resolved PR #2611 merge conflicts

openmmapi/src/LangevinMiddleIntegrator.cpp

@@ -80,7 +80,7 @@ void LangevinMiddleIntegrator::step(int steps) {
         throw OpenMMException("This Integrator is not bound to a context!");  
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
-        context->calcForcesAndEnergy(true, false);
+        context->calcForcesAndEnergy(true, false, getIntegrationForceGroups());
         kernel.getAs<IntegrateLangevinMiddleStepKernel>().execute(*context, *this);
     }
 }

openmmapi/src/LocalEnergyMinimizer.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -79,7 +79,7 @@ struct MinimizerData {
 static double computeForcesAndEnergy(Context& context, const vector<Vec3>& positions, lbfgsfloatval_t *g) {
     context.setPositions(positions);
     context.computeVirtualSites();
-    State state = context.getState(State::Forces | State::Energy);
+    State state = context.getState(State::Forces | State::Energy, false, context.getIntegrator().getIntegrationForceGroups());
     const vector<Vec3>& forces = state.getForces();
     const System& system = context.getSystem();
     for (int i = 0; i < forces.size(); i++) {

openmmapi/src/MonteCarloAnisotropicBarostatImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Lee-Ping Wang                                      *
  * Contributors:                                                              *
  *                                                                            *
@@ -72,7 +72,8 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
     
     // Compute the current potential energy.
     
-    double initialEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
+    int groups = context.getIntegrator().getIntegrationForceGroups();
+    double initialEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
     double pressure;
     
     // Choose which axis to modify at random.
@@ -114,7 +115,7 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
     
     // Compute the energy of the modified system.
     
-    double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
+    double finalEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
     double kT = BOLTZ*context.getParameter(MonteCarloAnisotropicBarostat::Temperature());
     double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
     if (w > 0 && SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() > std::exp(-w/kT)) {

openmmapi/src/MonteCarloBarostatImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -68,7 +68,8 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context, bool& forc
 
     // Compute the current potential energy.
 
-    double initialEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
+    int groups = context.getIntegrator().getIntegrationForceGroups();
+    double initialEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
 
     // Modify the periodic box size.
 
@@ -83,7 +84,7 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context, bool& forc
 
     // Compute the energy of the modified system.
     
-    double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
+    double finalEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
     double pressure = context.getParameter(MonteCarloBarostat::Pressure())*(AVOGADRO*1e-25);
     double kT = BOLTZ*context.getParameter(MonteCarloBarostat::Temperature());
     double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);

openmmapi/src/MonteCarloMembraneBarostatImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Lee-Ping Wang                                      *
  * Contributors:                                                              *
  *                                                                            *
@@ -70,7 +70,8 @@ void MonteCarloMembraneBarostatImpl::updateContextState(ContextImpl& context) {
     
     // Compute the current potential energy.
     
-    double initialEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
+    int groups = context.getIntegrator().getIntegrationForceGroups();
+    double initialEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
     double pressure = context.getParameter(MonteCarloMembraneBarostat::Pressure())*(AVOGADRO*1e-25);
     double tension = context.getParameter(MonteCarloMembraneBarostat::SurfaceTension())*(AVOGADRO*1e-25);
     
@@ -115,7 +116,7 @@ void MonteCarloMembraneBarostatImpl::updateContextState(ContextImpl& context) {
     
     // Compute the energy of the modified system.
     
-    double finalEnergy = context.getOwner().getState(State::Energy).getPotentialEnergy();
+    double finalEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
     double kT = BOLTZ*context.getParameter(MonteCarloMembraneBarostat::Temperature());
     double w = finalEnergy-initialEnergy + pressure*deltaVolume - tension*deltaArea - context.getMolecules().size()*kT*std::log(newVolume/volume);
     if (w > 0 && SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() > std::exp(-w/kT)) {

openmmapi/src/NoseHooverIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2019 Stanford University and the Authors.           *
+ * Portions copyright (c) 2019-2020 Stanford University and the Authors.      *
  * Authors: Andreas Krämer and Andrew C. Simmonett                            *
  * Contributors:                                                              *
  *                                                                            *
@@ -337,7 +337,7 @@ void NoseHooverIntegrator::step(int steps) {
     for (int i = 0; i < steps; ++i) {
         if(context->updateContextState())
             forcesAreValid = false;
-        context->calcForcesAndEnergy(true, false);
+        context->calcForcesAndEnergy(true, false, getIntegrationForceGroups());
         kernel.getAs<IntegrateNoseHooverStepKernel>().execute(*context, *this, forcesAreValid);
     }
 }

openmmapi/src/VariableLangevinIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -80,7 +80,7 @@ void VariableLangevinIntegrator::step(int steps) {
         throw OpenMMException("This Integrator is not bound to a context!");  
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
-        context->calcForcesAndEnergy(true, false);
+        context->calcForcesAndEnergy(true, false, getIntegrationForceGroups());
         setStepSize(kernel.getAs<IntegrateVariableLangevinStepKernel>().execute(*context, *this, std::numeric_limits<double>::infinity()));
     }
 }
@@ -90,7 +90,7 @@ void VariableLangevinIntegrator::stepTo(double time) {
         throw OpenMMException("This Integrator is not bound to a context!");
     while (time > context->getTime()) {
         context->updateContextState();
-        context->calcForcesAndEnergy(true, false);
+        context->calcForcesAndEnergy(true, false, getIntegrationForceGroups());
         setStepSize(kernel.getAs<IntegrateVariableLangevinStepKernel>().execute(*context, *this, time));
     }
 }

openmmapi/src/VariableVerletIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -74,7 +74,7 @@ void VariableVerletIntegrator::step(int steps) {
         throw OpenMMException("This Integrator is not bound to a context!");
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
-        context->calcForcesAndEnergy(true, false);
+        context->calcForcesAndEnergy(true, false, getIntegrationForceGroups());
         setStepSize(kernel.getAs<IntegrateVariableVerletStepKernel>().execute(*context, *this, std::numeric_limits<double>::infinity()));
     }
 }
@@ -84,7 +84,7 @@ void VariableVerletIntegrator::stepTo(double time) {
         throw OpenMMException("This Integrator is not bound to a context!");  
     while (time > context->getTime()) {
         context->updateContextState();
-        context->calcForcesAndEnergy(true, false);
+        context->calcForcesAndEnergy(true, false, getIntegrationForceGroups());
         setStepSize(kernel.getAs<IntegrateVariableVerletStepKernel>().execute(*context, *this, time));
     }
 }

openmmapi/src/VerletIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2020 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -73,7 +73,7 @@ void VerletIntegrator::step(int steps) {
         throw OpenMMException("This Integrator is not bound to a context!");
     for (int i = 0; i < steps; ++i) {
         context->updateContextState();
-        context->calcForcesAndEnergy(true, false);
+        context->calcForcesAndEnergy(true, false, getIntegrationForceGroups());
         kernel.getAs<IntegrateVerletStepKernel>().execute(*context, *this);
     }
 }

platforms/common/src/CommonKernels.cpp

@@ -5709,7 +5709,7 @@ void CommonIntegrateNoseHooverStepKernel::execute(ContextImpl& context, const No
 
     // If the atom reordering has occured, the forces from the previous step are permuted and thus invalid.
     // They need to be either sorted or recomputed; here we choose the latter.
-    if (!forcesAreValid || cc.getAtomsWereReordered()) context.calcForcesAndEnergy(true, false);
+    if (!forcesAreValid || cc.getAtomsWereReordered()) context.calcForcesAndEnergy(true, false, integrator.getIntegrationForceGroups());
 
     const auto& atomList = integrator.getAllThermostatedIndividualParticles();
     const auto& pairList = integrator.getAllThermostatedPairs();
@@ -6770,7 +6770,7 @@ void CommonIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
 
         // Record the variable names and flags for the force and energy in each step.
 
-        forceGroupFlags.resize(numSteps, -1);
+        forceGroupFlags.resize(numSteps, integrator.getIntegrationForceGroups());
         vector<string> forceGroupName;
         vector<string> energyGroupName;
         for (int i = 0; i < 32; i++) {
@@ -6957,7 +6957,7 @@ void CommonIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
                 if (cc.getUseMixedPrecision())
                     kernel->addArg(cc.getPosqCorrection());
                 else
-                    kernel->addArg(NULL);
+                    kernel->addArg(nullptr);
                 kernel->addArg(integration.getPosDelta());
                 kernel->addArg(cc.getVelm());
                 kernel->addArg(cc.getLongForceBuffer());
@@ -6992,7 +6992,7 @@ void CommonIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
                 if (cc.getUseMixedPrecision())
                     kernel->addArg(cc.getPosqCorrection());
                 else
-                    kernel->addArg(NULL);
+                    kernel->addArg(nullptr);
                 kernel->addArg(integration.getPosDelta());
             }
         }
@@ -7048,7 +7048,7 @@ void CommonIntegrateCustomStepKernel::prepareForComputation(ContextImpl& context
         if (cc.getUseMixedPrecision())
             kineticEnergyKernel->addArg(cc.getPosqCorrection());
         else
-            kineticEnergyKernel->addArg(NULL);
+            kineticEnergyKernel->addArg(nullptr);
         kineticEnergyKernel->addArg(integration.getPosDelta());
         kineticEnergyKernel->addArg(cc.getVelm());
         kineticEnergyKernel->addArg(cc.getLongForceBuffer());

platforms/common/src/IntegrationUtilities.cpp

@@ -549,7 +549,7 @@ IntegrationUtilities::IntegrationUtilities(ComputeContext& context, const System
     if (context.getUseMixedPrecision())
         vsitePositionKernel->addArg(context.getPosqCorrection());
     else
-        vsitePositionKernel->addArg(NULL);
+        vsitePositionKernel->addArg(nullptr);
     vsitePositionKernel->addArg(vsite2AvgAtoms);
     vsitePositionKernel->addArg(vsite2AvgWeights);
     vsitePositionKernel->addArg(vsite3AvgAtoms);
@@ -565,7 +565,7 @@ IntegrationUtilities::IntegrationUtilities(ComputeContext& context, const System
     if (context.getUseMixedPrecision())
         vsiteForceKernel->addArg(context.getPosqCorrection());
     else
-        vsiteForceKernel->addArg(NULL);
+        vsiteForceKernel->addArg(nullptr);
     vsiteForceKernel->addArg(); // Skip argument 2: the force array hasn't been created yet.
     vsiteForceKernel->addArg(vsite2AvgAtoms);
     vsiteForceKernel->addArg(vsite2AvgWeights);

platforms/common/src/kernels/cmapTorsionForce.cc

@@ -61,8 +61,8 @@ angleB = fmod(angleB+2.0f*PI, 2.0f*PI);
 int2 pos = MAP_POS[MAPS[index]];
 int size = pos.y;
 real delta = 2*PI/size;
-int s = (int) fmin(angleA/delta, size-1);
-int t = (int) fmin(angleB/delta, size-1);
+int s = (int) fmin(angleA/delta, (real) (size-1));
+int t = (int) fmin(angleB/delta, (real) (size-1));
 float4 c[4];
 int coeffIndex = pos.x+4*(s+size*t);
 c[0] = COEFF[coeffIndex];

platforms/common/src/kernels/customIntegratorPerDof.cc

@@ -3,8 +3,8 @@ typedef double TempType;
 typedef double3 TempType3;
 typedef double4 TempType4;
 
-#define make_TempType3(...) make_double3(__VA_ARGS__)
-#define make_TempType4(...) make_double4(__VA_ARGS__)
+#define make_TempType3 make_double3
+#define make_TempType4 make_double4
 #define convertToTempType3(a) make_double3((a).x, (a).y, (a).z)
 #define convertToTempType4(a) make_double4((a).x, (a).y, (a).z, (a).w)
 
@@ -16,8 +16,8 @@ typedef float TempType;
 typedef float3 TempType3;
 typedef float4 TempType4;
 
-#define make_TempType3(...) make_float3(__VA_ARGS__)
-#define make_TempType4(...) make_float4(__VA_ARGS__)
+#define make_TempType3 make_float3
+#define make_TempType4 make_float4
 #define convertToTempType3(a) make_float3((a).x, (a).y, (a).z)
 #define convertToTempType4(a) make_float4((a).x, (a).y, (a).z, (a).w)
 #endif

platforms/cpu/include/CpuNeighborList.h

@@ -51,7 +51,7 @@ public:
             const Vec3* periodicBoxVectors, bool usePeriodic, float maxDistance, ThreadPool& threads);
     int getNumBlocks() const;
     int getBlockSize() const;
-    const std::vector<int>& getSortedAtoms() const;
+    const std::vector<int32_t>& getSortedAtoms() const;
     const std::vector<int>& getBlockNeighbors(int blockIndex) const;
 
     /**

platforms/cpu/include/CpuNonbondedForceFvec.h

@@ -109,10 +109,8 @@ CpuNonbondedForceFvec<FVEC>::approximateFunctionFromTable(const std::vector<floa
     FVEC s1, s2;
     gatherVecPair(table.data(), index, s1, s2);
 
-    const auto coeff2 = x1-FVEC(index);
-    const auto coeff1 = 1.0f-coeff2;
-
-    return coeff1*s1 + coeff2*s2;
+    const auto coeff2 = x1 - FVEC(index);
+    return (s1 - coeff2 * s1) + coeff2 * s2;
 }
 
 template<typename FVEC>
@@ -140,7 +138,7 @@ void CpuNonbondedForceFvec<FVEC>::calculateBlockIxnHandler(int blockIndex, float
         using std::min;
         using std::max;
 
-        const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
+        const int32_t* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
         float minx, maxx, miny, maxy, minz, maxz;
         minx = maxx = posq[4*blockAtom[0]];
         miny = maxy = posq[4*blockAtom[0]+1];
@@ -183,7 +181,7 @@ template <int PERIODIC_TYPE, BlockType BLOCK_TYPE>
 void CpuNonbondedForceFvec<FVEC>::calculateBlockIxnImpl(int blockIndex, float* forces, double* totalEnergy, const fvec4& boxSize, const fvec4& invBoxSize, const fvec4& blockCenter) {
     // Load the positions and parameters of the atoms in the block.
 
-    const int* blockAtom = &neighborList->getSortedAtoms()[blockSize * blockIndex];
+    const int32_t* blockAtom = &neighborList->getSortedAtoms()[blockSize * blockIndex];
     fvec4 blockAtomPosq[blockSize];
     FVEC blockAtomForceX(0.0f), blockAtomForceY(0.0f), blockAtomForceZ(0.0f);
     FVEC blockAtomX, blockAtomY, blockAtomZ, blockAtomCharge;
@@ -216,6 +214,8 @@ void CpuNonbondedForceFvec<FVEC>::calculateBlockIxnImpl(int blockIndex, float* f
     // Loop over neighbors for this block.
     const auto& neighbors = neighborList->getBlockNeighbors(blockIndex);
     const auto& exclusions = neighborList->getBlockExclusions(blockIndex);
+    FVEC partialEnergy = {};
+
     for (int i = 0; i < (int) neighbors.size(); i++) {
         // Load the next neighbor.
         
@@ -230,7 +230,7 @@ void CpuNonbondedForceFvec<FVEC>::calculateBlockIxnImpl(int blockIndex, float* f
         getDeltaR<PERIODIC_TYPE>(atomPos, blockAtomX, blockAtomY, blockAtomZ, dx, dy, dz, r2, boxSize, invBoxSize);
 
         const auto exclNotMask = FVEC::expandBitsToMask(~exclusions[i]);
-        const auto include = blendZero(r2 < cutoffDistance*cutoffDistance, exclNotMask);
+        const auto include = blendZero(r2 < cutoffDistanceSquared, exclNotMask);
         if (!any(include))
             continue; // No interactions to compute.
 
@@ -296,7 +296,8 @@ void CpuNonbondedForceFvec<FVEC>::calculateBlockIxnImpl(int blockIndex, float* f
                     energy += chargeProd*inverseR;
             }
             energy = blendZero(energy, include);
-            *totalEnergy += reduceAdd(energy);
+
+            partialEnergy += energy;
         }
 
         // Accumulate forces.
@@ -313,6 +314,9 @@ void CpuNonbondedForceFvec<FVEC>::calculateBlockIxnImpl(int blockIndex, float* f
         newAtomForce.store(atomForce);
     }
     
+    if (totalEnergy)
+        *totalEnergy += reduceAdd(partialEnergy);
+
     // Record the forces on the block atoms.
     fvec4 f[blockSize];
     transpose(blockAtomForceX, blockAtomForceY, blockAtomForceZ, 0.0f, f);

platforms/cpu/sharedTarget/CMakeLists.txt

 FOREACH(file ${SOURCE_FILES})
-    IF(file MATCHES ".*Vec8.*")
-        IF(MSVC)
-            SET_SOURCE_FILES_PROPERTIES(${file} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} /arch:AVX /D__AVX__")
-        ELSEIF(X86)
-            SET_SOURCE_FILES_PROPERTIES(${file} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1 -mavx")
-        ELSE()
-            SET_SOURCE_FILES_PROPERTIES(${file} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
-        ENDIF()
-    ELSE()
-        IF(X86 AND NOT MSVC)
-            SET_SOURCE_FILES_PROPERTIES(${file} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1")
-        ENDIF()
+    IF(X86 AND NOT MSVC)
+        SET_SOURCE_FILES_PROPERTIES(${file} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1")
     ENDIF()
 ENDFOREACH(file)
+
+# Override some sources files with platform specific flags.
+IF(MSVC)
+    SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/platforms/cpu/src/CpuNonbondedForceAvx.cpp PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} /arch:AVX /D__AVX__")
+    SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/platforms/cpu/src/CpuNonbondedForceAvx2.cpp PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} /arch:AVX2 /D__AVX2__")
+ELSEIF(X86)
+    SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/platforms/cpu/src/CpuNonbondedForceAvx.cpp PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -mavx")
+    SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/platforms/cpu/src/CpuNonbondedForceAvx2.cpp PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -mavx2 -mfma")
+ENDIF()
+
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})

platforms/cpu/src/CpuBondForce.cpp

@@ -41,7 +41,7 @@ CpuBondForce::CpuBondForce() {
 void CpuBondForce::initialize(int numAtoms, int numBonds, int numAtomsPerBond, vector<vector<int> >& bondAtoms, ThreadPool& threads) {
     this->numBonds = numBonds;
     this->numAtomsPerBond = numAtomsPerBond;
-    this->bondAtoms = &bondAtoms[0];
+    this->bondAtoms = bondAtoms.empty() ? nullptr : bondAtoms.data();
     this->threads = &threads;
     int numThreads = threads.getNumThreads();
     int targetBondsPerThread = numBonds/numThreads;

platforms/cpu/src/CpuCustomGBForce.cpp

@@ -361,7 +361,7 @@ void CpuCustomGBForce::calculateParticlePairValue(int index, ThreadData& data, i
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
             const int blockSize = neighborList->getBlockSize();
-            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
+            const int32_t* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const auto& blockExclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {
@@ -456,7 +456,7 @@ void CpuCustomGBForce::calculateParticlePairEnergyTerm(int index, ThreadData& da
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
             const int blockSize = neighborList->getBlockSize();
-            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
+            const int32_t* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const auto& blockExclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {
@@ -543,7 +543,7 @@ void CpuCustomGBForce::calculateChainRuleForces(ThreadData& data, int numAtoms,
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
             const int blockSize = neighborList->getBlockSize();
-            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
+            const int32_t* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const auto& blockExclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {

platforms/cpu/src/CpuCustomNonbondedForce.cpp

@@ -193,7 +193,7 @@ void CpuCustomNonbondedForce::threadComputeForce(ThreadPool& threads, int thread
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
             const int blockSize = neighborList->getBlockSize();
-            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
+            const int32_t* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const auto& exclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {

platforms/cpu/src/CpuGayBerneForce.cpp

@@ -181,7 +181,7 @@ void CpuGayBerneForce::threadComputeForce(ThreadPool& threads, int threadIndex,
             if (blockIndex >= neighborList->getNumBlocks())
                 break;
             const int blockSize = neighborList->getBlockSize();
-            const int* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
+            const int32_t* blockAtom = &neighborList->getSortedAtoms()[blockSize*blockIndex];
             const vector<int>& neighbors = neighborList->getBlockNeighbors(blockIndex);
             const auto& exclusions = neighborList->getBlockExclusions(blockIndex);
             for (int i = 0; i < (int) neighbors.size(); i++) {