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Unverified Commit 6786cc75 authored by peastman's avatar peastman Committed by GitHub
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Merge pull request #2561 from peastman/middle 

Converted BAOABLangevinIntegrator to LangevinMiddleIntegrator
parents 3fdc297c cc59da1a
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platforms/cpu/include/CpuBAOABDynamics.h → platforms/cpu/include/CpuLangevinMiddleDynamics.h
View file @ 6786cc75
/* Portions copyright (c) 2013-2019 Stanford University and Simbios.
/* Portions copyright (c) 2013-2020 Stanford University and Simbios.
* Authors: Peter Eastman
* Contributors:
*
......@@ -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.
......@@ -45,25 +45,22 @@ 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.
*
* @param numberOfAtoms number of atoms
* @param atomCoordinates atom coordinates
* @param velocities velocities
* @param forces forces
* @param inverseMasses inverse atom masses
* @param xPrime xPrime
*/
void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses);
/**
* Second update step.
......@@ -94,7 +91,6 @@ private:
void threadUpdate1(int threadIndex);
void threadUpdate2(int threadIndex);
void threadUpdate3(int threadIndex);
void threadUpdate4(int threadIndex);
OpenMM::ThreadPool& threads;
OpenMM::CpuRandom& random;
std::vector<OpenMM_SFMT::SFMT> threadRandom;
......@@ -109,4 +105,4 @@ private:
} // namespace OpenMM
#endif // __CPU_BAOAB_DYNAMICS_H__
#endif // __CPU_LANGEVIN_MIDDLE_DYNAMICS_H__
platforms/cpu/src/CpuKernelFactory.cpp
View file @ 6786cc75
......@@ -61,7 +61,7 @@ KernelImpl* CpuKernelFactory::createKernelImpl(std::string name, const Platform&
return new CpuCalcGayBerneForceKernel(name, platform, data);
if (name == IntegrateLangevinStepKernel::Name())
return new CpuIntegrateLangevinStepKernel(name, platform, data);
if (name == IntegrateBAOABStepKernel::Name())
return new CpuIntegrateBAOABStepKernel(name, platform, data);
if (name == IntegrateLangevinMiddleStepKernel::Name())
return new CpuIntegrateLangevinMiddleStepKernel(name, platform, data);
throw OpenMMException((std::string("Tried to create kernel with illegal kernel name '") + name + "'").c_str());
}
platforms/cpu/src/CpuKernels.cpp
View file @ 6786cc75
......@@ -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) 2013-2019 Stanford University and the Authors. *
* Portions copyright (c) 2013-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -1361,12 +1361,12 @@ double CpuIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& context
return computeShiftedKineticEnergy(context, masses, 0.5*integrator.getStepSize());
}
CpuIntegrateBAOABStepKernel::~CpuIntegrateBAOABStepKernel() {
CpuIntegrateLangevinMiddleStepKernel::~CpuIntegrateLangevinMiddleStepKernel() {
if (dynamics)
delete dynamics;
}
void CpuIntegrateBAOABStepKernel::initialize(const System& system, const BAOABLangevinIntegrator& integrator) {
void CpuIntegrateLangevinMiddleStepKernel::initialize(const System& system, const LangevinMiddleIntegrator& integrator) {
int numParticles = system.getNumParticles();
masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i)
......@@ -1374,7 +1374,7 @@ void CpuIntegrateBAOABStepKernel::initialize(const System& system, const BAOABLa
data.random.initialize(integrator.getRandomNumberSeed(), data.threads.getNumThreads());
}
void CpuIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid) {
void CpuIntegrateLangevinMiddleStepKernel::execute(ContextImpl& context, const LangevinMiddleIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
......@@ -1385,18 +1385,18 @@ void CpuIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLange
if (dynamics)
delete dynamics;
dynamics = new CpuBAOABDynamics(context.getSystem().getNumParticles(), stepSize, friction, temperature, data.threads, data.random);
dynamics = new CpuLangevinMiddleDynamics(context.getSystem().getNumParticles(), stepSize, friction, temperature, data.threads, data.random);
dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
prevTemp = temperature;
prevFriction = friction;
prevStepSize = stepSize;
}
dynamics->update(context, posData, velData, masses, forcesAreValid, integrator.getConstraintTolerance());
dynamics->update(context, posData, velData, masses, integrator.getConstraintTolerance());
ReferencePlatform::PlatformData* refData = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
refData->time += stepSize;
refData->stepCount++;
}
double CpuIntegrateBAOABStepKernel::computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
double CpuIntegrateLangevinMiddleStepKernel::computeKineticEnergy(ContextImpl& context, const LangevinMiddleIntegrator& integrator) {
return computeShiftedKineticEnergy(context, masses, 0.0);
}
platforms/cpu/src/CpuBAOABDynamics.cpp → platforms/cpu/src/CpuLangevinMiddleDynamics.cpp
View file @ 6786cc75
/* Portions copyright (c) 2006-2019 Stanford University and Simbios.
/* Portions copyright (c) 2006-2020 Stanford University and Simbios.
* Authors: Peter Eastman
* Contributors:
*
......@@ -24,28 +23,25 @@
*/
#include "SimTKOpenMMUtilities.h"
#include "CpuBAOABDynamics.h"
#include "CpuLangevinMiddleDynamics.h"
using namespace OpenMM;
using namespace std;
CpuBAOABDynamics::CpuBAOABDynamics(int numberOfAtoms, double deltaT, double friction, double temperature, ThreadPool& threads, CpuRandom& random) :
ReferenceBAOABDynamics(numberOfAtoms, deltaT, friction, temperature), threads(threads), random(random) {
CpuLangevinMiddleDynamics::CpuLangevinMiddleDynamics(int numberOfAtoms, double deltaT, double friction, double temperature, ThreadPool& threads, CpuRandom& random) :
ReferenceLangevinMiddleDynamics(numberOfAtoms, deltaT, friction, temperature), threads(threads), random(random) {
}
CpuBAOABDynamics::~CpuBAOABDynamics() {
CpuLangevinMiddleDynamics::~CpuLangevinMiddleDynamics() {
}
void CpuBAOABDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& atomCoordinates, vector<Vec3>& velocities,
vector<Vec3>& forces, vector<double>& inverseMasses, vector<Vec3>& xPrime) {
void CpuLangevinMiddleDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses) {
// Record the parameters for the threads.
this->numberOfAtoms = numberOfAtoms;
this->atomCoordinates = &atomCoordinates[0];
this->velocities = &velocities[0];
this->forces = &forces[0];
this->inverseMasses = &inverseMasses[0];
this->xPrime = &xPrime[0];
// Signal the threads to start running and wait for them to finish.
......@@ -53,7 +49,7 @@ void CpuBAOABDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& atomCoordina
threads.waitForThreads();
}
void CpuBAOABDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordinates, vector<Vec3>& velocities,
void CpuLangevinMiddleDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordinates, vector<Vec3>& velocities,
vector<double>& inverseMasses, vector<Vec3>& xPrime) {
// Record the parameters for the threads.
......@@ -69,7 +65,7 @@ void CpuBAOABDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordina
threads.waitForThreads();
}
void CpuBAOABDynamics::updatePart3(ContextImpl& context, int numberOfAtoms, vector<Vec3>& atomCoordinates, vector<Vec3>& velocities,
void CpuLangevinMiddleDynamics::updatePart3(ContextImpl& context, int numberOfAtoms, vector<Vec3>& atomCoordinates, vector<Vec3>& velocities,
vector<double>& inverseMasses, vector<Vec3>& xPrime) {
// Record the parameters for the threads.
......@@ -83,26 +79,18 @@ void CpuBAOABDynamics::updatePart3(ContextImpl& context, int numberOfAtoms, vect
threads.execute([&] (ThreadPool& threads, int threadIndex) { threadUpdate3(threadIndex); });
threads.waitForThreads();
context.calcForcesAndEnergy(true, false);
threads.execute([&] (ThreadPool& threads, int threadIndex) { threadUpdate4(threadIndex); });
threads.waitForThreads();
}
void CpuBAOABDynamics::threadUpdate1(int threadIndex) {
const double halfdt = 0.5*getDeltaT();
void CpuLangevinMiddleDynamics::threadUpdate1(int threadIndex) {
int start = threadIndex*numberOfAtoms/threads.getNumThreads();
int end = (threadIndex+1)*numberOfAtoms/threads.getNumThreads();
for (int i = start; i < end; i++) {
if (inverseMasses[i] != 0.0) {
velocities[i] += (halfdt*inverseMasses[i])*forces[i];
xPrime[i] = atomCoordinates[i] + velocities[i]*halfdt;
oldx[i] = xPrime[i];
}
}
for (int i = start; i < end; i++)
if (inverseMasses[i] != 0.0)
velocities[i] += (getDeltaT()*inverseMasses[i])*forces[i];
}
void CpuBAOABDynamics::threadUpdate2(int threadIndex) {
void CpuLangevinMiddleDynamics::threadUpdate2(int threadIndex) {
const double halfdt = 0.5*getDeltaT();
const double kT = BOLTZ*getTemperature();
const double friction = getFriction();
......@@ -113,34 +101,22 @@ void CpuBAOABDynamics::threadUpdate2(int threadIndex) {
for (int i = start; i < end; i++) {
if (inverseMasses[i] != 0.0) {
velocities[i] += (xPrime[i]-oldx[i])/halfdt;
xPrime[i] = atomCoordinates[i] + velocities[i]*halfdt;
Vec3 noise(random.getGaussianRandom(threadIndex), random.getGaussianRandom(threadIndex), random.getGaussianRandom(threadIndex));
velocities[i] = vscale*velocities[i] + noisescale*sqrt(kT*inverseMasses[i])*noise;
atomCoordinates[i] = xPrime[i];
xPrime[i] = atomCoordinates[i] + velocities[i]*halfdt;
xPrime[i] = xPrime[i] + velocities[i]*halfdt;
oldx[i] = xPrime[i];
}
}
}
void CpuBAOABDynamics::threadUpdate3(int threadIndex) {
const double halfdt = 0.5*getDeltaT();
void CpuLangevinMiddleDynamics::threadUpdate3(int threadIndex) {
int start = threadIndex*numberOfAtoms/threads.getNumThreads();
int end = (threadIndex+1)*numberOfAtoms/threads.getNumThreads();
for (int i = start; i < end; ++i)
if (inverseMasses[i] != 0.0) {
velocities[i] += (xPrime[i]-oldx[i])/halfdt;
velocities[i] += (xPrime[i]-oldx[i])/getDeltaT();
atomCoordinates[i] = xPrime[i];
}
}
void CpuBAOABDynamics::threadUpdate4(int threadIndex) {
const double halfdt = 0.5*getDeltaT();
int start = threadIndex*numberOfAtoms/threads.getNumThreads();
int end = (threadIndex+1)*numberOfAtoms/threads.getNumThreads();
for (int i = start; i < end; ++i)
if (inverseMasses[i] != 0.0)
velocities[i] += (halfdt*inverseMasses[i])*forces[i];
}
platforms/cpu/src/CpuPlatform.cpp
View file @ 6786cc75
......@@ -74,7 +74,7 @@ CpuPlatform::CpuPlatform() {
registerKernelFactory(CalcCustomGBForceKernel::Name(), factory);
registerKernelFactory(CalcGayBerneForceKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateBAOABStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinMiddleStepKernel::Name(), factory);
platformProperties.push_back(CpuThreads());
platformProperties.push_back(CpuDeterministicForces());
int threads = getNumProcessors();
......
platforms/cpu/tests/TestCpuBAOABLangevinIntegrator.cpp → platforms/cpu/tests/TestCpuLangevinMiddleIntegrator.cpp
View file @ 6786cc75
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "CpuTests.h"
#include "TestBAOABLangevinIntegrator.h"
#include "TestLangevinMiddleIntegrator.h"
void runPlatformTests() {
}
platforms/cuda/src/CudaKernelFactory.cpp
View file @ 6786cc75
......@@ -121,8 +121,8 @@ KernelImpl* CudaKernelFactory::createKernelImpl(std::string name, const Platform
return new CommonIntegrateVerletStepKernel(name, platform, cu);
if (name == IntegrateLangevinStepKernel::Name())
return new CommonIntegrateLangevinStepKernel(name, platform, cu);
if (name == IntegrateBAOABStepKernel::Name())
return new CommonIntegrateBAOABStepKernel(name, platform, cu);
if (name == IntegrateLangevinMiddleStepKernel::Name())
return new CommonIntegrateLangevinMiddleStepKernel(name, platform, cu);
if (name == IntegrateBrownianStepKernel::Name())
return new CommonIntegrateBrownianStepKernel(name, platform, cu);
if (name == IntegrateVariableVerletStepKernel::Name())
......
platforms/cuda/src/CudaPlatform.cpp
View file @ 6786cc75
......@@ -98,7 +98,7 @@ CudaPlatform::CudaPlatform() {
registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateVelocityVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateBAOABStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinMiddleStepKernel::Name(), factory);
registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableLangevinStepKernel::Name(), factory);
......
platforms/cuda/tests/TestCudaBAOABLangevinIntegrator.cpp → platforms/cuda/tests/TestCudaLangevinMiddleIntegrator.cpp
View file @ 6786cc75
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "CudaTests.h"
#include "TestBAOABLangevinIntegrator.h"
#include "TestLangevinMiddleIntegrator.h"
void runPlatformTests() {
}
platforms/opencl/src/OpenCLKernelFactory.cpp
View file @ 6786cc75
......@@ -119,8 +119,8 @@ KernelImpl* OpenCLKernelFactory::createKernelImpl(std::string name, const Platfo
return new CommonIntegrateVerletStepKernel(name, platform, cl);
if (name == IntegrateLangevinStepKernel::Name())
return new CommonIntegrateLangevinStepKernel(name, platform, cl);
if (name == IntegrateBAOABStepKernel::Name())
return new CommonIntegrateBAOABStepKernel(name, platform, cl);
if (name == IntegrateLangevinMiddleStepKernel::Name())
return new CommonIntegrateLangevinMiddleStepKernel(name, platform, cl);
if (name == IntegrateBrownianStepKernel::Name())
return new CommonIntegrateBrownianStepKernel(name, platform, cl);
if (name == IntegrateVariableVerletStepKernel::Name())
......
platforms/opencl/src/OpenCLPlatform.cpp
View file @ 6786cc75
......@@ -89,7 +89,7 @@ OpenCLPlatform::OpenCLPlatform() {
registerKernelFactory(IntegrateVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateVelocityVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateBAOABStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinMiddleStepKernel::Name(), factory);
registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableVerletStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableLangevinStepKernel::Name(), factory);
......
platforms/opencl/tests/TestOpenCLBAOABLangevinIntegrator.cpp → platforms/opencl/tests/TestOpenCLLangevinMiddleIntegrator.cpp
View file @ 6786cc75
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "OpenCLTests.h"
#include "TestBAOABLangevinIntegrator.h"
#include "TestLangevinMiddleIntegrator.h"
void runPlatformTests() {
}
platforms/reference/include/ReferenceKernels.h
View file @ 6786cc75
......@@ -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) 2008-2019 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -45,7 +45,7 @@ namespace OpenMM {
class ReferenceObc;
class ReferenceAndersenThermostat;
class ReferenceBAOABDynamics;
class ReferenceLangevinMiddleDynamics;
class ReferenceCustomBondIxn;
class ReferenceCustomAngleIxn;
class ReferenceCustomTorsionIxn;
......@@ -1213,42 +1213,38 @@ private:
};
/**
* This kernel is invoked by BAOABLangevinIntegrator to take one time step.
* This kernel is invoked by LangevinMiddleIntegrator to take one time step.
*/
class ReferenceIntegrateBAOABStepKernel : public IntegrateBAOABStepKernel {
class ReferenceIntegrateLangevinMiddleStepKernel : public IntegrateLangevinMiddleStepKernel {
public:
ReferenceIntegrateBAOABStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateBAOABStepKernel(name, platform),
ReferenceIntegrateLangevinMiddleStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) : IntegrateLangevinMiddleStepKernel(name, platform),
data(data), dynamics(0) {
}
~ReferenceIntegrateBAOABStepKernel();
~ReferenceIntegrateLangevinMiddleStepKernel();
/**
* 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 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.
* @param integrator the LangevinMiddleIntegrator this kernel is being used for
*/
void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid);
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:
ReferencePlatform::PlatformData& data;
ReferenceBAOABDynamics* dynamics;
ReferenceLangevinMiddleDynamics* dynamics;
std::vector<double> masses;
double prevTemp, prevFriction, prevStepSize;
};
......
platforms/reference/include/ReferenceBAOABDynamics.h → platforms/reference/include/ReferenceLangevinMiddleDynamics.h
View file @ 6786cc75
/* Portions copyright (c) 2006-2019 Stanford University and Simbios.
/* Portions copyright (c) 2006-2020 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -22,8 +22,8 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __ReferenceBAOABDynamics_H__
#define __ReferenceBAOABDynamics_H__
#ifndef __ReferenceLangevinMiddleDynamics_H__
#define __ReferenceLangevinMiddleDynamics_H__
#include "ReferenceDynamics.h"
#include "openmm/internal/ContextImpl.h"
......@@ -31,7 +31,7 @@
namespace OpenMM {
class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
class OPENMM_EXPORT ReferenceLangevinMiddleDynamics : public ReferenceDynamics {
protected:
......@@ -52,7 +52,7 @@ class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
ReferenceBAOABDynamics(int numberOfAtoms, double deltaT, double friction, double temperature);
ReferenceLangevinMiddleDynamics(int numberOfAtoms, double deltaT, double friction, double temperature);
/**---------------------------------------------------------------------------------------
......@@ -60,7 +60,7 @@ class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
~ReferenceBAOABDynamics();
~ReferenceLangevinMiddleDynamics();
/**---------------------------------------------------------------------------------------
......@@ -79,29 +79,25 @@ class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
@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);
std::vector<OpenMM::Vec3>& velocities, std::vector<double>& masses, 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 inverseMasses inverse 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>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
virtual void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses);
/**---------------------------------------------------------------------------------------
......@@ -116,7 +112,7 @@ class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
virtual void updatePart2(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
/**---------------------------------------------------------------------------------------
......@@ -126,16 +122,15 @@ class OPENMM_EXPORT ReferenceBAOABDynamics : public ReferenceDynamics {
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param inverseMasses inverse atom masses
@param xPrime xPrime
--------------------------------------------------------------------------------------- */
virtual void updatePart3(OpenMM::ContextImpl& context, int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
};
} // namespace OpenMM
#endif // __ReferenceBAOABDynamics_H__
#endif // __ReferenceLangevinMiddleDynamics_H__
platforms/reference/src/ReferenceKernelFactory.cpp
View file @ 6786cc75
......@@ -94,8 +94,8 @@ KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Pla
return new ReferenceNoseHooverChainKernel(name, platform);
if (name == IntegrateLangevinStepKernel::Name())
return new ReferenceIntegrateLangevinStepKernel(name, platform, data);
if (name == IntegrateBAOABStepKernel::Name())
return new ReferenceIntegrateBAOABStepKernel(name, platform, data);
if (name == IntegrateLangevinMiddleStepKernel::Name())
return new ReferenceIntegrateLangevinMiddleStepKernel(name, platform, data);
if (name == IntegrateBrownianStepKernel::Name())
return new ReferenceIntegrateBrownianStepKernel(name, platform, data);
if (name == IntegrateVariableLangevinStepKernel::Name())
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 6786cc75
......@@ -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) 2008-2019 Stanford University and the Authors. *
* Portions copyright (c) 2008-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -33,7 +33,6 @@
#include "ReferenceObc.h"
#include "ReferenceAndersenThermostat.h"
#include "ReferenceAngleBondIxn.h"
#include "ReferenceBAOABDynamics.h"
#include "ReferenceBondForce.h"
#include "ReferenceBrownianDynamics.h"
#include "ReferenceCCMAAlgorithm.h"
......@@ -53,6 +52,7 @@
#include "ReferenceCustomTorsionIxn.h"
#include "ReferenceGayBerneForce.h"
#include "ReferenceHarmonicBondIxn.h"
#include "ReferenceLangevinMiddleDynamics.h"
#include "ReferenceLJCoulomb14.h"
#include "ReferenceLJCoulombIxn.h"
#include "ReferenceMonteCarloBarostat.h"
......@@ -2233,12 +2233,12 @@ double ReferenceIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& c
return computeShiftedKineticEnergy(context, masses, 0.5*integrator.getStepSize());
}
ReferenceIntegrateBAOABStepKernel::~ReferenceIntegrateBAOABStepKernel() {
ReferenceIntegrateLangevinMiddleStepKernel::~ReferenceIntegrateLangevinMiddleStepKernel() {
if (dynamics)
delete dynamics;
}
void ReferenceIntegrateBAOABStepKernel::initialize(const System& system, const BAOABLangevinIntegrator& integrator) {
void ReferenceIntegrateLangevinMiddleStepKernel::initialize(const System& system, const LangevinMiddleIntegrator& integrator) {
int numParticles = system.getNumParticles();
masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i)
......@@ -2246,7 +2246,7 @@ void ReferenceIntegrateBAOABStepKernel::initialize(const System& system, const B
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
}
void ReferenceIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid) {
void ReferenceIntegrateLangevinMiddleStepKernel::execute(ContextImpl& context, const LangevinMiddleIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
......@@ -2257,7 +2257,7 @@ void ReferenceIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOA
if (dynamics)
delete dynamics;
dynamics = new ReferenceBAOABDynamics(
dynamics = new ReferenceLangevinMiddleDynamics(
context.getSystem().getNumParticles(),
stepSize,
friction,
......@@ -2267,12 +2267,12 @@ void ReferenceIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOA
prevFriction = friction;
prevStepSize = stepSize;
}
dynamics->update(context, posData, velData, masses, forcesAreValid, integrator.getConstraintTolerance());
dynamics->update(context, posData, velData, masses, integrator.getConstraintTolerance());
data.time += stepSize;
data.stepCount++;
}
double ReferenceIntegrateBAOABStepKernel::computeKineticEnergy(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
double ReferenceIntegrateLangevinMiddleStepKernel::computeKineticEnergy(ContextImpl& context, const LangevinMiddleIntegrator& integrator) {
return computeShiftedKineticEnergy(context, masses, 0.0);
}
......
platforms/reference/src/ReferencePlatform.cpp
View file @ 6786cc75
......@@ -69,7 +69,7 @@ ReferencePlatform::ReferencePlatform() {
registerKernelFactory(IntegrateVelocityVerletStepKernel::Name(), factory);
registerKernelFactory(NoseHooverChainKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateBAOABStepKernel::Name(), factory);
registerKernelFactory(IntegrateLangevinMiddleStepKernel::Name(), factory);
registerKernelFactory(IntegrateBrownianStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableLangevinStepKernel::Name(), factory);
registerKernelFactory(IntegrateVariableVerletStepKernel::Name(), factory);
......
platforms/reference/src/SimTKReference/ReferenceBAOABDynamics.cpp → platforms/reference/src/SimTKReference/ReferenceLangevinMiddleDynamics.cpp
View file @ 6786cc75
/* Portions copyright (c) 2006-2019 Stanford University and Simbios.
/* Portions copyright (c) 2006-2020 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -26,7 +26,7 @@
#include <sstream>
#include "SimTKOpenMMUtilities.h"
#include "ReferenceBAOABDynamics.h"
#include "ReferenceLangevinMiddleDynamics.h"
#include "ReferencePlatform.h"
#include "ReferenceVirtualSites.h"
#include "openmm/OpenMMException.h"
......@@ -35,7 +35,7 @@
using std::vector;
using namespace OpenMM;
ReferenceBAOABDynamics::ReferenceBAOABDynamics(int numberOfAtoms,
ReferenceLangevinMiddleDynamics::ReferenceLangevinMiddleDynamics(int numberOfAtoms,
double deltaT, double friction,
double temperature) :
ReferenceDynamics(numberOfAtoms, deltaT, temperature), friction(friction) {
......@@ -44,29 +44,22 @@ ReferenceBAOABDynamics::ReferenceBAOABDynamics(int numberOfAtoms,
inverseMasses.resize(numberOfAtoms);
}
ReferenceBAOABDynamics::~ReferenceBAOABDynamics() {
ReferenceLangevinMiddleDynamics::~ReferenceLangevinMiddleDynamics() {
}
double ReferenceBAOABDynamics::getFriction() const {
double ReferenceLangevinMiddleDynamics::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 ReferenceLangevinMiddleDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses) {
for (int i = 0; i < numberOfAtoms; i++)
if (inverseMasses[i] != 0.0)
velocities[i] += (getDeltaT()*inverseMasses[i])*forces[i];
}
void ReferenceBAOABDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<double>& inverseMasses,
vector<Vec3>& xPrime) {
void ReferenceLangevinMiddleDynamics::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();
......@@ -75,37 +68,29 @@ void ReferenceBAOABDynamics::updatePart2(int numberOfAtoms, vector<Vec3>& atomCo
for (int i = 0; i < numberOfAtoms; i++) {
if (inverseMasses[i] != 0.0) {
velocities[i] += (xPrime[i]-oldx[i])/halfdt;
xPrime[i] = atomCoordinates[i] + velocities[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;
xPrime[i] = xPrime[i] + velocities[i]*halfdt;
oldx[i] = xPrime[i];
}
}
}
void ReferenceBAOABDynamics::updatePart3(OpenMM::ContextImpl& context, int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses,
vector<Vec3>& xPrime) {
const double halfdt = 0.5*getDeltaT();
void ReferenceLangevinMiddleDynamics::updatePart3(OpenMM::ContextImpl& context, int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<double>& inverseMasses, vector<Vec3>& xPrime) {
for (int i = 0; i < numberOfAtoms; i++) {
if (inverseMasses[i] != 0.0) {
velocities[i] += (xPrime[i]-oldx[i])/halfdt;
velocities[i] += (xPrime[i]-oldx[i])/getDeltaT();
atomCoordinates[i] = xPrime[i];
}
}
context.calcForcesAndEnergy(true, false);
for (int i = 0; i < numberOfAtoms; i++) {
if (inverseMasses[i] != 0.0)
velocities[i] += (halfdt*inverseMasses[i])*forces[i];
}
}
void ReferenceBAOABDynamics::update(ContextImpl& context, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<double>& masses, bool& forcesAreValid, double tolerance) {
void ReferenceLangevinMiddleDynamics::update(ContextImpl& context, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<double>& masses, double tolerance) {
int numberOfAtoms = context.getSystem().getNumParticles();
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (getTimeStep() == 0) {
......@@ -118,18 +103,14 @@ void ReferenceBAOABDynamics::update(ContextImpl& context, vector<Vec3>& atomCoor
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);
updatePart1(numberOfAtoms, velocities, forces, inverseMasses);
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
referenceConstraintAlgorithm->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
// 2nd update
......@@ -139,9 +120,7 @@ void ReferenceBAOABDynamics::update(ContextImpl& context, vector<Vec3>& atomCoor
// 3rd update
updatePart3(context, numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
updatePart3(context, numberOfAtoms, atomCoordinates, velocities, inverseMasses, xPrime);
ReferenceVirtualSites::computePositions(context.getSystem(), atomCoordinates);
incrementTimeStep();
......
platforms/reference/tests/TestReferenceBAOABLangevinIntegrator.cpp → platforms/reference/tests/TestReferenceLangevinMiddleIntegrator.cpp
View file @ 6786cc75
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "ReferenceTests.h"
#include "TestBAOABLangevinIntegrator.h"
#include "TestLangevinMiddleIntegrator.h"
void runPlatformTests() {
}
serialization/include/openmm/serialization/BAOABLangevinIntegratorProxy.h → serialization/include/openmm/serialization/LangevinMiddleIntegratorProxy.h
View file @ 6786cc75
#ifndef OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_
#define OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_
#ifndef OPENMM_LANGEVIN_MIDDLE_INTEGRATOR_PROXY_H_
#define OPENMM_LANGEVIN_MIDDLE_INTEGRATOR_PROXY_H_
#include "openmm/serialization/XmlSerializer.h"
namespace OpenMM {
class BAOABLangevinIntegratorProxy : public SerializationProxy {
class LangevinMiddleIntegratorProxy : public SerializationProxy {
public:
BAOABLangevinIntegratorProxy();
LangevinMiddleIntegratorProxy();
void serialize(const void* object, SerializationNode& node) const;
void* deserialize(const SerializationNode& node) const;
};
}
#endif /*OPENMM_BAOAB_LANGEVIN_INTEGRATOR_PROXY_H_*/
\ No newline at end of file
#endif /*OPENMM_LANGEVIN_MIDDLE_INTEGRATOR_PROXY_H_*/
\ No newline at end of file
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