Serialization for CustomCVForce

serialization/include/openmm/serialization/CustomCVForceProxy.h

+#ifndef OPENMM_CUSTOMCVFORCE_PROXY_H_
+#define OPENMM_CUSTOMCVFORCE_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) 2017 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 CustomCVForce objects.
+ */
+
+class OPENMM_EXPORT CustomCVForceProxy : public SerializationProxy {
+public:
+    CustomCVForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_CUSTOMCVFORCE_PROXY_H_*/

serialization/src/CustomCVForceProxy.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) 2010-2017 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/CustomCVForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/CustomCVForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+CustomCVForceProxy::CustomCVForceProxy() : SerializationProxy("CustomCVForce") {
+}
+
+void CustomCVForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 0);
+    const CustomCVForce& force = *reinterpret_cast<const CustomCVForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setStringProperty("energy", force.getEnergyFunction());
+    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& energyDerivs = node.createChildNode("EnergyParameterDerivatives");
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++) {
+        energyDerivs.createChildNode("Parameter").setStringProperty("name", force.getEnergyParameterDerivativeName(i));
+    }
+    SerializationNode& cvs = node.createChildNode("CollectiveVariables");
+    for (int i = 0; i < force.getNumCollectiveVariables(); i++) {
+        SerializationNode& node = cvs.createChildNode("CollectiveVariable").setStringProperty("name", force.getCollectiveVariableName(i));
+        node.createChildNode("Force", &force.getCollectiveVariable(i));
+    }
+    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* CustomCVForceProxy::deserialize(const SerializationNode& node) const {
+    int version = node.getIntProperty("version");
+    if (version != 0)
+        throw OpenMMException("Unsupported version number");
+    CustomCVForce* force = NULL;
+    try {
+        CustomCVForce* force = new CustomCVForce(node.getStringProperty("energy"));
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
+        for (auto& parameter : globalParams.getChildren())
+            force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
+        const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
+        for (auto& parameter : energyDerivs.getChildren())
+            force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
+        const SerializationNode& cvs = node.getChildNode("CollectiveVariables");
+        for (auto& cv : cvs.getChildren()) {
+            string name = cv.getStringProperty("name");
+            force->addCollectiveVariable(name, cv.getChildren()[0].decodeObject<Force>());
+        }
+        const SerializationNode& functions = node.getChildNode("Functions");
+        for (auto& function : functions.getChildren())
+            force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>());
+        return force;
+    }
+    catch (...) {
+        if (force != NULL)
+            delete force;
+        throw;
+    }
+}

serialization/src/SerializationProxyRegistration.cpp

@@ -38,6 +38,7 @@
 #include "openmm/CustomBondForce.h"
 #include "openmm/CustomCentroidBondForce.h"
 #include "openmm/CustomCompoundBondForce.h"
+#include "openmm/CustomCVForce.h"
 #include "openmm/CustomExternalForce.h"
 #include "openmm/CustomGBForce.h"
 #include "openmm/CustomHbondForce.h"
@@ -72,6 +73,7 @@
 #include "openmm/serialization/CustomBondForceProxy.h"
 #include "openmm/serialization/CustomCentroidBondForceProxy.h"
 #include "openmm/serialization/CustomCompoundBondForceProxy.h"
+#include "openmm/serialization/CustomCVForceProxy.h"
 #include "openmm/serialization/CustomExternalForceProxy.h"
 #include "openmm/serialization/CustomGBForceProxy.h"
 #include "openmm/serialization/CustomHbondForceProxy.h"
@@ -124,6 +126,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(CustomBondForce), new CustomBondForceProxy());
     SerializationProxy::registerProxy(typeid(CustomCentroidBondForce), new CustomCentroidBondForceProxy());
     SerializationProxy::registerProxy(typeid(CustomCompoundBondForce), new CustomCompoundBondForceProxy());
+    SerializationProxy::registerProxy(typeid(CustomCVForce), new CustomCVForceProxy());
     SerializationProxy::registerProxy(typeid(CustomExternalForce), new CustomExternalForceProxy());
     SerializationProxy::registerProxy(typeid(CustomGBForce), new CustomGBForceProxy());
     SerializationProxy::registerProxy(typeid(CustomHbondForce), new CustomHbondForceProxy());

serialization/tests/TestSerializeCustomCVForce.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) 2010-2017 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/CustomCVForce.h"
+#include "openmm/HarmonicAngleForce.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    CustomCVForce force("2*v1+v2");
+    force.setForceGroup(3);
+    force.addGlobalParameter("x", 1.3);
+    force.addGlobalParameter("y", 2.221);
+    force.addEnergyParameterDerivative("y");
+    HarmonicBondForce* v1 = new HarmonicBondForce();
+    v1->addBond(2, 3, 5.2, 1.1);
+    force.addCollectiveVariable("v1", v1);
+    HarmonicAngleForce* v2 = new HarmonicAngleForce();
+    v2->addAngle(3, 11, 15, 0.4, 0.2);
+    force.addCollectiveVariable("v2", v2);
+    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<CustomCVForce>(&force, "Force", buffer);
+    CustomCVForce* copy = XmlSerializer::deserialize<CustomCVForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    CustomCVForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.getEnergyFunction(), force2.getEnergyFunction());
+    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.getNumEnergyParameterDerivatives(), force2.getNumEnergyParameterDerivatives());
+    for (int i = 0; i < force.getNumEnergyParameterDerivatives(); i++)
+        ASSERT_EQUAL(force.getEnergyParameterDerivativeName(i), force2.getEnergyParameterDerivativeName(i));
+    ASSERT_EQUAL(force.getNumCollectiveVariables(), force2.getNumCollectiveVariables());
+    for (int i = 0; i < force.getNumCollectiveVariables(); i++) {
+        ASSERT_EQUAL(force.getCollectiveVariableName(i), force2.getCollectiveVariableName(i));
+        stringstream buffer1, buffer2;
+        XmlSerializer::serialize<Force>(&force.getCollectiveVariable(i), "Force", buffer1);
+        XmlSerializer::serialize<Force>(&force2.getCollectiveVariable(i), "Force", buffer2);
+        ASSERT_EQUAL(buffer1.str(), buffer2.str());
+    }
+    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;
+}