Support for serialization of Integrator base class, and two derived classes:...

Support for serialization of Integrator base class, and two derived classes: LangevinIntegrator and VerletIntegrator. Also added support for python serialization via a single deserializeIntegrator()

serialization/src/IntegratorProxy.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 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/IntegratorProxy.h"
+#include "openmm/serialization/SerializationNode.h"
+#include <OpenMM.h>
+
+using namespace std;
+using namespace OpenMM;
+
+IntegratorProxy::IntegratorProxy() : SerializationProxy("Integrator") {
+
+}
+
+void IntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+	node.createChildNode("Integrator", reinterpret_cast<const Integrator *>(object));
+}
+
+void* IntegratorProxy::deserialize(const SerializationNode& node) const {
+	return node.decodeObject<Integrator>();
+}
\ No newline at end of file

serialization/src/LangevinIntegratorProxy.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 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/LangevinIntegratorProxy.h"
+#include <OpenMM.h>
+
+using namespace std;
+using namespace OpenMM;
+
+LangevinIntegratorProxy::LangevinIntegratorProxy() : SerializationProxy("LangevinIntegrator") {
+
+}
+
+void LangevinIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const LangevinIntegrator& integrator = *reinterpret_cast<const LangevinIntegrator*>(object);
+    node.setDoubleProperty("stepSizeInPs", integrator.getStepSize());
+    node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
+    node.setDoubleProperty("temperature", integrator.getTemperature());
+    node.setDoubleProperty("friction", integrator.getFriction());
+    node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
+}
+
+void* LangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
+        throw OpenMMException("Unsupported version number");
+    LangevinIntegrator *integrator = new LangevinIntegrator(node.getDoubleProperty("temperature"),
+															node.getDoubleProperty("friction"),
+		                                                    node.getDoubleProperty("stepSizeInPs"));
+    integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
+    integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
+	return integrator;
+}
\ No newline at end of file

serialization/src/SerializationProxyRegistration.cpp

@@ -49,6 +49,8 @@
 #include "openmm/PeriodicTorsionForce.h"
 #include "openmm/RBTorsionForce.h"
 #include "openmm/System.h"
+#include "openmm/VerletIntegrator.h"
+#include "openmm/LangevinIntegrator.h"
 #include "openmm/serialization/SerializationProxy.h"
 #include "openmm/serialization/AndersenThermostatProxy.h"
 #include "openmm/serialization/CMAPTorsionForceProxy.h"
@@ -71,6 +73,9 @@
 #include "openmm/serialization/RBTorsionForceProxy.h"
 #include "openmm/serialization/SystemProxy.h"
 #include "openmm/serialization/StateProxy.h"
+#include "openmm/serialization/VerletIntegratorProxy.h"
+#include "openmm/serialization/LangevinIntegratorProxy.h"
+#include "openmm/serialization/IntegratorProxy.h"
 
 #if defined(WIN32)
     #include <windows.h>
@@ -108,4 +113,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(RBTorsionForce), new RBTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(System), new SystemProxy());
 	SerializationProxy::registerProxy(typeid(State), new StateProxy());
+	SerializationProxy::registerProxy(typeid(VerletIntegrator), new VerletIntegratorProxy());
+	SerializationProxy::registerProxy(typeid(LangevinIntegrator), new LangevinIntegratorProxy());
+	SerializationProxy::registerProxy(typeid(Integrator), new IntegratorProxy());
 }
\ No newline at end of file

serialization/src/VerletIntegratorProxy.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 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/VerletIntegratorProxy.h"
+#include <OpenMM.h>
+
+using namespace std;
+using namespace OpenMM;
+
+VerletIntegratorProxy::VerletIntegratorProxy() : SerializationProxy("VerletIntegrator") {
+
+}
+
+void VerletIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const VerletIntegrator& integrator = *reinterpret_cast<const VerletIntegrator*>(object);
+    node.setDoubleProperty("stepSizeInPs", integrator.getStepSize());
+    node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
+}
+
+void* VerletIntegratorProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
+        throw OpenMMException("Unsupported version number");
+    double stepSize = node.getDoubleProperty("stepSizeInPs");
+    double constraintTol = node.getDoubleProperty("constraintTolerance");
+    VerletIntegrator *integrator = new VerletIntegrator(stepSize);
+    integrator->setConstraintTolerance(constraintTol);
+	return integrator;
+}
\ No newline at end of file

wrappers/python/src/swig_doxygen/swigInputBuilder.py

@@ -401,6 +401,17 @@ class SwigInputBuilder:
             extendString +=    "           ss << inputString;\n" 
             extendString +=    "           return XmlSerializer::deserialize<OpenMM::System>( ss );\n"
             extendString +=    "       }\n"
+            extendString +=    "       static std::string serializeIntegrator( const OpenMM::Integrator *object ){\n"
+            extendString +=    "           std::stringstream ss;\n"
+            extendString +=    "           XmlSerializer::serialize<OpenMM::Integrator>( object, \"Integrator\", ss );\n"
+            extendString +=    "           return ss.str();\n"
+            extendString +=    "       }\n"
+            extendString +=    "\n"
+            extendString +=    "       static OpenMM::Integrator* deserializeIntegrator( const char* inputString ){\n"
+            extendString +=    "           std::stringstream ss;\n"
+            extendString +=    "           ss << inputString;\n" 
+            extendString +=    "           return XmlSerializer::deserialize<OpenMM::Integrator>( ss );\n"
+            extendString +=    "       }\n"
             extendString +=    "    };\n"   
 
             self.fOut.write("%s%s\n" % (INDENT, extendString))