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Unverified Commit 63a9e6c2 authored by Andy Simmonett's avatar Andy Simmonett
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Fix bug in NHC propagation, tests all pass

parent 55ff3ecd
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Showing with 140 additions and 118 deletions
openmmapi/src/VelocityVerletIntegrator.cpp
View file @ 63a9e6c2
......@@ -130,18 +130,14 @@ void VelocityVerletIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) {
context->updateContextState();
for(auto &nhc : noseHooverChains) {
kineticEnergy = nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, *nhc);
//std::cout << "ke " << kineticEnergy << std::endl;
scale = nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, *nhc, kineticEnergy, getStepSize());
//std::cout << "scl " << scale << std::endl;
nhcKernel.getAs<NoseHooverChainKernel>().scaleVelocities(*context, *nhc, scale);
}
vvKernel.getAs<IntegrateVelocityVerletStepKernel>().execute(*context, *this);
for(auto &nhc : noseHooverChains) {
kineticEnergy = nhcKernel.getAs<NoseHooverChainKernel>().computeMaskedKineticEnergy(*context, *nhc);
scale = nhcKernel.getAs<NoseHooverChainKernel>().propagateChain(*context, *nhc, kineticEnergy, getStepSize());
//std::cout << "ke " << kineticEnergy << " scale " << scale << std::endl;
nhcKernel.getAs<NoseHooverChainKernel>().scaleVelocities(*context, *nhc, scale);
}
}
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 63a9e6c2
......@@ -2433,7 +2433,7 @@ void ReferenceNoseHooverChainKernel::initialize() {
}
double ReferenceNoseHooverChainKernel::propagateChain(ContextImpl& context, const NoseHooverChain &nhc, double kineticEnergy, double timeStep) {
if (kineticEnergy < 1e-10) return 1.0; // (catches the problem of zero velocities in the first dynamics step, where we have nothing to scale)
if (kineticEnergy < 1e-8) return 1.0; // (catches the problem of zero velocities in the first dynamics step, where we have nothing to scale)
// Get the variables describing the NHC
int chainLength = nhc.getDefaultChainLength();
double temperature = nhc.getDefaultTemperature();
......@@ -2461,23 +2461,24 @@ double ReferenceNoseHooverChainKernel::propagateChain(ContextImpl& context, cons
}
double ReferenceNoseHooverChainKernel::computeHeatBathEnergy(ContextImpl& context, const NoseHooverChain &nhc) {
double energy = 0;
double potentialEnergy = 0;
double kineticEnergy = 0;
int chainLength = nhc.getDefaultChainLength();
double temperature = nhc.getDefaultTemperature();
double collisionFrequency = nhc.getDefaultCollisionFrequency();
double kT = temperature * BOLTZ;
int numDOFs = nhc.getDefaultNumDegreesOfFreedom();
for(int i = 0; i < chainLength; ++i) {
double mass = kT / (collisionFrequency * collisionFrequency);
mass *= i ? 1 : numDOFs;
double velocity = context.getParameter(nhc.Velocity(i));
// The kinetic energy of this bead
energy += 0.5 * mass * velocity * velocity;
// The potential energy of this bead
double position = context.getParameter(nhc.Position(i));
energy += numDOFs * kT * position;
double prefac = i ? 1 : numDOFs;
double mass = prefac * kT / (collisionFrequency * collisionFrequency);
double velocity = context.getParameter(nhc.Velocity(i));
// The kinetic energy of this bead
kineticEnergy += 0.5 * mass * velocity * velocity;
// The potential energy of this bead
double position = context.getParameter(nhc.Position(i));
potentialEnergy += prefac * kT * position;
}
return energy;
return kineticEnergy + potentialEnergy;
}
double ReferenceNoseHooverChainKernel::computeMaskedKineticEnergy(ContextImpl& context, const NoseHooverChain &noseHooverChain) {
......@@ -2520,11 +2521,9 @@ void ReferenceNoseHooverChainKernel::scaleVelocities(ContextImpl& context, const
if (parents.size() == 0){
// scale absolute velocities
for (auto m: mask){
//std::cout << m << " " << velocities[m] << " " << scaleFactor << std::endl;
velocities[m] *= scaleFactor;
}
} else {
std::cout << "OUCHH" << std::endl;
// scale velocities relative to parent
assert(parents.size() == mask.size());
for (int i=0; i < mask.size(); i++){
......
platforms/reference/src/SimTKReference/ReferenceNoseHooverChain.cpp
View file @ 63a9e6c2
......@@ -27,7 +27,6 @@
#include <sstream>
#include <exception>
#include <iostream>
#include <fenv.h>
#include "SimTKOpenMMUtilities.h"
#include "ReferenceNoseHooverChain.h"
......@@ -62,7 +61,6 @@ double ReferenceNoseHooverChain::propagate(double kineticEnergy, vector<double>&
std::vector<double> chainForces(chainLength, 0);
std::vector<double> chainMasses(chainLength, kT/(collisionFrequency*collisionFrequency));
chainMasses[0] *= numDOFs;
feenableexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW);
double KE2 = 2 * kineticEnergy;
chainForces[0] = (KE2 - numDOFs * kT) / chainMasses[0];
for (int bead = 0; bead < chainLength - 1; ++bead) {
......@@ -71,7 +69,7 @@ double ReferenceNoseHooverChain::propagate(double kineticEnergy, vector<double>&
for (int mts = 0; mts < numMTS; ++mts) {
for (const auto &ys : YSWeights) {
double wdt = ys * timeStep / numMTS;
chainVelocities.back() += 0.25 * wdt + chainForces.back();
chainVelocities.back() += 0.25 * wdt * chainForces.back();
for (int bead = chainLength - 2; bead >= 0; --bead) {
double aa = exp(-0.125 * wdt * chainVelocities[bead + 1]);
chainVelocities[bead] = aa * (chainVelocities[bead] * aa + 0.25 * wdt * chainForces[bead]);
......@@ -92,9 +90,6 @@ double ReferenceNoseHooverChain::propagate(double kineticEnergy, vector<double>&
chainForces[bead + 1] = (chainMasses[bead] * chainVelocities[bead] * chainVelocities[bead] - kT) / chainMasses[bead + 1];
}
chainVelocities[chainLength-1] += 0.25 * wdt * chainForces.back();
// std::cout << "P " << chainPositions.back() << std::endl;
// std::cout << "V " << chainVelocities.back() << std::endl;
// std::cout << "F " << chainForces.back() << std::endl;
} // YS loop
} // MTS loop
return scale;
......
platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp
View file @ 63a9e6c2
......@@ -24,6 +24,7 @@
#include <cstring>
#include <sstream>
#include <iostream>
#include "SimTKOpenMMUtilities.h"
#include "ReferenceVerletDynamics.h"
......
tests/TestNoseHooverThermostat.h
View file @ 63a9e6c2
......@@ -42,23 +42,24 @@
#include <iostream>
#include <iomanip>
#include <vector>
#include <algorithm>
using namespace OpenMM;
using namespace std;
#define DEBUG 0
void testHarmonicOscillator() {
const double mass = 1.0;
double temperature = 300;
double frequency = 1;
double mts = 3, ys = 3, chain_length = 1;
double mts = 1, ys = 1, chain_length = 3;
System system;
system.addParticle(mass);
vector<Vec3> positions(1);
positions[0] = Vec3(0.7, 0.8,0.6);
positions[0] = Vec3(0.5,0.5,0.5);
vector<Vec3> velocities(1);
velocities[0] = Vec3(0, 0, 0);
auto harmonic_restraint = new CustomExternalForce("x^2+y^2+z^2");
auto harmonic_restraint = new CustomExternalForce("0.5*(x^2+y^2+z^2)");
harmonic_restraint->addParticle(0);
system.addForce(harmonic_restraint);
VelocityVerletIntegrator integrator(0.001);
......@@ -67,117 +68,145 @@ void testHarmonicOscillator() {
context.setPositions(positions);
context.setVelocities(velocities);
double mean_temperature=0;
double mean_temperature=0;
// equilibration
// integrator.step(10000);
for (size_t i=0; i < 10000; i++){
integrator.step(2000);
for (size_t i=0; i < 2500; i++){
integrator.step(10);
State state = context.getState(State::Energy);
State state = context.getState(State::Energy | State::Positions | State::Velocities);
double kinetic_energy = state.getKineticEnergy();
double temp = kinetic_energy/(0.5*3*BOLTZ);
mean_temperature = (i*mean_temperature + temp)/(i+1);
//cout << kinetic_energy << " " << temp << " " << temperature << endl;
double PE = state.getPotentialEnergy();
double time = state.getTime();
double energy = kinetic_energy + PE + integrator.computeHeatBathEnergy();
#if DEBUG
std::cout << " Time: " << std::setw(4) << time
<< " Temperature: " << std::setw(8) << std::setprecision(3) << temp
<< " Mean Temp: " << std::setw(8) << std::setprecision(3) << mean_temperature
<< " Kinet Energy: " << std::setw(12) << std::setprecision(8) << kinetic_energy
<< " Poten Energy: " << std::setw(12) << std::setprecision(8) << PE
<< " Total Energy: " << std::setw(12) << std::setprecision(8) << energy << std::endl;
#endif
}
//cout << "Mean Temperature: " << mean_temperature;
#if DEBUG
std::cout << "Mean Temperature: " << mean_temperature << std::endl;;
#endif
ASSERT_EQUAL_TOL(temperature, mean_temperature, 0.02);
//ASSERT_USUALLY_EQUAL_TOL(3*0.5*BOLTZ*temperatureDrude, keInternal/numSteps, 0.01);
}
void testSingleBond() {
void testDimerBox(bool constrain=true) {
// Check conservation of system + bath energy for a harmonic oscillator
System system;
system.addParticle(2.0);
system.addParticle(2.0);
int numMolecules = 20;
double boxLength = 2; // nm
Vec3 a(boxLength, 0.0, 0.0);
Vec3 b(0.0, boxLength, 0.0);
Vec3 c(0.0, 0.0, boxLength);
double mass = 20;
double bondForceConstant = 30000; //0.001;
double bondLength = 0.1;
double bondLengthSquared = bondLength * bondLength;
int numDOF = 0;
NonbondedForce* forceField = new NonbondedForce();
HarmonicBondForce* bondForce = new HarmonicBondForce();
for(int molecule = 0; molecule < numMolecules; ++molecule) {
int particle1 = system.addParticle(mass);
int particle2 = system.addParticle(mass);
forceField->addParticle(0.0, 0.1, 1.0);
forceField->addParticle(0.0, 0.1, 1.0);
forceField->addException(particle1, particle2, 0, 0, 0);
bondForce->addBond(particle1, particle2, bondLength, bondForceConstant);
numDOF += 6;
if (constrain) {
system.addConstraint(particle1, particle2, bondLength);
numDOF -= 1;
}
}
forceField->setCutoffDistance(.99*boxLength/2);
forceField->setSwitchingDistance(.88*boxLength/2);
forceField->setUseSwitchingFunction(true);
forceField->setUseDispersionCorrection(false);
forceField->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
system.addForce(forceField);
system.addForce(bondForce);
system.setDefaultPeriodicBoxVectors(a, b, c);
std::vector<Vec3> positions(numMolecules*2);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numMolecules; i++) {
while (true) {
Vec3 pos = Vec3(boxLength*genrand_real2(sfmt), boxLength*genrand_real2(sfmt), boxLength*genrand_real2(sfmt));
Vec3 pos1 = pos + Vec3(0,0, bondLength/2);
Vec3 pos2 = pos + Vec3(0,0,-bondLength/2);
double minDist = 2*boxLength;
for (int j = 0; j < i; j++) {
Vec3 delta = pos1-positions[j];
minDist = std::min(minDist, sqrt(delta.dot(delta)));
delta = pos2-positions[j];
minDist = std::min(minDist, sqrt(delta.dot(delta)));
}
if (minDist > 0.15) {
positions[2*i+0] = pos1;
positions[2*i+1] = pos2;
break;
}
}
}
VelocityVerletIntegrator integrator(0.001);
double temperature = 300; // kelvin
double collisionFrequency = 0.1; // 1/ps
double collisionFrequency = 25; // 1/ps
int numMTS = 3;
int numYS = 3;
int chainLength = 5;
int numDOF = 6;
integrator.addNoseHooverChainThermostat(system, temperature, collisionFrequency,
chainLength, numMTS, numYS);
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
context.setVelocitiesToTemperature(temperature);
integrator.step(1500);
integrator.step(10000);
int nSteps = 2000;
double mean_temp = 0.0;
for (int i = 0; i < 10000000; ++i) {
State state = context.getState(State::Energy);
std::vector<double> energies(nSteps);
for (int i = 0; i < nSteps; ++i) {
integrator.step(1);
State state = context.getState(State::Energy | (constrain ? State::Positions : 0));
if (constrain) {
auto positions = state.getPositions();
for(int i = 0; i < numMolecules; ++i) {
Vec3 delta = positions[2*i+1] - positions[2*i];
double dR2 = delta.dot(delta);
ASSERT_EQUAL_TOL(bondLengthSquared, dR2, 1e-4);
}
}
double KE = state.getKineticEnergy();
double PE = state.getPotentialEnergy();
double time = state.getTime();
double temperature = 2 * KE / (BOLTZ * numDOF);
mean_temp = (i*mean_temp + temperature)/(i+1);
double instantaneous_temperature = 2 * KE / (BOLTZ * numDOF);
mean_temp = (i*mean_temp + instantaneous_temperature)/(i+1);
double energy = KE + PE + integrator.computeHeatBathEnergy();
if(i % 100 == 0)
std::cout << " Time: " << std::setw(4) << time
<< " Temperature: " << std::setw(8) << std::setprecision(3) << temperature
<< " Mean Temperature: " << std::setw(8) << std::setprecision(3) << mean_temp
<< " Total Energy: " << std::setw(12) << std::setprecision(8) << energy << std::endl;
integrator.step(1);
#if DEBUG
if(i % 10 == 0) std::cout << " Time: " << std::setw(4) << time
<< " Temperature: " << std::setw(8) << std::setprecision(3) << temperature
<< " Mean Temperature: " << std::setw(8) << std::setprecision(3) << mean_temp
<< " Total Energy: " << std::setw(12) << std::setprecision(8) << energy << std::endl;
#endif
energies[i] = energy;
}
double sum = std::accumulate(energies.begin(), energies.end(), 0.0);
double mean = sum / energies.size();
double sq_sum = std::inner_product(energies.begin(), energies.end(), energies.begin(), 0.0);
double std = std::sqrt(sq_sum / energies.size() - mean * mean);
double relative_std = std / mean;
//std::cout << "Relative STD of energy " << relative_std << std::endl;
// Check mean temperature
ASSERT_EQUAL_TOL(temperature, temperature, 1e-2);
// Check fluctuation of conserved (total bath + system) energy
ASSERT_EQUAL_TOL(relative_std, 0, 1e-4);
}
void testConstraints() {
const int numParticles = 8;
const int numConstraints = 5;
System system;
VelocityVerletIntegrator integrator(0.001);
integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) {
system.addParticle(i%2 == 0 ? 5.0 : 10.0);
forceField->addParticle((i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
}
system.addConstraint(0, 1, 1.0);
system.addConstraint(1, 2, 1.0);
system.addConstraint(2, 3, 1.0);
system.addConstraint(4, 5, 1.0);
system.addConstraint(6, 7, 1.0);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; ++i) {
positions[i] = Vec3(i/2, (i+1)/2, 0);
velocities[i] = Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5);
}
context.setPositions(positions);
context.setVelocities(velocities);
// Simulate it and see whether the constraints remain satisfied.
double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2;
double distance;
system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-4);
}
double energy = state.getPotentialEnergy()+state.getKineticEnergy();
if (i == 1)
initialEnergy = energy;
else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1);
}
}
void testNHCPropagation() {
// test if the velocity scale factor goes to one for a single particle
// with no forces in the system
......@@ -225,7 +254,9 @@ void testPropagateChainConsistentWithPythonReference() {
chainLength, numMTS, numYS);
Context context(system, integrator, platform);
double scale = integrator.propagateChain(kineticEnergy, chainID);
//std::cout << std::setw(12) << std::setprecision(10) << scale << std::endl;
#if DEBUG
std::cout << std::setw(12) << std::setprecision(10) << scale << std::endl;
#endif
ASSERT_EQUAL_TOL(0.9674732261005896, scale, 1e-5)
}
......@@ -233,14 +264,14 @@ void runPlatformTests();
int main(int argc, char* argv[]) {
try {
//initializeTests(argc, argv);
//testNHCPropagation();
//testPropagateChainConsistentWithPythonReference();
initializeTests(argc, argv);
testNHCPropagation();
testPropagateChainConsistentWithPythonReference();
testHarmonicOscillator();
//testSingleBond();
//testConstraints();
//runPlatformTests();
bool constrain;
constrain = false; testDimerBox(constrain);
constrain = true; testDimerBox(constrain);
runPlatformTests();
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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