| 34 |
|
* |
| 35 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 37 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 37 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 38 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 39 |
> |
* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). * |
| 40 |
|
* |
| 40 |
– |
* |
| 41 |
|
* randomBuilder.cpp |
| 42 |
|
* |
| 43 |
|
* Created by Charles F. Vardeman II on 10 Apr 2006. |
| 44 |
|
* @author Charles F. Vardeman II |
| 45 |
< |
* @version $Id: randomBuilder.cpp,v 1.8 2009-11-25 20:01:58 gezelter Exp $ |
| 45 |
> |
* @version $Id$ |
| 46 |
|
* |
| 47 |
|
*/ |
| 48 |
|
|
| 77 |
|
|
| 78 |
|
int main(int argc, char *argv []) { |
| 79 |
|
|
| 80 |
– |
// register force fields |
| 81 |
– |
registerForceFields(); |
| 80 |
|
registerLattice(); |
| 81 |
|
|
| 82 |
|
gengetopt_args_info args_info; |
| 168 |
|
std::vector<RealType> molFractions; |
| 169 |
|
std::vector<RealType> molecularMasses; |
| 170 |
|
std::vector<int> nMol; |
| 171 |
< |
int nComponents = components.size(); |
| 172 |
< |
|
| 171 |
> |
std::size_t nComponents = components.size(); |
| 172 |
> |
|
| 173 |
|
if (nComponents == 1) { |
| 174 |
|
molFractions.push_back(1.0); |
| 175 |
|
} else { |
| 176 |
|
if (args_info.molFraction_given == nComponents) { |
| 177 |
< |
for (int i = 0; i < nComponents; i++) { |
| 177 |
> |
for (std::size_t i = 0; i < nComponents; i++) { |
| 178 |
|
molFractions.push_back(args_info.molFraction_arg[i]); |
| 179 |
|
} |
| 180 |
|
} else if (args_info.molFraction_given == nComponents-1) { |
| 181 |
|
RealType remainingFraction = 1.0; |
| 182 |
< |
for (int i = 0; i < nComponents-1; i++) { |
| 182 |
> |
for (std::size_t i = 0; i < nComponents-1; i++) { |
| 183 |
|
molFractions.push_back(args_info.molFraction_arg[i]); |
| 184 |
|
remainingFraction -= molFractions[i]; |
| 185 |
|
} |
| 196 |
|
|
| 197 |
|
RealType totalFraction = 0.0; |
| 198 |
|
|
| 199 |
< |
for (int i = 0; i < nComponents; i++) { |
| 199 |
> |
for (std::size_t i = 0; i < nComponents; i++) { |
| 200 |
|
if (molFractions.at(i) < 0.0) { |
| 201 |
|
sprintf(painCave.errMsg, "One of the requested molFractions was" |
| 202 |
|
" less than zero!"); |
| 218 |
|
} |
| 219 |
|
|
| 220 |
|
int remaining = nSites; |
| 221 |
< |
for (int i=0; i < nComponents-1; i++) { |
| 221 |
> |
for (std::size_t i=0; i < nComponents-1; i++) { |
| 222 |
|
nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
| 223 |
|
remaining -= nMol.at(i); |
| 224 |
|
} |
| 228 |
|
|
| 229 |
|
int totalMolecules = 0; |
| 230 |
|
RealType totalMass = 0.0; |
| 231 |
< |
for (int i=0; i < nComponents; i++) { |
| 231 |
> |
for (std::size_t i=0; i < nComponents; i++) { |
| 232 |
|
molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
| 233 |
|
totalMolecules += nMol.at(i); |
| 234 |
< |
molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i), |
| 235 |
< |
oldInfo->getForceField())); |
| 234 |
> |
molecularMasses.push_back(MoLocator::getMolMass(oldInfo->getMoleculeStamp(i), |
| 235 |
> |
oldInfo->getForceField())); |
| 236 |
|
totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i); |
| 237 |
|
} |
| 238 |
|
RealType avgMass = totalMass / (RealType) totalMolecules; |
| 283 |
|
|
| 284 |
|
createMdFile(inputFileName, outputFileName, nMol); |
| 285 |
|
|
| 286 |
< |
if (oldInfo != NULL) |
| 289 |
< |
delete oldInfo; |
| 286 |
> |
delete oldInfo; |
| 287 |
|
|
| 288 |
|
// We need to read in the new SimInfo object, then Parse the |
| 289 |
|
// md file and set up the system |
| 314 |
|
// Randomize a vector of ints: |
| 315 |
|
|
| 316 |
|
vector<int> ids; |
| 317 |
< |
for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
| 317 |
> |
for (std::size_t i = 0; i < sites.size(); i++) ids.push_back(i); |
| 318 |
|
std::random_shuffle(ids.begin(), ids.end()); |
| 319 |
|
|
| 320 |
|
Molecule* mol; |
| 321 |
|
int l = 0; |
| 322 |
< |
for (int i = 0; i < nComponents; i++){ |
| 322 |
> |
for (std::size_t i = 0; i < nComponents; i++){ |
| 323 |
|
locator = new MoLocator(newInfo->getMoleculeStamp(i), |
| 324 |
|
newInfo->getForceField()); |
| 325 |
|
for (int n = 0; n < nMol.at(i); n++) { |
| 348 |
|
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 349 |
|
"generated.\n", outputFileName.c_str()); |
| 350 |
|
painCave.isFatal = 0; |
| 351 |
+ |
painCave.severity = OPENMD_INFO; |
| 352 |
|
simError(); |
| 353 |
|
return 0; |
| 354 |
|
} |
| 368 |
|
|
| 369 |
|
oldMdFile.getline(buffer, MAXLEN); |
| 370 |
|
|
| 371 |
< |
int i = 0; |
| 371 |
> |
std::size_t i = 0; |
| 372 |
|
while (!oldMdFile.eof()) { |
| 373 |
|
|
| 374 |
|
//correct molecule number |
| 375 |
|
if (strstr(buffer, "nMol") != NULL) { |
| 376 |
< |
if(i<nMol.size()){ |
| 376 |
> |
if (i<nMol.size()){ |
| 377 |
|
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
| 378 |
|
newMdFile << buffer << std::endl; |
| 379 |
|
i++; |
