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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 1.2 2006-05-17 21:51:42 tim 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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RealType latticeConstant; |
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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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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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| 234 |
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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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> |
createMdFile(inputFileName, outMdFileName, nComponents, numMol); |
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//fill Hmat |
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hmat(0, 0)= nx * latticeConstant; |
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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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| 274 |
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> |
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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 |
| 265 |
> |
|
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SimCreator newCreator; |
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< |
SimInfo* NewInfo = newCreator.createSim(outMdFileName, false); |
| 267 |
> |
SimInfo* newInfo = newCreator.createSim(outMdFileName, false); |
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|
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/* create Molocators */ |
| 270 |
< |
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; |
| 276 |
< |
mol = NewInfo->beginMolecule(mi); |
| 276 |
> |
mol = newInfo->beginMolecule(mi); |
| 277 |
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int l = 0; |
| 278 |
< |
for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
| 278 |
> |
for (mol = newInfo->beginMolecule(mi); mol != NULL; mol = newInfo->nextMolecule(mi)) { |
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locator->placeMol(latticeSites[l], latticeOrt[l], mol); |
| 280 |
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l++; |
| 281 |
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} |
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| 296 |
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| 283 |
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//create dumpwriter and write out the coordinates |
| 284 |
< |
oldInfo->setFinalConfigFileName(outInitFileName); |
| 285 |
< |
writer = new DumpWriter(oldInfo); |
| 284 |
> |
newInfo->setFinalConfigFileName(outMdFileName); |
| 285 |
> |
writer = new DumpWriter(newInfo); |
| 286 |
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|
| 287 |
|
if (writer == NULL) { |
| 288 |
|
std::cerr << "error in creating DumpWriter" << std::endl; |
| 289 |
|
exit(1); |
| 290 |
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} |
| 291 |
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| 292 |
< |
writer->writeDump(); |
| 293 |
< |
std::cout << "new initial configuration file: " << outInitFileName |
| 294 |
< |
<< " is generated." << std::endl; |
| 309 |
< |
|
| 310 |
< |
//delete objects |
| 311 |
< |
|
| 312 |
< |
//delete oldInfo and oldSimSetup |
| 313 |
< |
if (oldInfo != NULL) |
| 314 |
< |
delete oldInfo; |
| 315 |
< |
|
| 316 |
< |
if (writer != NULL) |
| 317 |
< |
delete writer; |
| 318 |
< |
|
| 319 |
< |
delete simpleLat; |
| 320 |
< |
|
| 292 |
> |
writer->writeEor(); |
| 293 |
> |
std::cout << "new OOPSE MD file: " << outMdFileName |
| 294 |
> |
<< " has been generated." << std::endl; |
| 295 |
|
return 0; |
| 296 |
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} |
| 297 |
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|
