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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 1.4 2006-10-10 02:44:13 gezelter Exp $ |
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* |
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*/ |
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void createMdFile(const std::string&oldMdFileName, |
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const std::string&newMdFileName, |
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< |
int components,int* numMol); |
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> |
int components, int* numMol); |
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int main(int argc, char *argv []) { |
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//register force fields |
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// register force fields |
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registerForceFields(); |
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registerLattice(); |
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gengetopt_args_info args_info; |
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std::string latticeType; |
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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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std::string outputFileName; |
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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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int nx, |
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ny, |
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nz; |
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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, ny, nz; |
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Mat3x3d hmat; |
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MoLocator *locator; |
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std::vector<Vector3d> latticePos; |
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simError(); |
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} |
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//get the number of unit cell |
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//get the number of unit cells in each direction: |
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nx = args_info.nx_arg; |
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if (nx <= 0) { |
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std::cerr << "The number of unit cell in h direction must be greater than 0" << std::endl; |
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exit(1); |
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sprintf(painCave.errMsg, "The number of unit cells in the x direction " |
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"must be greater than 0."); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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ny = args_info.ny_arg; |
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if (ny <= 0) { |
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std::cerr << "The number of unit cell in l direction must be greater than 0" << std::endl; |
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exit(1); |
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sprintf(painCave.errMsg, "The number of unit cells in the y direction " |
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"must be greater than 0."); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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nz = args_info.nz_arg; |
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if (nz <= 0) { |
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std::cerr << "The number of unit cell in k direction must be greater than 0" << std::endl; |
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exit(1); |
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sprintf(painCave.errMsg, "The number of unit cells in the z direction " |
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"must be greater than 0."); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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//get input file name |
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if (args_info.inputs_num) |
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inputFileName = args_info.inputs[0]; |
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else { |
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std::cerr << "You must specify a input file name.\n" << std::endl; |
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cmdline_parser_print_help(); |
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exit(1); |
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sprintf(painCave.errMsg, "No input .md file name was specified " |
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"on the command line"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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//parse md file and set up the system |
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SimCreator oldCreator; |
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SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
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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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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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if (oldInfo->getNMoleculeStamp() > 2) { |
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sprintf(painCave.errMsg, "randomBuilder can't yet build a system with " |
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"more than two components."); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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//get mass of molecule. |
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mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
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//creat lattice |
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// Create the lattice |
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|
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
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if (simpleLat == NULL) { |
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std::cerr << "Error in creating lattice" << std::endl; |
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exit(1); |
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sprintf(painCave.errMsg, "Error in creating lattice."); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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numMolPerCell = simpleLat->getNumSitesPerCell(); |
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//calculate lattice constant (in Angstrom) |
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// Calculate lattice constant (in Angstroms) |
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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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// Set the lattice constant |
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lc.push_back(latticeConstant); |
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simpleLat->setLatticeConstant(lc); |
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//calculate the total number of molecules |
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// Calculate the total number of molecules |
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int totMol = nx * ny * nz * numMolPerCell; |
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// Calculate the lattice sites and fill lattice vector. |
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vector<Vector3d> latticeSites; |
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// Calculate the lattice sites and fill the lattice vector. |
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|
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// Get the standard orientations of the cell sites |
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> |
latticeOrt = simpleLat->getLatticePointsOrt(); |
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> |
vector<Vector3d> sites; |
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> |
vector<Vector3d> orientations; |
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for(int i = 0; i < nx; i++) { |
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for(int j = 0; j < ny; j++) { |
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for(int k = 0; k < nz; k++) { |
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< |
//get the position of the cell sites |
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> |
// Get the position of the cell sites |
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> |
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simpleLat->getLatticePointsPos(latticePos, i, j, k); |
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for(int l = 0; l < numMolPerCell; l++) { |
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< |
latticeSites.push_back(latticePos[l]); |
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> |
sites.push_back(latticePos[l]); |
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> |
orientations.push_back(latticeOrt[l]); |
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} |
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} |
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} |
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} |
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< |
int numSites = latticeSites.size(); |
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> |
int numSites = sites.size(); |
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numMol = new int[nComponents]; |
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if (nComponents != args_info.molFraction_given && nComponents != 1){ |
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< |
std::cerr << "Number of components does not equal molFraction occurances." << std::endl; |
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< |
exit(1); |
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> |
sprintf(painCave.errMsg, "There needs to be the same number of " |
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> |
"molFraction arguments as there are components in the " |
| 236 |
> |
"<MetaData> block."); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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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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> |
for (int i = 0;i<nComponents-1;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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numMol[nComponents-1] = numSites - totComponents; |
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|
| 248 |
+ |
outputFileName = args_info.output_arg; |
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< |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
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< |
outMdFileName = outPrefix + ".md"; |
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> |
// create a new .md file on the fly which corrects the number of molecules |
| 251 |
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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); |
| 252 |
> |
createMdFile(inputFileName, outputFileName, nComponents, numMol); |
| 253 |
> |
|
| 254 |
> |
if (oldInfo != NULL) |
| 255 |
> |
delete oldInfo; |
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> |
|
| 257 |
> |
// We need to read in the new SimInfo object, then Parse the |
| 258 |
> |
// md file and set up the system |
| 259 |
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|
| 260 |
+ |
SimCreator newCreator; |
| 261 |
+ |
SimInfo* newInfo = newCreator.createSim(outputFileName, false); |
| 262 |
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| 263 |
+ |
// fill Hmat |
| 264 |
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|
| 265 |
< |
//determine the output file names |
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< |
if (args_info.output_given){ |
| 237 |
< |
outInitFileName = args_info.output_arg; |
| 238 |
< |
}else{ |
| 239 |
< |
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
| 240 |
< |
} |
| 241 |
< |
|
| 242 |
< |
//fill Hmat |
| 243 |
< |
hmat(0, 0)= nx * latticeConstant; |
| 265 |
> |
hmat(0, 0) = nx * latticeConstant; |
| 266 |
|
hmat(0, 1) = 0.0; |
| 267 |
|
hmat(0, 2) = 0.0; |
| 268 |
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| 274 |
|
hmat(2, 1) = 0.0; |
| 275 |
|
hmat(2, 2) = nz * latticeConstant; |
| 276 |
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|
| 277 |
< |
//set Hmat |
| 256 |
< |
oldInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 277 |
> |
// Set Hmat |
| 278 |
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|
| 279 |
< |
//place the molecules |
| 279 |
> |
newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 280 |
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|
| 281 |
+ |
// place the molecules |
| 282 |
+ |
|
| 283 |
|
curMolIndex = 0; |
| 284 |
|
|
| 285 |
< |
//get the orientation of the cell sites |
| 263 |
< |
//for the same type of molecule in same lattice, it will not change |
| 264 |
< |
latticeOrt = simpleLat->getLatticePointsOrt(); |
| 285 |
> |
// Randomize a vector of ints: |
| 286 |
|
|
| 287 |
< |
|
| 288 |
< |
/* Randomize position vector */ |
| 289 |
< |
std::random_shuffle(latticeSites.begin(), latticeSites.end()); |
| 287 |
> |
vector<int> ids; |
| 288 |
> |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
| 289 |
> |
std::random_shuffle(ids.begin(), ids.end()); |
| 290 |
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|
| 270 |
– |
|
| 271 |
– |
if (oldInfo != NULL) |
| 272 |
– |
delete oldInfo; |
| 273 |
– |
|
| 274 |
– |
|
| 275 |
– |
// We need to read in new siminfo object. |
| 276 |
– |
//parse md file and set up the system |
| 277 |
– |
//SimCreator NewCreator; |
| 278 |
– |
SimCreator newCreator; |
| 279 |
– |
SimInfo* NewInfo = newCreator.createSim(outMdFileName, false); |
| 280 |
– |
|
| 281 |
– |
/* create Molocators */ |
| 282 |
– |
locator = new MoLocator(NewInfo->getMoleculeStamp(0), NewInfo->getForceField()); |
| 283 |
– |
|
| 284 |
– |
|
| 285 |
– |
|
| 291 |
|
Molecule* mol; |
| 287 |
– |
SimInfo::MoleculeIterator mi; |
| 288 |
– |
mol = NewInfo->beginMolecule(mi); |
| 292 |
|
int l = 0; |
| 293 |
< |
for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
| 294 |
< |
locator->placeMol(latticeSites[l], latticeOrt[l], mol); |
| 295 |
< |
l++; |
| 293 |
> |
for (int i = 0; i < nComponents; i++){ |
| 294 |
> |
locator = new MoLocator(newInfo->getMoleculeStamp(i), |
| 295 |
> |
newInfo->getForceField()); |
| 296 |
> |
for (int n = 0; n < numMol[i]; n++) { |
| 297 |
> |
mol = newInfo->getMoleculeByGlobalIndex(l); |
| 298 |
> |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
| 299 |
> |
l++; |
| 300 |
> |
} |
| 301 |
|
} |
| 302 |
+ |
|
| 303 |
+ |
// Create DumpWriter and write out the coordinates |
| 304 |
|
|
| 305 |
+ |
writer = new DumpWriter(newInfo, outputFileName); |
| 306 |
|
|
| 296 |
– |
|
| 297 |
– |
//create dumpwriter and write out the coordinates |
| 298 |
– |
oldInfo->setFinalConfigFileName(outInitFileName); |
| 299 |
– |
writer = new DumpWriter(oldInfo); |
| 300 |
– |
|
| 307 |
|
if (writer == NULL) { |
| 308 |
< |
std::cerr << "error in creating DumpWriter" << std::endl; |
| 309 |
< |
exit(1); |
| 308 |
> |
sprintf(painCave.errMsg, "error in creating DumpWriter"); |
| 309 |
> |
painCave.isFatal = 1; |
| 310 |
> |
simError(); |
| 311 |
|
} |
| 312 |
|
|
| 313 |
|
writer->writeDump(); |
| 307 |
– |
std::cout << "new initial configuration file: " << outInitFileName |
| 308 |
– |
<< " is generated." << std::endl; |
| 314 |
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|
| 315 |
< |
//delete objects |
| 315 |
> |
// deleting the writer will put the closing at the end of the dump file. |
| 316 |
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|
| 317 |
< |
//delete oldInfo and oldSimSetup |
| 313 |
< |
if (oldInfo != NULL) |
| 314 |
< |
delete oldInfo; |
| 317 |
> |
delete writer; |
| 318 |
|
|
| 319 |
< |
if (writer != NULL) |
| 320 |
< |
delete writer; |
| 321 |
< |
|
| 322 |
< |
delete simpleLat; |
| 320 |
< |
|
| 319 |
> |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 320 |
> |
"generated.", outputFileName.c_str()); |
| 321 |
> |
painCave.isFatal = 0; |
| 322 |
> |
simError(); |
| 323 |
|
return 0; |
| 324 |
|
} |
| 325 |
|
|
| 326 |
< |
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
| 327 |
< |
int components,int* numMol) { |
| 326 |
> |
void createMdFile(const std::string&oldMdFileName, |
| 327 |
> |
const std::string&newMdFileName, |
| 328 |
> |
int components, int* numMol) { |
| 329 |
|
ifstream oldMdFile; |
| 330 |
|
ofstream newMdFile; |
| 331 |
|
const int MAXLEN = 65535; |
| 332 |
|
char buffer[MAXLEN]; |
| 333 |
|
|
| 334 |
|
//create new .md file based on old .md file |
| 335 |
+ |
|
| 336 |
|
oldMdFile.open(oldMdFileName.c_str()); |
| 337 |
|
newMdFile.open(newMdFileName.c_str()); |
| 338 |
|
|
| 344 |
|
//correct molecule number |
| 345 |
|
if (strstr(buffer, "nMol") != NULL) { |
| 346 |
|
if(i<components){ |
| 347 |
< |
sprintf(buffer, "\tnMol = %i;", numMol[i]); |
| 347 |
> |
sprintf(buffer, "\tnMol = %i;", numMol[i]); |
| 348 |
|
newMdFile << buffer << std::endl; |
| 349 |
|
i++; |
| 350 |
|
} |
