Renamed BAOABLangevinIntegrator to LangevinMiddleIntegrator

docs-source/usersguide/application.rst

@@ -120,7 +120,7 @@ steps.
         forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml')
         system = forcefield.createSystem(pdb.topology, nonbondedMethod=PME,
                 nonbondedCutoff=1*nanometer, constraints=HBonds)
-        integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+        integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
         simulation = Simulation(pdb.topology, system, integrator)
         simulation.context.setPositions(pdb.positions)
         simulation.minimizeEnergy()
@@ -210,10 +210,10 @@ convenient and less error-prone.  We could have equivalently specified
 The units system will be described in more detail later, in Section :ref:`units-and-dimensional-analysis`.
 ::
 
-    integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+    integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
 
 This line creates the integrator to use for advancing the equations of motion.
-It specifies a :class:`BAOABLangevinIntegrator`, which performs Langevin dynamics,
+It specifies a :class:`LangevinMiddleIntegrator`, which performs Langevin dynamics,
 and assigns it to a variable called :code:`integrator`\ .  It also specifies
 the values of three parameters that are specific to Langevin dynamics: the
 simulation temperature (300 K), the friction coefficient (1 ps\ :sup:`-1`\ ), and
@@ -295,7 +295,7 @@ found in OpenMM’s :file:`examples` folder with the name :file:`simulateAmber.p
         inpcrd = AmberInpcrdFile('input.inpcrd')
         system = prmtop.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer,
                 constraints=HBonds)
-        integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+        integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
         simulation = Simulation(prmtop.topology, system, integrator)
         simulation.context.setPositions(inpcrd.positions)
         if inpcrd.boxVectors is not None:
@@ -389,7 +389,7 @@ with the name :file:`simulateGromacs.py`.
                 includeDir='/usr/local/gromacs/share/gromacs/top')
         system = top.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer,
                 constraints=HBonds)
-        integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+        integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
         simulation = Simulation(top.topology, system, integrator)
         simulation.context.setPositions(gro.positions)
         simulation.minimizeEnergy()
@@ -453,7 +453,7 @@ on the :class:`CharmmPsfFile`.
         params = CharmmParameterSet('charmm22.rtf', 'charmm22.prm')
         system = psf.createSystem(params, nonbondedMethod=NoCutoff,
                 nonbondedCutoff=1*nanometer, constraints=HBonds)
-        integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+        integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
         simulation = Simulation(psf.topology, system, integrator)
         simulation.context.setPositions(pdb.positions)
         simulation.minimizeEnergy()
@@ -1031,7 +1031,7 @@ BAOAB Langevin Integrator
 In the examples of the previous sections, we used Langevin integration:
 ::
 
-    integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+    integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
 
 The three parameter values in this line are the simulation temperature (300 K),
 the friction coefficient (1 ps\ :sup:`-1`\ ), and the step size (0.004 ps).  You
@@ -1043,11 +1043,11 @@ equivalent.
 Langevin Integrator
 -------------------
 
-:code:`LangevinIntegrator` is very similar to :code:`BAOABLangevinIntegrator`,
+:code:`LangevinIntegrator` is very similar to :code:`LangevinMiddleIntegrator`,
 but it uses a different discretization of the Langevin equation.
-:code:`BAOABLangevinIntegrator` tends to produce more accurate configurational
+:code:`LangevinMiddleIntegrator` tends to produce more accurate configurational
 sampling, and therefore is preferred for most applications.  Also note that
-:code:`LangevinIntegrator` (unlike :code:`BAOABLangevinIntegrator`) is a leapfrog
+:code:`LangevinIntegrator` (unlike :code:`LangevinMiddleIntegrator`) is a leapfrog
 integrator, so the velocities are offset by half a time step from the positions.
 
 Leapfrog Verlet Integrator
@@ -1158,7 +1158,7 @@ previous section:
     system = prmtop.createSystem(nonbondedMethod=PME, nonbondedCutoff=1*nanometer,
             constraints=HBonds)
     system.addForce(MonteCarloBarostat(1*bar, 300*kelvin))
-    integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+    integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
     ...
 
 The parameters of the Monte Carlo barostat are the pressure (1 bar) and
@@ -1718,7 +1718,7 @@ executing 1000 time steps at each temperature:
         :autonumber:`Example,simulated annealing`
 
 This code needs very little explanation.  The loop is executed 100 times.  Each
-time through, it adjusts the temperature of the :class:`BAOABLangevinIntegrator` and then
+time through, it adjusts the temperature of the :class:`LangevinMiddleIntegrator` and then
 calls :code:`step(1000)` to take 1000 time steps.
 
 Applying an External Force to Particles: a Spherical Container
@@ -1750,7 +1750,7 @@ coordinates.  Here is the code to do it:
         system.addForce(force)
         for i in range(system.getNumParticles()):
             force.addParticle(i, [])
-        integrator = BAOABLangevinIntegrator(300*kelvin, 91/picosecond, 0.004*picoseconds)
+        integrator = LangevinMiddleIntegrator(300*kelvin, 91/picosecond, 0.004*picoseconds)
         ...
 
     .. caption::

docs-source/usersguide/library.rst

@@ -243,14 +243,14 @@ simulation might look like:
         angles->addAngle(angle[i].particle1, angle[i].particle2,
             angle[i].particle3, angle[i].angle, angle[i].k);
     // ...create and initialize other force field terms in the same way
-    BAOABLangevinIntegrator integrator(temperature, friction, stepSize);
+    LangevinMiddleIntegrator integrator(temperature, friction, stepSize);
     Context context(system, integrator);
     context.setPositions(initialPositions);
     context.setVelocities(initialVelocities);
     integrator.step(10000);
 
 We create a System, add various Forces to it, and set parameters on both the
-System and the Forces.  We then create a BAOABLangevinIntegrator, initialize a
+System and the Forces.  We then create a LangevinMiddleIntegrator, initialize a
 Context in which to run a simulation, and instruct the Integrator to advance the
 simulation for 10,000 time steps.
 
@@ -1631,7 +1631,7 @@ along with the handle :code:`omm`\ , back to the calling function.
     // best available Platform. Initialize the configuration from the default
     // positions we collected above. Initial velocities will be zero but could
     // have been set here.
-    omm->integrator = new OpenMM::BAOABLangevinIntegrator(temperature,
+    omm->integrator = new OpenMM::LangevinMiddleIntegrator(temperature,
     frictionInPs,
     stepSizeInFs * OpenMM::PsPerFs);
     omm->context    = new OpenMM::Context(*omm->system, *omm->integrator);

docs-source/usersguide/theory.rst

@@ -1353,8 +1353,8 @@ random number, and :math:`\alpha=\exp(-\gamma\Delta t)`.
 The same comments about the offset between positions and velocities apply to
 this integrator as to VerletIntegrator.
 
-BAOABLangevinIntegrator
-***********************
+LangevinMiddleIntegrator
+************************
 
 This integrator is similar to LangevinIntegerator, but it instead uses the BAOAB
 discretization. :cite:`Leimkuhler2013` In each step, the positions and velocities

examples/HelloSodiumChloride.cpp

@@ -249,7 +249,7 @@ myInitializeOpenMM( const MyAtomInfo    atoms[],
     // best available Platform. Initialize the configuration from the default
     // positions we collected above. Initial velocities will be zero but could
     // have been set here.
-    omm->integrator = new OpenMM::BAOABLangevinIntegrator(temperature, frictionInPs, 
+    omm->integrator = new OpenMM::LangevinMiddleIntegrator(temperature, frictionInPs, 
                                                      stepSizeInFs * OpenMM::PsPerFs);
     omm->context    = new OpenMM::Context(*omm->system, *omm->integrator);
     omm->context->setPositions(initialPosInNm);

examples/HelloSodiumChlorideInC.c

@@ -252,7 +252,7 @@ myInitializeOpenMM( const MyAtomInfo    atoms[],
      * best available Platform. Initialize the configuration from the default
      * positions we collected above. Initial velocities will be zero but could
      * have been set here. */
-    omm->integrator = (OpenMM_Integrator*)OpenMM_BAOABLangevinIntegrator_create(
+    omm->integrator = (OpenMM_Integrator*)OpenMM_LangevinMiddleIntegrator_create(
                                             temperature, frictionInPerPs, 
                                             stepSizeInFs * OpenMM_PsPerFs);
     omm->context    = OpenMM_Context_create(omm->system, omm->integrator);

examples/HelloSodiumChlorideInFortran.f90

@@ -171,7 +171,7 @@ SUBROUTINE myInitializeOpenMM(ommHandle, platformName)
     ! These are the objects we'll create here thare are stored in the
     ! Context for later access. Don't forget to delete them at the end.
     type (OpenMM_System)             system
-    type (OpenMM_BAOABLangevinIntegrator) langevin
+    type (OpenMM_LangevinMiddleIntegrator) langevin
     type (OpenMM_Context)            context
 
     ! These are temporary OpenMM objects used and discarded here.
@@ -236,11 +236,11 @@ SUBROUTINE myInitializeOpenMM(ommHandle, platformName)
     ! best available Platform. Initialize the configuration from the default
     ! positions we collected above. Initial velocities will be zero but could
     ! have been set here.
-    call OpenMM_BAOABLangevinIntegrator_create(langevin,                     &
+    call OpenMM_LangevinMiddleIntegrator_create(langevin,                     &
                                           Temperature, FrictionInPerPs, &
                                           StepSizeInFs * OpenMM_PsPerFs)
 
-    ! Convert BAOABLangevinIntegrator to generic Integrator type for this call.
+    ! Convert LangevinMiddleIntegrator to generic Integrator type for this call.
     call OpenMM_Context_create(context, system,                         &
                                transfer(langevin, OpenMM_Integrator(0)))
     call OpenMM_Context_setPositions(context, initialPosInNm)

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 = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
 simulation = Simulation(prmtop.topology, system, integrator)
 simulation.context.setPositions(inpcrd.positions)
 if inpcrd.boxVectors is not None:

examples/simulateCharmm.py

@@ -21,7 +21,7 @@ params = CharmmParameterSet('charmm22.rtf', 'charmm22.par')
 
 # Instantiate the system
 system = psf.createSystem(params, nonbondedMethod=NoCutoff, constraints=HBonds)
-integrator = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*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 = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*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 = BAOABLangevinIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
+integrator = LangevinMiddleIntegrator(300*kelvin, 1/picosecond, 0.004*picoseconds)
 simulation = Simulation(pdb.topology, system, integrator)
 simulation.context.setPositions(pdb.positions)
 simulation.minimizeEnergy()

olla/include/openmm/kernels.h

@@ -33,7 +33,7 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/AndersenThermostat.h"
-#include "openmm/BAOABLangevinIntegrator.h"
+#include "openmm/LangevinMiddleIntegrator.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
@@ -1129,36 +1129,36 @@ public:
 };
 
 /**
- * This kernel is invoked by BAOABLangevinIntegrator to take one time step.
+ * This kernel is invoked by LangevinMiddleIntegrator to take one time step.
  */
-class IntegrateBAOABStepKernel : public KernelImpl {
+class IntegrateLangevinMiddleStepKernel : public KernelImpl {
 public:
     static std::string Name() {
-        return "IntegrateBAOABStep";
+        return "IntegrateLangevinMiddleStep";
     }
-    IntegrateBAOABStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
+    IntegrateLangevinMiddleStepKernel(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
+     * @param integrator the LangevinMiddleIntegrator this kernel will be used for
      */
-    virtual void initialize(const System& system, const BAOABLangevinIntegrator& integrator) = 0;
+    virtual void initialize(const System& system, const LangevinMiddleIntegrator& 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 integrator the LangevinMiddleIntegrator this kernel is being used for
      */
-    virtual void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator) = 0;
+    virtual void execute(ContextImpl& context, const LangevinMiddleIntegrator& integrator) = 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
+     * @param integrator the LangevinMiddleIntegrator this kernel is being used for
      */
-    virtual double computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator) = 0;
+    virtual double computeKineticEnergy(ContextImpl& context, const LangevinMiddleIntegrator& integrator) = 0;
 };
 
 /**

openmmapi/include/OpenMM.h

@@ -33,7 +33,6 @@
  * -------------------------------------------------------------------------- */
 
 #include "openmm/AndersenThermostat.h"
-#include "openmm/BAOABLangevinIntegrator.h"
 #include "openmm/BrownianIntegrator.h"
 #include "openmm/CMAPTorsionForce.h"
 #include "openmm/CMMotionRemover.h"
@@ -57,6 +56,7 @@
 #include "openmm/HarmonicBondForce.h"
 #include "openmm/Integrator.h"
 #include "openmm/LangevinIntegrator.h"
+#include "openmm/LangevinMiddleIntegrator.h"
 #include "openmm/LocalEnergyMinimizer.h"
 #include "openmm/MonteCarloAnisotropicBarostat.h"
 #include "openmm/MonteCarloBarostat.h"

openmmapi/include/openmm/CustomIntegrator.h

@@ -236,7 +236,7 @@ namespace OpenMM {
  * </pre></tt>
  * 
  * The second one implements the algorithm used by the standard
- * BAOABLangevinIntegrator class.  kB is Boltzmann's constant.
+ * LangevinMiddleIntegrator class.  kB is Boltzmann's constant.
  * 
  * <tt><pre>
  * CustomIntegrator integrator(dt);

openmmapi/include/openmm/BAOABLangevinIntegrator.h → openmmapi/include/openmm/LangevinMiddleIntegrator.h

-#ifndef OPENMM_BAOABLANGEVININTEGRATOR_H_
-#define OPENMM_BAOABLANGEVININTEGRATOR_H_
+#ifndef OPENMM_LANGEVINMIDDLEINTEGRATOR_H_
+#define OPENMM_LANGEVINMIDDLEINTEGRATOR_H_
 
 /* -------------------------------------------------------------------------- *
  *                                   OpenMM                                   *
@@ -45,16 +45,16 @@ namespace OpenMM {
  * discretizations, such as the one used in LangevinIntegrator.
  */
 
-class OPENMM_EXPORT BAOABLangevinIntegrator : public Integrator {
+class OPENMM_EXPORT LangevinMiddleIntegrator : public Integrator {
 public:
     /**
-     * Create a BAOABLangevinIntegrator.
+     * Create a LangevinMiddleIntegrator.
      * 
      * @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);
+    LangevinMiddleIntegrator(double temperature, double frictionCoeff, double stepSize);
     /**
      * Get the temperature of the heat bath (in Kelvin).
      *
@@ -148,4 +148,4 @@ private:
 
 } // namespace OpenMM
 
-#endif /*OPENMM_BAOABLANGEVININTEGRATOR_H_*/
+#endif /*OPENMM_LANGEVINMIDDLEINTEGRATOR_H_*/

openmmapi/src/BAOABLangevinIntegrator.cpp → openmmapi/src/LangevinMiddleIntegrator.cpp

@@ -29,7 +29,7 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "openmm/BAOABLangevinIntegrator.h"
+#include "openmm/LangevinMiddleIntegrator.h"
 #include "openmm/Context.h"
 #include "openmm/OpenMMException.h"
 #include "openmm/internal/ContextImpl.h"
@@ -40,7 +40,7 @@ using namespace OpenMM;
 using std::string;
 using std::vector;
 
-BAOABLangevinIntegrator::BAOABLangevinIntegrator(double temperature, double frictionCoeff, double stepSize) {
+LangevinMiddleIntegrator::LangevinMiddleIntegrator(double temperature, double frictionCoeff, double stepSize) {
     setTemperature(temperature);
     setFriction(frictionCoeff);
     setStepSize(stepSize);
@@ -48,39 +48,39 @@ BAOABLangevinIntegrator::BAOABLangevinIntegrator(double temperature, double fric
     setRandomNumberSeed(0);
 }
 
-void BAOABLangevinIntegrator::initialize(ContextImpl& contextRef) {
+void LangevinMiddleIntegrator::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);
+    kernel = context->getPlatform().createKernel(IntegrateLangevinMiddleStepKernel::Name(), contextRef);
+    kernel.getAs<IntegrateLangevinMiddleStepKernel>().initialize(contextRef.getSystem(), *this);
 }
 
-void BAOABLangevinIntegrator::cleanup() {
+void LangevinMiddleIntegrator::cleanup() {
     kernel = Kernel();
 }
 
-vector<string> BAOABLangevinIntegrator::getKernelNames() {
+vector<string> LangevinMiddleIntegrator::getKernelNames() {
     std::vector<std::string> names;
-    names.push_back(IntegrateBAOABStepKernel::Name());
+    names.push_back(IntegrateLangevinMiddleStepKernel::Name());
     return names;
 }
 
-double BAOABLangevinIntegrator::computeKineticEnergy() {
-    return kernel.getAs<IntegrateBAOABStepKernel>().computeKineticEnergy(*context, *this);
+double LangevinMiddleIntegrator::computeKineticEnergy() {
+    return kernel.getAs<IntegrateLangevinMiddleStepKernel>().computeKineticEnergy(*context, *this);
 }
 
-bool BAOABLangevinIntegrator::kineticEnergyRequiresForce() const {
+bool LangevinMiddleIntegrator::kineticEnergyRequiresForce() const {
     return false;
 }
 
-void BAOABLangevinIntegrator::step(int steps) {
+void LangevinMiddleIntegrator::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();
         context->calcForcesAndEnergy(true, false);
-        kernel.getAs<IntegrateBAOABStepKernel>().execute(*context, *this);
+        kernel.getAs<IntegrateLangevinMiddleStepKernel>().execute(*context, *this);
     }
 }

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

@@ -905,34 +905,34 @@ private:
 };
 
 /**
- * This kernel is invoked by BAOABLangevinIntegrator to take one time step.
+ * This kernel is invoked by LangevinMiddleIntegrator to take one time step.
  */
-class CommonIntegrateBAOABStepKernel : public IntegrateBAOABStepKernel {
+class CommonIntegrateLangevinMiddleStepKernel : public IntegrateLangevinMiddleStepKernel {
 public:
-    CommonIntegrateBAOABStepKernel(std::string name, const Platform& platform, ComputeContext& cc) : IntegrateBAOABStepKernel(name, platform), cc(cc),
+    CommonIntegrateLangevinMiddleStepKernel(std::string name, const Platform& platform, ComputeContext& cc) : IntegrateLangevinMiddleStepKernel(name, platform), cc(cc),
             hasInitializedKernels(false) {
     }
     /**
      * 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
+     * @param integrator the LangevinMiddleIntegrator this kernel will be used for
      */
-    void initialize(const System& system, const BAOABLangevinIntegrator& integrator);
+    void initialize(const System& system, const LangevinMiddleIntegrator& 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 integrator the LangevinMiddleIntegrator this kernel is being used for
      */
-    void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator);
+    void execute(ContextImpl& context, const LangevinMiddleIntegrator& integrator);
     /**
      * Compute the kinetic energy.
      * 
      * @param context    the context in which to execute this kernel
-     * @param integrator the BAOABLangevinIntegrator this kernel is being used for
+     * @param integrator the LangevinMiddleIntegrator this kernel is being used for
      */
-    double computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator);
+    double computeKineticEnergy(ContextImpl& context, const LangevinMiddleIntegrator& integrator);
 private:
     ComputeContext& cc;
     double prevTemp, prevFriction, prevStepSize;

platforms/common/src/CommonKernels.cpp

@@ -5547,26 +5547,26 @@ double CommonIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& cont
     return cc.getIntegrationUtilities().computeKineticEnergy(0.5*integrator.getStepSize());
 }
 
-void CommonIntegrateBAOABStepKernel::initialize(const System& system, const BAOABLangevinIntegrator& integrator) {
+void CommonIntegrateLangevinMiddleStepKernel::initialize(const System& system, const LangevinMiddleIntegrator& integrator) {
     cc.initializeContexts();
     cc.setAsCurrent();
     cc.getIntegrationUtilities().initRandomNumberGenerator(integrator.getRandomNumberSeed());
-    ComputeProgram program = cc.compileProgram(CommonKernelSources::baoab);
-    kernel1 = program->createKernel("integrateBAOABPart1");
-    kernel2 = program->createKernel("integrateBAOABPart2");
-    kernel3 = program->createKernel("integrateBAOABPart3");
+    ComputeProgram program = cc.compileProgram(CommonKernelSources::langevinMiddle);
+    kernel1 = program->createKernel("integrateLangevinMiddlePart1");
+    kernel2 = program->createKernel("integrateLangevinMiddlePart2");
+    kernel3 = program->createKernel("integrateLangevinMiddlePart3");
     if (cc.getUseDoublePrecision() || cc.getUseMixedPrecision()) {
-        params.initialize<double>(cc, 2, "baoabParams");
+        params.initialize<double>(cc, 2, "langevinMiddleParams");
         oldDelta.initialize<mm_double4>(cc, cc.getPaddedNumAtoms(), "oldDelta");
     }
     else {
-        params.initialize<float>(cc, 2, "baoabParams");
+        params.initialize<float>(cc, 2, "langevinMiddleParams");
         oldDelta.initialize<mm_float4>(cc, cc.getPaddedNumAtoms(), "oldDelta");
     }
     prevStepSize = -1.0;
 }
 
-void CommonIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
+void CommonIntegrateLangevinMiddleStepKernel::execute(ContextImpl& context, const LangevinMiddleIntegrator& integrator) {
     IntegrationUtilities& integration = cc.getIntegrationUtilities();
     int numAtoms = cc.getNumAtoms();
     int paddedNumAtoms = cc.getPaddedNumAtoms();
@@ -5636,7 +5636,7 @@ void CommonIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLa
 #endif
 }
 
-double CommonIntegrateBAOABStepKernel::computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
+double CommonIntegrateLangevinMiddleStepKernel::computeKineticEnergy(ContextImpl& context, const LangevinMiddleIntegrator& integrator) {
     return cc.getIntegrationUtilities().computeKineticEnergy(0.0);
 }
 

platforms/common/src/kernels/baoab.cc → platforms/common/src/kernels/langevinMiddle.cc

 enum {VelScale, NoiseScale};
 
 /**
- * Perform the first part of BAOAB integration: velocity half step, then position half step.
+ * Perform the first part of integration: velocity step.
  */
 
-KERNEL void integrateBAOABPart1(int numAtoms, int paddedNumAtoms, GLOBAL mixed4* RESTRICT velm, GLOBAL const mm_long* RESTRICT force,
+KERNEL void integrateLangevinMiddlePart1(int numAtoms, int paddedNumAtoms, GLOBAL mixed4* RESTRICT velm, GLOBAL const mm_long* RESTRICT force,
         GLOBAL const mixed2* RESTRICT dt) {
     mixed fscale = dt[0].y/(mixed) 0x100000000;
     for (int index = GLOBAL_ID; index < numAtoms; index += GLOBAL_SIZE) {
@@ -19,11 +19,11 @@ KERNEL void integrateBAOABPart1(int numAtoms, int paddedNumAtoms, GLOBAL mixed4*
 }
 
 /**
- * Perform the second part of BAOAB integration: apply constraint forces to velocities, then interact with heat bath,
- * then position half step.
+ * Perform the second part of integration: position half step, then interact with heat bath,
+ * then another position half step.
  */
 
-KERNEL void integrateBAOABPart2(int numAtoms, GLOBAL mixed4* RESTRICT velm, GLOBAL mixed4* RESTRICT posDelta,
+KERNEL void integrateLangevinMiddlePart2(int numAtoms, GLOBAL mixed4* RESTRICT velm, GLOBAL mixed4* RESTRICT posDelta,
         GLOBAL mixed4* RESTRICT oldDelta, GLOBAL const mixed* RESTRICT paramBuffer, GLOBAL const mixed2* RESTRICT dt, GLOBAL const float4* RESTRICT random, unsigned int randomIndex
         ) {
     mixed vscale = paramBuffer[VelScale];
@@ -50,11 +50,11 @@ KERNEL void integrateBAOABPart2(int numAtoms, GLOBAL mixed4* RESTRICT velm, GLOB
 }
 
 /**
- * Perform the third part of BAOAB integration: apply constraint forces to velocities, then record
- * the constrained positions in preparation for computing forces.
+ * Perform the third part of integration: apply constraint forces to velocities, then record
+ * the constrained positions.
  */
 
-KERNEL void integrateBAOABPart3(int numAtoms, GLOBAL real4* RESTRICT posq, GLOBAL mixed4* RESTRICT velm,
+KERNEL void integrateLangevinMiddlePart3(int numAtoms, GLOBAL real4* RESTRICT posq, GLOBAL mixed4* RESTRICT velm,
          GLOBAL mixed4* RESTRICT posDelta, GLOBAL mixed4* RESTRICT oldDelta, GLOBAL const mixed2* RESTRICT dt
 #ifdef USE_MIXED_PRECISION
         , GLOBAL real4* RESTRICT posqCorrection

platforms/cpu/include/CpuKernels.h

@@ -32,7 +32,6 @@
  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
  * -------------------------------------------------------------------------- */
 
-#include "CpuBAOABDynamics.h"
 #include "CpuBondForce.h"
 #include "CpuCustomGBForce.h"
 #include "CpuCustomManyParticleForce.h"
@@ -40,6 +39,7 @@
 #include "CpuGayBerneForce.h"
 #include "CpuGBSAOBCForce.h"
 #include "CpuLangevinDynamics.h"
+#include "CpuLangevinMiddleDynamics.h"
 #include "CpuNeighborList.h"
 #include "CpuNonbondedForce.h"
 #include "CpuPlatform.h"
@@ -538,38 +538,38 @@ private:
 };
 
 /**
- * This kernel is invoked by BAOABLangevinIntegrator to take one time step.
+ * This kernel is invoked by LangevinMiddleIntegrator to take one time step.
  */
-class CpuIntegrateBAOABStepKernel : public IntegrateBAOABStepKernel {
+class CpuIntegrateLangevinMiddleStepKernel : public IntegrateLangevinMiddleStepKernel {
 public:
-    CpuIntegrateBAOABStepKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) : IntegrateBAOABStepKernel(name, platform),
+    CpuIntegrateLangevinMiddleStepKernel(std::string name, const Platform& platform, CpuPlatform::PlatformData& data) : IntegrateLangevinMiddleStepKernel(name, platform),
             data(data), dynamics(0) {
     }
-    ~CpuIntegrateBAOABStepKernel();
+    ~CpuIntegrateLangevinMiddleStepKernel();
     /**
      * 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
+     * @param integrator the LangevinMiddleIntegrator this kernel will be used for
      */
-    void initialize(const System& system, const BAOABLangevinIntegrator& integrator);
+    void initialize(const System& system, const LangevinMiddleIntegrator& 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 integrator the LangevinMiddleIntegrator this kernel is being used for
      */
-    void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator);
+    void execute(ContextImpl& context, const LangevinMiddleIntegrator& integrator);
     /**
      * Compute the kinetic energy.
      * 
      * @param context    the context in which to execute this kernel
-     * @param integrator the BAOABLangevinIntegrator this kernel is being used for
+     * @param integrator the LangevinMiddleIntegrator this kernel is being used for
      */
-    double computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator);
+    double computeKineticEnergy(ContextImpl& context, const LangevinMiddleIntegrator& integrator);
 private:
     CpuPlatform::PlatformData& data;
-    CpuBAOABDynamics* dynamics;
+    CpuLangevinMiddleDynamics* dynamics;
     std::vector<double> masses;
     double prevTemp, prevFriction, prevStepSize;
 };

platforms/cpu/include/CpuBAOABDynamics.h → platforms/cpu/include/CpuLangevinMiddleDynamics.h

@@ -23,17 +23,17 @@
  * WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-#ifndef __CPU_BAOAB_DYNAMICS_H__
-#define __CPU_BAOAB_DYNAMICS_H__
+#ifndef __CPU_LANGEVIN_MIDDLE_DYNAMICS_H__
+#define __CPU_LANGEVIN_MIDDLE_DYNAMICS_H__
 
-#include "ReferenceBAOABDynamics.h"
+#include "ReferenceLangevinMiddleDynamics.h"
 #include "CpuRandom.h"
 #include "openmm/internal/ThreadPool.h"
 #include "sfmt/SFMT.h"
 
 namespace OpenMM {
 
-class CpuBAOABDynamics : public ReferenceBAOABDynamics {
+class CpuLangevinMiddleDynamics : public ReferenceLangevinMiddleDynamics {
 public:
     /**
      * Constructor.
@@ -45,12 +45,12 @@ public:
      * @param threads        thread pool for parallelizing computation
      * @param random         random number generator
      */
-    CpuBAOABDynamics(int numberOfAtoms, double deltaT, double friction, double temperature, OpenMM::ThreadPool& threads, OpenMM::CpuRandom& random);
+    CpuLangevinMiddleDynamics(int numberOfAtoms, double deltaT, double friction, double temperature, OpenMM::ThreadPool& threads, OpenMM::CpuRandom& random);
 
     /**
      * Destructor.
      */
-    ~CpuBAOABDynamics();
+    ~CpuLangevinMiddleDynamics();
 
     /**
      * First update step.
@@ -105,4 +105,4 @@ private:
 
 } // namespace OpenMM
 
-#endif // __CPU_BAOAB_DYNAMICS_H__
+#endif // __CPU_LANGEVIN_MIDDLE_DYNAMICS_H__