Merge pull request #1119 from peastman/centroid

Created CustomCentroidBondForce

docs-source/usersguide/theory.rst

@@ -861,6 +861,28 @@ Parameters may be specified in two ways:
 * Per-bond parameters are defined by specifying a value for each bond.
 
 
+CustomCentroidBondForce
+***********************
+
+CustomCentroidBondForce is very similar to CustomCompoundBondForce, but instead
+of creating bonds between individual particles, the bonds are between the
+centers of groups of particles.  This is useful for purposes such as restraining
+the distance between two molecules or pinning the center of mass of a single
+molecule.
+
+The first step in computing this force is to calculate the center position of
+each defined group of particles.  This is calculated as a weighted average of
+the positions of all the particles in the group, with the weights being user
+defined.  The computation then proceeds exactly as with CustomCompoundBondForce,
+but the energy of each "bond" is now calculated based on the centers of a set
+of groups, rather than on the positions of individual particles.
+
+This class supports all the same function types and features as
+CustomCompoundBondForce.  In fact, any interaction that could be implemented
+with CustomCompoundBondForce can also be implemented with this class, simply by
+defining each group to contain only a single atom.
+
+
 CustomManyParticleForce
 ***********************
 

olla/include/openmm/kernels.h

@@ -38,6 +38,7 @@
 #include "openmm/CMMotionRemover.h"
 #include "openmm/CustomAngleForce.h"
 #include "openmm/CustomBondForce.h"
+#include "openmm/CustomCentroidBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"
 #include "openmm/CustomExternalForce.h"
 #include "openmm/CustomGBForce.h"
@@ -801,6 +802,41 @@ public:
     virtual void copyParametersToContext(ContextImpl& context, const CustomHbondForce& force) = 0;
 };
 
+/**
+ * This kernel is invoked by CustomCentroidBondForce to calculate the forces acting on the system and the energy of the system.
+ */
+class CalcCustomCentroidBondForceKernel : public KernelImpl {
+public:
+    static std::string Name() {
+        return "CalcCustomCentroidBondForce";
+    }
+    CalcCustomCentroidBondForceKernel(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 CustomCentroidBondForce this kernel will be used for
+     */
+    virtual void initialize(const System& system, const CustomCentroidBondForce& force) = 0;
+    /**
+     * Execute the kernel to calculate the forces and/or energy.
+     *
+     * @param context        the context in which to execute this kernel
+     * @param includeForces  true if forces should be calculated
+     * @param includeEnergy  true if the energy should be calculated
+     * @return the potential energy due to the force
+     */
+    virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CustomCentroidBondForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force) = 0;
+};
+
 /**
  * This kernel is invoked by CustomCompoundBondForce to calculate the forces acting on the system and the energy of the system.
  */

openmmapi/include/OpenMM.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009 Stanford University and the Authors.           *
+ * Portions copyright (c) 2009-2015 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -37,6 +37,7 @@
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
 #include "openmm/CustomBondForce.h"
+#include "openmm/CustomCentroidBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"
 #include "openmm/CustomAngleForce.h"
 #include "openmm/CustomTorsionForce.h"

openmmapi/include/openmm/CustomCentroidBondForce.h

+#ifndef OPENMM_CUSTOMCENTROIDBONDFORCE_H_
+#define OPENMM_CUSTOMCENTROIDBONDFORCE_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) 2008-2015 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "TabulatedFunction.h"
+#include "Force.h"
+#include "Vec3.h"
+#include <vector>
+#include "internal/windowsExport.h"
+
+namespace OpenMM {
+
+/**
+ * This class is similar to CustomCompoundBondForce, but instead of applying forces between individual particles,
+ * it applies them between the centers of groups of particles.  This is useful for a variety of purposes, such as
+ * restraints to keep two molecules from moving too far apart.
+ *
+ * When using this class, you define groups of particles, and the center of each group is calculated as a weighted
+ * average of the particle positions.  By default, the particle masses are used as weights, so the center position
+ * is the center of mass.  You can optionally specify different weights to use.  You then add bonds just as with
+ * CustomCompoundBondForce, but instead of specifying the particles that make up a bond, you specify the groups.
+ *
+ * When creating a CustomCentroidBondForce, you specify the number of groups involved in a bond, and an expression
+ * for the energy of each bond.  It may depend on the center positions of individual groups, the distances between
+ * the centers of pairs of groups, the angles formed by sets of three groups, and the dihedral angles formed by
+ * sets of four groups.
+ *
+ * We refer to the groups in a bond as g1, g2, g3, etc.  For each bond, CustomCentroidBondForce evaluates a
+ * user supplied algebraic expression to determine the interaction energy.  The expression may depend on the
+ * following variables and functions:
+ *
+ * <ul>
+ * <li>x1, y1, z1, x2, y2, z2, etc.: The x, y, and z coordinates of the centers of the groups.  For example, x1
+ * is the x coordinate of the center of group g1, and y3 is the y coordinate of the center of group g3.</li>
+ * <li>distance(g1, g2): the distance between the centers of groups g1 and g2 (where "g1" and "g2" may be replaced
+ * by the names of whichever groups you want to calculate the distance between).</li>
+ * <li>angle(g1, g2, g3): the angle formed by the centers of the three specified groups.</li>
+ * <li>dihedral(g1, g2, g3, g4): the dihedral angle formed by the centers of the four specified groups.</li>
+ * </ul>
+ *
+ * The expression also may involve tabulated functions, and may depend on arbitrary global and per-bond parameters.
+ *
+ * To use this class, create a CustomCentroidBondForce object, passing an algebraic expression to the constructor
+ * that defines the interaction energy of each bond.  Then call addPerBondParameter() to define per-bond
+ * parameters and addGlobalParameter() to define global parameters.  The values of per-bond parameters are specified
+ * as part of the system definition, while values of global parameters may be modified during a simulation by calling
+ * Context::setParameter().
+ *
+ * Next call addGroup() to define the particle groups.  Each group is specified by the particles it contains, and
+ * the weights to use when computing the center position.
+ *
+ * Then call addBond() to define bonds and specify their parameter values.  After a bond has been added, you can
+ * modify its parameters by calling setBondParameters().  This will have no effect on Contexts that already exist unless
+ * you call updateParametersInContext().
+ *
+ * As an example, the following code creates a CustomCentroidBondForce that implements a harmonic force between the
+ * centers of mass of two groups of particles.
+ * 
+ * <tt><pre>
+ * CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "0.5*k*distance(g1,g2)^2");
+ * force->addPerBondParameter("k");
+ * force->addGroup(particles1);
+ * force->addGroup(particles2);
+ * vector<int> bondGroups;
+ * bondGroups.push_back(0);
+ * bondGroups.push_back(1);
+ * vector<double> bondParameters;
+ * bondParameters.push_back(k);
+ * force->addBond(bondGroups, bondParameters);
+ * </pre></tt>
+ *
+ * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
+ * select(x,y,z) = z if x = 0, y otherwise.
+ *
+ * In addition, you can call addTabulatedFunction() to define a new function based on tabulated values.  You specify the function by
+ * creating a TabulatedFunction object.  That function can then appear in the expression.
+ */
+
+class OPENMM_EXPORT CustomCentroidBondForce : public Force {
+public:
+    /**
+     * Create a CustomCentroidBondForce.
+     *
+     * @param numGroups     the number of groups used to define each bond
+     * @param energy        an algebraic expression giving the interaction energy of each bond as a function
+     *                      of particle positions, inter-particle distances, angles, and dihedrals, and any global
+     *                      and per-bond parameters
+     */
+    explicit CustomCentroidBondForce(int numGroups, const std::string& energy);
+    ~CustomCentroidBondForce();
+    /**
+     * Get the number of groups used to define each bond.
+     */
+    int getNumGroupsPerBond() const {
+        return groupsPerBond;
+    }
+    /**
+     * Get the number of particle groups that have been defined.
+     */
+    int getNumGroups() const {
+        return groups.size();
+    }
+    /**
+     * Get the number of bonds for which force field parameters have been defined.
+     */
+    int getNumBonds() const {
+        return bonds.size();
+    }
+    /**
+     * Get the number of per-bond parameters that the interaction depends on.
+     */
+    int getNumPerBondParameters() const {
+        return bondParameters.size();
+    }
+    /**
+     * Get the number of global parameters that the interaction depends on.
+     */
+    int getNumGlobalParameters() const {
+        return globalParameters.size();
+    }
+    /**
+     * Get the number of tabulated functions that have been defined.
+     */
+    int getNumTabulatedFunctions() const {
+        return functions.size();
+    }
+    /**
+     * Get the number of tabulated functions that have been defined.
+     *
+     * @deprecated This method exists only for backward compatibility.  Use getNumTabulatedFunctions() instead.
+     */
+    int getNumFunctions() const {
+        return functions.size();
+    }
+    /**
+     * Get the algebraic expression that gives the interaction energy of each bond
+     */
+    const std::string& getEnergyFunction() const;
+    /**
+     * Set the algebraic expression that gives the interaction energy of each bond
+     */
+    void setEnergyFunction(const std::string& energy);
+    /**
+     * Add a new per-bond parameter that the interaction may depend on.
+     *
+     * @param name     the name of the parameter
+     * @return the index of the parameter that was added
+     */
+    int addPerBondParameter(const std::string& name);
+    /**
+     * Get the name of a per-bond parameter.
+     *
+     * @param index     the index of the parameter for which to get the name
+     * @return the parameter name
+     */
+    const std::string& getPerBondParameterName(int index) const;
+    /**
+     * Set the name of a per-bond parameter.
+     *
+     * @param index          the index of the parameter for which to set the name
+     * @param name           the name of the parameter
+     */
+    void setPerBondParameterName(int index, const std::string& name);
+    /**
+     * Add a new global parameter that the interaction may depend on.
+     *
+     * @param name             the name of the parameter
+     * @param defaultValue     the default value of the parameter
+     * @return the index of the parameter that was added
+     */
+    int addGlobalParameter(const std::string& name, double defaultValue);
+    /**
+     * Get the name of a global parameter.
+     *
+     * @param index     the index of the parameter for which to get the name
+     * @return the parameter name
+     */
+    const std::string& getGlobalParameterName(int index) const;
+    /**
+     * Set the name of a global parameter.
+     *
+     * @param index          the index of the parameter for which to set the name
+     * @param name           the name of the parameter
+     */
+    void setGlobalParameterName(int index, const std::string& name);
+    /**
+     * Get the default value of a global parameter.
+     *
+     * @param index     the index of the parameter for which to get the default value
+     * @return the parameter default value
+     */
+    double getGlobalParameterDefaultValue(int index) const;
+    /**
+     * Set the default value of a global parameter.
+     *
+     * @param index          the index of the parameter for which to set the default value
+     * @param name           the default value of the parameter
+     */
+    void setGlobalParameterDefaultValue(int index, double defaultValue);
+    /**
+     * Add a particle group.
+     *
+     * @param particles   the indices of the particles to include in the group
+     * @param weights     the weight to use for each particle when computing the center position.
+     *                    If this is omitted, then particle masses will be used as weights.
+     * @return the index of the group that was added
+     */
+    int addGroup(const std::vector<int>& particles, const std::vector<double>& weights = std::vector<double>());
+    /**
+     * Get the properties of a group.
+     *
+     * @param index       the index of the group to get
+     * @param particles   the indices of the particles in the group
+     * @param weights     the weight used for each particle when computing the center position.
+     *                    If no weights were specified, this vector will be empty indicating that particle
+     *                    masses should be used as weights.
+     */
+    void getGroupParameters(int index, std::vector<int>& particles, std::vector<double>& weights) const;
+    /**
+     * Set the properties of a group.
+     *
+     * @param index       the index of the group to set
+     * @param particles   the indices of the particles in the group
+     * @param weights     the weight to use for each particle when computing the center position.
+     *                    If this is omitted, then particle masses will be used as weights.
+     */
+    void setGroupParameters(int index, const std::vector<int>& particles, const std::vector<double>& weights = std::vector<double>());
+    /**
+     * Add a bond to the force
+     *
+     * @param groups      the indices of the groups the bond depends on
+     * @param parameters  the list of per-bond parameter values for the new bond
+     * @return the index of the bond that was added
+     */
+    int addBond(const std::vector<int>& groups, const std::vector<double>& parameters);
+    /**
+     * Get the properties of a bond.
+     *
+     * @param index       the index of the bond to get
+     * @param groups      the indices of the groups in the bond
+     * @param parameters  the list of per-bond parameter values for the bond
+     */
+    void getBondParameters(int index, std::vector<int>& groups, std::vector<double>& parameters) const;
+    /**
+     * Set the properties of a bond.
+     *
+     * @param index       the index of the bond to set
+     * @param groups      the indices of the groups in the bond
+     * @param parameters  the list of per-bond parameter values for the bond
+     */
+    void setBondParameters(int index, const std::vector<int>& groups, const std::vector<double>& parameters);
+    /**
+     * Add a tabulated function that may appear in the energy expression.
+     *
+     * @param name           the name of the function as it appears in expressions
+     * @param function       a TabulatedFunction object defining the function.  The TabulatedFunction
+     *                       should have been created on the heap with the "new" operator.  The
+     *                       Force takes over ownership of it, and deletes it when the Force itself is deleted.
+     * @return the index of the function that was added
+     */
+    int addTabulatedFunction(const std::string& name, TabulatedFunction* function);
+    /**
+     * Get a const reference to a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the TabulatedFunction object defining the function
+     */
+    const TabulatedFunction& getTabulatedFunction(int index) const;
+    /**
+     * Get a reference to a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the TabulatedFunction object defining the function
+     */
+    TabulatedFunction& getTabulatedFunction(int index);
+    /**
+     * Get the name of a tabulated function that may appear in the energy expression.
+     *
+     * @param index     the index of the function to get
+     * @return the name of the function as it appears in expressions
+     */
+    const std::string& getTabulatedFunctionName(int index) const;
+    /**
+     * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
+     * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInContext()
+     * to copy them over to the Context.
+     *
+     * This method has several limitations.  The only information it updates is the values of per-bond parameters.
+     * All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing
+     * the Context.  Neither the definitions of groups nor the set of groups involved in a bond can be changed, nor can new
+     * bonds be added.
+     */
+    void updateParametersInContext(Context& context);
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns false
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
+protected:
+    ForceImpl* createImpl() const;
+private:
+    class GroupInfo;
+    class BondInfo;
+    class BondParameterInfo;
+    class GlobalParameterInfo;
+    class FunctionInfo;
+    int groupsPerBond;
+    std::string energyExpression;
+    std::vector<BondParameterInfo> bondParameters;
+    std::vector<GlobalParameterInfo> globalParameters;
+    std::vector<GroupInfo> groups;
+    std::vector<BondInfo> bonds;
+    std::vector<FunctionInfo> functions;
+};
+
+/**
+ * This is an internal class used to record information about a group.
+ * @private
+ */
+class CustomCentroidBondForce::GroupInfo {
+public:
+    std::vector<int> particles;
+    std::vector<double> weights;
+    GroupInfo() {
+    }
+    GroupInfo(const std::vector<int>& particles, const std::vector<double>& weights) :
+        particles(particles), weights(weights) {
+    }
+};
+
+/**
+ * This is an internal class used to record information about a bond.
+ * @private
+ */
+class CustomCentroidBondForce::BondInfo {
+public:
+    std::vector<int> groups;
+    std::vector<double> parameters;
+    BondInfo() {
+    }
+    BondInfo(const std::vector<int>& groups, const std::vector<double>& parameters) :
+        groups(groups), parameters(parameters) {
+    }
+};
+
+/**
+ * This is an internal class used to record information about a per-bond parameter.
+ * @private
+ */
+class CustomCentroidBondForce::BondParameterInfo {
+public:
+    std::string name;
+    BondParameterInfo() {
+    }
+    BondParameterInfo(const std::string& name) : name(name) {
+    }
+};
+
+/**
+ * This is an internal class used to record information about a global parameter.
+ * @private
+ */
+class CustomCentroidBondForce::GlobalParameterInfo {
+public:
+    std::string name;
+    double defaultValue;
+    GlobalParameterInfo() {
+    }
+    GlobalParameterInfo(const std::string& name, double defaultValue) : name(name), defaultValue(defaultValue) {
+    }
+};
+
+/**
+ * This is an internal class used to record information about a tabulated function.
+ * @private
+ */
+class CustomCentroidBondForce::FunctionInfo {
+public:
+    std::string name;
+    TabulatedFunction* function;
+    FunctionInfo() {
+    }
+    FunctionInfo(const std::string& name, TabulatedFunction* function) : name(name), function(function) {
+    }
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUSTOMCENTROIDBONDFORCE_H_*/

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -231,7 +231,7 @@ public:
     /**
      * Set the properties of a bond.
      *
-     * @param index       the index of the bond group to set
+     * @param index       the index of the bond to set
      * @param particles   the indices of the particles in the bond
      * @param parameters  the list of per-bond parameter values for the bond
      */
@@ -323,7 +323,7 @@ private:
 };
 
 /**
- * This is an internal class used to record information about a bond or acceptor.
+ * This is an internal class used to record information about a bond.
  * @private
  */
 class CustomCompoundBondForce::BondInfo {
@@ -338,7 +338,7 @@ public:
 };
 
 /**
- * This is an internal class used to record information about a per-bond or per-acceptor parameter.
+ * This is an internal class used to record information about a per-bond parameter.
  * @private
  */
 class CustomCompoundBondForce::BondParameterInfo {

openmmapi/include/openmm/internal/CustomCentroidBondForceImpl.h

+#ifndef OPENMM_CUSTOMCENTROIDBONDFORCEIMPL_H_
+#define OPENMM_CUSTOMCENTROIDBONDFORCEIMPL_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) 2008-2015 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ForceImpl.h"
+#include "openmm/CustomCentroidBondForce.h"
+#include "openmm/Kernel.h"
+#include "openmm/System.h"
+#include "lepton/CustomFunction.h"
+#include "lepton/ExpressionTreeNode.h"
+#include "lepton/ParsedExpression.h"
+#include <utility>
+#include <map>
+#include <string>
+
+namespace OpenMM {
+
+/**
+ * This is the internal implementation of CustomCentroidBondForce.
+ */
+
+class OPENMM_EXPORT CustomCentroidBondForceImpl : public ForceImpl {
+public:
+    CustomCentroidBondForceImpl(const CustomCentroidBondForce& owner);
+    ~CustomCentroidBondForceImpl();
+    void initialize(ContextImpl& context);
+    const CustomCentroidBondForce& getOwner() const {
+        return owner;
+    }
+    void updateContextState(ContextImpl& context) {
+        // This force field doesn't update the state directly.
+    }
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
+    std::map<std::string, double> getDefaultParameters();
+    std::vector<std::string> getKernelNames();
+    std::vector<std::pair<int, int> > getBondedParticles() const;
+    void updateParametersInContext(ContextImpl& context);
+    /**
+     * This is a utility routine that parses the energy expression, identifies the angles and dihedrals
+     * in it, and replaces them with variables.
+     *
+     * @param force     the CustomCentroidBondForce to process
+     * @param functions definitions of custom function that may appear in the expression
+     * @param distances on exit, this will contain an entry for each distance used in the expression.  The key is the name
+     *                  of the corresponding variable, and the value is the list of particle indices.
+     * @param angles    on exit, this will contain an entry for each angle used in the expression.  The key is the name
+     *                  of the corresponding variable, and the value is the list of particle indices.
+     * @param dihedrals on exit, this will contain an entry for each dihedral used in the expression.  The key is the name
+     *                  of the corresponding variable, and the value is the list of particle indices.
+     * @return a Parsed expression for the energy
+     */
+    static Lepton::ParsedExpression prepareExpression(const CustomCentroidBondForce& force, const std::map<std::string, Lepton::CustomFunction*>& functions, std::map<std::string, std::vector<int> >& distances,
+            std::map<std::string, std::vector<int> >& angles, std::map<std::string, std::vector<int> >& dihedrals);
+    /**
+     * Compute the normalized weights to use for each particle in each group.
+     *
+     * @param force     the CustomCentroidBondForce to process
+     * @param system    the System it is part of
+     * @param weights   on exit, weights[i][j] contains the normalized weight for particle j in group i.
+     */
+    static void computeNormalizedWeights(const CustomCentroidBondForce& force, const System& system, std::vector<std::vector<double> >& weights);
+private:
+    class FunctionPlaceholder;
+    static Lepton::ExpressionTreeNode replaceFunctions(const Lepton::ExpressionTreeNode& node, std::map<std::string, int> atoms,
+            std::map<std::string, std::vector<int> >& distances, std::map<std::string, std::vector<int> >& angles,
+            std::map<std::string, std::vector<int> >& dihedrals);
+    void addBondsBetweenGroups(int group1, int group2, std::vector<std::pair<int, int> >& bonds) const;
+    const CustomCentroidBondForce& owner;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUSTOMCENTROIDBONDFORCEIMPL_H_*/

openmmapi/src/CustomCentroidBondForce.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) 2015 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/Force.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/CustomCentroidBondForce.h"
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/internal/CustomCentroidBondForceImpl.h"
+#include <cmath>
+#include <map>
+#include <set>
+#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;
+
+CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy) {
+}
+
+CustomCentroidBondForce::~CustomCentroidBondForce() {
+    for (int i = 0; i < (int) functions.size(); i++)
+        delete functions[i].function;
+}
+
+const string& CustomCentroidBondForce::getEnergyFunction() const {
+    return energyExpression;
+}
+
+void CustomCentroidBondForce::setEnergyFunction(const std::string& energy) {
+    energyExpression = energy;
+}
+
+int CustomCentroidBondForce::addPerBondParameter(const string& name) {
+    bondParameters.push_back(BondParameterInfo(name));
+    return bondParameters.size()-1;
+}
+
+const string& CustomCentroidBondForce::getPerBondParameterName(int index) const {
+    ASSERT_VALID_INDEX(index, bondParameters);
+    return bondParameters[index].name;
+}
+
+void CustomCentroidBondForce::setPerBondParameterName(int index, const string& name) {
+    ASSERT_VALID_INDEX(index, bondParameters);
+    bondParameters[index].name = name;
+}
+
+int CustomCentroidBondForce::addGlobalParameter(const string& name, double defaultValue) {
+    globalParameters.push_back(GlobalParameterInfo(name, defaultValue));
+    return globalParameters.size()-1;
+}
+
+const string& CustomCentroidBondForce::getGlobalParameterName(int index) const {
+    ASSERT_VALID_INDEX(index, globalParameters);
+    return globalParameters[index].name;
+}
+
+void CustomCentroidBondForce::setGlobalParameterName(int index, const string& name) {
+    ASSERT_VALID_INDEX(index, globalParameters);
+    globalParameters[index].name = name;
+}
+
+double CustomCentroidBondForce::getGlobalParameterDefaultValue(int index) const {
+    ASSERT_VALID_INDEX(index, globalParameters);
+    return globalParameters[index].defaultValue;
+}
+
+void CustomCentroidBondForce::setGlobalParameterDefaultValue(int index, double defaultValue) {
+    ASSERT_VALID_INDEX(index, globalParameters);
+    globalParameters[index].defaultValue = defaultValue;
+}
+
+int CustomCentroidBondForce::addGroup(const vector<int>& particles, const vector<double>& weights) {
+    if (particles.size() != weights.size() && weights.size() > 0)
+        throw OpenMMException("CustomCentroidBondForce: wrong number of weights specified for a group.");
+    groups.push_back(GroupInfo(particles, weights));
+    return groups.size()-1;
+}
+
+void CustomCentroidBondForce::getGroupParameters(int index, vector<int>& particles, std::vector<double>& weights) const {
+    ASSERT_VALID_INDEX(index, groups);
+    particles = groups[index].particles;
+    weights = groups[index].weights;
+}
+
+void CustomCentroidBondForce::setGroupParameters(int index, const vector<int>& particles, const vector<double>& weights) {
+    ASSERT_VALID_INDEX(index, groups);
+    if (particles.size() != weights.size() && weights.size() > 0)
+        throw OpenMMException("CustomCentroidBondForce: wrong number of weights specified for a group.");
+    groups[index].particles = particles;
+    groups[index].weights = weights;
+}
+
+int CustomCentroidBondForce::addBond(const vector<int>& groups, const vector<double>& parameters) {
+    if (groups.size() != groupsPerBond)
+        throw OpenMMException("CustomCentroidBondForce: wrong number of groups specified for a bond.");
+    bonds.push_back(BondInfo(groups, parameters));
+    return bonds.size()-1;
+}
+
+void CustomCentroidBondForce::getBondParameters(int index, vector<int>& groups, std::vector<double>& parameters) const {
+    ASSERT_VALID_INDEX(index, bonds);
+    groups = bonds[index].groups;
+    parameters = bonds[index].parameters;
+}
+
+void CustomCentroidBondForce::setBondParameters(int index, const vector<int>& groups, const vector<double>& parameters) {
+    ASSERT_VALID_INDEX(index, bonds);
+    if (groups.size() != groupsPerBond)
+        throw OpenMMException("CustomCentroidBondForce: wrong number of groups specified for a bond.");
+    bonds[index].groups = groups;
+    bonds[index].parameters = parameters;
+}
+
+int CustomCentroidBondForce::addTabulatedFunction(const std::string& name, TabulatedFunction* function) {
+    functions.push_back(FunctionInfo(name, function));
+    return functions.size()-1;
+}
+
+const TabulatedFunction& CustomCentroidBondForce::getTabulatedFunction(int index) const {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+TabulatedFunction& CustomCentroidBondForce::getTabulatedFunction(int index) {
+    ASSERT_VALID_INDEX(index, functions);
+    return *functions[index].function;
+}
+
+const string& CustomCentroidBondForce::getTabulatedFunctionName(int index) const {
+    ASSERT_VALID_INDEX(index, functions);
+    return functions[index].name;
+}
+
+ForceImpl* CustomCentroidBondForce::createImpl() const {
+    return new CustomCentroidBondForceImpl(*this);
+}
+
+void CustomCentroidBondForce::updateParametersInContext(Context& context) {
+    dynamic_cast<CustomCentroidBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+}

openmmapi/src/CustomCentroidBondForceImpl.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/OpenMMException.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/CustomCentroidBondForceImpl.h"
+#include "openmm/kernels.h"
+#include "lepton/Operation.h"
+#include "lepton/Parser.h"
+#include <sstream>
+#include <utility>
+
+using namespace OpenMM;
+using namespace std;
+using Lepton::CustomFunction;
+using Lepton::ExpressionTreeNode;
+using Lepton::Operation;
+using Lepton::ParsedExpression;
+
+/**
+ * This class serves as a placeholder for angles and dihedrals in expressions.
+ */
+class CustomCentroidBondForceImpl::FunctionPlaceholder : public CustomFunction {
+public:
+    int numArguments;
+    FunctionPlaceholder(int numArguments) : numArguments(numArguments) {
+    }
+    int getNumArguments() const {
+        return numArguments;
+    }
+    double evaluate(const double* arguments) const {
+        return 0.0;
+    }
+    double evaluateDerivative(const double* arguments, const int* derivOrder) const {
+        return 0.0;
+    }
+    CustomFunction* clone() const {
+        return new FunctionPlaceholder(numArguments);
+    }
+};
+
+CustomCentroidBondForceImpl::CustomCentroidBondForceImpl(const CustomCentroidBondForce& owner) : owner(owner) {
+}
+
+CustomCentroidBondForceImpl::~CustomCentroidBondForceImpl() {
+}
+
+void CustomCentroidBondForceImpl::initialize(ContextImpl& context) {
+    kernel = context.getPlatform().createKernel(CalcCustomCentroidBondForceKernel::Name(), context);
+
+    // Check for errors in the specification of parameters and exclusions.
+
+    const System& system = context.getSystem();
+    vector<int> particles;
+    vector<double> weights;
+    for (int i = 0; i < owner.getNumGroups(); i++) {
+        owner.getGroupParameters(i, particles, weights);
+        for (int j = 0; j < (int) particles.size(); j++)
+            if (particles[j] < 0 || particles[j] >= system.getNumParticles()) {
+                stringstream msg;
+                msg << "CustomCentroidBondForce: Illegal particle index for a group: ";
+                msg << particles[j];
+                throw OpenMMException(msg.str());
+            }
+        if (weights.size() != particles.size() && weights.size() > 0) {
+            stringstream msg;
+            msg << "CustomCentroidBondForce: Wrong number of weights for group ";
+            msg << i;
+            throw OpenMMException(msg.str());
+        }
+    }
+    vector<int> groups;
+    vector<double> parameters;
+    int numBondParameters = owner.getNumPerBondParameters();
+    for (int i = 0; i < owner.getNumBonds(); i++) {
+        owner.getBondParameters(i, groups, parameters);
+        for (int j = 0; j < (int) groups.size(); j++)
+            if (groups[j] < 0 || groups[j] >= owner.getNumGroups()) {
+                stringstream msg;
+                msg << "CustomCentroidBondForce: Illegal group index for a bond: ";
+                msg << groups[j];
+                throw OpenMMException(msg.str());
+            }
+        if (parameters.size() != numBondParameters) {
+            stringstream msg;
+            msg << "CustomCentroidBondForce: Wrong number of parameters for bond ";
+            msg << i;
+            throw OpenMMException(msg.str());
+        }
+    }
+    kernel.getAs<CalcCustomCentroidBondForceKernel>().initialize(context.getSystem(), owner);
+}
+
+double CustomCentroidBondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+    if ((groups&(1<<owner.getForceGroup())) != 0)
+        return kernel.getAs<CalcCustomCentroidBondForceKernel>().execute(context, includeForces, includeEnergy);
+    return 0.0;
+}
+
+vector<string> CustomCentroidBondForceImpl::getKernelNames() {
+    vector<string> names;
+    names.push_back(CalcCustomCentroidBondForceKernel::Name());
+    return names;
+}
+
+map<string, double> CustomCentroidBondForceImpl::getDefaultParameters() {
+    map<string, double> parameters;
+    for (int i = 0; i < owner.getNumGlobalParameters(); i++)
+        parameters[owner.getGlobalParameterName(i)] = owner.getGlobalParameterDefaultValue(i);
+    return parameters;
+}
+
+ParsedExpression CustomCentroidBondForceImpl::prepareExpression(const CustomCentroidBondForce& force, const map<string, CustomFunction*>& customFunctions, map<string, vector<int> >& distances,
+        map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
+    CustomCentroidBondForceImpl::FunctionPlaceholder custom(1);
+    CustomCentroidBondForceImpl::FunctionPlaceholder distance(2);
+    CustomCentroidBondForceImpl::FunctionPlaceholder angle(3);
+    CustomCentroidBondForceImpl::FunctionPlaceholder dihedral(4);
+    map<string, CustomFunction*> functions = customFunctions;
+    functions["distance"] = &distance;
+    functions["angle"] = &angle;
+    functions["dihedral"] = &dihedral;
+    ParsedExpression expression = Lepton::Parser::parse(force.getEnergyFunction(), functions);
+    map<string, int> groups;
+    for (int i = 0; i < force.getNumGroupsPerBond(); i++) {
+        stringstream name;
+        name << 'g' << (i+1);
+        groups[name.str()] = i;
+    }
+    return ParsedExpression(replaceFunctions(expression.getRootNode(), groups, distances, angles, dihedrals)).optimize();
+}
+
+ExpressionTreeNode CustomCentroidBondForceImpl::replaceFunctions(const ExpressionTreeNode& node, map<string, int> groups,
+        map<string, vector<int> >& distances, map<string, vector<int> >& angles, map<string, vector<int> >& dihedrals) {
+    const Operation& op = node.getOperation();
+    if (op.getId() != Operation::CUSTOM || (op.getName() != "distance" && op.getName() != "angle" && op.getName() != "dihedral"))
+    {
+        // This is not an angle or dihedral, so process its children.
+
+        vector<ExpressionTreeNode> children;
+        for (int i = 0; i < (int) node.getChildren().size(); i++)
+            children.push_back(replaceFunctions(node.getChildren()[i], groups, distances, angles, dihedrals));
+        return ExpressionTreeNode(op.clone(), children);
+    }
+    const Operation::Custom& custom = static_cast<const Operation::Custom&>(op);
+
+    // Identify the groups this term is based on.
+
+    int numArgs = custom.getNumArguments();
+    vector<int> indices(numArgs);
+    for (int i = 0; i < numArgs; i++) {
+        map<string, int>::const_iterator iter = groups.find(node.getChildren()[i].getOperation().getName());
+        if (iter == groups.end())
+            throw OpenMMException("CustomCentroidBondForce: Unknown group '"+node.getChildren()[i].getOperation().getName()+"'");
+        indices[i] = iter->second;
+    }
+
+    // Select a name for the variable and add it to the appropriate map.
+
+    stringstream variable;
+    if (numArgs == 2)
+        variable << "distance";
+    else if (numArgs == 3)
+        variable << "angle";
+    else
+        variable << "dihedral";
+    for (int i = 0; i < numArgs; i++)
+        variable << indices[i];
+    string name = variable.str();
+    if (numArgs == 2)
+        distances[name] = indices;
+    else if (numArgs == 3)
+        angles[name] = indices;
+    else
+        dihedrals[name] = indices;
+
+    // Return a new node that represents it as a simple variable.
+
+    return ExpressionTreeNode(new Operation::Variable(name));
+}
+
+vector<pair<int, int> > CustomCentroidBondForceImpl::getBondedParticles() const {
+    vector<pair<int, int> > bonds;
+    for (int i = 0; i < owner.getNumBonds(); i++) {
+        vector<int> groups;
+        vector<double> parameters;
+        owner.getBondParameters(i, groups, parameters);
+        for (int j = 1; j < groups.size(); j++)
+            for (int k = 0; k < j; k++)
+                addBondsBetweenGroups(j, k, bonds);
+    }
+    return bonds;
+}
+
+void CustomCentroidBondForceImpl::addBondsBetweenGroups(int group1, int group2, vector<pair<int, int> >& bonds) const {
+    vector<int> atoms1;
+    vector<int> atoms2;
+    vector<double> weights;
+    owner.getGroupParameters(group1, atoms1, weights);
+    owner.getGroupParameters(group2, atoms2, weights);
+    for (int i = 0; i < atoms1.size(); i++)
+        for (int j = 0; j < atoms2.size(); j++)
+            bonds.push_back(make_pair(atoms1[i], atoms2[j]));
+}
+
+void CustomCentroidBondForceImpl::updateParametersInContext(ContextImpl& context) {
+    kernel.getAs<CalcCustomCentroidBondForceKernel>().copyParametersToContext(context, owner);
+}
+
+void CustomCentroidBondForceImpl::computeNormalizedWeights(const CustomCentroidBondForce& force, const System& system, vector<vector<double> >& weights) {
+    int numGroups = force.getNumGroups();
+    weights.resize(numGroups);
+    for (int i = 0; i < numGroups; i++) {
+        vector<int> particles;
+        vector<double> groupWeights;
+        force.getGroupParameters(i, particles, groupWeights);
+        int numParticles = particles.size();
+
+        // If weights were not specified, use particle masses.
+
+        if (groupWeights.size() == 0) {
+            groupWeights.resize(numParticles);
+            for (int j = 0; j < numParticles; j++)
+                groupWeights[j] = system.getParticleMass(particles[j]);
+        }
+
+        // Normalize the weights.
+
+        double total = 0;
+        for (int j = 0; j < numParticles; j++)
+            total += groupWeights[j];
+        if (total == 0.0) {
+            stringstream msg;
+            msg << "CustomCentroidBondForce: Weights for group ";
+            msg << i;
+            msg << " add to 0";
+            throw OpenMMException(msg.str());
+        }
+        weights[i].resize(numParticles);
+        for (int j = 0; j < numParticles; j++)
+            weights[i][j] = groupWeights[j]/total;
+    }
+}

platforms/cuda/include/CudaKernels.h

@@ -922,6 +922,58 @@ private:
     CUfunction donorKernel, acceptorKernel;
 };
 
+/**
+ * This kernel is invoked by CustomCentroidBondForce to calculate the forces acting on the system.
+ */
+class CudaCalcCustomCentroidBondForceKernel : public CalcCustomCentroidBondForceKernel {
+public:
+    CudaCalcCustomCentroidBondForceKernel(std::string name, const Platform& platform, CudaContext& cu, const System& system) : CalcCustomCentroidBondForceKernel(name, platform),
+            cu(cu), params(NULL), globals(NULL), groupParticles(NULL), groupWeights(NULL), groupOffsets(NULL), groupForces(NULL), bondGroups(NULL), centerPositions(NULL), system(system) {
+    }
+    ~CudaCalcCustomCentroidBondForceKernel();
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     * @param force      the CustomCentroidBondForce this kernel will be used for
+     */
+    void initialize(const System& system, const CustomCentroidBondForce& force);
+    /**
+     * Execute the kernel to calculate the forces and/or energy.
+     *
+     * @param context        the context in which to execute this kernel
+     * @param includeForces  true if forces should be calculated
+     * @param includeEnergy  true if the energy should be calculated
+     * @return the potential energy due to the force
+     */
+    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CustomCentroidBondForce to copy the parameters from
+     */
+    void copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force);
+
+private:
+    int numGroups, numBonds;
+    CudaContext& cu;
+    CudaParameterSet* params;
+    CudaArray* globals;
+    CudaArray* groupParticles;
+    CudaArray* groupWeights;
+    CudaArray* groupOffsets;
+    CudaArray* groupForces;
+    CudaArray* bondGroups;
+    CudaArray* centerPositions;
+    std::vector<std::string> globalParamNames;
+    std::vector<float> globalParamValues;
+    std::vector<CudaArray*> tabulatedFunctions;
+    std::vector<void*> groupForcesArgs;
+    CUfunction computeCentersKernel, groupForcesKernel, applyForcesKernel;
+    const System& system;
+};
+
 /**
  * This kernel is invoked by CustomCompoundBondForce to calculate the forces acting on the system.
  */

platforms/cuda/src/CudaKernelFactory.cpp

@@ -104,6 +104,8 @@ KernelImpl* CudaKernelFactory::createKernelImpl(std::string name, const Platform
         return new CudaCalcCustomExternalForceKernel(name, platform, cu, context.getSystem());
     if (name == CalcCustomHbondForceKernel::Name())
         return new CudaCalcCustomHbondForceKernel(name, platform, cu, context.getSystem());
+    if (name == CalcCustomCentroidBondForceKernel::Name())
+        return new CudaCalcCustomCentroidBondForceKernel(name, platform, cu, context.getSystem());
     if (name == CalcCustomCompoundBondForceKernel::Name())
         return new CudaCalcCustomCompoundBondForceKernel(name, platform, cu, context.getSystem());
     if (name == CalcCustomManyParticleForceKernel::Name())

platforms/cuda/src/CudaPlatform.cpp

@@ -80,6 +80,7 @@ CudaPlatform::CudaPlatform() {
     registerKernelFactory(CalcCustomGBForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomExternalForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomHbondForceKernel::Name(), factory);
+    registerKernelFactory(CalcCustomCentroidBondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomCompoundBondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomManyParticleForceKernel::Name(), factory);
     registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);

platforms/cuda/src/kernels/customCentroidBond.cu

+/**
+ * Compute the center of each group.
+ */
+extern "C" __global__ void computeGroupCenters(const real4* __restrict__ posq, const int* __restrict__ groupParticles,
+        const real* __restrict__ groupWeights, const int* __restrict__ groupOffsets, real4* __restrict__ centerPositions) {
+    __shared__ volatile real3 temp[64];
+    for (int group = blockIdx.x; group < NUM_GROUPS; group += gridDim.x) {
+        // The threads in this block work together to compute the center one group.
+        
+        int firstIndex = groupOffsets[group];
+        int lastIndex = groupOffsets[group+1];
+        real3 center = make_real3(0, 0, 0);
+        for (int index = threadIdx.x; index < lastIndex-firstIndex; index += blockDim.x) {
+            int atom = groupParticles[firstIndex+index];
+            real weight = groupWeights[firstIndex+index];
+            real4 pos = posq[atom];
+            center.x += weight*pos.x;
+            center.y += weight*pos.y;
+            center.z += weight*pos.z;
+        }
+        
+        // Sum the values.
+        
+        int thread = threadIdx.x;
+        temp[thread].x = center.x;
+        temp[thread].y = center.y;
+        temp[thread].z = center.z;
+        __syncthreads();
+        if (thread < 32) {
+            temp[thread].x += temp[thread+32].x;
+            temp[thread].y += temp[thread+32].y;
+            temp[thread].z += temp[thread+32].z;
+            if (thread < 16) {
+                temp[thread].x += temp[thread+16].x;
+                temp[thread].y += temp[thread+16].y;
+                temp[thread].z += temp[thread+16].z;
+            }
+            if (thread < 8) {
+                temp[thread].x += temp[thread+8].x;
+                temp[thread].y += temp[thread+8].y;
+                temp[thread].z += temp[thread+8].z;
+            }
+            if (thread < 4) {
+                temp[thread].x += temp[thread+4].x;
+                temp[thread].y += temp[thread+4].y;
+                temp[thread].z += temp[thread+4].z;
+            }
+            if (thread < 2) {
+                temp[thread].x += temp[thread+2].x;
+                temp[thread].y += temp[thread+2].y;
+                temp[thread].z += temp[thread+2].z;
+            }
+        }
+        if (thread == 0)
+            centerPositions[group] = make_real4(temp[0].x+temp[1].x, temp[0].y+temp[1].y, temp[0].z+temp[1].z, 0);
+    }
+}
+
+/**
+ * Convert a real4 to a real3 by removing its last element.
+ */
+inline __device__ real3 trim(real4 v) {
+    return make_real3(v.x, v.y, v.z);
+}
+
+/**
+ * Compute the difference between two vectors, setting the fourth component to the squared magnitude.
+ */
+inline __device__ real4 delta(real4 vec1, real4 vec2) {
+    real4 result = make_real4(vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0);
+    result.w = result.x*result.x + result.y*result.y + result.z*result.z;
+    return result;
+}
+
+/**
+ * Compute the angle between two vectors.  The w component of each vector should contain the squared magnitude.
+ */
+__device__ real computeAngle(real4 vec1, real4 vec2) {
+    real dotProduct = vec1.x*vec2.x + vec1.y*vec2.y + vec1.z*vec2.z;
+    real cosine = dotProduct*RSQRT(vec1.w*vec2.w);
+    real angle;
+    if (cosine > 0.99f || cosine < -0.99f) {
+        // We're close to the singularity in acos(), so take the cross product and use asin() instead.
+
+        real3 crossProduct = cross(vec1, vec2);
+        real scale = vec1.w*vec2.w;
+        angle = ASIN(SQRT(dot(crossProduct, crossProduct)/scale));
+        if (cosine < 0.0f)
+            angle = M_PI-angle;
+    }
+    else
+       angle = ACOS(cosine);
+    return angle;
+}
+
+/**
+ * Compute the cross product of two vectors, setting the fourth component to the squared magnitude.
+ */
+inline __device__ real4 computeCross(real4 vec1, real4 vec2) {
+    real3 cp = cross(vec1, vec2);
+    return make_real4(cp.x, cp.y, cp.z, cp.x*cp.x+cp.y*cp.y+cp.z*cp.z);
+}
+
+/**
+ * Compute the forces on groups based on the bonds.
+ */
+extern "C" __global__ void computeGroupForces(unsigned long long* __restrict__ groupForce, real* __restrict__ energyBuffer, const real4* __restrict__ centerPositions,
+        const int* __restrict__ bondGroups
+        EXTRA_ARGS) {
+    real energy = 0;
+    for (int index = blockIdx.x*blockDim.x+threadIdx.x; index < NUM_BONDS; index += blockDim.x*gridDim.x) {
+        COMPUTE_FORCE
+    }
+    energyBuffer[blockIdx.x*blockDim.x+threadIdx.x] += energy;
+}
+
+/**
+ * Apply the forces from the group centers to the individual atoms.
+ */
+extern "C" __global__ void applyForcesToAtoms(const int* __restrict__ groupParticles, const real* __restrict__ groupWeights, const int* __restrict__ groupOffsets,
+        const long long* __restrict__ groupForce, unsigned long long* __restrict__ atomForce) {
+    for (int group = blockIdx.x; group < NUM_GROUPS; group += gridDim.x) {
+        long long fx = groupForce[group];
+        long long fy = groupForce[group+NUM_GROUPS];
+        long long fz = groupForce[group+NUM_GROUPS*2];
+        int firstIndex = groupOffsets[group];
+        int lastIndex = groupOffsets[group+1];
+        for (int index = threadIdx.x; index < lastIndex-firstIndex; index += blockDim.x) {
+            int atom = groupParticles[firstIndex+index];
+            real weight = groupWeights[firstIndex+index];
+            atomicAdd(&atomForce[atom], static_cast<unsigned long long>((long long) (fx*weight)));
+            atomicAdd(&atomForce[atom+PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (fy*weight)));
+            atomicAdd(&atomForce[atom+2*PADDED_NUM_ATOMS], static_cast<unsigned long long>((long long) (fz*weight)));
+        }
+    }
+}

platforms/cuda/tests/TestCudaCustomCentroidBondForce.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) 2015 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the reference implementation of CustomCompoundBondForce.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "CudaPlatform.h"
+#include "openmm/CustomCentroidBondForce.h"
+#include "openmm/CustomCompoundBondForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+CudaPlatform platform;
+
+const double TOL = 1e-5;
+
+void testHarmonicBond() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(2.0);
+    system.addParticle(3.0);
+    system.addParticle(4.0);
+    system.addParticle(5.0);
+    CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "k*distance(g1,g2)^2");
+    force->addPerBondParameter("k");
+    vector<int> particles1;
+    particles1.push_back(0);
+    particles1.push_back(1);
+    vector<int> particles2;
+    particles2.push_back(2);
+    particles2.push_back(3);
+    particles2.push_back(4);
+    force->addGroup(particles1);
+    force->addGroup(particles2);
+    vector<int> groups;
+    groups.push_back(0);
+    groups.push_back(1);
+    vector<double> parameters;
+    parameters.push_back(1.0);
+    force->addBond(groups, parameters);
+    system.addForce(force);
+    ASSERT(!system.usesPeriodicBoundaryConditions());
+
+    // The center of mass of group 0 is (1.5, 0, 0).
+
+    vector<Vec3> positions(5);
+    positions[0] = Vec3(2.5, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+
+    // The center of mass of group 1 is (-1, 0, 0).
+
+    positions[2] = Vec3(-6, 0, 0);
+    positions[3] = Vec3(-1, 0, 0);
+    positions[4] = Vec3(2, 0, 0);
+
+    // Check the forces and energy.
+
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(2.5*2.5, state.getPotentialEnergy(), TOL);
+    ASSERT_EQUAL_VEC(Vec3(-2*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(-2*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
+    ASSERT_EQUAL_VEC(Vec3(2*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
+    ASSERT_EQUAL_VEC(Vec3(2*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
+    ASSERT_EQUAL_VEC(Vec3(2*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
+
+    // Update the per-bond parameter and see if the results change.
+
+    parameters[0] = 2.0;
+    force->setBondParameters(0, groups, parameters);
+    force->updateParametersInContext(context);
+    state = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(2*2.5*2.5, state.getPotentialEnergy(), TOL);
+    ASSERT_EQUAL_VEC(Vec3(-4*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(-4*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
+    ASSERT_EQUAL_VEC(Vec3(4*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
+    ASSERT_EQUAL_VEC(Vec3(4*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
+    ASSERT_EQUAL_VEC(Vec3(4*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
+    
+    // All the particles should be treated as a single molecule.
+    
+    vector<std::vector<int> > molecules = context.getMolecules();
+    ASSERT_EQUAL(1, molecules.size());
+    ASSERT_EQUAL(5, molecules[0].size());
+}
+
+void testComplexFunction() {
+    int numParticles = 5;
+    System system;
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(2.0);
+    vector<double> table(20);
+    for (int i = 0; i < 20; i++)
+        table[i] = sin(0.11*i);
+
+    // When every group contains only one particle, a CustomCentroidBondForce is identical to a
+    // CustomCompoundBondForce.  Use that to test a complicated energy function with lots of terms.
+
+    CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+fn(distance(p1,p2))*angle(p3,p2,p4)+scale*dihedral(p2,p1,p4,p3)");
+    CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+fn(distance(g1,g2))*angle(g3,g2,g4)+scale*dihedral(g2,g1,g4,g3)");
+    compound->addGlobalParameter("scale", 0.5);
+    centroid->addGlobalParameter("scale", 0.5);
+    compound->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
+    centroid->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
+
+    // Add two bonds to the CustomCompoundBondForce.
+
+    vector<int> particles(4);
+    vector<double> parameters;
+    particles[0] = 0;
+    particles[1] = 1;
+    particles[2] = 2;
+    particles[3] = 3;
+    compound->addBond(particles, parameters);
+    particles[0] = 2;
+    particles[1] = 4;
+    particles[2] = 3;
+    particles[3] = 1;
+    compound->addBond(particles, parameters);
+
+    // Add identical bonds to the CustomCentroidBondForce.  As a stronger test, make sure that
+    // group number is different from particle number.
+
+    vector<int> groupMembers(1);
+    groupMembers[0] = 3;
+    centroid->addGroup(groupMembers);
+    groupMembers[0] = 0;
+    centroid->addGroup(groupMembers);
+    groupMembers[0] = 1;
+    centroid->addGroup(groupMembers);
+    groupMembers[0] = 2;
+    centroid->addGroup(groupMembers);
+    groupMembers[0] = 4;
+    centroid->addGroup(groupMembers);
+    vector<int> groups(4);
+    groups[0] = 1;
+    groups[1] = 2;
+    groups[2] = 3;
+    groups[3] = 0;
+    centroid->addBond(groups, parameters);
+    groups[0] = 3;
+    groups[1] = 4;
+    groups[2] = 0;
+    groups[3] = 2;
+    centroid->addBond(groups, parameters);
+
+    // Add both forces as different force groups, and create a context.
+
+    centroid->setForceGroup(1);
+    system.addForce(compound);
+    system.addForce(centroid);
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+
+    // Evaluate the force and energy for various positions and see if they match.
+
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < 10; i++) {
+        for (int j = 0; j < numParticles; j++)
+            positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
+        context.setPositions(positions);
+        State state1 = context.getState(State::Forces | State::Energy, false, 1<<0);
+        State state2 = context.getState(State::Forces | State::Energy, false, 1<<1);
+        ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), TOL);
+        for (int i = 0; i < numParticles; i++)
+            ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], TOL);
+    }
+}
+
+void testCustomWeights() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(2.0);
+    system.addParticle(3.0);
+    system.addParticle(4.0);
+    CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "distance(g1,g2)^2");
+    vector<int> particles(2);
+    vector<double> weights(2);
+    particles[0] = 0;
+    particles[1] = 1;
+    weights[0] = 0.5;
+    weights[1] = 1.5;
+    force->addGroup(particles, weights);
+    particles[0] = 2;
+    particles[1] = 3;
+    weights[0] = 2.0;
+    weights[1] = 1.0;
+    force->addGroup(particles, weights);
+    vector<int> groups;
+    groups.push_back(0);
+    groups.push_back(1);
+    vector<double> parameters;
+    force->addBond(groups, parameters);
+    system.addForce(force);
+
+    // The center of mass of group 0 is (0, 1, 0).
+
+    vector<Vec3> positions(4);
+    positions[0] = Vec3(0, 4, 0);
+    positions[1] = Vec3(0, 0, 0);
+
+    // The center of mass of group 1 is (0, 10, 0).
+
+    positions[2] = Vec3(0, 9, 0);
+    positions[3] = Vec3(0, 12, 0);
+
+    // Check the forces and energy.
+
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(9*9, state.getPotentialEnergy(), TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, 2*9*(0.5/2.0), 0), state.getForces()[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, 2*9*(1.5/2.0), 0), state.getForces()[1], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, -2*9*(2.0/3.0), 0), state.getForces()[2], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, -2*9*(1.0/3.0), 0), state.getForces()[3], TOL);
+}
+
+int main(int argc, char* argv[]) {
+    try {
+        if (argc > 1)
+            platform.setPropertyDefaultValue("CudaPrecision", string(argv[1]));
+        testHarmonicBond();
+        testComplexFunction();
+        testCustomWeights();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

platforms/opencl/include/OpenCLKernels.h

@@ -904,6 +904,57 @@ private:
     cl::Kernel donorKernel, acceptorKernel;
 };
 
+/**
+ * This kernel is invoked by CustomCentroidBondForce to calculate the forces acting on the system.
+ */
+class OpenCLCalcCustomCentroidBondForceKernel : public CalcCustomCentroidBondForceKernel {
+public:
+    OpenCLCalcCustomCentroidBondForceKernel(std::string name, const Platform& platform, OpenCLContext& cl, const System& system) : CalcCustomCentroidBondForceKernel(name, platform),
+            cl(cl), params(NULL), globals(NULL), groupParticles(NULL), groupWeights(NULL), groupOffsets(NULL), groupForces(NULL), bondGroups(NULL), centerPositions(NULL), system(system) {
+    }
+    ~OpenCLCalcCustomCentroidBondForceKernel();
+    /**
+     * Initialize the kernel.
+     *
+     * @param system     the System this kernel will be applied to
+     * @param force      the CustomCentroidBondForce this kernel will be used for
+     */
+    void initialize(const System& system, const CustomCentroidBondForce& force);
+    /**
+     * Execute the kernel to calculate the forces and/or energy.
+     *
+     * @param context        the context in which to execute this kernel
+     * @param includeForces  true if forces should be calculated
+     * @param includeEnergy  true if the energy should be calculated
+     * @return the potential energy due to the force
+     */
+    double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CustomCentroidBondForce to copy the parameters from
+     */
+    void copyParametersToContext(ContextImpl& context, const CustomCentroidBondForce& force);
+
+private:
+    int numGroups, numBonds;
+    OpenCLContext& cl;
+    OpenCLParameterSet* params;
+    OpenCLArray* globals;
+    OpenCLArray* groupParticles;
+    OpenCLArray* groupWeights;
+    OpenCLArray* groupOffsets;
+    OpenCLArray* groupForces;
+    OpenCLArray* bondGroups;
+    OpenCLArray* centerPositions;
+    std::vector<std::string> globalParamNames;
+    std::vector<cl_float> globalParamValues;
+    std::vector<OpenCLArray*> tabulatedFunctions;
+    cl::Kernel computeCentersKernel, groupForcesKernel, applyForcesKernel;
+    const System& system;
+};
+
 /**
  * This kernel is invoked by CustomCompoundBondForce to calculate the forces acting on the system.
  */

platforms/opencl/src/OpenCLKernelFactory.cpp

@@ -102,6 +102,8 @@ KernelImpl* OpenCLKernelFactory::createKernelImpl(std::string name, const Platfo
         return new OpenCLCalcCustomExternalForceKernel(name, platform, cl, context.getSystem());
     if (name == CalcCustomHbondForceKernel::Name())
         return new OpenCLCalcCustomHbondForceKernel(name, platform, cl, context.getSystem());
+    if (name == CalcCustomCentroidBondForceKernel::Name())
+        return new OpenCLCalcCustomCentroidBondForceKernel(name, platform, cl, context.getSystem());
     if (name == CalcCustomCompoundBondForceKernel::Name())
         return new OpenCLCalcCustomCompoundBondForceKernel(name, platform, cl, context.getSystem());
     if (name == CalcCustomManyParticleForceKernel::Name())

platforms/opencl/src/OpenCLPlatform.cpp

@@ -74,6 +74,7 @@ OpenCLPlatform::OpenCLPlatform() {
     registerKernelFactory(CalcCustomGBForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomExternalForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomHbondForceKernel::Name(), factory);
+    registerKernelFactory(CalcCustomCentroidBondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomCompoundBondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomManyParticleForceKernel::Name(), factory);
     registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);

platforms/opencl/src/kernels/customCentroidBond.cl

+#pragma OPENCL EXTENSION cl_khr_int64_base_atomics : enable
+
+/**
+ * Compute the center of each group.
+ */
+__kernel void computeGroupCenters(__global const real4* restrict posq, __global const int* restrict groupParticles,
+        __global const real* restrict groupWeights, __global const int* restrict groupOffsets, __global real4* restrict centerPositions) {
+    __local volatile real3 temp[64];
+    for (int group = get_group_id(0); group < NUM_GROUPS; group += get_num_groups(0)) {
+        // The threads in this block work together to compute the center one group.
+        
+        int firstIndex = groupOffsets[group];
+        int lastIndex = groupOffsets[group+1];
+        real3 center = (real3) 0;
+        for (int index = get_local_id(0); index < lastIndex-firstIndex; index += get_local_size(0)) {
+            int atom = groupParticles[firstIndex+index];
+            real weight = groupWeights[firstIndex+index];
+            real4 pos = posq[atom];
+            center.x += weight*pos.x;
+            center.y += weight*pos.y;
+            center.z += weight*pos.z;
+        }
+        
+        // Sum the values.
+        
+        int thread = get_local_id(0);
+        temp[thread].x = center.x;
+        temp[thread].y = center.y;
+        temp[thread].z = center.z;
+        __syncthreads();
+        if (thread < 32) {
+            temp[thread].x += temp[thread+32].x;
+            temp[thread].y += temp[thread+32].y;
+            temp[thread].z += temp[thread+32].z;
+            if (thread < 16) {
+                temp[thread].x += temp[thread+16].x;
+                temp[thread].y += temp[thread+16].y;
+                temp[thread].z += temp[thread+16].z;
+            }
+            if (thread < 8) {
+                temp[thread].x += temp[thread+8].x;
+                temp[thread].y += temp[thread+8].y;
+                temp[thread].z += temp[thread+8].z;
+            }
+            if (thread < 4) {
+                temp[thread].x += temp[thread+4].x;
+                temp[thread].y += temp[thread+4].y;
+                temp[thread].z += temp[thread+4].z;
+            }
+            if (thread < 2) {
+                temp[thread].x += temp[thread+2].x;
+                temp[thread].y += temp[thread+2].y;
+                temp[thread].z += temp[thread+2].z;
+            }
+        }
+        if (thread == 0)
+            centerPositions[group] = (real4) (temp[0].x+temp[1].x, temp[0].y+temp[1].y, temp[0].z+temp[1].z, 0);
+    }
+}
+
+/**
+ * Compute the difference between two vectors, setting the fourth component to the squared magnitude.
+ */
+real4 delta(real4 vec1, real4 vec2) {
+    real4 result = (real4) (vec1.x-vec2.x, vec1.y-vec2.y, vec1.z-vec2.z, 0);
+    result.w = result.x*result.x + result.y*result.y + result.z*result.z;
+    return result;
+}
+
+/**
+ * Compute the angle between two vectors.  The w component of each vector should contain the squared magnitude.
+ */
+real computeAngle(real4 vec1, real4 vec2) {
+    real dotProduct = vec1.x*vec2.x + vec1.y*vec2.y + vec1.z*vec2.z;
+    real cosine = dotProduct*RSQRT(vec1.w*vec2.w);
+    real angle;
+    if (cosine > 0.99f || cosine < -0.99f) {
+        // We're close to the singularity in acos(), so take the cross product and use asin() instead.
+
+        real4 crossProduct = cross(vec1, vec2);
+        real scale = vec1.w*vec2.w;
+        angle = asin(SQRT(dot(crossProduct, crossProduct)/scale));
+        if (cosine < 0)
+            angle = M_PI-angle;
+    }
+    else
+       angle = acos(cosine);
+    return angle;
+}
+
+/**
+ * Compute the cross product of two vectors, setting the fourth component to the squared magnitude.
+ */
+real4 computeCross(real4 vec1, real4 vec2) {
+    real4 result = cross(vec1, vec2);
+    result.w = result.x*result.x + result.y*result.y + result.z*result.z;
+    return result;
+}
+
+/**
+ * Compute the forces on groups based on the bonds.
+ */
+__kernel void computeGroupForces(__global long* restrict groupForce, __global real* restrict energyBuffer, __global const real4* restrict centerPositions,
+        __global const int* restrict bondGroups
+        EXTRA_ARGS) {
+    real energy = 0;
+    for (int index = get_global_id(0); index < NUM_BONDS; index += get_global_size(0)) {
+        COMPUTE_FORCE
+    }
+    energyBuffer[get_global_id(0)] += energy;
+}
+
+/**
+ * Apply the forces from the group centers to the individual atoms.
+ */
+__kernel void applyForcesToAtoms(__global const int* restrict groupParticles, __global const real* restrict groupWeights, __global const int* restrict groupOffsets,
+        __global const long* restrict groupForce, __global long* restrict atomForce) {
+    for (int group = get_group_id(0); group < NUM_GROUPS; group += get_num_groups(0)) {
+        long fx = groupForce[group];
+        long fy = groupForce[group+NUM_GROUPS];
+        long fz = groupForce[group+NUM_GROUPS*2];
+        int firstIndex = groupOffsets[group];
+        int lastIndex = groupOffsets[group+1];
+        for (int index = get_local_id(0); index < lastIndex-firstIndex; index += get_local_size(0)) {
+            int atom = groupParticles[firstIndex+index];
+            real weight = groupWeights[firstIndex+index];
+            atom_add(&atomForce[atom], (long) (fx*weight));
+            atom_add(&atomForce[atom+PADDED_NUM_ATOMS], (long) (fy*weight));
+            atom_add(&atomForce[atom+2*PADDED_NUM_ATOMS], (long) (fz*weight));
+        }
+    }
+}

platforms/opencl/tests/TestOpenCLCustomCentroidBondForce.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) 2015 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests the reference implementation of CustomCompoundBondForce.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/Context.h"
+#include "OpenCLPlatform.h"
+#include "openmm/CustomCentroidBondForce.h"
+#include "openmm/CustomCompoundBondForce.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+OpenCLPlatform platform;
+
+const double TOL = 1e-5;
+
+void testHarmonicBond() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(2.0);
+    system.addParticle(3.0);
+    system.addParticle(4.0);
+    system.addParticle(5.0);
+    CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "k*distance(g1,g2)^2");
+    force->addPerBondParameter("k");
+    vector<int> particles1;
+    particles1.push_back(0);
+    particles1.push_back(1);
+    vector<int> particles2;
+    particles2.push_back(2);
+    particles2.push_back(3);
+    particles2.push_back(4);
+    force->addGroup(particles1);
+    force->addGroup(particles2);
+    vector<int> groups;
+    groups.push_back(0);
+    groups.push_back(1);
+    vector<double> parameters;
+    parameters.push_back(1.0);
+    force->addBond(groups, parameters);
+    system.addForce(force);
+    ASSERT(!system.usesPeriodicBoundaryConditions());
+
+    // The center of mass of group 0 is (1.5, 0, 0).
+
+    vector<Vec3> positions(5);
+    positions[0] = Vec3(2.5, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+
+    // The center of mass of group 1 is (-1, 0, 0).
+
+    positions[2] = Vec3(-6, 0, 0);
+    positions[3] = Vec3(-1, 0, 0);
+    positions[4] = Vec3(2, 0, 0);
+
+    // Check the forces and energy.
+
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(2.5*2.5, state.getPotentialEnergy(), TOL);
+    ASSERT_EQUAL_VEC(Vec3(-2*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(-2*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
+    ASSERT_EQUAL_VEC(Vec3(2*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
+    ASSERT_EQUAL_VEC(Vec3(2*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
+    ASSERT_EQUAL_VEC(Vec3(2*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
+
+    // Update the per-bond parameter and see if the results change.
+
+    parameters[0] = 2.0;
+    force->setBondParameters(0, groups, parameters);
+    force->updateParametersInContext(context);
+    state = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(2*2.5*2.5, state.getPotentialEnergy(), TOL);
+    ASSERT_EQUAL_VEC(Vec3(-4*2.5*(1.0/3.0), 0, 0), state.getForces()[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(-4*2.5*(2.0/3.0), 0, 0), state.getForces()[1], TOL);
+    ASSERT_EQUAL_VEC(Vec3(4*2.5*(3.0/12.0), 0, 0), state.getForces()[2], TOL);
+    ASSERT_EQUAL_VEC(Vec3(4*2.5*(4.0/12.0), 0, 0), state.getForces()[3], TOL);
+    ASSERT_EQUAL_VEC(Vec3(4*2.5*(5.0/12.0), 0, 0), state.getForces()[4], TOL);
+    
+    // All the particles should be treated as a single molecule.
+    
+    vector<std::vector<int> > molecules = context.getMolecules();
+    ASSERT_EQUAL(1, molecules.size());
+    ASSERT_EQUAL(5, molecules[0].size());
+}
+
+void testComplexFunction() {
+    int numParticles = 5;
+    System system;
+    for (int i = 0; i < numParticles; i++)
+        system.addParticle(2.0);
+    vector<double> table(20);
+    for (int i = 0; i < 20; i++)
+        table[i] = sin(0.11*i);
+
+    // When every group contains only one particle, a CustomCentroidBondForce is identical to a
+    // CustomCompoundBondForce.  Use that to test a complicated energy function with lots of terms.
+
+    CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+fn(distance(p1,p2))*angle(p3,p2,p4)+scale*dihedral(p2,p1,p4,p3)");
+    CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+fn(distance(g1,g2))*angle(g3,g2,g4)+scale*dihedral(g2,g1,g4,g3)");
+    compound->addGlobalParameter("scale", 0.5);
+    centroid->addGlobalParameter("scale", 0.5);
+    compound->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
+    centroid->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
+
+    // Add two bonds to the CustomCompoundBondForce.
+
+    vector<int> particles(4);
+    vector<double> parameters;
+    particles[0] = 0;
+    particles[1] = 1;
+    particles[2] = 2;
+    particles[3] = 3;
+    compound->addBond(particles, parameters);
+    particles[0] = 2;
+    particles[1] = 4;
+    particles[2] = 3;
+    particles[3] = 1;
+    compound->addBond(particles, parameters);
+
+    // Add identical bonds to the CustomCentroidBondForce.  As a stronger test, make sure that
+    // group number is different from particle number.
+
+    vector<int> groupMembers(1);
+    groupMembers[0] = 3;
+    centroid->addGroup(groupMembers);
+    groupMembers[0] = 0;
+    centroid->addGroup(groupMembers);
+    groupMembers[0] = 1;
+    centroid->addGroup(groupMembers);
+    groupMembers[0] = 2;
+    centroid->addGroup(groupMembers);
+    groupMembers[0] = 4;
+    centroid->addGroup(groupMembers);
+    vector<int> groups(4);
+    groups[0] = 1;
+    groups[1] = 2;
+    groups[2] = 3;
+    groups[3] = 0;
+    centroid->addBond(groups, parameters);
+    groups[0] = 3;
+    groups[1] = 4;
+    groups[2] = 0;
+    groups[3] = 2;
+    centroid->addBond(groups, parameters);
+
+    // Add both forces as different force groups, and create a context.
+
+    centroid->setForceGroup(1);
+    system.addForce(compound);
+    system.addForce(centroid);
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+
+    // Evaluate the force and energy for various positions and see if they match.
+
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < 10; i++) {
+        for (int j = 0; j < numParticles; j++)
+            positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
+        context.setPositions(positions);
+        State state1 = context.getState(State::Forces | State::Energy, false, 1<<0);
+        State state2 = context.getState(State::Forces | State::Energy, false, 1<<1);
+        ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), TOL);
+        for (int i = 0; i < numParticles; i++)
+            ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], TOL);
+    }
+}
+
+void testCustomWeights() {
+    System system;
+    system.addParticle(1.0);
+    system.addParticle(2.0);
+    system.addParticle(3.0);
+    system.addParticle(4.0);
+    CustomCentroidBondForce* force = new CustomCentroidBondForce(2, "distance(g1,g2)^2");
+    vector<int> particles(2);
+    vector<double> weights(2);
+    particles[0] = 0;
+    particles[1] = 1;
+    weights[0] = 0.5;
+    weights[1] = 1.5;
+    force->addGroup(particles, weights);
+    particles[0] = 2;
+    particles[1] = 3;
+    weights[0] = 2.0;
+    weights[1] = 1.0;
+    force->addGroup(particles, weights);
+    vector<int> groups;
+    groups.push_back(0);
+    groups.push_back(1);
+    vector<double> parameters;
+    force->addBond(groups, parameters);
+    system.addForce(force);
+
+    // The center of mass of group 0 is (0, 1, 0).
+
+    vector<Vec3> positions(4);
+    positions[0] = Vec3(0, 4, 0);
+    positions[1] = Vec3(0, 0, 0);
+
+    // The center of mass of group 1 is (0, 10, 0).
+
+    positions[2] = Vec3(0, 9, 0);
+    positions[3] = Vec3(0, 12, 0);
+
+    // Check the forces and energy.
+
+    VerletIntegrator integrator(0.01);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    State state = context.getState(State::Forces | State::Energy);
+    ASSERT_EQUAL_TOL(9*9, state.getPotentialEnergy(), TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, 2*9*(0.5/2.0), 0), state.getForces()[0], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, 2*9*(1.5/2.0), 0), state.getForces()[1], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, -2*9*(2.0/3.0), 0), state.getForces()[2], TOL);
+    ASSERT_EQUAL_VEC(Vec3(0, -2*9*(1.0/3.0), 0), state.getForces()[3], TOL);
+}
+
+int main(int argc, char* argv[]) {
+    try {
+        if (argc > 1)
+            platform.setPropertyDefaultValue("OpenCLPrecision", string(argv[1]));
+        testHarmonicBond();
+        testComplexFunction();
+        testCustomWeights();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}