Changes for 8.1.1 (#4376)

openmm · Jan 2, 2024 · ec797ac · ec797ac
1 parent 43f571d
commit ec797ac
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Showing 5 changed files with 19 additions and 2 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -165,7 +165,7 @@ ENDIF (NOT CMAKE_CXX_FLAGS_RELEASE)
 SET(OPENMM_LIBRARY_NAME OpenMM)
 SET(OPENMM_MAJOR_VERSION 8)
 SET(OPENMM_MINOR_VERSION 1)
-SET(OPENMM_BUILD_VERSION 0)
+SET(OPENMM_BUILD_VERSION 1)
 
 ADD_DEFINITIONS(-DOPENMM_LIBRARY_NAME=${OPENMM_LIBRARY_NAME}
                 -DOPENMM_MAJOR_VERSION=${OPENMM_MAJOR_VERSION}

diff --git a/platforms/common/include/openmm/common/CommonKernels.h b/platforms/common/include/openmm/common/CommonKernels.h
@@ -1578,7 +1578,7 @@ class CommonApplyMonteCarloBarostatKernel : public ApplyMonteCarloBarostatKernel
     ComputeContext& cc;
     bool hasInitializedKernels, rigidMolecules, atomsWereReordered;
     int numMolecules;
-    ComputeArray savedPositions, savedFloatForces, savedLongForces;
+    ComputeArray savedPositions, savedFloatForces, savedLongForces, savedVelocities;
     ComputeArray moleculeAtoms;
     ComputeArray moleculeStartIndex;
     ComputeKernel kernel;

diff --git a/platforms/common/src/CommonKernels.cpp b/platforms/common/src/CommonKernels.cpp
@@ -7699,6 +7699,7 @@ void CommonApplyMonteCarloBarostatKernel::initialize(const System& system, const
     this->rigidMolecules = rigidMolecules;
     ContextSelector selector(cc);
     savedPositions.initialize(cc, cc.getPaddedNumAtoms(), cc.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4), "savedPositions");
+    savedVelocities.initialize(cc, cc.getPaddedNumAtoms(), cc.getUseDoublePrecision() || cc.getUseMixedPrecision() ? sizeof(mm_double4) : sizeof(mm_float4), "savedVelocities");
     savedLongForces.initialize<long long>(cc, cc.getPaddedNumAtoms()*3, "savedLongForces");
     try {
         cc.getFloatForceBuffer(); // This will throw an exception on the CUDA platform.
@@ -7714,6 +7715,7 @@ void CommonApplyMonteCarloBarostatKernel::initialize(const System& system, const
 void CommonApplyMonteCarloBarostatKernel::saveCoordinates(ContextImpl& context) {
     ContextSelector selector(cc);
     cc.getPosq().copyTo(savedPositions);
+    cc.getVelm().copyTo(savedVelocities);
     cc.getLongForceBuffer().copyTo(savedLongForces);
     if (savedFloatForces.isInitialized())
         cc.getFloatForceBuffer().copyTo(savedFloatForces);
@@ -7777,6 +7779,7 @@ void CommonApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context,
 void CommonApplyMonteCarloBarostatKernel::restoreCoordinates(ContextImpl& context) {
     ContextSelector selector(cc);
     savedPositions.copyTo(cc.getPosq());
+    savedVelocities.copyTo(cc.getVelm());
     savedLongForces.copyTo(cc.getLongForceBuffer());
     cc.setPosCellOffsets(lastPosCellOffsets);
     if (savedFloatForces.isInitialized())

diff --git a/platforms/cuda/src/kernels/findInteractingBlocks.cu b/platforms/cuda/src/kernels/findInteractingBlocks.cu
@@ -327,6 +327,13 @@ extern "C" __global__ __launch_bounds__(GROUP_SIZE,3) void findBlocksWithInterac
                     blockDelta.y = max(0.0f, fabs(blockDelta.y)-blockSizeX.y-largeSize.y);
                     blockDelta.z = max(0.0f, fabs(blockDelta.z)-blockSizeX.z-largeSize.z);
                     includeLargeBlock = (blockDelta.x*blockDelta.x+blockDelta.y*blockDelta.y+blockDelta.z*blockDelta.z < PADDED_CUTOFF_SQUARED);
+#ifdef TRICLINIC
+                    // The calculation to find the nearest periodic copy is only guaranteed to work if the nearest copy is less than half a box width away.
+                    // If there's any possibility we might have missed it, do a detailed check.
+
+                    if (periodicBoxSize.z/2-blockSizeX.z-largeSize.z < PADDED_CUTOFF || periodicBoxSize.y/2-blockSizeX.y-largeSize.y < PADDED_CUTOFF)
+                        includeLargeBlock = true;
+#endif
                 }
                 largeBlockFlags = BALLOT(includeLargeBlock);
                 loadedLargeBlocks = 32;

diff --git a/platforms/opencl/src/kernels/findInteractingBlocks.cl b/platforms/opencl/src/kernels/findInteractingBlocks.cl
@@ -196,6 +196,13 @@ __kernel void findBlocksWithInteractions(real4 periodicBoxSize, real4 invPeriodi
                     blockDelta.y = max((real) 0, fabs(blockDelta.y)-blockSizeX.y-largeSize.y);
                     blockDelta.z = max((real) 0, fabs(blockDelta.z)-blockSizeX.z-largeSize.z);
                     includeLargeBlock = (blockDelta.x*blockDelta.x+blockDelta.y*blockDelta.y+blockDelta.z*blockDelta.z < PADDED_CUTOFF_SQUARED);
+#ifdef TRICLINIC
+                    // The calculation to find the nearest periodic copy is only guaranteed to work if the nearest copy is less than half a box width away.
+                    // If there's any possibility we might have missed it, do a detailed check.
+
+                    if (periodicBoxSize.z/2-blockSizeX.z-largeSize.z < PADDED_CUTOFF || periodicBoxSize.y/2-blockSizeX.y-largeSize.y < PADDED_CUTOFF)
+                        includeLargeBlock = true;
+#endif
                 }
                 largeBlockFlags[get_local_id(0)] = includeLargeBlock;
                 loadedLargeBlocks = 32;