Merge pull request #3 from openmm/master

Sync with official repo

examples/simulateAmber.py

@@ -6,7 +6,7 @@ from sys import stdout
 prmtop = AmberPrmtopFile('input.prmtop')
 inpcrd = AmberInpcrdFile('input.inpcrd')
 system = prmtop.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
-integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
+integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
 simulation = Simulation(prmtop.topology, system, integrator)
 simulation.context.setPositions(inpcrd.positions)
 if inpcrd.boxVectors is not None:

examples/simulateCharmm.py

@@ -22,7 +22,7 @@ params = CharmmParameterSet('charmm22.rtf', 'charmm22.par')
 # Instantiate the system
 system = psf.createSystem(params, nonbondedMethod=NoCutoff,
                           nonbondedCutoff=None)
-integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
+integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
 simulation = Simulation(psf.topology, system, integrator)
 simulation.context.setPositions(pdb.getPositions())
 simulation.minimizeEnergy()

examples/simulateGromacs.py

@@ -6,7 +6,7 @@ from sys import stdout
 gro = GromacsGroFile('input.gro')
 top = GromacsTopFile('input.top', periodicBoxVectors=gro.getPeriodicBoxVectors())
 system = top.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
-integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
+integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
 simulation = Simulation(top.topology, system, integrator)
 simulation.context.setPositions(gro.positions)
 simulation.minimizeEnergy()

examples/simulatePdb.py

@@ -6,7 +6,7 @@ from sys import stdout
 pdb = PDBFile('input.pdb')
 forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
 system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1*nanometer, constraints=HBonds)
-integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
+integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
 simulation = Simulation(pdb.topology, system, integrator)
 simulation.context.setPositions(pdb.positions)
 simulation.minimizeEnergy()

olla/include/openmm/Platform.h

@@ -213,12 +213,17 @@ public:
      */
     static void loadPluginLibrary(const std::string& file);
     /**
-     * Load multiple dynamic libraries (DLLs) which contain OpenMM plugins from a single directory.
-     * This method loops over every file contained in the specified directory and calls loadPluginLibrary()
+     * Load multiple dynamic libraries (DLLs) which contain OpenMM plugins from one or more directories.
+     * Multiple fully-qualified paths can be joined together with ':' on unix-like systems
+     * (or ';' on windows-like systems); each will be searched for plugins, in-order. For example,
+     * '/foo/plugins:/bar/plugins' will search both `/foo/plugins` and `/bar/plugins`. If an
+     * identically-named plugin is encountered twice it will be loaded at both points; be careful!!!
+     *
+     * This method loops over every file contained in the specified directories and calls loadPluginLibrary()
      * for each one.  If an error occurs while trying to load a particular file, that file is simply
      * ignored. You can retrieve a list of all such errors by calling getPluginLoadFailures().
      *
-     * @param directory    the path to the directory containing libraries to load
+     * @param directory    a ':' (unix) or ';' (windows) deliminated list of paths containing libraries to load
      * @return the names of all files which were successfully loaded as libraries
      */
     static std::vector<std::string> loadPluginsFromDirectory(const std::string& directory);

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.
  */

olla/src/Platform.cpp

@@ -37,7 +37,6 @@
 #include "openmm/internal/ContextImpl.h"
 #ifdef WIN32
 #include <windows.h>
-#include <sstream>
 #else
 #ifndef __PNACL__
     #include <dlfcn.h>
@@ -45,6 +44,7 @@
 #include <dirent.h>
 #include <cstdlib>
 #endif
+#include <sstream>
 #include <set>
 #include <algorithm>
 
@@ -261,31 +261,42 @@ void Platform::loadPluginLibrary(const string& file) {
 vector<string> Platform::loadPluginsFromDirectory(const string& directory) {
     vector<string> files;
     char dirSeparator;
+    char pathSeparator;
+    stringstream sdirectory(directory);
 #ifdef WIN32
     dirSeparator = '\\';
+    pathSeparator = ';';
     WIN32_FIND_DATA fileInfo;
-    string filePattern(directory + dirSeparator + "*.dll");
+
+    for (string path; std::getline(sdirectory, path, pathSeparator);) {
+        string filePattern(path + dirSeparator + "*.dll");
         HANDLE findHandle = FindFirstFile(filePattern.c_str(), &fileInfo);
         if (findHandle != INVALID_HANDLE_VALUE) {
             do {
                 if (fileInfo.cFileName[0] != '.')
-                files.push_back(string(fileInfo.cFileName));
+                    files.push_back(path+dirSeparator+string(fileInfo.cFileName));
             } while (FindNextFile(findHandle, &fileInfo));
             FindClose(findHandle);
         }
+    }
     vector<HMODULE> plugins;
 #else
-    dirSeparator = '/';
     DIR* dir;
+    dirSeparator = '/';
+    pathSeparator = ':';
     struct dirent *entry;
-    dir = opendir(directory.c_str());
+
+    for (string path; std::getline(sdirectory, path, pathSeparator);) {
+        dir = opendir(path.c_str());
         if (dir != NULL) {
             while ((entry = readdir(dir)) != NULL) {
                 if (entry->d_name[0] != '.')
-                files.push_back(string(entry->d_name));
+                    files.push_back(path+dirSeparator+string(entry->d_name));
             }
             closedir(dir);
         }
+    }
+
     vector<void*> plugins;
 #endif
     vector<string> loadedLibraries;
@@ -294,7 +305,7 @@ vector<string> Platform::loadPluginsFromDirectory(const string& directory) {
 
     for (unsigned int i = 0; i < files.size(); ++i) {
         try {
-            plugins.push_back(loadOneLibrary(directory+dirSeparator+files[i]));
+            plugins.push_back(loadOneLibrary(files[i]));
             loadedLibraries.push_back(files[i]);
         } catch (OpenMMException& ex) {
 	    pluginLoadFailures.push_back(ex.what());

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();
+    /**
+     * Computing kinetic energy for this integrator does not require forces.
+     */
+    bool kineticEnergyRequiresForce() const;
+private:
+    double temperature, friction;
+    int randomNumberSeed;
+    bool forcesAreValid;
+    Kernel kernel;
+};
+
+} // namespace OpenMM
+
+#endif /*OPENMM_BAOABLANGEVININTEGRATOR_H_*/

openmmapi/include/openmm/BrownianIntegrator.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -133,6 +133,10 @@ protected:
      * Compute the kinetic energy of the system at the current time.
      */
     double computeKineticEnergy();
+    /**
+     * Computing kinetic energy for this integrator does not require forces.
+     */
+    bool kineticEnergyRequiresForce() const;
 private:
     double temperature, friction;
     int randomNumberSeed;

openmmapi/include/openmm/CustomIntegrator.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) 2011-2018 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -627,6 +627,10 @@ protected:
      * Compute the kinetic energy of the system at the current time.
      */
     double computeKineticEnergy();
+    /**
+     * Get whether computeKineticEnergy() expects forces to have been computed.
+     */
+    bool kineticEnergyRequiresForce() const;
 private:
     class ComputationInfo;
     class FunctionInfo;
@@ -639,7 +643,7 @@ private:
     std::string kineticEnergy;
     mutable bool globalsAreCurrent;
     int randomNumberSeed;
-    bool forcesAreValid;
+    bool forcesAreValid, keNeedsForce;
     Kernel kernel;
 };
 

openmmapi/include/openmm/Integrator.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) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -120,8 +120,19 @@ protected:
      * Compute the kinetic energy of the system at the current time.  This may be different from simply
      * mv<sup>2</sup>/2.  For example, a leapfrog integrator will store velocities offset by half a step,
      * but the kinetic energy should be computed at the current time, not delayed by half a step.
+     * 
+     * If kineticEnergyRequiresForce() returns true, this method can assume that valid forces
+     * have already been computed.
      */
     virtual double computeKineticEnergy() = 0;
+    /**
+     * Get whether computeKineticEnergy() expects forces to have been computed.  The default
+     * implementation returns true to be safe.  Non-leapfrog integrators can override this to
+     * return false, which makes calling getState() to query the energy less expensive.
+     */
+    virtual bool kineticEnergyRequiresForce() const {
+        return true;
+    }
 private:
     double stepSize, constraintTol;
 };

openmmapi/include/openmm/VariableLangevinIntegrator.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -39,7 +39,7 @@
 namespace OpenMM {
 
 /**
- * This is an error contolled, variable time step Integrator that simulates a System using Langevin
+ * This is an error controlled, variable time step Integrator that simulates a System using Langevin
  * dynamics.  It compares the result of the Langevin integrator to that of an
  * explicit Euler integrator, takes the difference between the two as a measure of the integration
  * error in each time step, and continuously adjusts the step size to keep the error below a
@@ -50,6 +50,10 @@ namespace OpenMM {
  * adjustable parameter that affects the step size and integration accuracy.  You
  * should try different values to find the largest one that produces a trajectory sufficiently
  * accurate for your purposes.  0.001 is often a good starting point.
+ * 
+ * You can optionally set a maximum step size it will ever use.  This is useful to prevent it
+ * from taking excessively large steps in usual situations, such as when the system is right at
+ * a local energy minimum.
  */
 
 class OPENMM_EXPORT VariableLangevinIntegrator : public Integrator {
@@ -108,6 +112,20 @@ public:
     void setErrorTolerance(double tol) {
         errorTol = tol;
     }
+    /**
+     * Get the maximum step size the integrator will ever use, in ps.  If this
+     * is 0 (the default), no limit will be applied to step sizes.
+     */
+    double getMaximumStepSize() const {
+        return maxStepSize;
+    }
+    /**
+     * Set the maximum step size the integrator will ever use, in ps.  If this
+     * is 0 (the default), no limit will be applied to step sizes.
+     */
+    void setMaximumStepSize(double size) {
+        maxStepSize = size;
+    }
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
      */
@@ -165,7 +183,7 @@ protected:
      */
     double computeKineticEnergy();
 private:
-    double temperature, friction, errorTol;
+    double temperature, friction, errorTol, maxStepSize;
     int randomNumberSeed;
     Kernel kernel;
 };

openmmapi/include/openmm/VariableVerletIntegrator.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -39,7 +39,7 @@
 namespace OpenMM {
 
 /**
- * This is an error contolled, variable time step Integrator that simulates a System using the
+ * This is an error controlled, variable time step Integrator that simulates a System using the
  * leap-frog Verlet algorithm.  It compares the result of the Verlet integrator to that of an
  * explicit Euler integrator, takes the difference between the two as a measure of the integration
  * error in each time step, and continuously adjusts the step size to keep the error below a
@@ -56,6 +56,10 @@ namespace OpenMM {
  * This makes it most appropriate for constant temperate simulations.  In constant energy simulations
  * where precise energy conservation over long time periods is important, a fixed step size Verlet
  * integrator may be more appropriate.
+ * 
+ * You can optionally set a maximum step size it will ever use.  This is useful to prevent it
+ * from taking excessively large steps in usual situations, such as when the system is right at
+ * a local energy minimum.
  */
 
 class OPENMM_EXPORT VariableVerletIntegrator : public Integrator {
@@ -78,6 +82,20 @@ public:
     void setErrorTolerance(double tol) {
         errorTol = tol;
     }
+    /**
+     * Get the maximum step size the integrator will ever use, in ps.  If this
+     * is 0 (the default), no limit will be applied to step sizes.
+     */
+    double getMaximumStepSize() const {
+        return maxStepSize;
+    }
+    /**
+     * Set the maximum step size the integrator will ever use, in ps.  If this
+     * is 0 (the default), no limit will be applied to step sizes.
+     */
+    void setMaximumStepSize(double size) {
+        maxStepSize = size;
+    }
     /**
      * Advance a simulation through time by taking a series of time steps.
      *
@@ -114,7 +132,7 @@ protected:
      */
     double computeKineticEnergy();
 private:
-    double errorTol;
+    double errorTol, maxStepSize;
     Kernel kernel;
 };
 

openmmapi/include/openmm/VirtualSite.h

@@ -112,7 +112,7 @@ public:
      * @param particle3    the index of the third particle
      * @param weight1      the weight factor (between 0 and 1) for the first particle
      * @param weight2      the weight factor (between 0 and 1) for the second particle
-     * @param weight2      the weight factor (between 0 and 1) for the third particle
+     * @param weight3      the weight factor (between 0 and 1) for the third particle
      */
     ThreeParticleAverageSite(int particle1, int particle2, int particle3, double weight1, double weight2, double weight3);
     /**

openmmapi/include/openmm/internal/MonteCarloAnisotropicBarostatImpl.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -35,7 +35,6 @@
 #include "ForceImpl.h"
 #include "openmm/MonteCarloAnisotropicBarostat.h"
 #include "openmm/Kernel.h"
-#include "sfmt/SFMT.h"
 #include <string>
 
 namespace OpenMM {
@@ -62,7 +61,6 @@ private:
     const MonteCarloAnisotropicBarostat& owner;
     int step, numAttempted[3], numAccepted[3];
     double volumeScale[3];
-    OpenMM_SFMT::SFMT random;
     Kernel kernel;
 };
 

openmmapi/include/openmm/internal/MonteCarloBarostatImpl.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -35,7 +35,6 @@
 #include "ForceImpl.h"
 #include "openmm/MonteCarloBarostat.h"
 #include "openmm/Kernel.h"
-#include "sfmt/SFMT.h"
 #include <string>
 
 namespace OpenMM {
@@ -62,7 +61,6 @@ private:
     const MonteCarloBarostat& owner;
     int step, numAttempted, numAccepted;
     double volumeScale;
-    OpenMM_SFMT::SFMT random;
     Kernel kernel;
 };
 

openmmapi/include/openmm/internal/MonteCarloMembraneBarostatImpl.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -35,7 +35,6 @@
 #include "ForceImpl.h"
 #include "openmm/MonteCarloMembraneBarostat.h"
 #include "openmm/Kernel.h"
-#include "sfmt/SFMT.h"
 #include <string>
 
 namespace OpenMM {
@@ -62,7 +61,6 @@ private:
     const MonteCarloMembraneBarostat& owner;
     int step, numAttempted[3], numAccepted[3];
     double volumeScale[3];
-    OpenMM_SFMT::SFMT random;
     Kernel kernel;
 };
 

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);
+}
+
+bool BAOABLangevinIntegrator::kineticEnergyRequiresForce() const {
+    return false;
+}
+
+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);
+    }
+}

openmmapi/src/BrownianIntegrator.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) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2019 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -71,6 +71,10 @@ double BrownianIntegrator::computeKineticEnergy() {
     return kernel.getAs<IntegrateBrownianStepKernel>().computeKineticEnergy(*context, *this);
 }
 
+bool BrownianIntegrator::kineticEnergyRequiresForce() const {
+    return false;
+}
+
 void BrownianIntegrator::step(int steps) {
     if (context == NULL)
         throw OpenMMException("This Integrator is not bound to a context!");