void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities,
vector<Vec3>& forces, vector<double>& masses, double maxStepSize, double tolerance) {
// first-time-through initialization
int numberOfAtoms = system.getNumParticles();
if (getTimeStep() == 0) {
// invert masses
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == 0.0)
inverseMasses[ii] = 0.0;
else
inverseMasses[ii] = 1.0/masses[ii];
}
}
double error = 0.0;
for (int i = 0; i < numberOfAtoms; ++i) {
for (int j = 0; j < 3; ++j) {
double xerror = inverseMasses[i]*forces[i][j];
error += xerror*xerror;
}
}
error = sqrt(error/(numberOfAtoms*3));
double newStepSize = sqrt(getAccuracy()/error);
if (getDeltaT() > 0.0f)
newStepSize = std::min(newStepSize, getDeltaT()*2.0f); // For safety, limit how quickly dt can increase.
if (newStepSize > getDeltaT() && newStepSize < 1.2f*getDeltaT())
newStepSize = getDeltaT(); // Keeping dt constant between steps improves the behavior of the integrator.
if (newStepSize > maxStepSize)
newStepSize = maxStepSize;
double vstep = 0.5f*(newStepSize+getDeltaT()); // The time interval by which to advance the velocities
setDeltaT(newStepSize);
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != 0.0)
for (int j = 0; j < 3; ++j) {
double vPrime = velocities[i][j] + inverseMasses[i]*forces[i][j]*vstep;
xPrime[i][j] = atomCoordinates[i][j] + vPrime*getDeltaT();
}
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
double velocityScale = 1.0/getDeltaT();
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != 0.0)
for (int j = 0; j < 3; ++j) {
velocities[i][j] = velocityScale*(xPrime[i][j] - atomCoordinates[i][j]);
atomCoordinates[i][j] = xPrime[i][j];
}
}
ReferenceVirtualSites::computePositions(system, atomCoordinates);
incrementTimeStep();
}
void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceVerletDynamics::update";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
// ---------------------------------------------------------------------------------------
// first-time-through initialization
int numberOfAtoms = system.getNumParticles();
if( getTimeStep() == 0 ){
// invert masses
for( int ii = 0; ii < numberOfAtoms; ii++ ){
if (masses[ii] == zero)
inverseMasses[ii] = zero;
else
inverseMasses[ii] = one/masses[ii];
}
}
// Perform the integration.
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != zero)
for (int j = 0; j < 3; ++j) {
velocities[i][j] += inverseMasses[i]*forces[i][j]*getDeltaT();
xPrime[i][j] = atomCoordinates[i][j] + velocities[i][j]*getDeltaT();
}
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
RealOpenMM velocityScale = static_cast<RealOpenMM>( 1.0/getDeltaT() );
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != zero)
for (int j = 0; j < 3; ++j) {
velocities[i][j] = velocityScale*(xPrime[i][j] - atomCoordinates[i][j]);
atomCoordinates[i][j] = xPrime[i][j];
}
}
ReferenceVirtualSites::computePositions(system, atomCoordinates);
incrementTimeStep();
}
void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceBrownianDynamics::update";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
// ---------------------------------------------------------------------------------------
// first-time-through initialization
int numberOfAtoms = system.getNumParticles();
if( getTimeStep() == 0 ){
// invert masses
for( int ii = 0; ii < numberOfAtoms; ii++ ){
if (masses[ii] == zero)
inverseMasses[ii] = zero;
else
inverseMasses[ii] = one/masses[ii];
}
}
// Perform the integration.
const RealOpenMM noiseAmplitude = static_cast<RealOpenMM>( sqrt(2.0*BOLTZ*getTemperature()*getDeltaT()/getFriction()) );
const RealOpenMM forceScale = getDeltaT()/getFriction();
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != zero)
for (int j = 0; j < 3; ++j) {
xPrime[i][j] = atomCoordinates[i][j] + forceScale*inverseMasses[i]*forces[i][j] + noiseAmplitude*SQRT(inverseMasses[i])*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
RealOpenMM velocityScale = static_cast<RealOpenMM>( 1.0/getDeltaT() );
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != zero)
for (int j = 0; j < 3; ++j) {
velocities[i][j] = velocityScale*(xPrime[i][j] - atomCoordinates[i][j]);
atomCoordinates[i][j] = xPrime[i][j];
}
}
ReferenceVirtualSites::computePositions(system, atomCoordinates);
incrementTimeStep();
}
void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceStochasticDynamics::update";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
// ---------------------------------------------------------------------------------------
// first-time-through initialization
int numberOfAtoms = system.getNumParticles();
if( getTimeStep() == 0 ){
// invert masses
for( int ii = 0; ii < numberOfAtoms; ii++ ){
if (masses[ii] == zero)
inverseMasses[ii] = zero;
else
inverseMasses[ii] = one/masses[ii];
}
}
// 1st update
updatePart1( numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime );
// 2nd update
updatePart2( numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime );
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates
RealOpenMM invStepSize = 1.0/getDeltaT();
for (int i = 0; i < numberOfAtoms; ++i)
if (masses[i] != zero)
for (int j = 0; j < 3; ++j) {
velocities[i][j] = invStepSize*(xPrime[i][j]-atomCoordinates[i][j]);
atomCoordinates[i][j] = xPrime[i][j];
}
ReferenceVirtualSites::computePositions(system, atomCoordinates);
incrementTimeStep();
}
TEST(TestControlBerendsenBins,SingleBin){
std::ifstream file("../foam-1728.json");
if(!file.is_open()){
std::cout<<"File not found"<<std::endl;
exit(0);
}
std::string jsonstr;
std::string line;
while (!file.eof()) {
getline(file, line);
jsonstr += line;
}
file.close();
rapidjson::Document document;
if(document.Parse<0>(jsonstr.c_str()).HasParseError()){
std::cout<<"Parsing error "<<std::endl;
exit(0);
}
const double stepSizeInFs = document["StepSizeInFs"].GetDouble();
const int numParticles = document["NumberAtoms"].GetInt();
std::string equationStr = document["Equation"].GetString();
const double rCut = document["rCut"].GetDouble();
const rapidjson::Value& b = document["Boxsize"];
double bx = b[(rapidjson::SizeType)0].GetDouble();
double by = b[(rapidjson::SizeType)1].GetDouble();
double bz = b[(rapidjson::SizeType)2].GetDouble();
int numSpecies = document["NumberSpecies"].GetInt();
std::vector<OpenMM::Vec3> posInNm;
std::vector<OpenMM::Vec3> velInNm;
OpenMM::Platform::loadPluginsFromDirectory(
OpenMM::Platform::getDefaultPluginsDirectory());
OpenMM::System system;
//add particles to the system by reading from json file
system.setDefaultPeriodicBoxVectors(OpenMM::Vec3(bx,0,0),OpenMM::Vec3(0,by,0),OpenMM::Vec3(0,0,bz));
const rapidjson::Value& mass = document["masses"];
const rapidjson::Value& pos = document["Positions"];
const rapidjson::Value& vel = document["Velocities"];
posInNm.clear();
velInNm.clear();
for(rapidjson::SizeType m=0;m<mass.Size();m++){
double tm = mass[(rapidjson::SizeType) m].GetDouble();
system.addParticle(tm);
posInNm.push_back(OpenMM::Vec3(pos[(rapidjson::SizeType) m]["0"].GetDouble(),
pos[(rapidjson::SizeType) m]["1"].GetDouble(),
pos[(rapidjson::SizeType) m]["2"].GetDouble()
));
velInNm.push_back(OpenMM::Vec3(vel[(rapidjson::SizeType) m]["0"].GetDouble(),
vel[(rapidjson::SizeType) m]["1"].GetDouble(),
vel[(rapidjson::SizeType) m]["2"].GetDouble()
));
}
std::cout<<"Initialized System with "<<system.getNumParticles()<<" Particles."<<std::endl;
OpenMM::CustomNonbondedForce* nonbonded = new OpenMM::CustomNonbondedForce(equationStr);
nonbonded->setNonbondedMethod(OpenMM::CustomNonbondedForce::CutoffPeriodic);
nonbonded->setCutoffDistance(rCut);// * OpenMM::NmPerAngstrom
nonbonded->addPerParticleParameter("Ar");//later on collect it from json string based on OF
for(int p=0;p<numParticles;p++){
std::vector<double> params(numSpecies);
params[0] = (double) 1;
nonbonded->addParticle(params);
}
system.addForce(nonbonded);
std::vector<std::string> ctools(1);
ctools[0] = "ControlBerendsenInBins";
OpenMM::Vec3 startPoint = OpenMM::Vec3((10*0.34),(0*0.34),(10*0.34));
OpenMM::Vec3 endPoint = OpenMM::Vec3((10*0.34),(20*0.34),(10*0.34));
OpenMM::ControlTools controls(ctools,(double)292,0.001,
startPoint,endPoint);
int num_plat = OpenMM::Platform::getNumPlatforms();
std::cout<<"Number of registered platforms: "<< num_plat <<std::endl;
for(int i=0;i<num_plat;i++)
{
OpenMM::Platform& tempPlatform = OpenMM::Platform::getPlatform(i);
std::string tempPlatformName = tempPlatform.getName();
std::cout<<"Platform "<<(i+1)<<" is "<<tempPlatformName.c_str()<<std::endl;
}
OpenMM::Platform& platform = OpenMM::Platform::getPlatformByName("OpenCL");
OpenMM::VelocityVerletIntegrator integrator(stepSizeInFs * OpenMM::PsPerFs);
OpenMM::Context context(system,integrator,platform,controls);
string Platformname = context.getPlatform().getName();
std::cout<<"Using OpenMM "<<Platformname.c_str()<<" Platform"<<std::endl;
context.setPositions(posInNm);
context.setVelocities(velInNm);
int nbs = context.getControls().getNBins();
printf("Using %d bins for the system\n",nbs);
//start the simulation loop
integrator.step(1);
printf("Finished initial integration\n");
int counter=0;
std::cout<<"starting the loop\n";
for(int frame=1;frame<400;++frame){
// OpenMM::State state = context.getState(OpenMM::State::Velocities);
// const double time = state.getTime();
double* mola = context.getControls().getBinTemperature();
// OpenMM::Vec3* tv = context.getControls().getTestVariable();
double gpuMol = 0.0;
for(int k=0;k<nbs;k++){
gpuMol += mola[k];
}
EXPECT_EQ((double) numParticles,gpuMol);
integrator.step(1);
}
std::cout<<"Simulation completed with counter value "<<counter<<std::endl;
}