Merge pull request #2561 from peastman/middle

Converted BAOABLangevinIntegrator to LangevinMiddleIntegrator

serialization/src/BAOABLangevinIntegratorProxy.cpp → serialization/src/LangevinMiddleIntegratorProxy.cpp

@@ -29,19 +29,19 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/serialization/BAOABLangevinIntegratorProxy.h"
+#include "openmm/serialization/LangevinMiddleIntegratorProxy.h"
 #include <OpenMM.h>
 
 using namespace std;
 using namespace OpenMM;
 
-BAOABLangevinIntegratorProxy::BAOABLangevinIntegratorProxy() : SerializationProxy("BAOABLangevinIntegrator") {
+LangevinMiddleIntegratorProxy::LangevinMiddleIntegratorProxy() : SerializationProxy("LangevinMiddleIntegrator") {
 
 }
 
-void BAOABLangevinIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+void LangevinMiddleIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
-    const BAOABLangevinIntegrator& integrator = *reinterpret_cast<const BAOABLangevinIntegrator*>(object);
+    const LangevinMiddleIntegrator& integrator = *reinterpret_cast<const LangevinMiddleIntegrator*>(object);
     node.setDoubleProperty("stepSize", integrator.getStepSize());
     node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
     node.setDoubleProperty("temperature", integrator.getTemperature());
@@ -49,10 +49,10 @@ void BAOABLangevinIntegratorProxy::serialize(const void* object, SerializationNo
     node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
 }
 
-void* BAOABLangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
+void* LangevinMiddleIntegratorProxy::deserialize(const SerializationNode& node) const {
     if (node.getIntProperty("version") != 1)
         throw OpenMMException("Unsupported version number");
-    BAOABLangevinIntegrator *integrator = new BAOABLangevinIntegrator(node.getDoubleProperty("temperature"),
+    LangevinMiddleIntegrator *integrator = new LangevinMiddleIntegrator(node.getDoubleProperty("temperature"),
             node.getDoubleProperty("friction"), node.getDoubleProperty("stepSize"));
     integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
     integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));

serialization/src/SerializationProxyRegistration.cpp

@@ -30,7 +30,6 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/AndersenThermostat.h"
-#include "openmm/BAOABLangevinIntegrator.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
@@ -52,6 +51,7 @@
 #include "openmm/HarmonicAngleForce.h"
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/LangevinIntegrator.h"
+#include "openmm/LangevinMiddleIntegrator.h"
 #include "openmm/MonteCarloAnisotropicBarostat.h"
 #include "openmm/MonteCarloBarostat.h"
 #include "openmm/MonteCarloMembraneBarostat.h"
@@ -67,7 +67,6 @@
 #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"
@@ -90,6 +89,7 @@
 #include "openmm/serialization/HarmonicAngleForceProxy.h"
 #include "openmm/serialization/HarmonicBondForceProxy.h"
 #include "openmm/serialization/LangevinIntegratorProxy.h"
+#include "openmm/serialization/LangevinMiddleIntegratorProxy.h"
 #include "openmm/serialization/MonteCarloAnisotropicBarostatProxy.h"
 #include "openmm/serialization/MonteCarloBarostatProxy.h"
 #include "openmm/serialization/MonteCarloMembraneBarostatProxy.h"
@@ -121,7 +121,6 @@ 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());
@@ -149,6 +148,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(HarmonicAngleForce), new HarmonicAngleForceProxy());
     SerializationProxy::registerProxy(typeid(HarmonicBondForce), new HarmonicBondForceProxy());
     SerializationProxy::registerProxy(typeid(LangevinIntegrator), new LangevinIntegratorProxy());
+    SerializationProxy::registerProxy(typeid(LangevinMiddleIntegrator), new LangevinMiddleIntegratorProxy());
     SerializationProxy::registerProxy(typeid(MonteCarloAnisotropicBarostat), new MonteCarloAnisotropicBarostatProxy());
     SerializationProxy::registerProxy(typeid(MonteCarloBarostat), new MonteCarloBarostatProxy());
     SerializationProxy::registerProxy(typeid(MonteCarloMembraneBarostat), new MonteCarloMembraneBarostatProxy());

serialization/tests/TestSerializeIntegrator.cpp

@@ -31,11 +31,11 @@
 
 #include "openmm/internal/AssertionUtilities.h"
 
-#include "openmm/BAOABLangevinIntegrator.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CompoundIntegrator.h"
 #include "openmm/CustomIntegrator.h"
 #include "openmm/LangevinIntegrator.h"
+#include "openmm/LangevinMiddleIntegrator.h"
 #include "openmm/VariableLangevinIntegrator.h"
 #include "openmm/VariableVerletIntegrator.h"
 #include "openmm/VerletIntegrator.h"
@@ -75,11 +75,11 @@ void testSerializeLangevinIntegrator() {
     delete intg2;
 }
 
-void testSerializeBAOABLangevinIntegrator() {
-    BAOABLangevinIntegrator *intg = new BAOABLangevinIntegrator(372.4, 1.234, 0.0018);
+void testSerializeLangevinMiddleIntegrator() {
+    LangevinMiddleIntegrator *intg = new LangevinMiddleIntegrator(372.4, 1.234, 0.0018);
     stringstream ss;
-    XmlSerializer::serialize<Integrator>(intg, "BAOABLangevinIntegrator", ss);
-    BAOABLangevinIntegrator *intg2 = dynamic_cast<BAOABLangevinIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
+    XmlSerializer::serialize<Integrator>(intg, "LangevinMiddleIntegrator", ss);
+    LangevinMiddleIntegrator *intg2 = dynamic_cast<LangevinMiddleIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
     ASSERT_EQUAL(intg->getConstraintTolerance(), intg2->getConstraintTolerance());
     ASSERT_EQUAL(intg->getStepSize(), intg2->getStepSize());
     ASSERT_EQUAL(intg->getTemperature(), intg2->getTemperature());
@@ -259,7 +259,7 @@ int main() {
         testSerializeVariableLangevinIntegrator();
         testSerializeVariableVerletIntegrator();
         testSerializeLangevinIntegrator();
-        testSerializeBAOABLangevinIntegrator();
+        testSerializeLangevinMiddleIntegrator();
         testSerializeCompoundIntegrator();
     }
     catch(const exception& e) {

tests/TestBAOABLangevinIntegrator.h → tests/TestLangevinMiddleIntegrator.h

@@ -34,7 +34,7 @@
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/System.h"
-#include "openmm/BAOABLangevinIntegrator.h"
+#include "openmm/LangevinMiddleIntegrator.h"
 #include "SimTKOpenMMRealType.h"
 #include "sfmt/SFMT.h"
 #include <iostream>
@@ -49,7 +49,7 @@ void testSingleBond() {
     System system;
     system.addParticle(2.0);
     system.addParticle(2.0);
-    BAOABLangevinIntegrator integrator(0, 0.1, 0.01);
+    LangevinMiddleIntegrator integrator(0, 0.1, 0.01);
     HarmonicBondForce* forceField = new HarmonicBondForce();
     forceField->addBond(0, 1, 1.5, 1);
     system.addForce(forceField);
@@ -93,7 +93,7 @@ void testTemperature() {
     const double temp = 100.0;
     System system;
     system.setDefaultPeriodicBoxVectors(Vec3(5, 0, 0), Vec3(0, 5, 0), Vec3(0, 0, 5));
-    BAOABLangevinIntegrator integrator(temp, 3.0, 0.01);
+    LangevinMiddleIntegrator integrator(temp, 3.0, 0.01);
     NonbondedForce* forceField = new NonbondedForce();
     forceField->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
     for (int i = 0; i < numParticles; ++i) {
@@ -130,7 +130,7 @@ void testConstraints() {
     const int numConstraints = 5;
     const double temp = 100.0;
     System system;
-    BAOABLangevinIntegrator integrator(temp, 2.0, 0.01);
+    LangevinMiddleIntegrator integrator(temp, 2.0, 0.01);
     integrator.setConstraintTolerance(1e-5);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
@@ -181,7 +181,7 @@ void testConstrainedMasslessParticles() {
     vector<Vec3> positions(2);
     positions[0] = Vec3(-1, 0, 0);
     positions[1] = Vec3(1, 0, 0);
-    BAOABLangevinIntegrator integrator(300.0, 2.0, 0.01);
+    LangevinMiddleIntegrator integrator(300.0, 2.0, 0.01);
     bool failed = false;
     try {
         // This should throw an exception.
@@ -208,7 +208,7 @@ void testRandomSeed() {
     const int numParticles = 8;
     const double temp = 100.0;
     System system;
-    BAOABLangevinIntegrator integrator(temp, 2.0, 0.01);
+    LangevinMiddleIntegrator integrator(temp, 2.0, 0.01);
     NonbondedForce* forceField = new NonbondedForce();
     for (int i = 0; i < numParticles; ++i) {
         system.addParticle(2.0);