Classes for FreeEnergy plugin serialization

plugins/freeEnergy/CMakeLists.txt

@@ -190,6 +190,11 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
   SET (TEST_PATH .)
 ENDIF (EXECUTABLE_OUTPUT_PATH)
 
+IF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
+    ADD_SUBDIRECTORY(serialization)
+ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
+
+
 #INCLUDE(ApiDoxygen.cmake)
 
 #ADD_SUBDIRECTORY(tests)

plugins/freeEnergy/serialization/CMakeLists.txt

+#---------------------------------------------------
+# freeEnergy Serialization Library
+#
+# Creates freeEnergy serializatin library, base name=freeEnergySerialization.
+# Default libraries are shared & optimized. Variants
+# are created for static (_static) and debug (_d).
+#
+# Windows:
+#   freeEnergySerialization[_d].dll
+#   freeEnergySerialization[_d].lib
+# Unix:
+#   libfreeEnergySerialization[_d].so
+#----------------------------------------------------
+
+# The source is organized into subdirectories, but we handle them all from
+# this CMakeLists file rather than letting CMake visit them as SUBDIRS.
+SET(OPENMM_SOURCE_SUBDIRS . ../../../serialization)
+SET(OPENMM_FREE_ENERGY_SOURCE_SUBDIRS . )
+
+# Collect up information about the version of the OpenMM library we're building
+# and make it available to the code so it can be built into the binaries.
+
+SET(OPENMM_FREE_ENERGY_LIBRARY_NAME OpenMMFreeEnergy )
+SET(OPENMM_SERIALIZATION_LIBRARY_NAME OpenMMSerialization)
+SET(OPENMM_FREE_ENERGY_SERIALIZATION_LIBRARY_NAME FreeEnergySerialization)
+
+# Ensure that debug libraries have "_d" appended to their names.
+# CMake gets this right on Windows automatically with this definition.
+IF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+    SET(CMAKE_DEBUG_POSTFIX "_d" CACHE INTERNAL "" FORCE)
+ENDIF (${CMAKE_GENERATOR} MATCHES "Visual Studio")
+
+# But on Unix or Cygwin we have to add the suffix manually
+IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+    SET(OPENMM_FREE_ENERGY_LIBRARY_NAME ${OPENMM_FREE_ENERGY_LIBRARY_NAME}_d)
+    SET(OPENMM_SERIALIZATION_LIBRARY_NAME ${OPENMM_SERIALIZATION_LIBRARY_NAME}_d)
+    SET(OPENMM_FREE_ENERGY_SERIALIZATION_LIBRARY_NAME ${OPENMM_FREE_ENERGY_SERIALIZATION_LIBRARY_NAME}_d)
+ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
+
+# These are all the places to search for header files which are
+# to be part of the API.
+SET(API_INCLUDE_DIRS) # start empty
+FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
+    # append
+    SET(API_INCLUDE_DIRS ${API_INCLUDE_DIRS}
+                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include
+                         ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include/internal)
+ENDFOREACH(subdir)
+
+# We'll need both *relative* path names, starting with their API_INCLUDE_DIRS,
+# and absolute pathnames.
+SET(API_REL_INCLUDE_FILES)   # start these out empty
+SET(API_ABS_INCLUDE_FILES)
+
+FOREACH(dir ${API_INCLUDE_DIRS})
+    FILE(GLOB fullpaths ${dir}/*.h)	# returns full pathnames
+    SET(API_ABS_INCLUDE_FILES ${API_ABS_INCLUDE_FILES} ${fullpaths})
+
+    FOREACH(pathname ${fullpaths})
+        GET_FILENAME_COMPONENT(filename ${pathname} NAME)
+        SET(API_REL_INCLUDE_FILES ${API_REL_INCLUDE_FILES} ${dir}/${filename})
+    ENDFOREACH(pathname)
+ENDFOREACH(dir)
+
+# collect up source files
+SET(SOURCE_FILES) # empty
+SET(SOURCE_INCLUDE_FILES)
+
+FOREACH(subdir ${OPENMM_FREE_ENERGY_SOURCE_SUBDIRS})
+    FILE(GLOB_RECURSE src_files   ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.cpp  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.c)
+    FILE(GLOB incl_files  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.h  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/src/*.hpp)
+    SET(SOURCE_FILES         ${SOURCE_FILES}         ${src_files})   #append
+    SET(SOURCE_INCLUDE_FILES ${SOURCE_INCLUDE_FILES} ${incl_files})
+    INCLUDE_DIRECTORIES(BEFORE  ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
+    INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../../serialization/${subdir}/include)
+ENDFOREACH(subdir)
+#Message( "API_REL_INCLUDE_FILES=${API_REL_INCLUDE_FILES}\n" )
+
+INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src )
+
+# Create the library
+ADD_LIBRARY(${OPENMM_FREE_ENERGY_SERIALIZATION_LIBRARY_NAME} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
+TARGET_LINK_LIBRARIES(${OPENMM_FREE_ENERGY_SERIALIZATION_LIBRARY_NAME} ${OPENMM_FREE_ENERGY_LIBRARY_NAME} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${SHARED_TARGET})
+SET_TARGET_PROPERTIES(${OPENMM_FREE_ENERGY_SERIALIZATION_LIBRARY_NAME} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL -DIEEE_8087")
+INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${OPENMM_FREE_ENERGY_SERIALIZATION_LIBRARY_NAME})
+
+ADD_SUBDIRECTORY(tests)

plugins/freeEnergy/serialization/include/openmm/serialization/FreeEnergyGBSAOBCSoftcoreForceProxy.h

+#ifndef OPENMM_FREE_ENERGY_GBSAOBC_SOFTCORE_FORCE_PROXY_H_
+#define OPENMM_FREE_ENERGY_GBSAOBC_SOFTCORE_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 PROSAOBCDED "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 GBSAOBCSoftcoreForce objects.
+ */
+
+class OPENMM_EXPORT GBSAOBCSoftcoreForceProxy : public SerializationProxy {
+public:
+    GBSAOBCSoftcoreForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_FREE_ENERGY_GBSAOBC_SOFTCORE_FORCE_PROXY_H_*/

plugins/freeEnergy/serialization/include/openmm/serialization/FreeEnergyGBVISoftcoreForceProxy.h

+#ifndef OPENMM_FREE_ENERGY_GBVI_SOFTCORE_FORCE_PROXY_H_
+#define OPENMM_FREE_ENERGY_GBVI_SOFTCORE_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 GBVISoftcoreForce objects.
+ */
+
+class OPENMM_EXPORT GBVISoftcoreForceProxy : public SerializationProxy {
+public:
+    GBVISoftcoreForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_FREE_ENERGY_GBVI_SOFTCORE_FORCE_PROXY_H_*/

plugins/freeEnergy/serialization/include/openmm/serialization/FreeEnergyNonbondedSoftcoreForceProxy.h

+#ifndef OPENMM_FREE_ENERGY_NONBONDED_SOFTCORE_FORCE_PROXY_H_
+#define OPENMM_FREE_ENERGY_NONBONDED_SOFTCORE_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 NonbondedSoftcoreForceProxy : public SerializationProxy {
+public:
+    NonbondedSoftcoreForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_FREE_ENERGY_NONBONDED_SOFTCORE_FORCE_PROXY_H_*/

plugins/freeEnergy/serialization/src/FreeEnergyGBSAOBCSoftcoreProxy.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/FreeEnergyGBSAOBCSoftcoreForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/GBSAOBCSoftcoreForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+GBSAOBCSoftcoreForceProxy::GBSAOBCSoftcoreForceProxy() : SerializationProxy("GBSAOBCSoftcoreForce") {
+}
+
+void GBSAOBCSoftcoreForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const GBSAOBCSoftcoreForce& force = *reinterpret_cast<const GBSAOBCSoftcoreForce*>(object);
+    //node.setIntProperty("method", (int) force.getNonbondedMethod());
+    //node.setDoubleProperty("cutoff", force.getCutoffDistance());
+    node.setDoubleProperty("soluteDielectric", force.getSoluteDielectric());
+    node.setDoubleProperty("solventDielectric", force.getSolventDielectric());
+    node.setDoubleProperty("nonPolarPrefactor", force.getNonPolarPrefactor());
+    SerializationNode& particles = node.createChildNode("Particles");
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        double charge, radius, scale, nonPolarScalingFactor;
+        force.getParticleParameters(i, charge, radius, scale, nonPolarScalingFactor);
+        particles.createChildNode("Particle").setDoubleProperty("q", charge).setDoubleProperty("r", radius).setDoubleProperty("scale", scale).setDoubleProperty("nonPolarScalingFactor", nonPolarScalingFactor);
+    }
+}
+
+void* GBSAOBCSoftcoreForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    GBSAOBCSoftcoreForce* force = new GBSAOBCSoftcoreForce();
+    try {
+        //force->setNonbondedMethod((GBSAOBCSoftcoreForce::NonbondedMethod) node.getIntProperty("method"));
+        //force->setCutoffDistance(node.getDoubleProperty("cutoff"));
+        force->setSoluteDielectric(node.getDoubleProperty("soluteDielectric"));
+        force->setSolventDielectric(node.getDoubleProperty("solventDielectric"));
+        force->setNonPolarPrefactor(node.getDoubleProperty("nonPolarPrefactor"));
+        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"), particle.getDoubleProperty("nonPolarScalingFactor"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/freeEnergy/serialization/src/FreeEnergyGBVISoftcoreProxy.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/FreeEnergyGBVISoftcoreForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/GBVISoftcoreForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+GBVISoftcoreForceProxy::GBVISoftcoreForceProxy() : SerializationProxy("GBVISoftcoreForce") {
+}
+
+void GBVISoftcoreForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const GBVISoftcoreForce& force = *reinterpret_cast<const GBVISoftcoreForce*>(object);
+    node.setIntProperty("method", (int) force.getNonbondedMethod());
+    node.setIntProperty("brScaleMethod", (int) force.getBornRadiusScalingMethod());
+    node.setDoubleProperty("cutoff", force.getCutoffDistance());
+    node.setDoubleProperty("soluteDielectric", force.getSoluteDielectric());
+    node.setDoubleProperty("solventDielectric", force.getSolventDielectric());
+    node.setDoubleProperty("quinticLwrLmtFctr", force.getQuinticLowerLimitFactor());
+    node.setDoubleProperty("quinticUpprBrLmt", force.getQuinticUpperBornRadiusLimit());
+    double alpha, beta, gamma;
+    force.getTanhParameters( alpha, beta, gamma );
+    node.setDoubleProperty("alphaT", alpha);
+    node.setDoubleProperty("betaT", beta);
+    node.setDoubleProperty("gammaT", gamma);
+    SerializationNode& particles = node.createChildNode("Particles");
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        double charge, radius, gamma, bornRadiusScaleFactor;
+        force.getParticleParameters(i, charge, radius, gamma, bornRadiusScaleFactor);
+        particles.createChildNode("Particle").setDoubleProperty("q", charge).setDoubleProperty("r", radius).setDoubleProperty("gamma", gamma).setDoubleProperty("bRSclFctr", bornRadiusScaleFactor);
+    }
+    SerializationNode& bonds = node.createChildNode("Bonds");
+    for (int i = 0; i < force.getNumBonds(); i++) {
+        int particle1, particle2;
+        double distance;
+        force.getBondParameters(i, particle1, particle2, distance);
+        bonds.createChildNode("Bond").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setDoubleProperty("d", distance);
+    }
+}
+
+void* GBVISoftcoreForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    GBVISoftcoreForce* force = new GBVISoftcoreForce();
+    try {
+        force->setNonbondedMethod((GBVISoftcoreForce::NonbondedSoftcoreMethod) node.getIntProperty("method"));
+        force->setBornRadiusScalingMethod((GBVISoftcoreForce::BornRadiusScalingSoftcoreMethod) node.getIntProperty("brScaleMethod"));
+        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
+        force->setSoluteDielectric(node.getDoubleProperty("soluteDielectric"));
+        force->setSolventDielectric(node.getDoubleProperty("solventDielectric"));
+        force->setQuinticLowerLimitFactor(node.getDoubleProperty("quinticLwrLmtFctr"));
+        force->setQuinticUpperBornRadiusLimit(node.getDoubleProperty("quinticUpprBrLmt"));
+        double alpha, beta, gamma;
+        alpha  = node.getDoubleProperty("alphaT");
+        beta   = node.getDoubleProperty("betaT");
+        gamma  = node.getDoubleProperty("gammaT");
+        force->setTanhParameters( alpha, beta, gamma );
+        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("gamma"), particle.getDoubleProperty("bRSclFctr"));
+        }
+        const SerializationNode& bonds = node.getChildNode("Bonds");
+        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
+            const SerializationNode& bond = bonds.getChildren()[i];
+            force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getDoubleProperty("d"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/freeEnergy/serialization/src/FreeEnergyNonbondedSoftcoreForceProxy.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/FreeEnergyNonbondedSoftcoreForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/NonbondedSoftcoreForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+NonbondedSoftcoreForceProxy::NonbondedSoftcoreForceProxy() : SerializationProxy("NonbondedSoftcoreForce") {
+}
+
+void NonbondedSoftcoreForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const NonbondedSoftcoreForce& force = *reinterpret_cast<const NonbondedSoftcoreForce*>(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, softcoreLJLambda;
+        force.getParticleParameters(i, charge, sigma, epsilon, softcoreLJLambda);
+        particles.createChildNode("Particle").setDoubleProperty("q", charge).setDoubleProperty("sig", sigma).setDoubleProperty("eps", epsilon).setDoubleProperty("lambda", softcoreLJLambda);
+    }
+    SerializationNode& exceptions = node.createChildNode("Exceptions");
+    for (int i = 0; i < force.getNumExceptions(); i++) {
+        int particle1, particle2;
+        double chargeProd, sigma, epsilon, softcoreLJLambda;
+        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).setDoubleProperty("lambda", softcoreLJLambda);
+    }
+}
+
+void* NonbondedSoftcoreForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    NonbondedSoftcoreForce* force = new NonbondedSoftcoreForce();
+    try {
+        force->setNonbondedMethod((NonbondedSoftcoreForce::NonbondedSoftcoreMethod) 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"), particle.getDoubleProperty("lambda"));
+        }
+        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.getIntProperty("p1"), exception.getIntProperty("p2"), exception.getDoubleProperty("q"), exception.getDoubleProperty("sig"), exception.getDoubleProperty("eps"), exception.getDoubleProperty("lambda"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/freeEnergy/serialization/src/FreeEnergySerializationProxyRegistration.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.                                     *
+ * -------------------------------------------------------------------------- */
+
+#ifdef WIN32
+#include <windows.h>
+#include <sstream>
+#else
+#include <dlfcn.h>
+#include <dirent.h>
+#include <cstdlib>
+#endif
+
+#include "openmm/OpenMMException.h"
+
+#include "openmm/NonbondedSoftcoreForce.h"
+#include "openmm/GBVISoftcoreForce.h"
+#include "openmm/GBSAOBCSoftcoreForce.h"
+
+#include "openmm/serialization/SerializationProxy.h"
+#include "openmm/serialization/FreeEnergyNonbondedSoftcoreForceProxy.h"
+#include "openmm/serialization/FreeEnergyGBSAOBCSoftcoreForceProxy.h"
+#include "openmm/serialization/FreeEnergyGBVISoftcoreForceProxy.h"
+
+#if defined(WIN32)
+    #include <windows.h>
+    extern "C" void registerFreeEnergySerializationProxies();
+    BOOL WINAPI DllMain(HANDLE hModule, DWORD  ul_reason_for_call, LPVOID lpReserved) {
+        if (ul_reason_for_call == DLL_PROCESS_ATTACH)
+            registerFreeEnergySerializationProxies();
+        return TRUE;
+    }
+#else
+    extern "C" void __attribute__((constructor)) registerFreeEnergySerializationProxies();
+#endif
+
+using namespace OpenMM;
+
+extern "C" void registerFreeEnergySerializationProxies() {
+    SerializationProxy::registerProxy(typeid(NonbondedSoftcoreForce), new NonbondedSoftcoreForceProxy());
+    SerializationProxy::registerProxy(typeid(GBSAOBCSoftcoreForce), new GBSAOBCSoftcoreForceProxy());
+    SerializationProxy::registerProxy(typeid(GBVISoftcoreForce), new GBVISoftcoreForceProxy());
+}

plugins/freeEnergy/serialization/tests/CMakeLists.txt

+#
+# Testing
+#
+
+ENABLE_TESTING()
+
+# Automatically create tests using files named "Test*.cpp"
+FILE(GLOB TEST_PROGS "*Test*.cpp")
+FOREACH(TEST_PROG ${TEST_PROGS})
+    GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
+
+    # All tests use shared libraries
+    ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
+    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${OPENMM_SERIALIZATION_LIBRARY_NAME} ${OPENMM_FREE_ENERGY_SERIALIZATION_LIBRARY_NAME} ${OPENMM_FREE_ENERGY_LIBRARY_NAME})
+    ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
+
+ENDFOREACH(TEST_PROG ${TEST_PROGS})

plugins/freeEnergy/serialization/tests/TestSerializeFreeEnergyGBSAOBCSoftcoreForce.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/GBSAOBCSoftcoreForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+
+    // Create a Force.
+
+    GBSAOBCSoftcoreForce force;
+    //force.setNonbondedMethod(GBSAOBCSoftcoreForce::CutoffPeriodic);
+    //force.setCutoffDistance(2.0);
+    force.setSoluteDielectric(5.1);
+    force.setSolventDielectric(50.0);
+    force.setNonPolarPrefactor(5.0);
+    force.addParticle(1, 0.1, 0.01, 0.5);
+    force.addParticle(0.5, 0.2, 0.02, 1.0);
+    force.addParticle(-0.5, 0.3, 0.03, 1.1);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<GBSAOBCSoftcoreForce>(&force, "Force", buffer);
+    GBSAOBCSoftcoreForce* copy = XmlSerializer::deserialize<GBSAOBCSoftcoreForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    GBSAOBCSoftcoreForce& 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.getNonPolarPrefactor(), force2.getNonPolarPrefactor());
+    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        double charge1, radius1, scale1, nonPolarScalingFactor1;
+        double charge2, radius2, scale2, nonPolarScalingFactor2;
+        force.getParticleParameters(i, charge1, radius1, scale1, nonPolarScalingFactor1);
+        force2.getParticleParameters(i, charge2, radius2, scale2, nonPolarScalingFactor2);
+        ASSERT_EQUAL(charge1, charge2);
+        ASSERT_EQUAL(radius1, radius2);
+        ASSERT_EQUAL(scale1, scale2);
+        ASSERT_EQUAL(nonPolarScalingFactor1, nonPolarScalingFactor2);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

plugins/freeEnergy/serialization/tests/TestSerializeFreeEnergyGBVISoftcoreForce.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/GBVISoftcoreForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    GBVISoftcoreForce force;
+    force.setNonbondedMethod(GBVISoftcoreForce::CutoffPeriodic);
+    force.setBornRadiusScalingMethod(GBVISoftcoreForce::QuinticSpline);
+    force.setCutoffDistance(2.0);
+    force.setSoluteDielectric(5.1);
+    force.setSolventDielectric(50.0);
+    force.setQuinticLowerLimitFactor(0.1);
+    force.setQuinticUpperBornRadiusLimit(5.1);
+    force.setTanhParameters(5.1, 4.2, 1.3);
+    
+    force.addParticle(1, 0.1, 0.01, 0.1);
+    force.addParticle(0.5, 0.2, 0.02, 0.2);
+    force.addParticle(-0.5, 0.3, 0.03, 0.3);
+    force.addBond(0, 1, 2.0);
+    force.addBond(3, 5, 1.2);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<GBVISoftcoreForce>(&force, "Force", buffer);
+    GBVISoftcoreForce* copy = XmlSerializer::deserialize<GBVISoftcoreForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    GBVISoftcoreForce& 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.getQuinticLowerLimitFactor(), force2.getQuinticLowerLimitFactor());
+    ASSERT_EQUAL(force.getQuinticUpperBornRadiusLimit(), force2.getQuinticUpperBornRadiusLimit());
+    ASSERT_EQUAL(force.getBornRadiusScalingMethod(), force2.getBornRadiusScalingMethod());
+    double alpha1, beta1, gamma1;
+    double alpha2, beta2, gamma2;
+    force.getTanhParameters( alpha1, beta1, gamma1 );
+    force2.getTanhParameters( alpha2, beta2, gamma2 );
+    ASSERT_EQUAL(alpha1, alpha2);
+    ASSERT_EQUAL(beta1, beta2);
+    ASSERT_EQUAL(gamma1, gamma2);
+    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        double charge1, radius1, scale1, bornRadiusScaleFactor1;
+        double charge2, radius2, scale2, bornRadiusScaleFactor2;
+        force.getParticleParameters(i, charge1, radius1, scale1, bornRadiusScaleFactor1);
+        force2.getParticleParameters(i, charge2, radius2, scale2, bornRadiusScaleFactor2);
+        ASSERT_EQUAL(charge1, charge2);
+        ASSERT_EQUAL(radius1, radius2);
+        ASSERT_EQUAL(scale1, scale2);
+        ASSERT_EQUAL(bornRadiusScaleFactor1, bornRadiusScaleFactor2);
+    }
+    ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
+    for (int i = 0; i < force.getNumBonds(); i++) {
+        int a1, a2, b1, b2;
+        double da, db;
+        force.getBondParameters(i, a1, a2, da);
+        force2.getBondParameters(i, b1, b2, db);
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(da, db);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}

plugins/freeEnergy/serialization/tests/TestSerializeFreeEnergyNonbondedSoftcoreForce.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/NonbondedSoftcoreForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+
+    // Create a Force.
+
+    NonbondedSoftcoreForce force;
+    force.setNonbondedMethod(NonbondedSoftcoreForce::CutoffPeriodic);
+    force.setCutoffDistance(2.0);
+    force.setEwaldErrorTolerance(1e-3);
+    force.setReactionFieldDielectric(50.0);
+    //force.setUseDispersionCorrection(false);
+    force.addParticle(1, 0.1, 0.01);
+    force.addParticle(0.5, 0.2, 0.02);
+    force.addParticle(-0.5, 0.3, 0.03);
+    force.addException(0, 1, 2, 0.5, 0.1);
+    force.addException(1, 2, 0.2, 0.4, 0.2);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<NonbondedSoftcoreForce>(&force, "Force", buffer);
+    NonbondedSoftcoreForce* copy = XmlSerializer::deserialize<NonbondedSoftcoreForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    NonbondedSoftcoreForce& force2 = *copy;
+    ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
+    ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
+    ASSERT_EQUAL(force.getEwaldErrorTolerance(), force2.getEwaldErrorTolerance());
+    ASSERT_EQUAL(force.getReactionFieldDielectric(), force2.getReactionFieldDielectric());
+    //ASSERT_EQUAL(force.getUseDispersionCorrection(), force2.getUseDispersionCorrection());
+    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        double charge1, sigma1, epsilon1, lambda1;
+        double charge2, sigma2, epsilon2, lambda2;
+        force.getParticleParameters(i, charge1, sigma1, epsilon1, lambda1);
+        force2.getParticleParameters(i, charge2, sigma2, epsilon2, lambda2);
+        ASSERT_EQUAL(charge1, charge2);
+        ASSERT_EQUAL(sigma1, sigma2);
+        ASSERT_EQUAL(epsilon1, epsilon2);
+        ASSERT_EQUAL(lambda1, lambda2);
+    }
+    ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
+    for (int i = 0; i < force.getNumExceptions(); i++) {
+        int a1, a2, b1, b2;
+        double charge1, sigma1, epsilon1, lambda1;
+        double charge2, sigma2, epsilon2, lambda2;
+        force.getExceptionParameters(i, a1, b1, charge1, sigma1, epsilon1, lambda1);
+        force2.getExceptionParameters(i, a2, b2, charge2, sigma2, epsilon2, lambda2);
+        ASSERT_EQUAL(a1, a2);
+        ASSERT_EQUAL(b1, b2);
+        ASSERT_EQUAL(charge1, charge2);
+        ASSERT_EQUAL(sigma1, sigma2);
+        ASSERT_EQUAL(epsilon1, epsilon2);
+        ASSERT_EQUAL(lambda1, lambda2);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}