96 |
|
|
97 |
|
} |
98 |
|
|
99 |
< |
SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { |
99 |
> |
SimInfo* SimCreator::createSim(const std::string & mdFileName, |
100 |
> |
bool loadInitCoords) { |
101 |
|
|
102 |
|
MakeStamps * stamps = new MakeStamps(); |
103 |
|
|
107 |
|
parseFile(mdFileName, stamps, simParams); |
108 |
|
|
109 |
|
//create the force field |
110 |
< |
ForceField * ff = ForceFieldFactory::getInstance()->createForceField( |
111 |
< |
simParams->getForceField()); |
110 |
> |
ForceField * ff = ForceFieldFactory::getInstance() |
111 |
> |
->createForceField(simParams->getForceField()); |
112 |
|
|
113 |
|
if (ff == NULL) { |
114 |
< |
sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", |
114 |
> |
sprintf(painCave.errMsg, |
115 |
> |
"ForceField Factory can not create %s force field\n", |
116 |
|
simParams->getForceField()); |
117 |
|
painCave.isFatal = 1; |
118 |
|
simError(); |
148 |
|
compList(stamps, simParams, moleculeStampPairs); |
149 |
|
|
150 |
|
//create SimInfo |
151 |
< |
SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); |
152 |
< |
|
151 |
> |
SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams); |
152 |
> |
|
153 |
|
//gather parameters (SimCreator only retrieves part of the parameters) |
154 |
|
gatherParameters(info, mdFileName); |
155 |
|
|
180 |
|
info->addExcludePairs(mol); |
181 |
|
} |
182 |
|
|
181 |
– |
|
182 |
– |
//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
183 |
– |
//eta, chi for NPT integrator) |
183 |
|
if (loadInitCoords) |
184 |
|
loadCoordinates(info); |
185 |
|
|
399 |
|
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
400 |
|
int i; |
401 |
|
char * id; |
403 |
– |
LinkedMolStamp* extractedStamp = NULL; |
402 |
|
MoleculeStamp * currentStamp; |
403 |
|
Component** the_components = simParams->getComponents(); |
404 |
|
int n_components = simParams->getNComponents(); |
419 |
|
} |
420 |
|
|
421 |
|
id = the_components[i]->getType(); |
422 |
< |
|
423 |
< |
extractedStamp = stamps->extractMolStamp(id); |
424 |
< |
if (extractedStamp == NULL) { |
422 |
> |
|
423 |
> |
currentStamp = stamps->getMolStamp(id); |
424 |
> |
if (currentStamp == NULL) { |
425 |
|
sprintf(painCave.errMsg, |
426 |
|
"SimCreator error: Component \"%s\" was not found in the " |
427 |
|
"list of declared molecules\n", id); |
430 |
|
simError(); |
431 |
|
} |
432 |
|
|
435 |
– |
currentStamp = extractedStamp->getStamp(); |
436 |
– |
|
437 |
– |
|
433 |
|
moleculeStampPairs.push_back( |
434 |
|
std::make_pair(currentStamp, the_components[i]->getNMol())); |
435 |
|
} //end for (i = 0; i < n_components; i++) |