Reference implementation of CustomCVForce

openmmapi/include/openmm/CustomCVForce.h

@@ -32,10 +32,11 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "TabulatedFunction.h"
 #include "Force.h"
-#include <vector>
+#include "TabulatedFunction.h"
 #include "internal/windowsExport.h"
+#include <string>
+#include <vector>
 
 namespace OpenMM {
 
@@ -236,6 +237,22 @@ public:
      *                       stored into this
      */
     void getCollectiveVariableValues(Context& context, std::vector<double>& values);
+    /**
+     * Get the inner Context used for evaluating collective variables.
+     * 
+     * When you create a Context for a System that contains a CustomCVForce, internally
+     * it creates a new System, adds the Forces that define the CVs to it, creates a new
+     * Context for that System, and uses it to evaluate the variables.  In most cases you
+     * can ignore all of this.  It is just an implementation detail.  However, there are
+     * a few cases where you need to directly access that internal Context.  For example,
+     * if you want to modify one of the Forces that defines a collective variable and
+     * call updateParametersInContext() on it, you need to pass that inner Context to it.
+     * This method returns a reference to it.
+     * 
+     * @param context    the Context containing the CustomCVForce
+     * @return the inner Context used to evaluate the collective variables
+     */
+    Context& getInnerContext(Context& context);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.

openmmapi/include/openmm/internal/CustomCVForceImpl.h

@@ -63,6 +63,7 @@ public:
     std::map<std::string, double> getDefaultParameters();
     std::vector<std::string> getKernelNames();
     void getCollectiveVariableValues(ContextImpl& context, std::vector<double>& values);
+    Context& getInnerContext();
 private:
     const CustomCVForce& owner;
     Kernel kernel;

openmmapi/src/ContextImpl.cpp

@@ -119,8 +119,6 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
     kernelNames.push_back(VirtualSitesKernel::Name());
     for (int i = 0; i < system.getNumForces(); ++i) {
         forceImpls.push_back(system.getForce(i).createImpl());
-        map<string, double> forceParameters = forceImpls[forceImpls.size()-1]->getDefaultParameters();
-        parameters.insert(forceParameters.begin(), forceParameters.end());
         vector<string> forceKernels = forceImpls[forceImpls.size()-1]->getKernelNames();
         kernelNames.insert(kernelNames.begin(), forceKernels.begin(), forceKernels.end());
     }
@@ -177,8 +175,11 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
     Vec3 periodicBoxVectors[3];
     system.getDefaultPeriodicBoxVectors(periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
     updateStateDataKernel.getAs<UpdateStateDataKernel>().setPeriodicBoxVectors(*this, periodicBoxVectors[0], periodicBoxVectors[1], periodicBoxVectors[2]);
-    for (size_t i = 0; i < forceImpls.size(); ++i)
+    for (size_t i = 0; i < forceImpls.size(); ++i) {
         forceImpls[i]->initialize(*this);
+        map<string, double> forceParameters = forceImpls[i]->getDefaultParameters();
+        parameters.insert(forceParameters.begin(), forceParameters.end());
+    }
     integrator.initialize(*this);
     updateStateDataKernel.getAs<UpdateStateDataKernel>().setVelocities(*this, vector<Vec3>(numParticles));
 }

openmmapi/src/CustomCVForce.cpp

@@ -148,6 +148,10 @@ ForceImpl* CustomCVForce::createImpl() const {
     return new CustomCVForceImpl(*this);
 }
 
+Context& CustomCVForce::getInnerContext(Context& context) {
+    return dynamic_cast<CustomCVForceImpl&>(getImplInContext(context)).getInnerContext();
+}
+
 bool CustomCVForce::usesPeriodicBoundaryConditions() const {
     for (auto& variable : variables)
         if (variable.variable->usesPeriodicBoundaryConditions())

openmmapi/src/CustomCVForceImpl.cpp

@@ -71,6 +71,8 @@ void CustomCVForceImpl::initialize(ContextImpl& context) {
     for (auto& name : platform.getPropertyNames())
         properties[name] = platform.getPropertyValue(context.getOwner(), name);
     innerContext = new Context(innerSystem, innerIntegrator, platform, properties);
+    vector<Vec3> positions(system.getNumParticles(), Vec3());
+    innerContext->setPositions(positions);
     
     // Create the kernel.
     
@@ -92,6 +94,7 @@ vector<string> CustomCVForceImpl::getKernelNames() {
 
 map<string, double> CustomCVForceImpl::getDefaultParameters() {
     map<string, double> parameters;
+    parameters.insert(innerContext->getParameters().begin(), innerContext->getParameters().end());
     for (int i = 0; i < owner.getNumGlobalParameters(); i++)
         parameters[owner.getGlobalParameterName(i)] = owner.getGlobalParameterDefaultValue(i);
     return parameters;
@@ -101,7 +104,11 @@ void CustomCVForceImpl::getCollectiveVariableValues(ContextImpl& context, vector
     kernel.getAs<CalcCustomCVForceKernel>().copyState(context, getContextImpl(*innerContext));
     values.clear();
     for (int i = 0; i < innerSystem.getNumForces(); i++) {
-        double value = innerContext->getState(State::Energy).getPotentialEnergy();
+        double value = innerContext->getState(State::Energy, false, 1<<i).getPotentialEnergy();
         values.push_back(value);
     }
 }
+
+Context& CustomCVForceImpl::getInnerContext() {
+    return *innerContext;
+}

platforms/reference/include/ReferenceCustomCVForce.h

+
+/* Portions copyright (c) 2017 Stanford University and Simbios.
+ * Contributors: Peter Eastman
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceCustomCVForce_H__
+#define __ReferenceCustomCVForce_H__
+
+#include "openmm/CustomCVForce.h"
+#include "openmm/internal/ContextImpl.h"
+#include "lepton/ExpressionProgram.h"
+#include <map>
+#include <string>
+#include <vector>
+
+namespace OpenMM {
+
+class ReferenceCustomCVForce {
+private:
+    Lepton::ExpressionProgram energyExpression;
+    std::vector<std::string> variableNames, paramDerivNames;
+    std::vector<Lepton::ExpressionProgram> variableDerivExpressions;
+    std::vector<Lepton::ExpressionProgram> paramDerivExpressions;
+
+public:
+    /**
+     * Constructor
+     */
+    ReferenceCustomCVForce(const OpenMM::CustomCVForce& force);
+
+    /**
+     * Destructor
+     */
+    ~ReferenceCustomCVForce();
+
+    /**
+     * Calculate the interaction.
+     * 
+     * @param innerContext       the context created by the force for evaluating collective variables
+     * @param atomCoordinates    atom coordinates
+     * @param globalParameters   the values of global parameters
+     * @param forces             the forces are added to this
+     * @param totalEnergy        the energy is added to this
+     * @param energyParamDerivs  parameter derivatives are added to this
+     */
+   void calculateIxn(ContextImpl& innerContext, std::vector<OpenMM::Vec3>& atomCoordinates,
+                     const std::map<std::string, double>& globalParameters,
+                     std::vector<OpenMM::Vec3>& forces, double* totalEnergy, std::map<std::string, double>& energyParamDerivs) const;
+};
+
+} // namespace OpenMM
+
+#endif // __ReferenceCustomCVForce_H__

platforms/reference/include/ReferenceKernels.h

@@ -45,6 +45,7 @@ class ReferenceObc;
 class ReferenceAndersenThermostat;
 class ReferenceCustomCentroidBondIxn;
 class ReferenceCustomCompoundBondIxn;
+class ReferenceCustomCVForce;
 class ReferenceCustomHbondIxn;
 class ReferenceCustomManyParticleIxn;
 class ReferenceGayBerneForce;
@@ -1006,6 +1007,43 @@ private:
     ReferenceGayBerneForce* ixn;
 };
 
+/**
+ * This kernel is invoked by CustomCVForce to calculate the forces acting on the system and the energy of the system.
+ */
+class ReferenceCalcCustomCVForceKernel : public CalcCustomCVForceKernel {
+public:
+    ReferenceCalcCustomCVForceKernel(std::string name, const Platform& platform) : CalcCustomCVForceKernel(name, platform), ixn(NULL) {
+    }
+    ~ReferenceCalcCustomCVForceKernel();
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     * @param force      the CustomCVForce this kernel will be used for
+     */
+    void initialize(const System& system, const CustomCVForce& force);
+    /**
+     * Execute the kernel to calculate the forces and/or energy.
+     *
+     * @param context        the context in which to execute this kernel
+     * @param innerContext   the context created by the CustomCVForce for computing collective variables
+     * @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, ContextImpl& innerContext, bool includeForces, bool includeEnergy);
+    /**
+     * Copy state information to the inner context.
+     *
+     * @param context        the context in which to execute this kernel
+     * @param innerContext   the context created by the CustomCVForce for computing collective variables
+     */
+    void copyState(ContextImpl& context, ContextImpl& innerContext);
+private:
+    ReferenceCustomCVForce* ixn;
+    std::vector<std::string> globalParameterNames, energyParamDerivNames;
+};
+
 /**
  * This kernel is invoked by VerletIntegrator to take one time step.
  */

platforms/reference/src/ReferenceKernelFactory.cpp

@@ -78,6 +78,8 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
         return new ReferenceCalcCustomCentroidBondForceKernel(name, platform);
     if (name == CalcCustomCompoundBondForceKernel::Name())
         return new ReferenceCalcCustomCompoundBondForceKernel(name, platform);
+    if (name == CalcCustomCVForceKernel::Name())
+        return new ReferenceCalcCustomCVForceKernel(name, platform);
     if (name == CalcCustomManyParticleForceKernel::Name())
         return new ReferenceCalcCustomManyParticleForceKernel(name, platform);
     if (name == CalcGayBerneForceKernel::Name())

platforms/reference/src/ReferenceKernels.cpp

@@ -42,6 +42,7 @@
 #include "ReferenceCustomBondIxn.h"
 #include "ReferenceCustomCentroidBondIxn.h"
 #include "ReferenceCustomCompoundBondIxn.h"
+#include "ReferenceCustomCVForce.h"
 #include "ReferenceCustomDynamics.h"
 #include "ReferenceCustomExternalIxn.h"
 #include "ReferenceCustomGBIxn.h"
@@ -2015,6 +2016,44 @@ void ReferenceCalcGayBerneForceKernel::copyParametersToContext(ContextImpl& cont
     ixn = new ReferenceGayBerneForce(force);
 }
 
+ReferenceCalcCustomCVForceKernel::~ReferenceCalcCustomCVForceKernel() {
+    if (ixn != NULL)
+        delete ixn;
+}
+
+void ReferenceCalcCustomCVForceKernel::initialize(const System& system, const CustomCVForce& force) {
+    for (int i = 0; i < force.getNumGlobalParameters(); i++)
+        globalParameterNames.push_back(force.getGlobalParameterName(i));
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        energyParamDerivNames.push_back(force.getEnergyParameterDerivativeName(i));
+    ixn = new ReferenceCustomCVForce(force);
+}
+
+double ReferenceCalcCustomCVForceKernel::execute(ContextImpl& context, ContextImpl& innerContext, bool includeForces, bool includeEnergy) {
+    copyState(context, innerContext);
+    vector<Vec3>& posData = extractPositions(context);
+    vector<Vec3>& forceData = extractForces(context);
+    double energy = 0;
+    map<string, double> globalParameters;
+    for (auto& name : globalParameterNames)
+        globalParameters[name] = context.getParameter(name);
+    map<string, double>& energyParamDerivs = extractEnergyParameterDerivatives(context);
+    ixn->calculateIxn(innerContext, posData, globalParameters, forceData, includeEnergy ? &energy : NULL, energyParamDerivs);
+    return energy;
+}
+
+void ReferenceCalcCustomCVForceKernel::copyState(ContextImpl& context, ContextImpl& innerContext) {
+    extractPositions(innerContext) = extractPositions(context);
+    extractVelocities(innerContext) = extractVelocities(context);
+    extractBoxSize(innerContext) = extractBoxSize(context);
+    for (int i = 0; i < 3; i++)
+        extractBoxVectors(innerContext)[i] = extractBoxVectors(context)[i];
+    reinterpret_cast<ReferencePlatform::PlatformData*>(innerContext.getPlatformData())->time = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData())->time;
+    map<string, double> innerParameters = innerContext.getParameters();
+    for (auto& param : innerParameters)
+        innerContext.setParameter(param.first, context.getParameter(param.first));
+}
+
 ReferenceIntegrateVerletStepKernel::~ReferenceIntegrateVerletStepKernel() {
     if (dynamics)
         delete dynamics;

platforms/reference/src/ReferencePlatform.cpp

@@ -64,6 +64,7 @@ ReferencePlatform::ReferencePlatform() {
     registerKernelFactory(CalcCustomHbondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomCentroidBondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomCompoundBondForceKernel::Name(), factory);
+    registerKernelFactory(CalcCustomCVForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomManyParticleForceKernel::Name(), factory);
     registerKernelFactory(CalcGayBerneForceKernel::Name(), factory);
     registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);

platforms/reference/src/SimTKReference/ReferenceCustomCVForce.cpp

+
+/* Portions copyright (c) 2009-2017 Stanford University and Simbios.
+ * Contributors: Peter Eastman
+ *
+ * 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 "ReferenceCustomCVForce.h"
+#include "ReferencePlatform.h"
+#include "ReferenceTabulatedFunction.h"
+#include "lepton/CustomFunction.h"
+#include "lepton/ParsedExpression.h"
+#include "lepton/Parser.h"
+
+using namespace OpenMM;
+using namespace std;
+
+ReferenceCustomCVForce::ReferenceCustomCVForce(const CustomCVForce& force) {
+    // Create custom functions for the tabulated functions.
+
+    map<string, Lepton::CustomFunction*> functions;
+    for (int i = 0; i < (int) force.getNumTabulatedFunctions(); i++)
+        functions[force.getTabulatedFunctionName(i)] = createReferenceTabulatedFunction(force.getTabulatedFunction(i));
+
+    // Create the expressions.
+
+    Lepton::ParsedExpression energyExpr = Lepton::Parser::parse(force.getEnergyFunction(), functions);
+    energyExpression = energyExpr.createProgram();
+    for (int i = 0; i < force.getNumCollectiveVariables(); i++) {
+        string name = force.getCollectiveVariableName(i);
+        variableNames.push_back(name);
+        variableDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
+    }
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        string name = force.getEnergyParameterDerivativeName(i);
+        paramDerivNames.push_back(name);
+        paramDerivExpressions.push_back(energyExpr.differentiate(name).optimize().createProgram());
+    }
+
+    // Delete the custom functions.
+
+    for (auto& function : functions)
+        delete function.second;
+}
+
+ReferenceCustomCVForce::~ReferenceCustomCVForce() {
+}
+
+void ReferenceCustomCVForce::calculateIxn(ContextImpl& innerContext, vector<Vec3>& atomCoordinates,
+                                          const map<string, double>& globalParameters, vector<Vec3>& forces,
+                                          double* totalEnergy, map<string, double>& energyParamDerivs) const {
+    // Compute the collective variables, and their derivatives with respect to particle positions.
+    
+    int numCVs = variableNames.size();
+    ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(innerContext.getPlatformData());
+    vector<Vec3>& innerForces = *((vector<Vec3>*) data->forces);
+    map<string, double>& innerDerivs = *((map<string, double>*) data->energyParameterDerivatives);
+    vector<double> cvValues;
+    vector<vector<Vec3> > cvForces;
+    vector<map<string, double> > cvDerivs;
+    for (int i = 0; i < numCVs; i++) {
+        cvValues.push_back(innerContext.calcForcesAndEnergy(true, true, 1<<i));
+        cvForces.push_back(innerForces);
+        cvDerivs.push_back(innerDerivs);
+    }
+    
+    // Compute the energy and forces.
+    
+    int numParticles = atomCoordinates.size();
+    map<string, double> variables = globalParameters;
+    for (int i = 0; i < numCVs; i++)
+        variables[variableNames[i]] = cvValues[i];
+    if (totalEnergy != NULL)
+        *totalEnergy += energyExpression.evaluate(variables);
+    for (int i = 0; i < numCVs; i++) {
+        double dEdV = variableDerivExpressions[i].evaluate(variables);
+        for (int j = 0; j < numParticles; j++)
+            forces[j] += cvForces[i][j]*dEdV;
+    }
+    
+    // Compute the energy parameter derivatives.
+    
+    for (int i = 0; i < paramDerivExpressions.size(); i++)
+        energyParamDerivs[paramDerivNames[i]] += paramDerivExpressions[i].evaluate(variables);
+    for (int i = 0; i < numCVs; i++) {
+        double dEdV = variableDerivExpressions[i].evaluate(variables);
+        for (auto& deriv : cvDerivs[i])
+            energyParamDerivs[deriv.first] += dEdV*deriv.second;
+    }
+}

platforms/reference/tests/TestReferenceCustomCVForce.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) 2017 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 "ReferenceTests.h"
+#include "TestCustomCVForce.h"
+
+void runPlatformTests() {
+}

tests/TestCustomCVForce.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) 2017 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 "openmm/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "openmm/CustomBondForce.h"
+#include "openmm/CustomCVForce.h"
+#include "openmm/CustomExternalForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+void testCVs() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    
+    // Create a CustomCVForce with two collective variables.
+    
+    CustomCVForce* cv = new CustomCVForce("v1+3*v2");
+    system.addForce(cv);
+    CustomBondForce* v1 = new CustomBondForce("2*r");
+    v1->addBond(0, 1);
+    cv->addCollectiveVariable("v1", v1);
+    CustomBondForce* v2 = new CustomBondForce("r");
+    v2->addBond(0, 2);
+    cv->addCollectiveVariable("v2", v2);
+    ASSERT(!cv->usesPeriodicBoundaryConditions());
+    
+    // Create a context for evaluating it.
+    
+    VerletIntegrator integrator(1.0);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(3);
+    positions[0] = Vec3(0, 0, 0);
+    positions[1] = Vec3(1.5, 0, 0);
+    positions[2] = Vec3(0, 0, 2.5);
+    context.setPositions(positions);
+    
+    // Verify the values of the collective variables.
+    
+    vector<double> values;
+    cv->getCollectiveVariableValues(context, values);
+    ASSERT_EQUAL_TOL(2*1.5, values[0], 1e-6);
+    ASSERT_EQUAL_TOL(2.5, values[1], 1e-6);
+    
+    // Verify the energy and forces.
+    
+    State state = context.getState(State::Energy | State::Forces);
+    ASSERT_EQUAL_TOL(2*1.5+3*2.5, state.getPotentialEnergy(), 1e-6);
+    ASSERT_EQUAL_VEC(Vec3(2.0, 0.0, 3.0), state.getForces()[0], 1e-6);
+    ASSERT_EQUAL_VEC(Vec3(-2.0, 0.0, 0.0), state.getForces()[1], 1e-6);
+    ASSERT_EQUAL_VEC(Vec3(0.0, 0.0, -3.0), state.getForces()[2], 1e-6);
+}
+
+void testEnergyParameterDerivatives() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    
+    // Create a CustomCVForce with one collective variable and two global parameters.
+    // The CV in turn depends on a global parameter.
+    
+    CustomCVForce* cv = new CustomCVForce("v1*g1+g2");
+    system.addForce(cv);
+    CustomBondForce* v1 = new CustomBondForce("r*g3");
+    v1->addGlobalParameter("g3", 2.0);
+    v1->addEnergyParameterDerivative("g3");
+    v1->addBond(0, 1);
+    cv->addCollectiveVariable("v1", v1);
+    cv->addGlobalParameter("g1", 1.5);
+    cv->addGlobalParameter("g2", -1.0);
+    cv->addEnergyParameterDerivative("g2");
+    cv->addEnergyParameterDerivative("g1");
+    
+    // Create a context for evaluating it.
+    
+    VerletIntegrator integrator(1.0);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(0, 0, 0);
+    positions[1] = Vec3(2.0, 0, 0);
+    context.setPositions(positions);
+
+    // Verify the energy and parameter derivatives.
+
+    State state = context.getState(State::Energy | State::ParameterDerivatives);
+    ASSERT_EQUAL_TOL(4.0*1.5-1.0, state.getPotentialEnergy(), 1e-6);
+    map<string, double> derivs = state.getEnergyParameterDerivatives();
+    ASSERT_EQUAL_TOL(4.0, derivs["g1"], 1e-6);
+    ASSERT_EQUAL_TOL(1.0, derivs["g2"], 1e-6);
+    ASSERT_EQUAL_TOL(2.0*1.5, derivs["g3"], 1e-6);
+}
+
+void testTabulatedFunction() {
+    const int xsize = 10;
+    const int ysize = 11;
+    const double xmin = 0.4;
+    const double xmax = 1.1;
+    const double ymin = 0.0;
+    const double ymax = 0.95;
+    System system;
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomCVForce* cv = new CustomCVForce("fn(x,y)+1");
+    CustomExternalForce* v1 = new CustomExternalForce("x");
+    v1->addParticle(0);
+    cv->addCollectiveVariable("x", v1);
+    CustomExternalForce* v2 = new CustomExternalForce("y");
+    v2->addParticle(0);
+    cv->addCollectiveVariable("y", v2);
+    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);
+        }
+    }
+    cv->addTabulatedFunction("fn", new Continuous2DFunction(xsize, ysize, table, xmin, xmax, ymin, ymax));
+    system.addForce(cv);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(1);
+    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[0] = Vec3(x, y, 1.5);
+            context.setPositions(positions);
+            State state = context.getState(State::Forces | State::Energy);
+            const vector<Vec3>& forces = state.getForces();
+            double energy = 1;
+            Vec3 force(0, 0, 0);
+            if (x >= xmin && x <= xmax && y >= ymin && y <= ymax) {
+                energy = sin(0.25*x)*cos(0.33*y)+1;
+                force[0] = -0.25*cos(0.25*x)*cos(0.33*y);
+                force[1] = 0.3*sin(0.25*x)*sin(0.33*y);
+            }
+            ASSERT_EQUAL_VEC(force, forces[0], 0.1);
+            ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
+        }
+    }
+}
+
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
+    try {
+        initializeTests(argc, argv);
+        testCVs();
+        testEnergyParameterDerivatives();
+        testTabulatedFunction();
+        runPlatformTests();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}