Implemented serialization of GayBerneForce

serialization/include/openmm/serialization/GayBerneForceProxy.h

+#ifndef OPENMM_GAYBERNEFORCE_PROXY_H_
+#define OPENMM_GAYBERNEFORCE_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) 2016 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 GayBerneForce objects.
+ */
+
+class OPENMM_EXPORT GayBerneForceProxy : public SerializationProxy {
+public:
+    GayBerneForceProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_GAYBERNEFORCE_PROXY_H_*/

serialization/src/GayBerneForceProxy.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) 2010-2016 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/GayBerneForceProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include "openmm/Force.h"
+#include "openmm/GayBerneForce.h"
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+GayBerneForceProxy::GayBerneForceProxy() : SerializationProxy("GayBerneForce") {
+}
+
+void GayBerneForceProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const GayBerneForce& force = *reinterpret_cast<const GayBerneForce*>(object);
+    node.setIntProperty("forceGroup", force.getForceGroup());
+    node.setIntProperty("method", (int) force.getNonbondedMethod());
+    node.setDoubleProperty("cutoff", force.getCutoffDistance());
+    node.setBoolProperty("useSwitchingFunction", force.getUseSwitchingFunction());
+    node.setDoubleProperty("switchingDistance", force.getSwitchingDistance());
+    SerializationNode& particles = node.createChildNode("Particles");
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        double sigma, epsilon, sx, sy, sz, ex, ey, ez;
+        int xparticle, yparticle;
+        force.getParticleParameters(i, sigma, epsilon, xparticle, yparticle, sx, sy, sz, ex, ey, ez);
+        particles.createChildNode("Particle").setDoubleProperty("sig", sigma).setDoubleProperty("eps", epsilon).setDoubleProperty("sx", sx)
+                .setDoubleProperty("sy", sy).setDoubleProperty("sz", sz).setDoubleProperty("ex", ex).setDoubleProperty("ey", ey).setDoubleProperty("ez", ez)
+                .setIntProperty("xparticle", xparticle).setIntProperty("yparticle", yparticle);
+    }
+    SerializationNode& exceptions = node.createChildNode("Exceptions");
+    for (int i = 0; i < force.getNumExceptions(); i++) {
+        int particle1, particle2;
+        double sigma, epsilon;
+        force.getExceptionParameters(i, particle1, particle2, sigma, epsilon);
+        exceptions.createChildNode("Exception").setIntProperty("p1", particle1).setIntProperty("p2", particle2).setDoubleProperty("sig", sigma).setDoubleProperty("eps", epsilon);
+    }
+}
+
+void* GayBerneForceProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    GayBerneForce* force = new GayBerneForce();
+    try {
+        force->setForceGroup(node.getIntProperty("forceGroup", 0));
+        force->setNonbondedMethod((GayBerneForce::NonbondedMethod) node.getIntProperty("method"));
+        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
+        force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction", false));
+        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
+        const SerializationNode& particles = node.getChildNode("Particles");
+        for (int i = 0; i < (int) particles.getChildren().size(); i++) {
+            const SerializationNode& particle = particles.getChildren()[i];
+            force->addParticle(particle.getDoubleProperty("sig"), particle.getDoubleProperty("eps"), particle.getIntProperty("xparticle"),
+                    particle.getIntProperty("yparticle"), particle.getDoubleProperty("sx"), particle.getDoubleProperty("sy"), particle.getDoubleProperty("sz"),
+                    particle.getDoubleProperty("ex"), particle.getDoubleProperty("ey"), particle.getDoubleProperty("ez"));
+        }
+        const SerializationNode& exceptions = node.getChildNode("Exceptions");
+        for (int i = 0; i < (int) exceptions.getChildren().size(); i++) {
+            const SerializationNode& exception = exceptions.getChildren()[i];
+            force->addException(exception.getIntProperty("p1"), exception.getIntProperty("p2"), exception.getDoubleProperty("sig"), exception.getDoubleProperty("eps"));
+        }
+    }
+    catch (...) {
+        delete force;
+        throw;
+    }
+    return force;
+}

serialization/src/SerializationProxyRegistration.cpp

@@ -6,7 +6,7 @@
  * 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.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@
 #include "openmm/CustomManyParticleForce.h"
 #include "openmm/CustomNonbondedForce.h"
 #include "openmm/CustomTorsionForce.h"
+#include "openmm/GayBerneForce.h"
 #include "openmm/GBSAOBCForce.h"
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/HarmonicBondForce.h"
@@ -78,6 +79,7 @@
 #include "openmm/serialization/CustomManyParticleForceProxy.h"
 #include "openmm/serialization/CustomNonbondedForceProxy.h"
 #include "openmm/serialization/CustomTorsionForceProxy.h"
+#include "openmm/serialization/GayBerneForceProxy.h"
 #include "openmm/serialization/GBSAOBCForceProxy.h"
 #include "openmm/serialization/HarmonicAngleForceProxy.h"
 #include "openmm/serialization/HarmonicBondForceProxy.h"
@@ -132,6 +134,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(Discrete1DFunction), new Discrete1DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Discrete2DFunction), new Discrete2DFunctionProxy());
     SerializationProxy::registerProxy(typeid(Discrete3DFunction), new Discrete3DFunctionProxy());
+    SerializationProxy::registerProxy(typeid(GayBerneForce), new GayBerneForceProxy());
     SerializationProxy::registerProxy(typeid(GBSAOBCForce), new GBSAOBCForceProxy());
     SerializationProxy::registerProxy(typeid(HarmonicAngleForce), new HarmonicAngleForceProxy());
     SerializationProxy::registerProxy(typeid(HarmonicBondForce), new HarmonicBondForceProxy());

serialization/tests/TestSerializeGayBerneForce.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) 2010-2016 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/GayBerneForce.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void testSerialization() {
+    // Create a Force.
+
+    GayBerneForce force;
+    force.setForceGroup(3);
+    force.setNonbondedMethod(GayBerneForce::CutoffPeriodic);
+    force.setSwitchingDistance(1.5);
+    force.setUseSwitchingFunction(true);
+    force.setCutoffDistance(2.0);
+    force.addParticle(0.1, 0.01, -1, -1, 0.5, 0.5, 0.5, 1.0, 1.0, 1.0);
+    force.addParticle(0.2, 0.02, -1, -1, 0.7, 0.7, 0.7, 1.2, 1.2, 1.2);
+    force.addParticle(0.3, 0.03, 1, 0, 0.8, 0.9, 1.0, 0.5, 0.6, 0.7);
+    force.addException(0, 1, 0.5, 0.1);
+    force.addException(1, 2, 0.4, 0.2);
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<GayBerneForce>(&force, "Force", buffer);
+    GayBerneForce* copy = XmlSerializer::deserialize<GayBerneForce>(buffer);
+
+    // Compare the two forces to see if they are identical.
+
+    GayBerneForce& force2 = *copy;
+    ASSERT_EQUAL(force.getForceGroup(), force2.getForceGroup());
+    ASSERT_EQUAL(force.getNonbondedMethod(), force2.getNonbondedMethod());
+    ASSERT_EQUAL(force.getSwitchingDistance(), force2.getSwitchingDistance());
+    ASSERT_EQUAL(force.getUseSwitchingFunction(), force2.getUseSwitchingFunction());
+    ASSERT_EQUAL(force.getCutoffDistance(), force2.getCutoffDistance());
+    ASSERT_EQUAL(force.getNumParticles(), force2.getNumParticles());
+    for (int i = 0; i < force.getNumParticles(); i++) {
+        double sigma1, epsilon1, sx1, sy1, sz1, ex1, ey1, ez1;
+        double sigma2, epsilon2, sx2, sy2, sz2, ex2, ey2, ez2;
+        int xparticle1, yparticle1, xparticle2, yparticle2;
+        force.getParticleParameters(i, sigma1, epsilon1, xparticle1, yparticle1, sx1, sy1, sz1, ex1, ey1, ez1);
+        force2.getParticleParameters(i, sigma2, epsilon2, xparticle2, yparticle2, sx2, sy2, sz2, ex2, ey2, ez2);
+        ASSERT_EQUAL(sigma1, sigma2);
+        ASSERT_EQUAL(epsilon1, epsilon2);
+        ASSERT_EQUAL(xparticle1, xparticle1);
+        ASSERT_EQUAL(xparticle2, xparticle2);
+        ASSERT_EQUAL(sx1, sx2);
+        ASSERT_EQUAL(sy1, sy2);
+        ASSERT_EQUAL(sz1, sz2);
+        ASSERT_EQUAL(ex1, ex2);
+        ASSERT_EQUAL(ey1, ey2);
+        ASSERT_EQUAL(ez1, ez2);
+    }
+    ASSERT_EQUAL(force.getNumExceptions(), force2.getNumExceptions());
+    for (int i = 0; i < force.getNumExceptions(); i++) {
+        int a1, a2, b1, b2;
+        double sigma1, epsilon1;
+        double sigma2, epsilon2;
+        force.getExceptionParameters(i, a1, b1, sigma1, epsilon1);
+        force2.getExceptionParameters(i, a2, b2, sigma2, epsilon2);
+        ASSERT_EQUAL(a1, a2);
+        ASSERT_EQUAL(b1, b2);
+        ASSERT_EQUAL(sigma1, sigma2);
+        ASSERT_EQUAL(epsilon1, epsilon2);
+    }
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}