More serialization proxies and associated tests

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

+#ifndef OPENMM_AMOEBA_TORSION_TORSION_FORCE_PROXY_H_
+#define OPENMM_AMOEBA_TORSION_TORSION_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 AmoebaTorsionTorsionForce objects.
+ */
+
+class OPENMM_EXPORT AmoebaTorsionTorsionForceProxy : public SerializationProxy {
+public:
+    AmoebaTorsionTorsionForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_AMOEBA_TORSION_TORSION_FORCE_PROXY_H_*/

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

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

plugins/amoeba/serialization/src/AmoebaSerializationProxyRegistration.cpp

@@ -45,6 +45,8 @@
 #include "openmm/AmoebaOutOfPlaneBendForce.h"
 #include "openmm/AmoebaPiTorsionForce.h"
 #include "openmm/AmoebaTorsionForce.h"
+#include "openmm/AmoebaTorsionTorsionForce.h"
+#include "openmm/AmoebaUreyBradleyForce.h"
 
 #include "openmm/serialization/SerializationProxy.h"
 #include "openmm/serialization/AmoebaHarmonicBondForceProxy.h"
@@ -53,6 +55,8 @@
 #include "openmm/serialization/AmoebaOutOfPlaneBendForceProxy.h"
 #include "openmm/serialization/AmoebaPiTorsionForceProxy.h"
 #include "openmm/serialization/AmoebaTorsionForceProxy.h"
+#include "openmm/serialization/AmoebaTorsionTorsionForceProxy.h"
+#include "openmm/serialization/AmoebaUreyBradleyForceProxy.h"
 
 #if defined(WIN32)
     #include <windows.h>
@@ -101,4 +105,6 @@ extern "C" void registerAmoebaSerializationProxies() {
     SerializationProxy::registerProxy(typeid(AmoebaOutOfPlaneBendForce), new AmoebaOutOfPlaneBendForceProxy());
     SerializationProxy::registerProxy(typeid(AmoebaPiTorsionForce), new AmoebaPiTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(AmoebaTorsionForce), new AmoebaTorsionForceProxy());
+    SerializationProxy::registerProxy(typeid(AmoebaTorsionTorsionForce), new AmoebaTorsionTorsionForceProxy());
+    SerializationProxy::registerProxy(typeid(AmoebaUreyBradleyForce), new AmoebaUreyBradleyForceProxy());
 }

plugins/amoeba/serialization/src/AmoebaTorsionForceProxy.cpp

@@ -41,15 +41,17 @@ using namespace std;
 AmoebaTorsionForceProxy::AmoebaTorsionForceProxy() : SerializationProxy("AmoebaTorsionForce") {
 }
 
-static void addTorsionValues( SerializationNode& torsion, std::vector<double>& torsionValues ){
+static void addTorsionValues( SerializationNode& torsion, const std::vector<double>& torsionValues ){
     for (int j = 0; j < torsionValues.size(); j++) {
         torsion.createChildNode("Value").setDoubleProperty("v", torsionValues[j]);
     }
 }
 
 static void loadTorsionValues( SerializationNode& torsion, std::vector<double>& torsionValues ){
-    for (int j = 0; j < torsionValues.size(); j++) {
-        torsion.createChildNode("Value").setDoubleProperty("v", torsionValues[j]);
+    int size = torsion.getIntProperty("size");
+    torsionValues.resize(size);
+    for (int j = 0; j < size; j++) {
+        torsionValues[j] = ( torsion.getChildren()[j].getDoubleProperty("v") );
     }
 }
 
@@ -58,39 +60,54 @@ void AmoebaTorsionForceProxy::serialize(const void* object, SerializationNode& n
     const AmoebaTorsionForce& force = *reinterpret_cast<const AmoebaTorsionForce*>(object);
     SerializationNode& bonds = node.createChildNode("Torsion");
     for (int i = 0; i < force.getNumTorsions(); i++) {
+
         int particle1, particle2, particle3, particle4;
         std::vector<double> torsion1;
         std::vector<double> torsion2;
         std::vector<double> torsion3;
         force.getTorsionParameters(i, particle1, particle2, particle3, particle4, torsion1, torsion2, torsion3);
-        bonds.createChildNode("Torsion").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4);
-        SerializationNode& torsion = bonds.createChildNode("Torsion1").setIntProperty("size", torsion1.size());
-        addTorsionValues( torsion, torsion1 );
-        torsion = bonds.createChildNode("Torsion2").setIntProperty("size", torsion2.size());
-        addTorsionValues( torsion, torsion2 );
-        torsion = bonds.createChildNode("Torsion3").setIntProperty("size", torsion3.size());
-        addTorsionValues( torsion, torsion3 );
+
+        SerializationNode& torsionBond        = bonds.createChildNode("Torsion");
+        torsionBond.setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4);
+
+        SerializationNode& torsionVector1     = torsionBond.createChildNode("Torsion1").setIntProperty("size", torsion1.size());
+        addTorsionValues( torsionVector1, torsion1 );
+
+        SerializationNode& torsionVector2     = torsionBond.createChildNode("Torsion2").setIntProperty("size", torsion2.size());
+        addTorsionValues( torsionVector2, torsion2 );
+
+        SerializationNode& torsionVector3     = torsionBond.createChildNode("Torsion3").setIntProperty("size", torsion3.size());
+        addTorsionValues( torsionVector3, torsion3 );
     }
 }
 
 void* AmoebaTorsionForceProxy::deserialize(const SerializationNode& node) const {
+
     if (node.getIntProperty("version") != 1)
         throw OpenMMException("Unsupported version number");
+
     AmoebaTorsionForce* force = new AmoebaTorsionForce();
-/*
     try {
         const SerializationNode& bonds     = node.getChildNode("Torsion");
-        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
-            const SerializationNode& bond = bonds.getChildren()[i];
-            //force->addTorsion(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"),  bond.getIntProperty("p4") );
-            std::vector<double> torsion1, std::vector<double> torsion2, std::vector<double> torsion3;
-            const SerializationNode& torsion = bond.getChildNode("Torsion1");
+        vector<SerializationNode> children = bonds.getChildren();
+        for (unsigned int i = 0; i < children.size(); i++) {
+            SerializationNode& bond = children[i];
+            std::vector<double> torsion1;
+            std::vector<double> torsion2;
+            std::vector<double> torsion3;
+            SerializationNode& torsionNode1 = bond.getChildNode("Torsion1");
+            loadTorsionValues( torsionNode1, torsion1 );
+            SerializationNode& torsionNode2 = bond.getChildNode("Torsion2");
+            loadTorsionValues( torsionNode2, torsion2 );
+            SerializationNode& torsionNode3 = bond.getChildNode("Torsion3");
+            loadTorsionValues( torsionNode3, torsion3 );
+            force->addTorsion(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"),  bond.getIntProperty("p4"), torsion1, torsion2, torsion3 );
         }
     }
     catch (...) {
         delete force;
         throw;
     }
-*/
+
     return force;
 }

plugins/amoeba/serialization/src/AmoebaTorsionTorsionForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/AmoebaTorsionTorsionForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/AmoebaTorsionTorsionForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+AmoebaTorsionTorsionForceProxy::AmoebaTorsionTorsionForceProxy() : SerializationProxy("AmoebaTorsionTorsionForce") {
+}
+
+static void loadGrid( const SerializationNode& grid, std::vector< std::vector< std::vector<double> > >& gridVector ){
+
+    const std::vector<SerializationNode>& gridSerializationRows  = grid.getChildren();
+    gridVector.resize( gridSerializationRows.size() );
+
+    for( unsigned int ii = 0; ii < gridSerializationRows.size(); ii++) {
+        const std::vector<SerializationNode>& gridSerializationColumns  = gridSerializationRows[ii].getChildren();
+        gridVector[ii].resize( gridSerializationColumns.size() );
+        for( unsigned int jj = 0; jj < gridSerializationColumns.size(); jj++) {
+            const SerializationNode& gridSerializationColumnNode = gridSerializationColumns[jj];
+            gridVector[ii][jj].resize( 6 );
+            gridVector[ii][jj][0] = gridSerializationColumnNode.getDoubleProperty( "x" );
+            gridVector[ii][jj][1] = gridSerializationColumnNode.getDoubleProperty( "y" );
+            gridVector[ii][jj][2] = gridSerializationColumnNode.getDoubleProperty( "f" );
+            gridVector[ii][jj][3] = gridSerializationColumnNode.getDoubleProperty( "fx" );
+            gridVector[ii][jj][4] = gridSerializationColumnNode.getDoubleProperty( "fy" );
+            gridVector[ii][jj][5] = gridSerializationColumnNode.getDoubleProperty( "fxy" );
+        }
+    }
+}
+
+void AmoebaTorsionTorsionForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const AmoebaTorsionTorsionForce& force = *reinterpret_cast<const AmoebaTorsionTorsionForce*>(object);
+
+    // grid[xIdx][yIdx][6 values]
+
+    // value0 = x-Grid value
+    // value1 = y-Grid value
+    // value2 = F          function value
+    // value3 = F_x        partial f wrt x
+    // value4 = F_y        partial f wrt y
+    // value5 = F_xy       partial f wrt x,y
+
+    SerializationNode& grids = node.createChildNode("TorsionTorsionGrids");
+    grids.setIntProperty("size", static_cast<int>(force.getNumTorsionTorsionGrids()));
+    for (int i = 0; i < force.getNumTorsionTorsionGrids(); i++) {
+
+        const std::vector< std::vector< std::vector<double> > > grid = force.getTorsionTorsionGrid( i );
+
+        unsigned int gridCount = 0;
+        unsigned int gridYsize =  grid[0].size();
+        for ( unsigned int ii = 0; ii < grid.size(); ii++) {
+            gridCount += grid[ii].size();
+        }
+
+        SerializationNode& gridNode = grids.createChildNode("TorsionTorsionGrid").setIntProperty("size", static_cast<int>(gridCount) );
+        for ( unsigned int ii = 0; ii < grid.size(); ii++) {
+            SerializationNode& gridSerializationRow = gridNode.createChildNode("RowNode");
+            gridSerializationRow.setIntProperty("dim", ii );
+            gridSerializationRow.setIntProperty("size", static_cast<int>(grid[ii].size() ) );
+            for ( unsigned int jj = 0; jj < grid[ii].size(); jj++) {
+                SerializationNode& gridSerializationColumnNode = gridSerializationRow.createChildNode("ColumnNode");
+                gridSerializationColumnNode.setIntProperty("dim", jj );
+                unsigned int index = 0;
+                gridSerializationColumnNode.setDoubleProperty("x",   grid[ii][jj][index++] );
+                gridSerializationColumnNode.setDoubleProperty("y",   grid[ii][jj][index++] );
+                gridSerializationColumnNode.setDoubleProperty("f",   grid[ii][jj][index++] );
+                gridSerializationColumnNode.setDoubleProperty("fx",  grid[ii][jj][index++] );
+                gridSerializationColumnNode.setDoubleProperty("fy",  grid[ii][jj][index++] );
+                gridSerializationColumnNode.setDoubleProperty("fxy", grid[ii][jj][index++] );
+            }
+        }
+    }
+
+    SerializationNode& bonds = node.createChildNode("TorsionTorsion");
+    for (int i = 0; i < force.getNumTorsionTorsions(); i++) {
+        int particle1, particle2, particle3, particle4, particle5;
+        int chiralCheckAtomIndex, gridIndex;
+        force.getTorsionTorsionParameters(i, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex );
+        bonds.createChildNode("TorsionTorsion").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setIntProperty("p3", particle3).setIntProperty("p4", particle4).setIntProperty("p5", particle5).setIntProperty("chiralCheckAtomIndex", chiralCheckAtomIndex).setIntProperty("gridIndex", gridIndex );
+
+    }
+}
+
+void* AmoebaTorsionTorsionForceProxy::deserialize(const SerializationNode& node) const {
+
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+
+    AmoebaTorsionTorsionForce* force = new AmoebaTorsionTorsionForce();
+    try {
+
+        const SerializationNode& grids                    = node.getChildNode("TorsionTorsionGrids");
+        const std::vector<SerializationNode>& gridList    = grids.getChildren();
+        for( unsigned int ii = 0; ii < gridList.size(); ii++) {
+            std::vector< std::vector< std::vector<double> > > gridVector;
+            loadGrid( gridList[ii], gridVector );
+            force->setTorsionTorsionGrid( ii, gridVector );
+        }
+
+        const SerializationNode& bonds     = node.getChildNode("TorsionTorsion");
+        vector<SerializationNode> children = bonds.getChildren();
+        for (unsigned int i = 0; i < children.size(); i++) {
+            SerializationNode& bond = children[i];
+            force->addTorsionTorsion(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getIntProperty("p3"),  bond.getIntProperty("p4"), bond.getIntProperty("p5"), bond.getIntProperty("chiralCheckAtomIndex"), bond.getIntProperty("gridIndex"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/amoeba/serialization/src/AmoebaUreyBradleyForceProxy.cpp

+/* -------------------------------------------------------------------------- *
+ *                                OpenMMAmoeba                                *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2010 Stanford University and the Authors.           *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/serialization/AmoebaUreyBradleyForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/AmoebaUreyBradleyForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+AmoebaUreyBradleyForceProxy::AmoebaUreyBradleyForceProxy() : SerializationProxy("AmoebaUreyBradleyForce") {
+}
+
+void AmoebaUreyBradleyForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const AmoebaUreyBradleyForce& force = *reinterpret_cast<const AmoebaUreyBradleyForce*>(object);
+    node.setDoubleProperty("UreyBradleyCubic", force.getAmoebaGlobalUreyBradleyCubic());
+    node.setDoubleProperty("UreyBradleyQuartic", force.getAmoebaGlobalUreyBradleyQuartic());
+    SerializationNode& bonds = node.createChildNode("Bonds");
+    for (int i = 0; i < force.getNumInteractions(); i++) {
+        int particle1, particle2;
+        double distance, k;
+        force.getUreyBradleyParameters(i, particle1, particle2, distance, k);
+        bonds.createChildNode("Bond").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setDoubleProperty("d", distance).setDoubleProperty("k", k);
+    }
+}
+
+void* AmoebaUreyBradleyForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    AmoebaUreyBradleyForce* force = new AmoebaUreyBradleyForce();
+    try {
+        force->setAmoebaGlobalUreyBradleyCubic(node.getDoubleProperty("UreyBradleyCubic"));
+        force->setAmoebaGlobalUreyBradleyQuartic(node.getDoubleProperty("UreyBradleyQuartic"));
+        const SerializationNode& bonds = node.getChildNode("Bonds");
+        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
+            const SerializationNode& bond = bonds.getChildren()[i];
+            force->addUreyBradley(bond.getIntProperty("p1"), bond.getIntProperty("p2"), bond.getDoubleProperty("d"), bond.getDoubleProperty("k"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionForce.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/AmoebaTorsionForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void loadTorsion( std::vector<double>& torsion, double offset ){
+    torsion.push_back( offset + 1.0 );
+    torsion.push_back( offset + 2.0 );
+//    torsion.push_back( offset + 3.0 );
+//    torsion.push_back( offset + 4.0 );
+}
+
+void compareTorsion( std::vector<double> torsionA, std::vector<double> torsionB ){
+    ASSERT_EQUAL(torsionA.size(), torsionB.size());
+    for (int i = 0; i < torsionA.size(); i++) {
+        ASSERT_EQUAL(torsionA[i], torsionB[i]);
+    }
+}
+
+void testSerialization() {
+    // Create a Force.
+
+    AmoebaTorsionForce force;
+    for( int ii = 0; ii < 5; ii++ ){
+        std::vector<double> torsion1;
+        std::vector<double> torsion2;
+        std::vector<double> torsion3;
+        loadTorsion( torsion1, static_cast<double>(5*ii) + 11.1);
+        loadTorsion( torsion2, static_cast<double>(5*ii) + 21.2);
+        loadTorsion( torsion3, static_cast<double>(5*ii) + 31.3);
+        force.addTorsion( ii, ii+1,ii+3, ii+4, torsion1, torsion2, torsion3 );
+    }
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<AmoebaTorsionForce>(&force, "Force", buffer);
+
+if( 0 ){
+FILE* filePtr = fopen("Torsion.xml", "w" );
+(void) fprintf( filePtr, "%s", buffer.str().c_str() );
+(void) fclose( filePtr );
+}
+
+    AmoebaTorsionForce* copy = XmlSerializer::deserialize<AmoebaTorsionForce>(buffer);
+
+    // Compare the two forces to see if they are identical.  
+    AmoebaTorsionForce& force2 = *copy;
+    ASSERT_EQUAL(force.getNumTorsions(), force2.getNumTorsions());
+    for (int i = 0; i < force.getNumTorsions(); i++) {
+
+        int a1, a2, a3, a4, b1, b2, b3, b4;
+
+        std::vector<double> torsion1a;
+        std::vector<double> torsion2a;
+        std::vector<double> torsion3a;
+        std::vector<double> torsion1b;
+        std::vector<double> torsion2b;
+        std::vector<double> torsion3b;
+
+        force.getTorsionParameters( i, a1, a2, a3, a4, torsion1a, torsion2a, torsion3a);
+        force2.getTorsionParameters( i, b1, b2, b3, b4, torsion1b, torsion2b, torsion3b);
+
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(a3, b3);
+        ASSERT_EQUAL(a4, b4);
+
+        compareTorsion( torsion1a, torsion1b );
+        compareTorsion( torsion2a, torsion2b );
+        compareTorsion( torsion3a, torsion3b );
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+

plugins/amoeba/serialization/tests/TestSerializeAmoebaTorsionTorsionForce.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/AmoebaTorsionTorsionForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+#include <stdlib.h>
+
+using namespace OpenMM;
+using namespace std;
+
+static void loadTorsionTorsionGrid( std::vector< std::vector< std::vector<double> > >& gridVector ){
+ 
+    static const int gridSize = 25;
+    gridVector.resize( gridSize );
+    for( int ii = 0; ii < gridSize; ii++ ){
+        gridVector[ii].resize( gridSize );
+        for( int jj = 0; jj < gridSize; jj++ ){
+            gridVector[ii][jj].resize( 6 );
+            for( int kk = 0; kk < 6; kk++ ){
+                gridVector[ii][jj][0] = -180.0 + 15.0*static_cast<double>(ii);
+                gridVector[ii][jj][1] = -180.0 + 15.0*static_cast<double>(jj);
+                gridVector[ii][jj][2] = static_cast<double>( rand());
+                gridVector[ii][jj][3] = static_cast<double>( rand());
+                gridVector[ii][jj][4] = static_cast<double>( rand());
+                gridVector[ii][jj][5] = static_cast<double>( rand());
+            }
+        }
+     }
+}
+
+static void compareGrids( const std::vector< std::vector< std::vector<double> > >& grid1, const std::vector< std::vector< std::vector<double> > >& grid2 ) {
+
+    ASSERT_EQUAL(grid1.size(), grid2.size());
+    for (int i = 0; i < grid1.size(); i++) {
+        ASSERT_EQUAL(grid1[i].size(), grid2[i].size());
+        for (int jj = 0; jj < grid1[i].size(); jj++) {
+            ASSERT_EQUAL(grid1[i][jj].size(), grid2[i][jj].size());
+            for (int kk = 0; kk < grid1[i][jj].size(); kk++) {
+                ASSERT_EQUAL(grid1[i][jj][kk], grid2[i][jj][kk]);
+            }
+        }
+    }
+}
+
+void testSerialization() {
+    // Create a Force.
+
+    AmoebaTorsionTorsionForce force;
+
+    for( int ii = 0; ii < 5; ii++ ){
+        std::vector< std::vector< std::vector<double> > > gridVector;
+        loadTorsionTorsionGrid( gridVector );
+        force.setTorsionTorsionGrid( ii, gridVector );
+    }
+    for( int ii = 0; ii < 5; ii++ ){
+        force.addTorsionTorsion( ii, ii+1,ii+3, ii+4, ii+5, ( (ii % 2 ) ? 1 : 0), (ii % 4) );
+    }
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<AmoebaTorsionTorsionForce>(&force, "Force", buffer);
+
+if( 0 ){
+FILE* filePtr = fopen("TorsionTorsion.xml", "w" );
+(void) fprintf( filePtr, "%s", buffer.str().c_str() );
+(void) fclose( filePtr );
+}
+
+    AmoebaTorsionTorsionForce* copy = XmlSerializer::deserialize<AmoebaTorsionTorsionForce>(buffer);
+
+    // Compare the two forces to see if they are identical.  
+
+    AmoebaTorsionTorsionForce & force2 = *copy;
+    ASSERT_EQUAL(force.getNumTorsionTorsions(), force2.getNumTorsionTorsions());
+    for (int i = 0; i < force.getNumTorsionTorsions(); i++) {
+
+        int a1, a2, a3, a4, a5, aChiral, aGridIndex, b1, b2, b3, b4, b5, bChiral, bGridIndex;
+
+        force.getTorsionTorsionParameters( i, a1, a2, a3, a4, a5, aChiral, aGridIndex);
+        force2.getTorsionTorsionParameters( i, b1, b2, b3, b4, b5, bChiral, bGridIndex);
+
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(a3, b3);
+        ASSERT_EQUAL(a4, b4);
+        ASSERT_EQUAL(a5, b5);
+        ASSERT_EQUAL(aChiral, bChiral);
+        ASSERT_EQUAL(aGridIndex, bGridIndex );
+    }
+
+    ASSERT_EQUAL(force.getNumTorsionTorsionGrids(), force2.getNumTorsionTorsionGrids());
+    for (int i = 0; i < force.getNumTorsionTorsionGrids(); i++) {
+        const std::vector< std::vector< std::vector<double> > >& grid1 = force.getTorsionTorsionGrid( i );
+        const std::vector< std::vector< std::vector<double> > >& grid2 = force2.getTorsionTorsionGrid( i );
+        compareGrids(grid1, grid2 );
+    }
+
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+

plugins/amoeba/serialization/tests/TestSerializeAmoebaUreyBradleyForce.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/AmoebaUreyBradleyForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    AmoebaUreyBradleyForce force;
+    force.setAmoebaGlobalUreyBradleyCubic( 12.3 );
+    force.setAmoebaGlobalUreyBradleyQuartic( 98.7 );
+    force.addUreyBradley(0, 1, 1.0, 2.0);
+    force.addUreyBradley(0, 2, 2.0, 2.1);
+    force.addUreyBradley(2, 3, 3.0, 2.2);
+    force.addUreyBradley(5, 1, 4.0, 2.3);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<AmoebaUreyBradleyForce>(&force, "Force", buffer);
+    AmoebaUreyBradleyForce* copy = XmlSerializer::deserialize<AmoebaUreyBradleyForce>(buffer);
+
+    // Compare the two forces to see if they are identical.  
+    AmoebaUreyBradleyForce& force2 = *copy;
+    ASSERT_EQUAL(force.getAmoebaGlobalUreyBradleyCubic(), force2.getAmoebaGlobalUreyBradleyCubic());
+    ASSERT_EQUAL(force.getAmoebaGlobalUreyBradleyQuartic(), force2.getAmoebaGlobalUreyBradleyQuartic());
+    ASSERT_EQUAL(force.getNumInteractions(), force2.getNumInteractions());
+    for (int i = 0; i < force.getNumInteractions(); i++) {
+        int a1, a2, b1, b2;
+        double da, db, ka, kb;
+        force.getUreyBradleyParameters(i, a1, a2, da, ka);
+        force2.getUreyBradleyParameters(i, b1, b2, db, kb);
+        ASSERT_EQUAL(a1, b1);
+        ASSERT_EQUAL(a2, b2);
+        ASSERT_EQUAL(da, db);
+        ASSERT_EQUAL(ka, kb);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+