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"platforms/opencl/include/OpenCLIntegrationUtilities.h" did not exist on "10379a9a4405bc4efa5f1ba0ab93b85b21404e44"
Commit 01da523c authored by Peter Eastman's avatar Peter Eastman
Browse files

Converted RPMD plugin to use a velocity verlet type integrator

parent f794f818
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Showing with 234 additions and 44 deletions
plugins/rpmd/openmmapi/include/openmm/RPMDIntegrator.h
View file @ 01da523c
......@@ -157,6 +157,10 @@ protected:
* It will also get called again if the application calls reinitialize() on the Context.
*/
void initialize(ContextImpl& context);
/**
* 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.
*/
......@@ -164,6 +168,7 @@ protected:
private:
double temperature, friction;
int numCopies, randomNumberSeed;
bool forcesAreValid;
ContextImpl* context;
Context* owner;
Kernel kernel;
......
plugins/rpmd/openmmapi/include/openmm/RpmdKernels.h
View file @ 01da523c
......@@ -64,8 +64,10 @@ public:
*
* @param context the context in which to execute this kernel
* @param integrator the RPMDIntegrator 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
*/
virtual void execute(ContextImpl& context, const RPMDIntegrator& integrator) = 0;
virtual void execute(ContextImpl& context, const RPMDIntegrator& integrator, bool forcesAreValid) = 0;
/**
* Get the positions of all particles in one copy of the system.
*/
......
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
View file @ 01da523c
......@@ -41,7 +41,8 @@ using namespace OpenMM;
using std::string;
using std::vector;
RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize) : owner(NULL), numCopies(numCopies) {
RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictionCoeff, double stepSize) :
owner(NULL), numCopies(numCopies), forcesAreValid(false) {
setTemperature(temperature);
setFriction(frictionCoeff);
setStepSize(stepSize);
......@@ -58,6 +59,10 @@ void RPMDIntegrator::initialize(ContextImpl& contextRef) {
dynamic_cast<IntegrateRPMDStepKernel&>(kernel.getImpl()).initialize(contextRef.getSystem(), *this);
}
void RPMDIntegrator::stateChanged(State::DataType changed) {
forcesAreValid = false;
}
vector<string> RPMDIntegrator::getKernelNames() {
std::vector<std::string> names;
names.push_back(IntegrateRPMDStepKernel::Name());
......@@ -79,8 +84,7 @@ State RPMDIntegrator::getState(int copy, int types) {
void RPMDIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) {
context->updateContextState();
context->calcForcesAndEnergy(true, false);
dynamic_cast<IntegrateRPMDStepKernel&>(kernel.getImpl()).execute(*context, *this);
dynamic_cast<IntegrateRPMDStepKernel&>(kernel.getImpl()).execute(*context, *this, forcesAreValid);
forcesAreValid = true;
}
}
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp
View file @ 01da523c
......@@ -70,9 +70,12 @@ void ReferenceIntegrateRPMDStepKernel::initialize(const System& system, const RP
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
}
void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDIntegrator& integrator) {
int numCopies = positions.size();
int numParticles = positions[0].size();
void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDIntegrator& integrator, bool forcesAreValid) {
const int numCopies = positions.size();
const int numParticles = positions[0].size();
const RealOpenMM dt = integrator.getStepSize();
const RealOpenMM halfdt = 0.5*dt;
const System& system = context.getSystem();
vector<RealVec>& pos = extractPositions(context);
vector<RealVec>& vel = extractVelocities(context);
vector<RealVec>& f = extractForces(context);
......@@ -95,29 +98,64 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
// Loop over copies and compute the force on each one.
if (!forcesAreValid) {
for (int i = 0; i < numCopies; i++) {
pos = positions[i];
vel = velocities[i];
context.calcForcesAndEnergy(true, false);
forces[i] = f;
}
}
// Apply the PILE-L thermostat.
vector<t_complex> p(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 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);
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]);
// Apply a local Langevin thermostat to the centroid mode.
p[0].re = p[0].re*c1_0 + c3_0*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
// Use critical damping white noise for the remaining modes.
for (int k = 1; k <= numCopies/2; k++) {
const bool isCenter = (numCopies%2 == 0 && k == numCopies/2);
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);
RealOpenMM rand1 = c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
RealOpenMM rand2 = (isCenter ? 0.0 : c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
p[k] = p[k]*c1 + t_complex(rand1, rand2);
if (k < numCopies-k)
p[numCopies-k] = p[numCopies-k]*c1 + t_complex(rand1, -rand2);
}
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &p[0], &p[0]);
for (int k = 0; k < numCopies; k++)
velocities[k][particle][component] = scale*p[k].re/system.getParticleMass(particle);
}
}
// Update velocities.
const RealOpenMM dt = integrator.getStepSize();
const System& system = context.getSystem();
for (int i = 0; i < numCopies; i++)
for (int j = 0; j < numParticles; j++)
velocities[i][j] += forces[i][j]*(dt/system.getParticleMass(j));
velocities[i][j] += forces[i][j]*(halfdt/system.getParticleMass(j));
// Evolve the free ring polymer by transforming to the frequency domain.
vector<t_complex> p(numCopies);
vector<t_complex> q(numCopies);
const RealOpenMM scale = 1.0/sqrt(numCopies);
const RealOpenMM hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
const RealOpenMM nkT = numCopies*BOLTZ*integrator.getTemperature();
const RealOpenMM twown = 2.0*nkT/hbar;
for (int particle = 0; particle < numParticles; particle++) {
for (int component = 0; component < 3; component++) {
for (int k = 0; k < numCopies; k++) {
......@@ -130,10 +168,11 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
for (int k = 1; k < numCopies; k++) {
const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
const RealOpenMM wt = wk*dt;
const RealOpenMM sinwt2 = sin(wt/2);
const RealOpenMM coswt = cos(wt);
const RealOpenMM sinwt = sin(wt);
const RealOpenMM wm = wk*system.getParticleMass(particle);
const t_complex pprime = p[k] - q[k]*(2.0*wm*sinwt2); // Advance momentum from t-dt/2 to t+dt/2
q[k] = p[k]*(2.0*sinwt2/wm) + q[k]*(1.0-4.0*sinwt2*sinwt2); // Advance position from t to t+dt
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;
}
fftpack_exec_1d(fft, FFTPACK_BACKWARD, &q[0], &q[0]);
......@@ -145,10 +184,27 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
}
}
// Apply the PILE-L thermostat.
// Calculate forces based on the updated positions.
for (int i = 0; i < numCopies; i++) {
pos = positions[i];
vel = velocities[i];
context.updateContextState();
positions[i] = pos;
velocities[i] = vel;
context.calcForcesAndEnergy(true, false);
forces[i] = f;
}
// Update velocities.
for (int i = 0; i < numCopies; i++)
for (int j = 0; j < numParticles; j++)
velocities[i][j] += forces[i][j]*(halfdt/system.getParticleMass(j));
// Apply the PILE-L thermostat again.
const RealOpenMM c1_0 = exp(-dt*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);
for (int component = 0; component < 3; component++) {
......@@ -165,7 +221,7 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
for (int k = 1; k <= numCopies/2; k++) {
const bool isCenter = (numCopies%2 == 0 && k == numCopies/2);
const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
const RealOpenMM c1 = exp(-2.0*wk*dt);
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);
RealOpenMM rand1 = c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
......@@ -179,8 +235,123 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
velocities[k][particle][component] = scale*p[k].re/system.getParticleMass(particle);
}
}
// Update the time.
context.setTime(context.getTime()+dt);
}
//void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDIntegrator& integrator, bool forcesAreValid) {
// int numCopies = positions.size();
// int numParticles = positions[0].size();
// 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.
//
// for (int i = 0; i < numCopies; i++) {
// pos = positions[i];
// vel = velocities[i];
// context.calcForcesAndEnergy(true, false);
// forces[i] = f;
// }
//
// // Update velocities.
//
// const RealOpenMM dt = integrator.getStepSize();
// const System& system = context.getSystem();
// for (int i = 0; i < numCopies; i++)
// for (int j = 0; j < numParticles; j++)
// velocities[i][j] += forces[i][j]*(dt/system.getParticleMass(j));
//
// // Evolve the free ring polymer by transforming to the frequency domain.
//
// vector<t_complex> p(numCopies);
// vector<t_complex> q(numCopies);
// const RealOpenMM scale = 1.0/sqrt(numCopies);
// const RealOpenMM hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
// const RealOpenMM nkT = numCopies*BOLTZ*integrator.getTemperature();
// const RealOpenMM twown = 2.0*nkT/hbar;
// for (int particle = 0; particle < numParticles; particle++) {
// 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);
// }
// 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));
// for (int k = 1; k < numCopies; k++) {
// const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
// const RealOpenMM wt = wk*dt;
// const RealOpenMM sinwt2 = sin(wt/2);
// const RealOpenMM wm = wk*system.getParticleMass(particle);
// const t_complex pprime = p[k] - q[k]*(2.0*wm*sinwt2); // Advance momentum from t-dt/2 to t+dt/2
// q[k] = p[k]*(2.0*sinwt2/wm) + q[k]*(1.0-4.0*sinwt2*sinwt2); // Advance position from t to t+dt
// p[k] = pprime;
// }
// fftpack_exec_1d(fft, FFTPACK_BACKWARD, &q[0], &q[0]);
// fftpack_exec_1d(fft, FFTPACK_BACKWARD, &p[0], &p[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);
// }
// }
// }
//
// // Apply the PILE-L thermostat.
//
// const RealOpenMM c1_0 = exp(-dt*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);
// 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]);
//
// // Apply a local Langevin thermostat to the centroid mode.
//
// p[0].re = p[0].re*c1_0 + c3_0*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
//
// // Use critical damping white noise for the remaining modes.
//
// for (int k = 1; k <= numCopies/2; k++) {
// const bool isCenter = (numCopies%2 == 0 && k == numCopies/2);
// const RealOpenMM wk = twown*sin(k*M_PI/numCopies);
// const RealOpenMM c1 = exp(-2.0*wk*dt);
// const RealOpenMM c2 = sqrt((1.0-c1*c1)/2) * (isCenter ? sqrt(2.0) : 1.0);
// const RealOpenMM c3 = c2*sqrt(system.getParticleMass(particle)*nkT);
// RealOpenMM rand1 = c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
// RealOpenMM rand2 = (isCenter ? 0.0 : c3*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber());
// p[k] = p[k]*c1 + t_complex(rand1, rand2);
// if (k < numCopies-k)
// p[numCopies-k] = p[numCopies-k]*c1 + t_complex(rand1, -rand2);
// }
// fftpack_exec_1d(fft, FFTPACK_BACKWARD, &p[0], &p[0]);
// for (int k = 0; k < numCopies; k++)
// velocities[k][particle][component] = scale*p[k].re/system.getParticleMass(particle);
// }
// }
//}
void ReferenceIntegrateRPMDStepKernel::setPositions(int copy, const vector<Vec3>& pos) {
int numParticles = positions[copy].size();
for (int i = 0; i < numParticles; i++)
......
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.h
View file @ 01da523c
......@@ -61,8 +61,10 @@ public:
*
* @param context the context in which to execute this kernel
* @param integrator the RPMDIntegrator 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
*/
void execute(ContextImpl& context, const RPMDIntegrator& integrator);
void execute(ContextImpl& context, const RPMDIntegrator& integrator, bool forcesAreValid);
/**
* Get the positions of all particles in one copy of the system.
*/
......
plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp
View file @ 01da523c
......@@ -40,6 +40,7 @@
#include "openmm/System.h"
#include "openmm/RPMDIntegrator.h"
#include "SimTKUtilities/SimTKOpenMMUtilities.h"
#include "sfmt/SFMT.h"
#include <iostream>
#include <vector>
......@@ -47,24 +48,29 @@ using namespace OpenMM;
using namespace std;
void testIntegration() {
const int numParticles = 5;
const int numCopies = 50;
const int numParticles = 1;
const int numCopies = 30;
const double temperature = 300.0;
System system;
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++) {
for (int i = 0; i < numParticles; i++)
system.addParticle(i+1);
positions[i] = Vec3(i, 0, 0);
}
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
for (int i = 0; i < numParticles-1; i++)
bonds->addBond(i, i+1, 1.0, 100.0);
RPMDIntegrator integ(numCopies, temperature, 1.0, 0.001);
Context context(system, integ);
context.setPositions(positions);
const int numSteps = 5000;
integ.step(1000);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numCopies; i++)
{
for (int j = 0; j < numParticles; j++)
positions[j] = Vec3(i+0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt));
integ.setPositions(i, positions);
}
const int numSteps = 100000;
integ.step(10000);
vector<double> ke(numCopies, 0.0);
vector<double> rg(numParticles, 0.0);
const RealOpenMM hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
......@@ -80,7 +86,7 @@ void testIntegration() {
for (int j = 0; j < numCopies; j++) {
totalEnergy += state[j].getKineticEnergy()+state[j].getPotentialEnergy();
for (int k = 0; k < numParticles; k++) {
Vec3 delta = state[j].getPositions()[k]-state[j].getPositions()[j == 0 ? numCopies-1 : j-1];
Vec3 delta = state[j].getPositions()[k]-state[j == 0 ? numCopies-1 : j-1].getPositions()[k];
totalEnergy += 0.5*system.getParticleMass(k)*wn*wn*delta.dot(delta);
}
}
......
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