Exemple #1
0
  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();    
  }    
Exemple #2
0
Vector3d Molecule::getComVel() {
    StuntDouble* sd;
    std::vector<StuntDouble*>::iterator i;
    Vector3d velCom;
    double totalMass = 0;
    double mass;
    
    for (sd = beginIntegrableObject(i); sd != NULL; sd = nextIntegrableObject(i)){
        mass = sd->getMass();
        totalMass += mass;
        velCom += sd->getVel() * mass;    
    }

    velCom /= totalMass;

    return velCom;
}
Exemple #3
0
  void NPT::moveB(void) {
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* sd;
    int index;
    Vector3d Tb;
    Vector3d ji;
    Vector3d sc;
    Vector3d vel;
    Vector3d frc;
    RealType mass;

    thermostat = snap->getThermostat();
    RealType oldChi  = thermostat.first;
    RealType prevChi;

    loadEta();
    
    //save velocity and angular momentum
    index = 0;
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j); sd != NULL;
	   sd = mol->nextIntegrableObject(j)) {
                
	oldVel[index] = sd->getVel();

        if (sd->isDirectional())
	   oldJi[index] = sd->getJ();

	++index;
      }
    }

    // do the iteration:
    instaVol =thermo.getVolume();

    for(int k = 0; k < maxIterNum_; k++) {
      instaTemp =thermo.getTemperature();
      instaPress =thermo.getPressure();

      // evolve chi another half step using the temperature at t + dt/2
      prevChi = thermostat.first;
      thermostat.first = oldChi + dt2 * (instaTemp / targetTemp - 1.0) / tt2;

      //evolve eta
      this->evolveEtaB();
      this->calcVelScale();

      index = 0;
      for (mol = info_->beginMolecule(i); mol != NULL; 
           mol = info_->nextMolecule(i)) {

	for (sd = mol->beginIntegrableObject(j); sd != NULL;
	     sd = mol->nextIntegrableObject(j)) {            

	  frc = sd->getFrc();
	  mass = sd->getMass();

	  getVelScaleB(sc, index);

	  // velocity half step
	  vel = oldVel[index] 
            + 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());

	    ji = oldJi[index] 
              + dt2*PhysicalConstants::energyConvert*Tb 
              - dt2*thermostat.first*oldJi[index];

	    sd->setJ(ji);
	  }

	  ++index;
	}
      }
        
      rattle_->constraintB();

      if ((fabs(prevChi - thermostat.first) <= chiTolerance) && 
          this->etaConverged())
	break;
    }

    //calculate integral of chidt
    thermostat.second += dt2 * thermostat.first;

    snap->setThermostat(thermostat);

    flucQ_->moveB();
    saveEta();
  }
Exemple #4
0
  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();
  }
Exemple #5
0
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;
}