Merge branch 'master' into nucleic

platforms/cpu/include/CpuNeighborList.h

@@ -35,6 +35,7 @@
 #include "AlignedArray.h"
 #include "RealVec.h"
 #include "windowsExportCpu.h"
+#include "openmm/internal/gmx_atomic.h"
 #include "openmm/internal/ThreadPool.h"
 #include <set>
 #include <utility>
@@ -74,6 +75,7 @@ private:
     int numAtoms;
     bool usePeriodic;
     float maxDistance;
+    gmx_atomic_t atomicCounter;
 };
 
 } // namespace OpenMM

platforms/cpu/sharedTarget/CMakeLists.txt

@@ -18,6 +18,6 @@ ENDFOREACH(file)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_SHARED_LIBRARY")
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_SHARED_LIBRARY")
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

platforms/cpu/src/CpuCustomGBForce.cpp

@@ -28,7 +28,7 @@
 #include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "CpuCustomGBForce.h"
-#include "gmx_atomic.h"
+#include "openmm/internal/gmx_atomic.h"
 
 using namespace OpenMM;
 using namespace std;

platforms/cpu/src/CpuCustomManyParticleForce.cpp

@@ -32,7 +32,7 @@
 #include "ReferenceTabulatedFunction.h"
 #include "openmm/internal/CustomManyParticleForceImpl.h"
 #include "lepton/CustomFunction.h"
-#include "gmx_atomic.h"
+#include "openmm/internal/gmx_atomic.h"
 
 using namespace OpenMM;
 using namespace std;

platforms/cpu/src/CpuCustomNonbondedForce.cpp

@@ -28,7 +28,7 @@
 #include "SimTKOpenMMUtilities.h"
 #include "ReferenceForce.h"
 #include "CpuCustomNonbondedForce.h"
-#include "gmx_atomic.h"
+#include "openmm/internal/gmx_atomic.h"
 
 using namespace OpenMM;
 using namespace std;

platforms/cpu/src/CpuGBSAOBCForce.cpp

@@ -25,7 +25,7 @@
 #include "CpuGBSAOBCForce.h"
 #include "SimTKOpenMMRealType.h"
 #include "openmm/internal/vectorize.h"
-#include "gmx_atomic.h"
+#include "openmm/internal/gmx_atomic.h"
 #include <algorithm>
 #include <cmath>
 #include <cstdlib>
@@ -279,7 +279,7 @@ void CpuGBSAOBCForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
             fvec4 r = sqrt(r2);
             fvec4 alpha2_ij = radii*bornRadii[atomJ];
             fvec4 D_ij = r2/(4.0f*alpha2_ij);
-            fvec4 expTerm(expf(-D_ij[0]), expf(-D_ij[1]), expf(-D_ij[2]), expf(-D_ij[3]));
+            fvec4 expTerm = exp(-D_ij);
             fvec4 denominator2 = r2 + alpha2_ij*expTerm;
             fvec4 denominator = sqrt(denominator2);
             fvec4 Gpol = (partialChargeI*posJ[3])/denominator; 

platforms/cpu/src/CpuKernelFactory.cpp

@@ -41,6 +41,8 @@ KernelImpl* CpuKernelFactory::createKernelImpl(std::string name, const Platform&
     CpuPlatform::PlatformData& data = CpuPlatform::getPlatformData(context);
     if (name == CalcForcesAndEnergyKernel::Name())
         return new CpuCalcForcesAndEnergyKernel(name, platform, data, context);
+    if (name == CalcHarmonicAngleForceKernel::Name())
+        return new CpuCalcHarmonicAngleForceKernel(name, platform, data);
     if (name == CalcPeriodicTorsionForceKernel::Name())
         return new CpuCalcPeriodicTorsionForceKernel(name, platform, data);
     if (name == CalcRBTorsionForceKernel::Name())

platforms/cpu/src/CpuKernels.cpp

@@ -30,6 +30,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "CpuKernels.h"
+#include "ReferenceAngleBondIxn.h"
 #include "ReferenceBondForce.h"
 #include "ReferenceConstraints.h"
 #include "ReferenceKernelFactory.h"
@@ -47,6 +48,7 @@
 #include "RealVec.h"
 #include "lepton/CompiledExpression.h"
 #include "lepton/CustomFunction.h"
+#include "lepton/Operation.h"
 #include "lepton/Parser.h"
 #include "lepton/ParsedExpression.h"
 
@@ -83,6 +85,17 @@ static ReferenceConstraints& extractConstraints(ContextImpl& context) {
     return *(ReferenceConstraints*) data->constraints;
 }
 
+/**
+ * Make sure an expression doesn't use any undefined variables.
+ */
+static void validateVariables(const Lepton::ExpressionTreeNode& node, const set<string>& variables) {
+    const Lepton::Operation& op = node.getOperation();
+    if (op.getId() == Lepton::Operation::VARIABLE && variables.find(op.getName()) == variables.end())
+        throw OpenMMException("Unknown variable in expression: "+op.getName());
+    for (int i = 0; i < (int) node.getChildren().size(); i++)
+        validateVariables(node.getChildren()[i], variables);
+}
+
 /**
  * Compute the kinetic energy of the system, possibly shifting the velocities in time to account
  * for a leapfrog integrator.
@@ -240,6 +253,64 @@ double CpuCalcForcesAndEnergyKernel::finishComputation(ContextImpl& context, boo
     return referenceKernel.getAs<ReferenceCalcForcesAndEnergyKernel>().finishComputation(context, includeForce, includeEnergy, groups, valid);
 }
 
+CpuCalcHarmonicAngleForceKernel::~CpuCalcHarmonicAngleForceKernel() {
+    if (angleIndexArray != NULL) {
+        for (int i = 0; i < numAngles; i++) {
+            delete[] angleIndexArray[i];
+            delete[] angleParamArray[i];
+        }
+        delete[] angleIndexArray;
+        delete[] angleParamArray;
+    }
+}
+
+void CpuCalcHarmonicAngleForceKernel::initialize(const System& system, const HarmonicAngleForce& force) {
+    numAngles = force.getNumAngles();
+    angleIndexArray = new int*[numAngles];
+    for (int i = 0; i < numAngles; i++)
+        angleIndexArray[i] = new int[3];
+    angleParamArray = new RealOpenMM*[numAngles];
+    for (int i = 0; i < numAngles; i++)
+        angleParamArray[i] = new RealOpenMM[2];
+    for (int i = 0; i < numAngles; ++i) {
+        int particle1, particle2, particle3;
+        double angle, k;
+        force.getAngleParameters(i, particle1, particle2, particle3, angle, k);
+        angleIndexArray[i][0] = particle1;
+        angleIndexArray[i][1] = particle2;
+        angleIndexArray[i][2] = particle3;
+        angleParamArray[i][0] = (RealOpenMM) angle;
+        angleParamArray[i][1] = (RealOpenMM) k;
+    }
+    bondForce.initialize(system.getNumParticles(), numAngles, 3, angleIndexArray, data.threads);
+}
+
+double CpuCalcHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
+    vector<RealVec>& posData = extractPositions(context);
+    vector<RealVec>& forceData = extractForces(context);
+    RealOpenMM energy = 0;
+    ReferenceAngleBondIxn angleBond;
+    bondForce.calculateForce(posData, angleParamArray, forceData, includeEnergy ? &energy : NULL, angleBond);
+    return energy;
+}
+
+void CpuCalcHarmonicAngleForceKernel::copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force) {
+    if (numAngles != force.getNumAngles())
+        throw OpenMMException("updateParametersInContext: The number of angles has changed");
+
+    // Record the values.
+
+    for (int i = 0; i < numAngles; ++i) {
+        int particle1, particle2, particle3;
+        double angle, k;
+        force.getAngleParameters(i, particle1, particle2, particle3, angle, k);
+        if (particle1 != angleIndexArray[i][0] || particle2 != angleIndexArray[i][1] || particle3 != angleIndexArray[i][2])
+            throw OpenMMException("updateParametersInContext: The set of particles in an angle has changed");
+        angleParamArray[i][0] = (RealOpenMM) angle;
+        angleParamArray[i][1] = (RealOpenMM) k;
+    }
+}
+
 CpuCalcPeriodicTorsionForceKernel::~CpuCalcPeriodicTorsionForceKernel() {
     if (torsionIndexArray != NULL) {
         for (int i = 0; i < numTorsions; i++) {
@@ -467,6 +538,7 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
         bonded14ParamArray[i][1] = static_cast<RealOpenMM>(4.0*depth);
         bonded14ParamArray[i][2] = static_cast<RealOpenMM>(charge);
     }
+    bondForce.initialize(system.getNumParticles(), num14, 2, bonded14IndexArray, data.threads);
     
     // Record other parameters.
     
@@ -527,7 +599,7 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
     if (nonbondedMethod != NoCutoff) {
         // Determine whether we need to recompute the neighbor list.
         
-        double padding = 0.15*nonbondedCutoff;
+        double padding = 0.25*nonbondedCutoff;
         bool needRecompute = false;
         double closeCutoff2 = 0.25*padding*padding;
         double farCutoff2 = 0.5*padding*padding;
@@ -599,9 +671,8 @@ double CpuCalcNonbondedForceKernel::execute(ContextImpl& context, bool includeFo
     }
     energy += nonbondedEnergy;
     if (includeDirect) {
-        ReferenceBondForce refBondForce;
         ReferenceLJCoulomb14 nonbonded14;
-        refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, includeEnergy ? &energy : NULL, nonbonded14);
+        bondForce.calculateForce(posData, bonded14ParamArray, forceData, includeEnergy ? &energy : NULL, nonbonded14);
         if (data.isPeriodic)
             energy += dispersionCoefficient/(boxVectors[0][0]*boxVectors[1][1]*boxVectors[2][2]);
     }
@@ -654,6 +725,19 @@ void CpuCalcNonbondedForceKernel::copyParametersToContext(ContextImpl& context,
         dispersionCoefficient = NonbondedForceImpl::calcDispersionCorrection(context.getSystem(), force);
 }
 
+void CpuCalcNonbondedForceKernel::getPMEParameters(double& alpha, int& nx, int& ny, int& nz) const {
+    if (nonbondedMethod != PME)
+        throw OpenMMException("getPMEParametersInContext: This Context is not using PME");
+    if (useOptimizedPme)
+        optimizedPme.getAs<const CalcPmeReciprocalForceKernel>().getPMEParameters(alpha, nx, ny, nz);
+    else {
+        alpha = ewaldAlpha;
+        nx = gridSize[0];
+        ny = gridSize[1];
+        nz = gridSize[2];
+    }
+}
+
 CpuCalcCustomNonbondedForceKernel::CpuCalcCustomNonbondedForceKernel(string name, const Platform& platform, CpuPlatform::PlatformData& data) :
             CalcCustomNonbondedForceKernel(name, platform), data(data), forceCopy(NULL), neighborList(NULL), nonbonded(NULL) {
 }
@@ -724,6 +808,14 @@ void CpuCalcCustomNonbondedForceKernel::initialize(const System& system, const C
         globalParameterNames.push_back(force.getGlobalParameterName(i));
         globalParamValues[force.getGlobalParameterName(i)] = force.getGlobalParameterDefaultValue(i);
     }
+    set<string> variables;
+    variables.insert("r");
+    for (int i = 0; i < numParameters; i++) {
+        variables.insert(parameterNames[i]+"1");
+        variables.insert(parameterNames[i]+"2");
+    }
+    variables.insert(globalParameterNames.begin(), globalParameterNames.end());
+    validateVariables(expression.getRootNode(), variables);
 
     // Delete the custom functions.
 
@@ -937,6 +1029,18 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
     vector<vector<Lepton::CompiledExpression> > valueGradientExpressions(force.getNumComputedValues());
     vector<Lepton::CompiledExpression> valueExpressions;
     vector<Lepton::CompiledExpression> energyExpressions;
+    set<string> particleVariables, pairVariables;
+    pairVariables.insert("r");
+    particleVariables.insert("x");
+    particleVariables.insert("y");
+    particleVariables.insert("z");
+    for (int i = 0; i < numPerParticleParameters; i++) {
+        particleVariables.insert(particleParameterNames[i]);
+        pairVariables.insert(particleParameterNames[i]+"1");
+        pairVariables.insert(particleParameterNames[i]+"2");
+    }
+    particleVariables.insert(globalParameterNames.begin(), globalParameterNames.end());
+    pairVariables.insert(globalParameterNames.begin(), globalParameterNames.end());
     for (int i = 0; i < force.getNumComputedValues(); i++) {
         string name, expression;
         CustomGBForce::ComputationType type;
@@ -945,15 +1049,21 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
         valueExpressions.push_back(ex.createCompiledExpression());
         valueTypes.push_back(type);
         valueNames.push_back(name);
-        if (i == 0)
+        if (i == 0) {
             valueDerivExpressions[i].push_back(ex.differentiate("r").createCompiledExpression());
+            validateVariables(ex.getRootNode(), pairVariables);
+        }
         else {
             valueGradientExpressions[i].push_back(ex.differentiate("x").createCompiledExpression());
             valueGradientExpressions[i].push_back(ex.differentiate("y").createCompiledExpression());
             valueGradientExpressions[i].push_back(ex.differentiate("z").createCompiledExpression());
             for (int j = 0; j < i; j++)
                 valueDerivExpressions[i].push_back(ex.differentiate(valueNames[j]).createCompiledExpression());
+            validateVariables(ex.getRootNode(), particleVariables);
         }
+        particleVariables.insert(name);
+        pairVariables.insert(name+"1");
+        pairVariables.insert(name+"2");
     }
 
     // Parse the expressions for energy terms.
@@ -975,10 +1085,12 @@ void CpuCalcCustomGBForceKernel::initialize(const System& system, const CustomGB
                 energyGradientExpressions[i].push_back(ex.differentiate("x").createCompiledExpression());
                 energyGradientExpressions[i].push_back(ex.differentiate("y").createCompiledExpression());
                 energyGradientExpressions[i].push_back(ex.differentiate("z").createCompiledExpression());
+                validateVariables(ex.getRootNode(), particleVariables);
             }
             else {
                 energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"1").createCompiledExpression());
                 energyDerivExpressions[i].push_back(ex.differentiate(valueNames[j]+"2").createCompiledExpression());
+                validateVariables(ex.getRootNode(), pairVariables);
             }
         }
     }

platforms/cpu/src/CpuLangevinDynamics.cpp

 
-/* Portions copyright (c) 2006-2013 Stanford University and Simbios.
+/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
  * Authors: Peter Eastman
  * Contributors: 
  *
@@ -49,6 +49,16 @@ public:
     CpuLangevinDynamics& owner;
 };
 
+class CpuLangevinDynamics::Update3Task : public ThreadPool::Task {
+public:
+    Update3Task(CpuLangevinDynamics& owner) : owner(owner) {
+    }
+    void execute(ThreadPool& threads, int threadIndex) {
+        owner.threadUpdate3(threadIndex);
+    }
+    CpuLangevinDynamics& owner;
+};
+
 CpuLangevinDynamics::CpuLangevinDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM tau, RealOpenMM temperature, ThreadPool& threads, CpuRandom& random) : 
            ReferenceStochasticDynamics(numberOfAtoms, deltaT, tau, temperature), threads(threads), random(random) {
 }
@@ -92,6 +102,23 @@ void CpuLangevinDynamics::updatePart2(int numberOfAtoms, vector<RealVec>& atomCo
     threads.waitForThreads();
 }
 
+void CpuLangevinDynamics::updatePart3(int numberOfAtoms, vector<RealVec>& atomCoordinates, vector<RealVec>& velocities,
+                                       vector<RealOpenMM>& inverseMasses, vector<RealVec>& xPrime) {
+    // Record the parameters for the threads.
+    
+    this->numberOfAtoms = numberOfAtoms;
+    this->atomCoordinates = &atomCoordinates[0];
+    this->velocities = &velocities[0];
+    this->inverseMasses = &inverseMasses[0];
+    this->xPrime = &xPrime[0];
+    
+    // Signal the threads to start running and wait for them to finish.
+    
+    Update3Task task(*this);
+    threads.execute(task);
+    threads.waitForThreads();
+}
+
 void CpuLangevinDynamics::threadUpdate1(int threadIndex) {
     const RealOpenMM tau = getTau();
     const RealOpenMM vscale = EXP(-getDeltaT()/tau);
@@ -122,3 +149,16 @@ void CpuLangevinDynamics::threadUpdate2(int threadIndex) {
         }
    }
 }
+
+void CpuLangevinDynamics::threadUpdate3(int threadIndex) {
+   const RealOpenMM invStepSize = 1.0/getDeltaT();
+    int start = threadIndex*numberOfAtoms/threads.getNumThreads();
+    int end = (threadIndex+1)*numberOfAtoms/threads.getNumThreads();
+
+   for (int i = start; i < end; ++i)
+       if (inverseMasses[i] != 0.0) {
+            velocities[i] = (xPrime[i]-atomCoordinates[i])*invStepSize;
+            atomCoordinates[i] = xPrime[i];
+       }
+}
+

platforms/cpu/src/CpuNeighborList.cpp

@@ -59,22 +59,25 @@ public:
  */
 class CpuNeighborList::Voxels {
 public:
-    Voxels(int blockSize, float vsy, float vsz, float miny, float maxy, float minz, float maxz, const RealVec* periodicBoxVectors, bool usePeriodic) :
-            blockSize(blockSize), voxelSizeY(vsy), voxelSizeZ(vsz), miny(miny), maxy(maxy), minz(minz), maxz(maxz), periodicBoxVectors(periodicBoxVectors), usePeriodic(usePeriodic) {
-        periodicBoxSize[0] = (float) periodicBoxVectors[0][0];
-        periodicBoxSize[1] = (float) periodicBoxVectors[1][1];
-        periodicBoxSize[2] = (float) periodicBoxVectors[2][2];
-        recipBoxSize[0] = (float) (1/periodicBoxVectors[0][0]);
-        recipBoxSize[1] = (float) (1/periodicBoxVectors[1][1]);
-        recipBoxSize[2] = (float) (1/periodicBoxVectors[2][2]);
-        triclinic = (periodicBoxVectors[0][1] != 0.0 || periodicBoxVectors[0][2] != 0.0 ||
-                     periodicBoxVectors[1][0] != 0.0 || periodicBoxVectors[1][2] != 0.0 ||
-                     periodicBoxVectors[2][0] != 0.0 || periodicBoxVectors[2][1] != 0.0);
+    Voxels(int blockSize, float vsy, float vsz, float miny, float maxy, float minz, float maxz, const RealVec* boxVectors, bool usePeriodic) :
+            blockSize(blockSize), voxelSizeY(vsy), voxelSizeZ(vsz), miny(miny), maxy(maxy), minz(minz), maxz(maxz), usePeriodic(usePeriodic) {
+        for (int i = 0; i < 3; i++)
+            for (int j = 0; j < 3; j++)
+                periodicBoxVectors[i][j] = (float) boxVectors[i][j];
+        periodicBoxSize[0] = (float) boxVectors[0][0];
+        periodicBoxSize[1] = (float) boxVectors[1][1];
+        periodicBoxSize[2] = (float) boxVectors[2][2];
+        recipBoxSize[0] = (float) (1/boxVectors[0][0]);
+        recipBoxSize[1] = (float) (1/boxVectors[1][1]);
+        recipBoxSize[2] = (float) (1/boxVectors[2][2]);
+        triclinic = (boxVectors[0][1] != 0.0 || boxVectors[0][2] != 0.0 ||
+                     boxVectors[1][0] != 0.0 || boxVectors[1][2] != 0.0 ||
+                     boxVectors[2][0] != 0.0 || boxVectors[2][1] != 0.0);
         if (usePeriodic) {
-            ny = (int) floorf(periodicBoxVectors[1][1]/voxelSizeY+0.5f);
-            nz = (int) floorf(periodicBoxVectors[2][2]/voxelSizeZ+0.5f);
-            voxelSizeY = periodicBoxVectors[1][1]/ny;
-            voxelSizeZ = periodicBoxVectors[2][2]/nz;
+            ny = (int) floorf(boxVectors[1][1]/voxelSizeY+0.5f);
+            nz = (int) floorf(boxVectors[2][2]/voxelSizeZ+0.5f);
+            voxelSizeY = boxVectors[1][1]/ny;
+            voxelSizeZ = boxVectors[2][2]/nz;
         }
         else {
             ny = max(1, (int) floorf((maxy-miny)/voxelSizeY+0.5f));
@@ -110,12 +113,10 @@ public:
     }
     
     /**
-     * Find the index of the first particle in voxel (y,z) whose x coordinate in >= the specified value.
+     * Find the index of the first particle in voxel (y,z) whose x coordinate is >= the specified value.
      */
-    int findLowerBound(int y, int z, double x) const {
+    int findLowerBound(int y, int z, double x, int lower, int upper) const {
         const vector<pair<float, int> >& bin = bins[y][z];
-        int lower = 0;
-        int upper = bin.size();
         while (lower < upper) {
             int middle = (lower+upper)/2;
             if (bin[middle].first < x)
@@ -127,12 +128,10 @@ public:
     }
     
     /**
-     * Find the index of the first particle in voxel (y,z) whose x coordinate in greater than the specified value.
+     * Find the index of the first particle in voxel (y,z) whose x coordinate is greater than the specified value.
      */
-    int findUpperBound(int y, int z, double x) const {
+    int findUpperBound(int y, int z, double x, int lower, int upper) const {
         const vector<pair<float, int> >& bin = bins[y][z];
-        int lower = 0;
-        int upper = bin.size();
         while (lower < upper) {
             int middle = (lower+upper)/2;
             if (bin[middle].first > x)
@@ -208,7 +207,7 @@ public:
 
             // Loop over voxels along the y axis.
 
-            int boxz = (int) floor((float) z/nz);
+            float boxz = floor((float) z/nz);
             int starty = centerVoxelIndex.y-dIndexY;
             int endy = centerVoxelIndex.y+dIndexY;
             float yoffset = (float) (usePeriodic ? boxz*periodicBoxVectors[2][1] : 0);
@@ -225,7 +224,7 @@ public:
                 voxelIndex.y = y;
                 if (usePeriodic)
                     voxelIndex.y = (y < 0 ? y+ny : (y >= ny ? y-ny : y));
-                int boxy = (int) floor((float) y/ny);
+                float boxy = floor((float) y/ny);
                 float xoffset = (float) (usePeriodic ? boxy*periodicBoxVectors[1][0]+boxz*periodicBoxVectors[2][0] : 0);
                 
                 // Identify the range of atoms within this bin we need to search.  When using periodic boundary
@@ -261,30 +260,34 @@ public:
                 int numRanges;
                 int rangeStart[2];
                 int rangeEnd[2];
-                rangeStart[0] = findLowerBound(voxelIndex.y, voxelIndex.z, minx);
+                int binSize = bins[voxelIndex.y][voxelIndex.z].size();
+                rangeStart[0] = findLowerBound(voxelIndex.y, voxelIndex.z, minx, 0, binSize);
                 if (needPeriodic) {
                     numRanges = 2;
-                    rangeEnd[0] = findUpperBound(voxelIndex.y, voxelIndex.z, maxx);
-                    if (rangeStart[0] > 0) {
+                    rangeEnd[0] = findUpperBound(voxelIndex.y, voxelIndex.z, maxx, rangeStart[0], binSize);
+                    if (rangeStart[0] > 0 && rangeEnd[0] < binSize)
+                        numRanges = 1;
+                    else if (rangeStart[0] > 0) {
                         rangeStart[1] = 0;
-                        rangeEnd[1] = min(findUpperBound(voxelIndex.y, voxelIndex.z, maxx-periodicBoxSize[0]), rangeStart[0]);
+                        rangeEnd[1] = min(findUpperBound(voxelIndex.y, voxelIndex.z, maxx-periodicBoxSize[0], 0, rangeStart[0]), rangeStart[0]);
                     }
                     else {
-                        rangeStart[1] = max(findLowerBound(voxelIndex.y, voxelIndex.z, minx+periodicBoxSize[0]), rangeEnd[0]);
+                        rangeStart[1] = max(findLowerBound(voxelIndex.y, voxelIndex.z, minx+periodicBoxSize[0], rangeEnd[0], binSize), rangeEnd[0]);
                         rangeEnd[1] = bins[voxelIndex.y][voxelIndex.z].size();
                     }
                 }
                 else {
                     numRanges = 1;
-                    rangeEnd[0] = findUpperBound(voxelIndex.y, voxelIndex.z, maxx);
+                    rangeEnd[0] = findUpperBound(voxelIndex.y, voxelIndex.z, maxx, rangeStart[0], binSize);
                 }
                 bool periodicRectangular = (needPeriodic && !triclinic);
                 
                 // Loop over atoms and check to see if they are neighbors of this block.
                 
+                const vector<pair<float, int> >& voxelBins = bins[voxelIndex.y][voxelIndex.z];
                 for (int range = 0; range < numRanges; range++) {
                     for (int item = rangeStart[range]; item < rangeEnd[range]; item++) {
-                        const int sortedIndex = bins[voxelIndex.y][voxelIndex.z][item].second;
+                        const int sortedIndex = voxelBins[item].second;
 
                         // Avoid duplicate entries.
                         if (sortedIndex >= lastSortedIndex)
@@ -361,7 +364,7 @@ private:
     int ny, nz;
     float periodicBoxSize[3], recipBoxSize[3];
     bool triclinic;
-    const RealVec* periodicBoxVectors;
+    float periodicBoxVectors[3][3];
     const bool usePeriodic;
     vector<vector<vector<pair<float, int> > > > bins;
 };
@@ -444,6 +447,7 @@ void CpuNeighborList::computeNeighborList(int numAtoms, const AlignedArray<float
 
     // Signal the threads to start running and wait for them to finish.
     
+    gmx_atomic_set(&atomicCounter, 0);
     threads.resumeThreads();
     threads.waitForThreads();
     
@@ -500,7 +504,11 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI
     vector<int> blockAtoms;
     vector<float> blockAtomX(blockSize), blockAtomY(blockSize), blockAtomZ(blockSize);
     vector<VoxelIndex> atomVoxelIndex;
-    for (int i = threadIndex; i < numBlocks; i += numThreads) {
+    while (true) {
+        int i = gmx_atomic_fetch_add(&atomicCounter, 1);
+        if (i >= numBlocks)
+            break;
+
         // Find the atoms in this block and compute their bounding box.
         
         int firstIndex = blockSize*i;
@@ -532,14 +540,24 @@ void CpuNeighborList::threadComputeNeighborList(ThreadPool& threads, int threadI
 
         // Record the exclusions for this block.
 
+        map<int, char> atomFlags;
         for (int j = 0; j < atomsInBlock; j++) {
             const set<int>& atomExclusions = (*exclusions)[sortedAtoms[firstIndex+j]];
             char mask = 1<<j;
-            for (int k = 0; k < (int) blockNeighbors[i].size(); k++) {
-                int atomIndex = blockNeighbors[i][k];
-                if (atomExclusions.find(atomIndex) != atomExclusions.end())
-                    blockExclusions[i][k] |= mask;
+            for (set<int>::const_iterator iter = atomExclusions.begin(); iter != atomExclusions.end(); ++iter) {
+                map<int, char>::iterator thisAtomFlags = atomFlags.find(*iter);
+                if (thisAtomFlags == atomFlags.end())
+                    atomFlags[*iter] = mask;
+                else
+                    thisAtomFlags->second |= mask;
+            }
         }
+        int numNeighbors = blockNeighbors[i].size();
+        for (int k = 0; k < numNeighbors; k++) {
+            int atomIndex = blockNeighbors[i][k];
+            map<int, char>::iterator thisAtomFlags = atomFlags.find(atomIndex);
+            if (thisAtomFlags != atomFlags.end())
+                blockExclusions[i][k] |= thisAtomFlags->second;
         }
     }
 }

platforms/cpu/src/CpuNonbondedForce.cpp

@@ -28,7 +28,7 @@
 #include "CpuNonbondedForce.h"
 #include "ReferenceForce.h"
 #include "ReferencePME.h"
-#include "gmx_atomic.h"
+#include "openmm/internal/gmx_atomic.h"
 #include <algorithm>
 
 // In case we're using some primitive version of Visual Studio this will
@@ -322,6 +322,14 @@ void CpuNonbondedForce::calculateDirectIxn(int numberOfAtoms, float* posq, const
     threads.execute(task);
     threads.waitForThreads();
     
+    // Signal the threads to subtract the exclusions.
+    
+    if (ewald || pme) {
+        gmx_atomic_set(&counter, 0);
+        threads.resumeThreads();
+        threads.waitForThreads();
+    }
+    
     // Combine the energies from all the threads.
     
     if (totalEnergy != NULL) {
@@ -354,8 +362,16 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
 
         // Now subtract off the exclusions, since they were implicitly included in the reciprocal space sum.
 
-        for (int i = threadIndex; i < numberOfAtoms; i += numThreads) {
+        threads.syncThreads();
+        const int groupSize = max(1, numberOfAtoms/(10*numThreads));
+        while (true) {
+            int start = gmx_atomic_fetch_add(reinterpret_cast<gmx_atomic_t*>(atomicCounter), groupSize);
+            if (start >= numberOfAtoms)
+                break;
+            int end = min(start+groupSize, numberOfAtoms);
+            for (int i = start; i < end; i++) {
                fvec4 posI((float) atomCoordinates[i][0], (float) atomCoordinates[i][1], (float) atomCoordinates[i][2], 0.0f);
+                float scaledChargeI = (float) (ONE_4PI_EPS0*posq[4*i+3]);
                 for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
                     if (*iter > i) {
                         int j = *iter;
@@ -364,18 +380,19 @@ void CpuNonbondedForce::threadComputeDirect(ThreadPool& threads, int threadIndex
                         float r2;
                         getDeltaR(posJ, posI, deltaR, r2, false, boxSize, invBoxSize);
                         float r = sqrtf(r2);
-                    float inverseR = 1/r;
-                    float chargeProd = ONE_4PI_EPS0*posq[4*i+3]*posq[4*j+3];
                         float alphaR = alphaEwald*r;
                         float erfAlphaR = erf(alphaR);
                         if (erfAlphaR > 1e-6f) {
-                        float dEdR = (float) (chargeProd * inverseR * inverseR * inverseR);
-                        dEdR = (float) (dEdR * (erfAlphaR-TWO_OVER_SQRT_PI*alphaR*exp(-alphaR*alphaR)));
+                            float inverseR = 1/r;
+                            float chargeProdOverR = scaledChargeI*posq[4*j+3]*inverseR;
+                            float dEdR = chargeProdOverR*inverseR*inverseR;
+                            dEdR = dEdR * (erfAlphaR-(float)TWO_OVER_SQRT_PI*alphaR*(float)exp(-alphaR*alphaR));
                             fvec4 result = deltaR*dEdR;
                             (fvec4(forces+4*i)-result).store(forces+4*i);
                             (fvec4(forces+4*j)+result).store(forces+4*j);
                             if (includeEnergy)
-                            threadEnergy[threadIndex] -= chargeProd*inverseR*erfAlphaR;
+                                threadEnergy[threadIndex] -= chargeProdOverR*erfAlphaR;
+                        }
                     }
                 }
             }

platforms/cpu/src/CpuPlatform.cpp

@@ -61,6 +61,7 @@ map<const ContextImpl*, CpuPlatform::PlatformData*> CpuPlatform::contextData;
 CpuPlatform::CpuPlatform() {
     CpuKernelFactory* factory = new CpuKernelFactory();
     registerKernelFactory(CalcForcesAndEnergyKernel::Name(), factory);
+    registerKernelFactory(CalcHarmonicAngleForceKernel::Name(), factory);
     registerKernelFactory(CalcPeriodicTorsionForceKernel::Name(), factory);
     registerKernelFactory(CalcRBTorsionForceKernel::Name(), factory);
     registerKernelFactory(CalcNonbondedForceKernel::Name(), factory);

platforms/cpu/src/CpuSETTLE.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) 2013 Stanford University and the Authors.           *
+ * Portions copyright (c) 2013-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -30,6 +30,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "CpuSETTLE.h"
+#include "openmm/internal/gmx_atomic.h"
 
 using namespace OpenMM;
 using namespace std;
@@ -39,10 +40,14 @@ public:
     ApplyToPositionsTask(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses,
             RealOpenMM tolerance, vector<ReferenceSETTLEAlgorithm*>& threadSettle) : atomCoordinates(atomCoordinates), atomCoordinatesP(atomCoordinatesP),
             inverseMasses(inverseMasses), tolerance(tolerance), threadSettle(threadSettle) {
+        gmx_atomic_set(&atomicCounter, 0);
     }
     void execute(ThreadPool& threads, int threadIndex) {
-        if (threadIndex < threadSettle.size()) {
-            threadSettle[threadIndex]->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
+        while (true) {
+            int index = gmx_atomic_fetch_add(&atomicCounter, 1);
+            if (index >= threadSettle.size())
+                break;
+            threadSettle[index]->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
         }
     }
     vector<OpenMM::RealVec>& atomCoordinates;
@@ -50,6 +55,7 @@ public:
     vector<RealOpenMM>& inverseMasses;
     RealOpenMM tolerance;
     vector<ReferenceSETTLEAlgorithm*>& threadSettle;
+    gmx_atomic_t atomicCounter;
 };
 
 class CpuSETTLE::ApplyToVelocitiesTask : public ThreadPool::Task {
@@ -57,10 +63,14 @@ public:
     ApplyToVelocitiesTask(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses,
             RealOpenMM tolerance, vector<ReferenceSETTLEAlgorithm*>& threadSettle) : atomCoordinates(atomCoordinates), velocities(velocities),
             inverseMasses(inverseMasses), tolerance(tolerance), threadSettle(threadSettle) {
+        gmx_atomic_set(&atomicCounter, 0);
     }
     void execute(ThreadPool& threads, int threadIndex) {
-        if (threadIndex < threadSettle.size()) {
-            threadSettle[threadIndex]->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
+        while (true) {
+            int index = gmx_atomic_fetch_add(&atomicCounter, 1);
+            if (index >= threadSettle.size())
+                break;
+            threadSettle[index]->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
         }
     }
     vector<OpenMM::RealVec>& atomCoordinates;
@@ -68,17 +78,18 @@ public:
     vector<RealOpenMM>& inverseMasses;
     RealOpenMM tolerance;
     vector<ReferenceSETTLEAlgorithm*>& threadSettle;
+    gmx_atomic_t atomicCounter;
 };
 
 CpuSETTLE::CpuSETTLE(const System& system, const ReferenceSETTLEAlgorithm& settle, ThreadPool& threads) : threads(threads) {
-    int numThreads = threads.getNumThreads();
+    int numBlocks = 10*threads.getNumThreads();
     int numClusters = settle.getNumClusters();
     vector<RealOpenMM> mass(system.getNumParticles());
     for (int i = 0; i < system.getNumParticles(); i++)
         mass[i] = system.getParticleMass(i);
-    for (int i = 0; i < numThreads; i++) {
-        int start = i*numClusters/numThreads;
-        int end = (i+1)*numClusters/numThreads;
+    for (int i = 0; i < numBlocks; i++) {
+        int start = i*numClusters/numBlocks;
+        int end = (i+1)*numClusters/numBlocks;
         if (start != end) {
             int numThreadClusters = end-start;
             vector<int> atom1(numThreadClusters), atom2(numThreadClusters), atom3(numThreadClusters);

platforms/cpu/staticTarget/CMakeLists.txt

@@ -17,6 +17,6 @@ ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${AP
 
 TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}_static ${PTHREADS_LIB_STATIC})
 #-DPTW32_STATIC_LIB only works for the windows pthreads.
-SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")
+SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})

platforms/cpu/tests/CMakeLists.txt

@@ -23,7 +23,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
     ELSE (OPENMM_BUILD_SHARED_LIB)
         TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET})
     ENDIF (OPENMM_BUILD_SHARED_LIB)
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
 
 ENDFOREACH(TEST_PROG ${TEST_PROGS})

platforms/cpu/tests/CpuTests.h

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#ifdef WIN32
+  #define _USE_MATH_DEFINES // Needed to get M_PI
+#endif
+#include "CpuPlatform.h"
+#include <cstdlib>
+#include <iostream>
+
+OpenMM::CpuPlatform platform;
+
+void initializeTests(int argc, char* argv[]) {
+    if (!OpenMM::CpuPlatform::isProcessorSupported()) {
+        std::cout << "CPU is not supported.  Exiting." << std::endl;
+        exit(0);
+    }
+}

platforms/cpu/tests/TestCpuCheckpoints.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2012-2015 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * 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 "CpuTests.h"
+#include "TestCheckpoints.h"
+
+void testCheckpoint() {
+    const int numParticles = 100;
+    const double boxSize = 5.0;
+    const double temperature = 200.0;
+    System system;
+    system.addForce(new AndersenThermostat(0.0, 100.0));
+    NonbondedForce* nonbonded = new NonbondedForce();
+    system.addForce(nonbonded);
+    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    vector<Vec3> positions(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        nonbonded->addParticle(i%2 == 0 ? 0.1 : -0.1, 0.2, 0.1);
+        bool clash;
+        do {
+            clash = false;
+            positions[i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
+            for (int j = 0; j < i; j++) {
+                Vec3 delta = positions[i]-positions[j];
+                if (sqrt(delta.dot(delta)) < 0.1)
+                    clash = true;
+            }
+        } while (clash);
+    }
+    VerletIntegrator integrator(0.001);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
+    context.setParameter(AndersenThermostat::Temperature(), temperature);
+    
+    // Run for a little while.
+    
+    integrator.step(100);
+    
+    // Record the current state and make a checkpoint.
+    
+    State s1 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    stringstream stream1(ios_base::out | ios_base::in | ios_base::binary);
+    context.createCheckpoint(stream1);
+    
+    // Continue the simulation for a few more steps and record the state again.
+    
+    integrator.step(10);
+    State s2 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    
+    // Restore from the checkpoint and see if everything gets restored correctly.
+    
+    context.setPeriodicBoxVectors(Vec3(2*boxSize, 0, 0), Vec3(0, 2*boxSize, 0), Vec3(0, 0, 2*boxSize));
+    context.setParameter(AndersenThermostat::Temperature(), temperature+10);
+    context.loadCheckpoint(stream1);
+    State s3 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    compareStates(s1, s3);
+    
+    // Now simulate from there and see if the trajectory is identical.
+    
+    integrator.step(10);
+    State s4 = context.getState(State::Positions | State::Velocities | State::Parameters);
+    compareStates(s2, s4);
+}
+
+void runPlatformTests() {
+    testCheckpoint();
+}

platforms/cpu/tests/TestCpuCustomGBForce.cpp

-
 /* -------------------------------------------------------------------------- *
  *                                   OpenMM                                   *
  * -------------------------------------------------------------------------- *
@@ -7,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -30,454 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests all the different force terms in the reference implementation of CustomGBForce.
- */
-
-#include "openmm/internal/AssertionUtilities.h"
-#include "sfmt/SFMT.h"
-#include "openmm/Context.h"
-#include "CpuPlatform.h"
-#include "openmm/CustomGBForce.h"
-#include "openmm/GBSAOBCForce.h"
-#include "openmm/GBVIForce.h"
-#include "openmm/OpenMMException.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include <iostream>
-#include <vector>
-#include <algorithm>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-void testOBC(GBSAOBCForce::NonbondedMethod obcMethod, CustomGBForce::NonbondedMethod customMethod) {
-    const int numMolecules = 70;
-    const int numParticles = numMolecules*2;
-    const double boxSize = 10.0;
-    const double cutoff = 2.0;
-    CpuPlatform platform;
-
-    // Create two systems: one with a GBSAOBCForce, and one using a CustomGBForce to implement the same interaction.
-
-    System standardSystem;
-    System customSystem;
-    for (int i = 0; i < numParticles; i++) {
-        standardSystem.addParticle(1.0);
-        customSystem.addParticle(1.0);
-    }
-    standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
-    customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
-    GBSAOBCForce* obc = new GBSAOBCForce();
-    CustomGBForce* custom = new CustomGBForce();
-    obc->setCutoffDistance(cutoff);
-    custom->setCutoffDistance(cutoff);
-    custom->addPerParticleParameter("q");
-    custom->addPerParticleParameter("radius");
-    custom->addPerParticleParameter("scale");
-    custom->addGlobalParameter("solventDielectric", obc->getSolventDielectric());
-    custom->addGlobalParameter("soluteDielectric", obc->getSoluteDielectric());
-    custom->addComputedValue("I", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
-                                  "U=r+sr2;"
-                                  "C=2*(1/or1-1/L)*step(sr2-r-or1);"
-                                  "L=max(or1, D);"
-                                  "D=abs(r-sr2);"
-                                  "sr2 = scale2*or2;"
-                                  "or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
-    custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
-                                  "psi=I*or; or=radius-0.009", CustomGBForce::SingleParticle);
-    custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935485*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
-    string invCutoffString = "";
-    if (obcMethod != GBSAOBCForce::NoCutoff) {
-        stringstream s;
-        s<<(1.0/cutoff);
-        invCutoffString = s.str();
-    }
-    custom->addEnergyTerm("138.935485*(1/soluteDielectric-1/solventDielectric)*q1*q2*("+invCutoffString+"-1/f);"
-                          "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
-    vector<Vec3> positions(numParticles);
-    vector<Vec3> velocities(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    vector<double> params(3);
-    for (int i = 0; i < numMolecules; i++) {
-        if (i < numMolecules/2) {
-            obc->addParticle(1.0, 0.2, 0.5);
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.5;
-            custom->addParticle(params);
-            obc->addParticle(-1.0, 0.1, 0.5);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        else {
-            obc->addParticle(1.0, 0.2, 0.8);
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.8;
-            custom->addParticle(params);
-            obc->addParticle(-1.0, 0.1, 0.8);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
-        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
-        velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-    }
-    obc->setNonbondedMethod(obcMethod);
-    custom->setNonbondedMethod(customMethod);
-    standardSystem.addForce(obc);
-    customSystem.addForce(custom);
-    VerletIntegrator integrator1(0.01);
-    VerletIntegrator integrator2(0.01);
-    Context context1(standardSystem, integrator1, platform);
-    context1.setPositions(positions);
-    context1.setVelocities(velocities);
-    State state1 = context1.getState(State::Forces | State::Energy);
-    Context context2(customSystem, integrator2, platform);
-    context2.setPositions(positions);
-    context2.setVelocities(velocities);
-    State state2 = context2.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
-    for (int i = 0; i < numParticles; i++) {
-        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
-    }
-    
-    // Try changing the particle parameters and make sure it's still correct.
-    
-    for (int i = 0; i < numMolecules/2; i++) {
-        obc->setParticleParameters(2*i, 1.1, 0.3, 0.6);
-        params[0] = 1.1;
-        params[1] = 0.3;
-        params[2] = 0.6;
-        custom->setParticleParameters(2*i, params);
-        obc->setParticleParameters(2*i+1, -1.1, 0.2, 0.4);
-        params[0] = -1.1;
-        params[1] = 0.2;
-        params[2] = 0.4;
-        custom->setParticleParameters(2*i+1, params);
-    }
-    obc->updateParametersInContext(context1);
-    custom->updateParametersInContext(context2);
-    state1 = context1.getState(State::Forces | State::Energy);
-    state2 = context2.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
-    for (int i = 0; i < numParticles; i++) {
-        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
-    }
-}
-
-void testMembrane() {
-    const int numMolecules = 70;
-    const int numParticles = numMolecules*2;
-    const double boxSize = 10.0;
-    CpuPlatform platform;
-
-    // Create a system with an implicit membrane.
-
-    System system;
-    for (int i = 0; i < numParticles; i++) {
-        system.addParticle(1.0);
-    }
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0.0, 0.0), Vec3(0.0, boxSize, 0.0), Vec3(0.0, 0.0, boxSize));
-    CustomGBForce* custom = new CustomGBForce();
-    custom->setCutoffDistance(2.0);
-    custom->addPerParticleParameter("q");
-    custom->addPerParticleParameter("radius");
-    custom->addPerParticleParameter("scale");
-    custom->addGlobalParameter("thickness", 3);
-    custom->addGlobalParameter("solventDielectric", 78.3);
-    custom->addGlobalParameter("soluteDielectric", 1);
-    custom->addComputedValue("Imol", "step(r+sr2-or1)*0.5*(1/L-1/U+0.25*(1/U^2-1/L^2)*(r-sr2*sr2/r)+0.5*log(L/U)/r+C);"
-                             "U=r+sr2;"
-                             "C=2*(1/or1-1/L)*step(sr2-r-or1);"
-                             "L=max(or1, D);"
-                             "D=abs(r-sr2);"
-                             "sr2 = scale2*or2;"
-                             "or1 = radius1-0.009; or2 = radius2-0.009", CustomGBForce::ParticlePairNoExclusions);
-    custom->addComputedValue("Imem", "(1/radius+2*log(2)/thickness)/(1+exp(7.2*(abs(z)+radius-0.5*thickness)))", CustomGBForce::SingleParticle);
-    custom->addComputedValue("B", "1/(1/or-tanh(1*psi-0.8*psi^2+4.85*psi^3)/radius);"
-                             "psi=max(Imol,Imem)*or; or=radius-0.009", CustomGBForce::SingleParticle);
-    custom->addEnergyTerm("28.3919551*(radius+0.14)^2*(radius/B)^6-0.5*138.935456*(1/soluteDielectric-1/solventDielectric)*q^2/B", CustomGBForce::SingleParticle);
-    custom->addEnergyTerm("-138.935456*(1/soluteDielectric-1/solventDielectric)*q1*q2/f;"
-                          "f=sqrt(r^2+B1*B2*exp(-r^2/(4*B1*B2)))", CustomGBForce::ParticlePairNoExclusions);
-    vector<Vec3> positions(numParticles);
-    vector<Vec3> velocities(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    vector<double> params(3);
-    for (int i = 0; i < numMolecules; i++) {
-        if (i < numMolecules/2) {
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.5;
-            custom->addParticle(params);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        else {
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.8;
-            custom->addParticle(params);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            custom->addParticle(params);
-        }
-        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
-        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
-        velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-    }
-    system.addForce(custom);
-    VerletIntegrator integrator(0.01);
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    context.setVelocities(velocities);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-
-    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-    double norm = 0.0;
-    for (int i = 0; i < (int) forces.size(); ++i)
-        norm += forces[i].dot(forces[i]);
-    norm = std::sqrt(norm);
-    const double stepSize = 1e-2;
-    double step = 0.5*stepSize/norm;
-    vector<Vec3> positions2(numParticles), positions3(numParticles);
-    for (int i = 0; i < (int) positions.size(); ++i) {
-        Vec3 p = positions[i];
-        Vec3 f = forces[i];
-        positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-        positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
-    }
-    context.setPositions(positions2);
-    State state2 = context.getState(State::Energy);
-    context.setPositions(positions3);
-    State state3 = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
-}
-
-void testTabulatedFunction() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomGBForce* force = new CustomGBForce();
-    force->addComputedValue("a", "0", CustomGBForce::ParticlePair);
-    force->addEnergyTerm("fn(r)+1", CustomGBForce::ParticlePair);
-    force->addParticle(vector<double>());
-    force->addParticle(vector<double>());
-    vector<double> table;
-    for (int i = 0; i < 21; i++)
-        table.push_back(std::sin(0.25*i));
-    force->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
-    system.addForce(force);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (int i = 1; i < 30; i++) {
-        double x = (7.0/30.0)*i;
-        positions[1] = Vec3(x, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        double force = (x < 1.0 || x > 6.0 ? 0.0 : -std::cos(x-1.0));
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : std::sin(x-1.0))+1.0;
-        ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
-        ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
-    }
-}
-
-void testMultipleChainRules() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomGBForce* force = new CustomGBForce();
-    force->addComputedValue("a", "2*r", CustomGBForce::ParticlePair);
-    force->addComputedValue("b", "a+1", CustomGBForce::SingleParticle);
-    force->addComputedValue("c", "2*b+a", CustomGBForce::SingleParticle);
-    force->addEnergyTerm("0.1*a+1*b+10*c", CustomGBForce::SingleParticle); // 0.1*(2*r) + 2*r+1 + 10*(3*a+2) = 0.2*r + 2*r+1 + 40*r+20+20*r = 62.2*r+21
-    force->addParticle(vector<double>());
-    force->addParticle(vector<double>());
-    system.addForce(force);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (int i = 1; i < 5; i++) {
-        positions[1] = Vec3(i, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(124.4, 0, 0), forces[0], 1e-4);
-        ASSERT_EQUAL_VEC(Vec3(-124.4, 0, 0), forces[1], 1e-4);
-        ASSERT_EQUAL_TOL(2*(62.2*i+21), state.getPotentialEnergy(), 0.02);
-    }
-}
-
-void testPositionDependence() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomGBForce* force = new CustomGBForce();
-    force->addComputedValue("a", "r", CustomGBForce::ParticlePair);
-    force->addComputedValue("b", "a+x*y", CustomGBForce::SingleParticle);
-    force->addEnergyTerm("b*z", CustomGBForce::SingleParticle);
-    force->addEnergyTerm("b1+b2", CustomGBForce::ParticlePair); // = 2*r+x1*y1+x2*y2
-    force->addParticle(vector<double>());
-    force->addParticle(vector<double>());
-    system.addForce(force);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    vector<Vec3> forces(2);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    for (int i = 0; i < 5; i++) {
-        positions[0] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        positions[1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        Vec3 delta = positions[0]-positions[1];
-        double r = sqrt(delta.dot(delta));
-        double energy = 2*r+positions[0][0]*positions[0][1]+positions[1][0]*positions[1][1];
-        for (int j = 0; j < 2; j++)
-            energy += positions[j][2]*(r+positions[j][0]*positions[j][1]);
-        Vec3 force1(-(1+positions[0][2])*delta[0]/r-(1+positions[0][2])*positions[0][1]-(1+positions[1][2])*delta[0]/r,
-                    -(1+positions[0][2])*delta[1]/r-(1+positions[0][2])*positions[0][0]-(1+positions[1][2])*delta[1]/r,
-                    -(1+positions[0][2])*delta[2]/r-(r+positions[0][0]*positions[0][1])-(1+positions[1][2])*delta[2]/r);
-        Vec3 force2((1+positions[0][2])*delta[0]/r+(1+positions[1][2])*delta[0]/r-(1+positions[1][2])*positions[1][1],
-                    (1+positions[0][2])*delta[1]/r+(1+positions[1][2])*delta[1]/r-(1+positions[1][2])*positions[1][0],
-                    (1+positions[0][2])*delta[2]/r+(1+positions[1][2])*delta[2]/r-(r+positions[1][0]*positions[1][1]));
-        ASSERT_EQUAL_VEC(force1, forces[0], 1e-4);
-        ASSERT_EQUAL_VEC(force2, forces[1], 1e-4);
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
-
-        // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-        double norm = 0.0;
-        for (int i = 0; i < (int) forces.size(); ++i)
-            norm += forces[i].dot(forces[i]);
-        norm = std::sqrt(norm);
-        const double stepSize = 1e-3;
-        double step = 0.5*stepSize/norm;
-        vector<Vec3> positions2(2), positions3(2);
-        for (int i = 0; i < (int) positions.size(); ++i) {
-            Vec3 p = positions[i];
-            Vec3 f = forces[i];
-            positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-            positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
-        }
-        context.setPositions(positions2);
-        State state2 = context.getState(State::Energy);
-        context.setPositions(positions3);
-        State state3 = context.getState(State::Energy);
-        ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-3);
-    }
-}
-
-void testExclusions() {
-    CpuPlatform platform;
-    for (int i = 3; i < 4; i++) {
-        System system;
-        system.addParticle(1.0);
-        system.addParticle(1.0);
-        VerletIntegrator integrator(0.01);
-        CustomGBForce* force = new CustomGBForce();
-        force->addComputedValue("a", "r", i < 2 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
-        force->addEnergyTerm("a", CustomGBForce::SingleParticle);
-        force->addEnergyTerm("(1+a1+a2)*r", i%2 == 0 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions);
-        force->addParticle(vector<double>());
-        force->addParticle(vector<double>());
-        force->addExclusion(0, 1);
-        system.addForce(force);
-        Context context(system, integrator, platform);
-        vector<Vec3> positions(2);
-        positions[0] = Vec3(0, 0, 0);
-        positions[1] = Vec3(1, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        double f, energy;
-        switch (i)
-        {
-            case 0: // e = 0
-                f = 0;
-                energy = 0;
-                break;
-            case 1: // e = r
-                f = 1;
-                energy = 1;
-                break;
-            case 2: // e = 2r
-                f = 2;
-                energy = 2;
-                break;
-            case 3: // e = 3r + 2r^2
-                f = 7;
-                energy = 5;
-                break;
-            default:
-                ASSERT(false);
-        }
-        ASSERT_EQUAL_VEC(Vec3(f, 0, 0), forces[0], 1e-4);
-        ASSERT_EQUAL_VEC(Vec3(-f, 0, 0), forces[1], 1e-4);
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
-
-        // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-        double norm = 0.0;
-        for (int i = 0; i < (int) forces.size(); ++i)
-            norm += forces[i].dot(forces[i]);
-        norm = std::sqrt(norm);
-        const double stepSize = 1e-3;
-        double step = stepSize/norm;
-        for (int i = 0; i < (int) positions.size(); ++i) {
-            Vec3 p = positions[i];
-            Vec3 f = forces[i];
-            positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-        }
-        context.setPositions(positions);
-        State state2 = context.getState(State::Energy);
-        ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/stepSize, 1e-3*abs(state.getPotentialEnergy()));
-    }
-}
+#include "CpuTests.h"
+#include "TestCustomGBForce.h"
 
-int main() {
-    try {
-        if (!CpuPlatform::isProcessorSupported()) {
-            cout << "CPU is not supported.  Exiting." << endl;
-            return 0;
-        }
-        testOBC(GBSAOBCForce::NoCutoff, CustomGBForce::NoCutoff);
-        testOBC(GBSAOBCForce::CutoffNonPeriodic, CustomGBForce::CutoffNonPeriodic);
-        testOBC(GBSAOBCForce::CutoffPeriodic, CustomGBForce::CutoffPeriodic);
-        testMembrane();
-        testTabulatedFunction();
-        testMultipleChainRules();
-        testPositionDependence();
-        testExclusions();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }

platforms/cpu/tests/TestCpuCustomManyParticleForce.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) 2014 Stanford University and the Authors.           *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,713 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CPU implementation of CustomManyParticleForce.
- */
+#include "CpuTests.h"
+#include "TestCustomManyParticleForce.h"
 
-#ifdef WIN32
-  #define _USE_MATH_DEFINES // Needed to get M_PI
-#endif
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CpuPlatform.h"
-#include "openmm/CustomCompoundBondForce.h"
-#include "openmm/CustomManyParticleForce.h"
-#include "openmm/System.h"
-#include "openmm/TabulatedFunction.h"
-#include "openmm/VerletIntegrator.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-Vec3 computeDelta(const Vec3& pos1, const Vec3& pos2, bool periodic, const Vec3* periodicBoxVectors) {
-    Vec3 diff = pos1-pos2;
-    if (periodic) {
-        diff -= periodicBoxVectors[2]*floor(diff[2]/periodicBoxVectors[2][2]+0.5);
-        diff -= periodicBoxVectors[1]*floor(diff[1]/periodicBoxVectors[1][1]+0.5);
-        diff -= periodicBoxVectors[0]*floor(diff[0]/periodicBoxVectors[0][0]+0.5);
-    }
-    return diff;
-}
-
-void validateAxilrodTeller(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize, bool triclinic) {
-    // Create a System and Context.
-
-    int numParticles = force->getNumParticles();
-    CustomManyParticleForce::NonbondedMethod nonbondedMethod = force->getNonbondedMethod();
-    System system;
-    for (int i = 0; i < numParticles; i++)
-        system.addParticle(1.0);
-    Vec3 boxVectors[3];
-    if (triclinic) {
-        boxVectors[0] = Vec3(boxSize, 0, 0);
-        boxVectors[1] = Vec3(0.2*boxSize, boxSize, 0);
-        boxVectors[2] = Vec3(-0.3*boxSize, -0.1*boxSize, boxSize);
-    }
-    else {
-        boxVectors[0] = Vec3(boxSize, 0, 0);
-        boxVectors[1] = Vec3(0, boxSize, 0);
-        boxVectors[2] = Vec3(0, 0, boxSize);
-    }
-    system.setDefaultPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
-    system.addForce(force);
-    VerletIntegrator integrator(0.001);
-    CpuPlatform platform;
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    State state1 = context.getState(State::Forces | State::Energy);
-    double c = context.getParameter("C");
-
-    // See if the energy matches the expected value.
-
-    double expectedEnergy = 0;
-    bool periodic = (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic);
-    for (int i = 0; i < (int) expectedSets.size(); i++) {
-        int p1 = expectedSets[i][0];
-        int p2 = expectedSets[i][1];
-        int p3 = expectedSets[i][2];
-        Vec3 d12 = computeDelta(positions[p2], positions[p1], periodic, boxVectors);
-        Vec3 d13 = computeDelta(positions[p3], positions[p1], periodic, boxVectors);
-        Vec3 d23 = computeDelta(positions[p3], positions[p2], periodic, boxVectors);
-        double r12 = sqrt(d12.dot(d12));
-        double r13 = sqrt(d13.dot(d13));
-        double r23 = sqrt(d23.dot(d23));
-        double ctheta1 = d12.dot(d13)/(r12*r13);
-        double ctheta2 = -d12.dot(d23)/(r12*r23);
-        double ctheta3 = d13.dot(d23)/(r13*r23);
-        double rprod = r12*r13*r23;
-        expectedEnergy += c*(1+3*ctheta1*ctheta2*ctheta3)/(rprod*rprod*rprod);
-    }
-    ASSERT_EQUAL_TOL(expectedEnergy, state1.getPotentialEnergy(), 1e-5);
-
-    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-    const vector<Vec3>& forces = state1.getForces();
-    double norm = 0.0;
-    for (int i = 0; i < (int) forces.size(); ++i)
-        norm += forces[i].dot(forces[i]);
-    norm = std::sqrt(norm);
-    const double stepSize = 1e-3;
-    double step = 0.5*stepSize/norm;
-    vector<Vec3> positions2(numParticles), positions3(numParticles);
-    for (int i = 0; i < (int) positions.size(); ++i) {
-        Vec3 p = positions[i];
-        Vec3 f = forces[i];
-        positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-        positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
-    }
-    context.setPositions(positions2);
-    State state2 = context.getState(State::Energy);
-    context.setPositions(positions3);
-    State state3 = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
-}
-
-void validateStillingerWeber(CustomManyParticleForce* force, const vector<Vec3>& positions, const vector<const int*>& expectedSets, double boxSize) {
-    // Create a System and Context.
-    
-    int numParticles = force->getNumParticles();
-    CustomManyParticleForce::NonbondedMethod nonbondedMethod = force->getNonbondedMethod();
-    System system;
-    for (int i = 0; i < numParticles; i++)
-        system.addParticle(1.0);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    system.addForce(force);
-    VerletIntegrator integrator(0.001);
-    CpuPlatform platform;
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    State state1 = context.getState(State::Forces | State::Energy);
-    double L = context.getParameter("L");
-    double eps = context.getParameter("eps");
-    double a = context.getParameter("a");
-    double gamma = context.getParameter("gamma");
-    double sigma = context.getParameter("sigma");
-    
-    // See if the energy matches the expected value.
-    
-    double expectedEnergy = 0;
-    for (int i = 0; i < (int) expectedSets.size(); i++) {
-        int p1 = expectedSets[i][0];
-        int p2 = expectedSets[i][1];
-        int p3 = expectedSets[i][2];
-        Vec3 d12 = positions[p2]-positions[p1];
-        Vec3 d13 = positions[p3]-positions[p1];
-        Vec3 d23 = positions[p3]-positions[p2];
-        if (nonbondedMethod == CustomManyParticleForce::CutoffPeriodic) {
-            for (int j = 0; j < 3; j++) {
-                d12[j] -= floor(d12[j]/boxSize+0.5f)*boxSize;
-                d13[j] -= floor(d13[j]/boxSize+0.5f)*boxSize;
-                d23[j] -= floor(d23[j]/boxSize+0.5f)*boxSize;
-            }
-        }
-        double r12 = sqrt(d12.dot(d12));
-        double r13 = sqrt(d13.dot(d13));
-        double r23 = sqrt(d23.dot(d23));
-        double ctheta1 = d12.dot(d13)/(r12*r13);
-        double ctheta2 = -d12.dot(d23)/(r12*r23);
-        double ctheta3 = d13.dot(d23)/(r13*r23);
-        expectedEnergy += L*eps*(ctheta1+1.0/3.0)*(ctheta1+1.0/3.0)*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));
-    }
-    ASSERT_EQUAL_TOL(expectedEnergy, state1.getPotentialEnergy(), 1e-5);
-
-    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-
-    const vector<Vec3>& forces = state1.getForces();
-    double norm = 0.0;
-    for (int i = 0; i < (int) forces.size(); ++i)
-        norm += forces[i].dot(forces[i]);
-    norm = std::sqrt(norm);
-    const double stepSize = 1e-3;
-    double step = 0.5*stepSize/norm;
-    vector<Vec3> positions2(numParticles), positions3(numParticles);
-    for (int i = 0; i < (int) positions.size(); ++i) {
-        Vec3 p = positions[i];
-        Vec3 f = forces[i];
-        positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-        positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
-    }
-    context.setPositions(positions2);
-    State state2 = context.getState(State::Energy);
-    context.setPositions(positions3);
-    State state3 = context.getState(State::Energy);
-    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
-}
-
-void testNoCutoff() {
-    CustomManyParticleForce* force = new CustomManyParticleForce(3,
-        "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
-        "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
-        "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
-    force->addGlobalParameter("C", 1.5);
-    vector<double> params;
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    vector<Vec3> positions;
-    positions.push_back(Vec3(0, 0, 0));
-    positions.push_back(Vec3(1, 0, 0));
-    positions.push_back(Vec3(0, 1.1, 0.3));
-    positions.push_back(Vec3(0.4, 0, -0.8));
-    int sets[4][3] = {{0,1,2}, {1,2,3}, {2,3,0}, {3,0,1}};
-    vector<const int*> expectedSets(&sets[0], &sets[4]);
-    validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
-}
-
-void testCutoff() {
-    CustomManyParticleForce* force = new CustomManyParticleForce(3,
-        "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
-        "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
-        "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
-    force->addGlobalParameter("C", 1.5);
-    force->setNonbondedMethod(CustomManyParticleForce::CutoffNonPeriodic);
-    force->setCutoffDistance(1.55);
-    vector<double> params;
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    vector<Vec3> positions;
-    positions.push_back(Vec3(0, 0, 0));
-    positions.push_back(Vec3(1, 0, 0));
-    positions.push_back(Vec3(0, 1.1, 0.3));
-    positions.push_back(Vec3(0.4, 0, -0.8));
-    positions.push_back(Vec3(0.2, 0.5, -0.1));
-    int sets[7][3] = {{0,1,2}, {0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,2,4}, {1,3,4}};
-    vector<const int*> expectedSets(&sets[0], &sets[7]);
-    validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
-}
-
-void testPeriodic() {
-    CustomManyParticleForce* force = new CustomManyParticleForce(3,
-        "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
-        "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
-        "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
-    force->addGlobalParameter("C", 1.5);
-    force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
-    force->setCutoffDistance(1.05);
-    vector<double> params;
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    vector<Vec3> positions;
-    positions.push_back(Vec3(0, 0, 0));
-    positions.push_back(Vec3(1, 0, 0));
-    positions.push_back(Vec3(0, 1.1, 0.3));
-    positions.push_back(Vec3(0.4, 0, -0.8));
-    positions.push_back(Vec3(0.2, 0.5, -0.1));
-    double boxSize = 2.1;
-    int sets[5][3] = {{0,1,3}, {0,1,4}, {0,2,4}, {0,3,4}, {1,3,4}};
-    vector<const int*> expectedSets(&sets[0], &sets[5]);
-    validateAxilrodTeller(force, positions, expectedSets, boxSize, false);
-}
-
-void testTriclinic() {
-    CustomManyParticleForce* force = new CustomManyParticleForce(3,
-        "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
-        "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
-        "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
-    force->addGlobalParameter("C", 1.5);
-    force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
-    force->setCutoffDistance(1.05);
-    vector<double> params;
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    vector<Vec3> positions;
-    positions.push_back(Vec3(0, 0, 0));
-    positions.push_back(Vec3(1, 0, 0));
-    positions.push_back(Vec3(0, 1.1, 0.3));
-    positions.push_back(Vec3(0.4, 0, -0.8));
-    positions.push_back(Vec3(0.2, 0.5, -0.1));
-    double boxSize = 2.1;
-    int sets[4][3] = {{0,1,3}, {0,1,4}, {0,3,4}, {1,3,4}};
-    vector<const int*> expectedSets(&sets[0], &sets[4]);
-    validateAxilrodTeller(force, positions, expectedSets, boxSize, true);
-}
-
-void testExclusions() {
-    CustomManyParticleForce* force = new CustomManyParticleForce(3,
-        "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
-        "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
-        "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
-    force->addGlobalParameter("C", 1.5);
-    vector<double> params;
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    vector<Vec3> positions;
-    positions.push_back(Vec3(0, 0, 0));
-    positions.push_back(Vec3(1, 0, 0));
-    positions.push_back(Vec3(0, 1.1, 0.3));
-    positions.push_back(Vec3(0.4, 0, -0.8));
-    positions.push_back(Vec3(0.2, 0.5, -0.1));
-    force->addExclusion(0, 2);
-    force->addExclusion(0, 3);
-    int sets[5][3] = {{0,1,4}, {1,2,3}, {1,2,4}, {1,3,4}, {2,3,4}};
-    vector<const int*> expectedSets(&sets[0], &sets[5]);
-    validateAxilrodTeller(force, positions, expectedSets, 2.0, false);
-}
-
-void testAllTerms() {
-    int numParticles = 4;
-    CpuPlatform platform;
-    
-    // Create a system with a CustomManyParticleForce.
-    
-    System system1;
-    CustomManyParticleForce* force1 = new CustomManyParticleForce(4,
-        "distance(p1,p2)+angle(p1,p4,p3)+dihedral(p1,p3,p2,p4)+x1+y4+z3");
-    system1.addForce(force1);
-    vector<double> params;
-    for (int i = 0; i < numParticles; i++) {
-        system1.addParticle(1.0);
-        force1->addParticle(params, i);
-    }
-    set<int> filter;
-    filter.insert(0);
-    force1->setTypeFilter(0, filter);
-    filter.clear();
-    filter.insert(1);
-    force1->setTypeFilter(1, filter);
-    filter.clear();
-    filter.insert(3);
-    force1->setTypeFilter(2, filter);
-    filter.clear();
-    filter.insert(2);
-    force1->setTypeFilter(3, filter);
-    
-    // Create a system that use a CustomCompoundBondForce to compute exactly the same interactions.
-    
-    System system2;
-    CustomCompoundBondForce* force2 = new CustomCompoundBondForce(4,
-        "distance(p1,p2)+angle(p1,p3,p4)+dihedral(p1,p4,p2,p3)+x1+y3+z4");
-    system2.addForce(force2);
-    vector<int> particles;
-    particles.push_back(0);
-    particles.push_back(1);
-    particles.push_back(2);
-    particles.push_back(3);
-    force2->addBond(particles, params);
-    for (int i = 0; i < numParticles; i++)
-        system2.addParticle(1.0);
-    
-    // Create contexts for both of them.
-
-    vector<Vec3> positions;
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    for (int i = 0; i < numParticles; i++)
-        positions.push_back(Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt)));
-    VerletIntegrator integrator1(0.001);
-    VerletIntegrator integrator2(0.001);
-    Context context1(system1, integrator1, platform);
-    Context context2(system2, integrator2, platform);
-    context1.setPositions(positions);
-    context2.setPositions(positions);
-    
-    // See if they produce identical forces and energies.
-    
-    State state1 = context1.getState(State::Forces | State::Energy);
-    State state2 = context2.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(state2.getPotentialEnergy(), state1.getPotentialEnergy(), 1e-4);
-    for (int i = 0; i < numParticles; i++)
-        ASSERT_EQUAL_VEC(state2.getForces()[i], state1.getForces()[i], 1e-4);
-}
-
-void testParameters() {
-    // Create a system.
-    
-    int numParticles = 5;
-    System system;
-    CustomManyParticleForce* force = new CustomManyParticleForce(3, "C*scale1*scale2*scale3*(distance(p1,p2)+distance(p2,p3)+distance(p1,p3))");
-    force->addGlobalParameter("C", 2.0);
-    force->addPerParticleParameter("scale");
-    vector<double> params(1);
-    vector<Vec3> positions;
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    for (int i = 0; i < numParticles; i++) {
-        params[0] = i+1;
-        force->addParticle(params);
-        positions.push_back(Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt)));
-        system.addParticle(1.0);
-    }
-    system.addForce(force);
-    VerletIntegrator integrator(0.001);
-    CpuPlatform platform;
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    
-    // See if the energy is correct.
-
-    State state = context.getState(State::Energy);
-    double expectedEnergy = 0;
-    for (int i = 0; i < numParticles; i++)
-        for (int j = i+1; j < numParticles; j++)
-            for (int k = j+1; k < numParticles; k++) {
-                Vec3 d12 = positions[j]-positions[i];
-                Vec3 d13 = positions[k]-positions[i];
-                Vec3 d23 = positions[k]-positions[j];
-                double r12 = sqrt(d12.dot(d12));
-                double r13 = sqrt(d13.dot(d13));
-                double r23 = sqrt(d23.dot(d23));
-                expectedEnergy += 2.0*(i+1)*(j+1)*(k+1)*(r12+r13+r23);
-            }
-    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
-    
-    // Modify the parameters.
-    
-    context.setParameter("C", 3.5);
-    for (int i = 0; i < numParticles; i++) {
-        params[0] = 0.5*i-0.1;
-        force->setParticleParameters(i, params, 0);
-    }
-    force->updateParametersInContext(context);
-    
-    // See if the energy is still correct.
-    
-    state = context.getState(State::Energy);
-    expectedEnergy = 0;
-    for (int i = 0; i < numParticles; i++)
-        for (int j = i+1; j < numParticles; j++)
-            for (int k = j+1; k < numParticles; k++) {
-                Vec3 d12 = positions[j]-positions[i];
-                Vec3 d13 = positions[k]-positions[i];
-                Vec3 d23 = positions[k]-positions[j];
-                double r12 = sqrt(d12.dot(d12));
-                double r13 = sqrt(d13.dot(d13));
-                double r23 = sqrt(d23.dot(d23));
-                expectedEnergy += 3.5*(0.5*i-0.1)*(0.5*j-0.1)*(0.5*k-0.1)*(r12+r13+r23);
-            }
-    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
-}
-
-void testTabulatedFunctions() {
-    int numParticles = 5;
-    
-    // Create two tabulated functions.
-    
-    vector<double> values;
-    values.push_back(0.0);
-    values.push_back(50.0);
-    Continuous1DFunction* f1 = new Continuous1DFunction(values, 0, 100);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    vector<double> c(numParticles);
-    for (int i = 0; i < numParticles; i++)
-        c[i] = genrand_real2(sfmt);
-    values.resize(numParticles*numParticles*numParticles);
-    for (int i = 0; i < numParticles; i++)
-        for (int j = 0; j < numParticles; j++)
-            for (int k = 0; k < numParticles; k++)
-                values[i+numParticles*j+numParticles*numParticles*k] = c[i]+c[j]+c[k];
-    Discrete3DFunction* f2 = new Discrete3DFunction(numParticles, numParticles, numParticles, values);
-    
-    // Create a system.
-    
-    System system;
-    CustomManyParticleForce* force = new CustomManyParticleForce(3, "f1(distance(p1,p2)+distance(p2,p3)+distance(p1,p3))*f2(atom1, atom2, atom3)");
-    force->addPerParticleParameter("atom");
-    force->addTabulatedFunction("f1", f1);
-    force->addTabulatedFunction("f2", f2);
-    vector<double> params(1);
-    vector<Vec3> positions;
-    for (int i = 0; i < numParticles; i++) {
-        params[0] = i;
-        force->addParticle(params);
-        positions.push_back(Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt)));
-        system.addParticle(1.0);
-    }
-    system.addForce(force);
-    VerletIntegrator integrator(0.001);
-    CpuPlatform platform;
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    
-    // See if the energy is correct.
-
-    State state = context.getState(State::Energy);
-    double expectedEnergy = 0;
-    for (int i = 0; i < numParticles; i++)
-        for (int j = i+1; j < numParticles; j++)
-            for (int k = j+1; k < numParticles; k++) {
-                Vec3 d12 = positions[j]-positions[i];
-                Vec3 d13 = positions[k]-positions[i];
-                Vec3 d23 = positions[k]-positions[j];
-                double r12 = sqrt(d12.dot(d12));
-                double r13 = sqrt(d13.dot(d13));
-                double r23 = sqrt(d23.dot(d23));
-                expectedEnergy += 0.5*(r12+r13+r23)*(c[i]+c[j]+c[k]);
-            }
-    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
-}
-
-void testTypeFilters() {
-    // Create a system.
-    
-    System system;
-    for (int i = 0; i < 5; i++)
-        system.addParticle(1.0);
-    CustomManyParticleForce* force = new CustomManyParticleForce(3, "c1*(distance(p1,p2)+distance(p1,p3))");
-    force->addPerParticleParameter("c");
-    double c[] = {1.0, 2.0, 1.3, 1.5, -2.1};
-    int type[] = {0, 1, 0, 1, 5};
-    vector<double> params(1);
-    for (int i = 0; i < 5; i++) {
-        params[0] = c[i];
-        force->addParticle(params, type[i]);
-    }
-    vector<Vec3> positions;
-    positions.push_back(Vec3(0, 0, 0));
-    positions.push_back(Vec3(1, 0, 0));
-    positions.push_back(Vec3(0, 1.1, 0.3));
-    positions.push_back(Vec3(0.4, 0, -0.8));
-    positions.push_back(Vec3(0.2, 0.5, -0.1));
-    set<int> f1, f2;
-    f1.insert(0);
-    f2.insert(1);
-    f2.insert(5);
-    force->setTypeFilter(0, f1);
-    force->setTypeFilter(1, f2);
-    force->setTypeFilter(2, f2);
-    system.addForce(force);
-    VerletIntegrator integrator(0.001);
-    CpuPlatform platform;
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    
-    // See if the energy is correct.
-
-    State state = context.getState(State::Energy);
-    double expectedEnergy = 0;
-    int sets[6][3] = {{0,1,3}, {0,1,4}, {0,3,4}, {2,1,3}, {2,1,4}, {2,3,4}};
-    for (int i = 0; i < 6; i++) {
-        int p1 = sets[i][0];
-        int p2 = sets[i][1];
-        int p3 = sets[i][2];
-            Vec3 d12 = positions[p2]-positions[p1];
-            Vec3 d13 = positions[p3]-positions[p1];
-            double r12 = sqrt(d12.dot(d12));
-            double r13 = sqrt(d13.dot(d13));
-            expectedEnergy += c[p1]*(r12+r13);
-    }
-    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-5);
-}
-
-void testLargeSystem() {
-    int gridSize = 8;
-    int numParticles = gridSize*gridSize*gridSize;
-    double boxSize = 3.0;
-    double spacing = boxSize/gridSize;
-    CpuPlatform platform;
-    CustomManyParticleForce* force = new CustomManyParticleForce(3,
-        "C*(1+3*cos(theta1)*cos(theta2)*cos(theta3))/(r12*r13*r23)^3;"
-        "theta1=angle(p1,p2,p3); theta2=angle(p2,p3,p1); theta3=angle(p3,p1,p2);"
-        "r12=distance(p1,p2); r13=distance(p1,p3); r23=distance(p2,p3)");
-    force->addGlobalParameter("C", 1.5);
-    force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
-    force->setCutoffDistance(0.6);
-    vector<double> params;
-    vector<Vec3> positions;
-    System system;
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                force->addParticle(params);
-                positions.push_back(Vec3((i+0.4*genrand_real2(sfmt))*spacing, (j+0.4*genrand_real2(sfmt))*spacing, (k+0.4*genrand_real2(sfmt))*spacing));
-                system.addParticle(1.0);
-            }
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    system.addForce(force);
-    VerletIntegrator integrator1(0.001);
-    VerletIntegrator integrator2(0.001);
-    Context context1(system, integrator1, Platform::getPlatformByName("Reference"));
-    Context context2(system, integrator2, platform);
-    context1.setPositions(positions);
-    context2.setPositions(positions);
-    State state1 = context1.getState(State::Forces | State::Energy);
-    State state2 = context2.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
-    for (int i = 0; i < numParticles; i++)
-        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
-}
-
-void testCentralParticleModeNoCutoff() {
-    CustomManyParticleForce* force = new CustomManyParticleForce(3,
-        "L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
-        "r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
-    force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
-    force->addGlobalParameter("L", 23.13);
-    force->addGlobalParameter("eps", 25.894776);
-    force->addGlobalParameter("a", 1.8);
-    force->addGlobalParameter("sigma", 0.23925);
-    force->addGlobalParameter("gamma", 1.2);
-    vector<double> params;
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    vector<Vec3> positions;
-    positions.push_back(Vec3(0, 0, 0));
-    positions.push_back(Vec3(0.1, 0, 0));
-    positions.push_back(Vec3(0, 0.11, 0.03));
-    positions.push_back(Vec3(0.04, 0, -0.08));
-    int sets[12][3] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,0,2}, {1,0,3}, {1, 2, 3}, {2,0,1}, {2,0,3}, {2, 1, 3}, {3,0,1}, {3,0,2}, {3,1,2}};
-    vector<const int*> expectedSets(&sets[0], &sets[12]);
-    validateStillingerWeber(force, positions, expectedSets, 2.0);
-}
-
-void testCentralParticleModeCutoff() {
-    CustomManyParticleForce* force = new CustomManyParticleForce(3,
-        "L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
-        "r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
-    force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
-    force->addGlobalParameter("L", 23.13);
-    force->addGlobalParameter("eps", 25.894776);
-    force->addGlobalParameter("a", 1.8);
-    force->addGlobalParameter("sigma", 0.23925);
-    force->addGlobalParameter("gamma", 1.2);
-    force->setNonbondedMethod(CustomManyParticleForce::CutoffNonPeriodic);
-    force->setCutoffDistance(0.155);
-    vector<double> params;
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    force->addParticle(params);
-    vector<Vec3> positions;
-    positions.push_back(Vec3(0, 0, 0));
-    positions.push_back(Vec3(0.1, 0, 0));
-    positions.push_back(Vec3(0, 0.11, 0.03));
-    positions.push_back(Vec3(0.04, 0, -0.08));
-    int sets[8][3] = {{0,1,2}, {0,1,3}, {0,2,3}, {1,0,2}, {1,0,3}, {1, 2, 3}, {2,0,1}, {3,0,1}};
-    vector<const int*> expectedSets(&sets[0], &sets[8]);
-    validateStillingerWeber(force, positions, expectedSets, 2.0);
-}
-
-void testCentralParticleModeLargeSystem() {
-    int gridSize = 8;
-    int numParticles = gridSize*gridSize*gridSize;
-    double boxSize = 2.0;
-    double spacing = boxSize/gridSize;
-    CpuPlatform platform;
-    CustomManyParticleForce* force = new CustomManyParticleForce(3,
-        "L*eps*(cos(theta1)+1/3)^2*exp(sigma*gamma/(r12-a*sigma))*exp(sigma*gamma/(r13-a*sigma));"
-        "r12 = distance(p1,p2); r13 = distance(p1,p3); theta1 = angle(p3,p1,p2)");
-    force->setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
-    force->addGlobalParameter("L", 23.13);
-    force->addGlobalParameter("eps", 25.894776);
-    force->addGlobalParameter("a", 1.8);
-    force->addGlobalParameter("sigma", 0.23925);
-    force->addGlobalParameter("gamma", 1.2);
-    force->setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
-    force->setCutoffDistance(1.8*0.23925);
-    vector<double> params;
-    vector<Vec3> positions;
-    System system;
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                force->addParticle(params);
-                positions.push_back(Vec3((i+0.4*genrand_real2(sfmt))*spacing, (j+0.4*genrand_real2(sfmt))*spacing, (k+0.4*genrand_real2(sfmt))*spacing));
-                system.addParticle(1.0);
-            }
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    system.addForce(force);
-    VerletIntegrator integrator1(0.001);
-    VerletIntegrator integrator2(0.001);
-    Context context1(system, integrator1, Platform::getPlatformByName("Reference"));
-    Context context2(system, integrator2, platform);
-    context1.setPositions(positions);
-    context2.setPositions(positions);
-    State state1 = context1.getState(State::Forces | State::Energy);
-    State state2 = context2.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
-    for (int i = 0; i < numParticles; i++)
-        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
-}
-
-int main() {
-    try {
-        if (!CpuPlatform::isProcessorSupported()) {
-            cout << "CPU is not supported.  Exiting." << endl;
-            return 0;
-        }
-        testNoCutoff();
-        testCutoff();
-        testPeriodic();
-        testTriclinic();
-        testExclusions();
-        testAllTerms();
-        testParameters();
-        testTabulatedFunctions();
-        testTypeFilters();
-        testLargeSystem();
-        testCentralParticleModeNoCutoff();
-        testCentralParticleModeCutoff();
-        testCentralParticleModeLargeSystem();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }

platforms/cpu/tests/TestCpuCustomNonbondedForce.cpp

-
 /* -------------------------------------------------------------------------- *
  *                                   OpenMM                                   *
  * -------------------------------------------------------------------------- *
@@ -7,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -30,962 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests all the different force terms in the reference implementation of CustomNonbondedForce.
- */
-
-#ifdef WIN32
-  #define _USE_MATH_DEFINES // Needed to get M_PI
-#endif
-#include "CpuPlatform.h"
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "openmm/CustomNonbondedForce.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/System.h"
-#include "openmm/VerletIntegrator.h"
-#include "sfmt/SFMT.h"
-#include <cmath>
-#include <iostream>
-#include <set>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-CpuPlatform platform;
-
-const double TOL = 1e-5;
-
-void testSimpleExpression() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* forceField = new CustomNonbondedForce("-0.1*r^3");
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(2, 0, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-    double force = 0.1*3*(2*2);
-    ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
-    ASSERT_EQUAL_TOL(-0.1*(2*2*2), state.getPotentialEnergy(), TOL);
-}
-
-void testParameters() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* forceField = new CustomNonbondedForce("scale*a*(r*b)^3; a=a1*a2; b=c+b1+b2");
-    forceField->addPerParticleParameter("a");
-    forceField->addPerParticleParameter("b");
-    forceField->addGlobalParameter("scale", 3.0);
-    forceField->addGlobalParameter("c", -1.0);
-    vector<double> params(2);
-    params[0] = 1.5;
-    params[1] = 2.0;
-    forceField->addParticle(params);
-    params[0] = 2.0;
-    params[1] = 3.0;
-    forceField->addParticle(params);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(2, 0, 0);
-    context.setPositions(positions);
-    context.setParameter("scale", 1.0);
-    context.setParameter("c", 0.0);
-    State state = context.getState(State::Forces | State::Energy);
-    vector<Vec3> forces = state.getForces();
-    double force = -3.0*3*5.0*(10*10);
-    ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
-    ASSERT_EQUAL_TOL(3.0*(10*10*10), state.getPotentialEnergy(), TOL);
-    
-    // Try changing the global parameters and make sure it's still correct.
-    
-    context.setParameter("scale", 1.5);
-    context.setParameter("c", 1.0);
-    state = context.getState(State::Forces | State::Energy);
-    forces = state.getForces();
-    force = -1.5*3.0*3*6.0*(12*12);
-    ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
-    ASSERT_EQUAL_TOL(1.5*3.0*(12*12*12), state.getPotentialEnergy(), TOL);
-    
-    // Try changing the per-particle parameters and make sure it's still correct.
-    
-    params[0] = 1.6;
-    params[1] = 2.1;
-    forceField->setParticleParameters(0, params);
-    params[0] = 1.9;
-    params[1] = 2.8;
-    forceField->setParticleParameters(1, params);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Forces | State::Energy);
-    forces = state.getForces();
-    force = -1.5*1.6*1.9*3*5.9*(11.8*11.8);
-    ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], TOL);
-    ASSERT_EQUAL_TOL(1.5*1.6*1.9*(11.8*11.8*11.8), state.getPotentialEnergy(), TOL);
-}
-
-void testExclusions() {
-    System system;
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* nonbonded = new CustomNonbondedForce("a*r; a=a1+a2");
-    nonbonded->addPerParticleParameter("a");
-    vector<double> params(1);
-    vector<Vec3> positions(4);
-    for (int i = 0; i < 4; i++) {
-        system.addParticle(1.0);
-        params[0] = i+1;
-        nonbonded->addParticle(params);
-        positions[i] = Vec3(i, 0, 0);
-    }
-    nonbonded->addExclusion(0, 1);
-    nonbonded->addExclusion(1, 2);
-    nonbonded->addExclusion(2, 3);
-    nonbonded->addExclusion(0, 2);
-    nonbonded->addExclusion(1, 3);
-    system.addForce(nonbonded);
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-    ASSERT_EQUAL_VEC(Vec3(1+4, 0, 0), forces[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[2], TOL);
-    ASSERT_EQUAL_VEC(Vec3(-(1+4), 0, 0), forces[3], TOL);
-    ASSERT_EQUAL_TOL((1+4)*3.0, state.getPotentialEnergy(), TOL);
-}
-
-void testCutoff() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* forceField = new CustomNonbondedForce("r");
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    forceField->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
-    forceField->setCutoffDistance(2.5);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(3);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, 2, 0);
-    positions[2] = Vec3(0, 3, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-    ASSERT_EQUAL_VEC(Vec3(0, 1, 0), forces[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, -1, 0), forces[2], TOL);
-    ASSERT_EQUAL_TOL(2.0+1.0, state.getPotentialEnergy(), TOL);
-}
-
-void testPeriodic() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* forceField = new CustomNonbondedForce("r");
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    forceField->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
-    forceField->setCutoffDistance(2.0);
-    system.setDefaultPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(3);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, 2.1, 0);
-    positions[2] = Vec3(0, 3, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-    ASSERT_EQUAL_VEC(Vec3(0, -2, 0), forces[0], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, 2, 0), forces[1], TOL);
-    ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[2], TOL);
-    ASSERT_EQUAL_TOL(1.9+1+0.9, state.getPotentialEnergy(), TOL);
-}
-
-void testTriclinic() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    Vec3 a(3.1, 0, 0);
-    Vec3 b(0.4, 3.5, 0);
-    Vec3 c(-0.1, -0.5, 4.0);
-    system.setDefaultPeriodicBoxVectors(a, b, c);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* nonbonded = new CustomNonbondedForce("r");
-    nonbonded->addParticle(vector<double>());
-    nonbonded->addParticle(vector<double>());
-    nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
-    const double cutoff = 1.5;
-    nonbonded->setCutoffDistance(cutoff);
-    system.addForce(nonbonded);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    for (int iteration = 0; iteration < 50; iteration++) {
-        // Generate random positions for the two particles.
-
-        positions[0] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
-        positions[1] = a*genrand_real2(sfmt) + b*genrand_real2(sfmt) + c*genrand_real2(sfmt);
-        context.setPositions(positions);
-
-        // Loop over all possible periodic copies and find the nearest one.
-
-        Vec3 delta;
-        double distance2 = 100.0;
-        for (int i = -1; i < 2; i++)
-            for (int j = -1; j < 2; j++)
-                for (int k = -1; k < 2; k++) {
-                    Vec3 d = positions[1]-positions[0]+a*i+b*j+c*k;
-                    if (d.dot(d) < distance2) {
-                        delta = d;
-                        distance2 = d.dot(d);
-                    }
-                }
-        double distance = sqrt(distance2);
-
-        // See if the force and energy are correct.
-
-        State state = context.getState(State::Forces | State::Energy);
-        if (distance >= cutoff) {
-            ASSERT_EQUAL(0.0, state.getPotentialEnergy());
-            ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[0], 0);
-            ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getForces()[1], 0);
-        }
-        else {
-            const Vec3 force = delta/sqrt(delta.dot(delta));
-            ASSERT_EQUAL_TOL(distance, state.getPotentialEnergy(), TOL);
-            ASSERT_EQUAL_VEC(force, state.getForces()[0], TOL);
-            ASSERT_EQUAL_VEC(-force, state.getForces()[1], TOL);
-        }
-    }
-}
-
-void testContinuous1DFunction() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r)+1");
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    vector<double> table;
-    for (int i = 0; i < 21; i++)
-        table.push_back(sin(0.25*i));
-    forceField->addTabulatedFunction("fn", new Continuous1DFunction(table, 1.0, 6.0));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (int i = 1; i < 30; i++) {
-        double x = (7.0/30.0)*i;
-        positions[1] = Vec3(x, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        double force = (x < 1.0 || x > 6.0 ? 0.0 : -cos(x-1.0));
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : sin(x-1.0))+1.0;
-        ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
-        ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
-    }
-    for (int i = 1; i < 20; i++) {
-        double x = 0.25*i+1.0;
-        positions[1] = Vec3(x, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Energy);
-        double energy = (x < 1.0 || x > 6.0 ? 0.0 : sin(x-1.0))+1.0;
-        ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4);
-    }
-}
-
-void testContinuous2DFunction() {
-    const int xsize = 20;
-    const int ysize = 21;
-    const double xmin = 0.4;
-    const double xmax = 1.5;
-    const double ymin = 0.0;
-    const double ymax = 2.1;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a)+1");
-    forceField->addGlobalParameter("a", 0.0);
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    vector<double> table(xsize*ysize);
-    for (int i = 0; i < xsize; i++) {
-        for (int j = 0; j < ysize; j++) {
-            double x = xmin + i*(xmax-xmin)/xsize;
-            double y = ymin + j*(ymax-ymin)/ysize;
-            table[i+xsize*j] = sin(0.25*x)*cos(0.33*y);
-        }
-    }
-    forceField->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
-        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
-            positions[1] = Vec3(x, 0, 0);
-            context.setParameter("a", y);
-            context.setPositions(positions);
-            State state = context.getState(State::Forces | State::Energy);
-            const vector<Vec3>& forces = state.getForces();
-            double energy = 1;
-            double force = 0;
-            if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
-                energy = sin(0.25*x)*cos(0.33*y)+1.0;
-                force = -0.25*cos(0.25*x)*cos(0.33*y);
-            }
-            ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
-            ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
-            ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.02);
-        }
-    }
-}
-
-void testContinuous3DFunction() {
-    const int xsize = 10;
-    const int ysize = 11;
-    const int zsize = 12;
-    const double xmin = 0.4;
-    const double xmax = 1.1;
-    const double ymin = 0.0;
-    const double ymax = 0.9;
-    const double zmin = 0.2;
-    const double zmax = 1.3;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a,b)+1");
-    forceField->addGlobalParameter("a", 0.0);
-    forceField->addGlobalParameter("b", 0.0);
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    vector<double> table(xsize*ysize*zsize);
-    for (int i = 0; i < xsize; i++) {
-        for (int j = 0; j < ysize; j++) {
-            for (int k = 0; k < zsize; k++) {
-                double x = xmin + i*(xmax-xmin)/xsize;
-                double y = ymin + j*(ymax-ymin)/ysize;
-                double z = zmin + k*(zmax-zmin)/zsize;
-                table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
-            }
-        }
-    }
-    forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
-        for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
-            for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
-                positions[1] = Vec3(x, 0, 0);
-                context.setParameter("a", y);
-                context.setParameter("b", z);
-                context.setPositions(positions);
-                State state = context.getState(State::Forces | State::Energy);
-                const vector<Vec3>& forces = state.getForces();
-                double energy = 1;
-                double force = 0;
-                if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
-                    energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1.0;
-                    force = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
-                }
-                ASSERT_EQUAL_VEC(Vec3(-force, 0, 0), forces[0], 0.1);
-                ASSERT_EQUAL_VEC(Vec3(force, 0, 0), forces[1], 0.1);
-                ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
-            }
-        }
-    }
-}
-
-void testDiscrete1DFunction() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r)+1");
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    vector<double> table;
-    for (int i = 0; i < 21; i++)
-        table.push_back(sin(0.25*i));
-    forceField->addTabulatedFunction("fn", new Discrete1DFunction(table));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (int i = 0; i < (int) table.size(); i++) {
-        positions[1] = Vec3(i, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
-        ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
-    }
-}
-
-void testDiscrete2DFunction() {
-    const int xsize = 10;
-    const int ysize = 5;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a)+1");
-    forceField->addGlobalParameter("a", 0.0);
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    vector<double> table;
-    for (int i = 0; i < xsize; i++)
-        for (int j = 0; j < ysize; j++)
-            table.push_back(sin(0.25*i)+cos(0.33*j));
-    forceField->addTabulatedFunction("fn", new Discrete2DFunction(xsize, ysize, table));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (int i = 0; i < (int) table.size(); i++) {
-        positions[1] = Vec3(i%xsize, 0, 0);
-        context.setPositions(positions);
-        context.setParameter("a", i/xsize);
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
-        ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
-    }
-}
-
-void testDiscrete3DFunction() {
-    const int xsize = 8;
-    const int ysize = 5;
-    const int zsize = 6;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* forceField = new CustomNonbondedForce("fn(r,a,b)+1");
-    forceField->addGlobalParameter("a", 0.0);
-    forceField->addGlobalParameter("b", 0.0);
-    forceField->addParticle(vector<double>());
-    forceField->addParticle(vector<double>());
-    vector<double> table;
-    for (int i = 0; i < xsize; i++)
-        for (int j = 0; j < ysize; j++)
-            for (int k = 0; k < zsize; k++)
-                table.push_back(sin(0.25*i)+cos(0.33*j)+0.12345*k);
-    forceField->addTabulatedFunction("fn", new Discrete3DFunction(xsize, ysize, zsize, table));
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    for (int i = 0; i < (int) table.size(); i++) {
-        positions[1] = Vec3(i%xsize, 0, 0);
-        context.setPositions(positions);
-        context.setParameter("a", (i/xsize)%ysize);
-        context.setParameter("b", i/(xsize*ysize));
-        State state = context.getState(State::Forces | State::Energy);
-        const vector<Vec3>& forces = state.getForces();
-        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[0], 1e-6);
-        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), forces[1], 1e-6);
-        ASSERT_EQUAL_TOL(table[i]+1.0, state.getPotentialEnergy(), 1e-6);
-    }
-}
-
-void testCoulombLennardJones() {
-    const int numMolecules = 300;
-    const int numParticles = numMolecules*2;
-    const double boxSize = 20.0;
-
-    // Create two systems: one with a NonbondedForce, and one using a CustomNonbondedForce to implement the same interaction.
-
-    System standardSystem;
-    System customSystem;
-    for (int i = 0; i < numParticles; i++) {
-        standardSystem.addParticle(1.0);
-        customSystem.addParticle(1.0);
-    }
-    NonbondedForce* standardNonbonded = new NonbondedForce();
-    CustomNonbondedForce* customNonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6)+138.935456*q/r; q=q1*q2; sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
-    customNonbonded->addPerParticleParameter("q");
-    customNonbonded->addPerParticleParameter("sigma");
-    customNonbonded->addPerParticleParameter("eps");
-    vector<Vec3> positions(numParticles);
-    vector<Vec3> velocities(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    vector<double> params(3);
-    for (int i = 0; i < numMolecules; i++) {
-        if (i < numMolecules/2) {
-            standardNonbonded->addParticle(1.0, 0.2, 0.1);
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.1;
-            customNonbonded->addParticle(params);
-            standardNonbonded->addParticle(-1.0, 0.1, 0.1);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            customNonbonded->addParticle(params);
-        }
-        else {
-            standardNonbonded->addParticle(1.0, 0.2, 0.2);
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.2;
-            customNonbonded->addParticle(params);
-            standardNonbonded->addParticle(-1.0, 0.1, 0.2);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            customNonbonded->addParticle(params);
-        }
-        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
-        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
-        velocities[2*i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        velocities[2*i+1] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt));
-        standardNonbonded->addException(2*i, 2*i+1, 0.0, 1.0, 0.0);
-        customNonbonded->addExclusion(2*i, 2*i+1);
-    }
-    standardNonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
-    customNonbonded->setNonbondedMethod(CustomNonbondedForce::NoCutoff);
-    standardSystem.addForce(standardNonbonded);
-    customSystem.addForce(customNonbonded);
-    VerletIntegrator integrator1(0.01);
-    VerletIntegrator integrator2(0.01);
-    Context context1(standardSystem, integrator1, platform);
-    Context context2(customSystem, integrator2, platform);
-    context1.setPositions(positions);
-    context2.setPositions(positions);
-    context1.setVelocities(velocities);
-    context2.setVelocities(velocities);
-    State state1 = context1.getState(State::Forces | State::Energy);
-    State state2 = context2.getState(State::Forces | State::Energy);
-    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-4);
-    for (int i = 0; i < numParticles; i++) {
-        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-4);
-    }
-}
-
-void testSwitchingFunction() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* nonbonded = new CustomNonbondedForce("10/r^2");
-    vector<double> params;
-    nonbonded->addParticle(params);
-    nonbonded->addParticle(params);
-    nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
-    nonbonded->setCutoffDistance(2.0);
-    nonbonded->setUseSwitchingFunction(true);
-    nonbonded->setSwitchingDistance(1.5);
-    system.addForce(nonbonded);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    
-    // Compute the interaction at various distances.
-    
-    for (double r = 1.0; r < 2.5; r += 0.1) {
-        positions[1] = Vec3(r, 0, 0);
-        context.setPositions(positions);
-        State state = context.getState(State::Forces | State::Energy);
-        
-        // See if the energy is correct.
-        
-        double expectedEnergy = 10/(r*r);
-        double switchValue;
-        if (r <= 1.5)
-            switchValue = 1;
-        else if (r >= 2.0)
-            switchValue = 0;
-        else {
-            double t = (r-1.5)/0.5;
-            switchValue = 1+t*t*t*(-10+t*(15-t*6));
-        }
-        ASSERT_EQUAL_TOL(switchValue*expectedEnergy, state.getPotentialEnergy(), TOL);
-        
-        // See if the force is the gradient of the energy.
-        
-        double delta = 1e-3;
-        positions[1] = Vec3(r-delta, 0, 0);
-        context.setPositions(positions);
-        double e1 = context.getState(State::Energy).getPotentialEnergy();
-        positions[1] = Vec3(r+delta, 0, 0);
-        context.setPositions(positions);
-        double e2 = context.getState(State::Energy).getPotentialEnergy();
-        ASSERT_EQUAL_TOL((e2-e1)/(2*delta), state.getForces()[0][0], 1e-3);
-    }
-}
-
-void testLongRangeCorrection() {
-    // Create a box of particles.
-
-    int gridSize = 5;
-    int numParticles = gridSize*gridSize*gridSize;
-    double boxSize = gridSize*0.7;
-    double cutoff = boxSize/3;
-    System standardSystem;
-    System customSystem;
-    VerletIntegrator integrator1(0.01);
-    VerletIntegrator integrator2(0.01);
-    NonbondedForce* standardNonbonded = new NonbondedForce();
-    CustomNonbondedForce* customNonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6); sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
-    customNonbonded->addPerParticleParameter("sigma");
-    customNonbonded->addPerParticleParameter("eps");
-    vector<Vec3> positions(numParticles);
-    int index = 0;
-    vector<double> params1(2);
-    params1[0] = 1.1;
-    params1[1] = 0.5;
-    vector<double> params2(2);
-    params2[0] = 1;
-    params2[1] = 1;
-    for (int i = 0; i < gridSize; i++)
-        for (int j = 0; j < gridSize; j++)
-            for (int k = 0; k < gridSize; k++) {
-                standardSystem.addParticle(1.0);
-                customSystem.addParticle(1.0);
-                if (index%2 == 0) {
-                    standardNonbonded->addParticle(0, params1[0], params1[1]);
-                    customNonbonded->addParticle(params1);
-                }
-                else {
-                    standardNonbonded->addParticle(0, params2[0], params2[1]);
-                    customNonbonded->addParticle(params2);
-                }
-                positions[index] = Vec3(i*boxSize/gridSize, j*boxSize/gridSize, k*boxSize/gridSize);
-                index++;
-            }
-    standardNonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    customNonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
-    standardNonbonded->setCutoffDistance(cutoff);
-    customNonbonded->setCutoffDistance(cutoff);
-    standardSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    customSystem.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    standardNonbonded->setUseDispersionCorrection(true);
-    customNonbonded->setUseLongRangeCorrection(true);
-    standardNonbonded->setUseSwitchingFunction(true);
-    customNonbonded->setUseSwitchingFunction(true);
-    standardNonbonded->setSwitchingDistance(0.8*cutoff);
-    customNonbonded->setSwitchingDistance(0.8*cutoff);
-    standardSystem.addForce(standardNonbonded);
-    customSystem.addForce(customNonbonded);
-
-    // Compute the correction for the standard force.
-
-    Context context1(standardSystem, integrator1, platform);
-    context1.setPositions(positions);
-    double standardEnergy1 = context1.getState(State::Energy).getPotentialEnergy();
-    standardNonbonded->setUseDispersionCorrection(false);
-    context1.reinitialize();
-    context1.setPositions(positions);
-    double standardEnergy2 = context1.getState(State::Energy).getPotentialEnergy();
-
-    // Compute the correction for the custom force.
-
-    Context context2(customSystem, integrator2, platform);
-    context2.setPositions(positions);
-    double customEnergy1 = context2.getState(State::Energy).getPotentialEnergy();
-    customNonbonded->setUseLongRangeCorrection(false);
-    context2.reinitialize();
-    context2.setPositions(positions);
-    double customEnergy2 = context2.getState(State::Energy).getPotentialEnergy();
-
-    // See if they agree.
-
-    ASSERT_EQUAL_TOL(standardEnergy1-standardEnergy2, customEnergy1-customEnergy2, 1e-4);
-}
-
-void testInteractionGroups() {
-    const int numParticles = 6;
-    System system;
-    VerletIntegrator integrator(0.01);
-    CustomNonbondedForce* nonbonded = new CustomNonbondedForce("v1+v2");
-    nonbonded->addPerParticleParameter("v");
-    vector<double> params(1, 0.001);
-    for (int i = 0; i < numParticles; i++) {
-        system.addParticle(1.0);
-        nonbonded->addParticle(params);
-        params[0] *= 10;
-    }
-    set<int> set1, set2, set3, set4;
-    set1.insert(2);
-    set2.insert(0);
-    set2.insert(1);
-    set2.insert(2);
-    set2.insert(3);
-    set2.insert(4);
-    set2.insert(5);
-    nonbonded->addInteractionGroup(set1, set2); // Particle 2 interacts with every other particle.
-    set3.insert(0);
-    set3.insert(1);
-    set4.insert(4);
-    set4.insert(5);
-    nonbonded->addInteractionGroup(set3, set4); // Particles 0 and 1 interact with 4 and 5.
-    nonbonded->addExclusion(1, 2); // Add an exclusion to make sure it gets skipped.
-    system.addForce(nonbonded);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(numParticles);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-    double expectedEnergy = 331.423; // Each digit is the number of interactions a particle particle is involved in.
-    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), TOL);
-}
-
-void testLargeInteractionGroup() {
-    const int numMolecules = 300;
-    const int numParticles = numMolecules*2;
-    const double boxSize = 20.0;
-    
-    // Create a large system.
-    
-    System system;
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    for (int i = 0; i < numParticles; i++)
-        system.addParticle(1.0);
-    CustomNonbondedForce* nonbonded = new CustomNonbondedForce("4*eps*((sigma/r)^12-(sigma/r)^6)+138.935456*q/r; q=q1*q2; sigma=0.5*(sigma1+sigma2); eps=sqrt(eps1*eps2)");
-    nonbonded->addPerParticleParameter("q");
-    nonbonded->addPerParticleParameter("sigma");
-    nonbonded->addPerParticleParameter("eps");
-    vector<Vec3> positions(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-    vector<double> params(3);
-    for (int i = 0; i < numMolecules; i++) {
-        if (i < numMolecules/2) {
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.1;
-            nonbonded->addParticle(params);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            nonbonded->addParticle(params);
-        }
-        else {
-            params[0] = 1.0;
-            params[1] = 0.2;
-            params[2] = 0.2;
-            nonbonded->addParticle(params);
-            params[0] = -1.0;
-            params[1] = 0.1;
-            nonbonded->addParticle(params);
-        }
-        positions[2*i] = Vec3(boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt), boxSize*genrand_real2(sfmt));
-        positions[2*i+1] = Vec3(positions[2*i][0]+1.0, positions[2*i][1], positions[2*i][2]);
-        nonbonded->addExclusion(2*i, 2*i+1);
-    }
-    nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
-    system.addForce(nonbonded);
-    
-    // Compute the forces.
-    
-    VerletIntegrator integrator(0.01);
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    State state1 = context.getState(State::Forces);
-    
-    // Modify the force so only one particle interacts with everything else.
-    
-    set<int> set1, set2;
-    set1.insert(151);
-    for (int i = 0; i < numParticles; i++)
-        set2.insert(i);
-    nonbonded->addInteractionGroup(set1, set2);
-    context.reinitialize();
-    context.setPositions(positions);
-    State state2 = context.getState(State::Forces);
-    
-    // The force on that one particle should be the same.
-    
-    ASSERT_EQUAL_VEC(state1.getForces()[151], state2.getForces()[151], 1e-4);
-    
-    // Modify the interaction group so it includes all interactions.  This should now reproduce the original forces
-    // on all atoms.
-
-    for (int i = 0; i < numParticles; i++)
-        set1.insert(i);
-    nonbonded->setInteractionGroupParameters(0, set1, set2);
-    context.reinitialize();
-    context.setPositions(positions);
-    State state3 = context.getState(State::Forces);
-    for (int i = 0; i < numParticles; i++)
-        ASSERT_EQUAL_VEC(state1.getForces()[i], state3.getForces()[i], 1e-4);
-}
-
-void testInteractionGroupLongRangeCorrection() {
-    const int numParticles = 10;
-    const double boxSize = 10.0;
-    const double cutoff = 0.5;
-    System system;
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    CustomNonbondedForce* nonbonded = new CustomNonbondedForce("c1*c2*r^-4");
-    nonbonded->addPerParticleParameter("c");
-    vector<Vec3> positions(numParticles);
-    vector<double> params(1);
-    for (int i = 0; i < numParticles; i++) {
-        system.addParticle(1.0);
-        params[0] = (i%2 == 0 ? 1.1 : 2.0);
-        nonbonded->addParticle(params);
-        positions[i] = Vec3(0.5*i, 0, 0);
-    }
-    nonbonded->setNonbondedMethod(CustomNonbondedForce::CutoffPeriodic);
-    nonbonded->setCutoffDistance(cutoff);
-    system.addForce(nonbonded);
-    
-    // Setup nonbonded groups.  They involve 1 interaction of type AA,
-    // 2 of type BB, and 5 of type AB.
-    
-    set<int> set1, set2, set3, set4, set5;
-    set1.insert(0);
-    set1.insert(1);
-    set1.insert(2);
-    nonbonded->addInteractionGroup(set1, set1);
-    set2.insert(3);
-    set3.insert(4);
-    set3.insert(6);
-    set3.insert(8);
-    nonbonded->addInteractionGroup(set2, set3);
-    set4.insert(5);
-    set5.insert(7);
-    set5.insert(9);
-    nonbonded->addInteractionGroup(set4, set5);
-    
-    // Compute energy with and without the correction.
-    
-    VerletIntegrator integrator(0.01);
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    double energy1 = context.getState(State::Energy).getPotentialEnergy();
-    nonbonded->setUseLongRangeCorrection(true);
-    context.reinitialize();
-    context.setPositions(positions);
-    double energy2 = context.getState(State::Energy).getPotentialEnergy();
-    
-    // Check the result.
-    
-    double sum = (1.1*1.1 + 2*2.0*2.0 + 5*1.1*2.0)*2.0;
-    int numPairs = (numParticles*(numParticles+1))/2;
-    double expected = 2*M_PI*numParticles*numParticles*sum/(numPairs*boxSize*boxSize*boxSize);
-    ASSERT_EQUAL_TOL(expected, energy2-energy1, 1e-4);
-}
-
-void testMultipleCutoffs() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    
-    // Add multiple nonbonded forces that have different cutoffs.
-    
-    CustomNonbondedForce* nonbonded1 = new CustomNonbondedForce("2*r");
-    nonbonded1->addParticle(vector<double>());
-    nonbonded1->addParticle(vector<double>());
-    nonbonded1->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
-    nonbonded1->setCutoffDistance(2.5);
-    system.addForce(nonbonded1);
-    CustomNonbondedForce* nonbonded2 = new CustomNonbondedForce("3*r");
-    nonbonded2->addParticle(vector<double>());
-    nonbonded2->addParticle(vector<double>());
-    nonbonded2->setNonbondedMethod(CustomNonbondedForce::CutoffNonPeriodic);
-    nonbonded2->setCutoffDistance(2.9);
-    nonbonded2->setForceGroup(1);
-    system.addForce(nonbonded2);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(0, 0, 0);
-    for (double r = 2.4; r < 3.2; r += 0.2) {
-        positions[1][1] = r;
-        context.setPositions(positions);
-        double e1 = (r < 2.5 ? 2.0*r : 0.0);
-        double e2 = (r < 2.9 ? 3.0*r : 0.0);
-        double f1 = (r < 2.5 ? 2.0 : 0.0);
-        double f2 = (r < 2.9 ? 3.0 : 0.0);
-        
-        // Check the first force.
-        
-        State state = context.getState(State::Forces | State::Energy, false, 1);
-        ASSERT_EQUAL_VEC(Vec3(0, f1, 0), state.getForces()[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, -f1, 0), state.getForces()[1], TOL);
-        ASSERT_EQUAL_TOL(e1, state.getPotentialEnergy(), TOL);
-        
-        // Check the second force.
-        
-        state = context.getState(State::Forces | State::Energy, false, 2);
-        ASSERT_EQUAL_VEC(Vec3(0, f2, 0), state.getForces()[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, -f2, 0), state.getForces()[1], TOL);
-        ASSERT_EQUAL_TOL(e2, state.getPotentialEnergy(), TOL);
-        
-        // Check the sum of both forces.
-
-        state = context.getState(State::Forces | State::Energy);
-        ASSERT_EQUAL_VEC(Vec3(0, f1+f2, 0), state.getForces()[0], TOL);
-        ASSERT_EQUAL_VEC(Vec3(0, -f1-f2, 0), state.getForces()[1], TOL);
-        ASSERT_EQUAL_TOL(e1+e2, state.getPotentialEnergy(), TOL);
-    }
-}
+#include "CpuTests.h"
+#include "TestCustomNonbondedForce.h"
 
-int main() {
-    try {
-        if (!CpuPlatform::isProcessorSupported()) {
-            cout << "CPU is not supported.  Exiting." << endl;
-            return 0;
-        }
-        testSimpleExpression();
-        testParameters();
-        testExclusions();
-        testCutoff();
-        testPeriodic();
-        testTriclinic();
-        testContinuous1DFunction();
-        testContinuous2DFunction();
-        testContinuous3DFunction();
-        testDiscrete1DFunction();
-        testDiscrete2DFunction();
-        testDiscrete3DFunction();
-        testCoulombLennardJones();
-        testSwitchingFunction();
-        testLongRangeCorrection();
-        testInteractionGroups();
-        testLargeInteractionGroup();
-        testInteractionGroupLongRangeCorrection();
-        testMultipleCutoffs();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }