Development

.github/workflows/ccpp.yml

@@ -9,5 +9,7 @@ jobs:
 
     steps:
     - uses: actions/checkout@v1
+    - name: Install clang-openmp
+      run: sudo apt install -y libomp-14-dev
     - name: metamake
       run: ./metamake.sh

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: check-yaml
+      - id: check-merge-conflict
+      - id: check-added-large-files

CHANGELOG.md

@@ -1,8 +1,27 @@
 # Change Log
 All notable changes to this project will be documented in this file.
 
+## [2.80] - 12/03/2025
++ Added Molecule Exchange move for two liquid boxes.
++ Add support for CUDA version 13 and earlier.
++ Upgraded to C++17.
++ Build for any CUDA architecture compatible with the corresponding CUDA version.
++ Improve OpenMP calls.
++ Performance improvements, including some GPU calls.
++ Enable non-integer values for MIE potential.
++ Upgrade Random123 to version 1.14 and cereal to version 1.3.2.
++ More error checking of incompatible configuration parameters.
++ Improvements to the build process with some new options.
++ Consolidate MPI builds into the metamake.sh script.
++ Many bug fixes, including some small memory leaks and other memory management issues.
++ Upgraded our CMake to 3.18.
+
+## [2.75] - 11/02/2022
++ Added support for the Non-equilibrium Molecule Transfer move.
++ Numerous bug fixes.
+
 ## [2.70] - 10/13/2020
-+ This release forcues on GPU performance improvements
++ This release focuses on GPU performance improvements
 + Using Random123 to be able to generate the same random number on GPU and port Translation and Rotation of molecules to the GPU
 + Upgraded to C++14
 + Lots of bug fixes
@@ -19,7 +38,7 @@ All notable changes to this project will be documented in this file.
 + Fixed a warning due to ignoring return value of fscanf
 
 ## [2.50] - 1/20/2020
-+ Addes support for force biased multiparticle move
++ Added 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
@@ -37,7 +56,7 @@ All notable changes to this project will be documented in this file.
 + 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
++ Reduced GOMC repository size
 
 ## [2.40] - 3/15/2019
 + Added support for Cyclic molecules.
@@ -56,7 +75,7 @@ All notable changes to this project will be documented in this file.
 
 ## [2.31] - 5/21/2018
 + Compiling problem fixed on CYGWIN
-+ Fix to the error checking of volume exchange if simulation volume became negative
++ Fix to the error checking of volume exchange if simulation volume became negative.
 + Fix the equation to impose fix angle if the angle is less than 90. Generate error if constrained angle is not possible.
 + Fixed a bug where move timings were 0 in windows.
 + Fixed the issue where input files imported from NVT to NPT had zero volume, default value of 500 will be assigned in those cases.
@@ -66,21 +85,21 @@ All notable changes to this project will be documented in this file.
 + Cleaned up the code and removed any memory leaks and bugs.
 + Redesigned Ewald, EwaldCached, and NoEwald to be more efficient and allocate less memory.
 + Added an error when multiple atoms have zero coordinates.
-+ Added an error when resorvoir is empty and should print an error message and exit.
++ Added an error when reservoir is empty and should print an error message and exit.
 + Fixed some typo in output.
 + Fix a bug where seed number output and input was not the same size, so we changed int to uint while reading to avoid overflow. They both use uint now.
 + Increase memory allocation for NPT simulation in Ewald.
 + Fixed a bug in PickWeighted() function where it was return a value larger than the array.
 + Printing individual timing information for each move.
-+ To avoid getting large energy we are recalculating the total system at equilbrium step.
++ To avoid getting large energy we are recalculating the total system at equilibrium step.
 + Print CBMC information including first atom trial, secondary atom trials, angle trials, and dihedral trials.
 + Fix a bug where in windows the clock() function was returning a wrong value
 + Fix compiler warning for macOS in ConfigSetup file
 
 ## [2.20] - 1/2/2018
 + Non orthogonal implementation
 + Removed CUB library from our source code and we will automatically download CUB library before compiling (newest version all the time!).
-+ Removed compute_20 and compute_21 since they are depricated and CUDA 9 will generate fatal error. 
++ Removed compute_20 and compute_21 since they are deprecated and CUDA 9 will generate fatal error. 
 + Fixed a problem where the input reader will skip random_seed because there was a "info" print in an "else if" and would block anything after that.
 + Fixed a bug in MoveSettings where two for loops where not initialized.
 + Fixed a bug where in simulation of polar molecules, if any atom of the molecule has no VDW parameter (e.g. water), there is a chance that during insertion, atom of opposite charge will overlap and generate a very large energy value. Current mechanism of avoiding overlap is not working properly
@@ -92,7 +111,7 @@ All notable changes to this project will be documented in this file.
 
 ## [2.1] - 9/4/2017
 + Adsorption
-+ Fixed the bug where GPU and CPU total energy calculations where slighty different.
++ Fixed the bug where GPU and CPU total energy calculations where slightly different.
 + Removed some unused variables
 + Removed some warnings
 + Fixed pow function ambiguity in some compilers like clang
@@ -114,13 +133,13 @@ All notable changes to this project will be documented in this file.
 + Bug Fixes
 
 ## [1.7] - 04/21/2016
-+ Fix the bug of free Ewald class, which returns memory segmentation fault if ewald is not activated.
++ Fix the bug of free Ewald class, which returns memory segmentation fault if Ewald is not activated.
 TO DO: IntraSwap does not work properly. The bug is going to be fixed.
 
 
 ##[1.6] - 04/01/2016
 + IntraSwap is added into the code.
-+ Blockoutput, fluctoutput are modified to print out ewald energies.
++ Blockoutput, fluctoutput are modified to print out Ewald energies.
 + Tests of this modification are not done yet.
 
 ## [1.7] - 03/24/2016
@@ -150,12 +169,12 @@ TO DO: IntraSwap does not work properly. The bug is going to be fixed.
 + Update CPUSide.cpp, move hist into the ifdef of GCMC. Target at the floating operation issue returned by NVT and GEMC simulations.
 
 ##[1.00] Ewald branch - 12/8/2015
-+ Improve the initialization of Ewald's parameters, so that non-ewald simulation can also run on ewald code without crashing.
++ Improve the initialization of Ewald's parameters, so that non-Ewald simulation can also run on Ewald code without crashing.
 + CMakeList.txt file is added.
 
 ##[1.00] - 12/4/2015
-+ Added Examples of water and DME for NVT and GCMC
-+ Added bin/linux, which contains all executable files for linux
++ Added Examples of water and DME for NVT and GCMC.
++ Added bin/linux, which contains all executable files for linux.
 
 ## [1.0] - 10/18/2015
 + Changes for input file system.

CMake/FileLists.cmake

@@ -3,22 +3,22 @@ set(sources
    src/BondAdjacencyList.cpp
    src/BoxDimensions.cpp
    src/BoxDimensionsNonOrth.cpp
+   src/CalculateEnergy.cpp
    src/CBMC.cpp
    src/CellList.cpp
+   src/Checkpoint.cpp
+   src/CheckpointOutput.cpp
+   src/CheckpointSetup.cpp
    src/ConfigSetup.cpp
    src/ConsoleOutput.cpp
    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/ExtendedSystem.cpp
+   src/ExtendedSystemOutput.cpp
    src/FFConst.cpp
    src/FFDihedrals.cpp
    src/FFParticle.cpp
@@ -39,8 +39,8 @@ set(sources
    src/OutputVars.cpp
    src/ParallelTemperingPreprocessor.cpp
    src/ParallelTemperingUtilities.cpp
-   src/PDBSetup.cpp
    src/PDBOutput.cpp
+   src/PDBSetup.cpp
    src/PRNGSetup.cpp
    src/PSFOutput.cpp
    src/Random123Wrapper.cpp
@@ -51,16 +51,16 @@ set(sources
    src/cbmc/DCCrankShaftAng.cpp
    src/cbmc/DCCrankShaftDih.cpp
    src/cbmc/DCCyclic.cpp
-   src/cbmc/DCGraph.cpp
    src/cbmc/DCFreeCycle.cpp
+   src/cbmc/DCFreeCycleSeed.cpp
    src/cbmc/DCFreeHedron.cpp
    src/cbmc/DCFreeHedronSeed.cpp
-   src/cbmc/DCFreeCycleSeed.cpp
-   src/cbmc/DCLinkedHedron.cpp
-   src/cbmc/DCLinkedCycle.cpp
+   src/cbmc/DCGraph.cpp
    src/cbmc/DCHedron.cpp
    src/cbmc/DCHedronCycle.cpp
    src/cbmc/DCLinear.cpp
+   src/cbmc/DCLinkedCycle.cpp
+   src/cbmc/DCLinkedHedron.cpp
    src/cbmc/DCOnSphere.cpp
    src/cbmc/DCRotateCOM.cpp
    src/cbmc/DCRotateOnAtom.cpp
@@ -90,10 +90,10 @@ set(headers
    src/EnergyTypes.h
    src/EnPartCntSampleOutput.h
    src/EnsemblePreprocessor.h
-   src/ExtendedSystem.h
-   src/ExtendedSystemOutput.h
    src/Ewald.h
    src/EwaldCached.h  
+   src/ExtendedSystem.h
+   src/ExtendedSystemOutput.h
    src/FFAngles.h
    src/FFBonds.h
    src/FFConst.h
@@ -104,6 +104,7 @@ set(headers
    src/FFShift.h
    src/FFSwitch.h
    src/FFSwitchMartini.h
+   src/FFTabulated.h
    src/FixedWidthReader.h
    src/Forcefield.h
    src/FreeEnergyOutput.h
@@ -153,21 +154,20 @@ set(headers
    src/cbmc/DCCyclic.h
    src/cbmc/DCData.h
    src/cbmc/DCFreeCycle.h
+   src/cbmc/DCFreeCycleSeed.h
    src/cbmc/DCFreeHedron.h
    src/cbmc/DCFreeHedronSeed.h
-   src/cbmc/DCFreeCycleSeed.h
-   src/cbmc/DCLinkedHedron.h
-   src/cbmc/DCLinkedCycle.h
    src/cbmc/DCGraph.h
    src/cbmc/DCHedron.h
    src/cbmc/DCHedronCycle.h
    src/cbmc/DCLinear.h
+   src/cbmc/DCLinkedCycle.h
+   src/cbmc/DCLinkedHedron.h
    src/cbmc/DCOnSphere.h
    src/cbmc/DCRotateCOM.h
    src/cbmc/DCRotateOnAtom.h
    src/cbmc/DCSingle.h
    src/cbmc/TrialMol.h
-   src/moves/NeMTMC.h
    src/moves/CrankShaft.h
    src/moves/IntraMoleculeExchange1.h
    src/moves/IntraMoleculeExchange2.h
@@ -176,11 +176,14 @@ set(headers
    src/moves/IntraTargetedSwap.h
    src/moves/MoleculeExchange1.h
    src/moves/MoleculeExchange2.h
+   src/moves/MoleculeExchange2Liq.h
    src/moves/MoleculeExchange3.h
+   src/moves/MoleculeExchange3Liq.h
    src/moves/MoleculeTransfer.h
    src/moves/MoveBase.h
    src/moves/MultiParticle.h
    src/moves/MultiParticleBrownianMotion.h
+   src/moves/NeMTMC.h
    src/moves/Regrowth.h
    src/moves/Rotation.h
    src/moves/TargetedSwap.h
@@ -191,35 +194,34 @@ set(libHeaders
    lib/AlphaNum.h
    lib/BasicTypes.h
    lib/BitLib.h
-   lib/Endian.h
+   lib/CircuitFinder.h
+   lib/FloydWarshallCycle.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)
+   lib/VectorLib.h)
 
 set(libSources
     lib/AlphaNum.cpp
     lib/CircuitFinder.cpp
     lib/FloydWarshallCycle.cpp)
 
 set(cudaHeaders
-    src/GPU/ConstantDefinitionsCUDAKernel.cuh
-    src/GPU/CalculateMinImageCUDAKernel.cuh
     src/GPU/CalculateEnergyCUDAKernel.cuh
-    src/GPU/CalculateForceCUDAKernel.cuh
     src/GPU/CalculateEwaldCUDAKernel.cuh
+    src/GPU/CalculateForceCUDAKernel.cuh
+    src/GPU/CalculateMinImageCUDAKernel.cuh
+    src/GPU/ConstantDefinitionsCUDAKernel.cuh
     src/GPU/CUDAMemoryManager.cuh
     src/GPU/TransformParticlesCUDAKernel.cuh
     src/GPU/VariablesCUDA.cuh)
 
 set(cudaSources
     src/GPU/CalculateEnergyCUDAKernel.cu
-    src/GPU/CalculateForceCUDAKernel.cu
     src/GPU/CalculateEwaldCUDAKernel.cu
+    src/GPU/CalculateForceCUDAKernel.cu
     src/GPU/ConstantDefinitionsCUDAKernel.cu
     src/GPU/CUDAMemoryManager.cu
     src/GPU/TransformParticlesCUDAKernel.cu)

CMake/GOMCCPUSetup.cmake

@@ -1,26 +1,31 @@
 #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")
 
-#Grand Canonical Monte Carlo
-set(GC_flags "-DENSEMBLE=3")
-set(GC_name "GOMC_CPU_GCMC")
+#NVT (Canonical) Ensemble
+set(NVT_flags "-DENSEMBLE=1")
+set(NVT_name "GOMC_CPU_NVT")
 
 #Gibbs Ensemble Monte Carlo
 set(GE_flags "-DENSEMBLE=2")
 set(GE_name "GOMC_CPU_GEMC")
 
-#NVT (Canonical) Ensemble
-set(NVT_flags "-DENSEMBLE=1")
-set(NVT_name "GOMC_CPU_NVT")
+#Grand Canonical Monte Carlo
+set(GC_flags "-DENSEMBLE=3")
+set(GC_name "GOMC_CPU_GCMC")
 
-set(CMAKE_CXX_STANDARD 14)
+#NPT (Isothermal-Isobaric) Ensemble
+set(NPT_flags "-DENSEMBLE=4")
+set(NPT_name "GOMC_CPU_NPT")
+
+set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED true)
 
 if(ENSEMBLE_NVT)
    add_executable(NVT ${sources} ${headers} ${libHeaders} ${libSources})
+   # Set compiler and linker flags for each compiler
+    target_compile_options(NVT
+       PUBLIC $<$<COMPILE_LANGUAGE:CXX>:${CMAKE_COMP_FLAGS}>)
+    target_link_options(NVT
+       PUBLIC $<$<LINK_LANGUAGE:CXX>:${CMAKE_LINK_FLAGS}>)
    set_target_properties(NVT PROPERTIES 
       OUTPUT_NAME ${NVT_name}
       COMPILE_FLAGS "${NVT_flags}")
@@ -35,6 +40,11 @@ endif()
 
 if(ENSEMBLE_GEMC)
    add_executable(GEMC ${sources} ${headers} ${libHeaders} ${libSources})
+   # Set compiler and linker flags for each compiler
+    target_compile_options(GEMC
+       PUBLIC $<$<COMPILE_LANGUAGE:CXX>:${CMAKE_COMP_FLAGS}>)
+    target_link_options(GEMC
+       PUBLIC $<$<LINK_LANGUAGE:CXX>:${CMAKE_LINK_FLAGS}>)
    set_target_properties(GEMC PROPERTIES 
       OUTPUT_NAME ${GE_name}
       COMPILE_FLAGS "${GE_flags}")
@@ -49,6 +59,11 @@ endif()
 
 if(ENSEMBLE_GCMC)
    add_executable(GCMC ${sources} ${headers} ${libHeaders} ${libSources})
+   # Set compiler and linker flags for each compiler
+    target_compile_options(GCMC
+       PUBLIC $<$<COMPILE_LANGUAGE:CXX>:${CMAKE_COMP_FLAGS}>)
+    target_link_options(GCMC
+       PUBLIC $<$<LINK_LANGUAGE:CXX>:${CMAKE_LINK_FLAGS}>)
    set_target_properties(GCMC PROPERTIES 
       OUTPUT_NAME ${GC_name}
       COMPILE_FLAGS "${GC_flags}")
@@ -63,6 +78,11 @@ endif()
 
 if(ENSEMBLE_NPT)
    add_executable(NPT ${sources} ${headers} ${libHeaders} ${libSources})
+   # Set compiler and linker flags for each compiler
+    target_compile_options(NPT
+       PUBLIC $<$<COMPILE_LANGUAGE:CXX>:${CMAKE_COMP_FLAGS}>)
+    target_link_options(NPT
+       PUBLIC $<$<LINK_LANGUAGE:CXX>:${CMAKE_LINK_FLAGS}>)
    set_target_properties(NPT PROPERTIES 
       OUTPUT_NAME ${NPT_name}
       COMPILE_FLAGS "${NPT_flags}")
@@ -74,4 +94,3 @@ if(ENSEMBLE_NPT)
       target_link_libraries(NPT ${MPI_LIBRARIES})
    endif()
 endif()
-