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;
}
OpenMM::System* AmberParm::createSystem(
OpenMM::NonbondedForce::NonbondedMethod nonbondedMethod,
double nonbondedCutoff,
std::string constraints,
bool rigidWater,
std::string implicitSolvent,
double implicitSolventKappa,
double implicitSolventSaltConc,
double temperature,
double soluteDielectric,
double solventDielectric,
bool removeCMMotion,
double ewaldErrorTolerance,
bool flexibleConstraints,
bool useSASA) {
OpenMM::System* system = new OpenMM::System();
// Make sure we have a legal choice for constraints and implicitSolvent
if (constraints != "None" && constraints != "HBonds" &&
constraints != "AllBonds") {
string msg = "constraints must be None, HBonds, or AllBonds; not " +
constraints;
throw AmberParmError(msg.c_str());
}
if (implicitSolvent != "None" && implicitSolvent != "HCT" &&
implicitSolvent != "OBC1" && implicitSolvent != "OBC2" &&
implicitSolvent != "GBn" && implicitSolvent != "GBn2") {
string msg = "implicitSolvent must be None, HCT, OBC1, OBC2, GBn, or "
"GBn2; not " + implicitSolvent;
throw AmberParmError(msg.c_str());
}
if (rigidWater && (constraints != "HBonds" && constraints != "AllBonds")) {
cerr << "rigidWater is incompatible with constraints=None; setting to "
<< "false" << endl;
}
// Catch illegal nonbonded choice for system
if (isPeriodic()) {
if (nonbondedMethod == OpenMM::NonbondedForce::CutoffNonPeriodic ||
nonbondedMethod == OpenMM::NonbondedForce::NoCutoff)
throw AmberParmError("Illegal nonbondedForce choice for periodic system");
} else {
if (nonbondedMethod == OpenMM::NonbondedForce::CutoffPeriodic ||
nonbondedMethod == OpenMM::NonbondedForce::PME ||
nonbondedMethod == OpenMM::NonbondedForce::Ewald)
throw AmberParmError("Illegal nonbondedForce choice for non-periodic system");
}
// Add all particles
for (atom_iterator it = AtomBegin(); it != AtomEnd(); it++) {
system->addParticle(it->getMass());
}
// Add constraints
bool hcons = constraints == "HBonds" || constraints == "AllBonds";
bool allcons = constraints == "AllBonds";
for (bond_iterator it = BondBegin(); it != BondEnd(); it++) {
Atom a1 = atoms_[it->getAtomI()];
Atom a2 = atoms_[it->getAtomJ()];
if (hcons && (a1.getElement() == 1 || a2.getElement() == 1)) {
system->addConstraint(it->getAtomI(), it->getAtomJ(),
it->getEquilibriumDistance()*NANOMETER_PER_ANGSTROM);
} else if (allcons) {
system->addConstraint(it->getAtomI(), it->getAtomJ(),
it->getEquilibriumDistance()*NANOMETER_PER_ANGSTROM);
}
}
// Add all bonds
if (!allcons || flexibleConstraints) {
OpenMM::HarmonicBondForce *bond_force = new OpenMM::HarmonicBondForce();
bond_force->setForceGroup(BOND_FORCE_GROUP);
double conv = ANGSTROM_PER_NANOMETER*ANGSTROM_PER_NANOMETER*JOULE_PER_CALORIE;
for (bond_iterator it=BondBegin(); it != BondEnd(); it++) {
// See if this bond needs to be skipped due to constraints
Atom a1 = atoms_[it->getAtomI()];
Atom a2 = atoms_[it->getAtomJ()];
if (hcons && (a1.getElement() == 1 || a2.getElement() == 1) &&
!flexibleConstraints) continue;
bond_force->addBond(it->getAtomI(), it->getAtomJ(),
it->getEquilibriumDistance()*NANOMETER_PER_ANGSTROM,
2*it->getForceConstant()*conv);
}
system->addForce(bond_force);
}
// Add all angles
OpenMM::HarmonicAngleForce *angle_force = new OpenMM::HarmonicAngleForce();
angle_force->setForceGroup(ANGLE_FORCE_GROUP);
for (angle_iterator it = AngleBegin(); it != AngleEnd(); it++) {
angle_force->addAngle(it->getAtomI(), it->getAtomJ(), it->getAtomK(),
it->getEquilibriumAngle()*RADIAN_PER_DEGREE,
2*it->getForceConstant()*JOULE_PER_CALORIE);
}
system->addForce(angle_force);
// Add all torsions
OpenMM::PeriodicTorsionForce *dihedral_force = new OpenMM::PeriodicTorsionForce();
dihedral_force->setForceGroup(DIHEDRAL_FORCE_GROUP);
for (dihedral_iterator it = DihedralBegin(); it != DihedralEnd(); it++) {
dihedral_force->addTorsion(it->getAtomI(), it->getAtomJ(),
it->getAtomK(), it->getAtomL(),
it->getPeriodicity(),
it->getPhase()*RADIAN_PER_DEGREE,
it->getForceConstant()*JOULE_PER_CALORIE);
}
system->addForce(dihedral_force);
// Add nonbonded force
OpenMM::NonbondedForce *nonb_frc = new OpenMM::NonbondedForce();
nonb_frc->setForceGroup(NONBONDED_FORCE_GROUP);
nonb_frc->setNonbondedMethod(nonbondedMethod);
if (nonbondedMethod != OpenMM::NonbondedForce::NoCutoff)
nonb_frc->setCutoffDistance(nonbondedCutoff*NANOMETER_PER_ANGSTROM);
const double ONE_SIXTH = 1.0 / 6.0;
const double SIGMA_SCALE = pow(2, -ONE_SIXTH) * 2 * NANOMETER_PER_ANGSTROM;
for (atom_iterator it = AtomBegin(); it != AtomEnd(); it++) {
nonb_frc->addParticle(it->getCharge(),
it->getLJRadius()*SIGMA_SCALE,
it->getLJEpsilon()*JOULE_PER_CALORIE);
}
// Now do exceptions
const double SIGMA_SCALE2 = pow(2, -ONE_SIXTH) * NANOMETER_PER_ANGSTROM;
for (dihedral_iterator it = DihedralBegin(); it != DihedralEnd(); it++) {
if (it->ignoreEndGroups()) continue;
Atom a1 = atoms_[it->getAtomI()];
Atom a2 = atoms_[it->getAtomL()];
double eps = sqrt(a1.getLJEpsilon() * a2.getLJEpsilon()) *
JOULE_PER_CALORIE / it->getScnb();
double sig = (a1.getLJRadius() + a2.getLJRadius()) * SIGMA_SCALE2;
nonb_frc->addException(it->getAtomI(), it->getAtomL(),
a1.getCharge()*a2.getCharge()/it->getScee(),
sig, eps);
}
// Now do exclusions
for (int i = 0; i < atoms_.size(); i++) {
if (exclusion_list_[i].size() == 0) continue; // No exclusions here
for (set<int>::const_iterator it = exclusion_list_[i].begin();
it != exclusion_list_[i].end(); it++) {
nonb_frc->addException(i, *it, 0.0, 1.0, 0.0);
}
}
// Set the ewald error tolerance
if (nonbondedMethod == OpenMM::NonbondedForce::PME ||
nonbondedMethod == OpenMM::NonbondedForce::Ewald)
nonb_frc->setEwaldErrorTolerance(ewaldErrorTolerance);
system->addForce(nonb_frc);
// See about removing the center of mass motion
if (removeCMMotion)
system->addForce(new OpenMM::CMMotionRemover());
// Add a box if necessary
if (isPeriodic())
system->setDefaultPeriodicBoxVectors(unit_cell_.getVectorA()/10,
unit_cell_.getVectorB()/10,
unit_cell_.getVectorC()/10);
// If no implicit solvent, we can return system now
if (implicitSolvent == "None")
return system;
// Otherwise, we need to add the GB force
if (implicitSolventKappa <= 0 && implicitSolventSaltConc > 0)
implicitSolventKappa = 50.33355 * 0.73 *
sqrt(implicitSolventSaltConc/(solventDielectric*temperature));
OpenMM::CustomGBForce *gb_frc = 0;
if (implicitSolvent == "HCT") {
gb_frc = GB_HCT(*this, solventDielectric, soluteDielectric, useSASA,
nonbondedCutoff, implicitSolventKappa);
} else if (implicitSolvent == "OBC1") {
gb_frc = GB_OBC1(*this, solventDielectric, soluteDielectric, useSASA,
nonbondedCutoff, implicitSolventKappa);
} else if (implicitSolvent == "OBC2") {
gb_frc = GB_OBC2(*this, solventDielectric, soluteDielectric, useSASA,
nonbondedCutoff, implicitSolventKappa);
} else if (implicitSolvent == "GBn") {
gb_frc = GB_GBn(*this, solventDielectric, soluteDielectric, useSASA,
nonbondedCutoff, implicitSolventKappa);
} else if (implicitSolvent == "GBn2") {
gb_frc = GB_GBn2(*this, solventDielectric, soluteDielectric, useSASA,
nonbondedCutoff, implicitSolventKappa);
} else {
stringstream iss;
iss << "Should not be here; bad GB model " << implicitSolvent;
throw InternalError(iss.str());
}
if (nonbondedMethod == OpenMM::NonbondedForce::NoCutoff)
gb_frc->setNonbondedMethod(OpenMM::CustomGBForce::NoCutoff);
else if (nonbondedMethod == OpenMM::NonbondedForce::CutoffNonPeriodic)
gb_frc->setNonbondedMethod(OpenMM::CustomGBForce::CutoffNonPeriodic);
else // all remaining options are periodic cutoff...
gb_frc->setNonbondedMethod(OpenMM::CustomGBForce::CutoffPeriodic);
gb_frc->setForceGroup(NONBONDED_FORCE_GROUP);
// Since we're using GB, we need to turn off the reaction field dielectric
nonb_frc->setReactionFieldDielectric(1.0);
system->addForce(gb_frc);
return system;
}
