Merge pull request #431 from GOMC-WSU/development

GOMC Release 2.75

CMake/FileLists.cmake

@@ -1,5 +1,6 @@
 set(sources 
    src/BlockOutput.cpp
+   src/BondAdjacencyList.cpp
    src/BoxDimensions.cpp
    src/BoxDimensionsNonOrth.cpp
    src/CBMC.cpp
@@ -9,9 +10,13 @@ set(sources
    src/Coordinates.cpp
    src/CPUSide.cpp
    src/CalculateEnergy.cpp
+   src/Checkpoint.cpp
    src/CheckpointOutput.cpp
    src/CheckpointSetup.cpp
+   src/DCDlib.cpp
    src/EnPartCntSampleOutput.cpp
+   src/ExtendedSystem.cpp
+   src/ExtendedSystemOutput.cpp
    src/Ewald.cpp
    src/EwaldCached.cpp
    src/FFConst.cpp
@@ -38,6 +43,7 @@ set(sources
    src/PDBOutput.cpp
    src/PRNGSetup.cpp
    src/PSFOutput.cpp
+   src/Random123Wrapper.cpp
    src/Reader.cpp
    src/Simulation.cpp
    src/StaticVals.cpp
@@ -63,11 +69,13 @@ set(sources
 
 set(headers
    src/BlockOutput.h
+   src/BondAdjacencyList.h
    src/BoxDimensions.h
    src/BoxDimensionsNonOrth.h
    src/CalculateEnergy.h
    src/CBMC.h
    src/CellList.h
+   src/Checkpoint.h
    src/CheckpointOutput.h
    src/CheckpointSetup.h
    src/Clock.h
@@ -78,9 +86,12 @@ set(headers
    src/Coordinates.h
    src/CoordinateSetup.h
    src/CPUSide.h
+   src/DCDlib.h
    src/EnergyTypes.h
    src/EnPartCntSampleOutput.h
    src/EnsemblePreprocessor.h
+   src/ExtendedSystem.h
+   src/ExtendedSystemOutput.h
    src/Ewald.h
    src/EwaldCached.h  
    src/FFAngles.h
@@ -98,6 +109,8 @@ set(headers
    src/FreeEnergyOutput.h
    src/FxdWidthWrtr.h
    src/Geometry.h
+   src/GOMCEventsProfile.h
+   src/GOMCEventsProfileDef.h
    src/HistOutput.h
    src/InputAbstracts.h
    src/InputFileReader.h
@@ -121,6 +134,7 @@ set(headers
    src/PRNG.h
    src/PRNGSetup.h
    src/PSFOutput.h
+   src/Random123Wrapper.h
    src/Reader.h
    src/SeedReader.h
    src/Setup.h
@@ -130,6 +144,7 @@ set(headers
    src/SubdividedArray.h
    src/System.h
    src/TransformMatrix.h
+   src/Velocity.h
    src/Writer.h
    src/XYZArray.h
    src/cbmc/DCComponent.h
@@ -152,35 +167,43 @@ set(headers
    src/cbmc/DCRotateOnAtom.h
    src/cbmc/DCSingle.h
    src/cbmc/TrialMol.h
-   src/moves/CFCMC.h
+   src/moves/NeMTMC.h
    src/moves/CrankShaft.h
    src/moves/IntraMoleculeExchange1.h
    src/moves/IntraMoleculeExchange2.h
    src/moves/IntraMoleculeExchange3.h
    src/moves/IntraSwap.h
+   src/moves/IntraTargetedSwap.h
    src/moves/MoleculeExchange1.h
    src/moves/MoleculeExchange2.h
    src/moves/MoleculeExchange3.h
    src/moves/MoleculeTransfer.h
    src/moves/MoveBase.h
    src/moves/MultiParticle.h
+   src/moves/MultiParticleBrownianMotion.h
    src/moves/Regrowth.h
    src/moves/Rotation.h
+   src/moves/TargetedSwap.h
    src/moves/Translate.h
    src/moves/VolumeTransfer.h)
 
 set(libHeaders
+   lib/AlphaNum.h
    lib/BasicTypes.h
    lib/BitLib.h
+   lib/Endian.h
    lib/GeomLib.h
    lib/Lambda.h
    lib/NumLib.h
    lib/StrLib.h
    lib/StrStrmLib.h
    lib/VectorLib.h
+   lib/CircuitFinder.h
    lib/FloydWarshallCycle.h)
 
 set(libSources
+    lib/AlphaNum.cpp
+    lib/CircuitFinder.cpp
     lib/FloydWarshallCycle.cpp)
 
 set(cudaHeaders

CMake/GOMCCPUSetup.cmake

@@ -1,5 +1,6 @@
 #EnsemblePreprocessor defines NVT = 1, GEMC = 2, GCMC = 3, NPT = 4
 #NPT (Isothermal-Isobaric) Ensemble
+
 set(NPT_flags "-DENSEMBLE=4")
 set(NPT_name "GOMC_CPU_NPT")
 

CMake/GOMCCUDASetup.cmake

@@ -5,22 +5,35 @@ if (CMAKE_BUILD_TYPE STREQUAL "Debug")
 	set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS} -g -G --keep")
 endif()
 
+
+set(GEN_COMP_flag "-DGOMC_CUDA -DTHRUST_IGNORE_DEPRECATED_CPP_DIALECT ")
+
+if (GOMC_NVTX_ENABLED)
+	message("-- Enabling profiling with NVTX for GPU")
+	set(GEN_COMP_flag "${GEN_COMP_flag} -DGOMC_NVTX_ENABLED")
+endif()
+
+
 include_directories(src/GPU)
 
-set(GPU_NPT_flags "-DENSEMBLE=4 -DGOMC_CUDA -DTHRUST_IGNORE_DEPRECATED_CPP_DIALECT")
+set(GPU_NPT_flags "-DENSEMBLE=4 ${GEN_COMP_flag}")
 set(GPU_NPT_name "GOMC_GPU_NPT")
-set(GPU_GC_flags "-DENSEMBLE=3 -DGOMC_CUDA -DTHRUST_IGNORE_DEPRECATED_CPP_DIALECT")
+set(GPU_GC_flags "-DENSEMBLE=3 ${GEN_COMP_flag}")
 set(GPU_GC_name "GOMC_GPU_GCMC")
-set(GPU_GE_flags "-DENSEMBLE=2 -DGOMC_CUDA -DTHRUST_IGNORE_DEPRECATED_CPP_DIALECT")
+set(GPU_GE_flags "-DENSEMBLE=2 ${GEN_COMP_flag}")
 set(GPU_GE_name "GOMC_GPU_GEMC")
-set(GPU_NVT_flags "-DENSEMBLE=1 -DGOMC_CUDA -DTHRUST_IGNORE_DEPRECATED_CPP_DIALECT")
+set(GPU_NVT_flags "-DENSEMBLE=1 ${GEN_COMP_flag}")
 set(GPU_NVT_name "GOMC_GPU_NVT")
 
 set(CMAKE_CUDA_STANDARD 14)
 set(CMAKE_CUDA_STANDARD_REQUIRED true)
 set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED true)
 
+# Set host compiler
+set(CCBIN "-ccbin=${CMAKE_CXX_COMPILER}")
+set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} ${CCBIN} -Wno-deprecated-gpu-targets" )
+
 include_directories(${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
 
 #####################################
@@ -30,6 +43,7 @@ if(ENSEMBLE_GPU_NVT)
     set_target_properties(GPU_NVT PROPERTIES
         CUDA_SEPARABLE_COMPILATION ON
         OUTPUT_NAME ${GPU_NVT_name}
+        CUDA_ARCHITECTURES "35;60;70;80"
         COMPILE_FLAGS "${GPU_NVT_flags}")
 	if (CMAKE_BUILD_TYPE STREQUAL "Debug")
 		message("-- Debug build type detected, GPU_NVT setting CUDA_RESOLVE_DEVICE_SYMBOLS ON")
@@ -49,6 +63,7 @@ if(ENSEMBLE_GPU_GEMC)
     set_target_properties(GPU_GEMC PROPERTIES
         CUDA_SEPARABLE_COMPILATION ON
         OUTPUT_NAME ${GPU_GE_name}
+        CUDA_ARCHITECTURES "35;60;70;80"
         COMPILE_FLAGS "${GPU_GE_flags}")
 	if (CMAKE_BUILD_TYPE STREQUAL "Debug")
 		message("-- Debug build type detected, GPU_GEMC setting CUDA_RESOLVE_DEVICE_SYMBOLS ON")
@@ -68,6 +83,7 @@ if(ENSEMBLE_GPU_GCMC)
     set_target_properties(GPU_GCMC PROPERTIES
         CUDA_SEPARABLE_COMPILATION ON
         OUTPUT_NAME ${GPU_GC_name}
+        CUDA_ARCHITECTURES "35;60;70;80"
         COMPILE_FLAGS "${GPU_GC_flags}")
 	if (CMAKE_BUILD_TYPE STREQUAL "Debug")
 		message("-- Debug build type detected, GPU_GCMC setting CUDA_RESOLVE_DEVICE_SYMBOLS ON")
@@ -87,6 +103,7 @@ if(ENSEMBLE_GPU_NPT)
     set_target_properties(GPU_NPT PROPERTIES
         CUDA_SEPARABLE_COMPILATION ON
         OUTPUT_NAME ${GPU_NPT_name}
+        CUDA_ARCHITECTURES "35;60;70;80"
         COMPILE_FLAGS "${GPU_NPT_flags}")
 	if (CMAKE_BUILD_TYPE STREQUAL "Debug")
 		message("-- Debug build type detected, GPU_NPT setting CUDA_RESOLVE_DEVICE_SYMBOLS ON")

CMakeLists.txt

@@ -32,11 +32,6 @@ set(ENSEMBLE_GPU_NPT ON CACHE BOOL "Build GPU NPT version")
 
 include(${PROJECT_SOURCE_DIR}/CMake/GOMCMPI.cmake)
 
-#enable config header
-configure_file(
-	"${PROJECT_SOURCE_DIR}/GOMC_Config.h.in"
-	"${PROJECT_BINARY_DIR}/GOMC_Config.h"
-	)
 include_directories("${PROJECT_BINARY_DIR}")
 
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
@@ -58,6 +53,25 @@ endif()
 
 # Set Source and Header files
 include(${PROJECT_SOURCE_DIR}/CMake/FileLists.cmake)
+include_directories(lib/cereal-1.3.0/include)
+
+
+#Optional CMake Argument
+option(GOMC_GTEST    "Build unit tests for GOMC" OFF)
+option(GOMC_GTEST_MPI    "Build unit tests for GOMC - MPI Enabled" OFF)
+
+#enable config header
+configure_file(
+	"${PROJECT_SOURCE_DIR}/GOMC_Config.h.in"
+	"${PROJECT_BINARY_DIR}/GOMC_Config.h"
+)
+
+# Enable google test
+# for now we will disable testing for intel compiler
+if(GOMC_GTEST OR GOMC_GTEST_MPI)
+  enable_testing()
+  include(test/GoogleTest.cmake)
+endif()
 
 # Find if CUDA exists and what is the version number
 include(CheckLanguage)

CONTRIBUTING.md

@@ -0,0 +1,26 @@
+To contribute to GOMC please follow this procedure:
+
+1)  Fork the GOMC repository
+
+2)  Clone your forked repository
+
+        git clone https://github.com/yourusername/GOMC.git
+
+2)  Checkout the development branch:
+
+        git checkout development
+
+3)  Create a new branch based of the development branch named after your new feature
+
+        git checkout -b nameofyourbranch
+
+4)  Development on this branch checking for consistent results with the development branch by using the GOMC_Examples.py script
+
+5)  When you are ready to add to GOMC, rebase your branch with the development branch.
+
+        git remote add upstream https://github.com/GOMC-WSU/GOMC.git
+        git rebase upstream/development
+
+6)  Retest with the GOMC_Examples.py script
+
+7)  If all the tests passed, open a pull request and select reviewers.

GOMC_Config.h.in

@@ -3,6 +3,13 @@
 #define GOMC_VERSION_MAJOR @GOMC_VERSION_MAJOR@
 #define GOMC_VERSION_MINOR @GOMC_VERSION_MINOR@
 
+
+/* Allow exposure of methods only used in unit testing */
+#cmakedefine01 GOMC_GTEST
+
+/* Allow exposure of methods only used in unit testing - MPI Enabled */
+#cmakedefine01 GOMC_GTEST_MPI
+
 /* Use MPI (with mpicc) for parallelization */
 #cmakedefine01 GOMC_LIB_MPI
 
@@ -14,4 +21,4 @@
 #define GOMC_MPI (GOMC_LIB_MPI || GOMC_THREAD_MPI)
 
 /* MPI_IN_PLACE exists for collective operations */
-#cmakedefine01 MPI_IN_PLACE_EXISTS
+#cmakedefine01 MPI_IN_PLACE_EXISTS