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; }