Merge pull request #1295 from peastman/centroid

Added serialization proxy for CustomCentroidBondForce

serialization/include/openmm/serialization/CustomCentroidBondForceProxy.h

+#ifndef OPENMM_CUSTOMCENTROIDBONDFORCE_PROXY_H_
+#define OPENMM_CUSTOMCENTROIDBONDFORCE_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) 2015 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 CustomCentroidBondForce objects.
+ */
+
+class OPENMM_EXPORT CustomCentroidBondForceProxy : public SerializationProxy {
+public:
+    CustomCentroidBondForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUSTOMCENTROIDBONDFORCE_PROXY_H_*/

serialization/src/CustomCentroidBondForceProxy.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) 2010-2015 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/CustomCentroidBondForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/CustomCentroidBondForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+CustomCentroidBondForceProxy::CustomCentroidBondForceProxy() : SerializationProxy("CustomCentroidBondForce") {
+}
+
+void CustomCentroidBondForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const CustomCentroidBondForce& force = *reinterpret_cast<const CustomCentroidBondForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setIntProperty("groups", force.getNumGroupsPerBond());
+    node.setStringProperty("energy", force.getEnergyFunction());
+    SerializationNode& perBondParams = node.createChildNode("PerBondParameters");
+    for (int i = 0; i < force.getNumPerBondParameters(); i++) {
+        perBondParams.createChildNode("Parameter").setStringProperty("name", force.getPerBondParameterName(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& groups = node.createChildNode("Groups");
+    for (int i = 0; i < force.getNumGroups(); i++) {
+        vector<int> particles;
+        vector<double> weights;
+        force.getGroupParameters(i, particles, weights);
+        SerializationNode& group = groups.createChildNode("Group");
+        for (int j = 0; j < (int) particles.size(); j++) {
+            SerializationNode& node = group.createChildNode("Particle");
+            node.setIntProperty("p", particles[j]);
+            node.setDoubleProperty("weight", weights[j]);
+        }
+    }
+    SerializationNode& bonds = node.createChildNode("Bonds");
+    for (int i = 0; i < force.getNumBonds(); i++) {
+        vector<int> groups;
+        vector<double> params;
+        force.getBondParameters(i, groups, params);
+        SerializationNode& node = bonds.createChildNode("Bond");
+        for (int j = 0; j < (int) groups.size(); j++) {
+            stringstream key;
+            key << "g";
+            key << j+1;
+            node.setIntProperty(key.str(), groups[j]);
+        }
+        for (int j = 0; j < (int) params.size(); j++) {
+            stringstream key;
+            key << "param";
+            key << j+1;
+            node.setDoubleProperty(key.str(), params[j]);
+        }
+    }
+    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* CustomCentroidBondForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    CustomCentroidBondForce* force = NULL;
+    try {
+        CustomCentroidBondForce* force = new CustomCentroidBondForce(node.getIntProperty("groups"), node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
+        for (int i = 0; i < (int) perBondParams.getChildren().size(); i++) {
+            const SerializationNode& parameter = perBondParams.getChildren()[i];
+            force->addPerBondParameter(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& groups = node.getChildNode("Groups");
+        for (int i = 0; i < (int) groups.getChildren().size(); i++) {
+            const SerializationNode& group = groups.getChildren()[i];
+            vector<int> particles;
+            vector<double> weights;
+            for (int j = 0; j < (int) group.getChildren().size(); j++) {
+                particles.push_back(group.getChildren()[j].getIntProperty("p"));
+                weights.push_back(group.getChildren()[j].getDoubleProperty("weight"));
+            }
+            force->addGroup(particles, weights);
+        }
+        const SerializationNode& bonds = node.getChildNode("Bonds");
+        vector<int> bondGroups(force->getNumGroupsPerBond());
+        vector<double> params(force->getNumPerBondParameters());
+        for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
+            const SerializationNode& bond = bonds.getChildren()[i];
+            for (int j = 0; j < (int) bondGroups.size(); j++) {
+                stringstream key;
+                key << "g";
+                key << j+1;
+                bondGroups[j] = bond.getIntProperty(key.str());
+            }
+            for (int j = 0; j < (int) params.size(); j++) {
+                stringstream key;
+                key << "param";
+                key << j+1;
+                params[j] = bond.getDoubleProperty(key.str());
+            }
+            force->addBond(bondGroups, params);
+        }
+        const SerializationNode& functions = node.getChildNode("Functions");
+        for (int i = 0; i < (int) functions.getChildren().size(); i++) {
+            const SerializationNode& function = functions.getChildren()[i];
+            if (function.hasProperty("type")) {
+                force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
+            }
+            else {
+                // This is an old file created before TabulatedFunction existed.
+
+                const SerializationNode& valuesNode = function.getChildNode("Values");
+                vector<double> values;
+                for (int j = 0; j < (int) valuesNode.getChildren().size(); j++)
+                    values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v"));
+                force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
+            }
+        }
+        return force;
+    }
+    catch (...) {
+        if (force != NULL)
+            delete force;
+        throw;
+    }
+}

serialization/src/SerializationProxyRegistration.cpp

@@ -36,6 +36,7 @@
 #include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomAngleForce.h"
 #include "openmm/CustomBondForce.h"
+#include "openmm/CustomCentroidBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"
 #include "openmm/CustomExternalForce.h"
 #include "openmm/CustomGBForce.h"
@@ -68,6 +69,7 @@
 #include "openmm/serialization/CompoundIntegratorProxy.h"
 #include "openmm/serialization/CustomAngleForceProxy.h"
 #include "openmm/serialization/CustomBondForceProxy.h"
+#include "openmm/serialization/CustomCentroidBondForceProxy.h"
 #include "openmm/serialization/CustomCompoundBondForceProxy.h"
 #include "openmm/serialization/CustomExternalForceProxy.h"
 #include "openmm/serialization/CustomGBForceProxy.h"
@@ -118,6 +120,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(Continuous3DFunction), new Continuous3DFunctionProxy());
     SerializationProxy::registerProxy(typeid(CustomAngleForce), new CustomAngleForceProxy());
     SerializationProxy::registerProxy(typeid(CustomBondForce), new CustomBondForceProxy());
+    SerializationProxy::registerProxy(typeid(CustomCentroidBondForce), new CustomCentroidBondForceProxy());
     SerializationProxy::registerProxy(typeid(CustomCompoundBondForce), new CustomCompoundBondForceProxy());
     SerializationProxy::registerProxy(typeid(CustomExternalForce), new CustomExternalForceProxy());
     SerializationProxy::registerProxy(typeid(CustomGBForce), new CustomGBForceProxy());

serialization/tests/TestSerializeCustomCentroidBondForce.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) 2010-2015 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/CustomCentroidBondForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    CustomCentroidBondForce force(3, "5*sin(distance(g1,g2))^2+y*z");
+    force.setForceGroup(3);
+    force.addGlobalParameter("x", 1.3);
+    force.addGlobalParameter("y", 2.221);
+    force.addPerBondParameter("z");
+    for (int i = 0; i < 3; i++) {
+        vector<int> particles;
+        vector<double> weights;
+        for (int j = 0; j < i+1; j++) {
+            particles.push_back(i+j);
+            weights.push_back(1.0/(i+1));
+        }
+        force.addGroup(particles, weights);
+    }
+    vector<int> groups(3);
+    vector<double> params(1);
+    groups[0] = 0;
+    groups[1] = 1;
+    groups[2] = 2;
+    params[0] = 1.0;
+    force.addBond(groups, params);
+    groups[0] = 2;
+    groups[1] = 3;
+    groups[2] = 4;
+    params[0] = -3.3;
+    force.addBond(groups, params);
+    groups[0] = 3;
+    groups[1] = 5;
+    groups[2] = 1;
+    params[0] = 2.1;
+    force.addBond(groups, params);
+    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<CustomCentroidBondForce>(&force, "Force", buffer);
+    CustomCentroidBondForce* copy = XmlSerializer::deserialize<CustomCentroidBondForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    CustomCentroidBondForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.getNumGroupsPerBond(), force2.getNumGroupsPerBond());
+    ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
+    ASSERT_EQUAL(force.getNumPerBondParameters(), force2.getNumPerBondParameters());
+    for (int i = 0; i < force.getNumPerBondParameters(); i++)
+        ASSERT_EQUAL(force.getPerBondParameterName(i), force2.getPerBondParameterName(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.getNumGroups(), force2.getNumGroups());
+    for (int i = 0; i < force.getNumGroups(); i++) {
+        vector<int> particles1, particles2;
+        vector<double> weights1, weights2;
+        force.getGroupParameters(i, particles1, weights1);
+        force2.getGroupParameters(i, particles2, weights2);
+        ASSERT_EQUAL(weights1.size(), weights2.size());
+        for (int j = 0; j < (int) weights1.size(); j++)
+            ASSERT_EQUAL(weights1[j], weights2[j]);
+        ASSERT_EQUAL(particles1.size(), particles2.size());
+        for (int j = 0; j < (int) particles1.size(); j++)
+            ASSERT_EQUAL(particles1[j], particles2[j]);
+    }
+    ASSERT_EQUAL(force.getNumBonds(), force2.getNumBonds());
+    for (int i = 0; i < force.getNumBonds(); i++) {
+        vector<int> groups1, groups2;
+        vector<double> params1, params2;
+        force.getBondParameters(i, groups1, params1);
+        force2.getBondParameters(i, groups2, params2);
+        ASSERT_EQUAL(params1.size(), params2.size());
+        for (int j = 0; j < (int) params1.size(); j++)
+            ASSERT_EQUAL(params1[j], params2[j]);
+        ASSERT_EQUAL(groups1.size(), groups2.size());
+        for (int j = 0; j < (int) groups1.size(); j++)
+            ASSERT_EQUAL(groups1[j], groups2[j]);
+    }
+    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;
+}