Merge remote-tracking branch 'upstream/master' into forcefield

plugins/amoeba/platforms/cuda/tests/TestCudaAmoebaGeneralizedKirkwoodForce.cpp

@@ -50,10 +50,36 @@
 using namespace OpenMM;
+using namespace std;
+
 const double TOL = 1e-4;
 extern "C" void registerAmoebaCudaKernelFactories();
+static void checkFiniteDifferences(vector<Vec3> forces, Context &context, vector<Vec3> positions)
+{
+    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
+
+    double norm = 0.0;
+    for (int i = 0; i < (int) forces.size(); ++i)
+        norm += forces[i].dot(forces[i]);
+    norm = std::sqrt(norm);
+    const double stepSize = 1e-3;
+    double step = 0.5*stepSize/norm;
+    vector<Vec3> positions2(forces.size()), positions3(forces.size());
+    for (int i = 0; i < (int) positions.size(); ++i) {
+        Vec3 p = positions[i];
+        Vec3 f = forces[i];
+        positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
+        positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
+    }
+    context.setPositions(positions2);
+    State state2 = context.getState(State::Energy);
+    context.setPositions(positions3);
+    State state3 = context.getState(State::Energy);
+    ASSERT_EQUAL_TOL(state3.getPotentialEnergy()+norm*stepSize, state2.getPotentialEnergy(), 1e-4);
+}
+
 // setup for 2 ammonia molecules
 static void setupMultipoleAmmonia(System& system, AmoebaGeneralizedKirkwoodForce* amoebaGeneralizedKirkwoodForce,
@@ -289,6 +315,10 @@ static void getForcesEnergyMultipoleAmmonia(Context& context, std::vector<Vec3>&
     State state                      = context.getState(State::Forces | State::Energy);
     forces                           = state.getForces();
     energy                           = state.getPotentialEnergy();
+    
+    // Check that the forces and energy are consistent.
+    
+    checkFiniteDifferences(forces, context, positions);
 }
 // setup for villin
@@ -6972,6 +7002,10 @@ static void setupAndGetForcesEnergyMultipoleVillin(AmoebaMultipoleForce::Polariz
     State state                      = context.getState(State::Forces | State::Energy);
     forces                           = state.getForces();
     energy                           = state.getPotentialEnergy();
+    
+    // Check that the forces and energy are consistent.
+    
+    checkFiniteDifferences(forces, context, positions);
 }
 // compare forces and energies 
@@ -7049,6 +7083,25 @@ static void testGeneralizedKirkwoodAmmoniaDirectPolarization() {
     compareForcesEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance);
 }
+static void testGeneralizedKirkwoodAmmoniaExtrapolatedPolarization() {
+
+    std::string testName      = "testGeneralizedKirkwoodAmmoniaExtrapolatedPolarization";
+
+    int numberOfParticles     = 8;
+    std::vector<Vec3> forces;
+    double energy;
+
+    System system;
+    AmoebaGeneralizedKirkwoodForce* amoebaGeneralizedKirkwoodForce  = new AmoebaGeneralizedKirkwoodForce();
+    setupMultipoleAmmonia(system, amoebaGeneralizedKirkwoodForce, AmoebaMultipoleForce::Direct, 0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    Context context(system, integrator, Platform::getPlatformByName("CUDA"));
+
+    // We don't have reference values for this case, but at least check that force and energy are consistent.
+
+    getForcesEnergyMultipoleAmmonia(context, forces, energy);
+}
+
 // test GK mutual polarization for system comprised of two ammonia molecules
 static void testGeneralizedKirkwoodAmmoniaMutualPolarization() {
@@ -7765,6 +7818,19 @@ static void testGeneralizedKirkwoodVillinDirectPolarization() {
     compareForceNormsEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance);
 }
+static void testGeneralizedKirkwoodVillinExtrapolatedPolarization() {
+
+    std::string testName      = "testGeneralizedKirkwoodVillinExtrapolatedPolarization";
+
+    int numberOfParticles     = 596;
+    std::vector<Vec3> forces;
+    double energy;
+
+    // We don't have reference values for this case, but at least check that force and energy are consistent.
+    
+    setupAndGetForcesEnergyMultipoleVillin(AmoebaMultipoleForce::Extrapolated, 0, forces, energy);
+}
+
 // test GK mutual polarization for villin system
 static void testGeneralizedKirkwoodVillinMutualPolarization() {
@@ -8401,9 +8467,10 @@ int main(int argc, char* argv[]) {
         testGeneralizedKirkwoodAmmoniaDirectPolarization();
         testGeneralizedKirkwoodAmmoniaMutualPolarization();
+        testGeneralizedKirkwoodAmmoniaExtrapolatedPolarization();
         testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm();
-
         testGeneralizedKirkwoodVillinDirectPolarization();
+        testGeneralizedKirkwoodVillinExtrapolatedPolarization();
         testGeneralizedKirkwoodVillinMutualPolarization();
     } catch(const std::exception& e) {

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.cpp

@@ -565,6 +565,8 @@ void ReferenceCalcAmoebaMultipoleForceKernel::initialize(const System& system, c
     if (polarizationType == AmoebaMultipoleForce::Mutual) {
         mutualInducedMaxIterations = force.getMutualInducedMaxIterations();
         mutualInducedTargetEpsilon = force.getMutualInducedTargetEpsilon();
+    } else if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
+        extrapolationCoefficients = force.getExtrapolationCoefficients();
     }
 
     // PME
@@ -667,6 +669,9 @@ AmoebaReferenceMultipoleForce* ReferenceCalcAmoebaMultipoleForceKernel::setupAmo
         amoebaReferenceMultipoleForce->setMaximumMutualInducedDipoleIterations(mutualInducedMaxIterations);
     } else if (polarizationType == AmoebaMultipoleForce::Direct) {
         amoebaReferenceMultipoleForce->setPolarizationType(AmoebaReferenceMultipoleForce::Direct);
+    } else if (polarizationType == AmoebaMultipoleForce::Extrapolated) {
+        amoebaReferenceMultipoleForce->setPolarizationType(AmoebaReferenceMultipoleForce::Extrapolated);
+        amoebaReferenceMultipoleForce->setExtrapolationCoefficients(extrapolationCoefficients);
     } else {
         throw OpenMMException("Polarization type not recognzied.");
     }

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h

@@ -432,6 +432,7 @@ private:
 
     int mutualInducedMaxIterations;
     RealOpenMM mutualInducedTargetEpsilon;
+    std::vector<double> extrapolationCoefficients;
 
     bool usePme;
     RealOpenMM alphaEwald;

plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceMultipoleForce.h

@@ -345,11 +345,16 @@ public:
          */
         Mutual = 0,
 
-        /** 
+        /**
          * Direct polarization
          */
-        Direct = 1 
-    };  
+        Direct = 1,
+
+        /**
+         * Extrapolated perturbation theory
+         */
+        Extrapolated = 2
+    };
 
     /**
      * Constructor
@@ -422,6 +427,15 @@ public:
      */
     RealOpenMM getMutualInducedDipoleEpsilon() const;
 
+    /**
+     * Set the coefficients for the µ_0, µ_1, µ_2, µ_n terms in the extrapolation
+     * theory algorithm for induced dipoles
+     *
+     * @param optCoefficients a vector whose mth entry specifies the coefficient for µ_m
+     *
+     */
+    void setExtrapolationCoefficients(const std::vector<RealOpenMM> &coefficients);
+
     /**
      * Set the target epsilon for converging mutual induced dipoles.
      *
@@ -624,10 +638,13 @@ protected:
      * Helper class used in calculating induced dipoles
      */
     struct UpdateInducedDipoleFieldStruct {
-            UpdateInducedDipoleFieldStruct(std::vector<OpenMM::RealVec>& inputFixed_E_Field, std::vector<OpenMM::RealVec>& inputInducedDipoles);
+            UpdateInducedDipoleFieldStruct(std::vector<OpenMM::RealVec>& inputFixed_E_Field, std::vector<OpenMM::RealVec>& inputInducedDipoles, std::vector<std::vector<RealVec> >& extrapolatedDipoles, std::vector<std::vector<RealOpenMM> >& extrapolatedDipoleFieldGradient);
             std::vector<OpenMM::RealVec>* fixedMultipoleField;
             std::vector<OpenMM::RealVec>* inducedDipoles;
+            std::vector<std::vector<RealVec> >* extrapolatedDipoles;
+            std::vector<std::vector<RealOpenMM> >* extrapolatedDipoleFieldGradient;
             std::vector<OpenMM::RealVec> inducedDipoleField;
+            std::vector<std::vector<RealOpenMM> > inducedDipoleFieldGradient;
     };
 
     unsigned int _numParticles;
@@ -651,10 +668,17 @@ protected:
     std::vector<RealVec> _fixedMultipoleFieldPolar;
     std::vector<RealVec> _inducedDipole;
     std::vector<RealVec> _inducedDipolePolar;
+    std::vector<std::vector<RealVec> > _ptDipoleP;
+    std::vector<std::vector<RealVec> > _ptDipoleD;
+    std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientP;
+    std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientD;
 
     int _mutualInducedDipoleConverged;
     int _mutualInducedDipoleIterations;
     int _maximumMutualInducedDipoleIterations;
+    int _maxPTOrder;
+    std::vector<RealOpenMM>  _extrapolationCoefficients;
+    std::vector<RealOpenMM>  _extPartCoefficients;
     RealOpenMM  _mutualInducedDipoleEpsilon;
     RealOpenMM  _mutualInducedDipoleTargetEpsilon;
     RealOpenMM  _polarSOR;
@@ -904,7 +928,7 @@ protected:
 
     /**
      * Calculate fields due induced dipoles at each site.
-     * 
+     *
      * @param particleI                 positions and parameters (charge, labFrame dipoles, quadrupoles, ...) for particle I
      * @param particleJ                 positions and parameters (charge, labFrame dipoles, quadrupoles, ...) for particle J
      * @param updateInducedDipoleFields vector of UpdateInducedDipoleFieldStruct containing input induced dipoles and output fields
@@ -920,6 +944,14 @@ protected:
      */
     virtual void calculateInducedDipoleFields(const std::vector<MultipoleParticleData>& particleData,
                                               std::vector<UpdateInducedDipoleFieldStruct>& updateInducedDipoleFields);
+    /**
+     * Calculated induced dipoles using extrapolated perturbation theory.
+     *
+     * @param particleData              vector of particle positions and parameters (charge, labFrame dipoles, quadrupoles, ...)
+     * @param updateInducedDipoleFields vector of UpdateInducedDipoleFieldStruct containing input induced dipoles and output fields
+     */
+    void convergeInduceDipolesByExtrapolation(const std::vector<MultipoleParticleData>& particleData,
+                                              std::vector<UpdateInducedDipoleFieldStruct>& calculateInducedDipoleField);
     /**
      * Converge induced dipoles.
      * 
@@ -1191,6 +1223,10 @@ private:
     std::vector<RealVec> _gkField;
     std::vector<RealVec> _inducedDipoleS;
     std::vector<RealVec> _inducedDipolePolarS;
+    std::vector<std::vector<RealVec> > _ptDipolePS;
+    std::vector<std::vector<RealVec> > _ptDipoleDS;
+    std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientPS;
+    std::vector<std::vector<RealOpenMM> > _ptDipoleFieldGradientDS;
 
     int _includeCavityTerm;
     RealOpenMM _probeRadius;

plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaGeneralizedKirkwoodForce.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
  * Authors: Mark Friedrichs                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -50,11 +50,36 @@
 using namespace OpenMM;
+using namespace std;
 extern "C" OPENMM_EXPORT void registerAmoebaReferenceKernelFactories();
 const double TOL = 1e-4;
+static void checkFiniteDifferences(vector<Vec3> forces, Context &context, vector<Vec3> positions)
+{
+    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
+
+    double norm = 0.0;
+    for (int i = 0; i < (int) forces.size(); ++i)
+        norm += forces[i].dot(forces[i]);
+    norm = std::sqrt(norm);
+    const double stepSize = 1e-3;
+    double step = 0.5*stepSize/norm;
+    vector<Vec3> positions2(forces.size()), positions3(forces.size());
+    for (int i = 0; i < (int) positions.size(); ++i) {
+        Vec3 p = positions[i];
+        Vec3 f = forces[i];
+        positions2[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step);
+        positions3[i] = Vec3(p[0]+f[0]*step, p[1]+f[1]*step, p[2]+f[2]*step);
+    }
+    context.setPositions(positions2);
+    State state2 = context.getState(State::Energy);
+    context.setPositions(positions3);
+    State state3 = context.getState(State::Energy);
+    ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state3.getPotentialEnergy())/stepSize, 1e-4);
+}
+
 // setup for 2 ammonia molecules
 static void setupMultipoleAmmonia(System& system, AmoebaGeneralizedKirkwoodForce* amoebaGeneralizedKirkwoodForce,
@@ -291,6 +316,10 @@ static void getForcesEnergyMultipoleAmmonia(Context& context, std::vector<Vec3>&
     State state                      = context.getState(State::Forces | State::Energy);
     forces                           = state.getForces();
     energy                           = state.getPotentialEnergy();
+    
+    // Check that the forces and energy are consistent.
+    
+    checkFiniteDifferences(forces, context, positions);
 }
 // setup for villin
@@ -6974,6 +7003,10 @@ static void setupAndGetForcesEnergyMultipoleVillin(AmoebaMultipoleForce::Polariz
     State state                      = context.getState(State::Forces | State::Energy);
     forces                           = state.getForces();
     energy                           = state.getPotentialEnergy();
+    
+    // Check that the forces and energy are consistent.
+    
+    checkFiniteDifferences(forces, context, positions);
 }
 // compare forces and energies 
@@ -7052,6 +7085,25 @@ static void testGeneralizedKirkwoodAmmoniaDirectPolarization() {
     compareForcesEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance);
 }
+static void testGeneralizedKirkwoodAmmoniaExtrapolatedPolarization() {
+
+    std::string testName      = "testGeneralizedKirkwoodAmmoniaExtrapolatedPolarization";
+
+    int numberOfParticles     = 8;
+    std::vector<Vec3> forces;
+    double energy;
+
+    System system;
+    AmoebaGeneralizedKirkwoodForce* amoebaGeneralizedKirkwoodForce  = new AmoebaGeneralizedKirkwoodForce();
+    setupMultipoleAmmonia(system, amoebaGeneralizedKirkwoodForce, AmoebaMultipoleForce::Direct, 0);
+    LangevinIntegrator integrator(0.0, 0.1, 0.01);
+    Context context(system, integrator, Platform::getPlatformByName("Reference"));
+
+    // We don't have reference values for this case, but at least check that force and energy are consistent.
+
+    getForcesEnergyMultipoleAmmonia(context, forces, energy);
+}
+
 // test GK mutual polarization for system comprised of two ammonia molecules
 static void testGeneralizedKirkwoodAmmoniaMutualPolarization() {
@@ -7770,6 +7822,19 @@ static void testGeneralizedKirkwoodVillinDirectPolarization() {
     compareForceNormsEnergy(testName, expectedEnergy, energy, expectedForces, forces, tolerance);
 }
+static void testGeneralizedKirkwoodVillinExtrapolatedPolarization() {
+
+    std::string testName      = "testGeneralizedKirkwoodVillinExtrapolatedPolarization";
+
+    int numberOfParticles     = 596;
+    std::vector<Vec3> forces;
+    double energy;
+
+    // We don't have reference values for this case, but at least check that force and energy are consistent.
+    
+    setupAndGetForcesEnergyMultipoleVillin(AmoebaMultipoleForce::Extrapolated, 0, forces, energy);
+}
+
 // test GK mutual polarization for villin system
 static void testGeneralizedKirkwoodVillinMutualPolarization() {
@@ -8405,8 +8470,10 @@ int main(int numberOfArguments, char* argv[]) {
         testGeneralizedKirkwoodAmmoniaMutualPolarization();
         testGeneralizedKirkwoodAmmoniaDirectPolarization();
+        testGeneralizedKirkwoodAmmoniaExtrapolatedPolarization();
         testGeneralizedKirkwoodAmmoniaMutualPolarizationWithCavityTerm();
         testGeneralizedKirkwoodVillinDirectPolarization();
+        testGeneralizedKirkwoodVillinExtrapolatedPolarization();
         testGeneralizedKirkwoodVillinMutualPolarization();
     }

plugins/amoeba/serialization/src/AmoebaAngleForceProxy.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,10 +42,11 @@ AmoebaAngleForceProxy::AmoebaAngleForceProxy() : SerializationProxy("AmoebaAngle
 }
 
 void AmoebaAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
 
     const AmoebaAngleForce& force = *reinterpret_cast<const AmoebaAngleForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("cubic",   force.getAmoebaGlobalAngleCubic());
     node.setDoubleProperty("quartic", force.getAmoebaGlobalAngleQuartic());
     node.setDoubleProperty("pentic",  force.getAmoebaGlobalAnglePentic());
@@ -61,11 +62,13 @@ void AmoebaAngleForceProxy::serialize(const void* object, SerializationNode& nod
 }
 
 void* AmoebaAngleForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaAngleForce* force = new AmoebaAngleForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setAmoebaGlobalAngleCubic(node.getDoubleProperty("cubic"));
         force->setAmoebaGlobalAngleQuartic(node.getDoubleProperty("quartic"));
         force->setAmoebaGlobalAnglePentic(node.getDoubleProperty("pentic"));

plugins/amoeba/serialization/src/AmoebaBondForceProxy.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ AmoebaBondForceProxy::AmoebaBondForceProxy() : SerializationProxy("AmoebaBondFor
 }
 
 void AmoebaBondForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaBondForce& force = *reinterpret_cast<const AmoebaBondForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("cubic",   force.getAmoebaGlobalBondCubic());
     node.setDoubleProperty("quartic", force.getAmoebaGlobalBondQuartic());
 
@@ -58,10 +59,13 @@ void AmoebaBondForceProxy::serialize(const void* object, SerializationNode& node
 }
 
 void* AmoebaBondForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaBondForce* force = new AmoebaBondForce();
     try {
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setAmoebaGlobalBondCubic(node.getDoubleProperty("cubic"));
         force->setAmoebaGlobalBondQuartic(node.getDoubleProperty("quartic"));
         const SerializationNode& bonds = node.getChildNode("Bonds");

plugins/amoeba/serialization/src/AmoebaGeneralizedKirkwoodForceProxy.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ AmoebaGeneralizedKirkwoodForceProxy::AmoebaGeneralizedKirkwoodForceProxy() : Ser
 }
 
 void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaGeneralizedKirkwoodForce& force = *reinterpret_cast<const AmoebaGeneralizedKirkwoodForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("GeneralizedKirkwoodSolventDielectric", force.getSolventDielectric());
     node.setDoubleProperty("GeneralizedKirkwoodSoluteDielectric",  force.getSoluteDielectric());
     //node.setDoubleProperty("GeneralizedKirkwoodDielectricOffset",  force.getDielectricOffset());
@@ -62,11 +63,13 @@ void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, Serializ
 }
 
 void* AmoebaGeneralizedKirkwoodForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaGeneralizedKirkwoodForce* force = new AmoebaGeneralizedKirkwoodForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setSolventDielectric(  node.getDoubleProperty("GeneralizedKirkwoodSolventDielectric"));
         force->setSoluteDielectric(   node.getDoubleProperty("GeneralizedKirkwoodSoluteDielectric"));
         //force->setDielectricOffset(   node.getDoubleProperty("GeneralizedKirkwoodDielectricOffset"));

plugins/amoeba/serialization/src/AmoebaInPlaneAngleForceProxy.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -43,9 +43,10 @@ AmoebaInPlaneAngleForceProxy::AmoebaInPlaneAngleForceProxy() : SerializationProx
 
 void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNode& node) const {
 
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaInPlaneAngleForce& force = *reinterpret_cast<const AmoebaInPlaneAngleForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("cubic",      force.getAmoebaGlobalInPlaneAngleCubic());
     node.setDoubleProperty("quartic",    force.getAmoebaGlobalInPlaneAngleQuartic());
     node.setDoubleProperty("pentic",     force.getAmoebaGlobalInPlaneAnglePentic());
@@ -61,11 +62,13 @@ void AmoebaInPlaneAngleForceProxy::serialize(const void* object, SerializationNo
 }
 
 void* AmoebaInPlaneAngleForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaInPlaneAngleForce* force = new AmoebaInPlaneAngleForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setAmoebaGlobalInPlaneAngleCubic( node.getDoubleProperty("cubic"));
         force->setAmoebaGlobalInPlaneAngleQuartic(node.getDoubleProperty("quartic"));
         force->setAmoebaGlobalInPlaneAnglePentic(node.getDoubleProperty("pentic"));

plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -68,9 +68,10 @@ void loadCovalentMap(const SerializationNode& map, std::vector< int >& covalentM
 }
 
 void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 4);
     const AmoebaMultipoleForce& force = *reinterpret_cast<const AmoebaMultipoleForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setIntProperty("nonbondedMethod",                  force.getNonbondedMethod());
     node.setIntProperty("polarizationType",                 force.getPolarizationType());
     //node.setIntProperty("pmeBSplineOrder",                  force.getPmeBSplineOrder());
@@ -87,6 +88,14 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
     force.getPmeGridDimensions(gridDimensions);
     SerializationNode& gridDimensionsNode  = node.createChildNode("MultipoleParticleGridDimension");
     gridDimensionsNode.setIntProperty("d0", gridDimensions[0]).setIntProperty("d1", gridDimensions[1]).setIntProperty("d2", gridDimensions[2]); 
+    
+    SerializationNode& coefficients = node.createChildNode("ExtrapolationCoefficients");
+    vector<double> coeff = force.getExtrapolationCoefficients();
+    for (int i = 0; i < coeff.size(); i++) {
+        stringstream key;
+        key << "c" << i;
+        coefficients.setDoubleProperty(key.str(), coeff[i]);
+    }
 
     std::vector<std::string> covalentTypes;
     getCovalentTypes(covalentTypes);
@@ -124,16 +133,17 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
 }
 
 void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") > 2)
+    int version = node.getIntProperty("version");
+    if (version < 0 || version > 4)
         throw OpenMMException("Unsupported version number");
     AmoebaMultipoleForce* force = new AmoebaMultipoleForce();
 
     try {
-
+        if (version > 3)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setNonbondedMethod(static_cast<AmoebaMultipoleForce::NonbondedMethod>(node.getIntProperty("nonbondedMethod")));
-        if (node.getIntProperty("version") == 2) {
+        if (version >= 2)
             force->setPolarizationType(static_cast<AmoebaMultipoleForce::PolarizationType>(node.getIntProperty("polarizationType")));
-        }
         //force->setPmeBSplineOrder(node.getIntProperty("pmeBSplineOrder"));
         //force->setMutualInducedIterationMethod(static_cast<AmoebaMultipoleForce::MutualInducedIterationMethod>(node.getIntProperty("mutualInducedIterationMethod")));
         force->setMutualInducedMaxIterations(node.getIntProperty("mutualInducedMaxIterations"));
@@ -151,6 +161,18 @@ void* AmoebaMultipoleForceProxy::deserialize(const SerializationNode& node) cons
         gridDimensions.push_back(gridDimensionsNode.getIntProperty("d2"));
         force->setPmeGridDimensions(gridDimensions);
     
+        if (version >= 3) {
+            const SerializationNode& coefficients = node.getChildNode("ExtrapolationCoefficients");
+            vector<double> coeff;
+            for (int i = 0; ; i++) {
+                stringstream key;
+                key << "c" << i;
+                if (coefficients.getProperties().find(key.str()) == coefficients.getProperties().end())
+                    break;
+                coeff.push_back(coefficients.getDoubleProperty(key.str()));
+            }
+            force->setExtrapolationCoefficients(coeff);
+        }
         std::vector<std::string> covalentTypes;
         getCovalentTypes(covalentTypes);
 

plugins/amoeba/serialization/src/AmoebaOutOfPlaneBendForceProxy.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,8 +42,9 @@ AmoebaOutOfPlaneBendForceProxy::AmoebaOutOfPlaneBendForceProxy() : Serialization
 }
 
 void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaOutOfPlaneBendForce& force = *reinterpret_cast<const AmoebaOutOfPlaneBendForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("cubic",   force.getAmoebaGlobalOutOfPlaneBendCubic());
     node.setDoubleProperty("quartic", force.getAmoebaGlobalOutOfPlaneBendQuartic());
     node.setDoubleProperty("pentic",  force.getAmoebaGlobalOutOfPlaneBendPentic());
@@ -59,11 +60,13 @@ void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, Serialization
 }
 
 void* AmoebaOutOfPlaneBendForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaOutOfPlaneBendForce* force = new AmoebaOutOfPlaneBendForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setAmoebaGlobalOutOfPlaneBendCubic(node.getDoubleProperty("cubic"));
         force->setAmoebaGlobalOutOfPlaneBendQuartic(node.getDoubleProperty("quartic"));
         force->setAmoebaGlobalOutOfPlaneBendPentic(node.getDoubleProperty("pentic"));

plugins/amoeba/serialization/src/AmoebaPiTorsionForceProxy.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,8 +42,9 @@ AmoebaPiTorsionForceProxy::AmoebaPiTorsionForceProxy() : SerializationProxy("Amo
 }
 
 void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     SerializationNode& bonds = node.createChildNode("PiTorsion");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumPiTorsions()); ii++) {
         int particle1, particle2, particle3, particle4, particle5, particle6;
@@ -54,10 +55,13 @@ void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode&
 }
 
 void* AmoebaPiTorsionForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaPiTorsionForce* force = new AmoebaPiTorsionForce();
     try {
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& bonds = node.getChildNode("PiTorsion");
         for (unsigned int ii = 0; ii < bonds.getChildren().size(); ii++) {
             const SerializationNode& bond = bonds.getChildren()[ii];

plugins/amoeba/serialization/src/AmoebaStretchBendForceProxy.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) 2010-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,8 +42,9 @@ AmoebaStretchBendForceProxy::AmoebaStretchBendForceProxy() : SerializationProxy(
 }
 
 void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 2);
+    node.setIntProperty("version", 3);
     const AmoebaStretchBendForce& force = *reinterpret_cast<const AmoebaStretchBendForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     SerializationNode& bonds = node.createChildNode("StretchBendAngles");
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumStretchBends()); ii++) {
         int particle1, particle2, particle3;
@@ -56,10 +57,12 @@ void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNod
 
 void* AmoebaStretchBendForceProxy::deserialize(const SerializationNode& node) const {
     int version = node.getIntProperty("version");
-    if (version != 1 && version != 2)
+    if (version < 1 || version > 3)
         throw OpenMMException("Unsupported version number");
     AmoebaStretchBendForce* force = new AmoebaStretchBendForce();
     try {
+        if (version > 2)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& bonds = node.getChildNode("StretchBendAngles");
         for (unsigned int ii = 0; ii < (int) bonds.getChildren().size(); ii++) {
             const SerializationNode& bond = bonds.getChildren()[ii];

plugins/amoeba/serialization/src/AmoebaTorsionTorsionForceProxy.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -63,8 +63,9 @@ static void loadGrid(const SerializationNode& grid, std::vector< std::vector< st
 }
 
 void AmoebaTorsionTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaTorsionTorsionForce& force = *reinterpret_cast<const AmoebaTorsionTorsionForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
 
     // grid[xIdx][yIdx][6 values]
 
@@ -116,12 +117,14 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
 
 void* AmoebaTorsionTorsionForceProxy::deserialize(const SerializationNode& node) const {
 
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
 
     AmoebaTorsionTorsionForce* force = new AmoebaTorsionTorsionForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         const SerializationNode& grids                    = node.getChildNode("TorsionTorsionGrids");
         const std::vector<SerializationNode>& gridList    = grids.getChildren();
         for (unsigned int ii = 0; ii < gridList.size(); ii++) {

plugins/amoeba/serialization/src/AmoebaVdwForceProxy.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,9 +42,10 @@ AmoebaVdwForceProxy::AmoebaVdwForceProxy() : SerializationProxy("AmoebaVdwForce"
 }
 
 void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaVdwForce& force = *reinterpret_cast<const AmoebaVdwForce*>(object);
 
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setStringProperty("SigmaCombiningRule", force.getSigmaCombiningRule());
     node.setStringProperty("EpsilonCombiningRule", force.getEpsilonCombiningRule());
     node.setDoubleProperty("VdwCutoff", force.getCutoff());
@@ -72,11 +73,13 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
 }
 
 void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaVdwForce* force = new AmoebaVdwForce();
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setSigmaCombiningRule(node.getStringProperty("SigmaCombiningRule"));
         force->setEpsilonCombiningRule(node.getStringProperty("EpsilonCombiningRule"));
         force->setCutoff(node.getDoubleProperty("VdwCutoff"));

plugins/amoeba/serialization/src/AmoebaWcaDispersionForceProxy.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -42,8 +42,9 @@ AmoebaWcaDispersionForceProxy::AmoebaWcaDispersionForceProxy() : SerializationPr
 }
 
 void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const AmoebaWcaDispersionForce& force = *reinterpret_cast<const AmoebaWcaDispersionForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
     node.setDoubleProperty("Epso",    force.getEpso());
     node.setDoubleProperty("Epsh",    force.getEpsh());
     node.setDoubleProperty("Rmino",   force.getRmino());
@@ -63,12 +64,14 @@ void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationN
 }
 
 void* AmoebaWcaDispersionForceProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     AmoebaWcaDispersionForce* force = new AmoebaWcaDispersionForce();
 
     try {
-
+        if (version > 1)
+            force->setForceGroup(node.getIntProperty("forceGroup", 0));
         force->setEpso(   node.getDoubleProperty("Epso"));
         force->setEpsh(   node.getDoubleProperty("Epsh"));
         force->setRmino(  node.getDoubleProperty("Rmino"));

plugins/amoeba/serialization/tests/TestSerializeAmoebaAngleForce.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ void testSerialization() {
     // Create a Force.
 
     AmoebaAngleForce force1;
+    force1.setForceGroup(3);
     force1.setAmoebaGlobalAngleCubic(12.3);
     force1.setAmoebaGlobalAngleQuartic(98.7);
     force1.setAmoebaGlobalAnglePentic(91.7);
@@ -62,6 +63,7 @@ void testSerialization() {
 
     // Compare the two forces to see if they are identical.  
     AmoebaAngleForce& force2 = *copy;
+    ASSERT_EQUAL(force1.getForceGroup(), force2.getForceGroup());
     ASSERT_EQUAL(force1.getAmoebaGlobalAngleCubic(),   force2.getAmoebaGlobalAngleCubic());
     ASSERT_EQUAL(force1.getAmoebaGlobalAngleQuartic(), force2.getAmoebaGlobalAngleQuartic());
     ASSERT_EQUAL(force1.getAmoebaGlobalAnglePentic(),  force2.getAmoebaGlobalAnglePentic());