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Commit c67aed53 authored by Peter Eastman's avatar Peter Eastman
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Cleaning up the RPMD code

parent c5e909d4
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Showing with 47 additions and 66 deletions
plugins/rpmd/openmmapi/include/openmm/RPMDIntegrator.h
View file @ c67aed53
......@@ -168,7 +168,7 @@ protected:
private:
double temperature, friction;
int numCopies, randomNumberSeed;
bool forcesAreValid;
bool forcesAreValid, hasSetPosition, hasSetVelocity;
ContextImpl* context;
Context* owner;
Kernel kernel;
......
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
View file @ c67aed53
......@@ -42,7 +42,7 @@ using std::string;
using std::vector;
RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize) :
owner(NULL), numCopies(numCopies), forcesAreValid(false) {
owner(NULL), numCopies(numCopies), forcesAreValid(false), hasSetPosition(false), hasSetVelocity(false) {
setTemperature(temperature);
setFriction(frictionCoeff);
setStepSize(stepSize);
......@@ -71,10 +71,12 @@ vector<string> RPMDIntegrator::getKernelNames() {
void RPMDIntegrator::setPositions(int copy, const vector<Vec3>& positions) {
dynamic_cast<IntegrateRPMDStepKernel&>(kernel.getImpl()).setPositions(copy, positions);
hasSetPosition = true;
}
void RPMDIntegrator::setVelocities(int copy, const vector<Vec3>& velocities) {
dynamic_cast<IntegrateRPMDStepKernel&>(kernel.getImpl()).setVelocities(copy, velocities);
hasSetVelocity = true;
}
State RPMDIntegrator::getState(int copy, int types) {
......@@ -83,6 +85,20 @@ State RPMDIntegrator::getState(int copy, int types) {
}
void RPMDIntegrator::step(int steps) {
if (!hasSetPosition) {
// Initialize the positions from the context.
State s = context->getOwner().getState(State::Positions);
for (int i = 0; i < numCopies; i++)
setPositions(i, s.getPositions());
}
if (!hasSetVelocity) {
// Initialize the velocities from the context.
State s = context->getOwner().getState(State::Velocities);
for (int i = 0; i < numCopies; i++)
setVelocities(i, s.getVelocities());
}
for (int i = 0; i < steps; ++i) {
dynamic_cast<IntegrateRPMDStepKernel&>(kernel.getImpl()).execute(*context, *this, forcesAreValid);
forcesAreValid = true;
......
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp
View file @ c67aed53
......@@ -79,22 +79,6 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& vel = extractVelocities(context);
vector<RealVec>& f = extractForces(context);
if (!hasSetPosition) {
// Initialize the positions from the context.
for (int i = 0; i < numCopies; i++)
for (int j = 0; j < numParticles; j++)
positions[i][j] = pos[j];
hasSetPosition = true;
}
if (!hasSetVelocity) {
// Initialize the velocities from the context.
for (int i = 0; i < numCopies; i++)
for (int j = 0; j < numParticles; j++)
velocities[i][j] = vel[j];
hasSetVelocity = true;
}
// Loop over copies and compute the force on each one.
......@@ -109,24 +93,24 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
// Apply the PILE-L thermostat.
vector<t_complex> p(numCopies);
vector<t_complex> v(numCopies);
vector<t_complex> q(numCopies);
const RealOpenMM hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
const RealOpenMM scale = 1.0/sqrt(numCopies);
const RealOpenMM scale = 1.0/sqrt((RealOpenMM) numCopies);
const RealOpenMM nkT = numCopies*BOLTZ*integrator.getTemperature();
const RealOpenMM twown = 2.0*nkT/hbar;
const RealOpenMM c1_0 = exp(-halfdt*integrator.getFriction());
const RealOpenMM c2_0 = sqrt(1.0-c1_0*c1_0);
for (int particle = 0; particle < numParticles; particle++) {
const RealOpenMM c3_0 = c2_0*sqrt(system.getParticleMass(particle)*nkT);
const RealOpenMM c3_0 = c2_0*sqrt(nkT/system.getParticleMass(particle));
for (int component = 0; component < 3; component++) {
for (int k = 0; k < numCopies; k++)
p[k] = t_complex(scale*velocities[k][particle][component]*system.getParticleMass(particle), 0.0);
fftpack_exec_1d(fft, FFTPACK_FORWARD, &p[0], &p[0]);
v[k] = t_complex(scale*velocities[k][particle][component], 0.0);
fftpack_exec_1d(fft, FFTPACK_FORWARD, &v[0], &v[0]);
// Apply a local Langevin thermostat to the centroid mode.
p[0].re = p[0].re*c1_0 + c3_0*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
v[0].re = v[0].re*c1_0 + c3_0*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
// Use critical damping white noise for the remaining modes.
......@@ -135,16 +119,16 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
const RealOpenMM c1 = exp(-2.0*wk*halfdt);
const RealOpenMM c2 = sqrt((1.0-c1*c1)/2) * (isCenter ? sqrt(2.0) : 1.0);
const RealOpenMM c3 = c2*sqrt(system.getParticleMass(particle)*nkT);
const RealOpenMM c3 = c2*sqrt(nkT/system.getParticleMass(particle));
RealOpenMM rand1 = c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
RealOpenMM rand2 = (isCenter ? 0.0 : c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
p[k] = p[k]*c1 + t_complex(rand1, rand2);
v[k] = v[k]*c1 + t_complex(rand1, rand2);
if (k < numCopies-k)
p[numCopies-k] = p[numCopies-k]*c1 + t_complex(rand1, -rand2);
v[numCopies-k] = v[numCopies-k]*c1 + t_complex(rand1, -rand2);
}
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &p[0], &p[0]);
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &v[0], &v[0]);
for (int k = 0; k < numCopies; k++)
velocities[k][particle][component] = scale*p[k].re/system.getParticleMass(particle);
velocities[k][particle][component] = scale*v[k].re;
}
}
......@@ -160,26 +144,26 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
for (int component = 0; component < 3; component++) {
for (int k = 0; k < numCopies; k++) {
q[k] = t_complex(scale*positions[k][particle][component], 0.0);
p[k] = t_complex(scale*velocities[k][particle][component]*system.getParticleMass(particle), 0.0);
v[k] = t_complex(scale*velocities[k][particle][component], 0.0);
}
fftpack_exec_1d(fft, FFTPACK_FORWARD, &q[0], &q[0]);
fftpack_exec_1d(fft, FFTPACK_FORWARD, &p[0], &p[0]);
q[0] += p[0]*(dt/system.getParticleMass(particle));
fftpack_exec_1d(fft, FFTPACK_FORWARD, &v[0], &v[0]);
q[0] += v[0]*dt;
for (int k = 1; k < numCopies; k++) {
const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
const RealOpenMM wt = wk*dt;
const RealOpenMM coswt = cos(wt);
const RealOpenMM sinwt = sin(wt);
const RealOpenMM wm = wk*system.getParticleMass(particle);
const t_complex pprime = p[k]*coswt - q[k]*(wm*sinwt); // Advance momentum from t to t+dt
q[k] = p[k]*(sinwt/wm) + q[k]*coswt; // Advance position from t to t+dt
p[k] = pprime;
const t_complex vprime = v[k]*coswt - q[k]*(wk*sinwt); // Advance velocity from t to t+dt
q[k] = v[k]*(sinwt/wk) + q[k]*coswt; // Advance position from t to t+dt
v[k] = vprime;
}
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &q[0], &q[0]);
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &p[0], &p[0]);
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &v[0], &v[0]);
for (int k = 0; k < numCopies; k++) {
positions[k][particle][component] = scale*q[k].re;
velocities[k][particle][component] = scale*p[k].re/system.getParticleMass(particle);
velocities[k][particle][component] = scale*v[k].re;
}
}
}
......@@ -206,15 +190,15 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
// Apply the PILE-L thermostat again.
for (int particle = 0; particle < numParticles; particle++) {
const RealOpenMM c3_0 = c2_0*sqrt(system.getParticleMass(particle)*nkT);
const RealOpenMM c3_0 = c2_0*sqrt(nkT/system.getParticleMass(particle));
for (int component = 0; component < 3; component++) {
for (int k = 0; k < numCopies; k++)
p[k] = t_complex(scale*velocities[k][particle][component]*system.getParticleMass(particle), 0.0);
fftpack_exec_1d(fft, FFTPACK_FORWARD, &p[0], &p[0]);
v[k] = t_complex(scale*velocities[k][particle][component], 0.0);
fftpack_exec_1d(fft, FFTPACK_FORWARD, &v[0], &v[0]);
// Apply a local Langevin thermostat to the centroid mode.
p[0].re = p[0].re*c1_0 + c3_0*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
v[0].re = v[0].re*c1_0 + c3_0*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
// Use critical damping white noise for the remaining modes.
......@@ -223,16 +207,16 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
const RealOpenMM c1 = exp(-2.0*wk*halfdt);
const RealOpenMM c2 = sqrt((1.0-c1*c1)/2) * (isCenter ? sqrt(2.0) : 1.0);
const RealOpenMM c3 = c2*sqrt(system.getParticleMass(particle)*nkT);
const RealOpenMM c3 = c2*sqrt(nkT/system.getParticleMass(particle));
RealOpenMM rand1 = c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
RealOpenMM rand2 = (isCenter ? 0.0 : c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
p[k] = p[k]*c1 + t_complex(rand1, rand2);
v[k] = v[k]*c1 + t_complex(rand1, rand2);
if (k < numCopies-k)
p[numCopies-k] = p[numCopies-k]*c1 + t_complex(rand1, -rand2);
v[numCopies-k] = v[numCopies-k]*c1 + t_complex(rand1, -rand2);
}
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &p[0], &p[0]);
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &v[0], &v[0]);
for (int k = 0; k < numCopies; k++)
velocities[k][particle][component] = scale*p[k].re/system.getParticleMass(particle);
velocities[k][particle][component] = scale*v[k].re;
}
}
......@@ -247,22 +231,6 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
// vector<RealVec>& pos = extractPositions(context);
// vector<RealVec>& vel = extractVelocities(context);
// vector<RealVec>& f = extractForces(context);
// if (!hasSetPosition) {
// // Initialize the positions from the context.
//
// for (int i = 0; i < numCopies; i++)
// for (int j = 0; j < numParticles; j++)
// positions[i][j] = pos[j];
// hasSetPosition = true;
// }
// if (!hasSetVelocity) {
// // Initialize the velocities from the context.
//
// for (int i = 0; i < numCopies; i++)
// for (int j = 0; j < numParticles; j++)
// velocities[i][j] = vel[j];
// hasSetVelocity = true;
// }
//
// // Loop over copies and compute the force on each one.
//
......@@ -356,14 +324,12 @@ void ReferenceIntegrateRPMDStepKernel::setPositions(int copy, const vector<Vec3>
int numParticles = positions[copy].size();
for (int i = 0; i < numParticles; i++)
positions[copy][i] = pos[i];
hasSetPosition = true;
}
void ReferenceIntegrateRPMDStepKernel::setVelocities(int copy, const vector<Vec3>& vel) {
int numParticles = velocities[copy].size();
for (int i = 0; i < numParticles; i++)
velocities[copy][i] = vel[i];
hasSetVelocity = true;
}
void ReferenceIntegrateRPMDStepKernel::copyToContext(int copy, ContextImpl& context) const {
......
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.h
View file @ c67aed53
......@@ -46,7 +46,7 @@ namespace OpenMM {
class ReferenceIntegrateRPMDStepKernel : public IntegrateRPMDStepKernel {
public:
ReferenceIntegrateRPMDStepKernel(std::string name, const Platform& platform) :
IntegrateRPMDStepKernel(name, platform), fft(NULL), hasSetPosition(false), hasSetVelocity(false) {
IntegrateRPMDStepKernel(name, platform), fft(NULL) {
}
~ReferenceIntegrateRPMDStepKernel();
/**
......@@ -82,7 +82,6 @@ private:
std::vector<std::vector<RealVec> > velocities;
std::vector<std::vector<RealVec> > forces;
fftpack* fft;
bool hasSetPosition, hasSetVelocity;
};
} // namespace OpenMM
......
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