Added serialization support for CustomManyParticleForce

serialization/include/openmm/serialization/CustomManyParticleForceProxy.h

+#ifndef OPENMM_CUSTOMMANYPARTICLEFORCE_PROXY_H_
+#define OPENMM_CUSTOMMANYPARTICLEFORCE_PROXY_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2014 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 CustomManyParticleForce objects.
+ */
+
+class OPENMM_EXPORT CustomManyParticleForceProxy : public SerializationProxy {
+public:
+    CustomManyParticleForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUSTOMMANYPARTICLEFORCE_PROXY_H_*/

serialization/src/CustomManyParticleForceProxy.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) 2010-2014 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/CustomManyParticleForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/CustomManyParticleForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+CustomManyParticleForceProxy::CustomManyParticleForceProxy() : SerializationProxy("CustomManyParticleForce") {
+}
+
+void CustomManyParticleForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const CustomManyParticleForce& force = *reinterpret_cast<const CustomManyParticleForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setIntProperty("particlesPerSet", force.getNumParticlesPerSet());
+    node.setStringProperty("energy", force.getEnergyFunction());
+    node.setIntProperty("method", (int) force.getNonbondedMethod());
+    node.setIntProperty("permutationMode", (int) force.getPermutationMode());
+    node.setDoubleProperty("cutoff", force.getCutoffDistance());
+    SerializationNode& perParticleParams = node.createChildNode("PerParticleParameters");
+    for (int i = 0; i < force.getNumPerParticleParameters(); i++) {
+        perParticleParams.createChildNode("Parameter").setStringProperty("name", force.getPerParticleParameterName(i));
+    }
+    SerializationNode& globalParams = node.createChildNode("GlobalParameters");
+    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
+        globalParams.createChildNode("Parameter").setStringProperty("name", force.getGlobalParameterName(i)).setDoubleProperty("default", force.getGlobalParameterDefaultValue(i));
+    }
+    SerializationNode& particles = node.createChildNode("Particles");
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        vector<double> params;
+        int type;
+        force.getParticleParameters(i, params, type);
+        SerializationNode& node = particles.createChildNode("Particle");
+        node.setIntProperty("type", type);
+        for (int j = 0; j < (int) params.size(); j++) {
+            stringstream key;
+            key << "param";
+            key << j+1;
+            node.setDoubleProperty(key.str(), params[j]);
+        }
+    }
+    SerializationNode& exclusions = node.createChildNode("Exclusions");
+    for (int i = 0; i < force.getNumExclusions(); i++) {
+        int particle1, particle2;
+        force.getExclusionParticles(i, particle1, particle2);
+        exclusions.createChildNode("Exclusion").setIntProperty("p1", particle1).setIntProperty("p2", particle2);
+    }
+    SerializationNode& filters = node.createChildNode("TypeFilters");
+    for (int i = 0; i < force.getNumParticlesPerSet(); i++) {
+        set<int> types;
+        force.getTypeFilter(i, types);
+        stringstream list;
+        bool first = true;
+        for (set<int>::const_iterator iter = types.begin(); iter != types.end(); ++iter) {
+            if (!first)
+                list << ",";
+            list << *iter;
+            first = false;
+        }
+        filters.createChildNode("Filter").setIntProperty("index", i).setStringProperty("types", list.str());
+    }
+    SerializationNode& functions = node.createChildNode("Functions");
+    for (int i = 0; i < force.getNumTabulatedFunctions(); i++)
+        functions.createChildNode("Function", &force.getTabulatedFunction(i)).setStringProperty("name", force.getTabulatedFunctionName(i));
+}
+
+void* CustomManyParticleForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    CustomManyParticleForce* force = NULL;
+    try {
+        CustomManyParticleForce* force = new CustomManyParticleForce(node.getIntProperty("particlesPerSet"), node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setNonbondedMethod((CustomManyParticleForce::NonbondedMethod) node.getIntProperty("method"));
+        force->setPermutationMode((CustomManyParticleForce::PermutationMode) node.getIntProperty("permutationMode"));
+        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
+        const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
+        for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
+            const SerializationNode& parameter = perParticleParams.getChildren()[i];
+            force->addPerParticleParameter(parameter.getStringProperty("name"));
+        }
+        const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
+        for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
+            const SerializationNode& parameter = globalParams.getChildren()[i];
+            force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
+        }
+        const SerializationNode& particles = node.getChildNode("Particles");
+        vector<double> params(force->getNumPerParticleParameters());
+        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
+            const SerializationNode& particle = particles.getChildren()[i];
+            for (int j = 0; j < (int) params.size(); j++) {
+                stringstream key;
+                key << "param";
+                key << j+1;
+                params[j] = particle.getDoubleProperty(key.str());
+            }
+            force->addParticle(params, particle.getIntProperty("type"));
+        }
+        const SerializationNode& exclusions = node.getChildNode("Exclusions");
+        for (int i = 0; i < (int) exclusions.getChildren().size(); i++) {
+            const SerializationNode& exclusion = exclusions.getChildren()[i];
+            force->addExclusion(exclusion.getIntProperty("p1"), exclusion.getIntProperty("p2"));
+        }
+        const SerializationNode& filters = node.getChildNode("TypeFilters");
+        for (int i = 0; i < (int) filters.getChildren().size(); i++) {
+            const SerializationNode& filter = filters.getChildren()[i];
+            string typesString = filter.getStringProperty("types");
+            vector<string> splitTypes;
+            size_t searchPos = 0, nextPos;
+            while ((nextPos = typesString.find_first_of(", ", searchPos)) != string::npos) {
+                splitTypes.push_back(typesString.substr(searchPos, nextPos-searchPos));
+                searchPos = nextPos+1;
+            }
+            splitTypes.push_back(typesString.substr(searchPos));
+            set<int> types;
+            for (int j = 0; j < (int) splitTypes.size(); j++) {
+                if (splitTypes[j].size() > 0) {
+                    int type;
+                    stringstream(splitTypes[j]) >> type;
+                    types.insert(type);
+                }
+            }
+            force->setTypeFilter(filter.getIntProperty("index"), types);
+        }
+        const SerializationNode& functions = node.getChildNode("Functions");
+        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
+            const SerializationNode& function = functions.getChildren()[i];
+            force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
+        }
+        return force;
+    }
+    catch (...) {
+        if (force != NULL)
+            delete force;
+        throw;
+    }
+}

serialization/src/SerializationProxyRegistration.cpp

@@ -40,6 +40,7 @@
 #include "openmm/CustomGBForce.h"
 #include "openmm/CustomHbondForce.h"
 #include "openmm/CustomIntegrator.h"
+#include "openmm/CustomManyParticleForce.h"
 #include "openmm/CustomNonbondedForce.h"
 #include "openmm/CustomTorsionForce.h"
 #include "openmm/GBSAOBCForce.h"
@@ -69,6 +70,7 @@
 #include "openmm/serialization/CustomGBForceProxy.h"
 #include "openmm/serialization/CustomHbondForceProxy.h"
 #include "openmm/serialization/CustomIntegratorProxy.h"
+#include "openmm/serialization/CustomManyParticleForceProxy.h"
 #include "openmm/serialization/CustomNonbondedForceProxy.h"
 #include "openmm/serialization/CustomTorsionForceProxy.h"
 #include "openmm/serialization/GBSAOBCForceProxy.h"
@@ -116,6 +118,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(CustomGBForce), new CustomGBForceProxy());
     SerializationProxy::registerProxy(typeid(CustomHbondForce), new CustomHbondForceProxy());
     SerializationProxy::registerProxy(typeid(CustomIntegrator), new CustomIntegratorProxy());
+    SerializationProxy::registerProxy(typeid(CustomManyParticleForce), new CustomManyParticleForceProxy());
     SerializationProxy::registerProxy(typeid(CustomNonbondedForce), new CustomNonbondedForceProxy());
     SerializationProxy::registerProxy(typeid(CustomTorsionForce), new CustomTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(Discrete1DFunction), new Discrete1DFunctionProxy());

serialization/tests/TestSerializeCustomManyParticleForce.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) 2010-2014 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/CustomManyParticleForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    CustomManyParticleForce force(3, "C*(a1+a2+a3)*(distance(p1,p2)+distance(p1,p3))");
+    force.setForceGroup(3);
+    force.setNonbondedMethod(CustomManyParticleForce::CutoffPeriodic);
+    force.setPermutationMode(CustomManyParticleForce::UniqueCentralParticle);
+    force.setCutoffDistance(2.1);
+    force.addGlobalParameter("C", 1.3);
+    force.addPerParticleParameter("a");
+    vector<double> params(1);
+    params[0] = 1.0;
+    force.addParticle(params, 0);
+    params[0] = -3.3;
+    force.addParticle(params, 2);
+    params[0] = 2.1;
+    force.addParticle(params, 3);
+    set<int> types1, types2;
+    types1.insert(0);
+    types2.insert(2);
+    types2.insert(3);
+    force.setTypeFilter(0, types1);
+    force.setTypeFilter(2, types2);
+    force.addExclusion(0, 1);
+    force.addExclusion(1, 2);
+    vector<double> values(10);
+    for (int i = 0; i < 10; i++)
+        values[i] = sin((double) i);
+    force.addTabulatedFunction("f", new Continuous1DFunction(values, 0.5, 1.5));
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<CustomManyParticleForce>(&force, "Force", buffer);
+    CustomManyParticleForce* copy = XmlSerializer::deserialize<CustomManyParticleForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    CustomManyParticleForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.getNumParticlesPerSet(), force2.getNumParticlesPerSet());
+    ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
+    ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
+    ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
+    ASSERT_EQUAL(force.getNumPerParticleParameters(), force2.getNumPerParticleParameters());
+    for (int i = 0; i < force.getNumPerParticleParameters(); i++)
+        ASSERT_EQUAL(force.getPerParticleParameterName(i), force2.getPerParticleParameterName(i));
+    ASSERT_EQUAL(force.getNumGlobalParameters(), force2.getNumGlobalParameters());
+    for (int i = 0; i < force.getNumGlobalParameters(); i++) {
+        ASSERT_EQUAL(force.getGlobalParameterName(i), force2.getGlobalParameterName(i));
+        ASSERT_EQUAL(force.getGlobalParameterDefaultValue(i), force2.getGlobalParameterDefaultValue(i));
+    }
+    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        vector<double> params1, params2;
+        int type1, type2;
+        force.getParticleParameters(i, params1, type1);
+        force2.getParticleParameters(i, params2, type2);
+        ASSERT_EQUAL(type1, type2);
+        ASSERT_EQUAL(params1.size(), params2.size());
+        for (int j = 0; j < (int) params1.size(); j++)
+            ASSERT_EQUAL(params1[j], params2[j]);
+    }
+    ASSERT_EQUAL(force.getNumExclusions(), force2.getNumExclusions());
+    for (int i = 0; i < force.getNumExclusions(); i++) {
+        int a1, a2, b1, b2;
+        force.getExclusionParticles(i, a1, b1);
+        force2.getExclusionParticles(i, a2, b2);
+        ASSERT_EQUAL(a1, a2);
+        ASSERT_EQUAL(b1, b2);
+    }
+    for (int i = 0; i < force.getNumParticlesPerSet(); i++) {
+        set<int> set1, set2;
+        force.getTypeFilter(i, set1);
+        force2.getTypeFilter(i, set2);
+        ASSERT_EQUAL_CONTAINERS(set1, set2);
+    }
+    ASSERT_EQUAL(force.getNumTabulatedFunctions(), force2.getNumTabulatedFunctions());
+    for (int i = 0; i < force.getNumTabulatedFunctions(); i++) {
+        double min1, min2, max1, max2;
+        vector<double> val1, val2;
+        dynamic_cast<Continuous1DFunction&>(force.getTabulatedFunction(i)).getFunctionParameters(val1, min1, max1);
+        dynamic_cast<Continuous1DFunction&>(force2.getTabulatedFunction(i)).getFunctionParameters(val2, min2, max2);
+        ASSERT_EQUAL(force.getTabulatedFunctionName(i), force2.getTabulatedFunctionName(i));
+        ASSERT_EQUAL(min1, min2);
+        ASSERT_EQUAL(max1, max2);
+        ASSERT_EQUAL(val1.size(), val2.size());
+        for (int j = 0; j < (int) val1.size(); j++)
+            ASSERT_EQUAL(val1[j], val2[j]);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}