Redesigned the API for specifying exclusions and 1-4 interactions.

CMakeLists.txt

@@ -47,7 +47,7 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
 
 INCLUDE(Dart)
 
-# SUBDIRS (platforms/reference/tests platforms/cuda)
+SUBDIRS (tests)
 
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.

olla/include/kernels.h

@@ -226,11 +226,8 @@ public:
      * 
      * @param system     the System this kernel will be applied to
      * @param force      the NonbondedForce this kernel will be used for
-     * @param exclusions the i'th element lists the indices of all particles with which the i'th particle should not interact through
-     *                   nonbonded forces.  Bonded 1-4 pairs are also included in this list, since they should be omitted from
-     *                   the standard nonbonded calculation.
      */
-    virtual void initialize(const System& system, const NonbondedForce& force, const std::vector<std::set<int> >& exclusions) = 0;
+    virtual void initialize(const System& system, const NonbondedForce& force) = 0;
     /**
      * Execute the kernel to calculate the forces.
      * 

openmmapi/include/NonbondedForce.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) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -35,6 +35,7 @@
 #include "Force.h"
 #include "Vec3.h"
 #include <map>
+#include <set>
 #include <vector>
 #include "internal/windowsExport.h"
 
@@ -46,16 +47,22 @@ namespace OpenMM {
  * periodic boundary conditions and cutoffs for long range interactions.  Lennard-Jones interactions are
  * calculated with the Lorentz-Bertelot combining rule: it uses the arithmetic mean of the sigmas and the
  * geometric mean of the epsilons for the two interacting particles.
- * 
- * If the System also contains a HarmonicBondForce, nonbonded interactions are automatically excluded between
- * particles which are separated by three or fewer bonds.  Most molecular force fields omit Coulomb and
- * Lennard-Jones interactions between particles separated by one or two bonds, while using modified parameters
- * for those separated by three bonds (known as "1-4 interactions").  This class lets you provide a list of
- * 1-4 interactions to include in the potential, along with the parameters to use for each one.
- * 
- * When creating a NonbondedForce, you specify the number of particles and the number of 1-4 interactions as
- * arguments to the constructor.  You then loop over them and call setParticleParameters() for each particle and
- * setNonbond14Parameters() for each 1-4 interaction.
+ *
+ * To use this class, create a NonbondedForce object, then call addParticle() once for each particle in the
+ * System to define its parameters.  The number of particles for which you define nonbonded parameters must
+ * be exactly equal to the number of particles in the System, or else an exception will be thrown when you
+ * try to create an OpenMMContext.  After a particle has been added, you can modify its force field parameters
+ * by calling setParticleParameters().
+ *
+ * NonbondedForce also lets you specify "exceptions", particular pairs of particles whose interactions should be
+ * computed based on different parameters than those defined for the individual particles.  This can be used to
+ * completely exclude certain interactions from the force calculation, or to alter how they interact with each other.
+ *
+ * Many molecular force fields omit Coulomb and Lennard-Jones interactions between particles separated by one
+ * or two bonds, while using modified parameters for those separated by three bonds (known as "1-4 interactions").
+ * This class provides a convenience method for this case called createExceptionsFromBonds().  You pass to it
+ * a list of bonds and the scale factors to use for 1-4 interactions.  It identifies all pairs of particles which
+ * are separated by 1, 2, or 3 bonds, then automatically creates exceptions for them.
  */
 
 class OPENMM_EXPORT NonbondedForce : public Force {
@@ -81,28 +88,26 @@ public:
          */
         CutoffPeriodic = 2,
         /**
-         * Using Ewald summation method for long-range electrostatics.
+         * Periodic boundary conditions are used, and Ewald summation is used to compute the interaction of each particle
+         * with all periodic copies of every other particle.
          */
         Ewald = 3
     };
     /**
      * Create a NonbondedForce.
-     * 
-     * @param numParticles        the number of particles in the system
-     * @param numNonbonded14      the number of nonbonded 1-4 terms in the potential function
      */
-    NonbondedForce(int numParticles, int numNonbonded14);
+    NonbondedForce();
     /**
-     * Get the number of particles in the system.
+     * Get the number of particles for which force field parameters have been defined.
      */
     int getNumParticles() const {
         return particles.size();
     }
     /**
-     * Get the number of nonbonded 1-4 terms in the potential function
+     * Get the number of special interactions that should be calculated differently from other interactions.
      */
-    int getNumNonbonded14() const {
-        return nb14s.size();
+    int getNumExceptions() const {
+        return exceptions.size();
     }
     /**
      * Get the method used for handling long range nonbonded interactions.
@@ -146,13 +151,25 @@ public:
      * @param c      the vector defining the third edge of the periodic box
      */
     void setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c);
+    /**
+     * Add the nonbonded force parameters for a particle.  This should be called once for each particle
+     * in the System.  When it is called for the i'th time, it specifies the parameters for the i'th particle.
+     * For calculating the Lennard-Jones interaction between two particles, the arithmetic mean of the sigmas
+     * and the geometric mean of the epsilons for the two interacting particles is used (the Lorentz-Bertelot
+     * combining rule).
+     *
+     * @param charge    the charge of the particle, measured in units of the proton charge
+     * @param sigma     the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
+     * @param epsilon   the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
+     */
+    void addParticle(double charge, double sigma, double epsilon);
     /**
      * Get the nonbonded force parameters for a particle.
-     * 
+     *
      * @param index     the index of the particle for which to get parameters
      * @param charge    the charge of the particle, measured in units of the proton charge
-     * @param sigma     the van der Waals radius of the particle (sigma in the Lennard Jones potential), measured in nm
-     * @param epsilon   the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kJ/mol
+     * @param sigma     the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
+     * @param epsilon   the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
      */
     void getParticleParameters(int index, double& charge, double& sigma, double& epsilon) const;
     /**
@@ -162,40 +179,71 @@ public:
      *
      * @param index     the index of the particle for which to set parameters
      * @param charge    the charge of the particle, measured in units of the proton charge
-     * @param sigma     the van der Waals radius of the particle (sigma in the Lennard Jones potential), measured in nm
-     * @param epsilon   the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kJ/mol
+     * @param sigma     the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
+     * @param epsilon   the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
      */
     void setParticleParameters(int index, double charge, double sigma, double epsilon);
     /**
-     * Get the force field parameters for a nonbonded 1-4 term.
+     * Add an interaction to the list of exceptions that should be calculated differently from other interactions.
+     * If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from
+     * force and energy calculations.
+     *
+     * In many cases, you can use createExceptionsFromBonds() rather than adding each exception explicitly.
+     *
+     * @param particle1  the index of the first particle involved in the interaction
+     * @param particle2  the index of the second particle involved in the interaction
+     * @param chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
+     * @param sigma      the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
+     * @param epsilon    the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
+     */
+    void addException(int particle1, int particle2, double chargeProd, double sigma, double epsilon);
+    /**
+     * Get the force field parameters for an interaction that should be calculated differently from others.
      * 
      * @param index      the index of the interaction for which to get parameters
      * @param particle1  the index of the first particle involved in the interaction
      * @param particle2  the index of the second particle involved in the interaction
      * @param chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
-     * @param sigma      the van der Waals radius of the particle (sigma in the Lennard Jones potential), measured in nm
-     * @param epsilon    the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kJ/mol
+     * @param sigma      the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
+     * @param epsilon    the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
      */
-    void getNonbonded14Parameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon) const;
+    void getExceptionParameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon) const;
     /**
-     * Set the force field parameters for a nonbonded 1-4 term.
+     * Set the force field parameters for an interaction that should be calculated differently from others.
+     * If chargeProd and epsilon are both equal to 0, this will cause the interaction to be completely omitted from
+     * force and energy calculations.
      * 
      * @param index      the index of the interaction for which to get parameters
      * @param particle1  the index of the first particle involved in the interaction
      * @param particle2  the index of the second particle involved in the interaction
      * @param chargeProd the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge squared
-     * @param sigma      the van der Waals radius of the particle (sigma in the Lennard Jones potential), measured in nm
-     * @param epsilon    the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kJ/mol
+     * @param sigma      the sigma parameter of the Lennard-Jones potential (corresponding to the van der Waals radius of the particle), measured in nm
+     * @param epsilon    the epsilon parameter of the Lennard-Jones potential (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
+     */
+    void setExceptionParameters(int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon);
+    /**
+     * Identify exceptions based on the molecular topology.  Particles which are separated by one or two bonds are set
+     * to not interact at all, while pairs of particles separated by three bonds (known as "1-4 interactions") have
+     * their Coulomb and Lennard-Jones interactions reduced by a fixed factor.
+     *
+     * @param bonds           the set of bonds based on which to construct exceptions.  Each element specifies the indices of
+     *                        two particles that are bonded to each other.
+     * @param coulomb14Scale  pairs of particles separated by three bonds will have the strength of their Coulomb interaction
+     *                        multiplied by this factor
+     * @param lj14Scale       pairs of particles separated by three bonds will have the strength of their Lennard-Jones interaction
+     *                        multiplied by this factor
      */
-    void setNonbonded14Parameters(int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon);
+    void createExceptionsFromBonds(const std::vector<std::pair<int, int> >& bonds, double coulomb14Scale, double lj14Scale);
 protected:
     ForceImpl* createImpl();
 private:
     class ParticleInfo;
-    class NB14Info;
+    class ExceptionInfo;
     NonbondedMethod nonbondedMethod;
     double cutoffDistance;
     Vec3 periodicBoxVectors[3];
+    void addExclusionsToSet(const std::vector<std::set<int> >& bonded12, std::set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const;
+
 
 // Retarded visual studio compiler complains about being unable to 
 // export private stl class members.
@@ -205,7 +253,7 @@ private:
 #pragma warning(disable:4251)
 #endif
     std::vector<ParticleInfo> particles;
-    std::vector<NB14Info> nb14s;
+    std::vector<ExceptionInfo> exceptions;
 #if defined(_MSC_VER)
 #pragma warning(pop)
 #endif
@@ -218,16 +266,22 @@ public:
     ParticleInfo() {
         charge = sigma = epsilon = 0.0;
     }
+    ParticleInfo(double charge, double sigma, double epsilon) :
+        charge(charge), sigma(sigma), epsilon(epsilon) {
+    }
 };
 
-class NonbondedForce::NB14Info {
+class NonbondedForce::ExceptionInfo {
 public:
     int particle1, particle2;
     double chargeProd, sigma, epsilon;
-    NB14Info() {
+    ExceptionInfo() {
         particle1 = particle2 = -1;
         chargeProd = sigma = epsilon = 0.0;
     }
+    ExceptionInfo(int particle1, int particle2, double chargeProd, double sigma, double epsilon) :
+        particle1(particle1), particle2(particle2), chargeProd(chargeProd), sigma(sigma), epsilon(epsilon) {
+    }
 };
 
 } // namespace OpenMM

openmmapi/include/internal/NonbondedForceImpl.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) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -63,8 +63,6 @@ public:
     }
     std::vector<std::string> getKernelNames();
 private:
-    void findExclusions(const std::vector<std::vector<int> >& bondIndices, std::vector<std::set<int> >& exclusions, std::set<std::pair<int, int> >& bonded14Indices) const;
-    void addExclusionsToSet(const std::vector<std::set<int> >& bonded12, std::set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const;
     NonbondedForce& owner;
     Kernel kernel;
 };

openmmapi/src/NonbondedForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -33,11 +33,15 @@
 #include "OpenMMException.h"
 #include "NonbondedForce.h"
 #include "internal/NonbondedForceImpl.h"
+#include <cmath>
+#include <utility>
 
 using namespace OpenMM;
+using std::pair;
+using std::set;
+using std::vector;
 
-NonbondedForce::NonbondedForce(int numParticles, int numNonbonded14) : particles(numParticles), nb14s(numNonbonded14),
-        nonbondedMethod(NoCutoff), cutoffDistance(1.0) {
+NonbondedForce::NonbondedForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0) {
     periodicBoxVectors[0] = Vec3(2, 0, 0);
     periodicBoxVectors[1] = Vec3(0, 2, 0);
     periodicBoxVectors[2] = Vec3(0, 0, 2);
@@ -77,6 +81,10 @@ void NonbondedForce::setPeriodicBoxVectors(Vec3 a, Vec3 b, Vec3 c) {
     periodicBoxVectors[2] = c;
 }
 
+void NonbondedForce::addParticle(double charge, double sigma, double epsilon) {
+    particles.push_back(ParticleInfo(charge, sigma, epsilon));
+}
+
 void NonbondedForce::getParticleParameters(int index, double& charge, double& sigma, double& epsilon) const {
     charge = particles[index].charge;
     sigma = particles[index].sigma;
@@ -89,22 +97,73 @@ void NonbondedForce::setParticleParameters(int index, double charge, double sigm
     particles[index].epsilon = epsilon;
 }
 
-void NonbondedForce::getNonbonded14Parameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon) const {
-    particle1 = nb14s[index].particle1;
-    particle2 = nb14s[index].particle2;
-    chargeProd = nb14s[index].chargeProd;
-    sigma = nb14s[index].sigma;
-    epsilon = nb14s[index].epsilon;
+void NonbondedForce::addException(int particle1, int particle2, double chargeProd, double sigma, double epsilon) {
+    exceptions.push_back(ExceptionInfo(particle1, particle2, chargeProd, sigma, epsilon));
+}
+void NonbondedForce::getExceptionParameters(int index, int& particle1, int& particle2, double& chargeProd, double& sigma, double& epsilon) const {
+    particle1 = exceptions[index].particle1;
+    particle2 = exceptions[index].particle2;
+    chargeProd = exceptions[index].chargeProd;
+    sigma = exceptions[index].sigma;
+    epsilon = exceptions[index].epsilon;
 }
 
-void NonbondedForce::setNonbonded14Parameters(int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon) {
-    nb14s[index].particle1 = particle1;
-    nb14s[index].particle2 = particle2;
-    nb14s[index].chargeProd = chargeProd;
-    nb14s[index].sigma = sigma;
-    nb14s[index].epsilon = epsilon;
+void NonbondedForce::setExceptionParameters(int index, int particle1, int particle2, double chargeProd, double sigma, double epsilon) {
+    exceptions[index].particle1 = particle1;
+    exceptions[index].particle2 = particle2;
+    exceptions[index].chargeProd = chargeProd;
+    exceptions[index].sigma = sigma;
+    exceptions[index].epsilon = epsilon;
 }
 
 ForceImpl* NonbondedForce::createImpl() {
     return new NonbondedForceImpl(*this);
 }
+
+void NonbondedForce::createExceptionsFromBonds(const vector<pair<int, int> >& bonds, double coulomb14Scale, double lj14Scale) {
+
+    // Find particles separated by 1, 2, or 3 bonds.
+
+    vector<set<int> > exclusions(particles.size());
+    vector<set<int> > bonded12(exclusions.size());
+    for (int i = 0; i < (int) bonds.size(); ++i) {
+        bonded12[bonds[i].first].insert(bonds[i].second);
+        bonded12[bonds[i].second].insert(bonds[i].first);
+    }
+    for (int i = 0; i < (int) exclusions.size(); ++i)
+        addExclusionsToSet(bonded12, exclusions[i], i, i, 2);
+
+    // Find particles separated by 1 or 2 bonds and create the exceptions.
+
+    for (int i = 0; i < (int) exclusions.size(); ++i) {
+        set<int> bonded13;
+        addExclusionsToSet(bonded12, bonded13, i, i, 1);
+        for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
+            if (*iter < i) {
+                if (bonded13.find(*iter) == bonded13.end()) {
+                    // This is a 1-4 interaction.
+
+                    const ParticleInfo& particle1 = particles[*iter];
+                    const ParticleInfo& particle2 = particles[i];
+                    const double chargeProd = coulomb14Scale*particle1.charge*particle2.charge;
+                    const double sigma = 0.5*(particle1.sigma+particle2.sigma);
+                    const double epsilon = lj14Scale*std::sqrt(particle1.epsilon*particle2.epsilon);
+                    addException(*iter, i, chargeProd, sigma, epsilon);
+                }
+                else {
+                    // This interaction should be completely excluded.
+
+                    addException(*iter, i, 0.0, 1.0, 0.0);
+                }
+            }
+    }
+}
+
+void NonbondedForce::addExclusionsToSet(const vector<set<int> >& bonded12, set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const {
+    for (set<int>::const_iterator iter = bonded12[fromParticle].begin(); iter != bonded12[fromParticle].end(); ++iter) {
+        if (*iter != baseParticle)
+            exclusions.insert(*iter);
+        if (currentLevel > 0)
+            addExclusionsToSet(bonded12, exclusions, baseParticle, *iter, currentLevel-1);
+    }
+}

openmmapi/src/NonbondedForceImpl.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -29,14 +29,17 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "OpenMMException.h"
 #include "internal/OpenMMContextImpl.h"
 #include "internal/NonbondedForceImpl.h"
 #include "kernels.h"
+#include <sstream>
 
 using namespace OpenMM;
 using std::pair;
 using std::vector;
 using std::set;
+using std::stringstream;
 
 NonbondedForceImpl::NonbondedForceImpl(NonbondedForce& owner) : owner(owner) {
 }
@@ -46,41 +49,41 @@ NonbondedForceImpl::~NonbondedForceImpl() {
 
 void NonbondedForceImpl::initialize(OpenMMContextImpl& context) {
     kernel = context.getPlatform().createKernel(CalcNonbondedForceKernel::Name(), context);
-    
-    // See if the system contains a HarmonicBondForce.  If so, use it to identify exclusions.
-    
-    System& system = context.getSystem();
-    vector<set<int> > exclusions(owner.getNumParticles());
-    vector<vector<int> > bondIndices;
-    set<pair<int, int> > bonded14set;
-    for (int i = 0; i < system.getNumForces(); i++) {
-        if (dynamic_cast<HarmonicBondForce*>(&system.getForce(i)) != NULL) {
-            const HarmonicBondForce& force = dynamic_cast<const HarmonicBondForce&>(system.getForce(i));
-            bondIndices.resize(force.getNumBonds());
-            for (int j = 0; j < force.getNumBonds(); ++j) {
-                int particle1, particle2;
-                double length, k;
-                force.getBondParameters(j, particle1, particle2, length, k);
-                bondIndices[j].push_back(particle1);
-                bondIndices[j].push_back(particle2);
-            }
-            break;
-        }
-    }
 
-    // Also treat constrained distances as bonds.
+    // Check for errors in the specification of exceptions.
 
-    int numBonds = bondIndices.size();
-    bondIndices.resize(numBonds+system.getNumConstraints());
-    for (int j = 0; j < system.getNumConstraints(); j++) {
+    System& system = context.getSystem();
+    if (owner.getNumParticles() != system.getNumParticles())
+        throw OpenMMException("NonbondedForce must have exactly as many particles as the System it belongs to.");
+    vector<set<int> > exceptions(owner.getNumParticles());
+    for (int i = 0; i < owner.getNumExceptions(); i++) {
         int particle1, particle2;
-        double distance;
-        system.getConstraintParameters(j, particle1, particle2, distance);
-        bondIndices[j+numBonds].push_back(particle1);
-        bondIndices[j+numBonds].push_back(particle2);
+        double chargeProd, sigma, epsilon;
+        owner.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
+        if (particle1 < 0 || particle1 >= owner.getNumParticles()) {
+            stringstream msg;
+            msg << "NonbondedForce: Illegal particle index for an exception: ";
+            msg << particle1;
+            throw OpenMMException(msg.str());
+        }
+        if (particle2 < 0 || particle2 >= owner.getNumParticles()) {
+            stringstream msg;
+            msg << "NonbondedForce: Illegal particle index for an exception: ";
+            msg << particle2;
+            throw OpenMMException(msg.str());
+        }
+        if (exceptions[particle1].count(particle2) > 0 || exceptions[particle2].count(particle1) > 0) {
+            stringstream msg;
+            msg << "NonbondedForce: Multiple exceptions are specified for particles ";
+            msg << particle1;
+            msg << " and ";
+            msg << particle2;
+            throw OpenMMException(msg.str());
+        }
+        exceptions[particle1].insert(particle2);
+        exceptions[particle2].insert(particle1);
     }
-    findExclusions(bondIndices, exclusions, bonded14set);
-    dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner, exclusions);
+    dynamic_cast<CalcNonbondedForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
 }
 
 void NonbondedForceImpl::calcForces(OpenMMContextImpl& context, Stream& forces) {
@@ -96,30 +99,3 @@ std::vector<std::string> NonbondedForceImpl::getKernelNames() {
     names.push_back(CalcNonbondedForceKernel::Name());
     return names;
 }
-
-void NonbondedForceImpl::findExclusions(const vector<vector<int> >& bondIndices, vector<set<int> >& exclusions, set<pair<int, int> >& bonded14Indices) const {
-    vector<set<int> > bonded12(exclusions.size());
-    for (int i = 0; i < (int) bondIndices.size(); ++i) {
-        bonded12[bondIndices[i][0]].insert(bondIndices[i][1]);
-        bonded12[bondIndices[i][1]].insert(bondIndices[i][0]);
-    }
-    for (int i = 0; i < (int) exclusions.size(); ++i)
-        addExclusionsToSet(bonded12, exclusions[i], i, i, 2);
-    for (int i = 0; i < (int) exclusions.size(); ++i) {
-        set<int> bonded13;
-        addExclusionsToSet(bonded12, bonded13, i, i, 1);
-        for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
-            if (*iter < i && bonded13.find(*iter) == bonded13.end())
-                bonded14Indices.insert(pair<int, int> (*iter, i));
-    }
-}
-
-void NonbondedForceImpl::addExclusionsToSet(const vector<set<int> >& bonded12, set<int>& exclusions, int baseParticle, int fromParticle, int currentLevel) const {
-    for (set<int>::const_iterator iter = bonded12[fromParticle].begin(); iter != bonded12[fromParticle].end(); ++iter) {
-        if (*iter != baseParticle)
-            exclusions.insert(*iter);
-        if (currentLevel > 0)
-            addExclusionsToSet(bonded12, exclusions, baseParticle, *iter, currentLevel-1);
-    }
-}
-

platforms/brook/src/BrookCalcNonbondedForceKernel.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Mark Friedrichs                                    *
  * Contributors:                                                              *
  *                                                                            *
@@ -129,7 +129,7 @@ int BrookCalcNonbondedForceKernel::setLog( FILE* log ){
  *
  */
 
-void BrookCalcNonbondedForceKernel::initialize( const System& system, const NonbondedForce& force, const std::vector<std::set<int> >& exclusions ){
+void BrookCalcNonbondedForceKernel::initialize( const System& system, const NonbondedForce& force ){
 
 // ---------------------------------------------------------------------------------------
 
@@ -172,7 +172,22 @@ void BrookCalcNonbondedForceKernel::initialize( const System& system, const Nonb
       nonbondedParameters[ii].push_back( charge  );
       nonbondedParameters[ii].push_back( radius  );
       nonbondedParameters[ii].push_back( depth   );
-   }   
+   }
+
+   // Go through the exclusions.
+
+   std::vector<std::set<int> >& exclusions(_numberOfParticles);
+   std::vector<int> nb14s;
+   for (int i = 0; i < force.getNumExceptions(); i++) {
+        int particle1, particle2;
+        double chargeProd, sigma, epsilon;
+        force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
+        exclusions[particle1].insert(particle2);
+        exclusions[particle2].insert(particle1);
+        exclusions.push_back(pair<int, int>(particle1, particle2));
+        if (chargeProd != 0.0 || epsilon != 0.0)
+            nb14s.push_back(i);
+   }
 
    brookNonBonded.setup( _numberOfParticles, nonbondedParameters, exclusions, getPlatform() );
    _openMMBrookInterface.setTriggerForceKernel( this );
@@ -188,7 +203,7 @@ void BrookCalcNonbondedForceKernel::initialize( const System& system, const Nonb
 
    // nonbonded 14 ixns
 
-   initialize14Interactions( system, force );
+   initialize14Interactions( system, force, nb14s );
 
 }
 
@@ -200,7 +215,7 @@ void BrookCalcNonbondedForceKernel::initialize( const System& system, const Nonb
  *
  */
 
-void BrookCalcNonbondedForceKernel::initialize14Interactions( const System& system, const NonbondedForce& force ){
+void BrookCalcNonbondedForceKernel::initialize14Interactions( const System& system, const NonbondedForce& force, const std::vector<int>& nb14s ){
 
 // ---------------------------------------------------------------------------------------
 
@@ -216,7 +231,7 @@ void BrookCalcNonbondedForceKernel::initialize14Interactions( const System& syst
 
    // create _brookBondParameters object containing particle indices/parameters
 
-   int numberOf14Forces         = force.getNumNonbonded14();
+   int numberOf14Forces         = nb14s.size();
    if( numberOf14Forces > 0 ){
 
       _brookBondParameters         = new BrookBondParameters( BondName, NumberOfParticlesInBond, NumberOfParametersInBond, numberOf14Forces, getLog() );
@@ -229,7 +244,7 @@ void BrookCalcNonbondedForceKernel::initialize14Interactions( const System& syst
          int particles[NumberOfParticlesInBond];
          double parameters[NumberOfParametersInBond];
    
-         force.getNonbonded14Parameters( ii, particle1, particle2, charge, radius, depth ); 
+         force.getExceptionParameters( nb14s[ii], particle1, particle2, charge, radius, depth );
    
 //(void) fprintf( log, "%s idx=%d [%d %d] [%f %f %f]\n", methodName.c_str(), ii, particle1, particle2, charge, radius, depth );
          particles[0]    = particle1;

platforms/brook/src/BrookCalcNonbondedForceKernel.h

@@ -54,12 +54,9 @@ class BrookCalcNonbondedForceKernel : public CalcNonbondedForceKernel {
        * 
        * @param system     the System this kernel will be applied to
        * @param force      the NonbondedForce this kernel will be used for
-       * @param exclusions the i'th element lists the indices of all particles with which the i'th particle should not interact through
-       *                   nonbonded forces.  Bonded 1-4 pairs are also included in this list, since they should be omitted from
-       *                   the standard nonbonded calculation.
        */
 
-      void initialize( const System& system, const NonbondedForce& force, const std::vector<std::set<int> >& exclusions );
+      void initialize( const System& system, const NonbondedForce& force );
   
       /** 
        * Initialize the 14 ixns 

platforms/brook/tests/TestBrookCMMotionRemover.cpp

@@ -88,10 +88,10 @@ void testMotionRemoval( FILE* log ) {
    bonds->setBondParameters(0, 2, 3, 2.0, 0.5);
    system.addForce(bonds);
 
-   NonbondedForce* nonbonded = new NonbondedForce(numberOfParticles, 0);
+   NonbondedForce* nonbonded = new NonbondedForce();
    for (int i = 0; i < numberOfParticles; ++i) {
        system.setParticleMass(i, (double) (i+1) );
-       nonbonded->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+       nonbonded->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(nonbonded);
 

platforms/brook/tests/TestBrookLangevinIntegrator.cpp

@@ -217,10 +217,10 @@ void testLangevinTemperature( FILE* log ){
 
    System system(numberOfParticles, 0);
    LangevinIntegrator integrator(temp, 0.2, 0.002);
-   NonbondedForce* forceField = new NonbondedForce(numberOfParticles, 0);
+   NonbondedForce* forceField = new NonbondedForce();
    for (int i = 0; i < numberOfParticles; ++i){
       system.setParticleMass(i, mass );
-      forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+      forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
    }
    system.addForce(forceField);
 
@@ -315,10 +315,10 @@ void testLangevinConstraints( FILE* log ){
    System system( numParticles, numConstraints );
    LangevinIntegrator integrator( temp, 2.0, 0.001 );
    integrator.setConstraintTolerance(1e-5);
-   NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+   NonbondedForce* forceField = new NonbondedForce();
    for (int i = 0; i < numParticles; ++i) {
        system.setParticleMass(i, mass);
-       forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+       forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
    }
    for (int i = 0; i < numConstraints; ++i){
        system.setConstraintParameters(i, 2*i, 2*i+1, 1.0);

platforms/brook/tests/TestBrookNonbondedForce.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2009 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -73,9 +73,9 @@ void testBrookCoulomb( FILE* log ){
 
    // int index, double charge, double radius, double depth
 
-   NonbondedForce* forceField = new NonbondedForce( numberOfParticles, 0 ); 
-   forceField->setParticleParameters(0, 0.5, 1, 0);
-   forceField->setParticleParameters(1, -1.5, 1, 0);
+   NonbondedForce* forceField = new NonbondedForce(); 
+   forceField->addParticle(0.5, 1, 0);
+   forceField->addParticle(-1.5, 1, 0);
    system.addForce(forceField);
 
    //(void) fprintf( log, "%s: Calling context\n",  methodName.c_str() );
@@ -141,9 +141,9 @@ void testBrookLJ( FILE* log ){
 
    // int index, double charge, double radius, double depth
 
-   NonbondedForce* forceField = new NonbondedForce( numberOfParticles, 0 ); 
-   forceField->setParticleParameters(0, 0, 1.2, 1); 
-   forceField->setParticleParameters(1, 0, 1.4, 2); 
+   NonbondedForce* forceField = new NonbondedForce(); 
+   forceField->addParticle(0, 1.2, 1);
+   forceField->addParticle(0, 1.4, 2);
    system.addForce(forceField);
 
    //(void) fprintf( log, "%s: Calling context\n",  methodName.c_str() );
@@ -208,13 +208,25 @@ void testBrookExclusionsAnd14( FILE* log ){
 
    // int index, double charge, double radius, double depth
 
-   HarmonicBondForce* bonds = new HarmonicBondForce(4);
-   bonds->setBondParameters(0, 0, 1, 1, 0); 
-   bonds->setBondParameters(1, 1, 2, 1, 0); 
-   bonds->setBondParameters(2, 2, 3, 1, 0); 
-   bonds->setBondParameters(3, 3, 4, 1, 0); 
-   system.addForce(bonds);
-   NonbondedForce* nonbonded = new NonbondedForce( numberOfParticles, 2); 
+   NonbondedForce* nonbonded = new NonbondedForce();
+   for (int i = 0; i < numberOfParticles; i++)
+       nonbonded->addParticle(0, 1.5, 0)
+   vector<pair<int, int> > bonds;
+   bonds.push_back(pair<int, int>(0, 1));
+   bonds.push_back(pair<int, int>(1, 2));
+   bonds.push_back(pair<int, int>(2, 3));
+   bonds.push_back(pair<int, int>(3, 4));
+   nonbonded->createExceptionsFromBonds(bonds, 0.0, 0.0);
+   int first14, second14;
+   for (int i = 0; i < nonbonded->getNumExceptions(); i++) {
+       int particle1, particle2;
+       double chargeProd, sigma, epsilon;
+       nonbonded->getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
+       if ((particle1 == 0 && particle2 == 3) || (particle1 == 3 && particle2 == 0))
+           first14 = i;
+       if ((particle1 == 1 && particle2 == 4) || (particle1 == 4 && particle2 == 1))
+           second14 = i;
+   }
    system.addForce(nonbonded);
 
    //(void) fprintf( log, "%s: Calling context\n",  methodName.c_str() );
@@ -240,8 +252,8 @@ void testBrookExclusionsAnd14( FILE* log ){
        }
        nonbonded->setParticleParameters(0, 0, 1.5, 1); 
        nonbonded->setParticleParameters(ii, 0, 1.5, 1); 
-       nonbonded->setNonbonded14Parameters(0, 0, 3, 0, 1.5, ii == 3 ? 0.5 : 0.0);
-       nonbonded->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0.0);
+       nonbonded->setExceptionParameters(first14, 0, 3, 0, 1.5, ii == 3 ? 0.5 : 0.0);
+       nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0.0);
        positions[ii] = Vec3(r, 0, 0); 
 
       context.reinitialize();
@@ -284,8 +296,8 @@ void testBrookExclusionsAnd14( FILE* log ){
 
       nonbonded->setParticleParameters( 0, 2, 1.5, 0 );
       nonbonded->setParticleParameters( ii, 2, 1.5, 0 );
-      nonbonded->setNonbonded14Parameters( 0, 0, 3, ii == 3 ? 4/1.2 : 0, 1.5, 0 );
-      nonbonded->setNonbonded14Parameters( 1, 1, 4, 0, 1.5, 0 );
+      nonbonded->setExceptionParameters( first14, 0, 3, ii == 3 ? 4/1.2 : 0, 1.5, 0 );
+      nonbonded->setExceptionParameters( second14, 1, 4, 0, 1.5, 0 );
 
       context.reinitialize();
 

platforms/brook/tests/TestBrookVerletIntegrator.cpp

@@ -183,10 +183,10 @@ void testVerletConstraints( FILE* log ){
    System system(numParticles, numConstraints);
    VerletIntegrator integrator(0.001);
    integrator.setConstraintTolerance(1e-5);
-   NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+   NonbondedForce* forceField = new NonbondedForce();
    for (int i = 0; i < numParticles; ++i) {
        system.setParticleMass(i, mass );
-       forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+       forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
    }
    for (int i = 0; i < numConstraints; ++i){
        system.setConstraintParameters(i, 2*i, 2*i+1, 1.0);

platforms/cuda/src/CudaKernels.cpp

@@ -238,14 +238,27 @@ double CudaCalcRBTorsionForceKernel::executeEnergy(OpenMMContextImpl& context) {
 CudaCalcNonbondedForceKernel::~CudaCalcNonbondedForceKernel() {
 }
 
-void CudaCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force, const std::vector<std::set<int> >& exclusions) {
+void CudaCalcNonbondedForceKernel::initialize(const System& system, const NonbondedForce& force) {
     if (data.primaryKernel == NULL)
         data.primaryKernel = this;
     data.hasNonbonded = true;
     numParticles = force.getNumParticles();
-    num14 = force.getNumNonbonded14();
     _gpuContext* gpu = data.gpu;
-    
+
+    // Identify which exceptions are 1-4 interactions.
+
+    vector<pair<int, int> > exclusions;
+    vector<int> nb14s;
+    for (int i = 0; i < force.getNumExceptions(); i++) {
+        int particle1, particle2;
+        double chargeProd, sigma, epsilon;
+        force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
+        exclusions.push_back(pair<int, int>(particle1, particle2));
+        if (chargeProd != 0.0 || epsilon != 0.0)
+            nb14s.push_back(i);
+    }
+    num14 = nb14s.size();
+
     // Initialize nonbonded interactions.
     
     {
@@ -262,9 +275,12 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
             q[i] = (float) charge;
             c6[i] = (float) (4*depth*pow(radius, 6.0));
             c12[i] = (float) (4*depth*pow(radius, 12.0));
-            exclusionList[i] = vector<int>(exclusions[i].begin(), exclusions[i].end());
             exclusionList[i].push_back(i);
         }
+        for (int i = 0; i < exclusions.size(); i++) {
+            exclusionList[exclusions[i].first].push_back(exclusions[i].second);
+            exclusionList[exclusions[i].second].push_back(exclusions[i].first);
+        }
         CudaNonbondedMethod method = NO_CUTOFF;
         if (force.getNonbondedMethod() != NonbondedForce::NoCutoff) {
             gpuSetNonbondedCutoff(gpu, force.getCutoffDistance(), 78.3f);
@@ -299,7 +315,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         vector<float> q2(num14);
         for (int i = 0; i < num14; i++) {
             double charge, sig, eps;
-            force.getNonbonded14Parameters(i, particle1[i], particle2[i], charge, sig, eps);
+            force.getExceptionParameters(nb14s[i], particle1[i], particle2[i], charge, sig, eps);
             c6[i] = (float) (4*eps*pow(sig, 6.0));
             c12[i] = (float) (4*eps*pow(sig, 12.0));
             q1[i] = (float) charge;

platforms/cuda/src/CudaKernels.h

@@ -215,11 +215,8 @@ public:
      * 
      * @param system     the System this kernel will be applied to
      * @param force      the NonbondedForce this kernel will be used for
-     * @param exclusions the i'th element lists the indices of all particles with which the i'th particle should not interact through
-     *                   nonbonded forces.  Bonded 1-4 pairs are also included in this list, since they should be omitted from
-     *                   the standard nonbonded calculation.
      */
-    void initialize(const System& system, const NonbondedForce& force, const std::vector<std::set<int> >& exclusions);
+    void initialize(const System& system, const NonbondedForce& force);
     /**
      * Execute the kernel to calculate the forces.
      * 

platforms/cuda/tests/TestCudaAndersenThermostat.cpp

@@ -55,10 +55,10 @@ void testTemperature() {
     CudaPlatform platform;
     System system(numParticles, 0);
     VerletIntegrator integrator(0.01);
-    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
         system.setParticleMass(i, 2.0);
-        forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
     AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
@@ -93,10 +93,10 @@ void testRandomSeed() {
     CudaPlatform platform;
     System system(numParticles, 0);
     VerletIntegrator integrator(0.01);
-    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
         system.setParticleMass(i, 2.0);
-        forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
     AndersenThermostat* thermostat = new AndersenThermostat(temp, collisionFreq);

platforms/cuda/tests/TestCudaBrownianIntegrator.cpp

@@ -132,10 +132,10 @@ void testConstraints() {
     System system(numParticles, numConstraints);
     BrownianIntegrator integrator(temp, 2.0, 0.001);
     integrator.setConstraintTolerance(1e-5);
-    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
         system.setParticleMass(i, 10.0);
-        forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
     }
     system.setConstraintParameters(0, 0, 1, 1.0);
     system.setConstraintParameters(1, 1, 2, 1.0);
@@ -178,10 +178,10 @@ void testRandomSeed() {
     CudaPlatform platform;
     System system(numParticles, 0);
     BrownianIntegrator integrator(temp, 2.0, 0.001);
-    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
         system.setParticleMass(i, 2.0);
-        forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
     vector<Vec3> positions(numParticles);

platforms/cuda/tests/TestCudaCMMotionRemover.cpp

@@ -67,10 +67,10 @@ void testMotionRemoval(Integrator& integrator) {
     HarmonicBondForce* bonds = new HarmonicBondForce(1);
     bonds->setBondParameters(0, 2, 3, 2.0, 0.5);
     system.addForce(bonds);
-    NonbondedForce* nonbonded = new NonbondedForce(numParticles, 0);
+    NonbondedForce* nonbonded = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
         system.setParticleMass(i, i+1);
-        nonbonded->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+        nonbonded->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(nonbonded);
     CMMotionRemover* remover = new CMMotionRemover();

platforms/cuda/tests/TestCudaEwald.cpp

@@ -58,9 +58,9 @@ void testEwald() {
     CudaPlatform platform;
     System system(2, 0);
     VerletIntegrator integrator(0.01);
-    NonbondedForce* nonbonded = new NonbondedForce(2, 0);
-    nonbonded->setParticleParameters(0, 1.0, 1, 0);
-    nonbonded->setParticleParameters(1, -1.0, 1, 0);
+    NonbondedForce* nonbonded = new NonbondedForce();
+    nonbonded->addParticle(1.0, 1, 0);
+    nonbonded->addParticle(-1.0, 1, 0);
     nonbonded->setNonbondedMethod(NonbondedForce::Ewald);
     const double cutoff = 2.0;
     nonbonded->setCutoffDistance(cutoff);
@@ -90,10 +90,10 @@ void testPeriodic() {
     HarmonicBondForce* bonds = new HarmonicBondForce(1);
     bonds->setBondParameters(0, 0, 1, 1, 0);
     system.addForce(bonds);
-    NonbondedForce* nonbonded = new NonbondedForce(3, 0);
-    nonbonded->setParticleParameters(0, 1.0, 1, 0);
-    nonbonded->setParticleParameters(1, 1.0, 1, 0);
-    nonbonded->setParticleParameters(2, 1.0, 1, 0);
+    NonbondedForce* nonbonded = new NonbondedForce();
+    nonbonded->addParticle(1.0, 1, 0);
+    nonbonded->addParticle(1.0, 1, 0);
+    nonbonded->addParticle(1.0, 1, 0);
     nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
     const double cutoff = 2.0;
     nonbonded->setCutoffDistance(cutoff);

platforms/cuda/tests/TestCudaGBSAOBCForce.cpp

@@ -57,9 +57,9 @@ void testSingleParticle() {
     system.setParticleMass(0, 2.0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
     GBSAOBCForce* gbsa = new GBSAOBCForce(1);
-    NonbondedForce* nonbonded = new NonbondedForce(1, 0);
+    NonbondedForce* nonbonded = new NonbondedForce();
     gbsa->setParticleParameters(0, 0.5, 0.15, 1);
-    nonbonded->setParticleParameters(0, 0.5, 1, 0);
+    nonbonded->addParticle(0.5, 1, 0);
     system.addForce(gbsa);
     system.addForce(nonbonded);
     OpenMMContext context(system, integrator, platform);
@@ -80,11 +80,11 @@ void testCutoffAndPeriodic() {
     System system(2, 0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
     GBSAOBCForce* gbsa = new GBSAOBCForce(2);
-    NonbondedForce* nonbonded = new NonbondedForce(2, 0);
+    NonbondedForce* nonbonded = new NonbondedForce();
     gbsa->setParticleParameters(0, -1, 0.15, 1);
-    nonbonded->setParticleParameters(0, -1, 1, 0);
+    nonbonded->addParticle(-1, 1, 0);
     gbsa->setParticleParameters(1, 1, 0.15, 1);
-    nonbonded->setParticleParameters(1, 1, 1, 0);
+    nonbonded->addParticle(1, 1, 0);
     const double cutoffDistance = 3.0;
     const double boxSize = 10.0;
     nonbonded->setCutoffDistance(cutoffDistance);
@@ -131,11 +131,11 @@ void testForce(int numParticles, NonbondedForce::NonbondedMethod method) {
     System system(numParticles, 0);
     LangevinIntegrator integrator(0, 0.1, 0.01);
     GBSAOBCForce* gbsa = new GBSAOBCForce(numParticles);
-    NonbondedForce* nonbonded = new NonbondedForce(numParticles, 0);
+    NonbondedForce* nonbonded = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
         double charge = i%2 == 0 ? -1 : 1;
         gbsa->setParticleParameters(i, charge, 0.15, 1);
-        nonbonded->setParticleParameters(i, charge, 1, 0);
+        nonbonded->addParticle(charge, 1, 0);
     }
     nonbonded->setNonbondedMethod(method);
     nonbonded->setCutoffDistance(3.0);

platforms/cuda/tests/TestCudaLangevinIntegrator.cpp

@@ -100,10 +100,10 @@ void testTemperature() {
     CudaPlatform platform;
     System system(numParticles, 0);
     LangevinIntegrator integrator(temp, 2.0, 0.01);
-    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
         system.setParticleMass(i, 2.0);
-        forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
     OpenMMContext context(system, integrator, platform);
@@ -137,10 +137,10 @@ void testConstraints() {
     System system(numParticles, numConstraints);
     LangevinIntegrator integrator(temp, 2.0, 0.01);
     integrator.setConstraintTolerance(1e-5);
-    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
         system.setParticleMass(i, 10.0);
-        forceField->setParticleParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
     }
     system.setConstraintParameters(0, 0, 1, 1.0);
     system.setConstraintParameters(1, 1, 2, 1.0);
@@ -183,10 +183,10 @@ void testRandomSeed() {
     CudaPlatform platform;
     System system(numParticles, 0);
     LangevinIntegrator integrator(temp, 2.0, 0.01);
-    NonbondedForce* forceField = new NonbondedForce(numParticles, 0);
+    NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
         system.setParticleMass(i, 2.0);
-        forceField->setParticleParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
     }
     system.addForce(forceField);
     vector<Vec3> positions(numParticles);