| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 44 |
|
* @file MoleculeCreator.cpp |
| 45 |
|
* @author tlin |
| 46 |
|
* @date 11/04/2004 |
| 46 |
– |
* @time 13:44am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 54 |
|
#include "brains/MoleculeCreator.hpp" |
| 55 |
|
#include "primitives/GhostBend.hpp" |
| 56 |
|
#include "primitives/GhostTorsion.hpp" |
| 57 |
< |
#include "types/DirectionalAtomType.hpp" |
| 57 |
> |
#include "types/AtomType.hpp" |
| 58 |
|
#include "types/FixedBondType.hpp" |
| 59 |
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#include "utils/simError.h" |
| 60 |
|
#include "utils/StringUtils.hpp" |
| 65 |
|
MoleculeStamp *molStamp, |
| 66 |
|
int stampId, int globalIndex, |
| 67 |
|
LocalIndexManager* localIndexMan) { |
| 68 |
< |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName()); |
| 69 |
< |
|
| 68 |
> |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName(), |
| 69 |
> |
molStamp->getRegion() ); |
| 70 |
> |
|
| 71 |
|
//create atoms |
| 72 |
|
Atom* atom; |
| 73 |
|
AtomStamp* currentAtomStamp; |
| 139 |
|
int nCutoffGroups = molStamp->getNCutoffGroups(); |
| 140 |
|
for (int i = 0; i < nCutoffGroups; ++i) { |
| 141 |
|
currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i); |
| 142 |
< |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp); |
| 142 |
> |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan); |
| 143 |
|
mol->addCutoffGroup(cutoffGroup); |
| 144 |
|
} |
| 145 |
|
|
| 170 |
|
// every single free atom |
| 171 |
|
|
| 172 |
|
for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
| 173 |
< |
cutoffGroup = createCutoffGroup(mol, *fai); |
| 173 |
> |
cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan); |
| 174 |
|
mol->addCutoffGroup(cutoffGroup); |
| 175 |
|
} |
| 176 |
|
//create constraints |
| 177 |
|
createConstraintPair(mol); |
| 178 |
|
createConstraintElem(mol); |
| 179 |
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|
| 180 |
+ |
// Does this molecule stamp define a total constrained charge value? |
| 181 |
+ |
// If so, let the created molecule know about it. |
| 182 |
+ |
|
| 183 |
+ |
if (molStamp->haveConstrainTotalCharge() ) { |
| 184 |
+ |
mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() ); |
| 185 |
+ |
} |
| 186 |
+ |
|
| 187 |
|
//the construction of this molecule is finished |
| 188 |
|
mol->complete(); |
| 189 |
|
|
| 206 |
|
painCave.isFatal = 1; |
| 207 |
|
simError(); |
| 208 |
|
} |
| 209 |
< |
|
| 209 |
> |
|
| 210 |
|
//below code still have some kind of hard-coding smell |
| 211 |
|
if (atomType->isDirectional()){ |
| 204 |
– |
|
| 205 |
– |
DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 206 |
– |
|
| 207 |
– |
if (dAtomType == NULL) { |
| 208 |
– |
sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType"); |
| 212 |
|
|
| 210 |
– |
painCave.isFatal = 1; |
| 211 |
– |
simError(); |
| 212 |
– |
} |
| 213 |
– |
|
| 213 |
|
DirectionalAtom* dAtom; |
| 214 |
< |
dAtom = new DirectionalAtom(dAtomType); |
| 214 |
> |
dAtom = new DirectionalAtom(atomType); |
| 215 |
|
atom = dAtom; |
| 216 |
|
} |
| 217 |
|
else{ |
| 448 |
|
} |
| 449 |
|
|
| 450 |
|
|
| 451 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
| 451 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, |
| 452 |
> |
CutoffGroupStamp* stamp, |
| 453 |
> |
LocalIndexManager* localIndexMan) { |
| 454 |
|
int nAtoms; |
| 455 |
|
CutoffGroup* cg; |
| 456 |
|
Atom* atom; |
| 462 |
|
assert(atom); |
| 463 |
|
cg->addAtom(atom); |
| 464 |
|
} |
| 465 |
< |
|
| 465 |
> |
|
| 466 |
> |
//set the local index of this cutoffGroup, global index will be set later |
| 467 |
> |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 468 |
> |
|
| 469 |
|
return cg; |
| 470 |
|
} |
| 471 |
< |
|
| 472 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
| 471 |
> |
|
| 472 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom, |
| 473 |
> |
LocalIndexManager* localIndexMan) { |
| 474 |
|
CutoffGroup* cg; |
| 475 |
|
cg = new CutoffGroup(); |
| 476 |
|
cg->addAtom(atom); |
| 477 |
+ |
|
| 478 |
+ |
//set the local index of this cutoffGroup, global index will be set later |
| 479 |
+ |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 480 |
+ |
|
| 481 |
|
return cg; |
| 482 |
|
} |
| 483 |
|
|
