Merge pull request #3 from openmm/master

Sync with official repo

plugins/amoeba/serialization/tests/TestSerializeAmoebaVdwForce.cpp

@@ -50,10 +50,11 @@ void testSerialization() {
     force1.setEpsilonCombiningRule("GEOMETRIC");
     force1.setCutoff(0.9);
     force1.setNonbondedMethod(AmoebaVdwForce::CutoffPeriodic);
+    force1.setAlchemicalMethod(AmoebaVdwForce::None);
 
-    force1.addParticle(0, 1.0, 2.0, 0.9);
-    force1.addParticle(1, 1.1, 2.1, 0.9);
-    force1.addParticle(2, 1.3, 4.1, 0.9);
+    force1.addParticle(0, 1.0, 2.0, 0.9, false);
+    force1.addParticle(1, 1.1, 2.1, 0.9, true);
+    force1.addParticle(2, 1.3, 4.1, 0.9, false);
     for (unsigned int ii = 0; ii < 3; ii++) {
         std::vector< int > exclusions;
         exclusions.push_back(ii);
@@ -76,6 +77,7 @@ void testSerialization() {
     ASSERT_EQUAL(force1.getEpsilonCombiningRule(),  force2.getEpsilonCombiningRule());
     ASSERT_EQUAL(force1.getCutoff(),                force2.getCutoff());
     ASSERT_EQUAL(force1.getNonbondedMethod(),       force2.getNonbondedMethod());
+    ASSERT_EQUAL(force1.getAlchemicalMethod(),      force2.getAlchemicalMethod());
 
     ASSERT_EQUAL(force1.getNumParticles(),          force2.getNumParticles());
 
@@ -87,13 +89,17 @@ void testSerialization() {
         double sigma1, epsilon1, reductionFactor1;
         double sigma2, epsilon2, reductionFactor2;
 
-        force1.getParticleParameters(ii, ivIndex1, sigma1, epsilon1, reductionFactor1);
-        force2.getParticleParameters(ii, ivIndex2, sigma2, epsilon2, reductionFactor2);
+        bool isAlchemical1;
+        bool isAlchemical2;
+
+        force1.getParticleParameters(ii, ivIndex1, sigma1, epsilon1, reductionFactor1, isAlchemical1);
+        force2.getParticleParameters(ii, ivIndex2, sigma2, epsilon2, reductionFactor2, isAlchemical2);
 
         ASSERT_EQUAL(ivIndex1,          ivIndex2);
         ASSERT_EQUAL(sigma1,            sigma2);
         ASSERT_EQUAL(epsilon1,          epsilon2);
         ASSERT_EQUAL(reductionFactor1,  reductionFactor2);
+        ASSERT_EQUAL(isAlchemical1,  isAlchemical2);
     }
     for (unsigned int ii = 0; ii < static_cast<unsigned int>(force1.getNumParticles()); ii++) {
 

plugins/amoeba/wrappers/Doxyfile.in

@@ -581,7 +581,7 @@ INPUT_ENCODING         = UTF-8
 # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx 
 # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
 
-FILE_PATTERNS          = 
+FILE_PATTERNS          = *.h
 
 # The RECURSIVE tag can be used to turn specify whether or not subdirectories 
 # should be searched for input files as well. Possible values are YES and NO. 

plugins/cpupme/src/CpuPmeKernels.h

@@ -51,7 +51,7 @@ namespace OpenMM {
 
 class OPENMM_EXPORT_PME CpuCalcPmeReciprocalForceKernel : public CalcPmeReciprocalForceKernel {
 public:
-    CpuCalcPmeReciprocalForceKernel(std::string name, const Platform& platform) : CalcPmeReciprocalForceKernel(name, platform),
+    CpuCalcPmeReciprocalForceKernel(const std::string& name, const Platform& platform) : CalcPmeReciprocalForceKernel(name, platform),
             hasCreatedPlan(false), isDeleted(false), realGrid(NULL), complexGrid(NULL) {
     }
     /**
@@ -144,7 +144,7 @@ private:
 
 class OPENMM_EXPORT_PME CpuCalcDispersionPmeReciprocalForceKernel : public CalcDispersionPmeReciprocalForceKernel {
 public:
-    CpuCalcDispersionPmeReciprocalForceKernel(std::string name, const Platform& platform) : CalcDispersionPmeReciprocalForceKernel(name, platform),
+    CpuCalcDispersionPmeReciprocalForceKernel(const std::string& name, const Platform& platform) : CalcDispersionPmeReciprocalForceKernel(name, platform),
             hasCreatedPlan(false), isDeleted(false), realGrid(NULL), complexGrid(NULL)  {
     }
     /**

plugins/cudacompiler/src/CudaCompilerKernels.h

@@ -44,7 +44,7 @@ namespace OpenMM {
  */
 class OPENMM_EXPORT_CUDACOMPILER CudaRuntimeCompilerKernel : public CudaCompilerKernel {
 public:
-    CudaRuntimeCompilerKernel(std::string name, const Platform& platform) : CudaCompilerKernel(name, platform) {
+    CudaRuntimeCompilerKernel(const std::string& name, const Platform& platform) : CudaCompilerKernel(name, platform) {
     }
     /**
      * Compile a kernel to PTX.

plugins/drude/platforms/cuda/src/CudaDrudeKernels.h

@@ -44,7 +44,7 @@ namespace OpenMM {
  */
 class CudaCalcDrudeForceKernel : public CalcDrudeForceKernel {
 public:
-    CudaCalcDrudeForceKernel(std::string name, const Platform& platform, CudaContext& cu) :
+    CudaCalcDrudeForceKernel(const std::string& name, const Platform& platform, CudaContext& cu) :
             CalcDrudeForceKernel(name, platform), cu(cu) {
     }
     /**
@@ -81,7 +81,7 @@ private:
  */
 class CudaIntegrateDrudeLangevinStepKernel : public IntegrateDrudeLangevinStepKernel {
 public:
-    CudaIntegrateDrudeLangevinStepKernel(std::string name, const Platform& platform, CudaContext& cu) :
+    CudaIntegrateDrudeLangevinStepKernel(const std::string& name, const Platform& platform, CudaContext& cu) :
             IntegrateDrudeLangevinStepKernel(name, platform), cu(cu) {
     }
     /**
@@ -119,7 +119,7 @@ private:
  */
 class CudaIntegrateDrudeSCFStepKernel : public IntegrateDrudeSCFStepKernel {
 public:
-    CudaIntegrateDrudeSCFStepKernel(std::string name, const Platform& platform, CudaContext& cu) :
+    CudaIntegrateDrudeSCFStepKernel(const std::string& name, const Platform& platform, CudaContext& cu) :
             IntegrateDrudeSCFStepKernel(name, platform), cu(cu), minimizerPos(NULL) {
     }
     ~CudaIntegrateDrudeSCFStepKernel();

plugins/drude/platforms/opencl/src/OpenCLDrudeKernels.h

@@ -44,7 +44,7 @@ namespace OpenMM {
  */
 class OpenCLCalcDrudeForceKernel : public CalcDrudeForceKernel {
 public:
-    OpenCLCalcDrudeForceKernel(std::string name, const Platform& platform, OpenCLContext& cl) :
+    OpenCLCalcDrudeForceKernel(const std::string& name, const Platform& platform, OpenCLContext& cl) :
             CalcDrudeForceKernel(name, platform), cl(cl) {
     }
     /**
@@ -81,7 +81,7 @@ private:
  */
 class OpenCLIntegrateDrudeLangevinStepKernel : public IntegrateDrudeLangevinStepKernel {
 public:
-    OpenCLIntegrateDrudeLangevinStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) :
+    OpenCLIntegrateDrudeLangevinStepKernel(const std::string& name, const Platform& platform, OpenCLContext& cl) :
             IntegrateDrudeLangevinStepKernel(name, platform), cl(cl), hasInitializedKernels(false) {
     }
     /**
@@ -120,7 +120,7 @@ private:
  */
 class OpenCLIntegrateDrudeSCFStepKernel : public IntegrateDrudeSCFStepKernel {
 public:
-    OpenCLIntegrateDrudeSCFStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) :
+    OpenCLIntegrateDrudeSCFStepKernel(const std::string& name, const Platform& platform, OpenCLContext& cl) :
             IntegrateDrudeSCFStepKernel(name, platform), cl(cl), hasInitializedKernels(false), minimizerPos(NULL) {
     }
     ~OpenCLIntegrateDrudeSCFStepKernel();

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp

@@ -43,22 +43,22 @@ using namespace std;
 
 static vector<Vec3>& extractPositions(ContextImpl& context) {
     ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
-    return *((vector<Vec3>*) data->positions);
+    return *data->positions;
 }
 
 static vector<Vec3>& extractVelocities(ContextImpl& context) {
     ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
-    return *((vector<Vec3>*) data->velocities);
+    return *data->velocities;
 }
 
 static vector<Vec3>& extractForces(ContextImpl& context) {
     ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
-    return *((vector<Vec3>*) data->forces);
+    return *data->forces;
 }
 
 static ReferenceConstraints& extractConstraints(ContextImpl& context) {
     ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
-    return *(ReferenceConstraints*) data->constraints;
+    return *data->constraints;
 }
 
 static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>& inverseMasses, double timeShift) {

plugins/drude/platforms/reference/src/ReferenceDrudeKernels.h

@@ -48,7 +48,7 @@ namespace OpenMM {
  */
 class ReferenceCalcDrudeForceKernel : public CalcDrudeForceKernel {
 public:
-    ReferenceCalcDrudeForceKernel(std::string name, const Platform& platform) : CalcDrudeForceKernel(name, platform) {
+    ReferenceCalcDrudeForceKernel(const std::string& name, const Platform& platform) : CalcDrudeForceKernel(name, platform) {
     }
     /**
      * Initialize the kernel.
@@ -85,7 +85,7 @@ private:
  */
 class ReferenceIntegrateDrudeLangevinStepKernel : public IntegrateDrudeLangevinStepKernel {
 public:
-    ReferenceIntegrateDrudeLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) :
+    ReferenceIntegrateDrudeLangevinStepKernel(const std::string& name, const Platform& platform, ReferencePlatform::PlatformData& data) :
         IntegrateDrudeLangevinStepKernel(name, platform), data(data) {
     }
     ~ReferenceIntegrateDrudeLangevinStepKernel();
@@ -126,7 +126,7 @@ private:
  */
 class ReferenceIntegrateDrudeSCFStepKernel : public IntegrateDrudeSCFStepKernel {
 public:
-    ReferenceIntegrateDrudeSCFStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) :
+    ReferenceIntegrateDrudeSCFStepKernel(const std::string& name, const Platform& platform, ReferencePlatform::PlatformData& data) :
         IntegrateDrudeSCFStepKernel(name, platform), data(data), minimizerPos(NULL) {
     }
     ~ReferenceIntegrateDrudeSCFStepKernel();

plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.h

@@ -45,7 +45,7 @@ namespace OpenMM {
  */
 class CudaIntegrateRPMDStepKernel : public IntegrateRPMDStepKernel {
 public:
-    CudaIntegrateRPMDStepKernel(std::string name, const Platform& platform, CudaContext& cu) :
+    CudaIntegrateRPMDStepKernel(const std::string& name, const Platform& platform, CudaContext& cu) :
             IntegrateRPMDStepKernel(name, platform), cu(cu) {
     }
     /**

plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.h

@@ -44,7 +44,7 @@ namespace OpenMM {
  */
 class OpenCLIntegrateRPMDStepKernel : public IntegrateRPMDStepKernel {
 public:
-    OpenCLIntegrateRPMDStepKernel(std::string name, const Platform& platform, OpenCLContext& cl) :
+    OpenCLIntegrateRPMDStepKernel(const std::string& name, const Platform& platform, OpenCLContext& cl) :
             IntegrateRPMDStepKernel(name, platform), cl(cl), hasInitializedKernel(false) {
     }
     /**

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp

@@ -39,17 +39,17 @@ using namespace std;
 
 static vector<Vec3>& extractPositions(ContextImpl& context) {
     ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
-    return *((vector<Vec3>*) data->positions);
+    return *data->positions;
 }
 
 static vector<Vec3>& extractVelocities(ContextImpl& context) {
     ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
-    return *((vector<Vec3>*) data->velocities);
+    return *data->velocities;
 }
 
 static vector<Vec3>& extractForces(ContextImpl& context) {
     ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
-    return *((vector<Vec3>*) data->forces);
+    return *data->forces;
 }
 
 ReferenceIntegrateRPMDStepKernel::~ReferenceIntegrateRPMDStepKernel() {

plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.h

@@ -45,7 +45,7 @@ namespace OpenMM {
  */
 class ReferenceIntegrateRPMDStepKernel : public IntegrateRPMDStepKernel {
 public:
-    ReferenceIntegrateRPMDStepKernel(std::string name, const Platform& platform) :
+    ReferenceIntegrateRPMDStepKernel(const std::string& name, const Platform& platform) :
             IntegrateRPMDStepKernel(name, platform), fft(NULL) {
     }
     ~ReferenceIntegrateRPMDStepKernel();

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/src/VariableLangevinIntegratorProxy.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Yutong Zhao                                        *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,22 +36,23 @@ using namespace std;
 using namespace OpenMM;
 
 VariableLangevinIntegratorProxy::VariableLangevinIntegratorProxy() : SerializationProxy("VariableLangevinIntegrator") {
-
 }
 
 void VariableLangevinIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const VariableLangevinIntegrator& integrator = *reinterpret_cast<const VariableLangevinIntegrator*>(object);
     node.setDoubleProperty("stepSize", integrator.getStepSize());
     node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
     node.setDoubleProperty("temperature", integrator.getTemperature());
     node.setDoubleProperty("friction", integrator.getFriction());
     node.setDoubleProperty("errorTol", integrator.getErrorTolerance());
+    node.setDoubleProperty("maxStepSize", integrator.getMaximumStepSize());
     node.setIntProperty("randomSeed", integrator.getRandomNumberSeed());
 }
 
 void* VariableLangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     VariableLangevinIntegrator *integrator = new VariableLangevinIntegrator(node.getDoubleProperty("temperature"),
                                                             node.getDoubleProperty("friction"),
@@ -59,5 +60,7 @@ void* VariableLangevinIntegratorProxy::deserialize(const SerializationNode& node
     integrator->setStepSize(node.getDoubleProperty("stepSize"));
     integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
     integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
+    if (version > 1)
+        integrator->setMaximumStepSize(node.getDoubleProperty("maxStepSize"));
     return integrator;
 }
\ No newline at end of file

serialization/src/VariableVerletIntegratorProxy.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Yutong Zhao                                        *
  * Contributors:                                                              *
  *                                                                            *
@@ -36,22 +36,25 @@ using namespace std;
 using namespace OpenMM;
 
 VariableVerletIntegratorProxy::VariableVerletIntegratorProxy() : SerializationProxy("VariableVerletIntegrator") {
-
 }
 
 void VariableVerletIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
-    node.setIntProperty("version", 1);
+    node.setIntProperty("version", 2);
     const VariableVerletIntegrator& integrator = *reinterpret_cast<const VariableVerletIntegrator*>(object);
     node.setDoubleProperty("errorTol", integrator.getErrorTolerance());
+    node.setDoubleProperty("maxStepSize", integrator.getMaximumStepSize());
     node.setDoubleProperty("stepSize", integrator.getStepSize());
     node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
 }
 
 void* VariableVerletIntegratorProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1)
+    int version = node.getIntProperty("version");
+    if (version < 1 || version > 2)
         throw OpenMMException("Unsupported version number");
     VariableVerletIntegrator *integrator = new VariableVerletIntegrator(node.getDoubleProperty("errorTol"));
     integrator->setStepSize(node.getDoubleProperty("stepSize"));
     integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
+    if (version > 1)
+        integrator->setMaximumStepSize(node.getDoubleProperty("maxStepSize"));
     return integrator;
 }
\ No newline at end of file

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;
@@ -89,29 +104,31 @@ void testSerializeBrownianIntegrator() {
 }
 
 void testSerializeVariableVerletIntegrator() {
-    VariableVerletIntegrator *intg = new VariableVerletIntegrator(0.04234);
+    VariableVerletIntegrator intg(0.04234);
+    intg.setMaximumStepSize(0.32);
     stringstream ss;
-    XmlSerializer::serialize<Integrator>(intg, "VariableVerletIntegrator", ss);
+    XmlSerializer::serialize<Integrator>(&intg, "VariableVerletIntegrator", ss);
     VariableVerletIntegrator *intg2 = dynamic_cast<VariableVerletIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
-    ASSERT_EQUAL(intg->getConstraintTolerance(), intg2->getConstraintTolerance());
-    ASSERT_EQUAL(intg->getStepSize(), intg2->getStepSize());
-    ASSERT_EQUAL(intg->getErrorTolerance(), intg2->getErrorTolerance());
-    delete intg;
+    ASSERT_EQUAL(intg.getConstraintTolerance(), intg2->getConstraintTolerance());
+    ASSERT_EQUAL(intg.getStepSize(), intg2->getStepSize());
+    ASSERT_EQUAL(intg.getErrorTolerance(), intg2->getErrorTolerance());
+    ASSERT_EQUAL(intg.getMaximumStepSize(), intg2->getMaximumStepSize());
     delete intg2;
 }
 
 void testSerializeVariableLangevinIntegrator() {
-    VariableLangevinIntegrator *intg = new VariableLangevinIntegrator(243.1, 3.234, 0.0021);
+    VariableLangevinIntegrator intg(243.1, 3.234, 0.0021);
+    intg.setMaximumStepSize(0.32);
     stringstream ss;
-    XmlSerializer::serialize<Integrator>(intg, "VariableLangevinIntegrator", ss);
+    XmlSerializer::serialize<Integrator>(&intg, "VariableLangevinIntegrator", ss);
     VariableLangevinIntegrator *intg2 = dynamic_cast<VariableLangevinIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
-    ASSERT_EQUAL(intg->getConstraintTolerance(), intg2->getConstraintTolerance());
-    ASSERT_EQUAL(intg->getStepSize(), intg2->getStepSize());
-    ASSERT_EQUAL(intg->getErrorTolerance(), intg2->getErrorTolerance());
-    ASSERT_EQUAL(intg->getFriction(), intg2->getFriction());
-    ASSERT_EQUAL(intg->getTemperature(), intg2->getTemperature());
-    ASSERT_EQUAL(intg->getRandomNumberSeed(), intg2->getRandomNumberSeed());
-    delete intg;
+    ASSERT_EQUAL(intg.getConstraintTolerance(), intg2->getConstraintTolerance());
+    ASSERT_EQUAL(intg.getStepSize(), intg2->getStepSize());
+    ASSERT_EQUAL(intg.getErrorTolerance(), intg2->getErrorTolerance());
+    ASSERT_EQUAL(intg.getFriction(), intg2->getFriction());
+    ASSERT_EQUAL(intg.getTemperature(), intg2->getTemperature());
+    ASSERT_EQUAL(intg.getRandomNumberSeed(), intg2->getRandomNumberSeed());
+    ASSERT_EQUAL(intg.getMaximumStepSize(), intg2->getMaximumStepSize());
     delete intg2;
 }
 
@@ -242,6 +259,7 @@ int main() {
         testSerializeVariableLangevinIntegrator();
         testSerializeVariableVerletIntegrator();
         testSerializeLangevinIntegrator();
+        testSerializeBAOABLangevinIntegrator();
         testSerializeCompoundIntegrator();
     }
     catch(const exception& e) {

serialization/tests/TestSerializeState.cpp

@@ -128,7 +128,7 @@ void testSerialization() {
 	map<string, double>::const_iterator it1=p1.begin();
 	map<string, double>::const_iterator it2=p2.begin();
 	//maps are ordered, so iterators should be in the same order. 
-	for (it1 = p1.begin(); it1 != p1.end(); it1++, it2++) {
+	for (it1 = p1.begin(); it1 != p1.end(); ++it1, ++it2) {
 		assert((it1->first).compare(it2->first) == 0);
 		ASSERT_EQUAL(it1->second, it2->second);
 	}

tests/TestBAOABLangevinIntegrator.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) 2008-2019 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/Context.h"
+#include "openmm/HarmonicBondForce.h"
+#include "openmm/NonbondedForce.h"
+#include "openmm/System.h"
+#include "openmm/BAOABLangevinIntegrator.h"
+#include "SimTKOpenMMRealType.h"
+#include "sfmt/SFMT.h"
+#include <iostream>
+#include <vector>
+
+using namespace OpenMM;
+using namespace std;
+
+const double TOL = 1e-5;
+
+void testSingleBond() {
+    System system;
+    system.addParticle(2.0);
+    system.addParticle(2.0);
+    BAOABLangevinIntegrator integrator(0, 0.1, 0.01);
+    HarmonicBondForce* forceField = new HarmonicBondForce();
+    forceField->addBond(0, 1, 1.5, 1);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    context.setPositions(positions);
+    
+    // This is simply a damped harmonic oscillator, so compare it to the analytical solution.
+    
+    double freq = std::sqrt(1-0.05*0.05);
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions | State::Velocities);
+        double time = state.getTime();
+        double expectedDist = 1.5+0.5*std::exp(-0.05*time)*std::cos(freq*time);
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedDist, 0, 0), state.getPositions()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedDist, 0, 0), state.getPositions()[1], 0.02);
+        double expectedSpeed = -0.5*std::exp(-0.05*time)*(0.05*std::cos(freq*time)+freq*std::sin(freq*time));
+        ASSERT_EQUAL_VEC(Vec3(-0.5*expectedSpeed, 0, 0), state.getVelocities()[0], 0.02);
+        ASSERT_EQUAL_VEC(Vec3(0.5*expectedSpeed, 0, 0), state.getVelocities()[1], 0.02);
+        integrator.step(1);
+    }
+    
+    // Now set the friction to 0 and see if it conserves energy.
+    
+    integrator.setFriction(0.0);
+    context.setPositions(positions);
+    State state = context.getState(State::Energy);
+    double initialEnergy = state.getKineticEnergy()+state.getPotentialEnergy();
+    for (int i = 0; i < 1000; ++i) {
+        state = context.getState(State::Energy);
+        double energy = state.getKineticEnergy()+state.getPotentialEnergy();
+        ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
+        integrator.step(1);
+    }
+}
+
+void testTemperature() {
+    const int numParticles = 8;
+    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);
+    NonbondedForce* forceField = new NonbondedForce();
+    forceField->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(2.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    }
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    for (int i = 0; i < numParticles; ++i)
+        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
+    context.setPositions(positions);
+    
+    // Let it equilibrate.
+    
+    integrator.step(5000);
+    
+    // Now run it for a while and see if the temperature is correct.
+    
+    double ke = 0.0;
+    int steps = 10000;
+    for (int i = 0; i < steps; ++i) {
+        State state = context.getState(State::Energy);
+        ke += state.getKineticEnergy();
+        integrator.step(1);
+    }
+    ke /= steps;
+    double expected = 0.5*numParticles*3*BOLTZ*temp;
+    ASSERT_USUALLY_EQUAL_TOL(expected, ke, 6/std::sqrt((double) steps));
+}
+
+void testConstraints() {
+    const int numParticles = 8;
+    const int numConstraints = 5;
+    const double temp = 100.0;
+    System system;
+    BAOABLangevinIntegrator integrator(temp, 2.0, 0.01);
+    integrator.setConstraintTolerance(1e-5);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(10.0);
+        forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
+    }
+    system.addConstraint(0, 1, 1.0);
+    system.addConstraint(1, 2, 1.0);
+    system.addConstraint(2, 3, 1.0);
+    system.addConstraint(4, 5, 1.0);
+    system.addConstraint(6, 7, 1.0);
+    system.addForce(forceField);
+    Context context(system, integrator, platform);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    OpenMM_SFMT::SFMT sfmt;
+    init_gen_rand(0, sfmt);
+
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = Vec3(i/2, (i+1)/2, 0);
+        velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
+    }
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+
+    // Simulate it and see whether the constraints remain satisfied.
+
+    for (int i = 0; i < 1000; ++i) {
+        State state = context.getState(State::Positions);
+        for (int j = 0; j < numConstraints; ++j) {
+            int particle1, particle2;
+            double distance;
+            system.getConstraintParameters(j, particle1, particle2, distance);
+            Vec3 p1 = state.getPositions()[particle1];
+            Vec3 p2 = state.getPositions()[particle2];
+            double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
+            ASSERT_EQUAL_TOL(distance, dist, 1e-4);
+        }
+        integrator.step(1);
+    }
+}
+
+void testConstrainedMasslessParticles() {
+    System system;
+    system.addParticle(0.0);
+    system.addParticle(1.0);
+    system.addConstraint(0, 1, 1.5);
+    vector<Vec3> positions(2);
+    positions[0] = Vec3(-1, 0, 0);
+    positions[1] = Vec3(1, 0, 0);
+    BAOABLangevinIntegrator integrator(300.0, 2.0, 0.01);
+    bool failed = false;
+    try {
+        // This should throw an exception.
+        
+        Context context(system, integrator, platform);
+    }
+    catch (exception& ex) {
+        failed = true;
+    }
+    ASSERT(failed);
+    
+    // Now make both particles massless, which should work.
+    
+    system.setParticleMass(1, 0.0);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocitiesToTemperature(300.0);
+    integrator.step(1);
+    State state = context.getState(State::Velocities);
+    ASSERT_EQUAL(0.0, state.getVelocities()[0][0]);
+}
+
+void testRandomSeed() {
+    const int numParticles = 8;
+    const double temp = 100.0;
+    System system;
+    BAOABLangevinIntegrator integrator(temp, 2.0, 0.01);
+    NonbondedForce* forceField = new NonbondedForce();
+    for (int i = 0; i < numParticles; ++i) {
+        system.addParticle(2.0);
+        forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
+    }
+    system.addForce(forceField);
+    vector<Vec3> positions(numParticles);
+    vector<Vec3> velocities(numParticles);
+    for (int i = 0; i < numParticles; ++i) {
+        positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
+        velocities[i] = Vec3(0, 0, 0);
+    }
+
+    // Try twice with the same random seed.
+
+    integrator.setRandomNumberSeed(5);
+    Context context(system, integrator, platform);
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state1 = context.getState(State::Positions);
+    context.reinitialize();
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state2 = context.getState(State::Positions);
+
+    // Try twice with a different random seed.
+
+    integrator.setRandomNumberSeed(10);
+    context.reinitialize();
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state3 = context.getState(State::Positions);
+    context.reinitialize();
+    context.setPositions(positions);
+    context.setVelocities(velocities);
+    integrator.step(10);
+    State state4 = context.getState(State::Positions);
+
+    // Compare the results.
+
+    for (int i = 0; i < numParticles; i++) {
+        for (int j = 0; j < 3; j++) {
+            ASSERT_EQUAL_TOL(state1.getPositions()[i][j], state2.getPositions()[i][j], 1e-6);
+            ASSERT_EQUAL_TOL(state3.getPositions()[i][j], state4.getPositions()[i][j], 1e-6);
+            ASSERT(state1.getPositions()[i][j] != state3.getPositions()[i][j]);
+        }
+    }
+}
+
+void runPlatformTests();
+
+int main(int argc, char* argv[]) {
+    try {
+        initializeTests(argc, argv);
+        testSingleBond();
+        testTemperature();
+        testConstraints();
+        testConstrainedMasslessParticles();
+        testRandomSeed();
+        runPlatformTests();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}