| 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). |
| 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 |
|
/** |
| 55 |
|
#include "brains/MoleculeCreator.hpp" |
| 56 |
|
#include "primitives/GhostBend.hpp" |
| 57 |
|
#include "primitives/GhostTorsion.hpp" |
| 58 |
< |
#include "types/DirectionalAtomType.hpp" |
| 58 |
> |
#include "types/AtomType.hpp" |
| 59 |
|
#include "types/FixedBondType.hpp" |
| 60 |
|
#include "utils/simError.h" |
| 61 |
|
#include "utils/StringUtils.hpp" |
| 67 |
|
int stampId, int globalIndex, |
| 68 |
|
LocalIndexManager* localIndexMan) { |
| 69 |
|
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName()); |
| 70 |
< |
|
| 70 |
> |
|
| 71 |
|
//create atoms |
| 72 |
|
Atom* atom; |
| 73 |
|
AtomStamp* currentAtomStamp; |
| 177 |
|
createConstraintPair(mol); |
| 178 |
|
createConstraintElem(mol); |
| 179 |
|
|
| 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 |
|
|
| 213 |
< |
painCave.isFatal = 1; |
| 214 |
< |
simError(); |
| 212 |
< |
} |
| 213 |
< |
|
| 214 |
< |
DirectionalAtom* dAtom; |
| 215 |
< |
dAtom = new DirectionalAtom(dAtomType); |
| 213 |
> |
DirectionalAtom* dAtom; |
| 214 |
> |
dAtom = new DirectionalAtom(atomType); |
| 215 |
|
atom = dAtom; |
| 216 |
|
} |
| 217 |
|
else{ |
