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* |
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* Created by Charles F. Vardeman II on 10 Apr 2006. |
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* @author Charles F. Vardeman II |
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* @version $Id: randomBuilder.cpp,v 1.1 2006-04-25 22:59:27 chuckv Exp $ |
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* @version $Id: randomBuilder.cpp,v 1.3 2006-10-09 22:16:44 gezelter Exp $ |
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* |
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*/ |
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std::string inputFileName; |
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std::string outPrefix; |
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std::string outMdFileName; |
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std::string outInitFileName; |
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Lattice *simpleLat; |
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int* numMol; |
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double latticeConstant; |
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std::vector<double> lc; |
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double mass; |
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const double rhoConvertConst = 1.661; |
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double density; |
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RealType latticeConstant; |
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std::vector<RealType> lc; |
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RealType mass; |
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const RealType rhoConvertConst = 1.661; |
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RealType density; |
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int nx, |
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ny, |
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nz; |
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Globals* simParams = oldInfo->getSimParams(); |
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int nComponents =simParams->getNComponents(); |
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if (oldInfo->getNMoleculeStamp()>= 2) { |
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if (oldInfo->getNMoleculeStamp() > 2) { |
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std::cerr << "can not build the system with more than two components" |
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<< std::endl; |
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exit(1); |
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//calculate lattice constant (in Angstrom) |
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latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
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1.0 / 3.0); |
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(RealType)(1.0 / 3.0)); |
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//set lattice constant |
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lc.push_back(latticeConstant); |
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} |
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int totComponents = 0; |
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for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */ |
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numMol[i] = int((double)numSites * args_info.molFraction_arg[i]); |
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numMol[i] = int((RealType)numSites * args_info.molFraction_arg[i]); |
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std::cout<<numMol[i]<<std::endl; |
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totComponents += numMol[i]; |
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} |
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outMdFileName = outPrefix + ".md"; |
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//creat new .md file on fly which corrects the number of molecule |
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createMdFile(inputFileName, outMdFileName, nComponents,numMol); |
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createMdFile(inputFileName, outMdFileName, nComponents, numMol); |
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//determine the output file names |
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if (args_info.output_given){ |
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outInitFileName = args_info.output_arg; |
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}else{ |
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outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
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} |
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//fill Hmat |
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hmat(0, 0)= nx * latticeConstant; |
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hmat(0, 1) = 0.0; |
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/* Randomize position vector */ |
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std::random_shuffle(latticeSites.begin(), latticeSites.end()); |
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if (oldInfo != NULL) |
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delete oldInfo; |
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// We need to read in new siminfo object. |
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//parse md file and set up the system |
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//SimCreator NewCreator; |
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// parse md file and set up the system |
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SimCreator newCreator; |
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SimInfo* NewInfo = newCreator.createSim(outMdFileName, false); |
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> |
SimInfo* newInfo = newCreator.createSim(outMdFileName, false); |
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/* create Molocators */ |
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locator = new MoLocator(NewInfo->getMoleculeStamp(0), NewInfo->getForceField()); |
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locator = new MoLocator(newInfo->getMoleculeStamp(0), newInfo->getForceField()); |
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Molecule* mol; |
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SimInfo::MoleculeIterator mi; |
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mol = NewInfo->beginMolecule(mi); |
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> |
mol = newInfo->beginMolecule(mi); |
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int l = 0; |
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< |
for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
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> |
for (mol = newInfo->beginMolecule(mi); mol != NULL; mol = newInfo->nextMolecule(mi)) { |
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locator->placeMol(latticeSites[l], latticeOrt[l], mol); |
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l++; |
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} |
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//create dumpwriter and write out the coordinates |
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< |
oldInfo->setFinalConfigFileName(outInitFileName); |
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< |
writer = new DumpWriter(oldInfo); |
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> |
newInfo->setFinalConfigFileName(outMdFileName); |
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> |
writer = new DumpWriter(newInfo); |
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|
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if (writer == NULL) { |
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std::cerr << "error in creating DumpWriter" << std::endl; |
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exit(1); |
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} |
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< |
writer->writeDump(); |
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< |
std::cout << "new initial configuration file: " << outInitFileName |
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< |
<< " is generated." << std::endl; |
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< |
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< |
//delete objects |
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< |
|
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< |
//delete oldInfo and oldSimSetup |
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< |
if (oldInfo != NULL) |
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< |
delete oldInfo; |
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< |
|
| 316 |
< |
if (writer != NULL) |
| 317 |
< |
delete writer; |
| 318 |
< |
|
| 319 |
< |
delete simpleLat; |
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< |
|
| 292 |
> |
writer->writeEor(); |
| 293 |
> |
std::cout << "new OOPSE MD file: " << outMdFileName |
| 294 |
> |
<< " has been generated." << std::endl; |
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return 0; |
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} |
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