Created MonteCarloFlexibleBarostat (#3284)

* Created MonteCarloFlexibleBarostat

* Improved test cases

* Documentation for MonteCarloFlexibleBarostat

* Added a missing include

* Serialization for MonteCarloFlexibleBarostat

* Added MonteCarloFlexibleBarostat to C++ API docs index

* Added citation for MonteCarloFlexibleBarostat

docs-source/api-c++/forces.rst

@@ -30,7 +30,6 @@ These classes implement forces that are widely used in biomolecular simulation.
     generated/GayBerneForce
     generated/HarmonicAngleForce
     generated/HarmonicBondForce
-    generated/HippoNonbondedForce
     generated/NonbondedForce
     generated/PeriodicTorsionForce
     generated/RBTorsionForce
@@ -49,6 +48,7 @@ These forces are used to implement the polarizable AMOEBA force fields.
     generated/AmoebaTorsionTorsionForce
     generated/AmoebaVdwForce
     generated/AmoebaWcaDispersionForce
+    generated/HippoNonbondedForce
 
 
 Pseudo-forces
@@ -67,6 +67,7 @@ be combined in arbitrary ways.
     generated/CMMotionRemover
     generated/MonteCarloAnisotropicBarostat
     generated/MonteCarloBarostat
+    generated/MonteCarloFlexibleBarostat
     generated/MonteCarloMembraneBarostat
     generated/RMSDForce
     generated/RPMDMonteCarloBarostat

docs-source/usersguide/references.bib

@@ -595,6 +595,17 @@
   pages =    {6363--6374},
 }
 
+@article{Vandenhaute2021
+   author = {Vandenhaute, Sander and Rogge, Sven M. J. and Van Speybroeck, Veronique},   
+   title = {Large-Scale Molecular Dynamics Simulations Reveal New Insights Into the Phase Transition Mechanisms in MIL-53(Al)},      
+   journal = {Frontiers in Chemistry},      
+   volume = {9},      
+   pages = {699},     
+   year = {2021},      
+   doi = {10.3389/fchem.2021.718920},      
+   type = {Journal Article}
+}
+
 @article{Wang2000
    author = {Wang, J. and Cieplak, P. and Kollman, P.A.},
    title = {How well does a restrained electrostatic potential ({RESP}) model perform in calculating conformational energies of organic and biological molecules?},

docs-source/usersguide/theory/02_standard_forces.rst

@@ -671,6 +671,16 @@ behavior of the periodic box:
   * inversely varying with the X and Y axes (so the total box volume does not
     change)
 
+MonteCarloFlexibleBarostat
+**************************
+
+MonteCarloFlexibleBarostat is very similar to MonteCarloBarostat, but it allows
+the periodic box to be fully flexible.\ :cite:`Vandenhaute2021`  Monte Carlo
+steps can change not just the lengths of the box sides, but also the angles.  It
+is especially useful for simulations of bulk materials where the shape of a
+crystal's unit cell may not be known in advance, or could even change with time
+as it transitions between phases.
+
 CMMotionRemover
 ***************
 

olla/include/openmm/kernels.h

@@ -1446,8 +1446,9 @@ public:
      *
      * @param system          the System this kernel will be applied to
      * @param barostat        the MonteCarloBarostat this kernel will be used for
+     * @param rigidMolecules  whether molecules should be kept rigid while scaling coordinates
      */
-    virtual void initialize(const System& system, const Force& barostat) = 0;
+    virtual void initialize(const System& system, const Force& barostat, bool rigidMolecules=true) = 0;
     /**
      * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
      * This version scales the x, y, and z positions independently.

openmmapi/include/OpenMM.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2009-2017 Stanford University and the Authors.      *
+ * Portions copyright (c) 2009-2021 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -60,6 +60,7 @@
 #include "openmm/LocalEnergyMinimizer.h"
 #include "openmm/MonteCarloAnisotropicBarostat.h"
 #include "openmm/MonteCarloBarostat.h"
+#include "openmm/MonteCarloFlexibleBarostat.h"
 #include "openmm/MonteCarloMembraneBarostat.h"
 #include "openmm/NonbondedForce.h"
 #include "openmm/Context.h"

openmmapi/include/openmm/MonteCarloFlexibleBarostat.h

+#ifndef OPENMM_MONTECARLOFLEXIBLEBAROSTAT_H_
+#define OPENMM_MONTECARLOFLEXIBLEBAROSTAT_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) 2010-2021 Stanford University and the Authors.      *
+ * Authors: Peter Eastman, Sander Vandenhaute                                 *
+ * 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 "Force.h"
+#include <string>
+#include "internal/windowsExport.h"
+
+namespace OpenMM {
+
+/**
+ * This class uses a Monte Carlo algorithm to adjust the size and shape of the periodic box, simulating the
+ * effect of constant pressure.
+ *
+ * This class is similar to MonteCarloBarostat, but it simulates a fully flexible periodic box
+ * in which all three lengths and all three angles are free to change independently.  It is primarily
+ * useful for simulations of bulk materials where the shape of a crystal's unit cell may not
+ * be known in advance, or could even change with time as it transitions between phases.
+ * 
+ * Like MonteCarloBarostat, the default behavior of this class is to scale the centroid position
+ * of each molecule while holding it rigid.  In simulations of materials where all atoms are
+ * covalently bonded to each other, this behavior will not work well since the entire system
+ * then consists of a single molecule.  You can use setScaleMoleculesAsRigid() to disable this
+ * behavior and instead have it scale the position of every atom independently.
+ * 
+ * This class assumes the simulation is also being run at constant temperature, and requires you
+ * to specify the system temperature (since it affects the acceptance probability for Monte Carlo
+ * moves).  It does not actually perform temperature regulation, however.  You must use another
+ * mechanism along with it to maintain the temperature, such as LangevinIntegrator or AndersenThermostat.
+ */
+
+class OPENMM_EXPORT MonteCarloFlexibleBarostat : public Force {
+public:
+    /**
+     * This is the name of the parameter which stores the current pressure acting on
+     * the system (in bar).
+     */
+    static const std::string& Pressure() {
+        static const std::string key = "MonteCarloPressure";
+        return key;
+    }
+    /**
+     * This is the name of the parameter which stores the current temperature at which the
+     * system is being maintained (in Kelvin)
+     */
+    static const std::string& Temperature() {
+        static const std::string key = "MonteCarloTemperature";
+        return key;
+    }
+    /**
+     * Create a MonteCarloFlexibleBarostat.
+     *
+     * @param defaultPressure         the default pressure acting on the system (in bar)
+     * @param defaultTemperature      the default temperature at which the system is being maintained (in Kelvin)
+     * @param frequency               the frequency at which Monte Carlo pressure changes should be attempted (in time steps)
+     * @param scaleMoleculesAsRigid   if true, coordinate scaling keeps molecules rigid, scaling only the center of mass
+     *                                of each one.  If false, every atom is scaled independently.
+     */
+    MonteCarloFlexibleBarostat(double defaultPressure, double defaultTemperature, int frequency = 25, bool scaleMoleculesAsRigid = true);
+    /**
+     * Get the default pressure acting on the system (in bar).
+     *
+     * @return the default pressure acting on the system, measured in bar.
+     */
+    double getDefaultPressure() const {
+        return defaultPressure;
+    }
+    /**
+     * Set the default pressure acting on the system.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param pressure   the default pressure acting on the system, measured in bar.
+     */
+    void setDefaultPressure(double pressure) {
+        defaultPressure = pressure;
+    }
+    /**
+     * Get the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
+     * 0, the barostat is disabled.
+     */
+    int getFrequency() const {
+        return frequency;
+    }
+    /**
+     * Set the frequency (in time steps) at which Monte Carlo pressure changes should be attempted.  If this is set to
+     * 0, the barostat is disabled.
+     */
+    void setFrequency(int freq) {
+        frequency = freq;
+    }
+    /**
+     * Get the default temperature at which the system is being maintained, measured in Kelvin.
+     */
+    double getDefaultTemperature() const {
+        return defaultTemperature;
+    }
+    /**
+     * Set the default temperature at which the system is being maintained.  This will affect any new Contexts you create,
+     * but not ones that already exist.
+     *
+     * @param temp     the system temperature, measured in Kelvin.
+     */
+    void setDefaultTemperature(double temp) {
+        defaultTemperature = temp;
+    }
+    /**
+     * Get the random number seed.  See setRandomNumberSeed() for details.
+     */
+    int getRandomNumberSeed() const {
+        return randomNumberSeed;
+    }
+    /**
+     * Set the random number seed.  It is guaranteed that if two simulations are run
+     * with different random number seeds, the sequence of Monte Carlo steps will be different.  On
+     * the other hand, no guarantees are made about the behavior of simulations that use the same seed.
+     * In particular, Platforms are permitted to use non-deterministic algorithms which produce different
+     * results on successive runs, even if those runs were initialized identically.
+     *
+     * If seed is set to 0 (which is the default value assigned), a unique seed is chosen when a Context
+     * is created from this Force. This is done to ensure that each Context receives unique random seeds
+     * without you needing to set them explicitly.
+     */
+    void setRandomNumberSeed(int seed) {
+        randomNumberSeed = seed;
+    }
+    /**
+     * Returns whether or not this force makes use of periodic boundary
+     * conditions.
+     *
+     * @returns true if force uses PBC and false otherwise
+     */
+    bool usesPeriodicBoundaryConditions() const {
+        return false;
+    }
+    /**
+     * Get whether scaling is applied to the centroid of each molecule while keeping
+     * the molecules rigid, or to each atom independently.
+     *
+     * @returns true if scaling is applied to molecule centroids, false if it is applied to each atom independently.
+     */
+    bool getScaleMoleculesAsRigid() const {
+        return scaleMoleculesAsRigid;
+    }
+    /**
+     * Set whether scaling is applied to the centroid of each molecule while keeping
+     * the molecules rigid, or to each atom independently.
+     */
+    void setScaleMoleculesAsRigid(bool rigid) {
+        scaleMoleculesAsRigid = rigid;
+    }
+protected:
+    ForceImpl* createImpl() const;
+private:
+    bool scaleMoleculesAsRigid;
+    double defaultPressure, defaultTemperature;
+    int frequency, randomNumberSeed;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_MONTECARLOFLEXIBLEBAROSTAT_H_*/

openmmapi/include/openmm/internal/MonteCarloFlexibleBarostatImpl.h

+#ifndef OPENMM_MONTECARLOFLEXIBLEBAROSTATIMPL_H_
+#define OPENMM_MONTECARLOFLEXIBLEBAROSTATIMPL_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) 2010-2021 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 "ForceImpl.h"
+#include "openmm/MonteCarloFlexibleBarostat.h"
+#include "openmm/Kernel.h"
+#include <string>
+
+namespace OpenMM {
+
+/**
+ * This is the internal implementation of MonteCarloFlexibleBarostat.
+ */
+
+class MonteCarloFlexibleBarostatImpl : public ForceImpl {
+public:
+    MonteCarloFlexibleBarostatImpl(const MonteCarloFlexibleBarostat& owner);
+    void initialize(ContextImpl& context);
+    const MonteCarloFlexibleBarostat& getOwner() const {
+        return owner;
+    }
+    void updateContextState(ContextImpl& context, bool& forcesInvalid);
+    double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
+        // This force doesn't apply forces to particles.
+        return 0.0;
+    }
+    std::map<std::string, double> getDefaultParameters();
+    std::vector<std::string> getKernelNames();
+private:
+    const MonteCarloFlexibleBarostat& owner;
+    int step, numAttempted, numAccepted;
+    double lengthScale;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_MONTECARLOFLEXIBLEBAROSTATIMPL_H_*/

openmmapi/src/MonteCarloAnisotropicBarostatImpl.cpp

@@ -41,8 +41,7 @@
 #include <algorithm>
 
 using namespace OpenMM;
-using namespace OpenMM_SFMT;
-using std::vector;
+using namespace std;
 
 MonteCarloAnisotropicBarostatImpl::MonteCarloAnisotropicBarostatImpl(const MonteCarloAnisotropicBarostat& owner) : owner(owner), step(0) {
 }
@@ -117,13 +116,12 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
     
     double finalEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
     double kT = BOLTZ*context.getParameter(MonteCarloAnisotropicBarostat::Temperature());
-    double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
-    if (w > 0 && SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() > std::exp(-w/kT)) {
+    double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*log(newVolume/volume);
+    if (w > 0 && SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() > exp(-w/kT)) {
         // Reject the step.
         
         kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
         context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
-        volume = newVolume;
     }
     else
         numAccepted[axis]++;
@@ -135,15 +133,15 @@ void MonteCarloAnisotropicBarostatImpl::updateContextState(ContextImpl& context)
             numAccepted[axis] = 0;
         }
         else if (numAccepted[axis] > 0.75*numAttempted[axis]) {
-            volumeScale[axis] = std::min(volumeScale[axis]*1.1, volume*0.3);
+            volumeScale[axis] = min(volumeScale[axis]*1.1, volume*0.3);
             numAttempted[axis] = 0;
             numAccepted[axis] = 0;
         }
     }
 }
 
-std::map<std::string, double> MonteCarloAnisotropicBarostatImpl::getDefaultParameters() {
-    std::map<std::string, double> parameters;
+map<string, double> MonteCarloAnisotropicBarostatImpl::getDefaultParameters() {
+    map<string, double> parameters;
     parameters[MonteCarloAnisotropicBarostat::PressureX()] = getOwner().getDefaultPressure()[0];
     parameters[MonteCarloAnisotropicBarostat::PressureY()] = getOwner().getDefaultPressure()[1];
     parameters[MonteCarloAnisotropicBarostat::PressureZ()] = getOwner().getDefaultPressure()[2];
@@ -151,8 +149,8 @@ std::map<std::string, double> MonteCarloAnisotropicBarostatImpl::getDefaultParam
     return parameters;
 }
 
-std::vector<std::string> MonteCarloAnisotropicBarostatImpl::getKernelNames() {
-    std::vector<std::string> names;
+vector<string> MonteCarloAnisotropicBarostatImpl::getKernelNames() {
+    vector<string> names;
     names.push_back(ApplyMonteCarloBarostatKernel::Name());
     return names;
 }

openmmapi/src/MonteCarloBarostatImpl.cpp

@@ -41,8 +41,7 @@
 #include <algorithm>
 
 using namespace OpenMM;
-using namespace OpenMM_SFMT;
-using std::vector;
+using namespace std;
 
 MonteCarloBarostatImpl::MonteCarloBarostatImpl(const MonteCarloBarostat& owner) : owner(owner), step(0) {
 }
@@ -78,7 +77,7 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context, bool& forc
     double volume = box[0][0]*box[1][1]*box[2][2];
     double deltaVolume = volumeScale*2*(SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber()-0.5);
     double newVolume = volume+deltaVolume;
-    double lengthScale = std::pow(newVolume/volume, 1.0/3.0);
+    double lengthScale = pow(newVolume/volume, 1.0/3.0);
     kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, lengthScale, lengthScale, lengthScale);
     context.getOwner().setPeriodicBoxVectors(box[0]*lengthScale, box[1]*lengthScale, box[2]*lengthScale);
 
@@ -87,13 +86,12 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context, bool& forc
     double finalEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
     double pressure = context.getParameter(MonteCarloBarostat::Pressure())*(AVOGADRO*1e-25);
     double kT = BOLTZ*context.getParameter(MonteCarloBarostat::Temperature());
-    double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*std::log(newVolume/volume);
-    if (w > 0 && SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() > std::exp(-w/kT)) {
+    double w = finalEnergy-initialEnergy + pressure*deltaVolume - context.getMolecules().size()*kT*log(newVolume/volume);
+    if (w > 0 && SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() > exp(-w/kT)) {
         // Reject the step.
 
         kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
         context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
-        volume = newVolume;
     }
     else {
         numAccepted++;
@@ -107,22 +105,22 @@ void MonteCarloBarostatImpl::updateContextState(ContextImpl& context, bool& forc
             numAccepted = 0;
         }
         else if (numAccepted > 0.75*numAttempted) {
-            volumeScale = std::min(volumeScale*1.1, volume*0.3);
+            volumeScale = min(volumeScale*1.1, volume*0.3);
             numAttempted = 0;
             numAccepted = 0;
         }
     }
 }
 
-std::map<std::string, double> MonteCarloBarostatImpl::getDefaultParameters() {
-    std::map<std::string, double> parameters;
+map<string, double> MonteCarloBarostatImpl::getDefaultParameters() {
+    map<string, double> parameters;
     parameters[MonteCarloBarostat::Pressure()] = getOwner().getDefaultPressure();
     parameters[MonteCarloBarostat::Temperature()] = getOwner().getDefaultTemperature();
     return parameters;
 }
 
-std::vector<std::string> MonteCarloBarostatImpl::getKernelNames() {
-    std::vector<std::string> names;
+vector<string> MonteCarloBarostatImpl::getKernelNames() {
+    vector<string> names;
     names.push_back(ApplyMonteCarloBarostatKernel::Name());
     return names;
 }

openmmapi/src/MonteCarloFlexibleBarostat.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) 2010-2021 Stanford University and the Authors.      *
+ * Authors: Peter Eastman, Sander Vandenhaute                                 *
+ * 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/MonteCarloFlexibleBarostat.h"
+#include "openmm/internal/MonteCarloFlexibleBarostatImpl.h"
+
+using namespace OpenMM;
+
+MonteCarloFlexibleBarostat::MonteCarloFlexibleBarostat(double defaultPressure, double defaultTemperature, int frequency, bool scaleMoleculesAsRigid) :
+        defaultPressure(defaultPressure), defaultTemperature(defaultTemperature), frequency(frequency), scaleMoleculesAsRigid(scaleMoleculesAsRigid) {
+    setRandomNumberSeed(0);
+}
+
+ForceImpl* MonteCarloFlexibleBarostat::createImpl() const {
+    return new MonteCarloFlexibleBarostatImpl(*this);
+}

openmmapi/src/MonteCarloFlexibleBarostatImpl.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) 2010-2021 Stanford University and the Authors.      *
+ * Authors: Peter Eastman, Sander Vandenhaute                                 *
+ * 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/MonteCarloFlexibleBarostatImpl.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/OSRngSeed.h"
+#include "openmm/Context.h"
+#include "openmm/kernels.h"
+#include "openmm/OpenMMException.h"
+#include "SimTKOpenMMUtilities.h"
+#include <cmath>
+#include <vector>
+#include <algorithm>
+
+using namespace OpenMM;
+using namespace std;
+
+MonteCarloFlexibleBarostatImpl::MonteCarloFlexibleBarostatImpl(const MonteCarloFlexibleBarostat& owner) : owner(owner), step(0) {
+}
+
+void MonteCarloFlexibleBarostatImpl::initialize(ContextImpl& context) {
+    if (!context.getSystem().usesPeriodicBoundaryConditions())
+        throw OpenMMException("A barostat cannot be used with a non-periodic system");
+    kernel = context.getPlatform().createKernel(ApplyMonteCarloBarostatKernel::Name(), context);
+    kernel.getAs<ApplyMonteCarloBarostatKernel>().initialize(context.getSystem(), owner, owner.getScaleMoleculesAsRigid());
+    Vec3 box[3];
+    context.getPeriodicBoxVectors(box[0], box[1], box[2]);
+    double volume = box[0][0]*box[1][1]*box[2][2];
+    lengthScale = 0.01*pow(volume, 1.0/3.0);
+    numAttempted = 0;
+    numAccepted = 0;
+    SimTKOpenMMUtilities::setRandomNumberSeed(owner.getRandomNumberSeed());
+}
+
+void MonteCarloFlexibleBarostatImpl::updateContextState(ContextImpl& context, bool& forcesInvalid) {
+    if (++step < owner.getFrequency() || owner.getFrequency() == 0)
+        return;
+    step = 0;
+
+    // Compute the current potential energy.
+
+    int groups = context.getIntegrator().getIntegrationForceGroups();
+    double initialEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
+    double pressure = context.getParameter(MonteCarloFlexibleBarostat::Pressure())*(AVOGADRO*1e-25);
+
+    // Generate trial box vectors
+
+    Vec3 box[3], trial[3];
+    context.getPeriodicBoxVectors(box[0], box[1], box[2]);
+    trial[0][0] = box[0][0] + lengthScale*2*(SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber()-0.5);
+    trial[1][0] = box[1][0] + lengthScale*2*(SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber()-0.5);
+    trial[1][1] = box[1][1] + lengthScale*2*(SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber()-0.5);
+    trial[2][0] = box[2][0] + lengthScale*2*(SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber()-0.5);
+    trial[2][1] = box[2][1] + lengthScale*2*(SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber()-0.5);
+    trial[2][2] = box[2][2] + lengthScale*2*(SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber()-0.5);
+
+    // Recompute reduced form by flipping/linear combinations.
+
+    for (auto i = 0; i < 3; i++)
+        if (trial[i][i] < 0)
+            trial[i] = -trial[i];
+    trial[2] -= trial[1]*round(trial[2][1]/trial[1][1]);
+    trial[2] -= trial[0]*round(trial[2][0]/trial[0][0]);
+    trial[1] -= trial[0]*round(trial[1][0]/trial[0][0]);
+    double volume = box[0][0]*box[1][1]*box[2][2];
+    double newVolume = trial[0][0]*trial[1][1]*trial[2][2];
+
+    // Scale particle coordinates and update box vectors in context.
+
+    kernel.getAs<ApplyMonteCarloBarostatKernel>().scaleCoordinates(context, trial[0][0]/box[0][0], trial[1][1]/box[1][1], trial[2][2]/box[2][2]);
+    context.getOwner().setPeriodicBoxVectors(trial[0], trial[1], trial[2]);
+
+    // Compute the energy of the modified system.
+
+    double numberOfScaledParticles;
+    if (owner.getScaleMoleculesAsRigid())
+        numberOfScaledParticles = context.getMolecules().size();
+    else
+        numberOfScaledParticles = context.getSystem().getNumParticles();
+    double finalEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
+    double kT = BOLTZ*context.getParameter(MonteCarloFlexibleBarostat::Temperature());
+    double w0 = finalEnergy-initialEnergy;
+    double w1 = pressure*(newVolume-volume);
+    double w2 = -(numberOfScaledParticles-2)*kT*log(newVolume/volume);
+    double w3 = -kT*log((trial[0][0]*trial[0][0]*trial[1][1])/(box[0][0]*box[0][0]*box[1][1]));
+    double w  = w0+w1+w2+w3;
+    if (w > 0 && SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() > exp(-w/kT)) {
+        // Reject the step.
+
+        kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
+        context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
+    }
+    else {
+        numAccepted++;
+        forcesInvalid = true;
+    }
+    numAttempted++;
+    if (numAttempted >= 10) {
+        if (numAccepted < 0.25*numAttempted) {
+            lengthScale /= 1.1;
+            numAttempted = 0;
+            numAccepted = 0;
+        }
+        else if (numAccepted > 0.75*numAttempted) {
+            lengthScale = min(lengthScale*1.1, pow(newVolume, 1.0/3.0)*0.3);
+            numAttempted = 0;
+            numAccepted = 0;
+        }
+    }
+
+}
+
+map<string, double> MonteCarloFlexibleBarostatImpl::getDefaultParameters() {
+    map<string, double> parameters;
+    parameters[MonteCarloFlexibleBarostat::Pressure()] = getOwner().getDefaultPressure();
+    parameters[MonteCarloFlexibleBarostat::Temperature()] = getOwner().getDefaultTemperature();
+    return parameters;
+}
+
+vector<string> MonteCarloFlexibleBarostatImpl::getKernelNames() {
+    vector<string> names;
+    names.push_back(ApplyMonteCarloBarostatKernel::Name());
+    return names;
+}
+

openmmapi/src/MonteCarloMembraneBarostatImpl.cpp

@@ -41,8 +41,7 @@
 #include <algorithm>
 
 using namespace OpenMM;
-using namespace OpenMM_SFMT;
-using std::vector;
+using namespace std;
 
 MonteCarloMembraneBarostatImpl::MonteCarloMembraneBarostatImpl(const MonteCarloMembraneBarostat& owner) : owner(owner), step(0) {
 }
@@ -118,13 +117,12 @@ void MonteCarloMembraneBarostatImpl::updateContextState(ContextImpl& context) {
     
     double finalEnergy = context.getOwner().getState(State::Energy, false, groups).getPotentialEnergy();
     double kT = BOLTZ*context.getParameter(MonteCarloMembraneBarostat::Temperature());
-    double w = finalEnergy-initialEnergy + pressure*deltaVolume - tension*deltaArea - context.getMolecules().size()*kT*std::log(newVolume/volume);
-    if (w > 0 && SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() > std::exp(-w/kT)) {
+    double w = finalEnergy-initialEnergy + pressure*deltaVolume - tension*deltaArea - context.getMolecules().size()*kT*log(newVolume/volume);
+    if (w > 0 && SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() > exp(-w/kT)) {
         // Reject the step.
         
         kernel.getAs<ApplyMonteCarloBarostatKernel>().restoreCoordinates(context);
         context.getOwner().setPeriodicBoxVectors(box[0], box[1], box[2]);
-        volume = newVolume;
     }
     else
         numAccepted[axis]++;
@@ -136,23 +134,23 @@ void MonteCarloMembraneBarostatImpl::updateContextState(ContextImpl& context) {
             numAccepted[axis] = 0;
         }
         else if (numAccepted[axis] > 0.75*numAttempted[axis]) {
-            volumeScale[axis] = std::min(volumeScale[axis]*1.1, volume*0.3);
+            volumeScale[axis] = min(volumeScale[axis]*1.1, volume*0.3);
             numAttempted[axis] = 0;
             numAccepted[axis] = 0;
         }
     }
 }
 
-std::map<std::string, double> MonteCarloMembraneBarostatImpl::getDefaultParameters() {
-    std::map<std::string, double> parameters;
+map<string, double> MonteCarloMembraneBarostatImpl::getDefaultParameters() {
+    map<string, double> parameters;
     parameters[MonteCarloMembraneBarostat::Pressure()] = getOwner().getDefaultPressure();
     parameters[MonteCarloMembraneBarostat::SurfaceTension()] = getOwner().getDefaultSurfaceTension();
     parameters[MonteCarloMembraneBarostat::Temperature()] = getOwner().getDefaultTemperature();
     return parameters;
 }
 
-std::vector<std::string> MonteCarloMembraneBarostatImpl::getKernelNames() {
-    std::vector<std::string> names;
+vector<string> MonteCarloMembraneBarostatImpl::getKernelNames() {
+    vector<string> names;
     names.push_back(ApplyMonteCarloBarostatKernel::Name());
     return names;
 }

platforms/common/include/openmm/common/CommonKernels.h

@@ -1533,8 +1533,9 @@ public:
      *
      * @param system     the System this kernel will be applied to
      * @param barostat   the MonteCarloBarostat this kernel will be used for
+     * @param rigidMolecules  whether molecules should be kept rigid while scaling coordinates
      */
-    void initialize(const System& system, const Force& barostat);
+    void initialize(const System& system, const Force& barostat, bool rigidMolecules=true);
     /**
      * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
      * This version scales the x, y, and z positions independently.
@@ -1557,7 +1558,7 @@ public:
     void restoreCoordinates(ContextImpl& context);
 private:
     ComputeContext& cc;
-    bool hasInitializedKernels;
+    bool hasInitializedKernels, rigidMolecules;
     int numMolecules;
     ComputeArray savedPositions, savedFloatForces, savedLongForces;
     ComputeArray moleculeAtoms;

platforms/common/src/CommonKernels.cpp

@@ -7680,7 +7680,8 @@ void CommonApplyAndersenThermostatKernel::execute(ContextImpl& context) {
     kernel->execute(cc.getNumAtoms());
 }
 
-void CommonApplyMonteCarloBarostatKernel::initialize(const System& system, const Force& thermostat) {
+void CommonApplyMonteCarloBarostatKernel::initialize(const System& system, const Force& thermostat, bool rigidMolecules) {
+    this->rigidMolecules = rigidMolecules;
     ContextSelector selector(cc);
     savedPositions.initialize(cc, cc.getPaddedNumAtoms(), cc.getUseDoublePrecision() ? sizeof(mm_double4) : sizeof(mm_float4), "savedPositions");
     savedLongForces.initialize<long long>(cc, cc.getPaddedNumAtoms()*3, "savedLongForces");
@@ -7702,7 +7703,14 @@ void CommonApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context,
 
         // Create the arrays with the molecule definitions.
 
-        vector<vector<int> > molecules = context.getMolecules();
+        vector<vector<int> > molecules;
+        if (rigidMolecules)
+            molecules = context.getMolecules();
+        else {
+            molecules.resize(cc.getNumAtoms());
+            for (int i = 0; i < molecules.size(); i++)
+                molecules[i].push_back(i);
+        }
         numMolecules = molecules.size();
         moleculeAtoms.initialize<int>(cc, cc.getNumAtoms(), "moleculeAtoms");
         moleculeStartIndex.initialize<int>(cc, numMolecules+1, "moleculeStartIndex");

platforms/cuda/tests/TestCudaMonteCarloFlexibleBarostat.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) 2021 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 "CudaTests.h"
+#include "TestMonteCarloFlexibleBarostat.h"
+
+void runPlatformTests() {
+}

platforms/opencl/tests/TestOpenCLMonteCarloFlexibleBarostat.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) 2021 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 "OpenCLTests.h"
+#include "TestMonteCarloFlexibleBarostat.h"
+
+void runPlatformTests() {
+}

platforms/reference/include/ReferenceKernels.h

@@ -1546,8 +1546,9 @@ public:
      *
      * @param system     the System this kernel will be applied to
      * @param barostat   the MonteCarloBarostat this kernel will be used for
+     * @param rigidMolecules  whether molecules should be kept rigid while scaling coordinates
      */
-    void initialize(const System& system, const Force& barostat);
+    void initialize(const System& system, const Force& barostat, bool rigidMolecules=true);
     /**
      * Attempt a Monte Carlo step, scaling particle positions (or cluster centers) by a specified value.
      * This version scales the x, y, and z positions independently.
@@ -1569,6 +1570,7 @@ public:
      */
     void restoreCoordinates(ContextImpl& context);
 private:
+    bool rigidMolecules;
     ReferenceMonteCarloBarostat* barostat;
 };
 

platforms/reference/src/ReferenceKernels.cpp

@@ -2703,12 +2703,21 @@ ReferenceApplyMonteCarloBarostatKernel::~ReferenceApplyMonteCarloBarostatKernel(
         delete barostat;
 }
 
-void ReferenceApplyMonteCarloBarostatKernel::initialize(const System& system, const Force& barostat) {
+void ReferenceApplyMonteCarloBarostatKernel::initialize(const System& system, const Force& barostat, bool rigidMolecules) {
+    this->rigidMolecules = rigidMolecules;
 }
 
 void ReferenceApplyMonteCarloBarostatKernel::scaleCoordinates(ContextImpl& context, double scaleX, double scaleY, double scaleZ) {
-    if (barostat == NULL)
+    if (barostat == NULL) {
+        if (rigidMolecules)
             barostat = new ReferenceMonteCarloBarostat(context.getSystem().getNumParticles(), context.getMolecules());
+        else {
+            vector<vector<int> > molecules(context.getSystem().getNumParticles());
+            for (int i = 0; i < molecules.size(); i++)
+                molecules[i].push_back(i);
+            barostat = new ReferenceMonteCarloBarostat(context.getSystem().getNumParticles(), molecules);
+        }
+    }
     vector<Vec3>& posData = extractPositions(context);
     Vec3* boxVectors = extractBoxVectors(context);
     barostat->applyBarostat(posData, boxVectors, scaleX, scaleY, scaleZ);

platforms/reference/tests/TestReferenceMonteCarloFlexibleBarostat.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) 2021 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 "ReferenceTests.h"
+#include "TestMonteCarloFlexibleBarostat.h"
+
+void runPlatformTests() {
+}

serialization/include/openmm/serialization/MonteCarloFlexibleBarostatProxy.h

+#ifndef OPENMM_MONTECARLOFLEXIBLEBAROSTAT_PROXY_H_
+#define OPENMM_MONTECARLOFLEXIBLEBAROSTAT_PROXY_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) 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/internal/windowsExport.h"
+#include "openmm/serialization/SerializationProxy.h"
+
+namespace OpenMM {
+
+/**
+ * This is a proxy for serializing MonteCarloFlexibleBarostat objects.
+ */
+
+class OPENMM_EXPORT MonteCarloFlexibleBarostatProxy : public SerializationProxy {
+public:
+    MonteCarloFlexibleBarostatProxy();
+    void serialize(const void* object, SerializationNode& node) const;
+    void* deserialize(const SerializationNode& node) const;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_MONTECARLOFLEXIBLEBAROSTAT_PROXY_H_*/