Merge branch 'master' of github.com:pandegroup/openmm into genpt

openmmapi/src/CustomCentroidBondForceImpl.cpp

@@ -150,24 +150,37 @@ ParsedExpression CustomCentroidBondForceImpl::prepareExpression(const CustomCent
     functions["dihedral"] = &dihedral;
     ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions);
     map<string, int> groups;
+    set<string> variables;
     for (int i = 0; i < force.getNumGroupsPerBond(); i++) {
-        stringstream name;
+        stringstream name, x, y, z;
         name << 'g' << (i+1);
+        x << 'x' << (i+1);
+        y << 'y' << (i+1);
+        z << 'z' << (i+1);
         groups[name.str()] = i;
+        variables.insert(x.str());
+        variables.insert(y.str());
+        variables.insert(z.str());
     }
-    return ParsedExpression(replaceFunctions(expression.getRootNode(), groups, distances, angles, dihedrals)).optimize();
+    for (int i = 0; i < force.getNumGlobalParameters(); i++)
+        variables.insert(force.getGlobalParameterName(i));
+    for (int i = 0; i < force.getNumPerBondParameters(); i++)
+        variables.insert(force.getPerBondParameterName(i));
+    return ParsedExpression(replaceFunctions(expression.getRootNode(), groups, distances, angles, dihedrals, variables)).optimize();
 }
 
 ExpressionTreeNode CustomCentroidBondForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> groups,
-        map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
+        map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals, set<string>& variables) {
     const Operation& op = node.getOperation();
+    if (op.getId() == Operation::VARIABLE && variables.find(op.getName()) == variables.end())
+        throw OpenMMException("CustomCentroidBondForce: Unknown variable '"+op.getName()+"'");
     if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
     {
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
         for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], groups, distances, angles, dihedrals));
+            children.push_back(replaceFunctions(node.getChildren()[i], groups, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

openmmapi/src/CustomCompoundBondForceImpl.cpp

@@ -136,24 +136,37 @@ ParsedExpression CustomCompoundBondForceImpl::prepareExpression(const CustomComp
     functions["dihedral"] = &dihedral;
     ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions);
     map<string, int> atoms;
+    set<string> variables;
     for (int i = 0; i < force.getNumParticlesPerBond(); i++) {
-        stringstream name;
+        stringstream name, x, y, z;
         name << 'p' << (i+1);
+        x << 'x' << (i+1);
+        y << 'y' << (i+1);
+        z << 'z' << (i+1);
         atoms[name.str()] = i;
+        variables.insert(x.str());
+        variables.insert(y.str());
+        variables.insert(z.str());
     }
-    return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals)).optimize();
+    for (int i = 0; i < force.getNumGlobalParameters(); i++)
+        variables.insert(force.getGlobalParameterName(i));
+    for (int i = 0; i < force.getNumPerBondParameters(); i++)
+        variables.insert(force.getPerBondParameterName(i));
+    return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals, variables)).optimize();
 }
 
 ExpressionTreeNode CustomCompoundBondForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms,
-        map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
+        map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals, set<string>& variables) {
     const Operation& op = node.getOperation();
+    if (op.getId() == Operation::VARIABLE && variables.find(op.getName()) == variables.end())
+        throw OpenMMException("CustomCompoundBondForce: Unknown variable '"+op.getName()+"'");
     if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
     {
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
         for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals));
+            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

openmmapi/src/CustomExternalForce.cpp

@@ -119,3 +119,7 @@ ForceImpl* CustomExternalForce::createImpl() const {
 void CustomExternalForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomExternalForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+bool CustomExternalForce::usesPeriodicBoundaryConditions() const {
+    return (energyExpression.find("periodicdistance") != string::npos);
+}

openmmapi/src/CustomHbondForceImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -215,19 +215,28 @@ ParsedExpression CustomHbondForceImpl::prepareExpression(const CustomHbondForce&
     atoms["d1"] = 3;
     atoms["d2"] = 4;
     atoms["d3"] = 5;
-    return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals)).optimize();
+    set<string> variables;
+    for (int i = 0; i < force.getNumPerDonorParameters(); i++)
+        variables.insert(force.getPerDonorParameterName(i));
+    for (int i = 0; i < force.getNumPerAcceptorParameters(); i++)
+        variables.insert(force.getPerAcceptorParameterName(i));
+    for (int i = 0; i < force.getNumGlobalParameters(); i++)
+        variables.insert(force.getGlobalParameterName(i));
+    return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals, variables)).optimize();
 }
 
 ExpressionTreeNode CustomHbondForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms,
-        map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
+        map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals, set<string>& variables) {
     const Operation& op = node.getOperation();
+    if (op.getId() == Operation::VARIABLE && variables.find(op.getName()) == variables.end())
+        throw OpenMMException("CustomHBondForce: Unknown variable '"+op.getName()+"'");
     if (op.getId() != Operation::CUSTOM || op.getNumArguments() < 2)
     {
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
         for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals));
+            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

openmmapi/src/CustomManyParticleForceImpl.cpp

@@ -165,24 +165,40 @@ ParsedExpression CustomManyParticleForceImpl::prepareExpression(const CustomMany
     functions["dihedral"] = &dihedral;
     ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions);
     map<string, int> atoms;
+    set<string> variables;
     for (int i = 0; i < force.getNumParticlesPerSet(); i++) {
-        stringstream name;
+        stringstream name, x, y, z;
         name << 'p' << (i+1);
+        x << 'x' << (i+1);
+        y << 'y' << (i+1);
+        z << 'z' << (i+1);
         atoms[name.str()] = i;
+        variables.insert(x.str());
+        variables.insert(y.str());
+        variables.insert(z.str());
+        for (int j = 0; j < force.getNumPerParticleParameters(); j++) {
+            stringstream param;
+            param << force.getPerParticleParameterName(j) << (i+1);
+            variables.insert(param.str());
+        }
     }
-    return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals)).optimize();
+    for (int i = 0; i < force.getNumGlobalParameters(); i++)
+        variables.insert(force.getGlobalParameterName(i));
+    return ParsedExpression(replaceFunctions(expression.getRootNode(), atoms, distances, angles, dihedrals, variables)).optimize();
 }
 
 ExpressionTreeNode CustomManyParticleForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> atoms,
-        map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
+        map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals, set<string>& variables) {
     const Operation& op = node.getOperation();
+    if (op.getId() == Operation::VARIABLE && variables.find(op.getName()) == variables.end())
+        throw OpenMMException("CustomManyParticleForce: Unknown variable '"+op.getName()+"'");
     if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
     {
         // This is not an angle or dihedral, so process its children.
 
         vector<ExpressionTreeNode> children;
         for (int i = 0; i < (int) node.getChildren().size(); i++)
-            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals));
+            children.push_back(replaceFunctions(node.getChildren()[i], atoms, distances, angles, dihedrals, variables));
         return ExpressionTreeNode(op.clone(), children);
     }
     const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);

platforms/cpu/include/CpuKernels.h

@@ -92,6 +92,46 @@ private:
     Kernel referenceKernel;
 };
 
+/**
+ * This kernel is invoked by HarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
+ */
+class CpuCalcHarmonicAngleForceKernel : public CalcHarmonicAngleForceKernel {
+public:
+    CpuCalcHarmonicAngleForceKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) :
+            CalcHarmonicAngleForceKernel(name, platform), data(data), angleIndexArray(NULL), angleParamArray(NULL) {
+    }
+    ~CpuCalcHarmonicAngleForceKernel();
+    /**
+     * Initialize the kernel.
+     * 
+     * @param system     the System this kernel will be applied to
+     * @param force      the HarmonicAngleForce this kernel will be used for
+     */
+    void initialize(const System& system, const HarmonicAngleForce& force);
+    /**
+     * Execute the kernel to calculate the forces and/or energy.
+     *
+     * @param context        the context in which to execute this kernel
+     * @param includeForces  true if forces should be calculated
+     * @param includeEnergy  true if the energy should be calculated
+     * @return the potential energy due to the force
+     */
+    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the HarmonicAngleForce to copy the parameters from
+     */
+    void copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force);
+private:
+    CpuPlatform::PlatformData& data;
+    int numAngles;
+    int **angleIndexArray;
+    RealOpenMM **angleParamArray;
+    CpuBondForce bondForce;
+};
+
 /**
  * This kernel is invoked by PeriodicTorsionForce to calculate the forces acting on the system and the energy of the system.
  */
@@ -229,6 +269,7 @@ private:
     CpuNeighborList* neighborList;
     CpuNonbondedForce* nonbonded;
     Kernel optimizedPme;
+    CpuBondForce bondForce;
 };
 
 /**

platforms/cpu/include/CpuLangevinDynamics.h

 
-/* Portions copyright (c) 2013 Stanford University and Simbios.
+/* Portions copyright (c) 2013-2015 Stanford University and Simbios.
  * Authors: Peter Eastman
  * Contributors: 
  *
@@ -37,6 +37,7 @@ class CpuLangevinDynamics : public ReferenceStochasticDynamics {
 public:
     class Update1Task;
     class Update2Task;
+    class Update3Task;
     /**
      * Constructor.
      *
@@ -80,9 +81,21 @@ public:
     void updatePart2(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
                      std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime);
 
+    /**  
+     * Third update
+     * 
+     * @param numberOfAtoms       number of atoms
+     * @param atomCoordinates     atom coordinates
+     * @param velocities          velocities
+     * @param inverseMasses       inverse atom masses
+     */
+    void updatePart3(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
+                     std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime);
+
 private:
     void threadUpdate1(int threadIndex);
     void threadUpdate2(int threadIndex);
+    void threadUpdate3(int threadIndex);
     OpenMM::ThreadPool& threads;
     OpenMM::CpuRandom& random;
     std::vector<OpenMM_SFMT::SFMT> threadRandom;

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.
     
@@ -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]);
     }
@@ -737,6 +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.
 
@@ -950,6 +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;
@@ -958,15 +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.
@@ -988,10 +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/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/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() {
 }

platforms/cpu/tests/TestCpuEwald.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,311 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the Ewald summation method CPU implementation of NonbondedForce.
- */
+#include "CpuTests.h"
+#include "TestEwald.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CpuPlatform.h"
-#include "ReferencePlatform.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/System.h"
-#include "openmm/LangevinIntegrator.h"
-#include "openmm/VerletIntegrator.h"
-#include "openmm/internal/ContextImpl.h"
-#include "openmm/internal/NonbondedForceImpl.h"
-#include "SimTKOpenMMRealType.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-CpuPlatform platform;
-
-const double TOL = 1e-5;
-
-void testEwaldPME(bool includeExceptions) {
-
-//      Use amorphous NaCl system for the tests
-
-    const int numParticles = 894;
-    const double cutoff = 1.2;
-    const double boxSize = 3.00646;
-    double tol = 1e-5;
-
-    ReferencePlatform reference;
-    System system;
-    NonbondedForce* nonbonded = new NonbondedForce();
-    nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
-    nonbonded->setCutoffDistance(cutoff);
-    nonbonded->setEwaldErrorTolerance(tol);
-
-    for (int i = 0; i < numParticles/2; i++)
-        system.addParticle(22.99);
-    for (int i = 0; i < numParticles/2; i++)
-        system.addParticle(35.45);
-    for (int i = 0; i < numParticles/2; i++)
-        nonbonded->addParticle(1.0, 1.0,0.0);
-    for (int i = 0; i < numParticles/2; i++)
-        nonbonded->addParticle(-1.0, 1.0,0.0);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    system.addForce(nonbonded);
-
-    vector<Vec3> positions(numParticles);
-    #include "nacl_amorph.dat"
-    if (includeExceptions) {
-        // Add some exclusions.
-
-        for (int i = 0; i < numParticles-1; i++) {
-            Vec3 delta = positions[i]-positions[i+1];
-            if (sqrt(delta.dot(delta)) < 0.5*cutoff)
-                nonbonded->addException(i, i+1, i%2 == 0 ? 0.0 : 0.5, 1.0, 0.0);
-        }
-    }
-
-//    (1)  Check whether the Reference and CPU platforms agree when using Ewald Method
-
-    VerletIntegrator integrator1(0.01);
-    VerletIntegrator integrator2(0.01);
-    Context cpuContext(system, integrator1, platform);
-    Context referenceContext(system, integrator2, reference);
-    cpuContext.setPositions(positions);
-    referenceContext.setPositions(positions);
-    State cpuState = cpuContext.getState(State::Forces | State::Energy);
-    State referenceState = referenceContext.getState(State::Forces | State::Energy);
-    tol = 1e-2;
-    for (int i = 0; i < numParticles; i++) {
-        ASSERT_EQUAL_VEC(referenceState.getForces()[i], cpuState.getForces()[i], tol);
-    }
-    tol = 1e-5;
-    ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cpuState.getPotentialEnergy(), tol);
-
-//    (2) Check whether Ewald method in CPU is self-consistent
-
-    double norm = 0.0;
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 f = cpuState.getForces()[i];
-        norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
-    }
-
-    norm = std::sqrt(norm);
-    const double delta = 5e-3;
-    double step = delta/norm;
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 p = positions[i];
-        Vec3 f = cpuState.getForces()[i];
-        positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-    }
-    VerletIntegrator integrator3(0.01);
-    Context cpuContext2(system, integrator3, platform);
-    cpuContext2.setPositions(positions);
-
-    tol = 1e-2;
-    State cpuState2 = cpuContext2.getState(State::Energy);
-    ASSERT_EQUAL_TOL(norm, (cpuState2.getPotentialEnergy()-cpuState.getPotentialEnergy())/delta, tol)
-
-//    (3)  Check whether the Reference and CPU platforms agree when using PME
-
-    nonbonded->setNonbondedMethod(NonbondedForce::PME);
-    cpuContext.reinitialize();
-    referenceContext.reinitialize();
-    cpuContext.setPositions(positions);
-    referenceContext.setPositions(positions);
-    cpuState = cpuContext.getState(State::Forces | State::Energy);
-    referenceState = referenceContext.getState(State::Forces | State::Energy);
-    tol = 1e-2;
-    for (int i = 0; i < numParticles; i++) {
-        ASSERT_EQUAL_VEC(referenceState.getForces()[i], cpuState.getForces()[i], tol);
-    }
-    tol = 1e-5;
-    ASSERT_EQUAL_TOL(referenceState.getPotentialEnergy(), cpuState.getPotentialEnergy(), tol);
-
-//    (4) Check whether PME method in CPU is self-consistent
-
-    norm = 0.0;
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 f = cpuState.getForces()[i];
-        norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
-    }
-
-    norm = std::sqrt(norm);
-    step = delta/norm;
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 p = positions[i];
-        Vec3 f = cpuState.getForces()[i];
-        positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
-    }
-    VerletIntegrator integrator4(0.01);
-    Context cpuContext3(system, integrator4, platform);
-    cpuContext3.setPositions(positions);
-
-    tol = 1e-2;
-    State cpuState3 = cpuContext3.getState(State::Energy);
-    ASSERT_EQUAL_TOL(norm, (cpuState3.getPotentialEnergy()-cpuState.getPotentialEnergy())/delta, tol)
-}
-
-void testEwald2Ions() {
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    VerletIntegrator integrator(0.01);
-    NonbondedForce* nonbonded = new NonbondedForce();
-    nonbonded->addParticle(1.0, 1, 0);
-    nonbonded->addParticle(-1.0, 1, 0);
-    nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
-    const double cutoff = 2.0;
-    nonbonded->setCutoffDistance(cutoff);
-    nonbonded->setEwaldErrorTolerance(TOL);
-    system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
-    system.addForce(nonbonded);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(3.048000,2.764000,3.156000);
-    positions[1] = Vec3(2.809000,2.888000,2.571000);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    const vector<Vec3>& forces = state.getForces();
-
-    ASSERT_EQUAL_VEC(Vec3(-123.711,  64.1877, -302.716), forces[0], 10*TOL);
-    ASSERT_EQUAL_VEC(Vec3( 123.711, -64.1877,  302.716), forces[1], 10*TOL);
-    ASSERT_EQUAL_TOL(-217.276, state.getPotentialEnergy(), 0.01/*10*TOL*/);
-}
-
-void testTriclinic() {
-    // Create a triclinic box containing eight particles.
-
-    System system;
-    system.setDefaultPeriodicBoxVectors(Vec3(2.5, 0, 0), Vec3(0.5, 3.0, 0), Vec3(0.7, 0.9, 3.5));
-    for (int i = 0; i < 8; i++)
-        system.addParticle(1.0);
-    NonbondedForce* force = new NonbondedForce();
-    system.addForce(force);
-    force->setNonbondedMethod(NonbondedForce::PME);
-    force->setCutoffDistance(1.0);
-    force->setPMEParameters(3.45891, 32, 40, 48);
-    for (int i = 0; i < 4; i++)
-        force->addParticle(-1, 0.440104, 0.4184); // Cl parameters
-    for (int i = 0; i < 4; i++)
-        force->addParticle(1, 0.332840, 0.0115897); // Na parameters
-    vector<Vec3> positions(8);
-    positions[0] = Vec3(1.744, 2.788, 3.162);
-    positions[1] = Vec3(1.048, 0.762, 2.340);
-    positions[2] = Vec3(2.489, 1.570, 2.817);
-    positions[3] = Vec3(1.027, 1.893, 3.271);
-    positions[4] = Vec3(0.937, 0.825, 0.009);
-    positions[5] = Vec3(2.290, 1.887, 3.352);
-    positions[6] = Vec3(1.266, 1.111, 2.894);
-    positions[7] = Vec3(0.933, 1.862, 3.490);
-
-    // Compute the forces and energy.
-
-    VerletIntegrator integ(0.001);
-    Context context(system, integ, platform);
-    context.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-
-    // Compare them to values computed by Gromacs.
-
-    double expectedEnergy = -963.370;
-    vector<Vec3> expectedForce(8);
-    expectedForce[0] = Vec3(4.25253e+01, -1.23503e+02, 1.22139e+02);
-    expectedForce[1] = Vec3(9.74752e+01, 1.68213e+02, 1.93169e+02);
-    expectedForce[2] = Vec3(-1.50348e+02, 1.29165e+02, 3.70435e+02);
-    expectedForce[3] = Vec3(9.18644e+02, -3.52571e+00, -1.34772e+03);
-    expectedForce[4] = Vec3(-1.61193e+02, 9.01528e+01, -7.12904e+01);
-    expectedForce[5] = Vec3(2.82630e+02, 2.78029e+01, -3.72864e+02);
-    expectedForce[6] = Vec3(-1.47454e+02, -2.14448e+02, -3.55789e+02);
-    expectedForce[7] = Vec3(-8.82195e+02, -7.39132e+01, 1.46202e+03);
-    for (int i = 0; i < 8; i++) {
-        ASSERT_EQUAL_VEC(expectedForce[i], state.getForces()[i], 1e-4);
-    }
-    ASSERT_EQUAL_TOL(expectedEnergy, state.getPotentialEnergy(), 1e-4);
-}
-
-void testErrorTolerance(NonbondedForce::NonbondedMethod method) {
-    // Create a cloud of random point charges.
-
-    const int numParticles = 51;
-    const double boxWidth = 5.0;
-    System system;
-    system.setDefaultPeriodicBoxVectors(Vec3(boxWidth, 0, 0), Vec3(0, boxWidth, 0), Vec3(0, 0, boxWidth));
-    NonbondedForce* force = new NonbondedForce();
-    system.addForce(force);
-    vector<Vec3> positions(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    for (int i = 0; i < numParticles; i++) {
-        system.addParticle(1.0);
-        force->addParticle(-1.0+i*2.0/(numParticles-1), 1.0, 0.0);
-        positions[i] = Vec3(boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt), boxWidth*genrand_real2(sfmt));
-    }
-    force->setNonbondedMethod(method);
-
-    // For various values of the cutoff and error tolerance, see if the actual error is reasonable.
-
-    for (double cutoff = 1.0; cutoff < boxWidth/2; cutoff *= 1.2) {
-        force->setCutoffDistance(cutoff);
-        vector<Vec3> refForces;
-        double norm = 0.0;
-        for (double tol = 5e-5; tol < 1e-3; tol *= 2.0) {
-            force->setEwaldErrorTolerance(tol);
-            VerletIntegrator integrator(0.01);
-            Context context(system, integrator, platform);
-            context.setPositions(positions);
-            State state = context.getState(State::Forces);
-            if (refForces.size() == 0) {
-                refForces = state.getForces();
-                for (int i = 0; i < numParticles; i++)
-                    norm += refForces[i].dot(refForces[i]);
-                norm = sqrt(norm);
-            }
-            else {
-                double diff = 0.0;
-                for (int i = 0; i < numParticles; i++) {
-                    Vec3 delta = refForces[i]-state.getForces()[i];
-                    diff += delta.dot(delta);
-                }
-                diff = sqrt(diff)/norm;
-                ASSERT(diff < 2*tol);
-            }
-            if (method == NonbondedForce::PME) {
-                // See if the PME parameters were calculated correctly.
-
-                double expectedAlpha, actualAlpha;
-                int expectedSize[3], actualSize[3];
-                NonbondedForceImpl::calcPMEParameters(system, *force, expectedAlpha, expectedSize[0], expectedSize[1], expectedSize[2]);
-                force->getPMEParametersInContext(context, actualAlpha, actualSize[0], actualSize[1], actualSize[2]);
-                ASSERT_EQUAL_TOL(expectedAlpha, actualAlpha, 1e-5);
-                for (int i = 0; i < 3; i++) {
-                    ASSERT(actualSize[i] >= expectedSize[i]);
-                    ASSERT(actualSize[i] < expectedSize[i]+10);
-                }
-            }
-        }
-    }
-}
-
-int main(int argc, char* argv[]) {
-    try {
-        if (!CpuPlatform::isProcessorSupported()) {
-            cout << "CPU is not supported.  Exiting." << endl;
-            return 0;
-        }
-        testEwaldPME(false);
-        testEwaldPME(true);
-//        testEwald2Ions();
-        testTriclinic();
-        testErrorTolerance(NonbondedForce::Ewald);
-        testErrorTolerance(NonbondedForce::PME);
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }

platforms/cpu/tests/TestCpuGBSAOBCForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,244 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the CPU implementation of GBSAOBCForce.
- */
+#include "CpuTests.h"
+#include "TestGBSAOBCForce.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CpuPlatform.h"
-#include "openmm/GBSAOBCForce.h"
-#include "openmm/System.h"
-#include "openmm/LangevinIntegrator.h"
-#include "openmm/NonbondedForce.h"
-#include "SimTKOpenMMRealType.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-void testSingleParticle() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(2.0);
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForce* forceField = new GBSAOBCForce();
-    forceField->addParticle(0.5, 0.15, 1);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, 0, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-    double bornRadius = 0.15-0.009; // dielectric offset
-    double eps0 = EPSILON0;
-    double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
-    double extendedRadius = 0.15+0.14; // probe radius
-    double nonpolarEnergy = 4*PI_M*2.25936*extendedRadius*extendedRadius*std::pow(0.15/bornRadius, 6.0);
-    ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
-    
-    // Change the parameters and see if it is still correct.
-    
-    forceField->setParticleParameters(0, 0.4, 0.25, 1);
-    forceField->updateParametersInContext(context);
-    state = context.getState(State::Energy);
-    bornRadius = 0.25-0.009; // dielectric offset
-    bornEnergy = (-0.4*0.4/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
-    extendedRadius = 0.25+0.14;
-    nonpolarEnergy = 4*PI_M*2.25936*extendedRadius*extendedRadius*std::pow(0.25/bornRadius, 6.0);
-    ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
-}
-
-void testGlobalSettings() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(2.0);
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForce* forceField = new GBSAOBCForce();
-    forceField->addParticle(0.5, 0.15, 1);
-    const double soluteDielectric = 2.1;
-    const double solventDielectric = 35.0;
-    const double surfaceAreaEnergy = 0.75;
-    forceField->setSoluteDielectric(soluteDielectric);
-    forceField->setSolventDielectric(solventDielectric);
-    forceField->setSurfaceAreaEnergy(surfaceAreaEnergy);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(1);
-    positions[0] = Vec3(0, 0, 0);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-    double bornRadius = 0.15-0.009; // dielectric offset
-    double eps0 = EPSILON0;
-    double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/soluteDielectric-1.0/solventDielectric)/bornRadius;
-    double extendedRadius = 0.15+0.14; // probe radius
-    double nonpolarEnergy = 4*PI_M*surfaceAreaEnergy*extendedRadius*extendedRadius*std::pow(0.15/bornRadius, 6.0);
-    ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
-}
-
-void testCutoffAndPeriodic() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(1.0);
-    system.addParticle(1.0);
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-    GBSAOBCForce* gbsa = new GBSAOBCForce();
-    NonbondedForce* nonbonded = new NonbondedForce();
-    gbsa->addParticle(-1, 0.15, 1);
-    nonbonded->addParticle(-1, 1, 0);
-    gbsa->addParticle(1, 0.15, 1);
-    nonbonded->addParticle(1, 1, 0);
-    const double cutoffDistance = 3.0;
-    const double boxSize = 10.0;
-    nonbonded->setCutoffDistance(cutoffDistance);
-    gbsa->setCutoffDistance(cutoffDistance);
-    system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    system.addForce(gbsa);
-    system.addForce(nonbonded);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(0, 0, 0);
-    positions[1] = Vec3(2, 0, 0);
-
-    // Calculate the forces for both cutoff and periodic with two different atom positions.
-
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
-    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffNonPeriodic);
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    State state1 = context.getState(State::Forces);
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
-    context.reinitialize();
-    context.setPositions(positions);
-    State state2 = context.getState(State::Forces);
-    positions[1][0]+= boxSize;
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
-    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffNonPeriodic);
-    context.reinitialize();
-    context.setPositions(positions);
-    State state3 = context.getState(State::Forces);
-    nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
-    gbsa->setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
-    context.reinitialize();
-    context.setPositions(positions);
-    State state4 = context.getState(State::Forces);
-
-    // All forces should be identical, exception state3 which should be zero.
-
-    ASSERT_EQUAL_VEC(state1.getForces()[0], state2.getForces()[0], 0.01);
-    ASSERT_EQUAL_VEC(state1.getForces()[1], state2.getForces()[1], 0.01);
-    ASSERT_EQUAL_VEC(state1.getForces()[0], state4.getForces()[0], 0.01);
-    ASSERT_EQUAL_VEC(state1.getForces()[1], state4.getForces()[1], 0.01);
-    ASSERT_EQUAL_VEC(state3.getForces()[0], Vec3(0, 0, 0), 0.01);
-    ASSERT_EQUAL_VEC(state3.getForces()[1], Vec3(0, 0, 0), 0.01);
-}
-
-void testForce(int numParticles, NonbondedForce::NonbondedMethod method, GBSAOBCForce::NonbondedMethod method2) {
-    CpuPlatform platform;
-    ReferencePlatform reference;
-    System system;
-    GBSAOBCForce* gbsa = new GBSAOBCForce();
-    NonbondedForce* nonbonded = new NonbondedForce();
-    for (int i = 0; i < numParticles; ++i) {
-        system.addParticle(1.0);
-        double charge = i%2 == 0 ? -1 : 1;
-        gbsa->addParticle(charge, 0.15, 1);
-        nonbonded->addParticle(charge, 1, 0);
-    }
-    nonbonded->setNonbondedMethod(method);
-    gbsa->setNonbondedMethod(method2);
-    nonbonded->setCutoffDistance(3.0);
-    gbsa->setCutoffDistance(3.0);
-    int grid = (int) floor(0.5+pow(numParticles, 1.0/3.0));
-    if (method == NonbondedForce::CutoffPeriodic) {
-        double boxSize = (grid+1)*1.1;
-        system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
-    }
-    system.addForce(gbsa);
-    system.addForce(nonbonded);
-    LangevinIntegrator integrator1(0, 0.1, 0.01);
-    LangevinIntegrator integrator2(0, 0.1, 0.01);
-    Context context(system, integrator1, platform);
-    Context refContext(system, integrator2, reference);
-
-    // Set random (but uniformly distributed) positions for all the particles.
-
-    vector<Vec3> positions(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    for (int i = 0; i < grid; i++)
-        for (int j = 0; j < grid; j++)
-            for (int k = 0; k < grid; k++)
-                positions[i*grid*grid+j*grid+k] = Vec3(i*1.1, j*1.1, k*1.1);
-    for (int i = 0; i < numParticles; ++i)
-        positions[i] = positions[i] + Vec3(0.5*genrand_real2(sfmt), 0.5*genrand_real2(sfmt), 0.5*genrand_real2(sfmt));
-    context.setPositions(positions);
-    refContext.setPositions(positions);
-    State state = context.getState(State::Forces | State::Energy);
-    State refState = refContext.getState(State::Forces | State::Energy);
-
-    // Make sure the CPU and Reference platforms agree.
-
-    double norm = 0.0;
-    double diff = 0.0;
-    for (int i = 0; i < numParticles; ++i) {
-        Vec3 f = state.getForces()[i];
-        norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
-        Vec3 delta = f-refState.getForces()[i];
-        diff += delta[0]*delta[0] + delta[1]*delta[1] + delta[2]*delta[2];
-    }
-    norm = std::sqrt(norm);
-    diff = std::sqrt(diff);
-    ASSERT_EQUAL_TOL(0.0, diff, 0.001*norm);
-    ASSERT_EQUAL_TOL(state.getPotentialEnergy(), refState.getPotentialEnergy(), 1e-3);
-
-    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
-    // (This doesn't work with cutoffs, since the energy changes discontinuously at the cutoff distance.)
-
-    if (method == NonbondedForce::NoCutoff)
-    {
-        const double delta = 0.3;
-        double step = 0.5*delta/norm;
-        vector<Vec3> positions2(numParticles), positions3(numParticles);
-        for (int i = 0; i < numParticles; ++i) {
-            Vec3 p = positions[i];
-            Vec3 f = state.getForces()[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())/delta, 1e-2)
-    }
-}
-
-int main() {
-    try {
-        if (!CpuPlatform::isProcessorSupported()) {
-            cout << "CPU is not supported.  Exiting." << endl;
-            return 0;
-        }
-        testSingleParticle();
-        testGlobalSettings();
-        testCutoffAndPeriodic();
-        for (int i = 5; i < 11; i++) {
-            testForce(i*i*i, NonbondedForce::NoCutoff, GBSAOBCForce::NoCutoff);
-            testForce(i*i*i, NonbondedForce::CutoffNonPeriodic, GBSAOBCForce::CutoffNonPeriodic);
-            testForce(i*i*i, NonbondedForce::CutoffPeriodic, GBSAOBCForce::CutoffPeriodic);
-        }
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }

platforms/cpu/tests/TestCpuHarmonicAngleForce.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) 2008-2015 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 "TestHarmonicAngleForce.h"
+
+void testParallelComputation() {
+    System system;
+    const int numParticles = 200;
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(1.0);
+    HarmonicAngleForce* force = new HarmonicAngleForce();
+    for (int i = 2; i < numParticles; i++)
+        force->addAngle(i-2, i-1, i, 1.1, i);
+    system.addForce(force);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; i++)
+        positions[i] = Vec3(i, i%2, 0);
+    VerletIntegrator integrator1(0.01);
+    ReferencePlatform reference;
+    Context context1(system, integrator1, reference);
+    context1.setPositions(positions);
+    State state1 = context1.getState(State::Forces | State::Energy);
+    VerletIntegrator integrator2(0.01);
+    Context context2(system, integrator2, platform);
+    context2.setPositions(positions);
+    State state2 = context2.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
+    for (int i = 0; i < numParticles; i++)
+        ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
+}
+
+void runPlatformTests() {
+    testParallelComputation();
+}

platforms/cpu/tests/TestCpuLangevinIntegrator.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2015 Stanford University and the Authors.           *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,255 +29,8 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-/**
- * This tests the reference implementation of LangevinIntegrator.
- */
+#include "CpuTests.h"
+#include "TestLangevinIntegrator.h"
 
-#include "openmm/internal/AssertionUtilities.h"
-#include "openmm/Context.h"
-#include "CpuPlatform.h"
-#include "openmm/HarmonicBondForce.h"
-#include "openmm/NonbondedForce.h"
-#include "openmm/System.h"
-#include "openmm/LangevinIntegrator.h"
-#include "SimTKOpenMMRealType.h"
-#include "sfmt/SFMT.h"
-#include <iostream>
-#include <vector>
-
-using namespace OpenMM;
-using namespace std;
-
-const double TOL = 1e-5;
-
-void testSingleBond() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(2.0);
-    system.addParticle(2.0);
-    LangevinIntegrator integrator(0, 0.1, 0.01);
-    HarmonicBondForce* forceField = new HarmonicBondForce();
-    forceField->addBond(0, 1, 1.5, 1);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(-1, 0, 0);
-    positions[1] = Vec3(1, 0, 0);
-    context.setPositions(positions);
-    
-    // This is simply a damped harmonic oscillator, so compare it to the analytical solution.
-    
-    double freq = std::sqrt(1-0.05*0.05);
-    for (int i = 0; i < 1000; ++i) {
-        State state = context.getState(State::Positions | State::Velocities);
-        double time = state.getTime();
-        double expectedDist = 1.5+0.5*std::exp(-0.05*time)*std::cos(freq*time);
-        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
-        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
-        double expectedSpeed = -0.5*std::exp(-0.05*time)*(0.05*std::cos(freq*time)+freq*std::sin(freq*time));
-        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
-        ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
-        integrator.step(1);
-    }
-    
-    // Not set the friction to a tiny value and see if it conserves energy.
-    
-    integrator.setFriction(5e-5);
-    context.setPositions(positions);
-    State state = context.getState(State::Energy);
-    double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
-    for (int i = 0; i < 1000; ++i) {
-        state = context.getState(State::Energy);
-        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
-        ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
-        integrator.step(1);
-    }
-}
-
-void testTemperature() {
-    const int numParticles = 8;
-    const double temp = 100.0;
-    CpuPlatform platform;
-    System system;
-    LangevinIntegrator integrator(temp, 2.0, 0.01);
-    NonbondedForce* forceField = new NonbondedForce();
-    for (int i = 0; i < numParticles; ++i) {
-        system.addParticle(2.0);
-        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
-    }
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(numParticles);
-    for (int i = 0; i < numParticles; ++i)
-        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
-    context.setPositions(positions);
-    
-    // Let it equilibrate.
-    
-    integrator.step(10000);
-    
-    // Now run it for a while and see if the temperature is correct.
-    
-    double ke = 0.0;
-    for (int i = 0; i < 10000; ++i) {
-        State state = context.getState(State::Energy);
-        ke += state.getKineticEnergy();
-        integrator.step(1);
-    }
-    ke /= 10000;
-    double expected = 0.5*numParticles*3*BOLTZ*temp;
-    ASSERT_USUALLY_EQUAL_TOL(expected, ke, 6/std::sqrt(10000.0));
-}
-
-void testConstraints() {
-    const int numParticles = 8;
-    const double temp = 100.0;
-    CpuPlatform platform;
-    System system;
-    LangevinIntegrator integrator(temp, 2.0, 0.01);
-    integrator.setConstraintTolerance(1e-5);
-    NonbondedForce* forceField = new NonbondedForce();
-    for (int i = 0; i < numParticles; ++i) {
-        system.addParticle(10.0);
-        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
-    }
-    for (int i = 0; i < numParticles-1; ++i)
-        system.addConstraint(i, i+1, 1.0);
-    system.addForce(forceField);
-    Context context(system, integrator, platform);
-    vector<Vec3> positions(numParticles);
-    vector<Vec3> velocities(numParticles);
-    OpenMM_SFMT::SFMT sfmt;
-    init_gen_rand(0, sfmt);
-
-    for (int i = 0; i < numParticles; ++i) {
-        positions[i] = Vec3(i/2, (i+1)/2, 0);
-        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
-    }
-    context.setPositions(positions);
-    context.setVelocities(velocities);
-    
-    // Simulate it and see whether the constraints remain satisfied.
-    
-    for (int i = 0; i < 1000; ++i) {
-        State state = context.getState(State::Positions);
-        for (int j = 0; j < numParticles-1; ++j) {
-            Vec3 p1 = state.getPositions()[j];
-            Vec3 p2 = state.getPositions()[j+1];
-            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
-            ASSERT_EQUAL_TOL(1.0, dist, 2e-5);
-        }
-        integrator.step(1);
-    }
-}
-
-void testConstrainedMasslessParticles() {
-    CpuPlatform platform;
-    System system;
-    system.addParticle(0.0);
-    system.addParticle(1.0);
-    system.addConstraint(0, 1, 1.5);
-    vector<Vec3> positions(2);
-    positions[0] = Vec3(-1, 0, 0);
-    positions[1] = Vec3(1, 0, 0);
-    LangevinIntegrator integrator(300.0, 2.0, 0.01);
-    bool failed = false;
-    try {
-        // This should throw an exception.
-        
-        Context context(system, integrator, platform);
-    }
-    catch (exception& ex) {
-        failed = true;
-    }
-    ASSERT(failed);
-    
-    // Now make both particles massless, which should work.
-    
-    system.setParticleMass(1, 0.0);
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    context.setVelocitiesToTemperature(300.0);
-    integrator.step(1);
-    State state = context.getState(State::Velocities | State::Positions);
-    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
-}
-
-void testRandomSeed() {
-    const int numParticles = 8;
-    const double temp = 100.0;
-    const double collisionFreq = 10.0;
-    CpuPlatform platform;
-    System system;
-    LangevinIntegrator integrator(temp, 2.0, 0.01);
-    NonbondedForce* forceField = new NonbondedForce();
-    for (int i = 0; i < numParticles; ++i) {
-        system.addParticle(2.0);
-        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
-    }
-    system.addForce(forceField);
-    vector<Vec3> positions(numParticles);
-    vector<Vec3> velocities(numParticles);
-    for (int i = 0; i < numParticles; ++i) {
-        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
-        velocities[i] = Vec3(0, 0, 0);
-    }
-
-    // Try twice with the same random seed.
-
-    integrator.setRandomNumberSeed(5);
-    Context context(system, integrator, platform);
-    context.setPositions(positions);
-    context.setVelocities(velocities);
-    integrator.step(10);
-    State state1 = context.getState(State::Positions);
-    context.reinitialize();
-    context.setPositions(positions);
-    context.setVelocities(velocities);
-    integrator.step(10);
-    State state2 = context.getState(State::Positions);
-
-    // Try twice with a different random seed.
-
-    integrator.setRandomNumberSeed(10);
-    context.reinitialize();
-    context.setPositions(positions);
-    context.setVelocities(velocities);
-    integrator.step(10);
-    State state3 = context.getState(State::Positions);
-    context.reinitialize();
-    context.setPositions(positions);
-    context.setVelocities(velocities);
-    integrator.step(10);
-    State state4 = context.getState(State::Positions);
-
-    // Compare the results.
-
-    for (int i = 0; i < numParticles; i++) {
-        for (int j = 0; j < 3; j++) {
-            ASSERT_EQUAL_TOL(state1.getPositions()[i][j], state2.getPositions()[i][j], 1e-5);
-            ASSERT_EQUAL_TOL(state3.getPositions()[i][j], state4.getPositions()[i][j], 1e-5);
-            ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
-        }
-    }
-}
-
-int main() {
-    try {
-        if (!CpuPlatform::isProcessorSupported()) {
-            cout << "CPU is not supported.  Exiting." << endl;
-            return 0;
-        }
-        testSingleBond();
-        testTemperature();
-        testConstraints();
-        testConstrainedMasslessParticles();
-        testRandomSeed();
-    }
-    catch(const exception& e) {
-        cout << "exception: " << e.what() << endl;
-        return 1;
-    }
-    cout << "Done" << endl;
-    return 0;
+void runPlatformTests() {
 }