Created CustomNonbondedForce, including reference implementation.

libraries/lepton/include/lepton/ExpressionProgram.h

@@ -55,6 +55,7 @@ class ParsedExpression;
 
 class LEPTON_EXPORT ExpressionProgram {
 public:
+    ExpressionProgram();
     ExpressionProgram(const ExpressionProgram& program);
     ~ExpressionProgram();
     ExpressionProgram& operator=(const ExpressionProgram& program);

libraries/lepton/include/lepton/Operation.h

@@ -34,6 +34,7 @@
 
 #include "windowsIncludes.h"
 #include "CustomFunction.h"
+#include "Exception.h"
 #include <cmath>
 #include <map>
 #include <string>
@@ -170,7 +171,7 @@ public:
     double evaluate(double* args, const std::map<std::string, double>& variables) const {
         std::map<std::string, double>::const_iterator iter = variables.find(name);
         if (iter == variables.end())
-            throw std::exception();
+            throw Exception("No value specified for variable "+name);
         return iter->second;
     }
     ExpressionTreeNode differentiate(const std::vector<ExpressionTreeNode>& children, const std::vector<ExpressionTreeNode>& childDerivs, const std::string& variable) const;

libraries/lepton/src/ExpressionProgram.cpp

@@ -36,6 +36,9 @@
 using namespace Lepton;
 using namespace std;
 
+ExpressionProgram::ExpressionProgram() : maxArgs(0), stackSize(0) {
+}
+
 ExpressionProgram::ExpressionProgram(const ParsedExpression& expression) : maxArgs(0), stackSize(0) {
     buildProgram(expression.getRootNode());
     int currentStackSize = 0;

olla/include/openmm/kernels.h

@@ -35,6 +35,7 @@
 #include "openmm/AndersenThermostat.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMMotionRemover.h"
+#include "openmm/CustomNonbondedForce.h"
 #include "openmm/GBSAOBCForce.h"
 #include "openmm/GBVIForce.h"
 #include "openmm/HarmonicAngleForce.h"
@@ -277,6 +278,43 @@ public:
     virtual double executeEnergy(ContextImpl& context) = 0;
 };
 
+/**
+ * This kernel is invoked by CustomNonbondedForce to calculate the forces acting on the system and the energy of the system.
+ */
+class CalcCustomNonbondedForceKernel : public KernelImpl {
+public:
+    enum NonbondedMethod {
+        NoCutoff = 0,
+        CutoffNonPeriodic = 1,
+        CutoffPeriodic = 2
+    };
+    static std::string Name() {
+        return "CalcCustomNonbondedForce";
+    }
+    CalcCustomNonbondedForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
+    }
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     * @param force      the CustomNonbondedForce this kernel will be used for
+     */
+    virtual void initialize(const System& system, const CustomNonbondedForce& force) = 0;
+    /**
+     * Execute the kernel to calculate the forces.
+     *
+     * @param context    the context in which to execute this kernel
+     */
+    virtual void executeForces(ContextImpl& context) = 0;
+    /**
+     * Execute the kernel to calculate the energy.
+     *
+     * @param context    the context in which to execute this kernel
+     * @return the potential energy due to the CustomNonbondedForce
+     */
+    virtual double executeEnergy(ContextImpl& context) = 0;
+};
+
 /**
  * This kernel is invoked by GBSAOBCForce to calculate the forces acting on the system and the energy of the system.
  */

openmmapi/include/OpenMM.h

@@ -35,6 +35,7 @@
 #include "openmm/AndersenThermostat.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMMotionRemover.h"
+#include "openmm/CustomNonbondedForce.h"
 #include "openmm/Force.h"
 #include "openmm/GBSAOBCForce.h"
 #include "openmm/GBVIForce.h"

openmmapi/include/openmm/CustomNonbondedForce.h

+#ifndef OPENMM_CUSTOMNONBONDEDFORCE_H_
+#define OPENMM_CUSTOMNONBONDEDFORCE_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) 2008-2009 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 "Force.h"
+#include "Vec3.h"
+#include <map>
+#include <set>
+#include <utility>
+#include <vector>
+#include "internal/windowsExport.h"
+
+namespace OpenMM {
+
+/**
+ * This class is still under development.
+ */
+
+class OPENMM_EXPORT CustomNonbondedForce : public Force {
+public:
+    /**
+     * This is an enumeration of the different methods that may be used for handling long range nonbonded forces.
+     */
+    enum NonbondedMethod {
+        /**
+         * No cutoff is applied to nonbonded interactions.  The full set of N^2 interactions is computed exactly.
+         * This necessarily means that periodic boundary conditions cannot be used.  This is the default.
+         */
+        NoCutoff = 0,
+        /**
+         * Interactions beyond the cutoff distance are ignored.
+         */
+        CutoffNonPeriodic = 1,
+        /**
+         * Periodic boundary conditions are used, so that each particle interacts only with the nearest periodic copy of
+         * each other particle.  Interactions beyond the cutoff distance are ignored.
+         */
+        CutoffPeriodic = 2,
+    };
+    /**
+     * Create a CustomNonbondedForce.
+     *
+     * @param energy    an algebraic expression giving the interaction energy between two particles
+     */
+    CustomNonbondedForce(const std::string& energy);
+    /**
+     * Get the number of particles for which force field parameters have been defined.
+     */
+    int getNumParticles() const {
+        return particles.size();
+    }
+    /**
+     * Get the number of special interactions that should be calculated differently from other interactions.
+     */
+    int getNumExceptions() const {
+        return exceptions.size();
+    }
+    /**
+     * Get the number of per-particle parameters that the interaction depends on.
+     */
+    int getNumParameters() const {
+        return combiningRules.size();
+    }
+    /**
+     * Get the algebraic expression that gives the interaction energy between two particles
+     */
+    const std::string& getEnergyFunction() const;
+    /**
+     * SDet the algebraic expression that gives the interaction energy between two particles
+     */
+    void setEnergyFunction(const std::string& energy);
+    /**
+     * Get the method used for handling long range nonbonded interactions.
+     */
+    NonbondedMethod getNonbondedMethod() const;
+    /**
+     * Set the method used for handling long range nonbonded interactions.
+     */
+    void setNonbondedMethod(NonbondedMethod method);
+    /**
+     * Get the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
+     * is NoCutoff, this value will have no effect.
+     */
+    double getCutoffDistance() const;
+    /**
+     * Set the cutoff distance (in nm) being used for nonbonded interactions.  If the NonbondedMethod in use
+     * is NoCutoff, this value will have no effect.
+     */
+    void setCutoffDistance(double distance);
+    /**
+     * Get the vectors which define the axes of the periodic box (measured in nm).  If the NonbondedMethod
+     * in use does not use periodic boundary conditions, these values will have no effect.
+     *
+     * Currently, only rectangular boxes are supported.  This means that a, b, and c must be aligned with the
+     * x, y, and z axes respectively.  Future releases may support arbitrary triclinic boxes.
+     *
+     * @param a      on exit, this contains the vector defining the first edge of the periodic box
+     * @param b      on exit, this contains the vector defining the second edge of the periodic box
+     * @param c      on exit, this contains the vector defining the third edge of the periodic box
+     */
+    void getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const;
+    /**
+     * Set the vectors which define the axes of the periodic box (measured in nm).  If the NonbondedMethod
+     * in use does not use periodic boundary conditions, these values will have no effect.
+     *
+     * Currently, only rectangular boxes are supported.  This means that a, b, and c must be aligned with the
+     * x, y, and z axes respectively.  Future releases may support arbitrary triclinic boxes.
+     *
+     * @param a      the vector defining the first edge of the periodic box
+     * @param b      the vector defining the second edge of the periodic box
+     * @param c      the vector defining the third edge of the periodic box
+     */
+    void setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c);
+    /**
+     * Add a new per-particle parmeter that the interaction may depend on.
+     *
+     * @param combiningRule    an algebraic expression giving the combining rule for this parameter
+     * @return the index of the parameter that was added
+     */
+    int addParameter(const std::string& combiningRule);
+    /**
+     * Get the combining rule for a per-particle parameter.
+     *
+     * @param index     the index of the parameter for which to get the combining rule
+     * @return an algebraic expression giving the combining rule for the parameter
+     */
+    const std::string& getParameterCombiningRule(int index) const;
+    /**
+     * Set the combining rule for a per-particle parameter.
+     *
+     * @param index          the index of the parameter for which to set the combining rule
+     * @param combiningRule  an algebraic expression giving the combining rule for the parameter
+     */
+    void setParameterCombiningRule(int index, const std::string& combiningRule);
+    /**
+     * Add the nonbonded force parameters for a particle.  This should be called once for each particle
+     * in the System.  When it is called for the i'th time, it specifies the parameters for the i'th particle.
+     *
+     * @param parameters    the list of parameters for the new particle
+     * @return the index of the particle that was added
+     */
+    int addParticle(const std::vector<double>& parameters);
+    /**
+     * Get the nonbonded force parameters for a particle.
+     *
+     * @param index       the index of the particle for which to get parameters
+     * @param parameters  the list of parameters for the specified particle
+     */
+    void getParticleParameters(int index, std::vector<double>& parameters) const;
+    /**
+     * Set the nonbonded force parameters for a particle.
+     *
+     * @param index       the index of the particle for which to set parameters
+     * @param parameters  the list of parameters for the specified particle
+     */
+    void setParticleParameters(int index, const std::vector<double>& parameters);
+    /**
+     * Add an interaction to the list of exceptions that should be calculated differently from other interactions.
+     *
+     * @param particle1  the index of the first particle involved in the interaction
+     * @param particle2  the index of the second particle involved in the interaction
+     * @param parameters the list of parameters for the new interaction.  If this is an empty (zero length) vector, it
+     *                   will cause the interaction to be completely omitted from force and energy calculations.
+     * @param replace    determines the behavior if there is already an exception for the same two particles.  If true, the existing one is replaced.  If false,
+     *                   an exception is thrown.
+     * @return the index of the exception that was added
+     */
+    int addException(int particle1, int particle2, const std::vector<double>& parameters, bool replace = false);
+    /**
+     * Get the force field parameters for an interaction that should be calculated differently from others.
+     *
+     * @param index      the index of the interaction for which to get parameters
+     * @param particle1  the index of the first particle involved in the interaction
+     * @param particle2  the index of the second particle involved in the interaction
+     * @param parameters the list of parameters for the interaction.  If this is an empty (zero length) vector, it means
+     *                   the interaction will be completely omitted from force and energy calculations.
+     */
+    void getExceptionParameters(int index, int& particle1, int& particle2, std::vector<double>& parameters) const;
+    /**
+     * Set the force field parameters for an interaction that should be calculated differently from others.
+     *
+     * @param index      the index of the interaction for which to get parameters
+     * @param particle1  the index of the first particle involved in the interaction
+     * @param particle2  the index of the second particle involved in the interaction
+     * @param parameters the list of parameters for the interaction.  If this is an empty (zero length) vector, it
+     *                   will cause the interaction to be completely omitted from force and energy calculations.
+     */
+    void setExceptionParameters(int index, int particle1, int particle2, const std::vector<double>& parameters);
+protected:
+    ForceImpl* createImpl();
+private:
+    class ParticleInfo;
+    class ExceptionInfo;
+    NonbondedMethod nonbondedMethod;
+    double cutoffDistance;
+    Vec3 periodicBoxVectors[3];
+    std::string energyExpression;
+    std::vector<std::string> combiningRules;
+    std::vector<ParticleInfo> particles;
+    std::vector<ExceptionInfo> exceptions;
+    std::map<std::pair<int, int>, int> exceptionMap;
+};
+
+class CustomNonbondedForce::ParticleInfo {
+public:
+    std::vector<double> parameters;
+    ParticleInfo() {
+    }
+    ParticleInfo(const std::vector<double>& parameters) : parameters(parameters) {
+    }
+};
+
+class CustomNonbondedForce::ExceptionInfo {
+public:
+    int particle1, particle2;
+    std::vector<double> parameters;
+    ExceptionInfo() {
+        particle1 = particle2 = -1;
+    }
+    ExceptionInfo(int particle1, int particle2, const std::vector<double>& parameters) :
+        particle1(particle1), particle2(particle2), parameters(parameters) {
+    }
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUSTOMNONBONDEDFORCE_H_*/

openmmapi/include/openmm/internal/CustomNonbondedForceImpl.h

+#ifndef OPENMM_CUSTOMNONBONDEDFORCEIMPL_H_
+#define OPENMM_CUSTOMNONBONDEDFORCEIMPL_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) 2008-2009 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 "ForceImpl.h"
+#include "openmm/CustomNonbondedForce.h"
+#include "openmm/Kernel.h"
+#include <utility>
+#include <string>
+
+namespace OpenMM {
+
+/**
+ * This is the internal implementation of CustomNonbondedForce.
+ */
+
+class CustomNonbondedForceImpl : public ForceImpl {
+public:
+    CustomNonbondedForceImpl(CustomNonbondedForce& owner);
+    ~CustomNonbondedForceImpl();
+    void initialize(ContextImpl& context);
+    CustomNonbondedForce& getOwner() {
+        return owner;
+    }
+    void updateContextState(ContextImpl& context) {
+        // This force field doesn't update the state directly.
+    }
+    void calcForces(ContextImpl& context, Stream& forces);
+    double calcEnergy(ContextImpl& context);
+    std::map<std::string, double> getDefaultParameters() {
+        return std::map<std::string, double>(); // This force field doesn't define any parameters.
+    }
+    std::vector<std::string> getKernelNames();
+private:
+    CustomNonbondedForce& owner;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUSTOMNONBONDEDFORCEIMPL_H_*/

openmmapi/src/CustomNonbondedForce.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) 2008-2009 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/Force.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/CustomNonbondedForce.h"
+#include "openmm/internal/CustomNonbondedForceImpl.h"
+#include <cmath>
+#include <map>
+#include <sstream>
+#include <utility>
+
+using namespace OpenMM;
+using std::map;
+using std::pair;
+using std::set;
+using std::string;
+using std::stringstream;
+using std::vector;
+
+CustomNonbondedForce::CustomNonbondedForce(const string& energy) : energyExpression(energy), nonbondedMethod(NoCutoff), cutoffDistance(1.0) {
+    periodicBoxVectors[0] = Vec3(2, 0, 0);
+    periodicBoxVectors[1] = Vec3(0, 2, 0);
+    periodicBoxVectors[2] = Vec3(0, 0, 2);
+}
+
+const string& CustomNonbondedForce::getEnergyFunction() const {
+    return energyExpression;
+}
+
+void CustomNonbondedForce::setEnergyFunction(const std::string& energy) {
+    energyExpression = energy;
+}
+
+CustomNonbondedForce::NonbondedMethod CustomNonbondedForce::getNonbondedMethod() const {
+    return nonbondedMethod;
+}
+
+void CustomNonbondedForce::setNonbondedMethod(NonbondedMethod method) {
+    nonbondedMethod = method;
+}
+
+double CustomNonbondedForce::getCutoffDistance() const {
+    return cutoffDistance;
+}
+
+void CustomNonbondedForce::setCutoffDistance(double distance) {
+    cutoffDistance = distance;
+}
+
+void CustomNonbondedForce::getPeriodicBoxVectors(Vec3& a, Vec3& b, Vec3& c) const {
+    a = periodicBoxVectors[0];
+    b = periodicBoxVectors[1];
+    c = periodicBoxVectors[2];
+}
+
+void CustomNonbondedForce::setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c) {
+    if (a[1] != 0.0 || a[2] != 0.0)
+        throw OpenMMException("First periodic box vector must be parallel to x.");
+    if (b[0] != 0.0 || b[2] != 0.0)
+        throw OpenMMException("Second periodic box vector must be parallel to y.");
+    if (c[0] != 0.0 || c[1] != 0.0)
+        throw OpenMMException("Third periodic box vector must be parallel to z.");
+    periodicBoxVectors[0] = a;
+    periodicBoxVectors[1] = b;
+    periodicBoxVectors[2] = c;
+}
+
+int CustomNonbondedForce::addParameter(const string& combiningRule) {
+    combiningRules.push_back(combiningRule);
+    return combiningRules.size()-1;
+}
+
+const string& CustomNonbondedForce::getParameterCombiningRule(int index) const {
+    return combiningRules[index];
+}
+
+void CustomNonbondedForce::setParameterCombiningRule(int index, const string& combiningRule) {
+    combiningRules[index] = combiningRule;
+}
+
+int CustomNonbondedForce::addParticle(const vector<double>& parameters) {
+    particles.push_back(ParticleInfo(parameters));
+    return particles.size()-1;
+}
+
+void CustomNonbondedForce::getParticleParameters(int index, std::vector<double>& parameters) const {
+    parameters = particles[index].parameters;
+}
+
+void CustomNonbondedForce::setParticleParameters(int index, const vector<double>& parameters) {
+    particles[index].parameters = parameters;
+}
+
+int CustomNonbondedForce::addException(int particle1, int particle2, const vector<double>& parameters, bool replace) {
+    map<pair<int, int>, int>::iterator iter = exceptionMap.find(pair<int, int>(particle1, particle2));
+    int newIndex;
+    if (iter == exceptionMap.end())
+        iter = exceptionMap.find(pair<int, int>(particle2, particle1));
+    if (iter != exceptionMap.end()) {
+        if (!replace) {
+            stringstream msg;
+            msg << "CustomNonbondedForce: There is already an exception for particles ";
+            msg << particle1;
+            msg << " and ";
+            msg << particle2;
+            throw OpenMMException(msg.str());
+        }
+        exceptions[iter->second] = ExceptionInfo(particle1, particle2, parameters);
+        newIndex = iter->second;
+        exceptionMap.erase(iter->first);
+    }
+    else {
+        exceptions.push_back(ExceptionInfo(particle1, particle2, parameters));
+        newIndex = exceptions.size()-1;
+    }
+    exceptionMap[pair<int, int>(particle1, particle2)] = newIndex;
+    return newIndex;
+}
+void CustomNonbondedForce::getExceptionParameters(int index, int& particle1, int& particle2, vector<double>& parameters) const {
+    particle1 = exceptions[index].particle1;
+    particle2 = exceptions[index].particle2;
+    parameters = exceptions[index].parameters;
+}
+
+void CustomNonbondedForce::setExceptionParameters(int index, int particle1, int particle2, const vector<double>& parameters) {
+    exceptions[index].particle1 = particle1;
+    exceptions[index].particle2 = particle2;
+    exceptions[index].parameters = parameters;
+}
+
+ForceImpl* CustomNonbondedForce::createImpl() {
+    return new CustomNonbondedForceImpl(*this);
+}

openmmapi/src/CustomNonbondedForceImpl.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) 2008-2009 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/OpenMMException.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/CustomNonbondedForceImpl.h"
+#include "openmm/kernels.h"
+#include <sstream>
+
+using namespace OpenMM;
+using std::pair;
+using std::vector;
+using std::set;
+using std::stringstream;
+
+CustomNonbondedForceImpl::CustomNonbondedForceImpl(CustomNonbondedForce& owner) : owner(owner) {
+}
+
+CustomNonbondedForceImpl::~CustomNonbondedForceImpl() {
+}
+
+void CustomNonbondedForceImpl::initialize(ContextImpl& context) {
+    kernel = context.getPlatform().createKernel(CalcCustomNonbondedForceKernel::Name(), context);
+
+    // Check for errors in the specification of parameters and exceptions.
+
+    System& system = context.getSystem();
+    if (owner.getNumParticles() != system.getNumParticles())
+        throw OpenMMException("CustomNonbondedForce must have exactly as many particles as the System it belongs to.");
+    vector<set<int> > exceptions(owner.getNumParticles());
+    vector<double> parameters;
+    int numParameters = owner.getNumParameters();
+    for (int i = 0; i < owner.getNumParticles(); i++) {
+        owner.getParticleParameters(i, parameters);
+        if (parameters.size() != numParameters) {
+            stringstream msg;
+            msg << "CustomNonbondedForce: Wrong number of parameters for particle ";
+            msg << i;
+            throw OpenMMException(msg.str());
+        }
+    }
+    for (int i = 0; i < owner.getNumExceptions(); i++) {
+        int particle1, particle2;
+        owner.getExceptionParameters(i, particle1, particle2, parameters);
+        if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
+            stringstream msg;
+            msg << "CustomNonbondedForce: Illegal particle index for an exception: ";
+            msg << particle1;
+            throw OpenMMException(msg.str());
+        }
+        if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
+            stringstream msg;
+            msg << "CustomNonbondedForce: Illegal particle index for an exception: ";
+            msg << particle2;
+            throw OpenMMException(msg.str());
+        }
+        if (exceptions[particle1].count(particle2) > 0 || exceptions[particle2].count(particle1) > 0) {
+            stringstream msg;
+            msg << "CustomNonbondedForce: Multiple exceptions are specified for particles ";
+            msg << particle1;
+            msg << " and ";
+            msg << particle2;
+            throw OpenMMException(msg.str());
+        }
+        if (parameters.size() != 0 && parameters.size() != numParameters) {
+            stringstream msg;
+            msg << "CustomNonbondedForce: Wrong number of parameters for exception ";
+            msg << i;
+            throw OpenMMException(msg.str());
+        }
+        exceptions[particle1].insert(particle2);
+        exceptions[particle2].insert(particle1);
+    }
+    dynamic_cast<CalcCustomNonbondedForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
+}
+
+void CustomNonbondedForceImpl::calcForces(ContextImpl& context, Stream& forces) {
+    dynamic_cast<CalcCustomNonbondedForceKernel&>(kernel.getImpl()).executeForces(context);
+}
+
+double CustomNonbondedForceImpl::calcEnergy(ContextImpl& context) {
+    return dynamic_cast<CalcCustomNonbondedForceKernel&>(kernel.getImpl()).executeEnergy(context);
+}
+
+std::vector<std::string> CustomNonbondedForceImpl::getKernelNames() {
+    std::vector<std::string> names;
+    names.push_back(CalcCustomNonbondedForceKernel::Name());
+    return names;
+}
+

platforms/reference/src/ReferenceKernelFactory.cpp

@@ -44,6 +44,8 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
         return new ReferenceUpdateTimeKernel(name, platform, data);
     if (name == CalcNonbondedForceKernel::Name())
         return new ReferenceCalcNonbondedForceKernel(name, platform);
+    if (name == CalcCustomNonbondedForceKernel::Name())
+        return new ReferenceCalcCustomNonbondedForceKernel(name, platform);
     if (name == CalcHarmonicBondForceKernel::Name())
         return new ReferenceCalcHarmonicBondForceKernel(name, platform);
     if (name == CalcHarmonicAngleForceKernel::Name())

platforms/reference/src/ReferenceKernels.cpp

@@ -38,6 +38,7 @@
 #include "SimTKReference/ReferenceBondForce.h"
 #include "SimTKReference/ReferenceBrownianDynamics.h"
 #include "SimTKReference/ReferenceCCMAAlgorithm.h"
+#include "SimTKReference/ReferenceCustomNonbondedIxn.h"
 #include "SimTKReference/ReferenceHarmonicBondIxn.h"
 #include "SimTKReference/ReferenceLJCoulomb14.h"
 #include "SimTKReference/ReferenceLJCoulombIxn.h"
@@ -52,6 +53,8 @@
 #include "openmm/internal/ContextImpl.h"
 #include "openmm/Integrator.h"
 #include "SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "lepton/Parser.h"
+#include "lepton/ParsedExpression.h"
 #include <cmath>
 #include <limits>
 
@@ -470,6 +473,115 @@ double ReferenceCalcNonbondedForceKernel::executeEnergy(ContextImpl& context) {
     return energy;
 }
 
+ReferenceCalcCustomNonbondedForceKernel::~ReferenceCalcCustomNonbondedForceKernel() {
+    disposeRealArray(particleParamArray, numParticles);
+    disposeIntArray(exclusionArray, numParticles);
+    disposeIntArray(bonded14IndexArray, num14);
+    disposeRealArray(bonded14ParamArray, num14);
+    if (neighborList != NULL)
+        delete neighborList;
+}
+
+void ReferenceCalcCustomNonbondedForceKernel::initialize(const System& system, const CustomNonbondedForce& force) {
+
+    // Identify which exceptions are 1-4 interactions.
+
+    numParticles = force.getNumParticles();
+    exclusions.resize(numParticles);
+    vector<int> nb14s;
+    vector<double> parameters;
+    for (int i = 0; i < force.getNumExceptions(); i++) {
+        int particle1, particle2;
+        force.getExceptionParameters(i, particle1, particle2, parameters);
+        exclusions[particle1].insert(particle2);
+        exclusions[particle2].insert(particle1);
+        if (parameters.size() > 0)
+            nb14s.push_back(i);
+    }
+
+    // Build the arrays.
+
+    num14 = nb14s.size();
+    int numParameters = force.getNumParameters();
+    bonded14IndexArray = allocateIntArray(num14, 2);
+    bonded14ParamArray = allocateRealArray(num14, numParameters);
+    particleParamArray = allocateRealArray(numParticles, numParameters);
+    for (int i = 0; i < numParticles; ++i) {
+        force.getParticleParameters(i, parameters);
+        for (int j = 0; j < numParameters; j++)
+            particleParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
+    }
+    this->exclusions = exclusions;
+    exclusionArray = new int*[numParticles];
+    for (int i = 0; i < numParticles; ++i) {
+        exclusionArray[i] = new int[exclusions[i].size()+1];
+        exclusionArray[i][0] = exclusions[i].size();
+        int index = 0;
+        for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
+            exclusionArray[i][++index] = *iter;
+    }
+    for (int i = 0; i < num14; ++i) {
+        int particle1, particle2;
+        force.getExceptionParameters(nb14s[i], particle1, particle2, parameters);
+        bonded14IndexArray[i][0] = particle1;
+        bonded14IndexArray[i][1] = particle2;
+        for (int j = 0; j < numParameters; j++)
+            bonded14ParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
+    }
+    nonbondedMethod = CalcCustomNonbondedForceKernel::NonbondedMethod(force.getNonbondedMethod());
+    nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
+    Vec3 boxVectors[3];
+    force.getPeriodicBoxVectors(boxVectors[0], boxVectors[1], boxVectors[2]);
+    periodicBoxSize[0] = (RealOpenMM) boxVectors[0][0];
+    periodicBoxSize[1] = (RealOpenMM) boxVectors[1][1];
+    periodicBoxSize[2] = (RealOpenMM) boxVectors[2][2];
+    if (nonbondedMethod == NoCutoff)
+        neighborList = NULL;
+    else
+        neighborList = new NeighborList();
+
+    // Parse the various expressions used to calculate the force.
+
+    Lepton::ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction()).optimize();
+    energyExpression = expression.createProgram();
+    forceExpression = expression.differentiate("r").optimize().createProgram();
+    for (int i = 0; i < numParameters; i++)
+        combiningRules.push_back(Lepton::Parser::parse(force.getParameterCombiningRule(i)).optimize().createProgram());
+}
+
+void ReferenceCalcCustomNonbondedForceKernel::executeForces(ContextImpl& context) {
+    RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
+    RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
+    ReferenceCustomNonbondedIxn ixn(energyExpression, forceExpression, combiningRules);
+    bool periodic = (nonbondedMethod == CutoffPeriodic);
+    if (nonbondedMethod != NoCutoff) {
+        computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
+        ixn.setUseCutoff(nonbondedCutoff, *neighborList);
+    }
+    if (periodic)
+        ixn.setPeriodic(periodicBoxSize);
+    ixn.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, 0);
+    ixn.calculateExceptionIxn(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, 0);
+}
+
+double ReferenceCalcCustomNonbondedForceKernel::executeEnergy(ContextImpl& context) {
+    RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
+    RealOpenMM** forceData = allocateRealArray(numParticles, 3);
+    RealOpenMM energy = 0;
+    ReferenceCustomNonbondedIxn ixn(energyExpression, forceExpression, combiningRules);
+    bool periodic = (nonbondedMethod == CutoffPeriodic);
+    if (nonbondedMethod != NoCutoff) {
+        computeNeighborListVoxelHash(*neighborList, numParticles, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
+        ixn.setUseCutoff(nonbondedCutoff, *neighborList);
+    }
+    if (periodic)
+        ixn.setPeriodic(periodicBoxSize);
+    ixn.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, &energy);
+    ixn.calculateExceptionIxn(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, &energy);
+    disposeRealArray(forceData, numParticles);
+    return energy;
+}
+
 ReferenceCalcGBSAOBCForceKernel::~ReferenceCalcGBSAOBCForceKernel() {
     if (obc) {
         // delete obc->getObcParameters();

platforms/reference/src/ReferenceKernels.h

@@ -36,6 +36,7 @@
 #include "openmm/kernels.h"
 #include "SimTKUtilities/SimTKOpenMMRealType.h"
 #include "SimTKReference/ReferenceNeighborList.h"
+#include "lepton/ExpressionProgram.h"
 
 class CpuObc;
 class CpuGBVI;
@@ -274,6 +275,46 @@ private:
     NeighborList* neighborList;
 };
 
+/**
+ * This kernel is invoked by CustomNonbondedForce to calculate the forces acting on the system.
+ */
+class ReferenceCalcCustomNonbondedForceKernel : public CalcCustomNonbondedForceKernel {
+public:
+    ReferenceCalcCustomNonbondedForceKernel(std::string name, const Platform& platform) : CalcCustomNonbondedForceKernel(name, platform) {
+    }
+    ~ReferenceCalcCustomNonbondedForceKernel();
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     * @param force      the CustomNonbondedForce this kernel will be used for
+     */
+    void initialize(const System& system, const CustomNonbondedForce& force);
+    /**
+     * Execute the kernel to calculate the forces.
+     *
+     * @param context    the context in which to execute this kernel
+     */
+    void executeForces(ContextImpl& context);
+    /**
+     * Execute the kernel to calculate the energy.
+     *
+     * @param context    the context in which to execute this kernel
+     * @return the potential energy due to the CustomNonbondedForce
+     */
+    double executeEnergy(ContextImpl& context);
+private:
+    int numParticles, num14;
+    int **exclusionArray, **bonded14IndexArray;
+    RealOpenMM **particleParamArray, **bonded14ParamArray;
+    RealOpenMM nonbondedCutoff, periodicBoxSize[3];
+    std::vector<std::set<int> > exclusions;
+    Lepton::ExpressionProgram energyExpression, forceExpression;
+    std::vector<Lepton::ExpressionProgram> combiningRules;
+    NonbondedMethod nonbondedMethod;
+    NeighborList* neighborList;
+};
+
 /**
  * This kernel is invoked by GBSAOBCForce to calculate the forces acting on the system.
  */

platforms/reference/src/ReferencePlatform.cpp

@@ -46,6 +46,7 @@ ReferencePlatform::ReferencePlatform() {
     registerKernelFactory(CalcPeriodicTorsionForceKernel::Name(), factory);
     registerKernelFactory(CalcRBTorsionForceKernel::Name(), factory);
     registerKernelFactory(CalcNonbondedForceKernel::Name(), factory);
+    registerKernelFactory(CalcCustomNonbondedForceKernel::Name(), factory);
     registerKernelFactory(CalcGBSAOBCForceKernel::Name(), factory);
     registerKernelFactory(CalcGBVIForceKernel::Name(), factory);
     registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);

platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp

+
+/* Portions copyright (c) 2009 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 <string.h>
+#include <sstream>
+
+#include "../SimTKUtilities/SimTKOpenMMCommon.h"
+#include "../SimTKUtilities/SimTKOpenMMLog.h"
+#include "../SimTKUtilities/SimTKOpenMMUtilities.h"
+#include "ReferenceForce.h"
+#include "ReferenceCustomNonbondedIxn.h"
+
+using std::map;
+using std::string;
+using std::stringstream;
+using std::vector;
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceCustomNonbondedIxn constructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::ExpressionProgram& energyExpression,
+        const Lepton::ExpressionProgram& forceExpression, const std::vector<Lepton::ExpressionProgram>& combiningRules) :
+            cutoff(false), periodic(false), energyExpression(energyExpression), forceExpression(forceExpression),
+            combiningRules(combiningRules) {
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+    for (int i = 0; i < combiningRules.size(); i++) {
+        stringstream name;
+        name << "param" << i;
+        paramNames.push_back(name.str());
+    }
+}
+
+/**---------------------------------------------------------------------------------------
+
+   ReferenceCustomNonbondedIxn destructor
+
+   --------------------------------------------------------------------------------------- */
+
+ReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn( ){
+
+   // ---------------------------------------------------------------------------------------
+
+   // static const char* methodName = "\nReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn";
+
+   // ---------------------------------------------------------------------------------------
+
+}
+
+  /**---------------------------------------------------------------------------------------
+
+     Set the force to use a cutoff.
+
+     @param distance            the cutoff distance
+     @param neighbors           the neighbor list to use
+
+     @return ReferenceForce::DefaultReturn
+
+     --------------------------------------------------------------------------------------- */
+
+  int ReferenceCustomNonbondedIxn::setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors ) {
+
+    cutoff = true;
+    cutoffDistance = distance;
+    neighborList = &neighbors;
+
+    return ReferenceForce::DefaultReturn;
+  }
+
+  /**---------------------------------------------------------------------------------------
+
+     Set the force to use periodic boundary conditions.  This requires that a cutoff has
+     also been set, and the smallest side of the periodic box is at least twice the cutoff
+     distance.
+
+     @param boxSize             the X, Y, and Z widths of the periodic box
+
+     @return ReferenceForce::DefaultReturn
+
+     --------------------------------------------------------------------------------------- */
+
+  int ReferenceCustomNonbondedIxn::setPeriodic( RealOpenMM* boxSize ) {
+
+    assert(cutoff);
+    assert(boxSize[0] >= 2.0*cutoffDistance);
+    assert(boxSize[1] >= 2.0*cutoffDistance);
+    assert(boxSize[2] >= 2.0*cutoffDistance);
+    periodic = true;
+    periodicBoxSize[0] = boxSize[0];
+    periodicBoxSize[1] = boxSize[1];
+    periodicBoxSize[2] = boxSize[2];
+    return ReferenceForce::DefaultReturn;
+
+  }
+
+
+/**---------------------------------------------------------------------------------------
+
+   Calculate the custom pair ixn
+
+   @param numberOfAtoms    number of atoms
+   @param atomCoordinates  atom coordinates
+   @param atomParameters   atom parameters                             atomParameters[atomIndex][paramterIndex]
+   @param exclusions       atom exclusion indices                      exclusions[atomIndex][atomToExcludeIndex]
+                           exclusions[atomIndex][0] = number of exclusions
+                           exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
+                           interacting w/ atom atomIndex
+   @param fixedParameters  non atom parameters (not currently used)
+   @param forces           force array (forces added)
+   @param energyByAtom     atom energy
+   @param totalEnergy      total energy
+
+   @return ReferenceForce::DefaultReturn
+
+   --------------------------------------------------------------------------------------- */
+
+int ReferenceCustomNonbondedIxn::calculatePairIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                                             RealOpenMM** atomParameters, int** exclusions,
+                                             RealOpenMM* fixedParameters, RealOpenMM** forces,
+                                             RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {
+
+   map<string, double> variablesForParams;
+   map<string, double> variablesForForce;
+   if (cutoff) {
+       for (int i = 0; i < (int) neighborList->size(); i++) {
+           OpenMM::AtomPair pair = (*neighborList)[i];
+
+           // Apply the combining rules to compute the force field parameters.
+
+           for (int j = 0; j < combiningRules.size(); j++) {
+               variablesForParams["particle1"] = atomParameters[pair.first][j];
+               variablesForParams["particle2"] = atomParameters[pair.second][j];
+               variablesForForce[paramNames[j]] = combiningRules[j].evaluate(variablesForParams);
+           }
+           calculateOneIxn(pair.first, pair.second, atomCoordinates, variablesForForce, forces, energyByAtom, totalEnergy);
+       }
+   }
+   else {
+       // allocate and initialize exclusion array
+
+       int* exclusionIndices = new int[numberOfAtoms];
+       for( int ii = 0; ii < numberOfAtoms; ii++ ){
+          exclusionIndices[ii] = -1;
+       }
+
+       for( int ii = 0; ii < numberOfAtoms; ii++ ){
+
+          // set exclusions
+
+          for( int jj = 1; jj <= exclusions[ii][0]; jj++ ){
+             exclusionIndices[exclusions[ii][jj]] = ii;
+          }
+
+          // loop over atom pairs
+
+          for( int jj = ii+1; jj < numberOfAtoms; jj++ ){
+
+             if( exclusionIndices[jj] != ii ){
+
+                 // Apply the combining rules to compute the force field parameters.
+
+                 for (int j = 0; j < combiningRules.size(); j++) {
+                     variablesForParams["particle1"] = atomParameters[ii][j];
+                     variablesForParams["particle2"] = atomParameters[jj][j];
+                     variablesForForce[paramNames[j]] = combiningRules[j].evaluate(variablesForParams);
+                 }
+                 calculateOneIxn(ii, jj, atomCoordinates, variablesForForce, forces, energyByAtom, totalEnergy);
+             }
+          }
+       }
+
+       delete[] exclusionIndices;
+   }
+
+   return ReferenceForce::DefaultReturn;
+}
+/**---------------------------------------------------------------------------------------
+
+   Calculate custom pair ixn for exceptions
+
+   @param numberOfExceptions   number of exceptions
+   @param atomIndices          indices of atoms participating in exception ixn: atomIndices[exceptionIndex][indices]
+   @param atomCoordinates      atom coordinates: atomCoordinates[atomIndex][3]
+   @param parameters           parameters: parameters[exceptionIndex][*]; contents of array
+                               depend on ixn
+   @param forces               force array (forces added to current values): forces[atomIndex][3]
+   @param totalEnergy          totalEnergy: sum over { energies[atomIndex] }
+
+   --------------------------------------------------------------------------------------- */
+
+void ReferenceCustomNonbondedIxn::calculateExceptionIxn( int numberOfExceptions, int** atomIndices, RealOpenMM** atomCoordinates,
+                            RealOpenMM** parameters, RealOpenMM** forces,
+                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {
+
+    map<string, double> variables;
+    for (int i = 0; i < numberOfExceptions; i++) {
+        for (int j = 0; j < combiningRules.size(); j++)
+            variables[paramNames[j]] = parameters[i][j];
+        calculateOneIxn(atomIndices[i][0], atomIndices[i][1], atomCoordinates, variables, forces, energyByAtom, totalEnergy);
+    }
+}
+
+  /**---------------------------------------------------------------------------------------
+
+     Calculate one pair ixn between two atoms
+
+     @param ii               the index of the first atom
+     @param jj               the index of the second atom
+     @param atomCoordinates  atom coordinates
+     @param atomParameters   atom parameters (charges, c6, c12, ...)     atomParameters[atomIndex][paramterIndex]
+     @param forces           force array (forces added)
+     @param energyByAtom     atom energy
+     @param totalEnergy      total energy
+
+     --------------------------------------------------------------------------------------- */
+
+void ReferenceCustomNonbondedIxn::calculateOneIxn( int ii, int jj, RealOpenMM** atomCoordinates,
+                        map<string, double>& variables, RealOpenMM** forces,
+                        RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {
+
+    // ---------------------------------------------------------------------------------------
+
+    static const std::string methodName = "\nReferenceCustomNonbondedIxn::calculateOneIxn";
+
+    // ---------------------------------------------------------------------------------------
+
+    // constants -- reduce Visual Studio warnings regarding conversions between float & double
+
+    static const RealOpenMM zero        =  0.0;
+    static const RealOpenMM one         =  1.0;
+    static const RealOpenMM two         =  2.0;
+    static const RealOpenMM three       =  3.0;
+    static const RealOpenMM six         =  6.0;
+    static const RealOpenMM twelve      = 12.0;
+    static const RealOpenMM oneM        = -1.0;
+
+    // get deltaR, R2, and R between 2 atoms
+
+    RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
+    if (periodic)
+        ReferenceForce::getDeltaRPeriodic( atomCoordinates[jj], atomCoordinates[ii], periodicBoxSize, deltaR );
+    else
+        ReferenceForce::getDeltaR( atomCoordinates[jj], atomCoordinates[ii], deltaR );
+    if (cutoff && deltaR[ReferenceForce::RIndex] >= cutoffDistance)
+        return;
+
+    // accumulate forces
+
+    variables["r"] = deltaR[ReferenceForce::RIndex];
+    RealOpenMM dEdR = forceExpression.evaluate(variables)/(deltaR[ReferenceForce::RIndex]);
+    for( int kk = 0; kk < 3; kk++ ){
+       RealOpenMM force  = -dEdR*deltaR[kk];
+       forces[ii][kk]   += force;
+       forces[jj][kk]   -= force;
+    }
+
+    // accumulate energies
+
+    if( totalEnergy || energyByAtom ) {
+        RealOpenMM energy = energyExpression.evaluate(variables);
+        if( totalEnergy )
+           *totalEnergy += energy;
+        if( energyByAtom ){
+           energyByAtom[ii] += energy;
+           energyByAtom[jj] += energy;
+        }
+    }
+  }
+
+

platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.h

+
+/* Portions copyright (c) 2009 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 __ReferenceCustomNonbondedxIxn_H__
+#define __ReferenceCustomNonbondedxIxn_H__
+
+#include "ReferencePairIxn.h"
+#include "ReferenceNeighborList.h"
+#include "lepton/ExpressionProgram.h"
+#include <map>
+#include <vector>
+
+// ---------------------------------------------------------------------------------------
+
+class ReferenceCustomNonbondedIxn : public ReferencePairIxn {
+
+   private:
+
+      bool cutoff;
+      bool periodic;
+      const OpenMM::NeighborList* neighborList;
+      RealOpenMM periodicBoxSize[3];
+      RealOpenMM cutoffDistance;
+      Lepton::ExpressionProgram energyExpression;
+      Lepton::ExpressionProgram forceExpression;
+      std::vector<Lepton::ExpressionProgram> combiningRules;
+      std::vector<std::string> paramNames;
+
+      /**---------------------------------------------------------------------------------------
+
+         Calculate custom pair ixn between two atoms
+
+         @param atom1            the index of the first atom
+         @param atom2            the index of the second atom
+         @param atomCoordinates  atom coordinates
+         @param atomParameters   atomParameters[atomIndex][parameterIndex]
+         @param forces           force array (forces added)
+         @param energyByAtom     atom energy
+         @param totalEnergy      total energy
+
+         --------------------------------------------------------------------------------------- */
+
+      void calculateOneIxn( int atom1, int atom2, RealOpenMM** atomCoordinates,
+                            std::map<std::string, double>& variables, RealOpenMM** forces,
+                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
+
+
+   public:
+
+      /**---------------------------------------------------------------------------------------
+
+         Constructor
+
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceCustomNonbondedIxn(const Lepton::ExpressionProgram& energyExpression, const Lepton::ExpressionProgram& forceExpression,
+                                   const std::vector<Lepton::ExpressionProgram>& combiningRules);
+
+      /**---------------------------------------------------------------------------------------
+
+         Destructor
+
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceCustomNonbondedIxn( );
+
+      /**---------------------------------------------------------------------------------------
+
+         Set the force to use a cutoff.
+
+         @param distance            the cutoff distance
+         @param neighbors           the neighbor list to use
+
+         @return ReferenceForce::DefaultReturn
+
+         --------------------------------------------------------------------------------------- */
+
+      int setUseCutoff( RealOpenMM distance, const OpenMM::NeighborList& neighbors );
+
+      /**---------------------------------------------------------------------------------------
+
+         Set the force to use periodic boundary conditions.  This requires that a cutoff has
+         already been set, and the smallest side of the periodic box is at least twice the cutoff
+         distance.
+
+         @param boxSize             the X, Y, and Z widths of the periodic box
+
+         @return ReferenceForce::DefaultReturn
+
+         --------------------------------------------------------------------------------------- */
+
+      int setPeriodic( RealOpenMM* boxSize );
+
+      /**---------------------------------------------------------------------------------------
+
+         Calculate custom pair ixn
+
+         @param numberOfAtoms    number of atoms
+         @param atomCoordinates  atom coordinates
+         @param atomParameters   atom parameters (charges, c6, c12, ...)     atomParameters[atomIndex][paramterIndex]
+         @param exclusions       atom exclusion indices                      exclusions[atomIndex][atomToExcludeIndex]
+                                 exclusions[atomIndex][0] = number of exclusions
+                                 exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
+                                 interacting w/ atom atomIndex
+         @param fixedParameters  non atom parameters (not currently used)
+         @param forces           force array (forces added)
+         @param energyByAtom     atom energy
+         @param totalEnergy      total energy
+
+         @return ReferenceForce::DefaultReturn
+
+         --------------------------------------------------------------------------------------- */
+
+      int calculatePairIxn( int numberOfAtoms, RealOpenMM** atomCoordinates,
+                            RealOpenMM** atomParameters, int** exclusions,
+                            RealOpenMM* fixedParameters, RealOpenMM** forces,
+                            RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
+
+      /**---------------------------------------------------------------------------------------
+
+         Calculate custom pair ixn for exceptions
+
+         @param numberOfExceptions   number of exceptions
+         @param atomIndices          indices of atoms participating in exception ixn: atomIndices[exceptionIndex][indices]
+         @param atomCoordinates      atom coordinates: atomCoordinates[atomIndex][3]
+         @param parameters           parameters: parameters[excptionIndex][*]; contents of array
+                                     depend on ixn
+         @param forces               force array (forces added to current values): forces[atomIndex][3]
+         @param energyByAtom         atom energy
+         @param totalEnergy          total energy
+
+         --------------------------------------------------------------------------------------- */
+
+      void calculateExceptionIxn( int numberOfExceptions, int** atomIndices, RealOpenMM** atomCoordinates,
+                                    RealOpenMM** parameters, RealOpenMM** forces,
+                                    RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const;
+
+// ---------------------------------------------------------------------------------------
+
+};
+
+#endif // __ReferenceCustomNonbondedxIxn_H__

platforms/reference/tests/TestReferenceCustomNonbondedForce.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 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests all the different force terms in the reference implementation of CustomNonbondedForce.
+ */
+
+#include "../../../tests/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "ReferencePlatform.h"
+#include "openmm/CustomNonbondedForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testSimpleExpression() {
+    ReferencePlatform platform;
+    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() {
+    ReferencePlatform platform;
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(1.0);
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* forceField = new CustomNonbondedForce("param0*(r*param1)^3");
+    forceField->addParameter("particle1*particle2");
+    forceField->addParameter("particle1+particle2");
+    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);
+    State state = context.getState(State::Forces | State::Energy);
+    const 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);
+}
+
+void testExceptions() {
+    ReferencePlatform platform;
+    System system;
+    VerletIntegrator integrator(0.01);
+    CustomNonbondedForce* nonbonded = new CustomNonbondedForce("param0*r");
+    nonbonded->addParameter("particle1+particle2");
+    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->addException(0, 1, vector<double>());
+    nonbonded->addException(1, 2, vector<double>());
+    nonbonded->addException(2, 3, vector<double>());
+    params[0] = 0.5;
+    nonbonded->addException(0, 2, params);
+    nonbonded->addException(1, 3, params);
+    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(0.5+1+4, 0, 0), forces[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0.5, 0, 0), forces[1], TOL);
+    ASSERT_EQUAL_VEC(Vec3(-0.5, 0, 0), forces[2], TOL);
+    ASSERT_EQUAL_VEC(Vec3(-(0.5+1+4), 0, 0), forces[3], TOL);
+    ASSERT_EQUAL_TOL((1+4)*3+0.5*2+0.5*2, state.getPotentialEnergy(), TOL);
+}
+
+void testCutoff() {
+    ReferencePlatform platform;
+    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+1, state.getPotentialEnergy(), TOL);
+}
+
+void testPeriodic() {
+    ReferencePlatform platform;
+    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);
+    forceField->setPeriodicBoxVectors(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);
+}
+
+int main() {
+    try {
+        testSimpleExpression();
+        testParameters();
+        testExceptions();
+        testCutoff();
+        testPeriodic();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}