Serialization for BAOABLangevinIntegrator

serialization/include/openmm/serialization/BAOABLangevinIntegratorProxy.h

+#ifndef OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_
+#define OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_
+
+#include "openmm/serialization/XmlSerializer.h"
+
+namespace OpenMM {
+
+class BAOABLangevinIntegratorProxy : public SerializationProxy {
+public:
+    BAOABLangevinIntegratorProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+}
+
+#endif /*OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_*/
\ No newline at end of file

serialization/src/BAOABLangevinIntegratorProxy.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) 2010-2019 Stanford University and the Authors.      *
+ * Authors: Peter Eastman, Yutong Zhao                                        *
+ * 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/BAOABLangevinIntegratorProxy.h"
+#include <OpenMM.h>
+
+using namespace std;
+using namespace OpenMM;
+
+BAOABLangevinIntegratorProxy::BAOABLangevinIntegratorProxy() : SerializationProxy("BAOABLangevinIntegrator") {
+
+}
+
+void BAOABLangevinIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const BAOABLangevinIntegrator& integrator = *reinterpret_cast<const BAOABLangevinIntegrator*>(object);
+    node.setDoubleProperty("stepSize", integrator.getStepSize());
+    node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
+    node.setDoubleProperty("temperature", integrator.getTemperature());
+    node.setDoubleProperty("friction", integrator.getFriction());
+    node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
+}
+
+void* BAOABLangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    BAOABLangevinIntegrator *integrator = new BAOABLangevinIntegrator(node.getDoubleProperty("temperature"),
+            node.getDoubleProperty("friction"), node.getDoubleProperty("stepSize"));
+    integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
+    integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
+    return integrator;
+}
\ No newline at end of file

serialization/src/SerializationProxyRegistration.cpp

@@ -30,6 +30,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/AndersenThermostat.h"
+#include "openmm/BAOABLangevinIntegrator.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
@@ -65,6 +66,7 @@
 #include "openmm/VerletIntegrator.h"
 
 #include "openmm/serialization/SerializationProxy.h"
+#include "openmm/serialization/BAOABLangevinIntegratorProxy.h"
 #include "openmm/serialization/BrownianIntegratorProxy.h"
 #include "openmm/serialization/AndersenThermostatProxy.h"
 #include "openmm/serialization/CMAPTorsionForceProxy.h"
@@ -117,6 +119,7 @@ using namespace OpenMM;
 
 extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(AndersenThermostat), new AndersenThermostatProxy());
+    SerializationProxy::registerProxy(typeid(BAOABLangevinIntegrator), new BAOABLangevinIntegratorProxy());
     SerializationProxy::registerProxy(typeid(BrownianIntegrator), new BrownianIntegratorProxy());
     SerializationProxy::registerProxy(typeid(CMAPTorsionForce), new CMAPTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(CMMotionRemover), new CMMotionRemoverProxy());

serialization/tests/TestSerializeIntegrator.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) 2010-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Yutong Zhao                                        *
  * Contributors:                                                              *
  *                                                                            *
@@ -31,6 +31,7 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 
+#include "openmm/BAOABLangevinIntegrator.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomIntegrator.h"
@@ -74,6 +75,20 @@ void testSerializeLangevinIntegrator() {
     delete intg2;
 }
 
+void testSerializeBAOABLangevinIntegrator() {
+    BAOABLangevinIntegrator *intg = new BAOABLangevinIntegrator(372.4, 1.234, 0.0018);
+    stringstream ss;
+    XmlSerializer::serialize<Integrator>(intg, "BAOABLangevinIntegrator", ss);
+    BAOABLangevinIntegrator *intg2 = dynamic_cast<BAOABLangevinIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
+    ASSERT_EQUAL(intg->getConstraintTolerance(), intg2->getConstraintTolerance());
+    ASSERT_EQUAL(intg->getStepSize(), intg2->getStepSize());
+    ASSERT_EQUAL(intg->getTemperature(), intg2->getTemperature());
+    ASSERT_EQUAL(intg->getFriction(), intg2->getFriction());
+    ASSERT_EQUAL(intg->getRandomNumberSeed(), intg2->getRandomNumberSeed());
+    delete intg;
+    delete intg2;
+}
+
 void testSerializeBrownianIntegrator() {
     BrownianIntegrator *intg = new BrownianIntegrator(243.1, 3.234, 0.0021);
     stringstream ss;
@@ -244,6 +259,7 @@ int main() {
         testSerializeVariableLangevinIntegrator();
         testSerializeVariableVerletIntegrator();
         testSerializeLangevinIntegrator();
+        testSerializeBAOABLangevinIntegrator();
         testSerializeCompoundIntegrator();
     }
     catch(const exception& e) {