More serialization proxies

plugins/amoeba/serialization/include/openmm/serialization/AmoebaGeneralizedKirkwoodForceProxy.h

+#ifndef OPENMM_AMOEBA_GENERALIZED_KIRKWOOD_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_GENERALIZED_KIRKWOOD_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * 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) 2010 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 AmoebaUreyBradleyForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaGeneralizedKirkwoodForceProxy : public SerializationProxy {
+public:
+    AmoebaGeneralizedKirkwoodForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_GENERALIZED_KIRKWOOD_FORCE_PROXY_H_*/

plugins/amoeba/serialization/include/openmm/serialization/AmoebaMultipole.h

+#ifndef OPENMM_AMOEBA_MULTIPOLE_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_MULTIPOLE_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * 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) 2010 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 AmoebaUreyBradleyForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaMultipole : public SerializationProxy {
+public:
+    AmoebaMultipole();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_UREY_BRADLEY_FORCE_PROXY_H_*/

plugins/amoeba/serialization/include/openmm/serialization/AmoebaStretchBendForceProxy.h

+#ifndef OPENMM_AMOEBA_STRETCH_BEND_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_STRETCH_BEND_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * 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) 2010 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 AmoebaUreyBradleyForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaStretchBendForceProxy : public SerializationProxy {
+public:
+    AmoebaStretchBendForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_STRETCH_BEND_FORCE_PROXY_H_*/

plugins/amoeba/serialization/include/openmm/serialization/AmoebaVdwForceProxy.h

+#ifndef OPENMM_AMOEBA_VDW_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_VDW_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * 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) 2010 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 AmoebaUreyBradleyForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaVdwForceProxy : public SerializationProxy {
+public:
+    AmoebaVdwForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_VDW_FORCE_PROXY_H_*/

plugins/amoeba/serialization/include/openmm/serialization/AmoebaWcaDispersionForceProxy.h

+#ifndef OPENMM_AMOEBA_WCA_DISPERSION_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_WCA_DISPERSION_FORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * 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) 2010 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 AmoebaUreyBradleyForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaWcaDispersionForceProxy : public SerializationProxy {
+public:
+    AmoebaWcaDispersionForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_WCA_DISPERSION_FORCE_PROXY_H_*/

plugins/amoeba/serialization/src/AmoebaSerializationProxyRegistration.cpp

@@ -47,6 +47,7 @@
 #include "openmm/AmoebaTorsionForce.h"
 #include "openmm/AmoebaTorsionTorsionForce.h"
 #include "openmm/AmoebaUreyBradleyForce.h"
+#include "openmm/AmoebaVdwForce.h"
 
 #include "openmm/serialization/SerializationProxy.h"
 #include "openmm/serialization/AmoebaHarmonicBondForceProxy.h"
@@ -57,6 +58,7 @@
 #include "openmm/serialization/AmoebaTorsionForceProxy.h"
 #include "openmm/serialization/AmoebaTorsionTorsionForceProxy.h"
 #include "openmm/serialization/AmoebaUreyBradleyForceProxy.h"
+#include "openmm/serialization/AmoebaVdwForceProxy.h"
 
 #if defined(WIN32)
     #include <windows.h>
@@ -107,4 +109,5 @@ extern "C" void registerAmoebaSerializationProxies() {
     SerializationProxy::registerProxy(typeid(AmoebaTorsionForce), new AmoebaTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(AmoebaTorsionTorsionForce), new AmoebaTorsionTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(AmoebaUreyBradleyForce), new AmoebaUreyBradleyForceProxy());
+    SerializationProxy::registerProxy(typeid(AmoebaVdwForce), new AmoebaVdwForceProxy());
 }

plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * 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) 2010 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/AmoebaVdwForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/AmoebaVdwForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+AmoebaVdwForceProxy::AmoebaVdwForceProxy() : SerializationProxy("AmoebaVdwForce") {
+}
+
+void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const AmoebaVdwForce& force = *reinterpret_cast<const AmoebaVdwForce*>(object);
+    node.setStringProperty("SigmaCombiningRule", force.getSigmaCombiningRule());
+    node.setStringProperty("EpsilonCombiningRule", force.getEpsilonCombiningRule());
+    node.setDoubleProperty("VdwCutoff", force.getCutoff());
+    node.setIntProperty("VdwUseNeighborList", force.getUseNeighborList());
+    node.setIntProperty("VdwPBC", force.getPBC());
+    SerializationNode& particles = node.createChildNode("VdwParticles");
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        int ivIndex, classIndex;
+        double sigma, epsilon, reductionFactor;
+        force.getParticleParameters( i,  ivIndex, classIndex, sigma, epsilon, reductionFactor );
+        particles.createChildNode("Particle").setIntProperty("index", i).setIntProperty("ivIndex", ivIndex).setIntProperty("classIndex", classIndex).setDoubleProperty("sig", sigma).setDoubleProperty("eps", epsilon).setDoubleProperty("red", reductionFactor);
+    }
+
+    SerializationNode& particleExclusions = node.createChildNode("VdwParticleExclusions");
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        std::vector< int > exclusions;
+        force.getParticleExclusions( i,  exclusions );
+        SerializationNode& particle = particleExclusions.createChildNode("ParticleExclusion");
+        particle.setIntProperty("size", exclusions.size() );
+        particle.setIntProperty("index", i );
+        for (unsigned int jj = 0; jj < exclusions.size(); jj++) {
+            particle.createChildNode("ParticleExclusion").setIntProperty( "ex", exclusions[jj] );
+        }
+    }
+}
+
+void* AmoebaVdwForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    AmoebaVdwForce* force = new AmoebaVdwForce();
+    try {
+
+        force->setSigmaCombiningRule( node.getStringProperty( "SigmaCombiningRule" ) );
+        force->setEpsilonCombiningRule( node.getStringProperty( "EpsilonCombiningRule" ) );
+        force->setCutoff( node.getDoubleProperty( "VdwCutoff" ) );
+        force->setUseNeighborList( node.getIntProperty( "VdwUseNeighborList" ) );
+        force->setPBC( node.getIntProperty( "VdwPBC" ) );
+
+        const SerializationNode& particles = node.getChildNode("VdwParticles");
+        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
+            const SerializationNode& particle = particles.getChildren()[i];
+            force->addParticle(particle.getIntProperty("ivIndex"), particle.getIntProperty("classIndex"), particle.getDoubleProperty("sig"), particle.getDoubleProperty("eps"), particle.getDoubleProperty("red"));
+        }
+
+        // exclusions
+
+        const SerializationNode& particleExclusions = node.getChildNode("VdwParticleExclusions");
+        for (int i = 0; i < (int) particleExclusions.getChildren().size(); i++) {
+            const SerializationNode& particleExclusion = particleExclusions.getChildren()[i];
+            std::vector< int > exclusions;
+            for (unsigned int jj = 0; jj < particleExclusion.getChildren().size(); jj++) {
+                exclusions.push_back( particleExclusion.getChildren()[jj].getIntProperty("ex") );
+            }
+            int index = particleExclusion.getIntProperty( "index" );
+            force->setParticleExclusions( index, exclusions );
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * 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) 2010 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 "../../../tests/AssertionUtilities.h"
+#include "openmm/AmoebaVdwForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    AmoebaVdwForce force;
+    force.setSigmaCombiningRule( "GEOMETRIC" );
+    force.setEpsilonCombiningRule( "GEOMETRIC" );
+    force.setCutoff( 0.9 );
+    force.setUseNeighborList( 1 );
+    force.setPBC( 1 );
+
+    force.addParticle(0, 1, 1.0, 2.0, 0.9);
+    force.addParticle(1, 0, 1.1, 2.1, 0.9);
+    force.addParticle(2, 3, 1.3, 4.1, 0.9);
+    for( unsigned int ii = 0; ii < 3; ii++ ){
+        std::vector< int > exclusions;
+        exclusions.push_back( ii );
+        exclusions.push_back( ii + 1 );
+        exclusions.push_back( ii + 10 );
+        force.setParticleExclusions( ii, exclusions );
+    }
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<AmoebaVdwForce>(&force, "Force", buffer);
+if( 1 ){
+FILE* filePtr = fopen("Vdw.xml", "w" );
+(void) fprintf( filePtr, "%s", buffer.str().c_str() );
+(void) fclose( filePtr );
+}
+
+    AmoebaVdwForce* copy = XmlSerializer::deserialize<AmoebaVdwForce>(buffer);
+
+    // Compare the two forces to see if they are identical.  
+    AmoebaVdwForce& force2 = *copy;
+    ASSERT_EQUAL(force.getSigmaCombiningRule(), force2.getSigmaCombiningRule());
+    ASSERT_EQUAL(force.getEpsilonCombiningRule(), force2.getEpsilonCombiningRule());
+    ASSERT_EQUAL(force.getCutoff(), force2.getCutoff());
+    ASSERT_EQUAL(force.getUseNeighborList(), force2.getUseNeighborList());
+    ASSERT_EQUAL(force.getPBC(), force2.getPBC());
+    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        int ivIndex1, classIndex1;
+        int ivIndex2, classIndex2;
+        double sigma1, epsilon1, reductionFactor1;
+        double sigma2, epsilon2, reductionFactor2;
+        force.getParticleParameters( i, ivIndex1, classIndex1, sigma1, epsilon1, reductionFactor1 );
+        force2.getParticleParameters(i, ivIndex2, classIndex2, sigma2, epsilon2, reductionFactor2 );
+        ASSERT_EQUAL(ivIndex1, ivIndex2 );
+        ASSERT_EQUAL(classIndex1, classIndex2 );
+        ASSERT_EQUAL(sigma1, sigma2);
+        ASSERT_EQUAL(epsilon1, epsilon2);
+        ASSERT_EQUAL(reductionFactor1, reductionFactor2);
+    }
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        std::vector< int > exclusions1;
+        std::vector< int > exclusions2;
+        force.getParticleExclusions(  i, exclusions1 );
+        force2.getParticleExclusions( i, exclusions2 );
+        ASSERT_EQUAL(exclusions1.size(), exclusions2.size());
+        for (unsigned int ii = 0; ii < exclusions1.size(); ii++) {
+            int hit = 0;
+            for (unsigned int jj = 0; jj < exclusions2.size() && hit == 0; jj++) {
+                if( exclusions2[jj] == exclusions1[ii] )hit++;
+            }
+            ASSERT_EQUAL(hit, 1);
+        }
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+