Merge pull request #1982 from peastman/rmsd

Created RMSDForce

platforms/reference/include/ReferenceRMSDForce.h

+/* Portions copyright (c) 2018 Stanford University and Simbios.
+ * Contributors: Peter Eastman
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
+ * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+#ifndef __ReferenceRMSDForce_H__
+#define __ReferenceRMSDForce_H__
+
+#include "openmm/RMSDForce.h"
+#include <vector>
+
+namespace OpenMM {
+
+class ReferenceRMSDForce {
+private:
+    std::vector<OpenMM::Vec3> referencePos;
+    std::vector<int> particles;
+
+public:
+    /**
+     * Constructor
+     */
+    ReferenceRMSDForce(std::vector<OpenMM::Vec3>& referencePos, std::vector<int>& particles);
+
+    /**
+     * Destructor
+     */
+    ~ReferenceRMSDForce();
+
+    /**
+     * Calculate the interaction.
+     * 
+     * @param atomCoordinates    atom coordinates
+     * @param forces             the forces are added to this
+     * @return the energy of the interaction
+     */
+   double calculateIxn(std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& forces) const;
+};
+
+} // namespace OpenMM
+
+#endif // __ReferenceRMSDForce_H__

platforms/reference/src/ReferenceKernelFactory.cpp

@@ -80,6 +80,8 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
         return new ReferenceCalcCustomCompoundBondForceKernel(name, platform);
     if (name == CalcCustomCVForceKernel::Name())
         return new ReferenceCalcCustomCVForceKernel(name, platform);
+    if (name == CalcRMSDForceKernel::Name())
+        return new ReferenceCalcRMSDForceKernel(name, platform);
     if (name == CalcCustomManyParticleForceKernel::Name())
         return new ReferenceCalcCustomManyParticleForceKernel(name, platform);
     if (name == CalcGayBerneForceKernel::Name())

platforms/reference/src/ReferenceKernels.cpp

@@ -57,6 +57,7 @@
 #include "ReferenceMonteCarloBarostat.h"
 #include "ReferenceProperDihedralBond.h"
 #include "ReferenceRbDihedralBond.h"
+#include "ReferenceRMSDForce.h"
 #include "ReferenceStochasticDynamics.h"
 #include "ReferenceTabulatedFunction.h"
 #include "ReferenceVariableStochasticDynamics.h"
@@ -2055,6 +2056,43 @@ void ReferenceCalcCustomCVForceKernel::copyState(ContextImpl& context, ContextIm
         innerContext.setParameter(param.first, context.getParameter(param.first));
 }
 
+void ReferenceCalcRMSDForceKernel::initialize(const System& system, const RMSDForce& force) {
+    particles = force.getParticles();
+    if (particles.size() == 0)
+        for (int i = 0; i < system.getNumParticles(); i++)
+            particles.push_back(i);
+    referencePos = force.getReferencePositions();
+    Vec3 center;
+    for (int i : particles)
+        center += referencePos[i];
+    center /= particles.size();
+    for (Vec3& p : referencePos)
+        p -= center;
+}
+
+double ReferenceCalcRMSDForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
+    vector<Vec3>& posData = extractPositions(context);
+    vector<Vec3>& forceData = extractForces(context);
+    ReferenceRMSDForce rmsd(referencePos, particles);
+    return rmsd.calculateIxn(posData, forceData);
+}
+
+void ReferenceCalcRMSDForceKernel::copyParametersToContext(ContextImpl& context, const RMSDForce& force) {
+    if (referencePos.size() != force.getReferencePositions().size())
+        throw OpenMMException("updateParametersInContext: The number of reference positions has changed");
+    particles = force.getParticles();
+    if (particles.size() == 0)
+        for (int i = 0; i < referencePos.size(); i++)
+            particles.push_back(i);
+    referencePos = force.getReferencePositions();
+    Vec3 center;
+    for (int i : particles)
+        center += referencePos[i];
+    center /= particles.size();
+    for (Vec3& p : referencePos)
+        p -= center;
+}
+
 ReferenceIntegrateVerletStepKernel::~ReferenceIntegrateVerletStepKernel() {
     if (dynamics)
         delete dynamics;

platforms/reference/src/ReferencePlatform.cpp

@@ -65,6 +65,7 @@ ReferencePlatform::ReferencePlatform() {
     registerKernelFactory(CalcCustomCentroidBondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomCompoundBondForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomCVForceKernel::Name(), factory);
+    registerKernelFactory(CalcRMSDForceKernel::Name(), factory);
     registerKernelFactory(CalcCustomManyParticleForceKernel::Name(), factory);
     registerKernelFactory(CalcGayBerneForceKernel::Name(), factory);
     registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);

platforms/reference/src/SimTKReference/ReferenceRMSDForce.cpp

+/* Portions copyright (c) 2018 Stanford University and Simbios.
+ * Contributors: Peter Eastman
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * "Software"), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject
+ * to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ * IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
+ * LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+ * OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+#include "ReferenceRMSDForce.h"
+#include "jama_eig.h"
+
+using namespace OpenMM;
+using namespace std;
+
+ReferenceRMSDForce::ReferenceRMSDForce(vector<Vec3>& referencePos, vector<int>& particles) :
+        referencePos(referencePos), particles(particles) {
+}
+
+ReferenceRMSDForce::~ReferenceRMSDForce() {
+}
+
+double ReferenceRMSDForce::calculateIxn(vector<Vec3>& atomCoordinates, vector<Vec3>& forces) const {
+    // Compute the RMSD and its gradient using the algorithm described in Coutsias et al,
+    // "Using quaternions to calculate RMSD" (doi: 10.1002/jcc.20110).  First subtract
+    // the centroid from the atom positions.  The reference positions have already been centered.
+    
+    int numParticles = particles.size();
+    Vec3 center;
+    for (int i : particles)
+        center += atomCoordinates[i];
+    center /= numParticles;
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; i++)
+        positions[i] = atomCoordinates[particles[i]]-center;
+    
+    // Compute the correlation matrix.
+    
+    double R[3][3] = {{0, 0, 0}, {0, 0, 0}, {0, 0, 0}};
+    for (int i = 0; i < 3; i++)
+        for (int j = 0; j < 3; j++)
+            for (int k = 0; k < numParticles; k++) {
+                int index = particles[k];
+                R[i][j] += positions[k][i]*referencePos[index][j];
+            }
+
+    // Compute the F matrix.
+
+    Array2D<double> F(4, 4);
+    F[0][0] =  R[0][0] + R[1][1] + R[2][2];
+    F[1][0] =  R[1][2] - R[2][1];
+    F[2][0] =  R[2][0] - R[0][2];
+    F[3][0] =  R[0][1] - R[1][0];
+
+    F[0][1] =  R[1][2] - R[2][1];
+    F[1][1] =  R[0][0] - R[1][1] - R[2][2];
+    F[2][1] =  R[0][1] + R[1][0];
+    F[3][1] =  R[0][2] + R[2][0];
+
+    F[0][2] =  R[2][0] - R[0][2];
+    F[1][2] =  R[0][1] + R[1][0];
+    F[2][2] = -R[0][0] + R[1][1] - R[2][2];
+    F[3][2] =  R[1][2] + R[2][1];
+
+    F[0][3] =  R[0][1] - R[1][0];
+    F[1][3] =  R[0][2] + R[2][0];
+    F[2][3] =  R[1][2] + R[2][1];
+    F[3][3] = -R[0][0] - R[1][1] + R[2][2];
+
+    // Find the maximum eigenvalue and eigenvector.
+
+    JAMA::Eigenvalue<double> eigen(F);
+    Array1D<double> values;
+    eigen.getRealEigenvalues(values);
+    Array2D<double> vectors;
+    eigen.getV(vectors);
+
+    // Compute the RMSD.
+    
+    double sum = 0.0;
+    for (int i = 0; i < numParticles; i++) {
+        int index = particles[i];
+        sum += positions[i].dot(positions[i]) + referencePos[index].dot(referencePos[index]);
+    }
+    double msd = (sum-2*values[3])/numParticles;
+    if (msd < 1e-20) {
+        // The particles are perfectly aligned, so all the forces should be zero.
+        // Numerical error can lead to NaNs, so just return 0 now.
+        return 0.0;
+    }
+    double rmsd = sqrt(msd);
+
+    // Compute the rotation matrix.
+
+    double q[] = {vectors[0][3], vectors[1][3], vectors[2][3], vectors[3][3]};
+    double q00 = q[0]*q[0], q01 = q[0]*q[1], q02 = q[0]*q[2], q03 = q[0]*q[3];
+    double q11 = q[1]*q[1], q12 = q[1]*q[2], q13 = q[1]*q[3];
+    double q22 = q[2]*q[2], q23 = q[2]*q[3];
+    double q33 = q[3]*q[3];
+    double U[3][3] = {{q00+q11-q22-q33, 2*(q12-q03), 2*(q13+q02)},
+                      {2*(q12+q03), q00-q11+q22-q33, 2*(q23-q01)},
+                      {2*(q13-q02), 2*(q23+q01), q00-q11-q22+q33}};
+
+    // Rotate the reference positions and compute the forces.
+    
+    for (int i = 0; i < numParticles; i++) {
+        const Vec3& p = referencePos[particles[i]];
+        Vec3 rotatedRef(U[0][0]*p[0] + U[1][0]*p[1] + U[2][0]*p[2],
+                        U[0][1]*p[0] + U[1][1]*p[1] + U[2][1]*p[2],
+                        U[0][2]*p[0] + U[1][2]*p[1] + U[2][2]*p[2]);
+        forces[particles[i]] -= (positions[i]-rotatedRef) / (rmsd*numParticles);
+    }
+    return rmsd;
+}

platforms/reference/tests/TestReferenceRMSDForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2018 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "ReferenceTests.h"
+#include "TestRMSDForce.h"
+
+void runPlatformTests() {
+}

serialization/include/openmm/serialization/RMSDForceProxy.h

+#ifndef OPENMM_RMSDFORCE_PROXY_H_
+#define OPENMM_RMSDFORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2018 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing RMSDForce objects.
+ */
+
+class OPENMM_EXPORT RMSDForceProxy : public SerializationProxy {
+public:
+    RMSDForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_RMSDFORCE_PROXY_H_*/

serialization/src/RMSDForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2018 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/RMSDForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/RMSDForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+RMSDForceProxy::RMSDForceProxy() : SerializationProxy("RMSDForce") {
+}
+
+void RMSDForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 0);
+    const RMSDForce& force = *reinterpret_cast<const RMSDForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
+    SerializationNode& positionsNode = node.createChildNode("ReferencePositions");
+    for (const Vec3& pos : force.getReferencePositions())
+       positionsNode.createChildNode("Position").setDoubleProperty("x", pos[0]).setDoubleProperty("y", pos[1]).setDoubleProperty("z", pos[2]);
+    SerializationNode& particlesNode = node.createChildNode("Particles");
+    for (int i : force.getParticles())
+       particlesNode.createChildNode("Particle").setIntProperty("index", i);
+}
+
+void* RMSDForceProxy::deserialize(const SerializationNode& node) const {
+    int version = node.getIntProperty("version");
+    if (version != 0)
+        throw OpenMMException("Unsupported version number");
+    RMSDForce* force = NULL;
+    try {
+        vector<Vec3> positions;
+        for (auto& pos : node.getChildNode("ReferencePositions").getChildren())
+            positions.push_back(Vec3(pos.getDoubleProperty("x"), pos.getDoubleProperty("y"), pos.getDoubleProperty("z")));
+        vector<int> particles;
+        for (auto& particle : node.getChildNode("Particles").getChildren())
+            particles.push_back(particle.getIntProperty("index"));
+        force = new RMSDForce(positions, particles);
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        return force;
+    }
+    catch (...) {
+        if (force != NULL)
+            delete force;
+        throw;
+    }
+}

serialization/src/SerializationProxyRegistration.cpp

@@ -57,6 +57,7 @@
 #include "openmm/NonbondedForce.h"
 #include "openmm/PeriodicTorsionForce.h"
 #include "openmm/RBTorsionForce.h"
+#include "openmm/RMSDForce.h"
 #include "openmm/System.h"
 #include "openmm/TabulatedFunction.h"
 #include "openmm/VariableLangevinIntegrator.h"
@@ -92,6 +93,7 @@
 #include "openmm/serialization/NonbondedForceProxy.h"
 #include "openmm/serialization/PeriodicTorsionForceProxy.h"
 #include "openmm/serialization/RBTorsionForceProxy.h"
+#include "openmm/serialization/RMSDForceProxy.h"
 #include "openmm/serialization/StateProxy.h"
 #include "openmm/serialization/SystemProxy.h"
 #include "openmm/serialization/TabulatedFunctionProxies.h"
@@ -148,6 +150,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(NonbondedForce), new NonbondedForceProxy());
     SerializationProxy::registerProxy(typeid(PeriodicTorsionForce), new PeriodicTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(RBTorsionForce), new RBTorsionForceProxy());
+    SerializationProxy::registerProxy(typeid(RMSDForce), new RMSDForceProxy());
     SerializationProxy::registerProxy(typeid(System), new SystemProxy());
     SerializationProxy::registerProxy(typeid(State), new StateProxy());
     SerializationProxy::registerProxy(typeid(VariableLangevinIntegrator), new VariableLangevinIntegratorProxy());

serialization/tests/TestSerializeRMSDForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2018 Stanford University and the Authors.            *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/RMSDForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    vector<Vec3> refPos;
+    for (int i = 0; i < 10; i++)
+        refPos.push_back(Vec3(i/5.0, i*1.2, i*i/3.5));
+    vector<int> particles;
+    for (int i = 0; i < 5; i++)
+        particles.push_back(i*i);
+    RMSDForce force(refPos, particles);
+    force.setForceGroup(3);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<RMSDForce>(&force, "Force", buffer);
+    RMSDForce* copy = XmlSerializer::deserialize<RMSDForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    RMSDForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.getReferencePositions().size(), force2.getReferencePositions().size());
+    for (int i = 0; i < force.getReferencePositions().size(); i++)
+        ASSERT_EQUAL_VEC(force.getReferencePositions()[i], force2.getReferencePositions()[i], 0.0);
+    ASSERT_EQUAL(force.getParticles().size(), force2.getParticles().size());
+    for (int i = 0; i < force.getParticles().size(); i++)
+        ASSERT_EQUAL(force.getParticles()[i], force2.getParticles()[i]);
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

tests/TestRMSDForce.h

+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2018 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/RMSDForce.h"
+#include "openmm/Context.h"
+#include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "sfmt/SFMT.h"
+#include <cmath>
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+double estimateRMSD(vector<Vec3>& positions, vector<Vec3>& referencePos, vector<int>& particles) {
+    // Estimate the RMSD.  For simplicity we omit the orientation alignment, but they should
+    // already be almost perfectly aligned.
+    
+    Vec3 center1, center2;
+    for (int i : particles) {
+        center1 += referencePos[i];
+        center2 += positions[i];
+    }
+    center1 /= particles.size();
+    center2 /= particles.size();
+    double estimate = 0.0;
+    for (int i : particles) {
+        Vec3 delta = (referencePos[i]-center1) - (positions[i]-center2);
+        estimate += delta.dot(delta);
+    }
+    return sqrt(estimate/particles.size());
+}
+
+void testRMSD() {
+    const int numParticles = 20;
+    System system;
+    vector<Vec3> referencePos(numParticles);
+    vector<Vec3> positions(numParticles);
+    vector<int> particles;
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(1.0);
+        referencePos[i] = Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*10;
+        positions[i] = referencePos[i] + Vec3(genrand_real2(sfmt), genrand_real2(sfmt), genrand_real2(sfmt))*0.2;
+        if (i%5 != 0)
+            particles.push_back(i);
+    }
+    RMSDForce* force = new RMSDForce(referencePos, particles);
+    system.addForce(force);
+    VerletIntegrator integrator(0.001);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    double estimate = estimateRMSD(positions, referencePos, particles);
+    
+    // Have the force compute the RMSD.  It should be very slightly less than
+    // what we calculated above (since that omitted the rotation).
+    
+    State state1 = context.getState(State::Energy);
+    double rmsd = state1.getPotentialEnergy();
+    ASSERT(rmsd <= estimate);
+    ASSERT(rmsd > 0.9*estimate);
+
+    // Translate and rotate all the particles.  This should have no effect on the RMSD.
+
+    vector<Vec3> transformedPos(numParticles);
+    double cs = cos(1.1), sn = sin(1.1);
+    for (int i = 0; i < numParticles; i++) {
+        Vec3 p = positions[i];
+        transformedPos[i] = Vec3( cs*p[0] + sn*p[1] + 0.1,
+                                 -sn*p[0] + cs*p[1] - 11.3,
+                                  p[2] + 1.5);
+    }
+    context.setPositions(transformedPos);
+    state1 = context.getState(State::Energy | State::Forces);
+    ASSERT_EQUAL_TOL(rmsd, state1.getPotentialEnergy(), 1e-4);
+
+    // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount.
+
+    const vector<Vec3>& forces = state1.getForces();
+    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 = 0.1;
+    double step = 0.5*stepSize/norm;
+    vector<Vec3> positions2(numParticles), positions3(numParticles);
+    for (int i = 0; i < (int) positions.size(); ++i) {
+        Vec3 p = transformedPos[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-3);
+    
+    // Check that updateParametersInContext() works correctly.
+    
+    context.setPositions(transformedPos);
+    force->setReferencePositions(transformedPos);
+    force->updateParametersInContext(context);
+    ASSERT_EQUAL_TOL(0.0, context.getState(State::Energy).getPotentialEnergy(), 1e-2);
+    context.setPositions(referencePos);
+    ASSERT_EQUAL_TOL(rmsd, context.getState(State::Energy).getPotentialEnergy(), 1e-4);
+
+    // Verify that giving an empty list of particles is interpreted to mean all particles.
+
+    vector<int> allParticles;
+    for (int i = 0; i < numParticles; i++)
+        allParticles.push_back(i);
+    estimate = estimateRMSD(positions, referencePos, allParticles);
+    force->setParticles(allParticles);
+    force->setReferencePositions(referencePos);
+    force->updateParametersInContext(context);
+    context.setPositions(positions);
+    double rmsd1 = context.getState(State::Energy).getPotentialEnergy();
+    force->setParticles(vector<int>());
+    force->updateParametersInContext(context);
+    double rmsd2 = context.getState(State::Energy).getPotentialEnergy();
+    ASSERT_EQUAL_TOL(rmsd1, rmsd2, 1e-4);
+    ASSERT(rmsd1 <= estimate);
+    ASSERT(rmsd1 > 0.9*estimate);
+}
+
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
+    try {
+        initializeTests(argc, argv);
+        testRMSD();
+        runPlatformTests();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -453,5 +453,7 @@ UNITS = {
 ("DrudeSCFIntegrator", "getMinimizationErrorTolerance") : ("unit.kilojoules_per_mole/unit.nanometer", ()),
 ("RPMDIntegrator", "getContractions") : (None, ()),
 ("RPMDIntegrator", "getTotalEnergy") : ("unit.kilojoules_per_mole", ()),
+("RMSDForce", "getReferencePositions") : ("unit.nanometer", ()),
+("RMSDForce", "getParticles") : (None, ()),
 }
 

wrappers/python/src/swig_doxygen/swig_lib/python/typemaps.i

@@ -415,11 +415,14 @@ int Py_SequenceToVecVecVecDouble(PyObject* obj, std::vector<std::vector<std::vec
     $1 = &v;
 }
 %typemap(typecheck, precedence=SWIG_TYPECHECK_DOUBLE_ARRAY, fragment="Py_SequenceToVecVec3") const std::vector<Vec3>& {
-    std::vector<double> v;
+    std::vector<Vec3> v;
     int res=0;
     res = Py_SequenceToVecVec3($input, v);
     $1 = SWIG_IsOK(res);
 }
+%typemap(out) const std::vector<Vec3>& {
+    $result = copyVVec3ToList(*$1);
+}
 
 
 // typemap for const vector<double>