resolved PR #2611 merge conflicts

platforms/cpu/src/CpuKernels.cpp

@@ -712,12 +712,23 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
 void CpuCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const NonbondedForce& force) {
     if (force.getNumParticles() != numParticles)
         throw OpenMMException("updateParametersInContext: The number of particles has changed");
+
+    // Identify which exceptions are 1-4 interactions.
+
+    set<int> exceptionsWithOffsets;
+    for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
+        string param;
+        int exception;
+        double charge, sigma, epsilon;
+        force.getExceptionParameterOffset(i, param, exception, charge, sigma, epsilon);
+        exceptionsWithOffsets.insert(exception);
+    }
     vector<int> nb14s;
     for (int i = 0; i < force.getNumExceptions(); i++) {
         int particle1, particle2;
         double chargeProd, sigma, epsilon;
         force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
-        if (chargeProd != 0.0 || epsilon != 0.0)
+        if (chargeProd != 0.0 || epsilon != 0.0 || exceptionsWithOffsets.find(i) != exceptionsWithOffsets.end())
             nb14s.push_back(i);
     }
     if (nb14s.size() != num14)

platforms/cpu/src/CpuNeighborList.cpp

@@ -501,7 +501,7 @@ int CpuNeighborList::getBlockSize() const {
     return blockSize;
 }
 
-const std::vector<int>& CpuNeighborList::getSortedAtoms() const {
+const std::vector<int32_t>& CpuNeighborList::getSortedAtoms() const {
     return sortedAtoms;
 }
 

platforms/cpu/src/CpuNonbondedForceVec8.cpp → platforms/cpu/src/CpuNonbondedForceAvx.cpp

@@ -27,9 +27,9 @@
 
 #ifdef __AVX__
 
-#include "openmm/internal/vectorize8.h"
+#include "openmm/internal/vectorizeAvx.h"
 
-bool isVec8Supported() {
+bool isAvxSupported() {
     // Make sure the CPU supports AVX.
     int cpuInfo[4];
     cpuid(cpuInfo, 0);
@@ -40,16 +40,16 @@ bool isVec8Supported() {
     return false;
 }
 
-OpenMM::CpuNonbondedForce* createCpuNonbondedForceVec8() {
+OpenMM::CpuNonbondedForce* createCpuNonbondedForceAvx() {
     return new OpenMM::CpuNonbondedForceFvec<fvec8>();
 }
 
 #else
-bool isVec8Supported() {
+bool isAvxSupported() {
     return false;
 }
 
-OpenMM::CpuNonbondedForce* createCpuNonbondedForceVec8() {
+OpenMM::CpuNonbondedForce* createCpuNonbondedForceAvx() {
    throw OpenMM::OpenMMException("Internal error: OpenMM was compiled without AVX support");
 }
 #endif

platforms/cpu/src/CpuNonbondedForceAvx2.cpp

+
+/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
+ * Contributors: Daniel Towner
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
+ * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+#include "CpuNonbondedForceFvec.h"
+#include "openmm/OpenMMException.h"
+
+#ifdef __AVX2__
+
+#include "openmm/internal/vectorizeAvx2.h"
+OpenMM::CpuNonbondedForce* createCpuNonbondedForceAvx2() {
+    return new OpenMM::CpuNonbondedForceFvec<fvecAvx2>();
+}
+
+#else
+
+bool isAvx2Supported() {
+    return false;
+}
+
+OpenMM::CpuNonbondedForce* createCpuNonbondedForceAvx2() {
+   throw OpenMM::OpenMMException("Internal error: OpenMM was compiled without AVX2 support");
+}
+#endif

platforms/cpu/src/CpuNonbondedForceFvec.cpp

@@ -25,19 +25,25 @@
 #include "CpuNonbondedForceFvec.h"
 
 OpenMM::CpuNonbondedForce* createCpuNonbondedForceVec4();
-OpenMM::CpuNonbondedForce* createCpuNonbondedForceVec8();
+OpenMM::CpuNonbondedForce* createCpuNonbondedForceAvx();
+OpenMM::CpuNonbondedForce* createCpuNonbondedForceAvx2();
 
-bool isVec8Supported();
+bool isAvxSupported();
+bool isAvx2Supported();
+
+#include <iostream>
 
 OpenMM::CpuNonbondedForce* createCpuNonbondedForceVec() {
-    if (isVec8Supported())
-        return createCpuNonbondedForceVec8();
+    if (isAvx2Supported())
+        return createCpuNonbondedForceAvx2();
+    else if (isAvxSupported())
+        return createCpuNonbondedForceAvx();
     else
         return createCpuNonbondedForceVec4();
 }
 
 int getVecBlockSize() {
-    if (isVec8Supported())
+    if (isAvx2Supported() || isAvxSupported())
         return 8;
     else
         return 4;

platforms/opencl/tests/TestOpenCLCheckpoints.cpp

@@ -95,9 +95,12 @@ void testCheckpoint() {
     
     // Create a new Context that uses multiple devices.
 
-    string deviceIndex = platform.getPropertyValue(context, OpenCLPlatform::OpenCLDeviceIndex());
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     VerletIntegrator integrator2(0.001);
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);

platforms/opencl/tests/TestOpenCLCustomAngleForce.cpp

@@ -50,9 +50,13 @@ void testParallelComputation() {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/opencl/tests/TestOpenCLCustomBondForce.cpp

@@ -50,9 +50,13 @@ void testParallelComputation() {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/opencl/tests/TestOpenCLCustomCompoundBondForce.cpp

@@ -54,9 +54,13 @@ void testParallelComputation() {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/opencl/tests/TestOpenCLCustomExternalForce.cpp

@@ -53,9 +53,13 @@ void testParallelComputation() {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/opencl/tests/TestOpenCLCustomNonbondedForce.cpp

@@ -58,9 +58,13 @@ void testParallelComputation() {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/opencl/tests/TestOpenCLCustomTorsionForce.cpp

@@ -50,9 +50,13 @@ void testParallelComputation() {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/opencl/tests/TestOpenCLHarmonicAngleForce.cpp

@@ -51,9 +51,13 @@ void testParallelComputation() {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/opencl/tests/TestOpenCLHarmonicBondForce.cpp

@@ -50,9 +50,13 @@ void testParallelComputation() {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+    
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/opencl/tests/TestOpenCLNonbondedForce.cpp

@@ -62,9 +62,13 @@ void testParallelComputation(NonbondedForce::NonbondedMethod method) {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/opencl/tests/TestOpenCLPeriodicTorsionForce.cpp

@@ -49,9 +49,13 @@ void testParallelComputation() {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/opencl/tests/TestOpenCLRBTorsionForce.cpp

@@ -49,9 +49,13 @@ void testParallelComputation() {
     context1.setPositions(positions);
     State state1 = context1.getState(State::Forces | State::Energy);
     VerletIntegrator integrator2(0.01);
-    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
+
     map<string, string> props;
+    string deviceIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLDeviceIndex());
     props[OpenCLPlatform::OpenCLDeviceIndex()] = deviceIndex+","+deviceIndex;
+    string platformIndex = platform.getPropertyValue(context1, OpenCLPlatform::OpenCLPlatformIndex());
+    props[OpenCLPlatform::OpenCLPlatformIndex()] = platformIndex;
+
     Context context2(system, integrator2, platform, props);
     context2.setPositions(positions);
     State state2 = context2.getState(State::Forces | State::Energy);

platforms/reference/src/ReferenceKernels.cpp

@@ -1015,12 +1015,23 @@ double ReferenceCalcNonbondedForceKernel::execute(ContextImpl& context, bool inc
 void ReferenceCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context, const NonbondedForce& force) {
     if (force.getNumParticles() != numParticles)
         throw OpenMMException("updateParametersInContext: The number of particles has changed");
+
+    // Identify which exceptions are 1-4 interactions.
+
+    set<int> exceptionsWithOffsets;
+    for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
+        string param;
+        int exception;
+        double charge, sigma, epsilon;
+        force.getExceptionParameterOffset(i, param, exception, charge, sigma, epsilon);
+        exceptionsWithOffsets.insert(exception);
+    }
     vector<int> nb14s;
     for (int i = 0; i < force.getNumExceptions(); i++) {
         int particle1, particle2;
         double chargeProd, sigma, epsilon;
         force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
-        if (chargeProd != 0.0 || epsilon != 0.0)
+        if (chargeProd != 0.0 || epsilon != 0.0 || exceptionsWithOffsets.find(i) != exceptionsWithOffsets.end())
             nb14s.push_back(i);
     }
     if (nb14s.size() != num14)

platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp

 
-/* Portions copyright (c) 2011-2017 Stanford University and Simbios.
+/* Portions copyright (c) 2011-2020 Stanford University and Simbios.
  * Contributors: Peter Eastman
  *
  * Permission is hereby granted, free of charge, to any person obtaining
@@ -171,7 +171,7 @@ void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<double>& m
 
     // Record the force group flags for each step.
 
-    forceGroupFlags.resize(numSteps, -1);
+    forceGroupFlags.resize(numSteps, integrator.getIntegrationForceGroups());
     for (int i = 0; i < numSteps; i++)
         if (forceGroup[i] > -1)
             forceGroupFlags[i] = 1<<forceGroup[i];

platforms/reference/src/SimTKReference/ReferenceNoseHooverDynamics.cpp

@@ -26,6 +26,7 @@
 #include <iostream>
 #include <sstream>
 
+#include "openmm/Integrator.h"
 #include "openmm/OpenMMException.h"
 #include "SimTKOpenMMUtilities.h"
 #include "openmm/internal/ContextImpl.h"
@@ -55,7 +56,7 @@ void ReferenceNoseHooverDynamics::step1(OpenMM::ContextImpl &context, const Open
                                           double maxPairDistance) {
 
     // first-time-through initialization
-    if (!forcesAreValid) context.calcForcesAndEnergy(true, false);
+    if (!forcesAreValid) context.calcForcesAndEnergy(true, false, context.getIntegrator().getIntegrationForceGroups());
 
     if (getTimeStep() == 0) {
        // invert masses