}/lib/eigen)
+enable_testing()
+
+include_directories(  
+    ${CMAKE_SOURCE_DIR}/lib/cereal/include
+    ${CMAKE_SOURCE_DIR}/lib/eigen
+    ${CMAKE_SOURCE_DIR}/include
+    ${CMAKE_SOURCE_DIR}/include/COVID
+    ${CMAKE_SOURCE_DIR}/include/3body
+    ${CMAKE_SOURCE_DIR}/include/music
+    ${CMAKE_SOURCE_DIR}/include/tests
+    ${gtest_SOURCE_DIR}/include
+    ${gtest_SOURCE_DIR}
+)
+
+set(SOURCES_COVID
+    src/dynamic_model.cc
+    src/generative_function.cc
+    src/feature_selection_function.cc
+    src/COVID/run_COVID_dcm.cc
+    src/COVID/DEM_COVID.cc
+    src/COVID/import_COVID.cc
+    src/COVID/dynamic_COVID_model.cc
+    src/COVID/generative_COVID.cc
+    src/COVID/feature_selection_COVID.cc
+    src/utility.cc
+)
+
+set(SOURCES_3BODY
+    src/dynamic_model.cc
+    src/generative_function.cc
+    src/feature_selection_function.cc
+    src/3body/run_3body_dcm.cc
+    src/3body/DEM_3body.cc
+    src/3body/dynamic_3body_model.cc
+    src/3body/generative_3body.cc
+    src/3body/feature_selection_3body.cc
+    src/utility.cc
+)
+
+set(SOURCES_MUSIC
+    src/dynamic_model.cc
+    src/generative_function.cc
+    src/music/run_music_dcm.cc
+    src/music/DEM_music.cc
+    src/music/dynamic_music_model.cc
+    src/music/generative_music.cc
+    src/utility.cc
+)
+
+set(SOURCES_TESTS
+    src/COVID/import_COVID.cc
+    tests/import_COVID_test.cc
+    src/feature_selection_function.cc
+    src/COVID/feature_selection_COVID.cc
+    tests/feature_selection_COVID_test.cc
+    src/generative_function.cc
+    src/COVID/generative_COVID.cc
+    tests/generative_COVID_test.cc
+    src/utility.cc
+    tests/utility_test.cc
+    src/dynamic_model.cc
+    src/generative_function.cc
+    src/feature_selection_function.cc
+    src/3body/dynamic_3body_model.cc
+    src/3body/generative_3body.cc
+    src/3body/feature_selection_3body.cc
+    tests/dynamic_3body_model_test.cc
+
+)
+
+set(SOURCES_SERIALIZATION_TESTS
+    src/dynamic_model.cc
+    src/generative_function.cc
+    src/feature_selection_function.cc
+    src/3body/dynamic_3body_model.cc
+    src/3body/generative_3body.cc
+    src/3body/feature_selection_3body.cc
+    src/COVID/import_COVID.cc
+    src/COVID/dynamic_COVID_model.cc
+    src/COVID/generative_COVID.cc
+    src/COVID/feature_selection_COVID.cc    
+    src/utility.cc
+    tests/serialization_test.cc
+)
+
+set(SOURCES_TESTS_ELLIOT
+    src/COVID/import_COVID.cc
+    src/feature_selection_function.cc
+    src/COVID/feature_selection_COVID.cc
+    src/generative_function.cc
+    src/COVID/generative_COVID.cc
+    tests/generative_COVID_test.cc
+    src/utility.cc
+    src/dynamic_model.cc
+    src/generative_function.cc
+    src/log_likelihood_function.cc
+    src/feature_selection_function.cc
+    src/3body/dynamic_3body_model.cc
+    src/3body/generative_3body.cc
+    src/3body/log_likelihood_3body.cc
+    src/3body/feature_selection_3body.cc
+)
+
+find_package(OpenMP)
+
+SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS}-O3")
+SET(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS}-O3")
+
+add_executable(dcm_covid ${SOURCES_COVID})
+target_link_libraries(dcm_covid PUBLIC OpenMP::OpenMP_CXX)
+set_target_properties(dcm_covid PROPERTIES LDFLAGS "-fopenmp -march=native -O3")
+set_target_properties(dcm_covid PROPERTIES COMPILE_FLAGS "-fopenmp -lpthread -march=native -O3")
+
+add_executable(dcm_3body ${SOURCES_3BODY})
+target_link_libraries(dcm_3body PUBLIC OpenMP::OpenMP_CXX)
+set_target_properties(dcm_3body PROPERTIES COMPILE_FLAGS "-g -fopenmp -lpthread -march=native -O3")
+
+add_executable(run_tests ${SOURCES_TESTS})
+target_link_libraries(run_tests PUBLIC gtest_main PUBLIC OpenMP::OpenMP_CXX)
+set_target_properties(run_tests PROPERTIES COMPILE_FLAGS "-g -fopenmp -lpthread -march=native -O3")
+
+add_executable(run_serialization_tests ${SOURCES_SERIALIZATION_TESTS})
+target_link_libraries(run_serialization_tests PUBLIC gtest_main PUBLIC OpenMP::OpenMP_CXX PUBLIC)
+set_target_properties(run_serialization_tests PROPERTIES COMPILE_FLAGS "-g -fopenmp -lpthread -march=native -O3")
diff --git a/COPYING.BSD3 b/COPYING.BSD3
@@ -0,0 +1,9 @@
+BSD 3-Clause License
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+    Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+    Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+    The names of its contributors may not be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.