Reference implementation of BAOABLangevinIntegrator

olla/include/openmm/kernels.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) 2008-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -33,6 +33,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/AndersenThermostat.h"
+#include "openmm/BAOABLangevinIntegrator.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
@@ -1090,6 +1091,43 @@ public:
     virtual double computeKineticEnergy(ContextImpl& context, const LangevinIntegrator& integrator) = 0;
 };
 
+/**
+ * This kernel is invoked by BAOABLangevinIntegrator to take one time step.
+ */
+class IntegrateBAOABStepKernel : public KernelImpl {
+public:
+    static std::string Name() {
+        return "IntegrateBAOABStep";
+    }
+    IntegrateBAOABStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
+    }
+    /**
+     * Initialize the kernel.
+     * 
+     * @param system     the System this kernel will be applied to
+     * @param integrator the BAOABLangevinIntegrator this kernel will be used for
+     */
+    virtual void initialize(const System& system, const BAOABLangevinIntegrator& integrator) = 0;
+    /**
+     * Execute the kernel.
+     * 
+     * @param context    the context in which to execute this kernel
+     * @param integrator the BAOABLangevinIntegrator this kernel is being used for
+     * @param forcesAreValid if the context has been modified since the last time step, this will be
+     *                       false to show that cached forces are invalid and must be recalculated.
+     *                       On exit, this should specify whether the cached forces are valid at the
+     *                       end of the step.
+     */
+    virtual void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid) = 0;
+    /**
+     * Compute the kinetic energy.
+     * 
+     * @param context    the context in which to execute this kernel
+     * @param integrator the BAOABLangevinIntegrator this kernel is being used for
+     */
+    virtual double computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator) = 0;
+};
+
 /**
  * This kernel is invoked by BrownianIntegrator to take one time step.
  */

openmmapi/include/OpenMM.h

@@ -33,6 +33,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/AndersenThermostat.h"
+#include "openmm/BAOABLangevinIntegrator.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"

openmmapi/include/openmm/BAOABLangevinIntegrator.h

+#ifndef OPENMM_BAOABLANGEVININTEGRATOR_H_
+#define OPENMM_BAOABLANGEVININTEGRATOR_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 "Integrator.h"
+#include "openmm/Kernel.h"
+#include "internal/windowsExport.h"
+
+namespace OpenMM {
+
+/**
+ * This is an Integrator which simulates a System using Langevin dynamics, with
+ * the BAOAB discretization of Leimkuhler and Matthews (http://dx.doi.org/10.1093/amrx/abs010).
+ * This method tend to produce more accurate configurational sampling than other
+ * discretizations, such as the one used in LangevinIntegrator.
+ */
+
+class OPENMM_EXPORT BAOABLangevinIntegrator : public Integrator {
+public:
+    /**
+     * Create a BAOABLangevinIntegrator.
+     * 
+     * @param temperature    the temperature of the heat bath (in Kelvin)
+     * @param frictionCoeff  the friction coefficient which couples the system to the heat bath (in inverse picoseconds)
+     * @param stepSize       the step size with which to integrate the system (in picoseconds)
+     */
+    BAOABLangevinIntegrator(double temperature, double frictionCoeff, double stepSize);
+    /**
+     * Get the temperature of the heat bath (in Kelvin).
+     *
+     * @return the temperature of the heat bath, measured in Kelvin
+     */
+    double getTemperature() const {
+        return temperature;
+    }
+    /**
+     * Set the temperature of the heat bath (in Kelvin).
+     *
+     * @param temp    the temperature of the heat bath, measured in Kelvin
+     */
+    void setTemperature(double temp) {
+        temperature = temp;
+    }
+    /**
+     * Get the friction coefficient which determines how strongly the system is coupled to
+     * the heat bath (in inverse ps).
+     *
+     * @return the friction coefficient, measured in 1/ps
+     */
+    double getFriction() const {
+        return friction;
+    }
+    /**
+     * Set the friction coefficient which determines how strongly the system is coupled to
+     * the heat bath (in inverse ps).
+     *
+     * @param coeff    the friction coefficient, measured in 1/ps
+     */
+    void setFriction(double coeff) {
+        friction = coeff;
+    }
+    /**
+     * Get the random number seed.  See setRandomNumberSeed() for details.
+     */
+    int getRandomNumberSeed() const {
+        return randomNumberSeed;
+    }
+    /**
+     * Set the random number seed.  The precise meaning of this parameter is undefined, and is left up
+     * to each Platform to interpret in an appropriate way.  It is guaranteed that if two simulations
+     * are run with different random number seeds, the sequence of random forces 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 Integrator. 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;
+    }
+    /**
+     * Advance a simulation through time by taking a series of time steps.
+     * 
+     * @param steps   the number of time steps to take
+     */
+    void step(int steps);
+protected:
+    /**
+     * This will be called by the Context when it is created.  It informs the Integrator
+     * of what context it will be integrating, and gives it a chance to do any necessary initialization.
+     * It will also get called again if the application calls reinitialize() on the Context.
+     */
+    void initialize(ContextImpl& context);
+    /**
+     * This will be called by the Context when it is destroyed to let the Integrator do any necessary
+     * cleanup.  It will also get called again if the application calls reinitialize() on the Context.
+     */
+    void cleanup();
+    /**
+     * When the user modifies the state, we need to mark that the forces need to be recalculated.
+     */
+    void stateChanged(State::DataType changed);
+    /**
+     * Get the names of all Kernels used by this Integrator.
+     */
+    std::vector<std::string> getKernelNames();
+    /**
+     * Compute the kinetic energy of the system at the current time.
+     */
+    double computeKineticEnergy();
+private:
+    double temperature, friction;
+    int randomNumberSeed;
+    bool forcesAreValid;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_BAOABLANGEVININTEGRATOR_H_*/

openmmapi/src/BAOABLangevinIntegrator.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) 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/BAOABLangevinIntegrator.h"
+#include "openmm/Context.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/kernels.h"
+#include <string>
+
+using namespace OpenMM;
+using std::string;
+using std::vector;
+
+BAOABLangevinIntegrator::BAOABLangevinIntegrator(double temperature, double frictionCoeff, double stepSize) {
+    setTemperature(temperature);
+    setFriction(frictionCoeff);
+    setStepSize(stepSize);
+    setConstraintTolerance(1e-5);
+    setRandomNumberSeed(0);
+    forcesAreValid = false;
+}
+
+void BAOABLangevinIntegrator::initialize(ContextImpl& contextRef) {
+    if (owner != NULL && &contextRef.getOwner() != owner)
+        throw OpenMMException("This Integrator is already bound to a context");
+    context = &contextRef;
+    owner = &contextRef.getOwner();
+    kernel = context->getPlatform().createKernel(IntegrateBAOABStepKernel::Name(), contextRef);
+    kernel.getAs<IntegrateBAOABStepKernel>().initialize(contextRef.getSystem(), *this);
+}
+
+void BAOABLangevinIntegrator::cleanup() {
+    kernel = Kernel();
+}
+
+void BAOABLangevinIntegrator::stateChanged(State::DataType changed) {
+    forcesAreValid = false;
+}
+
+vector<string> BAOABLangevinIntegrator::getKernelNames() {
+    std::vector<std::string> names;
+    names.push_back(IntegrateBAOABStepKernel::Name());
+    return names;
+}
+
+double BAOABLangevinIntegrator::computeKineticEnergy() {
+    return kernel.getAs<IntegrateBAOABStepKernel>().computeKineticEnergy(*context, *this);
+}
+
+void BAOABLangevinIntegrator::step(int steps) {
+    if (context == NULL)
+        throw OpenMMException("This Integrator is not bound to a context!");  
+    for (int i = 0; i < steps; ++i) {
+        context->updateContextState();
+        kernel.getAs<IntegrateBAOABStepKernel>().execute(*context, *this, forcesAreValid);
+    }
+}

platforms/reference/include/ReferenceBAOABDynamics.h

+
+/* Portions copyright (c) 2006-2019 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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.
+ */
+
+#ifndef __ReferenceBAOABDynamics_H__
+#define __ReferenceBAOABDynamics_H__
+
+#include "ReferenceDynamics.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/windowsExport.h"
+
+namespace OpenMM {
+
+class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
+
+   protected:
+
+      std::vector<OpenMM::Vec3> xPrime, oldx;
+      std::vector<double> inverseMasses;
+      double friction;
+      
+   public:
+
+      /**---------------------------------------------------------------------------------------
+      
+         Constructor
+
+         @param numberOfAtoms  number of atoms
+         @param deltaT         delta t for dynamics
+         @param friction       friction coefficient
+         @param temperature    temperature
+      
+         --------------------------------------------------------------------------------------- */
+
+       ReferenceBAOABDynamics(int numberOfAtoms, double deltaT, double friction, double temperature);
+
+      /**---------------------------------------------------------------------------------------
+      
+         Destructor
+      
+         --------------------------------------------------------------------------------------- */
+
+       ~ReferenceBAOABDynamics();
+
+      /**---------------------------------------------------------------------------------------
+      
+         Get friction coefficient
+      
+         --------------------------------------------------------------------------------------- */
+      
+      double getFriction() const;
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Update
+      
+         @param context             the context this integrator is updating
+         @param system              the System to be integrated
+         @param atomCoordinates     atom coordinates
+         @param velocities          velocities
+         @param masses              atom masses
+         @param forcesAreValid      whether the current forces are valid or need to be recomputed
+         @param tolerance           the constraint tolerance
+      
+         --------------------------------------------------------------------------------------- */
+     
+      void update(OpenMM::ContextImpl& context, std::vector<OpenMM::Vec3>& atomCoordinates,
+                  std::vector<OpenMM::Vec3>& velocities, std::vector<double>& masses, bool& forcesAreValid, double tolerance);
+     
+      /**---------------------------------------------------------------------------------------
+      
+         First update; based on code in update.c do_update_sd() Gromacs 3.1.4
+      
+         @param numberOfAtoms       number of atoms
+         @param atomCoordinates     atom coordinates
+         @param velocities          velocities
+         @param forces              forces
+         @param masses              atom masses
+         @param xPrime              xPrime
+      
+         --------------------------------------------------------------------------------------- */
+      
+      virtual void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
+                       std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, std::vector<OpenMM::Vec3>& xPrime);
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Second update
+      
+         @param numberOfAtoms       number of atoms
+         @param atomCoordinates     atom coordinates
+         @param velocities          velocities
+         @param masses              atom masses
+      
+         --------------------------------------------------------------------------------------- */
+      
+      virtual void updatePart2(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
+                       std::vector<double>& masses, std::vector<OpenMM::Vec3>& xPrime);
+      
+      /**---------------------------------------------------------------------------------------
+      
+         Third update
+      
+         @param numberOfAtoms       number of atoms
+         @param atomCoordinates     atom coordinates
+         @param velocities          velocities
+         @param forces              forces
+         @param masses              atom masses
+      
+         --------------------------------------------------------------------------------------- */
+      
+      virtual void updatePart3(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
+                       std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, std::vector<OpenMM::Vec3>& xPrime);
+};
+
+} // namespace OpenMM
+
+#endif // __ReferenceBAOABDynamics_H__

platforms/reference/include/ReferenceKernels.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) 2008-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -45,6 +45,7 @@ namespace OpenMM {
 
 class ReferenceObc;
 class ReferenceAndersenThermostat;
+class ReferenceBAOABDynamics;
 class ReferenceCustomBondIxn;
 class ReferenceCustomAngleIxn;
 class ReferenceCustomTorsionIxn;
@@ -1170,6 +1171,47 @@ private:
     double prevTemp, prevFriction, prevStepSize;
 };
 
+/**
+ * This kernel is invoked by LangevinIntegrator to take one time step.
+ */
+class ReferenceIntegrateBAOABStepKernel : public IntegrateBAOABStepKernel {
+public:
+    ReferenceIntegrateBAOABStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateBAOABStepKernel(name, platform),
+        data(data), dynamics(0) {
+    }
+    ~ReferenceIntegrateBAOABStepKernel();
+    /**
+     * Initialize the kernel, setting up the particle masses.
+     * 
+     * @param system     the System this kernel will be applied to
+     * @param integrator the BAOABLangevinIntegrator this kernel will be used for
+     */
+    void initialize(const System& system, const BAOABLangevinIntegrator& integrator);
+    /**
+     * Execute the kernel.
+     * 
+     * @param context    the context in which to execute this kernel
+     * @param integrator the BAOABLangevinIntegrator this kernel is being used for
+     * @param forcesAreValid if the context has been modified since the last time step, this will be
+     *                       false to show that cached forces are invalid and must be recalculated.
+     *                       On exit, this should specify whether the cached forces are valid at the
+     *                       end of the step.
+     */
+    void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid);
+    /**
+     * Compute the kinetic energy.
+     * 
+     * @param context    the context in which to execute this kernel
+     * @param integrator the BAOABLangevinIntegrator this kernel is being used for
+     */
+    double computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator);
+private:
+    ReferencePlatform::PlatformData& data;
+    ReferenceBAOABDynamics* dynamics;
+    std::vector<double> masses;
+    double prevTemp, prevFriction, prevStepSize;
+};
+
 /**
  * This kernel is invoked by BrownianIntegrator to take one time step.
  */

platforms/reference/src/ReferenceKernelFactory.cpp

@@ -90,6 +90,8 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
         return new ReferenceIntegrateVerletStepKernel(name, platform, data);
     if (name == IntegrateLangevinStepKernel::Name())
         return new ReferenceIntegrateLangevinStepKernel(name, platform, data);
+    if (name == IntegrateBAOABStepKernel::Name())
+        return new ReferenceIntegrateBAOABStepKernel(name, platform, data);
     if (name == IntegrateBrownianStepKernel::Name())
         return new ReferenceIntegrateBrownianStepKernel(name, platform, data);
     if (name == IntegrateVariableLangevinStepKernel::Name())

platforms/reference/src/ReferenceKernels.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) 2008-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -33,6 +33,7 @@
 #include "ReferenceObc.h"
 #include "ReferenceAndersenThermostat.h"
 #include "ReferenceAngleBondIxn.h"
+#include "ReferenceBAOABDynamics.h"
 #include "ReferenceBondForce.h"
 #include "ReferenceBrownianDynamics.h"
 #include "ReferenceCCMAAlgorithm.h"
@@ -2149,6 +2150,49 @@ double ReferenceIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& c
     return computeShiftedKineticEnergy(context, masses, 0.5*integrator.getStepSize());
 }
 
+ReferenceIntegrateBAOABStepKernel::~ReferenceIntegrateBAOABStepKernel() {
+    if (dynamics)
+        delete dynamics;
+}
+
+void ReferenceIntegrateBAOABStepKernel::initialize(const System& system, const BAOABLangevinIntegrator& integrator) {
+    int numParticles = system.getNumParticles();
+    masses.resize(numParticles);
+    for (int i = 0; i < numParticles; ++i)
+        masses[i] = system.getParticleMass(i);
+    SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
+}
+
+void ReferenceIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid) {
+    double temperature = integrator.getTemperature();
+    double friction = integrator.getFriction();
+    double stepSize = integrator.getStepSize();
+    vector<Vec3>& posData = extractPositions(context);
+    vector<Vec3>& velData = extractVelocities(context);
+    if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
+        // Recreate the computation objects with the new parameters.
+        
+        if (dynamics)
+            delete dynamics;
+        dynamics = new ReferenceBAOABDynamics(
+                context.getSystem().getNumParticles(), 
+                stepSize, 
+                friction, 
+                temperature);
+        dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
+        prevTemp = temperature;
+        prevFriction = friction;
+        prevStepSize = stepSize;
+    }
+    dynamics->update(context, posData, velData, masses, forcesAreValid, integrator.getConstraintTolerance());
+    data.time += stepSize;
+    data.stepCount++;
+}
+
+double ReferenceIntegrateBAOABStepKernel::computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
+    return computeShiftedKineticEnergy(context, masses, 0.0);
+}
+
 ReferenceIntegrateBrownianStepKernel::~ReferenceIntegrateBrownianStepKernel() {
     if (dynamics)
         delete dynamics;

platforms/reference/src/ReferencePlatform.cpp

@@ -67,6 +67,7 @@ ReferencePlatform::ReferencePlatform() {
     registerKernelFactory(CalcGayBerneForceKernel::Name(), factory);
     registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
     registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
+    registerKernelFactory(IntegrateBAOABStepKernel::Name(), factory);
     registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
     registerKernelFactory(IntegrateVariableLangevinStepKernel::Name(), factory);
     registerKernelFactory(IntegrateVariableVerletStepKernel::Name(), factory);

platforms/reference/src/SimTKReference/ReferenceBAOABDynamics.cpp

+
+/* Portions copyright (c) 2006-2019 Stanford University and Simbios.
+ * Contributors: Pande Group
+ *
+ * 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 <cstring>
+#include <sstream>
+
+#include "SimTKOpenMMUtilities.h"
+#include "ReferenceBAOABDynamics.h"
+#include "ReferencePlatform.h"
+#include "ReferenceVirtualSites.h"
+#include "openmm/OpenMMException.h"
+#include "openmm/internal/ContextImpl.h"
+
+using std::vector;
+using namespace OpenMM;
+
+ReferenceBAOABDynamics::ReferenceBAOABDynamics(int numberOfAtoms,
+                                               double deltaT, double friction,
+                                               double temperature) : 
+           ReferenceDynamics(numberOfAtoms, deltaT, temperature), friction(friction) {
+   xPrime.resize(numberOfAtoms);
+   oldx.resize(numberOfAtoms);
+   inverseMasses.resize(numberOfAtoms);
+}
+
+ReferenceBAOABDynamics::~ReferenceBAOABDynamics() {
+}
+
+double ReferenceBAOABDynamics::getFriction() const {
+   return friction;
+}
+
+void ReferenceBAOABDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& atomCoordinates,
+                                              vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses,
+                                              vector<Vec3>& xPrime) {
+    const double halfdt = 0.5*getDeltaT();
+    for (int i = 0; i < numberOfAtoms; i++) {
+        if (inverseMasses[i] != 0.0) {
+            velocities[i] += (halfdt*inverseMasses[i])*forces[i];
+            xPrime[i] = atomCoordinates[i] + velocities[i]*halfdt;
+            oldx[i] = xPrime[i];
+        }
+    }
+}
+
+void ReferenceBAOABDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordinates,
+                                              vector<Vec3>& velocities, vector<double>& inverseMasses,
+                                              vector<Vec3>& xPrime) {
+    const double halfdt = 0.5*getDeltaT();
+    const double kT = BOLTZ*getTemperature();
+    const double friction = getFriction();
+    const double vscale = exp(-getDeltaT()*friction);
+    const double noisescale = sqrt(1-vscale*vscale);
+
+    for (int i = 0; i < numberOfAtoms; i++) {
+        if (inverseMasses[i] != 0.0) {
+            velocities[i] += (xPrime[i]-oldx[i])/halfdt;
+            velocities[i] = vscale*velocities[i] + noisescale*sqrt(kT*inverseMasses[i])*Vec3(
+                    SimTKOpenMMUtilities::getNormallyDistributedRandomNumber(),
+                    SimTKOpenMMUtilities::getNormallyDistributedRandomNumber(),
+                    SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
+            atomCoordinates[i] = xPrime[i];
+            xPrime[i] = atomCoordinates[i] + velocities[i]*halfdt;
+            oldx[i] = xPrime[i];
+        }
+    }
+}
+
+void ReferenceBAOABDynamics::updatePart3(int numberOfAtoms, vector<Vec3>& atomCoordinates,
+                                              vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses,
+                                              vector<Vec3>& xPrime) {
+    const double halfdt = 0.5*getDeltaT();
+    for (int i = 0; i < numberOfAtoms; i++) {
+        if (inverseMasses[i] != 0.0) {
+            velocities[i] += (xPrime[i]-oldx[i])/halfdt;
+            velocities[i] += (halfdt*inverseMasses[i])*forces[i];
+            atomCoordinates[i] = xPrime[i];
+        }
+    }
+}
+
+void ReferenceBAOABDynamics::update(ContextImpl& context, vector<Vec3>& atomCoordinates,
+                                          vector<Vec3>& velocities, vector<double>& masses, bool& forcesAreValid, double tolerance) {
+    int numberOfAtoms = context.getSystem().getNumParticles();
+    ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
+    if (getTimeStep() == 0) {
+        // Invert masses
+
+        for (int ii = 0; ii < numberOfAtoms; ii++) {
+            if (masses[ii] == 0.0)
+                inverseMasses[ii] = 0.0;
+            else
+                inverseMasses[ii] = 1.0/masses[ii];
+        }
+    }
+    if (!forcesAreValid) {
+        context.calcForcesAndEnergy(true, false);
+        forcesAreValid = true;
+    }
+    ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
+    vector<Vec3>& forces = *data->forces;
+
+    // 1st update
+
+    updatePart1(numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
+    if (referenceConstraintAlgorithm)
+        referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
+
+    // 2nd update
+
+    updatePart2(numberOfAtoms, atomCoordinates, velocities, inverseMasses, xPrime);
+    if (referenceConstraintAlgorithm)
+        referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
+
+    // 3rd update
+
+    context.calcForcesAndEnergy(true, false);
+    updatePart3(numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
+    if (referenceConstraintAlgorithm)
+        referenceConstraintAlgorithm->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
+
+    ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
+    incrementTimeStep();
+}

platforms/reference/tests/TestReferenceBAOABLangevinIntegrator.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) 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 "ReferenceTests.h"
+#include "TestBAOABLangevinIntegrator.h"
+
+void runPlatformTests() {
+}

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;
+}