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Commit ba9f6b0a authored by Peter Eastman's avatar Peter Eastman
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Converted from BAOAB to leapfrog

parent ff555815
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Showing with 64 additions and 212 deletions
olla/include/openmm/kernels.h
View file @ ba9f6b0a
......@@ -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: *
* *
......@@ -1150,12 +1150,8 @@ public:
*
* @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;
virtual void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator) = 0;
/**
* Compute the kinetic energy.
*
......
openmmapi/include/openmm/BAOABLangevinIntegrator.h
View file @ ba9f6b0a
......@@ -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: *
* *
......@@ -128,10 +128,6 @@ protected:
* 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.
*/
......@@ -147,7 +143,6 @@ protected:
private:
double temperature, friction;
int randomNumberSeed;
bool forcesAreValid;
Kernel kernel;
};
......
openmmapi/src/BAOABLangevinIntegrator.cpp
View file @ ba9f6b0a
......@@ -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: *
* *
......@@ -46,7 +46,6 @@ BAOABLangevinIntegrator::BAOABLangevinIntegrator(double temperature, double fric
setStepSize(stepSize);
setConstraintTolerance(1e-5);
setRandomNumberSeed(0);
forcesAreValid = false;
}
void BAOABLangevinIntegrator::initialize(ContextImpl& contextRef) {
......@@ -62,10 +61,6 @@ 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());
......@@ -73,7 +68,6 @@ vector<string> BAOABLangevinIntegrator::getKernelNames() {
}
double BAOABLangevinIntegrator::computeKineticEnergy() {
forcesAreValid = false;
return kernel.getAs<IntegrateBAOABStepKernel>().computeKineticEnergy(*context, *this);
}
......@@ -85,8 +79,8 @@ 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) {
if (context->updateContextState())
forcesAreValid = false;
kernel.getAs<IntegrateBAOABStepKernel>().execute(*context, *this, forcesAreValid);
context->updateContextState();
context->calcForcesAndEnergy(true, false);
kernel.getAs<IntegrateBAOABStepKernel>().execute(*context, *this);
}
}
platforms/common/include/openmm/common/CommonKernels.h
View file @ ba9f6b0a
......@@ -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: *
* *
......@@ -924,12 +924,8 @@ public:
*
* @param context the context in which to execute this kernel
* @param integrator the BAOABLangevinIntegrator this kernel is being used for
* @param forcesAreValid if the context has been modified since the last time step, this will be
* false to show that cached forces are invalid and must be recalculated.
* On exit, this should specify whether the cached forces are valid at the
* end of the step.
*/
void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid);
void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator);
/**
* Compute the kinetic energy.
*
......@@ -942,7 +938,7 @@ private:
double prevTemp, prevFriction, prevStepSize;
bool hasInitializedKernels;
ComputeArray params, oldDelta;
ComputeKernel kernel1, kernel2, kernel3, kernel4;
ComputeKernel kernel1, kernel2, kernel3;
};
/**
......
platforms/common/src/CommonKernels.cpp
View file @ ba9f6b0a
......@@ -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: *
* *
......@@ -5555,7 +5555,6 @@ void CommonIntegrateBAOABStepKernel::initialize(const System& system, const BAOA
kernel1 = program->createKernel("integrateBAOABPart1");
kernel2 = program->createKernel("integrateBAOABPart2");
kernel3 = program->createKernel("integrateBAOABPart3");
kernel4 = program->createKernel("integrateBAOABPart4");
if (cc.getUseDoublePrecision() || cc.getUseMixedPrecision()) {
params.initialize<double>(cc, 2, "baoabParams");
oldDelta.initialize<mm_double4>(cc, cc.getPaddedNumAtoms(), "oldDelta");
......@@ -5567,7 +5566,7 @@ void CommonIntegrateBAOABStepKernel::initialize(const System& system, const BAOA
prevStepSize = -1.0;
}
void CommonIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid) {
void CommonIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
IntegrationUtilities& integration = cc.getIntegrationUtilities();
int numAtoms = cc.getNumAtoms();
int paddedNumAtoms = cc.getPaddedNumAtoms();
......@@ -5577,11 +5576,8 @@ void CommonIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLa
kernel1->addArg(paddedNumAtoms);
kernel1->addArg(cc.getVelm());
kernel1->addArg(cc.getLongForceBuffer());
kernel1->addArg(integration.getPosDelta());
kernel1->addArg(oldDelta);
kernel1->addArg(integration.getStepSize());
kernel2->addArg(numAtoms);
kernel2->addArg(cc.getPosq());
kernel2->addArg(cc.getVelm());
kernel2->addArg(integration.getPosDelta());
kernel2->addArg(oldDelta);
......@@ -5589,8 +5585,6 @@ void CommonIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLa
kernel2->addArg(integration.getStepSize());
kernel2->addArg(integration.getRandom());
kernel2->addArg(); // Random index will be set just before it is executed.
if (cc.getUseMixedPrecision())
kernel2->addArg(cc.getPosqCorrection());
kernel3->addArg(numAtoms);
kernel3->addArg(cc.getPosq());
kernel3->addArg(cc.getVelm());
......@@ -5599,15 +5593,6 @@ void CommonIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLa
kernel3->addArg(integration.getStepSize());
if (cc.getUseMixedPrecision())
kernel3->addArg(cc.getPosqCorrection());
kernel4->addArg(numAtoms);
kernel4->addArg(paddedNumAtoms);
kernel4->addArg(cc.getVelm());
kernel4->addArg(cc.getLongForceBuffer());
kernel4->addArg(integration.getStepSize());
}
if (!forcesAreValid) {
context.calcForcesAndEnergy(true, false);
forcesAreValid = true;
}
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
......@@ -5630,15 +5615,12 @@ void CommonIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLa
// Perform the integration.
kernel2->setArg(8, integration.prepareRandomNumbers(cc.getPaddedNumAtoms()));
kernel2->setArg(7, integration.prepareRandomNumbers(cc.getPaddedNumAtoms()));
kernel1->execute(numAtoms);
integration.applyConstraints(integrator.getConstraintTolerance());
integration.applyVelocityConstraints(integrator.getConstraintTolerance());
kernel2->execute(numAtoms);
integration.applyConstraints(integrator.getConstraintTolerance());
kernel3->execute(numAtoms);
context.calcForcesAndEnergy(true, false);
kernel4->execute(numAtoms);
integration.applyVelocityConstraints(integrator.getConstraintTolerance());
integration.computeVirtualSites();
// Update the time and step count.
......@@ -5646,8 +5628,6 @@ void CommonIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLa
cc.setTime(cc.getTime()+stepSize);
cc.setStepCount(cc.getStepCount()+1);
cc.reorderAtoms();
if (cc.getAtomsWereReordered())
forcesAreValid = false;
// Reduce UI lag.
......
platforms/common/src/kernels/baoab.cc
View file @ ba9f6b0a
......@@ -4,10 +4,9 @@ enum {VelScale, NoiseScale};
* Perform the first part of BAOAB integration: velocity half step, then position half step.
*/
KERNEL void integrateBAOABPart1(int numAtoms, int paddedNumAtoms, GLOBAL mixed4* RESTRICT velm, GLOBAL const mm_long* RESTRICT force, GLOBAL mixed4* RESTRICT posDelta,
GLOBAL mixed4* RESTRICT oldDelta, GLOBAL const mixed2* RESTRICT dt) {
mixed halfdt = 0.5*dt[0].y;
mixed fscale = halfdt/(mixed) 0x100000000;
KERNEL void integrateBAOABPart1(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) {
mixed4 velocity = velm[index];
if (velocity.w != 0.0) {
......@@ -15,9 +14,6 @@ KERNEL void integrateBAOABPart1(int numAtoms, int paddedNumAtoms, GLOBAL mixed4*
velocity.y += fscale*velocity.w*force[index+paddedNumAtoms];
velocity.z += fscale*velocity.w*force[index+paddedNumAtoms*2];
velm[index] = velocity;
mixed4 delta = make_mixed4(halfdt*velocity.x, halfdt*velocity.y, halfdt*velocity.z, 0);
posDelta[index] = delta;
oldDelta[index] = delta;
}
}
}
......@@ -27,47 +23,24 @@ KERNEL void integrateBAOABPart1(int numAtoms, int paddedNumAtoms, GLOBAL mixed4*
* then position half step.
*/
KERNEL void integrateBAOABPart2(int numAtoms, GLOBAL real4* RESTRICT posq, GLOBAL mixed4* RESTRICT velm, GLOBAL mixed4* RESTRICT posDelta,
KERNEL void integrateBAOABPart2(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
#ifdef USE_MIXED_PRECISION
, GLOBAL real4* RESTRICT posqCorrection
#endif
) {
mixed vscale = paramBuffer[VelScale];
mixed noisescale = paramBuffer[NoiseScale];
mixed halfdt = 0.5*dt[0].y;
mixed invHalfdt = 1/halfdt;
int index = GLOBAL_ID;
randomIndex += index;
while (index < numAtoms) {
mixed4 velocity = velm[index];
if (velocity.w != 0.0) {
mixed4 delta = posDelta[index];
mixed4 delta = make_mixed4(halfdt*velocity.x, halfdt*velocity.y, halfdt*velocity.z, 0);
mixed sqrtInvMass = SQRT(velocity.w);
velocity.x += (delta.x-oldDelta[index].x)*invHalfdt;
velocity.y += (delta.y-oldDelta[index].y)*invHalfdt;
velocity.z += (delta.z-oldDelta[index].z)*invHalfdt;
velocity.x = vscale*velocity.x + noisescale*sqrtInvMass*random[randomIndex].x;
velocity.y = vscale*velocity.y + noisescale*sqrtInvMass*random[randomIndex].y;
velocity.z = vscale*velocity.z + noisescale*sqrtInvMass*random[randomIndex].z;
velm[index] = velocity;
#ifdef USE_MIXED_PRECISION
real4 pos1 = posq[index];
real4 pos2 = posqCorrection[index];
mixed4 pos = make_mixed4(pos1.x+(mixed)pos2.x, pos1.y+(mixed)pos2.y, pos1.z+(mixed)pos2.z, pos1.w);
#else
real4 pos = posq[index];
#endif
pos.x += delta.x;
pos.y += delta.y;
pos.z += delta.z;
#ifdef USE_MIXED_PRECISION
posq[index] = make_real4((real) pos.x, (real) pos.y, (real) pos.z, (real) pos.w);
posqCorrection[index] = make_real4(pos.x-(real) pos.x, pos.y-(real) pos.y, pos.z-(real) pos.z, 0);
#else
posq[index] = pos;
#endif
delta = make_mixed4(halfdt*velocity.x, halfdt*velocity.y, halfdt*velocity.z, 0);
delta += make_mixed4(halfdt*velocity.x, halfdt*velocity.y, halfdt*velocity.z, 0);
posDelta[index] = delta;
oldDelta[index] = delta;
}
......@@ -87,15 +60,14 @@ KERNEL void integrateBAOABPart3(int numAtoms, GLOBAL real4* RESTRICT posq, GLOBA
, GLOBAL real4* RESTRICT posqCorrection
#endif
) {
mixed halfdt = 0.5*dt[0].y;
mixed invHalfdt = 1/halfdt;
mixed invDt = 1/dt[0].y;
for (int index = GLOBAL_ID; index < numAtoms; index += GLOBAL_SIZE) {
mixed4 velocity = velm[index];
if (velocity.w != 0.0) {
mixed4 delta = posDelta[index];
velocity.x += (delta.x-oldDelta[index].x)*invHalfdt;
velocity.y += (delta.y-oldDelta[index].y)*invHalfdt;
velocity.z += (delta.z-oldDelta[index].z)*invHalfdt;
velocity.x += (delta.x-oldDelta[index].x)*invDt;
velocity.y += (delta.y-oldDelta[index].y)*invDt;
velocity.z += (delta.z-oldDelta[index].z)*invDt;
velm[index] = velocity;
#ifdef USE_MIXED_PRECISION
real4 pos1 = posq[index];
......@@ -116,22 +88,3 @@ KERNEL void integrateBAOABPart3(int numAtoms, GLOBAL real4* RESTRICT posq, GLOBA
}
}
}
/**
* Perform the fourth part of BAOAB integration: velocity half step.
*/
KERNEL void integrateBAOABPart4(int numAtoms, int paddedNumAtoms, GLOBAL mixed4* RESTRICT velm,
GLOBAL const mm_long* RESTRICT force, GLOBAL const mixed2* RESTRICT dt) {
mixed halfdt = 0.5*dt[0].y;
mixed fscale = halfdt/(mixed) 0x100000000;
for (int index = GLOBAL_ID; index < numAtoms; index += GLOBAL_SIZE) {
mixed4 velocity = velm[index];
if (velocity.w != 0.0) {
velocity.x += fscale*velocity.w*force[index];
velocity.y += fscale*velocity.w*force[index+paddedNumAtoms];
velocity.z += fscale*velocity.w*force[index+paddedNumAtoms*2];
velm[index] = velocity;
}
}
}
platforms/cpu/include/CpuBAOABDynamics.h
View file @ ba9f6b0a
/* Portions copyright (c) 2013-2019 Stanford University and Simbios.
/* Portions copyright (c) 2013-2020 Stanford University and Simbios.
* Authors: Peter Eastman
* Contributors:
*
......@@ -56,14 +56,11 @@ public:
* 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;
......
platforms/cpu/include/CpuKernels.h
View file @ ba9f6b0a
......@@ -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) 2013-2019 Stanford University and the Authors. *
* Portions copyright (c) 2013-2020 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -558,12 +558,8 @@ public:
*
* @param context the context in which to execute this kernel
* @param integrator the BAOABLangevinIntegrator this kernel is being used for
* @param forcesAreValid if the context has been modified since the last time step, this will be
* false to show that cached forces are invalid and must be recalculated.
* On exit, this should specify whether the cached forces are valid at the
* end of the step.
*/
void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid);
void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator);
/**
* Compute the kinetic energy.
*
......
platforms/cpu/src/CpuBAOABDynamics.cpp
View file @ ba9f6b0a
/* Portions copyright (c) 2006-2019 Stanford University and Simbios.
/* Portions copyright (c) 2006-2020 Stanford University and Simbios.
* Authors: Peter Eastman
* Contributors:
*
......@@ -36,16 +35,13 @@ CpuBAOABDynamics::CpuBAOABDynamics(int numberOfAtoms, double deltaT, double fric
CpuBAOABDynamics::~CpuBAOABDynamics() {
}
void CpuBAOABDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& atomCoordinates, vector<Vec3>& velocities,
vector<Vec3>& forces, vector<double>& inverseMasses, vector<Vec3>& xPrime) {
void CpuBAOABDynamics::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.
......@@ -83,23 +79,15 @@ 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();
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) {
......@@ -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();
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/CpuKernels.cpp
View file @ ba9f6b0a
......@@ -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: *
* *
......@@ -1366,7 +1366,7 @@ 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 CpuIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
......@@ -1383,7 +1383,7 @@ void CpuIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLange
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++;
......
platforms/reference/include/ReferenceBAOABDynamics.h
View file @ ba9f6b0a
/* 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
......@@ -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);
/**---------------------------------------------------------------------------------------
......@@ -126,14 +122,13 @@ 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
......
platforms/reference/include/ReferenceKernels.h
View file @ ba9f6b0a
......@@ -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: *
* *
......@@ -1233,12 +1233,8 @@ public:
*
* @param context the context in which to execute this kernel
* @param integrator the BAOABLangevinIntegrator this kernel is being used for
* @param forcesAreValid if the context has been modified since the last time step, this will be
* false to show that cached forces are invalid and must be recalculated.
* On exit, this should specify whether the cached forces are valid at the
* end of the step.
*/
void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator, bool& forcesAreValid);
void execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator);
/**
* Compute the kinetic energy.
*
......
platforms/reference/src/ReferenceKernels.cpp
View file @ ba9f6b0a
......@@ -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: *
* *
......@@ -2238,7 +2238,7 @@ 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 ReferenceIntegrateBAOABStepKernel::execute(ContextImpl& context, const BAOABLangevinIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
......@@ -2259,7 +2259,7 @@ 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++;
}
......
platforms/reference/src/SimTKReference/ReferenceBAOABDynamics.cpp
View file @ ba9f6b0a
/* 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
......@@ -51,22 +51,15 @@ double ReferenceBAOABDynamics::getFriction() const {
return friction;
}
void ReferenceBAOABDynamics::updatePart1(int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& inverseMasses,
vector<Vec3>& xPrime) {
const double halfdt = 0.5*getDeltaT();
for (int i = 0; i < numberOfAtoms; i++) {
if (inverseMasses[i] != 0.0) {
velocities[i] += (halfdt*inverseMasses[i])*forces[i];
xPrime[i] = atomCoordinates[i] + velocities[i]*halfdt;
oldx[i] = xPrime[i];
}
}
void ReferenceBAOABDynamics::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) {
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();
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) {
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();
......
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