コード例 #1
0
ファイル: nanorodBuilder.cpp プロジェクト: jmichalka/OpenMD
int main(int argc, char *argv []) {
  
  registerLattice();
  
  gengetopt_args_info args_info;
  std::string latticeType;
  std::string inputFileName;
  std::string outputFileName;
  MoLocator* locator;
  int nComponents;
  double latticeConstant;
  RealType rodRadius;
  RealType rodLength;
  Mat3x3d hmat;
  DumpWriter *writer;
  
  // Parse Command Line Arguments
  if (cmdline_parser(argc, argv, &args_info) != 0)
    exit(1);
         
  /* get lattice type */
  latticeType = "FCC";

  /* get input file name */
  if (args_info.inputs_num)
    inputFileName = args_info.inputs[0];
  else {
    sprintf(painCave.errMsg, "No input .omd file name was specified "
            "on the command line");
    painCave.isFatal = 1;
    cmdline_parser_print_help();
    simError();
  }
  
  /* parse md file and set up the system */
  SimCreator oldCreator;
  SimInfo* oldInfo = oldCreator.createSim(inputFileName, false);
  
  latticeConstant = args_info.latticeConstant_arg;
  rodRadius = args_info.radius_arg;
  rodLength = args_info.length_arg;
  Globals* simParams = oldInfo->getSimParams();
  
  vector<Vector3d> sites;
  vector<Vector3d> orientations;

  if (args_info.ellipsoid_flag) {
    shapedLatticeEllipsoid nanoEllipsoid(latticeConstant, latticeType,
                                         rodLength, rodRadius);
    sites = nanoEllipsoid.getSites();
    orientations = nanoEllipsoid.getOrientations();
  } else {
    
    /* Create nanorod */
    shapedLatticeRod nanoRod(latticeConstant, latticeType,
                             rodRadius, rodLength);
    /* Build a lattice and get lattice points for this lattice constant */
    sites = nanoRod.getSites();
    orientations = nanoRod.getOrientations();
  }

  std::vector<std::size_t> vacancyTargets;
  vector<bool> isVacancy;
  
  Vector3d myLoc;
  RealType myR;
 
  for (std::size_t i = 0; i < sites.size(); i++) 
    isVacancy.push_back(false);
  
  // cerr << "checking vacancyPercent" << "\n";
  if (args_info.vacancyPercent_given) {
    // cerr << "vacancyPercent given" << "\n";
    if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) {
      sprintf(painCave.errMsg, 
	      "vacancyPercent was set to a non-sensical value.");
      painCave.isFatal = 1;
      simError();
    } else {
      RealType vF = args_info.vacancyPercent_arg / 100.0;
      //  cerr << "vacancyPercent = " << vF << "\n";
      RealType vIR;
      RealType vOR;
      if (args_info.vacancyInnerRadius_given) {
        vIR = args_info.vacancyInnerRadius_arg;
      } else {
        vIR = 0.0;
      }
      if (args_info.vacancyOuterRadius_given) {
        vOR = args_info.vacancyOuterRadius_arg;
      } else {
        vOR = rodRadius;
      }
      if (vIR >= 0.0 && vOR <= rodRadius && vOR >= vIR) {
        
        for (std::size_t i = 0; i < sites.size(); i++) {
          myLoc = sites[i];
          myR = myLoc.length();
          if (myR >= vIR && myR <= vOR) {
            vacancyTargets.push_back(i);
          }          
        }
        std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end());
        
	std::size_t nTargets = vacancyTargets.size();
        vacancyTargets.resize((int)(vF * nTargets));
        
                  
        sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n"
                "\tsites between %lf and %lf.", (int) vacancyTargets.size(), 
                vIR, vOR); 
        painCave.isFatal = 0;
        painCave.severity = OPENMD_INFO;
        simError();

        isVacancy.clear();
        for (std::size_t i = 0; i < sites.size(); i++) {
          bool vac = false;
          for (std::size_t j = 0; j < vacancyTargets.size(); j++) {
            if (i == vacancyTargets[j]) vac = true;
          }
          isVacancy.push_back(vac);
        }
               
      } else {
        sprintf(painCave.errMsg, "Something is strange about the vacancy\n"
                "\tinner or outer radii.  Check their values.");
        painCave.isFatal = 1;
        simError();
      }
    }
  }
  
  /* Get number of lattice sites */
  std::size_t nSites = sites.size() - vacancyTargets.size();
  
  // cerr << "sites.size() = " << sites.size() << "\n";
  // cerr << "nSites = " << nSites << "\n";
  // cerr << "vacancyTargets = " << vacancyTargets.size() << "\n";

  std::vector<Component*> components = simParams->getComponents();
  std::vector<RealType> molFractions;
  std::vector<RealType> shellRadii;
  std::vector<int> nMol;
  std::map<int, int> componentFromSite;
  nComponents = components.size();
  // cerr << "nComponents = " << nComponents << "\n";

  if (args_info.molFraction_given && args_info.shellRadius_given) {
    sprintf(painCave.errMsg, "Specify either molFraction or shellRadius "
            "arguments, but not both!");
    painCave.isFatal = 1;
    simError();
  }
  
  if (nComponents == 1) {
    molFractions.push_back(1.0);    
    shellRadii.push_back(rodRadius);
  } else if (args_info.molFraction_given) {
    if ((int)args_info.molFraction_given == nComponents) {
      for (int i = 0; i < nComponents; i++) {
        molFractions.push_back(args_info.molFraction_arg[i]);
      }
    } else if ((int)args_info.molFraction_given == nComponents-1) {
      RealType remainingFraction = 1.0;
      for (int i = 0; i < nComponents-1; i++) {
        molFractions.push_back(args_info.molFraction_arg[i]);
        remainingFraction -= molFractions[i];
      }
      molFractions.push_back(remainingFraction);
    } else {    
      sprintf(painCave.errMsg, "nanorodBuilder can't figure out molFractions "
              "for all of the components in the <MetaData> block.");
      painCave.isFatal = 1;
      simError();
    }
  } else if ((int)args_info.shellRadius_given) {
    if ((int)args_info.shellRadius_given == nComponents) {
      for (int i = 0; i < nComponents; i++) {
        shellRadii.push_back(args_info.shellRadius_arg[i]);
      }
    } else if ((int)args_info.shellRadius_given == nComponents-1) {
      for (int i = 0; i < nComponents-1; i++) {
        shellRadii.push_back(args_info.shellRadius_arg[i]);
      }
      shellRadii.push_back(rodRadius);
    } else {    
      sprintf(painCave.errMsg, "nanorodBuilder can't figure out the\n"
              "\tshell radii for all of the components in the <MetaData> block.");
      painCave.isFatal = 1;
      simError();
    }
  } else {
    sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n"
            "\tbut have not specified either molFraction or shellRadius arguments.");
    painCave.isFatal = 1;
    simError();
  }
  
  if (args_info.molFraction_given) {
    RealType totalFraction = 0.0;
    
    /* Do some simple sanity checking*/
    
    for (int i = 0; i < nComponents; i++) {
      if (molFractions.at(i) < 0.0) {
        sprintf(painCave.errMsg, "One of the requested molFractions was"
                " less than zero!");
        painCave.isFatal = 1;
        simError();
      }
      if (molFractions.at(i) > 1.0) {
        sprintf(painCave.errMsg, "One of the requested molFractions was"
                " greater than one!");
        painCave.isFatal = 1;
        simError();
      }
      totalFraction += molFractions.at(i);
    }
    if (abs(totalFraction - 1.0) > 1e-6) {
      sprintf(painCave.errMsg, 
	      "The sum of molFractions was not close enough to 1.0");
      painCave.isFatal = 1;
      simError();
    }
    
    int remaining = nSites;
    for (int i=0; i < nComponents-1; i++) {    
      nMol.push_back(int((RealType)nSites * molFractions.at(i)));
      remaining -= nMol.at(i);
    }
    nMol.push_back(remaining);
    
    // recompute actual mol fractions and perform final sanity check:
    
    std::size_t totalMolecules = 0;
    for (int i=0; i < nComponents; i++) {
      molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites;
      totalMolecules += nMol.at(i);
    }
    if (totalMolecules != nSites) {
      sprintf(painCave.errMsg, 
	      "Computed total number of molecules is not equal "
              "to the number of lattice sites!");
      painCave.isFatal = 1;
      simError();
    }
  } else {

    for (unsigned int i = 0; i < shellRadii.size(); i++) {
      if (shellRadii.at(i) > rodRadius + 1e-6 ) {
        sprintf(painCave.errMsg, 
		"One of the shellRadius values exceeds the rod Radius.");
        painCave.isFatal = 1;
        simError();
      } 
      if (shellRadii.at(i) <= 0.0 ) {
        sprintf(painCave.errMsg, 
		"One of the shellRadius values is smaller than zero!");
        painCave.isFatal = 1;
        simError();
      }
    }
  }

  vector<int> ids;           
  if ((int)args_info.molFraction_given){
    //  cerr << "molFraction given 2" << "\n";
    sprintf(painCave.errMsg, 
	    "Creating a randomized spherically-capped nanorod.");
    painCave.isFatal = 0;
    painCave.severity = OPENMD_INFO;
    simError();
    /* Random rod is the default case*/

    for (std::size_t i = 0; i < sites.size(); i++) 
      if (!isVacancy[i]) ids.push_back(i);
    
    std::random_shuffle(ids.begin(), ids.end());
    
  } else{ 
    sprintf(painCave.errMsg, "Creating an fcc nanorod.");
    painCave.isFatal = 0;
    painCave.severity = OPENMD_INFO;
    simError();

    // RealType smallestSoFar;
    int myComponent = -1;
    nMol.clear();
    nMol.resize(nComponents);

    // cerr << "shellRadii[0] " << shellRadii[0] << "\n";
    // cerr << "rodRadius " << rodRadius << "\n";

    for (unsigned int i = 0; i < sites.size(); i++) {
      myLoc = sites[i];
      myR = myLoc.length();
      // smallestSoFar = rodRadius;  
      // cerr << "vac = " << isVacancy[i]<< "\n";
    
      if (!isVacancy[i]) {


        // for (int j = 0; j < nComponents; j++) {
        //   if (myR <= shellRadii[j]) {
        //     if (shellRadii[j] <= smallestSoFar) {
        //       smallestSoFar = shellRadii[j];
        //       myComponent = j;
        //     }
        //   }
        // }
	myComponent = 0;
        componentFromSite[i] = myComponent;
        nMol[myComponent]++;
	//	cerr << "nMol for myComp(" << myComponent<<") = " << nMol[myComponent] << "\n";
      }
    }       
  }
  //     cerr << "nMol = " << nMol.at(0) << "\n";

  outputFileName = args_info.output_arg;
   
  //creat new .omd file on fly which corrects the number of molecule    

  createMdFile(inputFileName, outputFileName, nMol);
  
  delete oldInfo;
  
  SimCreator newCreator;
  SimInfo* NewInfo = newCreator.createSim(outputFileName, false);
    
  // Place molecules
  Molecule* mol;
  SimInfo::MoleculeIterator mi;
  mol = NewInfo->beginMolecule(mi);

  int l = 0;

  for (int i = 0; i < nComponents; i++){
    locator = new MoLocator(NewInfo->getMoleculeStamp(i), 
                            NewInfo->getForceField());
    
    //   cerr << "nMol = " << nMol.at(i) << "\n";
    if (!args_info.molFraction_given) {
      for (unsigned int n = 0; n < sites.size(); n++) {
        if (!isVacancy[n]) {
          if (componentFromSite[n] == i) {
            mol = NewInfo->getMoleculeByGlobalIndex(l);
            locator->placeMol(sites[n], orientations[n], mol);
            l++;
          }
        }
      }
    } else {
      for (int n = 0; n < nMol.at(i); n++) {
        mol = NewInfo->getMoleculeByGlobalIndex(l);
        locator->placeMol(sites[ids[l]], orientations[ids[l]], mol);
        l++;
      }
    }
  }
  
  //fill Hmat
  hmat(0, 0)=  10.0*rodRadius;
  hmat(0, 1) = 0.0;
  hmat(0, 2) = 0.0;
  
  hmat(1, 0) = 0.0;
  hmat(1, 1) = 10.0*rodRadius;
  hmat(1, 2) = 0.0;
  
  hmat(2, 0) = 0.0;
  hmat(2, 1) = 0.0;
  hmat(2, 2) = 5.0*rodLength + 2.0*rodRadius;
  
  //set Hmat
  NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat);
  
  
  //create dumpwriter and write out the coordinates
  writer = new DumpWriter(NewInfo, outputFileName);
  
  if (writer == NULL) {
    sprintf(painCave.errMsg, "Error in creating dumpwriter object ");
    painCave.isFatal = 1;
    simError();
  }
  
  writer->writeDump();

  // deleting the writer will put the closing at the end of the dump file

  delete writer;

  // cleanup a by calling sim error.....
  sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been "
          "generated.\n", outputFileName.c_str());
  painCave.isFatal = 0;
  painCave.severity = OPENMD_INFO;
  simError();
  return 0;
}
コード例 #2
0
ファイル: omd2omd.cpp プロジェクト: hsidky/OpenMD
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;
}