Small fix for travis, make NHC public and add serialization code

olla/include/openmm/kernels.h

@@ -55,7 +55,6 @@
 #include "openmm/KernelImpl.h"
 #include "openmm/LangevinIntegrator.h"
 #include "openmm/MonteCarloBarostat.h"
-#include "openmm/internal/NoseHooverChain.h"
 #include "openmm/PeriodicTorsionForce.h"
 #include "openmm/RBTorsionForce.h"
 #include "openmm/RMSDForce.h"
@@ -65,6 +64,7 @@
 #include "openmm/VariableVerletIntegrator.h"
 #include "openmm/VerletIntegrator.h"
 #include "openmm/NoseHooverIntegrator.h"
+#include "openmm/NoseHooverChain.h"
 #include <iosfwd>
 #include <set>
 #include <string>

openmmapi/include/OpenMM.h

@@ -75,6 +75,7 @@
 #include "openmm/Vec3.h"
 #include "openmm/VerletIntegrator.h"
 #include "openmm/NoseHooverIntegrator.h"
+#include "openmm/NoseHooverChain.h"
 #include "openmm/VirtualSite.h"
 #include "openmm/Platform.h"
 #include "openmm/serialization/XmlSerializer.h"

openmmapi/include/openmm/internal/NoseHooverChain.h → openmmapi/include/openmm/NoseHooverChain.h

@@ -36,7 +36,7 @@
 #include <string>
 #include <vector>
 #include "openmm/OpenMMException.h"
-#include "windowsExport.h"
+#include "internal/windowsExport.h"
 
 namespace OpenMM {
 

openmmapi/include/openmm/NoseHooverIntegrator.h

@@ -35,7 +35,7 @@
 #include "Integrator.h"
 #include "openmm/State.h"
 #include "openmm/Kernel.h"
-#include "internal/NoseHooverChain.h"
+#include "NoseHooverChain.h"
 #include "internal/windowsExport.h"
 
 namespace OpenMM {
@@ -118,7 +118,7 @@ public:
     /**
      * Get the temperature of the i-th chain for controling absolute particle motion (in Kelvin).
      * 
-     * @param chainID the index of the Nose-Hoover chain (default=0).
+     * @param chainID the index of the Nose-Hoover chain thermostat (default=0).
      * 
      * @return the temperature.
      */
@@ -127,13 +127,13 @@ public:
      * set the (absolute motion) temperature of the i-th chain.
      *
      * @param temperature the temperature for the Nose-Hoover chain thermostat (in Kelvin).
-     * @param chainID The id of the Nose-Hoover chain for which the temperature is set (default=0).
+     * @param chainID The id of the Nose-Hoover chain thermostat for which the temperature is set (default=0).
      */
     void setTemperature(double temperature, int chainID=0);
     /**
      * Get the temperature of the i-th chain for controling pairs' relative particle motion (in Kelvin).
      *
-     * @param chainID the index of the Nose-Hoover chain (default=0).
+     * @param chainID the index of the Nose-Hoover chain thermostat (default=0).
      *
      * @return the temperature.
      */
@@ -142,13 +142,13 @@ public:
      * set the (relative pair motion) temperature of the i-th chain.
      *
      * @param temperature the temperature for the Nose-Hoover chain thermostat (in Kelvin).
-     * @param chainID The id of the Nose-Hoover chain for which the temperature is set (default=0).
+     * @param chainID The id of the Nose-Hoover chain thermostat for which the temperature is set (default=0).
      */
     void setRelativeTemperature(double temperature, int chainID=0);
     /**
      * Get the collision frequency for absolute motion of the i-th chain (in 1/picosecond).
      * 
-     * @param chainID the index of the Nose-Hoover chain (default=0).
+     * @param chainID the index of the Nose-Hoover chain thermostat (default=0).
      *
      * @return the collision frequency.
      */
@@ -157,13 +157,13 @@ public:
      * Set the collision frequency for absolute motion of the i-th chain.
      *
      * @param frequency the collision frequency in picosecond.
-     * @param chainID the index of the Nose-Hoover chain (default=0).
+     * @param chainID the index of the Nose-Hoover chain thermostat (default=0).
      */
     void setCollisionFrequency(double frequency, int chainID=0);
     /**
      * Get the collision frequency for pairs' relative motion of the i-th chain (in 1/picosecond).
      *
-     * @param chainID the index of the Nose-Hoover chain (default=0).
+     * @param chainID the index of the Nose-Hoover chain thermostat (default=0).
      *
      * @return the collision frequency.
      */
@@ -172,7 +172,7 @@ public:
      * Set the collision frequency for pairs' relative motion of the i-th chain.
      *
      * @param frequency the collision frequency in picosecond.
-     * @param chainID the index of the Nose-Hoover chain (default=0).
+     * @param chainID the index of the Nose-Hoover chain thermostat (default=0).
      */
     void setRelativeCollisionFrequency(double frequency, int chainID=0);
     /**
@@ -183,9 +183,15 @@ public:
     /**
      * Get the number of Nose-Hoover chains registered with this integrator.
      */
-    int getNumNoseHooverChains() const {
+    int getNumNoseHooverThermostats() const {
         return noseHooverChains.size();
     }
+    /**
+     * Get the NoseHooverChain thermostat 
+     *
+     * @param chainID the index of the Nose-Hoover chain thermostat (default=0).
+     */
+    const NoseHooverChain& getNoseHooverThermostat(int chainID=0) const ;
     /**
      * This will be called by the Context when the user modifies aspects of the context state, such
      * as positions, velocities, or parameters.  This gives the Integrator a chance to discard cached
@@ -198,7 +204,13 @@ public:
     virtual void stateChanged(State::DataType changed) {
        if (State::Positions == changed) forcesAreValid = false;
     }
-
+    /**
+     * Return false, if this integrator was set up with the 'default constructor' that thermostats the whole system,
+     * true otherwise. Required for serialization.
+     */
+    bool hasSubsystemThermostats() const {
+        return hasSubsystemThermostats_;
+    }
 protected:
    /**
      * Advance any Nose-Hoover chains associated with this integrator and determine
@@ -236,6 +248,7 @@ protected:
     std::vector<NoseHooverChain> noseHooverChains;
     bool forcesAreValid;
     Kernel vvKernel, nhcKernel;
+    bool hasSubsystemThermostats_;
 };
 
 } // namespace OpenMM

openmmapi/src/NoseHooverChain.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/internal/NoseHooverChain.h"
+#include "openmm/NoseHooverChain.h"
 #include "openmm/OpenMMException.h"
 
 using namespace OpenMM;

openmmapi/src/NoseHooverIntegrator.cpp

@@ -33,7 +33,7 @@
 #include "openmm/Context.h"
 #include "openmm/Force.h"
 #include "openmm/System.h"
-#include "openmm/internal/NoseHooverChain.h"
+#include "openmm/NoseHooverChain.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/CMMotionRemover.h"
 #include "openmm/internal/ContextImpl.h"
@@ -48,13 +48,17 @@ using std::string;
 using std::vector;
 
 NoseHooverIntegrator::NoseHooverIntegrator(double stepSize):
-    forcesAreValid(false)
+    forcesAreValid(false),
+    hasSubsystemThermostats_(true)
 {
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
 }
 NoseHooverIntegrator::NoseHooverIntegrator(double temperature, double collisionFrequency, double stepSize,
-                                           int chainLength, int numMTS, int numYoshidaSuzuki) : forcesAreValid(false) {
+                                           int chainLength, int numMTS, int numYoshidaSuzuki) : 
+    forcesAreValid(false),
+    hasSubsystemThermostats_(false) {
+
     setStepSize(stepSize);
     setConstraintTolerance(1e-5);
     addThermostat(temperature, collisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
@@ -69,7 +73,7 @@ std::pair<double, double> NoseHooverIntegrator::propagateChain(std::pair<double,
 
 int NoseHooverIntegrator::addThermostat(double temperature, double collisionFrequency,
                                         int chainLength, int numMTS, int numYoshidaSuzuki) {
-
+    hasSubsystemThermostats_ = false;
     return addSubsystemThermostat(std::vector<int>(), std::vector<std::pair<int, int>>(), temperature,
                                   collisionFrequency, temperature, collisionFrequency, chainLength, numMTS, numYoshidaSuzuki);
 }
@@ -80,6 +84,14 @@ int NoseHooverIntegrator::addSubsystemThermostat(const std::vector<int>& thermos
                                                  double relativeTemperature, double relativeCollisionFrequency,
                                                  int chainLength, int numMTS, int numYoshidaSuzuki) {
     int chainID = noseHooverChains.size();
+    // check if one thermostat already applies to all atoms or pairs
+    if ( (chainID > 0) && (noseHooverChains[0].getThermostatedAtoms().size()*noseHooverChains[0].getThermostatedPairs().size() == 0) ) {
+        throw OpenMMException(
+            "Cannot add thermostat, since one of the thermostats already in the integrator applies to all particles. "
+            "To manually add thermostats, use the constructor that takes only the "
+            "step size as an input argument."
+        );
+    }
     int nDOF = 0; // is set in initializeThermostats()
     noseHooverChains.emplace_back(temperature, relativeTemperature,
                                  collisionFrequency, relativeCollisionFrequency,
@@ -89,6 +101,10 @@ int NoseHooverIntegrator::addSubsystemThermostat(const std::vector<int>& thermos
     return chainID;
 }
 
+const NoseHooverChain& NoseHooverIntegrator::getNoseHooverThermostat(int chainID) const {
+    ASSERT_VALID_INDEX(chainID, noseHooverChains);
+    return noseHooverChains[chainID];
+}
 
 void NoseHooverIntegrator::initializeThermostats(const System &system) {
 

platforms/opencl/include/OpenCLKernels.h

@@ -36,13 +36,13 @@
 #include "openmm/kernels.h"
 #include "openmm/internal/CompiledExpressionSet.h"
 #include "openmm/internal/CustomIntegratorUtilities.h"
-#include "openmm/internal/NoseHooverChain.h"
 #include "lepton/CompiledExpression.h"
 #include "lepton/ExpressionProgram.h"
 #include "openmm/System.h"
 
 namespace OpenMM {
 
+
 /**
  * This kernel is invoked at the beginning and end of force and energy computations.  It gives the
  * Platform a chance to clear buffers and do other initialization at the beginning, and to do any

plugins/drude/openmmapi/src/DrudeNoseHooverIntegrator.cpp

@@ -51,6 +51,7 @@ DrudeNoseHooverIntegrator::DrudeNoseHooverIntegrator(double temperature, double
                                                      double stepSize, int chainLength, int numMTS, int numYoshidaSuzuki) :
     NoseHooverIntegrator(stepSize) {
 
+    hasSubsystemThermostats_ = false;
     addSubsystemThermostat(std::vector<int>(), std::vector<std::pair<int, int>>(), temperature,
                            collisionFrequency, drudeTemperature, drudeCollisionFrequency,
                            chainLength, numMTS, numYoshidaSuzuki);

plugins/drude/tests/TestDrudeNoseHoover.h

@@ -30,7 +30,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/internal/AssertionUtilities.h"
-#include "openmm/internal/NoseHooverChain.h"
+#include "openmm/NoseHooverChain.h"
 #include "openmm/CMMotionRemover.h"
 #include "openmm/DrudeNoseHooverIntegrator.h"
 #include "openmm/Context.h"

serialization/include/openmm/serialization/NoseHooverIntegratorProxy.h

+#ifndef OPENMM_NOSE_HOOVER_INTEGRATOR_PROXY_H_
+#define OPENMM_NOSE_HOOVER_INTEGRATOR_PROXY_H_
+
+#include "openmm/serialization/XmlSerializer.h"
+
+namespace OpenMM {
+
+class NoseHooverIntegratorProxy : public SerializationProxy {
+public:
+    NoseHooverIntegratorProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+}
+
+#endif /*OPENMM_NOSE_HOOVER_INTEGRATOR_PROXY_H_*/

serialization/src/NoseHooverIntegratorProxy.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: Andrew C. Simmonett, Andreas Krämer                               *
+ * 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/NoseHooverIntegratorProxy.h"
+#include <vector>
+#include <OpenMM.h>
+
+using namespace std;
+using namespace OpenMM;
+
+NoseHooverIntegratorProxy::NoseHooverIntegratorProxy() : SerializationProxy("NoseHooverIntegrator") {
+
+}
+
+void NoseHooverIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
+    node.setIntProperty("version", 1);
+    const NoseHooverIntegrator& integrator = *reinterpret_cast<const NoseHooverIntegrator*>(object);
+    node.setDoubleProperty("stepSize", integrator.getStepSize());
+    node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
+    node.setBoolProperty("hasSubsystemThermostats", integrator.hasSubsystemThermostats());
+    if (integrator.hasSubsystemThermostats()) {
+        // Serialize all thermostats separately
+        for (int i = 0; i < integrator.getNumNoseHooverThermostats(); i++){
+            const auto& chain = integrator.getNoseHooverThermostat(i);
+            auto& chainNode = node.createChildNode("Thermostat");
+            chainNode.setDoubleProperty("temperature", chain.getDefaultTemperature());
+            chainNode.setDoubleProperty("collisionFrequency", chain.getDefaultCollisionFrequency());
+            chainNode.setDoubleProperty("relativeTemperature", chain.getDefaultRelativeTemperature());
+            chainNode.setDoubleProperty("relativeCollisionFrequency", chain.getDefaultRelativeCollisionFrequency());
+            chainNode.setIntProperty("chainLength", chain.getDefaultChainLength());
+            chainNode.setIntProperty("numMTS", chain.getDefaultNumMultiTimeSteps());
+            chainNode.setIntProperty("numYS", chain.getDefaultNumYoshidaSuzukiTimeSteps());
+            auto& particlesNode = chainNode.createChildNode("ThermostatedAtoms");
+            for (int particle: chain.getThermostatedAtoms()){
+                particlesNode.createChildNode("Particle").setIntProperty("index", particle);
+            }
+            auto& pairsNode = chainNode.createChildNode("ThermostatedPairs");
+            for (auto& pair: chain.getThermostatedPairs()){
+                auto& pairNode = pairsNode.createChildNode("Pair");
+                pairNode.setIntProperty("index1", pair.first);
+                pairNode.setIntProperty("index2", pair.second);
+            }
+        }
+    } else { // Serialize standard thermostat
+        node.setDoubleProperty("temperature", integrator.getTemperature());
+        node.setDoubleProperty("collisionFrequency", integrator.getCollisionFrequency());
+        node.setIntProperty("chainLength", integrator.getNoseHooverThermostat().getDefaultChainLength());
+        node.setIntProperty("numMTS", integrator.getNoseHooverThermostat().getDefaultNumMultiTimeSteps());
+        node.setIntProperty("numYS", integrator.getNoseHooverThermostat().getDefaultNumYoshidaSuzukiTimeSteps());
+    }
+
+}
+
+void* NoseHooverIntegratorProxy::deserialize(const SerializationNode& node) const {
+    if (node.getIntProperty("version") != 1)
+        throw OpenMMException("Unsupported version number");
+    NoseHooverIntegrator* integrator;
+    if (node.getBoolProperty("hasSubsystemThermostats")){
+        // deserialize all chains
+        integrator = new NoseHooverIntegrator(node.getDoubleProperty("stepSize"));
+        for (auto& chainNode : node.getChildren()) {
+            // particles
+            const auto& particlesNode = chainNode.getChildNode("ThermostatedAtoms");
+            vector<int> particles;
+            for (auto& particleNode: particlesNode.getChildren()){
+                particles.push_back(particleNode.getIntProperty("index"));
+            }
+            // pairs
+            const auto& pairsNode = chainNode.getChildNode("ThermostatedPairs");
+            vector<pair<int, int>> pairs;
+            for (auto& pairNode: pairsNode.getChildren()){
+                pairs.emplace_back(pairNode.getIntProperty("index1"), pairNode.getIntProperty("index2"));
+            }
+            integrator->addSubsystemThermostat(
+                particles, pairs, 
+                chainNode.getDoubleProperty("temperature"),
+                chainNode.getDoubleProperty("collisionFrequency"),
+                chainNode.getDoubleProperty("relativeTemperature"),
+                chainNode.getDoubleProperty("relativeCollisionFrequency"),
+                chainNode.getIntProperty("chainLength"),
+                chainNode.getIntProperty("numMTS"),
+                chainNode.getIntProperty("numYS")
+            );
+        }
+    } else {
+        integrator = new NoseHooverIntegrator(
+            node.getDoubleProperty("temperature"),
+            node.getDoubleProperty("collisionFrequency"),
+            node.getDoubleProperty("stepSize"),
+            node.getIntProperty("chainLength"),
+            node.getIntProperty("numMTS"),
+            node.getIntProperty("numYS")
+        );
+    }
+    integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
+
+    return integrator;
+}

serialization/src/SerializationProxyRegistration.cpp

@@ -55,6 +55,7 @@
 #include "openmm/MonteCarloBarostat.h"
 #include "openmm/MonteCarloMembraneBarostat.h"
 #include "openmm/NonbondedForce.h"
+#include "openmm/NoseHooverIntegrator.h"
 #include "openmm/PeriodicTorsionForce.h"
 #include "openmm/RBTorsionForce.h"
 #include "openmm/RMSDForce.h"
@@ -91,6 +92,7 @@
 #include "openmm/serialization/MonteCarloBarostatProxy.h"
 #include "openmm/serialization/MonteCarloMembraneBarostatProxy.h"
 #include "openmm/serialization/NonbondedForceProxy.h"
+#include "openmm/serialization/NoseHooverIntegratorProxy.h"
 #include "openmm/serialization/PeriodicTorsionForceProxy.h"
 #include "openmm/serialization/RBTorsionForceProxy.h"
 #include "openmm/serialization/RMSDForceProxy.h"
@@ -148,6 +150,7 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(MonteCarloBarostat), new MonteCarloBarostatProxy());
     SerializationProxy::registerProxy(typeid(MonteCarloMembraneBarostat), new MonteCarloMembraneBarostatProxy());
     SerializationProxy::registerProxy(typeid(NonbondedForce), new NonbondedForceProxy());
+    SerializationProxy::registerProxy(typeid(NoseHooverIntegrator), new NoseHooverIntegratorProxy());
     SerializationProxy::registerProxy(typeid(PeriodicTorsionForce), new PeriodicTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(RBTorsionForce), new RBTorsionForceProxy());
     SerializationProxy::registerProxy(typeid(RMSDForce), new RMSDForceProxy());
@@ -156,4 +159,4 @@ extern "C" void registerSerializationProxies() {
     SerializationProxy::registerProxy(typeid(VariableLangevinIntegrator), new VariableLangevinIntegratorProxy());
     SerializationProxy::registerProxy(typeid(VariableVerletIntegrator), new VariableVerletIntegratorProxy());
     SerializationProxy::registerProxy(typeid(VerletIntegrator), new VerletIntegratorProxy());
-}
+}
\ No newline at end of file

serialization/tests/TestSerializeNoseHooverIntegrator.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) 2010-2014 Stanford University and the Authors.      *
+ * Authors: Andrew C. Simmonett and Andreas Kraemer
+ * 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/NoseHooverIntegrator.h"
+#include "openmm/serialization/XmlSerializer.h"
+#include "openmm/System.h"
+#include "openmm/Context.h"
+#include <iostream>
+#include <sstream>
+
+using namespace OpenMM;
+using namespace std;
+
+void assertIntegratorsEqual(const NoseHooverIntegrator& integrator1, const NoseHooverIntegrator& integrator2){
+    ASSERT_EQUAL(integrator1.getStepSize(), integrator2.getStepSize());
+    ASSERT_EQUAL(integrator1.getConstraintTolerance(), integrator2.getConstraintTolerance());
+    ASSERT_EQUAL(integrator1.getNumNoseHooverThermostats(), integrator2.getNumNoseHooverThermostats());
+    for (int i = 0; i < integrator1.getNumNoseHooverThermostats(); i++) {
+        const auto &thermostat1 = integrator1.getNoseHooverThermostat(i);
+        const auto &thermostat2 = integrator2.getNoseHooverThermostat(i);
+        ASSERT_EQUAL(thermostat1.getDefaultTemperature(), thermostat2.getDefaultTemperature());
+        ASSERT_EQUAL(thermostat1.getDefaultCollisionFrequency(), thermostat2.getDefaultCollisionFrequency());
+        ASSERT_EQUAL(thermostat1.getDefaultRelativeTemperature(), thermostat2.getDefaultRelativeTemperature());
+        ASSERT_EQUAL(thermostat1.getDefaultRelativeCollisionFrequency(), thermostat2.getDefaultRelativeCollisionFrequency());
+        ASSERT_EQUAL(thermostat1.getDefaultChainLength(), thermostat2.getDefaultChainLength());
+        ASSERT_EQUAL(thermostat1.getDefaultNumMultiTimeSteps(), thermostat2.getDefaultNumMultiTimeSteps());
+        ASSERT_EQUAL(thermostat1.getDefaultNumYoshidaSuzukiTimeSteps(), thermostat2.getDefaultNumYoshidaSuzukiTimeSteps());
+        ASSERT_EQUAL(thermostat1.getDefaultChainID(), thermostat2.getDefaultChainID());
+        const auto &thermostat1Atoms = thermostat1.getThermostatedAtoms();
+        const auto &thermostat2Atoms = thermostat2.getThermostatedAtoms();
+        ASSERT_EQUAL(thermostat1Atoms.size(), thermostat2Atoms.size());
+        for (int j = 0; j < thermostat1Atoms.size(); ++j) {
+            ASSERT_EQUAL(thermostat1Atoms[j], thermostat2Atoms[j]);
+        }
+        const auto &thermostat1Pairs = thermostat1.getThermostatedPairs();
+        const auto &thermostat2Pairs = thermostat2.getThermostatedPairs();
+        ASSERT_EQUAL(thermostat1Pairs.size(), thermostat2Pairs.size());
+        for (int j = 0; j < thermostat1Pairs.size(); ++j) {
+            ASSERT_EQUAL(thermostat1Pairs[j].first, thermostat2Pairs[j].first);
+            ASSERT_EQUAL(thermostat1Pairs[j].second, thermostat2Pairs[j].second);
+        }
+    }
+}
+
+void testSerialization() {
+
+    // Check with custom subsystem thermostats
+
+    NoseHooverIntegrator integrator_sub (0.0006);
+    integrator_sub.setConstraintTolerance(0.0404);
+    integrator_sub.addSubsystemThermostat(
+        {0,1,2,3,4,7}, {{0,7}}, 301.1, 1.1, 1.2, 1.3, 9, 2, 5
+    );
+
+    // Serialize and then deserialize it.
+
+    stringstream buffer;
+    XmlSerializer::serialize<NoseHooverIntegrator>(&integrator_sub, "Integrator", buffer);
+    NoseHooverIntegrator* copy = XmlSerializer::deserialize<NoseHooverIntegrator>(buffer);
+    assertIntegratorsEqual(integrator_sub, *copy);
+
+    // Check with default constructor
+
+    System system;
+    for (int i=0; i<10; i++) system.addParticle(1.0);
+    NoseHooverIntegrator integrator(331, 1.1, 0.004, 5, 5, 5);
+    Context context(system, integrator);
+
+    // Serialize and then deserialize it.
+    stringstream buffer2;
+    XmlSerializer::serialize<NoseHooverIntegrator>(&integrator, "Integrator", buffer2);
+    copy = XmlSerializer::deserialize<NoseHooverIntegrator>(buffer2);
+    // for thermostats that apply to the whole system, the particles are not serialized ...
+    ASSERT_EQUAL(copy->getNoseHooverThermostat(0).getThermostatedAtoms().size(), 0);
+
+    // ... but assigned when creating a context.
+    Context context2(system, *copy);
+    assertIntegratorsEqual(integrator, *copy);
+
+}
+
+int main() {
+    try {
+        testSerialization();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}
+

tests/TestNoseHooverThermostat.h

@@ -30,7 +30,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/internal/AssertionUtilities.h"
-#include "openmm/internal/NoseHooverChain.h"
+#include "openmm/NoseHooverChain.h"
 #include "openmm/NoseHooverIntegrator.h"
 #include "openmm/Context.h"
 #include "openmm/State.h"

wrappers/python/setup.py

@@ -193,7 +193,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
         extra_compile_args.append('/EHsc')
     else:
         if platform.system() == 'Darwin':
-            extra_compile_args += ['-std=c++11 -stdlib=libc++', '-mmacosx-version-min=10.7']
+            extra_compile_args += ['-stdlib=libc++', '-mmacosx-version-min=10.7']
             extra_link_args += ['-stdlib=libc++', '-mmacosx-version-min=10.7', '-Wl', '-rpath', openmm_lib_path]
             # Hard-code CC and CXX to clang, since gcc/g++ will *not* work with
             # Anaconda, despite the fact that distutils will try to use them.

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -482,9 +482,9 @@ UNITS = {
 ("RPMDIntegrator", "getState"): (None,(None, None, None, None)),
 ("RMSDForce", "getReferencePositions") : ("unit.nanometer", ()),
 ("RMSDForce", "getParticles") : (None, ()),
-#("NoseHooverChain", "getThermostatedPairs") : (None, ()),
-#("NoseHooverChain", "getThermostatedAtoms") : (None, ()),
-#("NoseHooverChain", "getDefaultYoshidaSuzukiWeights") : (None, ()),
+("NoseHooverChain", "getThermostatedPairs") : (None, ()),
+("NoseHooverChain", "getThermostatedAtoms") : (None, ()),
+("NoseHooverChain", "getDefaultYoshidaSuzukiWeights") : (None, ()),
 ("NoseHooverIntegrator", "setTemperature") : (None, ("unit.kelvin", None)),
 ("NoseHooverIntegrator", "setRelativeTemperature") : (None, ("unit.kelvin", None) ),
 ("NoseHooverIntegrator", "setCollisionFrequency") : (None, ("unit.picosecond**-1", None)),
@@ -492,6 +492,7 @@ UNITS = {
 ("NoseHooverIntegrator", "computeHeatBathEnergy") : ( "unit.kilojoules_per_mole", ()),
 ("NoseHooverIntegrator", "addThermostat"): (None, ("unit.kelvin", "unit.picosecond**-1", None, None, None)),
 ("NoseHooverIntegrator", "addSubsystemThermostat"):
-    (None, (None, None, "unit.kelvin", "unit.picosecond**-1", "unit.kelvin", "unit.picosecond**-1", None, None, None))
+    (None, (None, None, "unit.kelvin", "unit.picosecond**-1", "unit.kelvin", "unit.picosecond**-1", None, None, None)),
+("NoseHooverIntegrator", "getNumNoseHooverThermostats") : (None, ()),
+("NoseHooverIntegrator", "getNoseHooverThermostat") : (None, ()),
 }
-