| 146 |
|
compList(stamps, simParams, moleculeStampPairs); |
| 147 |
|
|
| 148 |
|
//create SimInfo |
| 149 |
< |
SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); |
| 150 |
< |
|
| 149 |
> |
SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams); |
| 150 |
> |
|
| 151 |
|
//gather parameters (SimCreator only retrieves part of the parameters) |
| 152 |
|
gatherParameters(info, mdFileName); |
| 153 |
|
|
| 178 |
|
info->addExcludePairs(mol); |
| 179 |
|
} |
| 180 |
|
|
| 181 |
– |
|
| 182 |
– |
//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
| 183 |
– |
//eta, chi for NPT integrator) |
| 181 |
|
if (loadInitCoords) |
| 182 |
|
loadCoordinates(info); |
| 183 |
|
|
| 397 |
|
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
| 398 |
|
int i; |
| 399 |
|
char * id; |
| 403 |
– |
LinkedMolStamp* extractedStamp = NULL; |
| 400 |
|
MoleculeStamp * currentStamp; |
| 401 |
|
Component** the_components = simParams->getComponents(); |
| 402 |
|
int n_components = simParams->getNComponents(); |
| 417 |
|
} |
| 418 |
|
|
| 419 |
|
id = the_components[i]->getType(); |
| 420 |
< |
|
| 421 |
< |
extractedStamp = stamps->extractMolStamp(id); |
| 422 |
< |
if (extractedStamp == NULL) { |
| 420 |
> |
|
| 421 |
> |
currentStamp = stamps->getMolStamp(id); |
| 422 |
> |
if (currentStamp == NULL) { |
| 423 |
|
sprintf(painCave.errMsg, |
| 424 |
|
"SimCreator error: Component \"%s\" was not found in the " |
| 425 |
|
"list of declared molecules\n", id); |
| 428 |
|
simError(); |
| 429 |
|
} |
| 430 |
|
|
| 435 |
– |
currentStamp = extractedStamp->getStamp(); |
| 436 |
– |
|
| 437 |
– |
|
| 431 |
|
moleculeStampPairs.push_back( |
| 432 |
|
std::make_pair(currentStamp, the_components[i]->getNMol())); |
| 433 |
|
} //end for (i = 0; i < n_components; i++) |
