Continuing to implement serialization

serialization/CMakeLists.txt

@@ -77,7 +77,7 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 # Create the library
 ADD_LIBRARY(${OPENMM_SERIALIZATION_LIBRARY_NAME} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 TARGET_LINK_LIBRARIES(${OPENMM_SERIALIZATION_LIBRARY_NAME} debug ${OPENMM_LIBRARY_NAME}_d optimized ${OPENMM_LIBRARY_NAME})
-SET_TARGET_PROPERTIES(${OPENMM_SERIALIZATION_LIBRARY_NAME} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL")
+SET_TARGET_PROPERTIES(${OPENMM_SERIALIZATION_LIBRARY_NAME} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
 INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${OPENMM_SERIALIZATION_LIBRARY_NAME})
 
 ADD_SUBDIRECTORY(tests)

serialization/include/openmm/serialization/AndersenThermostatProxy.h

+#ifndef OPENMM_ANDERSENTHERMOSTAT_PROXY_H_
+#define OPENMM_ANDERSENTHERMOSTAT_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) 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 AndersenThermostat objects.
+ */
+
+class OPENMM_EXPORT AndersenThermostatProxy : public SerializationProxy {
+public:
+    AndersenThermostatProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_ANDERSENTHERMOSTAT_PROXY_H_*/

serialization/include/openmm/serialization/GBSAOBCForceProxy.h

+#ifndef OPENMM_GBSAOBCFORCE_PROXY_H_
+#define OPENMM_GBSAOBCFORCE_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) 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 GBSAOBCForce objects.
+ */
+
+class OPENMM_EXPORT GBSAOBCForceProxy : public SerializationProxy {
+public:
+    GBSAOBCForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_GBSAOBCFORCE_PROXY_H_*/

serialization/include/openmm/serialization/NonbondedForceProxy.h

+#ifndef OPENMM_NONBONDEDFORCE_PROXY_H_
+#define OPENMM_NONBONDEDFORCE_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) 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 NonbondedForce objects.
+ */
+
+class OPENMM_EXPORT NonbondedForceProxy : public SerializationProxy {
+public:
+    NonbondedForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_NONBONDEDFORCE_PROXY_H_*/

serialization/include/openmm/serialization/PeriodicTorsionForceProxy.h

+#ifndef OPENMM_PERIODICTORSIONFORCE_PROXY_H_
+#define OPENMM_PERIODICTORSIONFORCE_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) 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 PeriodicTorsionForce objects.
+ */
+
+class OPENMM_EXPORT PeriodicTorsionForceProxy : public SerializationProxy {
+public:
+    PeriodicTorsionForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_PERIODICTORSIONFORCE_PROXY_H_*/

serialization/include/openmm/serialization/RBTorsionForceProxy.h

+#ifndef OPENMM_RBTORSIONFORCE_PROXY_H_
+#define OPENMM_RBTORSIONFORCE_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) 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 RBTorsionForce objects.
+ */
+
+class OPENMM_EXPORT RBTorsionForceProxy : public SerializationProxy {
+public:
+    RBTorsionForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_RBTORSIONFORCE_PROXY_H_*/

serialization/src/AndersenThermostatProxy.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) 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/AndersenThermostatProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/AndersenThermostat.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+AndersenThermostatProxy::AndersenThermostatProxy() : SerializationProxy("AndersenThermostat") {
+}
+
+void AndersenThermostatProxy::serialize(const void* object, SerializationNode& node) const {
+    const AndersenThermostat& force = *reinterpret_cast<const AndersenThermostat*>(object);
+    node.setDoubleProperty("temperature", force.getDefaultTemperature());
+    node.setDoubleProperty("frequency", force.getDefaultCollisionFrequency());
+    node.setIntProperty("randomSeed", force.getRandomNumberSeed());
+}
+
+void* AndersenThermostatProxy::deserialize(const SerializationNode& node) const {
+    AndersenThermostat* force = NULL;
+    try {
+        AndersenThermostat* force = new AndersenThermostat(node.getDoubleProperty("temperature"), node.getDoubleProperty("frequency"));
+        force->setRandomNumberSeed(node.getIntProperty("randomSeed"));
+        return force;
+    }
+    catch (...) {
+        if (force != NULL)
+            delete force;
+        throw;
+    }
+}

serialization/src/GBSAOBCForceProxy.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) 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/GBSAOBCForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/GBSAOBCForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+GBSAOBCForceProxy::GBSAOBCForceProxy() : SerializationProxy("GBSAOBCForce") {
+}
+
+void GBSAOBCForceProxy::serialize(const void* object, SerializationNode& node) const {
+    const GBSAOBCForce& force = *reinterpret_cast<const GBSAOBCForce*>(object);
+    node.setIntProperty("method", (int) force.getNonbondedMethod());
+    node.setDoubleProperty("cutoff", force.getCutoffDistance());
+    node.setDoubleProperty("soluteDielectric", force.getSoluteDielectric());
+    node.setDoubleProperty("solventDielectric", force.getSolventDielectric());
+    SerializationNode& particles = node.createChildNode("Particles");
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        double charge, radius, scale;
+        force.getParticleParameters(i, charge, radius, scale);
+        particles.createChildNode("Particle").setDoubleProperty("q", charge).setDoubleProperty("r", radius).setDoubleProperty("scale", scale);
+    }
+}
+
+void* GBSAOBCForceProxy::deserialize(const SerializationNode& node) const {
+    GBSAOBCForce* force = new GBSAOBCForce();
+    try {
+        force->setNonbondedMethod((GBSAOBCForce::NonbondedMethod) node.getIntProperty("method"));
+        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
+        force->setSoluteDielectric(node.getDoubleProperty("soluteDielectric"));
+        force->setSolventDielectric(node.getDoubleProperty("solventDielectric"));
+        const SerializationNode& particles = node.getChildNode("Particles");
+        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
+            const SerializationNode& particle = particles.getChildren()[i];
+            force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("r"), particle.getDoubleProperty("scale"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

serialization/src/HarmonicAngleForceProxy.cpp

@@ -55,10 +55,10 @@ void HarmonicAngleForceProxy::serialize(const void* object, SerializationNode& n
 void* HarmonicAngleForceProxy::deserialize(const SerializationNode& node) const {
     HarmonicAngleForce* force = new HarmonicAngleForce();
     try {
-        const SerializationNode& bonds = node.getChildNode("Angles");
-        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
-            const SerializationNode& constraint = bonds.getChildren()[i];
-            force->addAngle(constraint.getDoubleProperty("p1"), constraint.getDoubleProperty("p2"), constraint.getDoubleProperty("p3"), constraint.getDoubleProperty("a"), constraint.getDoubleProperty("k"));
+        const SerializationNode& angles = node.getChildNode("Angles");
+        for (int i = 0; i < (int) angles.getChildren().size(); i++) {
+            const SerializationNode& angle = angles.getChildren()[i];
+            force->addAngle(angle.getDoubleProperty("p1"), angle.getDoubleProperty("p2"), angle.getDoubleProperty("p3"), angle.getDoubleProperty("a"), angle.getDoubleProperty("k"));
         }
     }
     catch (...) {

serialization/src/HarmonicBondForceProxy.cpp

@@ -57,8 +57,8 @@ void* HarmonicBondForceProxy::deserialize(const SerializationNode& node) const {
     try {
         const SerializationNode& bonds = node.getChildNode("Bonds");
         for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
-            const SerializationNode& constraint = bonds.getChildren()[i];
-            force->addBond(constraint.getDoubleProperty("p1"), constraint.getDoubleProperty("p2"), constraint.getDoubleProperty("d"), constraint.getDoubleProperty("k"));
+            const SerializationNode& bond = bonds.getChildren()[i];
+            force->addBond(bond.getDoubleProperty("p1"), bond.getDoubleProperty("p2"), bond.getDoubleProperty("d"), bond.getDoubleProperty("k"));
         }
     }
     catch (...) {

serialization/src/NonbondedForceProxy.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) 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/NonbondedForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/NonbondedForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+NonbondedForceProxy::NonbondedForceProxy() : SerializationProxy("NonbondedForce") {
+}
+
+void NonbondedForceProxy::serialize(const void* object, SerializationNode& node) const {
+    const NonbondedForce& force = *reinterpret_cast<const NonbondedForce*>(object);
+    node.setIntProperty("method", (int) force.getNonbondedMethod());
+    node.setDoubleProperty("cutoff", force.getCutoffDistance());
+    node.setDoubleProperty("ewaldTolerance", force.getEwaldErrorTolerance());
+    node.setDoubleProperty("rfDielectric", force.getReactionFieldDielectric());
+    node.setIntProperty("dispersionCorrection", force.getUseDispersionCorrection());
+    SerializationNode& particles = node.createChildNode("Particles");
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        double charge, sigma, epsilon;
+        force.getParticleParameters(i, charge, sigma, epsilon);
+        particles.createChildNode("Particle").setDoubleProperty("q", charge).setDoubleProperty("sig", sigma).setDoubleProperty("eps", epsilon);
+    }
+    SerializationNode& exceptions = node.createChildNode("Exceptions");
+    for (int i = 0; i < force.getNumExceptions(); i++) {
+        int particle1, particle2;
+        double chargeProd, sigma, epsilon;
+        force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
+        exceptions.createChildNode("Exception").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setDoubleProperty("q", chargeProd).setDoubleProperty("sig", sigma).setDoubleProperty("eps", epsilon);
+    }
+}
+
+void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
+    NonbondedForce* force = new NonbondedForce();
+    try {
+        force->setNonbondedMethod((NonbondedForce::NonbondedMethod) node.getIntProperty("method"));
+        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
+        force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance"));
+        force->setReactionFieldDielectric(node.getDoubleProperty("rfDielectric"));
+        force->setUseDispersionCorrection(node.getIntProperty("dispersionCorrection"));
+        const SerializationNode& particles = node.getChildNode("Particles");
+        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
+            const SerializationNode& particle = particles.getChildren()[i];
+            force->addParticle(particle.getDoubleProperty("q"), particle.getDoubleProperty("sig"), particle.getDoubleProperty("eps"));
+        }
+        const SerializationNode& exceptions = node.getChildNode("Exceptions");
+        for (int i = 0; i < (int) exceptions.getChildren().size(); i++) {
+            const SerializationNode& exception = exceptions.getChildren()[i];
+            force->addException(exception.getDoubleProperty("p1"), exception.getDoubleProperty("p2"), exception.getDoubleProperty("q"), exception.getDoubleProperty("sig"), exception.getDoubleProperty("eps"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

serialization/src/PeriodicTorsionForceProxy.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) 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/PeriodicTorsionForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/PeriodicTorsionForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+PeriodicTorsionForceProxy::PeriodicTorsionForceProxy() : SerializationProxy("PeriodicTorsionForce") {
+}
+
+void PeriodicTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
+    const PeriodicTorsionForce& force = *reinterpret_cast<const PeriodicTorsionForce*>(object);
+    SerializationNode& torsions = node.createChildNode("Torsions");
+    for (int i = 0; i < force.getNumTorsions(); i++) {
+        int particle1, particle2, particle3, particle4, periodicity;
+        double phase, k;
+        force.getTorsionParameters(i, particle1, particle2, particle3, particle4, periodicity, phase, k);
+        torsions.createChildNode("Torsion").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4).setIntProperty("periodicity", periodicity).setDoubleProperty("phase", phase).setDoubleProperty("k", k);
+    }
+}
+
+void* PeriodicTorsionForceProxy::deserialize(const SerializationNode& node) const {
+    PeriodicTorsionForce* force = new PeriodicTorsionForce();
+    try {
+        const SerializationNode& torsions = node.getChildNode("Torsions");
+        for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
+            const SerializationNode& torsion = torsions.getChildren()[i];
+            force->addTorsion(torsion.getDoubleProperty("p1"), torsion.getDoubleProperty("p2"), torsion.getDoubleProperty("p3"), torsion.getDoubleProperty("p4"),
+                    torsion.getIntProperty("periodicity"), torsion.getDoubleProperty("phase"), torsion.getDoubleProperty("k"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

serialization/src/RBTorsionForceProxy.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) 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/RBTorsionForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/RBTorsionForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+RBTorsionForceProxy::RBTorsionForceProxy() : SerializationProxy("RBTorsionForce") {
+}
+
+void RBTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
+    const RBTorsionForce& force = *reinterpret_cast<const RBTorsionForce*>(object);
+    SerializationNode& torsions = node.createChildNode("Torsions");
+    for (int i = 0; i < force.getNumTorsions(); i++) {
+        int particle1, particle2, particle3, particle4;
+        double c0, c1, c2, c3, c4, c5;
+        force.getTorsionParameters(i, particle1, particle2, particle3, particle4, c0, c1, c2, c3, c4, c5);
+        torsions.createChildNode("Torsion").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4).setDoubleProperty("c0", c0).setDoubleProperty("c1", c1).setDoubleProperty("c2", c2).setDoubleProperty("c3", c3).setDoubleProperty("c4", c4).setDoubleProperty("c5", c5);
+    }
+}
+
+void* RBTorsionForceProxy::deserialize(const SerializationNode& node) const {
+    RBTorsionForce* force = new RBTorsionForce();
+    try {
+        const SerializationNode& torsions = node.getChildNode("Torsions");
+        for (int i = 0; i < (int) torsions.getChildren().size(); i++) {
+            const SerializationNode& torsion = torsions.getChildren()[i];
+            force->addTorsion(torsion.getDoubleProperty("p1"), torsion.getDoubleProperty("p2"), torsion.getDoubleProperty("p3"), torsion.getDoubleProperty("p4"),
+                    torsion.getDoubleProperty("c0"), torsion.getDoubleProperty("c1"), torsion.getDoubleProperty("c2"),
+                    torsion.getDoubleProperty("c3"), torsion.getDoubleProperty("c4"), torsion.getDoubleProperty("c5"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}
+

serialization/src/SerializationNode.cpp

@@ -36,6 +36,9 @@
 using namespace OpenMM;
 using namespace std;
 
+extern "C" char* g_fmt(char*, double);
+extern "C" double strtod(const char* s00, char** se);
+
 const string& SerializationNode::getName() const {
     return name;
 }
@@ -122,25 +125,20 @@ double SerializationNode::getDoubleProperty(const string& name) const {
     map<string, string>::const_iterator iter = properties.find(name);
     if (iter == properties.end())
         throw OpenMMException("Unknown property '"+name+"' in node '"+getName()+"'");
-    double value;
-    stringstream(iter->second) >> value;
-    return value;
+    return strtod(iter->second.c_str(), NULL);
 }
 
 double SerializationNode::getDoubleProperty(const string& name, double defaultValue) const {
     map<string, string>::const_iterator iter = properties.find(name);
     if (iter == properties.end())
         return defaultValue;
-    double value;
-    stringstream(iter->second) >> value;
-    return value;
+    return strtod(iter->second.c_str(), NULL);
 }
 
 SerializationNode& SerializationNode::setDoubleProperty(const string& name, double value) {
-    stringstream s;
-    s.precision(16);
-    s << value;
-    properties[name] = s.str();
+    char buffer[32];
+    g_fmt(buffer, value);
+    properties[name] = string(buffer);
     return *this;
 }
 

serialization/src/SerializationProxyRegistration.cpp

@@ -29,12 +29,22 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
+#include "openmm/AndersenThermostat.h"
 #include "openmm/HarmonicAngleForce.h"
+#include "openmm/GBSAOBCForce.h"
 #include "openmm/HarmonicBondForce.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/PeriodicTorsionForce.h"
+#include "openmm/RBTorsionForce.h"
 #include "openmm/System.h"
 #include "openmm/serialization/SerializationProxy.h"
+#include "openmm/serialization/AndersenThermostatProxy.h"
+#include "openmm/serialization/GBSAOBCForceProxy.h"
 #include "openmm/serialization/HarmonicAngleForceProxy.h"
 #include "openmm/serialization/HarmonicBondForceProxy.h"
+#include "openmm/serialization/NonbondedForceProxy.h"
+#include "openmm/serialization/PeriodicTorsionForceProxy.h"
+#include "openmm/serialization/RBTorsionForceProxy.h"
 #include "openmm/serialization/SystemProxy.h"
 
 #if defined(WIN32)
@@ -52,7 +62,12 @@
 using namespace OpenMM;
 
 extern "C" void registerSerializationProxies() {
+    SerializationProxy::registerProxy(typeid(AndersenThermostat), new AndersenThermostatProxy());
+    SerializationProxy::registerProxy(typeid(GBSAOBCForce), new GBSAOBCForceProxy());
     SerializationProxy::registerProxy(typeid(HarmonicAngleForce), new HarmonicAngleForceProxy());
     SerializationProxy::registerProxy(typeid(HarmonicBondForce), new HarmonicBondForceProxy());
+    SerializationProxy::registerProxy(typeid(NonbondedForce), new NonbondedForceProxy());
+    SerializationProxy::registerProxy(typeid(PeriodicTorsionForce), new PeriodicTorsionForceProxy());
+    SerializationProxy::registerProxy(typeid(RBTorsionForce), new RBTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(System), new SystemProxy());
 }
\ No newline at end of file

serialization/src/g_fmt.cpp

+/****************************************************************
+ *
+ * The author of this software is David M. Gay.
+ *
+ * Copyright (c) 1991, 1996 by Lucent Technologies.
+ *
+ * Permission to use, copy, modify, and distribute this software for any
+ * purpose without fee is hereby granted, provided that this entire notice
+ * is included in all copies of any software which is or includes a copy
+ * or modification of this software and in all copies of the supporting
+ * documentation for such software.
+ *
+ * THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED
+ * WARRANTY.  IN PARTICULAR, NEITHER THE AUTHOR NOR LUCENT MAKES ANY
+ * REPRESENTATION OR WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY
+ * OF THIS SOFTWARE OR ITS FITNESS FOR ANY PARTICULAR PURPOSE.
+ *
+ ***************************************************************/
+
+/* g_fmt(buf,x) stores the closest decimal approximation to x in buf;
+ * it suffices to declare buf
+ *	char buf[32];
+ */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+ extern char *dtoa(double, int, int, int *, int *, char **);
+ extern char *g_fmt(char *, double);
+ extern void freedtoa(char*);
+#ifdef __cplusplus
+	}
+#endif
+
+ char *
+g_fmt(register char *b, double x)
+{
+	register int i, k;
+	register char *s;
+	int decpt, j, sign;
+	char *b0, *s0, *se;
+
+	b0 = b;
+#ifdef IGNORE_ZERO_SIGN
+	if (!x) {
+		*b++ = '0';
+		*b = 0;
+		goto done;
+		}
+#endif
+	s = s0 = dtoa(x, 0, 0, &decpt, &sign, &se);
+	if (sign)
+		*b++ = '-';
+	if (decpt == 9999) /* Infinity or Nan */ {
+		while(*b++ = *s++);
+		goto done0;
+		}
+	if (decpt <= -4 || decpt > se - s + 5) {
+		*b++ = *s++;
+		if (*s) {
+			*b++ = '.';
+			while(*b = *s++)
+				b++;
+			}
+		*b++ = 'e';
+		/* sprintf(b, "%+.2d", decpt - 1); */
+		if (--decpt < 0) {
+			*b++ = '-';
+			decpt = -decpt;
+			}
+		else
+			*b++ = '+';
+		for(j = 2, k = 10; 10*k <= decpt; j++, k *= 10);
+		for(;;) {
+			i = decpt / k;
+			*b++ = i + '0';
+			if (--j <= 0)
+				break;
+			decpt -= i*k;
+			decpt *= 10;
+			}
+		*b = 0;
+		}
+	else if (decpt <= 0) {
+		*b++ = '.';
+		for(; decpt < 0; decpt++)
+			*b++ = '0';
+		while(*b++ = *s++);
+		}
+	else {
+		while(*b = *s++) {
+			b++;
+			if (--decpt == 0 && *s)
+				*b++ = '.';
+			}
+		for(; decpt > 0; decpt--)
+			*b++ = '0';
+		*b = 0;
+		}
+ done0:
+	freedtoa(s0);
+ done:
+	return b0;
+	}

serialization/tests/TestSerializeAndersenThermostat.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) 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/AndersenThermostat.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    AndersenThermostat force(250.0, 0.2);
+    force.setRandomNumberSeed(3);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<AndersenThermostat>(&force, "Force", buffer);
+    AndersenThermostat* copy = XmlSerializer::deserialize<AndersenThermostat>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    AndersenThermostat& force2 = *copy;
+    ASSERT_EQUAL(force.getDefaultTemperature(), force2.getDefaultTemperature());
+    ASSERT_EQUAL(force.getDefaultCollisionFrequency(), force2.getDefaultCollisionFrequency());
+    ASSERT_EQUAL(force.getRandomNumberSeed(), force2.getRandomNumberSeed());
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+

serialization/tests/TestSerializeGBSAOBCForce.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) 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/GBSAOBCForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    GBSAOBCForce force;
+    force.setNonbondedMethod(GBSAOBCForce::CutoffPeriodic);
+    force.setCutoffDistance(2.0);
+    force.setSoluteDielectric(5.1);
+    force.setSolventDielectric(50.0);
+    force.addParticle(1, 0.1, 0.01);
+    force.addParticle(0.5, 0.2, 0.02);
+    force.addParticle(-0.5, 0.3, 0.03);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<GBSAOBCForce>(&force, "Force", buffer);
+    GBSAOBCForce* copy = XmlSerializer::deserialize<GBSAOBCForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    GBSAOBCForce& force2 = *copy;
+    ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
+    ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
+    ASSERT_EQUAL(force.getSoluteDielectric(), force2.getSoluteDielectric());
+    ASSERT_EQUAL(force.getSolventDielectric(), force2.getSolventDielectric());
+    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        double charge1, radius1, scale1;
+        double charge2, radius2, scale2;
+        force.getParticleParameters(i, charge1, radius1, scale1);
+        force2.getParticleParameters(i, charge2, radius2, scale2);
+        ASSERT_EQUAL(charge1, charge2);
+        ASSERT_EQUAL(radius1, radius2);
+        ASSERT_EQUAL(scale1, scale2);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

serialization/tests/TestSerializeHarmonicAngleForce.cpp

@@ -53,7 +53,7 @@ void testSerialization() {
     XmlSerializer::serialize<HarmonicAngleForce>(&force, "Force", buffer);
     HarmonicAngleForce* copy = XmlSerializer::deserialize<HarmonicAngleForce>(buffer);
 
-    // Compare the two systems to see if they are identical.
+    // Compare the two forces to see if they are identical.
 
     HarmonicAngleForce& force2 = *copy;
     ASSERT_EQUAL(force.getNumAngles(), force2.getNumAngles());
@@ -61,7 +61,7 @@ void testSerialization() {
         int a1, a2, a3, b1, b2, b3;
         double da, db, ka, kb;
         force.getAngleParameters(i, a1, a2, a3, da, ka);
-        force.getAngleParameters(i, b1, b2, b3, db, kb);
+        force2.getAngleParameters(i, b1, b2, b3, db, kb);
         ASSERT_EQUAL(a1, b1);
         ASSERT_EQUAL(a2, b2);
         ASSERT_EQUAL(a3, b3);