Wolf final

CMake/FileLists.cmake

@@ -48,6 +48,9 @@ set(sources
    src/Simulation.cpp
    src/StaticVals.cpp
    src/System.cpp
+   src/Wolf.cpp
+   src/WolfCalibration.cpp
+   src/WolfCalibrationOutput.cpp
    src/cbmc/DCCrankShaftAng.cpp
    src/cbmc/DCCrankShaftDih.cpp
    src/cbmc/DCCyclic.cpp
@@ -114,6 +117,7 @@ set(headers
    src/HistOutput.h
    src/InputAbstracts.h
    src/InputFileReader.h
+   src/MemoryTracker.h
    src/MersenneTwister.h
    src/MoleculeKind.h
    src/MoleculeLookup.h
@@ -146,6 +150,9 @@ set(headers
    src/TransformMatrix.h
    src/Velocity.h
    src/Writer.h
+   src/Wolf.h
+   src/WolfCalibration.h
+   src/WolfCalibrationOutput.h
    src/XYZArray.h
    src/cbmc/DCComponent.h
    src/cbmc/DCCrankShaftAng.h
@@ -173,7 +180,6 @@ set(headers
    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

CMake/GOMCCUDASetup.cmake

@@ -43,6 +43,7 @@ if(ENSEMBLE_GPU_NVT)
     set_target_properties(GPU_NVT PROPERTIES
         CUDA_SEPARABLE_COMPILATION ON
         OUTPUT_NAME ${GPU_NVT_name}
+        CUDA_ARCHITECTURES "35;60;70"
         COMPILE_FLAGS "${GPU_NVT_flags}")
 	if (CMAKE_BUILD_TYPE STREQUAL "Debug")
 		message("-- Debug build type detected, GPU_NVT setting CUDA_RESOLVE_DEVICE_SYMBOLS ON")
@@ -62,6 +63,7 @@ if(ENSEMBLE_GPU_GEMC)
     set_target_properties(GPU_GEMC PROPERTIES
         CUDA_SEPARABLE_COMPILATION ON
         OUTPUT_NAME ${GPU_GE_name}
+        CUDA_ARCHITECTURES "35;60;70"
         COMPILE_FLAGS "${GPU_GE_flags}")
 	if (CMAKE_BUILD_TYPE STREQUAL "Debug")
 		message("-- Debug build type detected, GPU_GEMC setting CUDA_RESOLVE_DEVICE_SYMBOLS ON")
@@ -81,6 +83,7 @@ if(ENSEMBLE_GPU_GCMC)
     set_target_properties(GPU_GCMC PROPERTIES
         CUDA_SEPARABLE_COMPILATION ON
         OUTPUT_NAME ${GPU_GC_name}
+        CUDA_ARCHITECTURES "35;60;70"
         COMPILE_FLAGS "${GPU_GC_flags}")
 	if (CMAKE_BUILD_TYPE STREQUAL "Debug")
 		message("-- Debug build type detected, GPU_GCMC setting CUDA_RESOLVE_DEVICE_SYMBOLS ON")
@@ -100,6 +103,7 @@ if(ENSEMBLE_GPU_NPT)
     set_target_properties(GPU_NPT PROPERTIES
         CUDA_SEPARABLE_COMPILATION ON
         OUTPUT_NAME ${GPU_NPT_name}
+        CUDA_ARCHITECTURES "35;60;70"
         COMPILE_FLAGS "${GPU_NPT_flags}")
 	if (CMAKE_BUILD_TYPE STREQUAL "Debug")
 		message("-- Debug build type detected, GPU_NPT setting CUDA_RESOLVE_DEVICE_SYMBOLS ON")

lib/Endian.h

@@ -37,6 +37,7 @@
  */
 
 #include <stdlib.h>
+#include <stdint.h>
 
 #define bswap_64(x)                            \
   ((((x) & 0xff00000000000000ull) >> 56)       \

metamake.sh

@@ -38,27 +38,28 @@ then
 			echo "==== GOMC needs CUB library to run..."
 			echo "==== Finding latest CUB library..."
 
+
 			# download the download html page
-			wget https://nvlabs.github.io/cub/download_cub.html > /dev/null 2>&1
+			#wget https://nvlabs.github.io/cub/download_cub.html > /dev/null 2>&1
 
 			# find the lines that have the link
-			grep "https://github.com/NVlabs/" download_cub.html > link_lines
+			#grep "https://github.com/NVlabs/" download_cub.html > link_lines
 
 			# the last line is the easiest to find the link
-			awk '/./{line=$0} END{print line}' link_lines > last_line
+			#awk '/./{line=$0} END{print line}' link_lines > last_line
 
 			# the substring between two quotes is the link!!!!
-			LINK="$(awk -F'"' '{ print $2 }' last_line)"
-			echo "==== Link found at ${LINK}"
+			#LINK="$(awk -F'"' '{ print $2 }' last_line)"
+			#echo "==== Link found at ${LINK}"
 
 			# remove any temporary files
-			rm link_lines
-			rm download_cub.html
-			rm last_line
+			#rm link_lines
+			#rm download_cub.html
+			#rm last_line
 
 			# download the zip file 
 			echo "==== Downloading the CUB library... (Shouldn't take too long)"
-			wget "${LINK}" > /dev/null 2>&1
+			wget https://github.com/NVIDIA/cub/archive/refs/tags/1.8.0.zip > /dev/null 2>&1
 
 			#unzip
 			echo "==== Extracting the CUB library..."
@@ -151,12 +152,26 @@ else
 		ENSEMBLES+="GOMC_NPT_MPI_Test "
 		ENSEMBLES+="GOMC_GCMC_MPI_Test "
 		ENSEMBLES+="GOMC_GEMC_MPI_Test "
+		if(( use_cuda ))
+		then
+        	ENSEMBLES+="GOMC_GPU_NVT_MPI_Test "
+        	ENSEMBLES+="GOMC_GPU_NPT_MPI_Test "
+        	ENSEMBLES+="GOMC_GPU_GCMC_MPI_Test "
+        	ENSEMBLES+="GOMC_GPU_GEMC_MPI_Test "
+		fi
         CMAKEARGS+="-DGOMC_GTEST_MPI=on "
     else
         ENSEMBLES+="GOMC_NVT_Test "
         ENSEMBLES+="GOMC_NPT_Test "
         ENSEMBLES+="GOMC_GCMC_Test "
         ENSEMBLES+="GOMC_GEMC_Test "
+		if(( use_cuda ))
+		then
+        	ENSEMBLES+="GOMC_GPU_NVT_Test "
+        	ENSEMBLES+="GOMC_GPU_NPT_Test "
+        	ENSEMBLES+="GOMC_GPU_GCMC_Test "
+        	ENSEMBLES+="GOMC_GPU_GEMC_Test "
+		fi
         CMAKEARGS+="-DGOMC_GTEST=on "
     fi
     export CC="$(which gcc 2> /dev/null)"

src/BlockOutput.cpp

@@ -217,7 +217,7 @@ void BlockAverages::InitWatchSingle(config_setup::TrackedVars const& tracked)
     blocks[out::PRESSURE_IDX].SetRef(&var->pressure[b], b);
     blocks[out::MOL_NUM_IDX].SetRef(&var->numByBox[b], b);
     blocks[out::DENSITY_IDX].SetRef(&var->densityTot[b], b);
-    blocks[out::COMPRESSIBILITY_IDX].SetRef(&var->compressability[b], b);
+    blocks[out::COMPRESSIBILITY_IDX].SetRef(&var->compressibility[b], b);
     blocks[out::ENTHALPY_IDX].SetRef(&var->enthalpy[b], b);
     blocks[out::SURF_TENSION_IDX].SetRef(&var->surfaceTens[b], b);
 #if ENSEMBLE == GEMC

src/BoxDimensions.h

@@ -130,6 +130,10 @@ class BoxDimensions
   bool InRcut(double & distSq, XYZArray const& arr1,
               const uint i, XYZArray const& arr2, const uint j,
               const uint b) const;
+
+  bool InRcut(double & distSq, double cutoff, XYZ & dist,
+                                  XYZArray const& arr, const uint i,
+                                  const uint j, const uint b) const;
   /*
     bool InRcut(double distSq) const
     {
@@ -247,6 +251,14 @@ inline bool BoxDimensions::InRcut(double & distSq, XYZ & dist,
   return (rCutSq[b] > distSq);
 }
 
+inline bool BoxDimensions::InRcut(double & distSq, double cutoff, XYZ & dist,
+                                  XYZArray const& arr, const uint i,
+                                  const uint j, const uint b) const
+{
+  dist = MinImage(arr.Difference(i, j), b);
+  distSq = dist.x * dist.x + dist.y * dist.y + dist.z * dist.z;
+  return (cutoff > distSq);
+}
 
 inline bool BoxDimensions::InRcut(double & distSq, XYZ & dist,
                                   XYZArray const& arr1, const uint i,

src/CPUSide.cpp

@@ -15,7 +15,8 @@ CPUSide::CPUSide(System & sys, StaticVals & statV, Setup & set) :
   psf(statV.mol, sys, set), 
   xstBinary(sys, statV),
   console(varRef), block(varRef),
-  hist(varRef), checkpoint(sys, statV)
+  hist(varRef), checkpoint(sys, statV),
+  wolfCalibration(sys, statV)
 #if ENSEMBLE == GCMC
   , sample_N_E(varRef)
 #endif
@@ -45,6 +46,8 @@ void CPUSide::Init( PDBSetup const& pdbSet,
     outObj.push_back(&block);
   if (out.restart.settings.enable)
     outObj.push_back(&checkpoint);
+  if (out.wolfCalibration.settings.enable)
+    outObj.push_back(&wolfCalibration);
 
 #if ENSEMBLE == GCMC
   outObj.push_back(&hist);

src/CPUSide.h

@@ -19,6 +19,7 @@ along with this program, also can be found at <http://www.gnu.org/licenses/>.
 #include "CheckpointOutput.h"
 #include "EnPartCntSampleOutput.h"
 #include "FreeEnergyOutput.h"
+#include "WolfCalibrationOutput.h"
 #include "PSFOutput.h"
 
 #include <vector>
@@ -50,6 +51,7 @@ struct CPUSide {
   BlockAverages block;
   Histogram hist;
   CheckpointOutput checkpoint;
+  WolfCalibrationOutput wolfCalibration;
 #if ENSEMBLE == GCMC
   EnPartCntSample sample_N_E;
 #endif