Merge pull request #155 from GOMC-WSU/development

Release v2.50

.github/ISSUE_TEMPLATE/bug_report.md

@@ -22,7 +22,7 @@ Please include all the files you used to run the simulation.
 **Please complete the following information:**
  - OS: [e.g. Ubuntu, Fedora, CentOS, Windows, Cygwin, macOS, ...]
  - Ensemble: [e.g. NPT, NVT, GEMC, GCMC]
- - Code version [e.g. 2.31]
+ - Code version [e.g. 2.40]
 
 **Additional context**
 Add any other context about the problem here.

.gitignore

@@ -33,6 +33,9 @@
 *.app
 
 bin
+bin_MPI
 lib/cub
+.vscode
 .idea
-cmake-build-debug
+cmake-build-debug
+.vscode

CHANGELOG.md

@@ -1,6 +1,27 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.50] - 1/20/2020
++ Addes support for force biased multiparticle move
++ Added support for free energy calculations using TI and FEP methods
++ Support for multiple simulation with different temperatures using MPI
++ Added support for Exponential-6 forcefield
++ Support for restarting simulation using checkpoint 
++ Added support for new GPU architectures 7.0 and 7.5
++ Added an error message when GPU version was used but there was no GPU present (#126)
++ Read PDB file more efficiently when recalculating trajectory (#131)
++ Fixed detecting simulation box shape (orthogonal and non-orthogonal) (#134)
++ Fixed bugs in PDB reader and support for HETATM field in PDB file
++ Fixed bugs in PSF reader
++ Fixed Case sensitive keywords (#100)
++ Fixed the timing report on Windows (#89)
++ Added minimum volume in case the difference in box sizes were large (#94)
++ Fixed the issue where cutoff value is larger than half of minimum box length (#98)
++ Added an error message when charges detected and ewald was set to false (#99)
++ Fixed compiling issue on Visual Studio (#110)
++ Fixed the issue where GOMC did not read CHARMM parameter files missing Urey-Bradley terms (#147)
++ Reduced GOMC reposity size
+
 ## [2.40] - 3/15/2019
 + Added support for Cyclic molecules.
 + Added Inter Molecular Exchange Monte Carlo move in GCMC and GEMC simulation.

CMake/FileLists.cmake

@@ -19,6 +19,7 @@ set(sources
    src/FFParticle.cpp
    src/FFSetup.cpp
    src/Forcefield.cpp
+   src/FreeEnergyOutput.cpp
    src/Geometry.cpp
    src/HistOutput.cpp
    src/InputFileReader.cpp
@@ -31,6 +32,7 @@ set(sources
    src/NoEwald.cpp
    src/OutConst.cpp
    src/OutputVars.cpp
+   src/ParallelTemperingPreprocessor.cpp
    src/PDBSetup.cpp
    src/PDBOutput.cpp
    src/PRNGSetup.cpp
@@ -84,13 +86,15 @@ set(headers
    src/FFBonds.h
    src/FFConst.h
    src/FFDihedrals.h
+   src/FFExp6.h
    src/FFParticle.h
    src/FFSetup.h
    src/FFShift.h
    src/FFSwitch.h
    src/FFSwitchMartini.h
    src/FixedWidthReader.h
    src/Forcefield.h
+   src/FreeEnergyOutput.h
    src/FxdWidthWrtr.h
    src/Geometry.h
    src/HistOutput.h
@@ -108,6 +112,7 @@ set(headers
    src/OutConst.h
    src/OutputAbstracts.h
    src/OutputVars.h
+   src/ParallelTemperingPreprocessor.h
    src/PDBConst.h
    src/PDBOutput.h
    src/PDBSetup.h
@@ -145,6 +150,7 @@ set(headers
    src/cbmc/DCRotateOnAtom.h
    src/cbmc/DCSingle.h
    src/cbmc/TrialMol.h
+   src/moves/CFCMC.h
    src/moves/CrankShaft.h
    src/moves/IntraMoleculeExchange1.h
    src/moves/IntraMoleculeExchange2.h
@@ -155,6 +161,7 @@ set(headers
    src/moves/MoleculeExchange3.h
    src/moves/MoleculeTransfer.h
    src/moves/MoveBase.h
+   src/moves/MultiParticle.h
    src/moves/Regrowth.h
    src/moves/Rotation.h
    src/moves/Translate.h
@@ -164,6 +171,7 @@ set(libHeaders
    lib/BasicTypes.h
    lib/BitLib.h
    lib/GeomLib.h
+   lib/Lambda.h
    lib/NumLib.h
    lib/StrLib.h
    lib/StrStrmLib.h

CMake/GOMCCPUSetup.cmake

@@ -7,6 +7,9 @@ if(ENSEMBLE_NVT)
       #needed for hostname
       target_link_libraries(NVT ws2_32)
    endif()
+   if(MPI_FOUND)
+      target_link_libraries(NVT ${MPI_LIBRARIES})
+   endif()
 endif()
 
 if(ENSEMBLE_GEMC)
@@ -18,6 +21,9 @@ if(ENSEMBLE_GEMC)
       #needed for hostname
       target_link_libraries(GEMC ws2_32)
    endif()
+   if(MPI_FOUND)
+      target_link_libraries(GEMC ${MPI_LIBRARIES})
+   endif()
 endif()
 
 if(ENSEMBLE_GCMC)
@@ -29,6 +35,9 @@ if(ENSEMBLE_GCMC)
       #needed for hostname
       target_link_libraries(GCMC ws2_32)
    endif()
+   if(MPI_FOUND)
+      target_link_libraries(GCMC ${MPI_LIBRARIES})
+   endif()
 endif()
 
 if(ENSEMBLE_NPT)
@@ -40,5 +49,8 @@ if(ENSEMBLE_NPT)
       #needed for hostname
       target_link_libraries(NPT ws2_32)
    endif()
+   if(MPI_FOUND)
+      target_link_libraries(NPT ${MPI_LIBRARIES})
+   endif()
 endif()
 

CMake/GOMCCUDASetup.cmake

@@ -7,7 +7,13 @@ set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-Xcompiler -D__CORRECT_ISO_CPP11_MATH_H_P
 set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode arch=compute_30,code=sm_30)
 set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode arch=compute_35,code=sm_35)
 set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode arch=compute_50,code=sm_50)
+set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode=arch=compute_70,code=sm_70)
+set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode=arch=compute_70,code=compute_70)
+set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode=arch=compute_75,code=sm_75)
+set(CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS};-gencode=arch=compute_75,code=compute_75)
 include_directories(src/GPU)
+#set(CUDA_VERBOSE_BUILD ON)
+set(CUDA_SEPARABLE_COMPILATION ON)
 
 set(GPU_NPT_flags "-DENSEMBLE=4 -DGOMC_CUDA")
 set(GPU_NPT_name "GOMC_GPU_NPT")
@@ -29,6 +35,9 @@ if(ENSEMBLE_GPU_NVT)
         #needed for hostname
         target_link_libraries(GPU_NVT ws2_32)
     endif()
+    if(MPI_FOUND)
+	target_link_libraries(GPU_NVT ${MPI_LIBRARIES})
+    endif()
 endif()
 
 if(ENSEMBLE_GPU_GEMC)
@@ -41,6 +50,9 @@ if(ENSEMBLE_GPU_GEMC)
         #needed for hostname
         target_link_libraries(GPU_GEMC ws2_32)
     endif()
+    if(MPI_FOUND)
+	target_link_libraries(GPU_GEMC ${MPI_LIBRARIES})
+    endif()
 endif()
 
 if(ENSEMBLE_GPU_GCMC)
@@ -53,6 +65,9 @@ if(ENSEMBLE_GPU_GCMC)
         #needed for hostname
         target_link_libraries(GPU_GCMC ws2_32)
     endif()
+    if(MPI_FOUND)
+	target_link_libraries(GPU_GCMC ${MPI_LIBRARIES})
+    endif()
 endif()
 
 if(ENSEMBLE_GPU_NPT)
@@ -65,4 +80,7 @@ if(ENSEMBLE_GPU_NPT)
         #needed for hostname
         target_link_libraries(GPU_NPT ws2_32)
     endif()
+    if(MPI_FOUND)
+	target_link_libraries(GPU_NPT ${MPI_LIBRARIES})
+    endif()
 endif()