Merge pull request #1837 from peastman/cv

Created CustomCVForce

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 +1007,44 @@ 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
+     * @param innerContext   the context created by the CustomCVForce for computing collective variables
+     */
+    void initialize(const System& system, const CustomCVForce& force, ContextImpl& innerContext);
+    /**
+     * 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, ContextImpl& innerContext) {
+    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);
+    Vec3 a, b, c;
+    context.getPeriodicBoxVectors(a, b, c);
+    innerContext.setPeriodicBoxVectors(a, b, c);
+    innerContext.setTime(context.getTime());
+    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() {
+}

serialization/include/openmm/serialization/CustomCVForceProxy.h

+#ifndef OPENMM_CUSTOMCVFORCE_PROXY_H_
+#define OPENMM_CUSTOMCVFORCE_PROXY_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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing CustomCVForce objects.
+ */
+
+class OPENMM_EXPORT CustomCVForceProxy : public SerializationProxy {
+public:
+    CustomCVForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUSTOMCVFORCE_PROXY_H_*/

serialization/src/CustomCVForceProxy.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) 2010-2017 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 "openmm/serialization/CustomCVForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/CustomCVForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+CustomCVForceProxy::CustomCVForceProxy() : SerializationProxy("CustomCVForce") {
+}
+
+void CustomCVForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 0);
+    const CustomCVForce& force = *reinterpret_cast<const CustomCVForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("energy", force.getEnergyFunction());
+    SerializationNode& globalParams = node.createChildNode("GlobalParameters");
+    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
+        globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
+    }
+    SerializationNode& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
+    }
+    SerializationNode& cvs = node.createChildNode("CollectiveVariables");
+    for (int i = 0; i < force.getNumCollectiveVariables(); i++) {
+        SerializationNode& node = cvs.createChildNode("CollectiveVariable").setStringProperty("name", force.getCollectiveVariableName(i));
+        node.createChildNode("Force", &force.getCollectiveVariable(i));
+    }
+    SerializationNode& functions = node.createChildNode("Functions");
+    for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
+        functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
+}
+
+void* CustomCVForceProxy::deserialize(const SerializationNode& node) const {
+    int version = node.getIntProperty("version");
+    if (version != 0)
+        throw OpenMMException("Unsupported version number");
+    CustomCVForce* force = NULL;
+    try {
+        CustomCVForce* force = new CustomCVForce(node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
+        for (auto& parameter : globalParams.getChildren())
+            force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
+        const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
+        for (auto& parameter : energyDerivs.getChildren())
+            force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
+        const SerializationNode& cvs = node.getChildNode("CollectiveVariables");
+        for (auto& cv : cvs.getChildren()) {
+            string name = cv.getStringProperty("name");
+            force->addCollectiveVariable(name, cv.getChildren()[0].decodeObject<Force>());
+        }
+        const SerializationNode& functions = node.getChildNode("Functions");
+        for (auto& function : functions.getChildren())
+            force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
+        return force;
+    }
+    catch (...) {
+        if (force != NULL)
+            delete force;
+        throw;
+    }
+}

serialization/src/SerializationProxyRegistration.cpp

@@ -38,6 +38,7 @@
 #include "openmm/CustomBondForce.h"
 #include "openmm/CustomCentroidBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"
+#include "openmm/CustomCVForce.h"
 #include "openmm/CustomExternalForce.h"
 #include "openmm/CustomGBForce.h"
 #include "openmm/CustomHbondForce.h"
@@ -72,6 +73,7 @@
 #include "openmm/serialization/CustomBondForceProxy.h"
 #include "openmm/serialization/CustomCentroidBondForceProxy.h"
 #include "openmm/serialization/CustomCompoundBondForceProxy.h"
+#include "openmm/serialization/CustomCVForceProxy.h"
 #include "openmm/serialization/CustomExternalForceProxy.h"
 #include "openmm/serialization/CustomGBForceProxy.h"
 #include "openmm/serialization/CustomHbondForceProxy.h"
@@ -124,6 +126,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(CustomBondForce), new CustomBondForceProxy());
     SerializationProxy::registerProxy(typeid(CustomCentroidBondForce), new CustomCentroidBondForceProxy());
     SerializationProxy::registerProxy(typeid(CustomCompoundBondForce), new CustomCompoundBondForceProxy());
+    SerializationProxy::registerProxy(typeid(CustomCVForce), new CustomCVForceProxy());
     SerializationProxy::registerProxy(typeid(CustomExternalForce), new CustomExternalForceProxy());
     SerializationProxy::registerProxy(typeid(CustomGBForce), new CustomGBForceProxy());
     SerializationProxy::registerProxy(typeid(CustomHbondForce), new CustomHbondForceProxy());

serialization/tests/TestSerializeCustomCVForce.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) 2010-2017 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 "openmm/internal/AssertionUtilities.h"
+#include "openmm/CustomCVForce.h"
+#include "openmm/HarmonicAngleForce.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    CustomCVForce force("2*v1+v2");
+    force.setForceGroup(3);
+    force.addGlobalParameter("x", 1.3);
+    force.addGlobalParameter("y", 2.221);
+    force.addEnergyParameterDerivative("y");
+    HarmonicBondForce* v1 = new HarmonicBondForce();
+    v1->addBond(2, 3, 5.2, 1.1);
+    force.addCollectiveVariable("v1", v1);
+    HarmonicAngleForce* v2 = new HarmonicAngleForce();
+    v2->addAngle(3, 11, 15, 0.4, 0.2);
+    force.addCollectiveVariable("v2", v2);
+    vector<double> values(10);
+    for (int i = 0; i < 10; i++)
+        values[i] = sin((double) i);
+    force.addTabulatedFunction("f", new Continuous1DFunction(values, 0.5, 1.5));
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<CustomCVForce>(&force, "Force", buffer);
+    CustomCVForce* copy = XmlSerializer::deserialize<CustomCVForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    CustomCVForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
+    ASSERT_EQUAL(force.getNumGlobalParameters(), force2.getNumGlobalParameters());
+    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
+        ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
+        ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
+    }
+    ASSERT_EQUAL(force.getNumEnergyParameterDerivatives(), force2.getNumEnergyParameterDerivatives());
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        ASSERT_EQUAL(force.getEnergyParameterDerivativeName(i), force2.getEnergyParameterDerivativeName(i));
+    ASSERT_EQUAL(force.getNumCollectiveVariables(), force2.getNumCollectiveVariables());
+    for (int i = 0; i < force.getNumCollectiveVariables(); i++) {
+        ASSERT_EQUAL(force.getCollectiveVariableName(i), force2.getCollectiveVariableName(i));
+        stringstream buffer1, buffer2;
+        XmlSerializer::serialize<Force>(&force.getCollectiveVariable(i), "Force", buffer1);
+        XmlSerializer::serialize<Force>(&force2.getCollectiveVariable(i), "Force", buffer2);
+        ASSERT_EQUAL(buffer1.str(), buffer2.str());
+    }
+    ASSERT_EQUAL(force.getNumTabulatedFunctions(), force2.getNumTabulatedFunctions());
+    for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
+        double min1, min2, max1, max2;
+        vector<double> val1, val2;
+        dynamic_cast<Continuous1DFunction&>(force.getTabulatedFunction(i)).getFunctionParameters(val1, min1, max1);
+        dynamic_cast<Continuous1DFunction&>(force2.getTabulatedFunction(i)).getFunctionParameters(val2, min2, max2);
+        ASSERT_EQUAL(force.getTabulatedFunctionName(i), force2.getTabulatedFunctionName(i));
+        ASSERT_EQUAL(min1, min2);
+        ASSERT_EQUAL(max1, max2);
+        ASSERT_EQUAL(val1.size(), val2.size());
+        for (int j = 0; j < (int) val1.size(); j++)
+            ASSERT_EQUAL(val1[j], val2[j]);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

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/CustomNonbondedForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "sfmt/SFMT.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 testReordering() {
+    // Create a larger system with a nonbonded force, since that will trigger atom
+    // reordering on the GPU.
+    
+    const int numParticles = 100;
+    System system;
+    CustomCVForce* cv = new CustomCVForce("2*v2");
+    CustomNonbondedForce* v1 = new CustomNonbondedForce("r");
+    v1->addPerParticleParameter("a");
+    CustomBondForce* v2 = new CustomBondForce("r+1");
+    v2->addBond(5, 10);
+    cv->addCollectiveVariable("v1", v1);
+    cv->addCollectiveVariable("v2", v2);
+    cv->setForceGroup(2);
+    system.addForce(cv);
+    CustomNonbondedForce* nb = new CustomNonbondedForce("r^2");
+    nb->addPerParticleParameter("a");
+    system.addForce(nb);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<Vec3> positions;
+    vector<double> params(1);
+    for (int i = 0; i < numParticles; i++) {
+        system.addParticle(1.0);
+        params[0] = i%2;
+        v1->addParticle(params);
+        params[0] = (i < numParticles/2 ? 2.0 : 3.0);
+        nb->addParticle(params);
+        positions.push_back(Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*10);
+    }
+    
+    // Make sure it works correctly.
+    
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    State state = context.getState(State::Energy | State::Forces, false, 1<<2);
+    Vec3 delta = positions[5]-positions[10];
+    double r = sqrt(delta.dot(delta));
+    ASSERT_EQUAL_TOL(2*(r+1), state.getPotentialEnergy(), 1e-5);
+    ASSERT_EQUAL_VEC(-delta*2/r, state.getForces()[5], 1e-5);
+    ASSERT_EQUAL_VEC(delta*2/r, state.getForces()[10], 1e-5);
+}
+
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
+    try {
+        initializeTests(argc, argv);
+        testCVs();
+        testEnergyParameterDerivatives();
+        testTabulatedFunction();
+        testReordering();
+        runPlatformTests();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

wrappers/python/src/swig_doxygen/swigInputBuilder.py

@@ -280,6 +280,11 @@ class SwigInputBuilder:
             self.fOut.write(",\n         OpenMM::%s" % name)
         self.fOut.write(");\n\n")
 
+        self.fOut.write("%factory(OpenMM::Force& OpenMM::CustomCVForce::getCollectiveVariable")
+        for name in sorted(forceSubclassList):
+            self.fOut.write(",\n         OpenMM::%s" % name)
+        self.fOut.write(");\n\n")
+
         self.fOut.write("%factory(OpenMM::Integrator* OpenMM::Integrator::__copy__")
         for name in sorted(integratorSubclassList):
             self.fOut.write(",\n         OpenMM::%s" % name)

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -142,6 +142,8 @@ STEAL_OWNERSHIP = {("Platform", "registerPlatform") : [0],
                    ("CustomHbondForce", "addTabulatedFunction") : [1],
                    ("CustomCompoundBondForce", "addTabulatedFunction") : [1],
                    ("CustomManyParticleForce", "addTabulatedFunction") : [1],
+                   ("CustomCVForce", "addTabulatedFunction") : [1],
+                   ("CustomCVForce", "addCollectiveVariable") : [1],
                    ("CompoundIntegrator", "addIntegrator") : [0],
 }
 
@@ -390,6 +392,8 @@ UNITS = {
 ("CustomTorsionForce", "getPerTorsionParameterName") : (None, ()),
 ("CustomTorsionForce", "getGlobalParameterName") : (None, ()),
 ("CustomTorsionForce", "getTorsionParameters") : (None, ()),
+("CustomCVForce", "getCollectiveVariable") : (None, ()),
+("CustomCVForce", "getInnerContext") : (None, ()),
 ("DrudeForce", "getParticleParameters") : (None, (None, None, None, None, None, 'unit.elementary_charge', 'unit.nanometer**3', None, None)),
 ("DrudeForce", "getNumScreenedPairs") : (None, ()),
 ("DrudeForce", "getScreenedPairParameters") : (None, ()),