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Commit 3e7616fc authored by Peter Eastman's avatar Peter Eastman
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RPMD supports virtual sites

parent 63955548
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Showing with 284 additions and 103 deletions
plugins/rpmd/openmmapi/src/RPMDIntegrator.cpp
View file @ 3e7616fc
......@@ -54,12 +54,8 @@ RPMDIntegrator::RPMDIntegrator(int numCopies, double temperature, double frictio
void RPMDIntegrator::initialize(ContextImpl& contextRef) {
if (owner != NULL && &contextRef.getOwner() != owner)
throw OpenMMException("This Integrator is already bound to a context");
const System& system = contextRef.getSystem();
if (system.getNumConstraints() > 0)
if (contextRef.getSystem().getNumConstraints() > 0)
throw OpenMMException("RPMDIntegrator cannot be used with Systems that include constraints");
for (int i = 0; i < system.getNumParticles(); i++)
if (system.isVirtualSite(i))
throw OpenMMException("RPMDIntegrator cannot be used with Systems that include virtual sites");
context = &contextRef;
owner = &contextRef.getOwner();
kernel = context->getPlatform().createKernel(IntegrateRPMDStepKernel::Name(), contextRef);
......
plugins/rpmd/platforms/cuda/src/CudaRpmdKernels.cpp
View file @ 3e7616fc
......@@ -187,6 +187,7 @@ void CudaIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
void* copyToContextArgs[] = {&velocities->getDevicePointer(), &cu.getVelm().getDevicePointer(), &positions->getDevicePointer(),
&cu.getPosq().getDevicePointer(), &cu.getAtomIndexArray().getDevicePointer(), &i};
cu.executeKernel(copyToContextKernel, copyToContextArgs, cu.getNumAtoms());
context.computeVirtualSites();
context.updateContextState();
context.calcForcesAndEnergy(true, false);
if (cu.getAtomsWereReordered() && cu.getNonbondedUtilities().getUsePeriodic()) {
......
plugins/rpmd/platforms/cuda/src/kernels/rpmd.cu
View file @ 3e7616fc
......@@ -38,6 +38,8 @@ extern "C" __global__ void applyPileThermostat(mixed4* velm, float4* random, uns
for (int particle = (blockIdx.x*blockDim.x+threadIdx.x)/NUM_COPIES; particle < NUM_ATOMS; particle += numBlocks) {
mixed4 particleVelm = velm[particle+indexInBlock*PADDED_NUM_ATOMS];
mixed invMass = particleVelm.w;
if (invMass == 0)
continue;
mixed c3_0 = c2_0*SQRT(nkT*invMass);
// Forward FFT.
......@@ -100,6 +102,8 @@ extern "C" __global__ void integrateStep(mixed4* posq, mixed4* velm, long long*
int index = particle+indexInBlock*PADDED_NUM_ATOMS;
int forceIndex = particle+indexInBlock*PADDED_NUM_ATOMS*3;
mixed4 particleVelm = velm[index];
if (particleVelm.w == 0)
continue;
particleVelm.x += forceScale*force[forceIndex]*(0.5f*dt*particleVelm.w);
particleVelm.y += forceScale*force[forceIndex+PADDED_NUM_ATOMS]*(0.5f*dt*particleVelm.w);
particleVelm.z += forceScale*force[forceIndex+PADDED_NUM_ATOMS*2]*(0.5f*dt*particleVelm.w);
......@@ -118,6 +122,8 @@ extern "C" __global__ void integrateStep(mixed4* posq, mixed4* velm, long long*
for (int particle = (blockIdx.x*blockDim.x+threadIdx.x)/NUM_COPIES; particle < NUM_ATOMS; particle += numBlocks) {
mixed4 particlePosq = posq[particle+indexInBlock*PADDED_NUM_ATOMS];
mixed4 particleVelm = velm[particle+indexInBlock*PADDED_NUM_ATOMS];
if (particleVelm.w == 0)
continue;
// Forward FFT.
......@@ -173,6 +179,8 @@ extern "C" __global__ void advanceVelocities(mixed4* velm, long long* force, mix
int index = particle+indexInBlock*PADDED_NUM_ATOMS;
int forceIndex = particle+indexInBlock*PADDED_NUM_ATOMS*3;
mixed4 particleVelm = velm[index];
if (particleVelm.w == 0)
continue;
particleVelm.x += forceScale*force[forceIndex]*(0.5f*dt*particleVelm.w);
particleVelm.y += forceScale*force[forceIndex+PADDED_NUM_ATOMS]*(0.5f*dt*particleVelm.w);
particleVelm.z += forceScale*force[forceIndex+PADDED_NUM_ATOMS*2]*(0.5f*dt*particleVelm.w);
......
plugins/rpmd/platforms/cuda/tests/TestCudaRpmd.cpp
View file @ 3e7616fc
......@@ -38,9 +38,11 @@
#include "openmm/Context.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/Platform.h"
#include "openmm/System.h"
#include "openmm/RPMDIntegrator.h"
#include "openmm/VirtualSite.h"
#include "SimTKUtilities/SimTKOpenMMUtilities.h"
#include "sfmt/SFMT.h"
#include <iostream>
......@@ -272,6 +274,87 @@ void testCMMotionRemoval() {
}
}
void testVirtualSites() {
const int gridSize = 3;
const int numMolecules = gridSize*gridSize*gridSize;
const int numParticles = numMolecules*3;
const int numCopies = 10;
const double spacing = 2.0;
const double cutoff = 3.0;
const double boxSize = spacing*(gridSize+1);
const double temperature = 300.0;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setCutoffDistance(cutoff);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.addForce(nonbonded);
// Create a cloud of molecules.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numMolecules; i++) {
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
nonbonded->addParticle(-0.2, 0.2, 0.2);
nonbonded->addParticle(0.1, 0.2, 0.2);
nonbonded->addParticle(0.1, 0.2, 0.2);
nonbonded->addException(3*i, 3*i+1, 0, 1, 0);
nonbonded->addException(3*i, 3*i+2, 0, 1, 0);
nonbonded->addException(3*i+1, 3*i+2, 0, 1, 0);
bonds->addBond(3*i, 3*i+1, 1.0, 10000.0);
system.setVirtualSite(3*i+2, new TwoParticleAverageSite(3*i, 3*i+1, 0.5, 0.5));
}
RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001);
Platform& platform = Platform::getPlatformByName("CUDA");
Context context(system, integ, platform);
for (int copy = 0; copy < numCopies; copy++) {
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
Vec3 pos = Vec3(spacing*(i+0.02*genrand_real2(sfmt)), spacing*(j+0.02*genrand_real2(sfmt)), spacing*(k+0.02*genrand_real2(sfmt)));
int index = k+gridSize*(j+gridSize*i);
positions[3*index] = pos;
positions[3*index+1] = Vec3(pos[0]+1.0, pos[1], pos[2]);
positions[3*index+2] = Vec3();
}
integ.setPositions(copy, positions);
}
// Check the temperature and virtual site locations.
const int numSteps = 1000;
integ.step(1000);
vector<double> ke(numCopies, 0.0);
for (int i = 0; i < numSteps; i++) {
integ.step(1);
vector<State> state(numCopies);
for (int j = 0; j < numCopies; j++) {
state[j] = integ.getState(j, State::Positions | State::Velocities | State::Forces, true);
const vector<Vec3>& pos = state[j].getPositions();
for (int k = 0; k < numMolecules; k++)
ASSERT_EQUAL_VEC((pos[3*k]+pos[3*k+1])*0.5, pos[3*k+2], 1e-5);
}
for (int j = 0; j < numParticles; j++) {
for (int k = 0; k < numCopies; k++) {
Vec3 v = state[k].getVelocities()[j];
ke[k] += 0.5*system.getParticleMass(j)*v.dot(v);
}
}
}
double meanKE = 0.0;
for (int i = 0; i < numCopies; i++)
meanKE += ke[i];
meanKE /= numSteps*numCopies;
double expectedKE = 0.5*numCopies*(2*numMolecules)*3*BOLTZ*temperature;
ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
}
int main(int argc, char* argv[]) {
try {
registerRPMDCudaKernelFactories();
......@@ -280,6 +363,7 @@ int main(int argc, char* argv[]) {
testFreeParticles();
testParaHydrogen();
testCMMotionRemoval();
testVirtualSites();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/rpmd/platforms/opencl/src/OpenCLRpmdKernels.cpp
View file @ 3e7616fc
......@@ -198,6 +198,7 @@ void OpenCLIntegrateRPMDStepKernel::computeForces(ContextImpl& context) {
for (int i = 0; i < numCopies; i++) {
copyToContextKernel.setArg<cl_int>(5, i);
cl.executeKernel(copyToContextKernel, cl.getNumAtoms());
context.computeVirtualSites();
context.updateContextState();
context.calcForcesAndEnergy(true, false);
if (cl.getAtomsWereReordered() && cl.getNonbondedUtilities().getUsePeriodic()) {
......
plugins/rpmd/platforms/opencl/src/kernels/rpmd.cl
View file @ 3e7616fc
......@@ -38,6 +38,8 @@ __kernel void applyPileThermostat(__global mixed4* velm, __global float4* random
for (int particle = get_global_id(0)/NUM_COPIES; particle < NUM_ATOMS; particle += numBlocks) {
mixed4 particleVelm = velm[particle+indexInBlock*PADDED_NUM_ATOMS];
mixed invMass = particleVelm.w;
if (invMass == 0)
continue;
mixed c3_0 = c2_0*sqrt(nkT*invMass);
// Forward FFT.
......@@ -97,6 +99,8 @@ __kernel void integrateStep(__global mixed4* posq, __global mixed4* velm, __glob
for (int particle = get_global_id(0)/NUM_COPIES; particle < NUM_ATOMS; particle += numBlocks) {
int index = particle+indexInBlock*PADDED_NUM_ATOMS;
mixed4 particleVelm = velm[index];
if (particleVelm.w == 0)
continue;
particleVelm.xyz += convert_mixed4(force[index]).xyz*(0.5f*dt*particleVelm.w);
velm[index] = particleVelm;
}
......@@ -113,6 +117,8 @@ __kernel void integrateStep(__global mixed4* posq, __global mixed4* velm, __glob
for (int particle = get_global_id(0)/NUM_COPIES; particle < NUM_ATOMS; particle += numBlocks) {
mixed4 particlePosq = posq[particle+indexInBlock*PADDED_NUM_ATOMS];
mixed4 particleVelm = velm[particle+indexInBlock*PADDED_NUM_ATOMS];
if (particleVelm.w == 0)
continue;
// Forward FFT.
......@@ -166,6 +172,8 @@ __kernel void advanceVelocities(__global mixed4* velm, __global real4* force, mi
for (int particle = get_global_id(0)/NUM_COPIES; particle < NUM_ATOMS; particle += numBlocks) {
int index = particle+indexInBlock*PADDED_NUM_ATOMS;
mixed4 particleVelm = velm[index];
if (particleVelm.w == 0)
continue;
particleVelm.xyz += convert_mixed4(force[index]).xyz*(0.5f*dt*particleVelm.w);
velm[index] = particleVelm;
}
......
plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp
View file @ 3e7616fc
......@@ -38,9 +38,11 @@
#include "openmm/Context.h"
#include "openmm/CustomNonbondedForce.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/Platform.h"
#include "openmm/System.h"
#include "openmm/RPMDIntegrator.h"
#include "openmm/VirtualSite.h"
#include "SimTKUtilities/SimTKOpenMMUtilities.h"
#include "sfmt/SFMT.h"
#include <iostream>
......@@ -273,6 +275,87 @@ void testCMMotionRemoval() {
}
}
void testVirtualSites() {
const int gridSize = 3;
const int numMolecules = gridSize*gridSize*gridSize;
const int numParticles = numMolecules*3;
const int numCopies = 10;
const double spacing = 2.0;
const double cutoff = 3.0;
const double boxSize = spacing*(gridSize+1);
const double temperature = 300.0;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setCutoffDistance(cutoff);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.addForce(nonbonded);
// Create a cloud of molecules.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numMolecules; i++) {
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
nonbonded->addParticle(-0.2, 0.2, 0.2);
nonbonded->addParticle(0.1, 0.2, 0.2);
nonbonded->addParticle(0.1, 0.2, 0.2);
nonbonded->addException(3*i, 3*i+1, 0, 1, 0);
nonbonded->addException(3*i, 3*i+2, 0, 1, 0);
nonbonded->addException(3*i+1, 3*i+2, 0, 1, 0);
bonds->addBond(3*i, 3*i+1, 1.0, 10000.0);
system.setVirtualSite(3*i+2, new TwoParticleAverageSite(3*i, 3*i+1, 0.5, 0.5));
}
RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001);
Platform& platform = Platform::getPlatformByName("OpenCL");
Context context(system, integ, platform);
for (int copy = 0; copy < numCopies; copy++) {
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
Vec3 pos = Vec3(spacing*(i+0.02*genrand_real2(sfmt)), spacing*(j+0.02*genrand_real2(sfmt)), spacing*(k+0.02*genrand_real2(sfmt)));
int index = k+gridSize*(j+gridSize*i);
positions[3*index] = pos;
positions[3*index+1] = Vec3(pos[0]+1.0, pos[1], pos[2]);
positions[3*index+2] = Vec3();
}
integ.setPositions(copy, positions);
}
// Check the temperature and virtual site locations.
const int numSteps = 1000;
integ.step(1000);
vector<double> ke(numCopies, 0.0);
for (int i = 0; i < numSteps; i++) {
integ.step(1);
vector<State> state(numCopies);
for (int j = 0; j < numCopies; j++) {
state[j] = integ.getState(j, State::Positions | State::Velocities | State::Forces, true);
const vector<Vec3>& pos = state[j].getPositions();
for (int k = 0; k < numMolecules; k++)
ASSERT_EQUAL_VEC((pos[3*k]+pos[3*k+1])*0.5, pos[3*k+2], 1e-5);
}
for (int j = 0; j < numParticles; j++) {
for (int k = 0; k < numCopies; k++) {
Vec3 v = state[k].getVelocities()[j];
ke[k] += 0.5*system.getParticleMass(j)*v.dot(v);
}
}
}
double meanKE = 0.0;
for (int i = 0; i < numCopies; i++)
meanKE += ke[i];
meanKE /= numSteps*numCopies;
double expectedKE = 0.5*numCopies*(2*numMolecules)*3*BOLTZ*temperature;
ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
}
int main(int argc, char* argv[]) {
try {
registerRPMDOpenCLKernelFactories();
......@@ -281,6 +364,7 @@ int main(int argc, char* argv[]) {
testFreeParticles();
testParaHydrogen();
testCMMotionRemoval();
testVirtualSites();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
plugins/rpmd/platforms/reference/src/ReferenceRpmdKernels.cpp
View file @ 3e7616fc
......@@ -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) 2011 Stanford University and the Authors. *
* Portions copyright (c) 2011-2013 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -86,6 +86,7 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
for (int i = 0; i < numCopies; i++) {
pos = positions[i];
vel = velocities[i];
context.computeVirtualSites();
context.calcForcesAndEnergy(true, false);
forces[i] = f;
}
......@@ -102,6 +103,8 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
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++) {
if (system.getParticleMass(particle) == 0.0)
continue;
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++)
......@@ -136,11 +139,14 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
for (int i = 0; i < numCopies; i++)
for (int j = 0; j < numParticles; j++)
if (system.getParticleMass(j) != 0.0)
velocities[i][j] += forces[i][j]*(halfdt/system.getParticleMass(j));
// Evolve the free ring polymer by transforming to the frequency domain.
for (int particle = 0; particle < numParticles; particle++) {
if (system.getParticleMass(particle) == 0.0)
continue;
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);
......@@ -173,6 +179,7 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
for (int i = 0; i < numCopies; i++) {
pos = positions[i];
vel = velocities[i];
context.computeVirtualSites();
context.updateContextState();
positions[i] = pos;
velocities[i] = vel;
......@@ -184,11 +191,14 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
for (int i = 0; i < numCopies; i++)
for (int j = 0; j < numParticles; j++)
if (system.getParticleMass(j) != 0.0)
velocities[i][j] += forces[i][j]*(halfdt/system.getParticleMass(j));
// Apply the PILE-L thermostat again.
for (int particle = 0; particle < numParticles; particle++) {
if (system.getParticleMass(particle) == 0.0)
continue;
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++)
......@@ -224,101 +234,6 @@ void ReferenceIntegrateRPMDStepKernel::execute(ContextImpl& context, const RPMDI
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);
//
// // 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);
// }
// }
//}
double ReferenceIntegrateRPMDStepKernel::computeKineticEnergy(ContextImpl& context, const RPMDIntegrator& integrator) {
System& system = context.getSystem();
int numParticles = system.getNumParticles();
......
plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp
View file @ 3e7616fc
......@@ -37,9 +37,11 @@
#include "openmm/CMMotionRemover.h"
#include "openmm/Context.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
#include "openmm/Platform.h"
#include "openmm/System.h"
#include "openmm/RPMDIntegrator.h"
#include "openmm/VirtualSite.h"
#include "SimTKUtilities/SimTKOpenMMUtilities.h"
#include "sfmt/SFMT.h"
#include <iostream>
......@@ -154,10 +156,92 @@ void testCMMotionRemoval() {
}
}
void testVirtualSites() {
const int gridSize = 3;
const int numMolecules = gridSize*gridSize*gridSize;
const int numParticles = numMolecules*3;
const int numCopies = 10;
const double spacing = 2.0;
const double cutoff = 3.0;
const double boxSize = spacing*(gridSize+1);
const double temperature = 300.0;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setCutoffDistance(cutoff);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.addForce(nonbonded);
// Create a cloud of molecules.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numMolecules; i++) {
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
nonbonded->addParticle(-0.2, 0.2, 0.2);
nonbonded->addParticle(0.1, 0.2, 0.2);
nonbonded->addParticle(0.1, 0.2, 0.2);
nonbonded->addException(3*i, 3*i+1, 0, 1, 0);
nonbonded->addException(3*i, 3*i+2, 0, 1, 0);
nonbonded->addException(3*i+1, 3*i+2, 0, 1, 0);
bonds->addBond(3*i, 3*i+1, 1.0, 10000.0);
system.setVirtualSite(3*i+2, new TwoParticleAverageSite(3*i, 3*i+1, 0.5, 0.5));
}
RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001);
Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform);
for (int copy = 0; copy < numCopies; copy++) {
for (int i = 0; i < gridSize; i++)
for (int j = 0; j < gridSize; j++)
for (int k = 0; k < gridSize; k++) {
Vec3 pos = Vec3(spacing*(i+0.02*genrand_real2(sfmt)), spacing*(j+0.02*genrand_real2(sfmt)), spacing*(k+0.02*genrand_real2(sfmt)));
int index = k+gridSize*(j+gridSize*i);
positions[3*index] = pos;
positions[3*index+1] = Vec3(pos[0]+1.0, pos[1], pos[2]);
positions[3*index+2] = Vec3();
}
integ.setPositions(copy, positions);
}
// Check the temperature and virtual site locations.
const int numSteps = 1000;
integ.step(1000);
vector<double> ke(numCopies, 0.0);
for (int i = 0; i < numSteps; i++) {
integ.step(1);
vector<State> state(numCopies);
for (int j = 0; j < numCopies; j++) {
state[j] = integ.getState(j, State::Positions | State::Velocities | State::Forces, true);
const vector<Vec3>& pos = state[j].getPositions();
for (int k = 0; k < numMolecules; k++)
ASSERT_EQUAL_VEC((pos[3*k]+pos[3*k+1])*0.5, pos[3*k+2], 1e-5);
}
for (int j = 0; j < numParticles; j++) {
for (int k = 0; k < numCopies; k++) {
Vec3 v = state[k].getVelocities()[j];
ke[k] += 0.5*system.getParticleMass(j)*v.dot(v);
}
}
}
double meanKE = 0.0;
for (int i = 0; i < numCopies; i++)
meanKE += ke[i];
meanKE /= numSteps*numCopies;
double expectedKE = 0.5*numCopies*(2*numMolecules)*3*BOLTZ*temperature;
ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
}
int main() {
try {
testFreeParticles();
testCMMotionRemoval();
testVirtualSites();
}
catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl;
......
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