void NVE::moveA(){
SimInfo::MoleculeIterator i;
Molecule::IntegrableObjectIterator j;
Molecule* mol;
StuntDouble* sd;
Vector3d vel;
Vector3d pos;
Vector3d frc;
Vector3d Tb;
Vector3d ji;
RealType mass;
for (mol = info_->beginMolecule(i); mol != NULL;
mol = info_->nextMolecule(i)) {
for (sd = mol->beginIntegrableObject(j); sd != NULL;
sd = mol->nextIntegrableObject(j)) {
vel = sd->getVel();
pos = sd->getPos();
frc = sd->getFrc();
mass = sd->getMass();
// velocity half step
vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
// position whole step
pos += dt * vel;
sd->setVel(vel);
sd->setPos(pos);
if (sd->isDirectional()){
// get and convert the torque to body frame
Tb = sd->lab2Body(sd->getTrq());
// get the angular momentum, and propagate a half step
ji = sd->getJ();
ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
rotAlgo_->rotate(sd, ji, dt);
sd->setJ(ji);
}
}
}
flucQ_->moveA();
rattle_->constraintA();
}
int main(int argc, char* argv[]){
registerHydrodynamicsModels();
gengetopt_args_info args_info;
std::string dumpFileName;
std::string mdFileName;
std::string prefix;
//parse the command line option
if (cmdline_parser (argc, argv, &args_info) != 0) {
exit(1) ;
}
//get the dumpfile name and meta-data file name
if (args_info.input_given){
dumpFileName = args_info.input_arg;
} else {
strcpy( painCave.errMsg,
"No input file name was specified.\n" );
painCave.isFatal = 1;
simError();
}
if (args_info.output_given){
prefix = args_info.output_arg;
} else {
prefix = getPrefix(dumpFileName);
}
std::string outputFilename = prefix + ".diff";
//parse md file and set up the system
SimCreator creator;
SimInfo* info = creator.createSim(dumpFileName, true);
SimInfo::MoleculeIterator mi;
Molecule* mol;
Molecule::IntegrableObjectIterator ii;
StuntDouble* sd;
Mat3x3d identMat;
identMat(0,0) = 1.0;
identMat(1,1) = 1.0;
identMat(2,2) = 1.0;
Globals* simParams = info->getSimParams();
RealType temperature(0.0);
RealType viscosity(0.0);
if (simParams->haveViscosity()) {
viscosity = simParams->getViscosity();
} else {
sprintf(painCave.errMsg, "viscosity must be set\n");
painCave.isFatal = 1;
simError();
}
if (simParams->haveTargetTemp()) {
temperature = simParams->getTargetTemp();
} else {
sprintf(painCave.errMsg, "target temperature must be set\n");
painCave.isFatal = 1;
simError();
}
std::map<std::string, SDShape> uniqueStuntDoubles;
for (mol = info->beginMolecule(mi); mol != NULL;
mol = info->nextMolecule(mi)) {
for (sd = mol->beginIntegrableObject(ii); sd != NULL;
sd = mol->nextIntegrableObject(ii)) {
if (uniqueStuntDoubles.find(sd->getType()) == uniqueStuntDoubles.end()) {
sd->setPos(V3Zero);
sd->setA(identMat);
if (sd->isRigidBody()) {
RigidBody* rb = static_cast<RigidBody*>(sd);
rb->updateAtoms();
}
SDShape tmp;
tmp.shape = ShapeBuilder::createShape(sd);
tmp.sd = sd;
uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(sd->getType(), tmp));
}
}
}
std::map<std::string, SDShape>::iterator si;
for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) {
HydrodynamicsModel* model;
Shape* shape = si->second.shape;
StuntDouble* sd = si->second.sd;;
if (args_info.model_given) {
model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info);
} else if (shape->hasAnalyticalSolution()) {
model = new AnalyticalModel(sd, info);
} else {
model = new BeadModel(sd, info);
}
model->init();
std::ofstream ofs;
std::stringstream outputBeads;
outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz";
ofs.open(outputBeads.str().c_str());
model->writeBeads(ofs);
ofs.close();
//if beads option is turned on, skip the calculation
if (!args_info.beads_flag) {
model->calcHydroProps(shape, viscosity, temperature);
std::ofstream outputDiff;
outputDiff.open(outputFilename.c_str());
model->writeHydroProps(outputDiff);
outputDiff.close();
}
delete model;
}
//MemoryUtils::deletePointers(shapes);
delete info;
}
void NPT::moveA() {
SimInfo::MoleculeIterator i;
Molecule::IntegrableObjectIterator j;
Molecule* mol;
StuntDouble* sd;
Vector3d Tb, ji;
RealType mass;
Vector3d vel;
Vector3d pos;
Vector3d frc;
Vector3d sc;
int index;
thermostat = snap->getThermostat();
loadEta();
instaTemp =thermo.getTemperature();
press = thermo.getPressureTensor();
instaPress = PhysicalConstants::pressureConvert* (press(0, 0) + press(1, 1) + press(2, 2)) / 3.0;
instaVol =thermo.getVolume();
Vector3d COM = thermo.getCom();
//evolve velocity half step
calcVelScale();
for (mol = info_->beginMolecule(i); mol != NULL;
mol = info_->nextMolecule(i)) {
for (sd = mol->beginIntegrableObject(j); sd != NULL;
sd = mol->nextIntegrableObject(j)) {
vel = sd->getVel();
frc = sd->getFrc();
mass = sd->getMass();
getVelScaleA(sc, vel);
// velocity half step (use chi from previous step here):
vel += dt2*PhysicalConstants::energyConvert/mass* frc - dt2*sc;
sd->setVel(vel);
if (sd->isDirectional()) {
// get and convert the torque to body frame
Tb = sd->lab2Body(sd->getTrq());
// get the angular momentum, and propagate a half step
ji = sd->getJ();
ji += dt2*PhysicalConstants::energyConvert * Tb
- dt2*thermostat.first* ji;
rotAlgo_->rotate(sd, ji, dt);
sd->setJ(ji);
}
}
}
// evolve chi and eta half step
thermostat.first += dt2 * (instaTemp / targetTemp - 1.0) / tt2;
evolveEtaA();
//calculate the integral of chidt
thermostat.second += dt2 * thermostat.first;
flucQ_->moveA();
index = 0;
for (mol = info_->beginMolecule(i); mol != NULL;
mol = info_->nextMolecule(i)) {
for (sd = mol->beginIntegrableObject(j); sd != NULL;
sd = mol->nextIntegrableObject(j)) {
oldPos[index++] = sd->getPos();
}
}
//the first estimation of r(t+dt) is equal to r(t)
for(int k = 0; k < maxIterNum_; k++) {
index = 0;
for (mol = info_->beginMolecule(i); mol != NULL;
mol = info_->nextMolecule(i)) {
for (sd = mol->beginIntegrableObject(j); sd != NULL;
sd = mol->nextIntegrableObject(j)) {
vel = sd->getVel();
pos = sd->getPos();
this->getPosScale(pos, COM, index, sc);
pos = oldPos[index] + dt * (vel + sc);
sd->setPos(pos);
++index;
}
}
rattle_->constraintA();
}
// Scale the box after all the positions have been moved:
this->scaleSimBox();
snap->setThermostat(thermostat);
saveEta();
}
int main(int argc, char* argv[]){
gengetopt_args_info args_info;
string dumpFileName;
string outFileName;
//parse the command line option
if (cmdline_parser (argc, argv, &args_info) != 0) {
exit(1) ;
}
//get the dumpfile name and meta-data file name
if (args_info.input_given){
dumpFileName = args_info.input_arg;
} else {
strcpy( painCave.errMsg,
"No input file name was specified.\n" );
painCave.isFatal = 1;
simError();
}
if (args_info.output_given){
outFileName = args_info.output_arg;
} else {
strcpy( painCave.errMsg,
"No output file name was specified.\n" );
painCave.isFatal = 1;
simError();
}
Vector3i repeat = Vector3i(args_info.repeatX_arg,
args_info.repeatY_arg,
args_info.repeatZ_arg);
Mat3x3d repeatD = Mat3x3d(0.0);
repeatD(0,0) = repeat.x();
repeatD(1,1) = repeat.y();
repeatD(2,2) = repeat.z();
Vector3d translate = Vector3d(args_info.translateX_arg,
args_info.translateY_arg,
args_info.translateZ_arg);
//parse md file and set up the system
SimCreator oldCreator;
SimInfo* oldInfo = oldCreator.createSim(dumpFileName, false);
Globals* simParams = oldInfo->getSimParams();
std::vector<Component*> components = simParams->getComponents();
std::vector<int> nMol;
for (vector<Component*>::iterator i = components.begin();
i !=components.end(); ++i) {
int nMolOld = (*i)->getNMol();
int nMolNew = nMolOld * repeat.x() * repeat.y() * repeat.z();
nMol.push_back(nMolNew);
}
createMdFile(dumpFileName, outFileName, nMol);
SimCreator newCreator;
SimInfo* newInfo = newCreator.createSim(outFileName, false);
DumpReader* dumpReader = new DumpReader(oldInfo, dumpFileName);
int nframes = dumpReader->getNFrames();
DumpWriter* writer = new DumpWriter(newInfo, outFileName);
if (writer == NULL) {
sprintf(painCave.errMsg, "error in creating DumpWriter");
painCave.isFatal = 1;
simError();
}
SimInfo::MoleculeIterator miter;
Molecule::IntegrableObjectIterator iiter;
Molecule::RigidBodyIterator rbIter;
Molecule* mol;
StuntDouble* sd;
StuntDouble* sdNew;
RigidBody* rb;
Mat3x3d oldHmat;
Mat3x3d newHmat;
Snapshot* oldSnap;
Snapshot* newSnap;
Vector3d oldPos;
Vector3d newPos;
for (int i = 0; i < nframes; i++){
cerr << "frame = " << i << "\n";
dumpReader->readFrame(i);
oldSnap = oldInfo->getSnapshotManager()->getCurrentSnapshot();
newSnap = newInfo->getSnapshotManager()->getCurrentSnapshot();
newSnap->setID( oldSnap->getID() );
newSnap->setTime( oldSnap->getTime() );
oldHmat = oldSnap->getHmat();
newHmat = repeatD*oldHmat;
newSnap->setHmat(newHmat);
newSnap->setThermostat( oldSnap->getThermostat() );
newSnap->setBarostat( oldSnap->getBarostat() );
int newIndex = 0;
for (mol = oldInfo->beginMolecule(miter); mol != NULL;
mol = oldInfo->nextMolecule(miter)) {
for (int ii = 0; ii < repeat.x(); ii++) {
for (int jj = 0; jj < repeat.y(); jj++) {
for (int kk = 0; kk < repeat.z(); kk++) {
Vector3d trans = Vector3d(ii, jj, kk);
for (sd = mol->beginIntegrableObject(iiter); sd != NULL;
sd = mol->nextIntegrableObject(iiter)) {
oldPos = sd->getPos() + translate;
oldSnap->wrapVector(oldPos);
newPos = oldPos + trans * oldHmat;
sdNew = newInfo->getIOIndexToIntegrableObject(newIndex);
sdNew->setPos( newPos );
sdNew->setVel( sd->getVel() );
if (sd->isDirectional()) {
sdNew->setA( sd->getA() );
sdNew->setJ( sd->getJ() );
}
newIndex++;
}
}
}
}
}
//update atoms of rigidbody
for (mol = newInfo->beginMolecule(miter); mol != NULL;
mol = newInfo->nextMolecule(miter)) {
//change the positions of atoms which belong to the rigidbodies
for (rb = mol->beginRigidBody(rbIter); rb != NULL;
rb = mol->nextRigidBody(rbIter)) {
rb->updateAtoms();
rb->updateAtomVel();
}
}
writer->writeDump();
}
// deleting the writer will put the closing at the end of the dump file.
delete writer;
delete oldInfo;
}