| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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/** |
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* @file MoleculeCreator.cpp |
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* @author tlin |
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* @date 11/04/2004 |
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– |
* @time 13:44am |
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* @version 1.0 |
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*/ |
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|
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#include "brains/MoleculeCreator.hpp" |
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#include "primitives/GhostBend.hpp" |
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#include "primitives/GhostTorsion.hpp" |
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#include "types/DirectionalAtomType.hpp" |
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> |
#include "types/AtomType.hpp" |
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#include "types/FixedBondType.hpp" |
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#include "utils/simError.h" |
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#include "utils/StringUtils.hpp" |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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Molecule* MoleculeCreator::createMolecule(ForceField* ff, |
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MoleculeStamp *molStamp, |
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int stampId, int globalIndex, |
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LocalIndexManager* localIndexMan) { |
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< |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName()); |
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< |
|
| 68 |
> |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName(), |
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> |
molStamp->getRegion() ); |
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> |
|
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//create atoms |
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Atom* atom; |
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AtomStamp* currentAtomStamp; |
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int nCutoffGroups = molStamp->getNCutoffGroups(); |
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for (int i = 0; i < nCutoffGroups; ++i) { |
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currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i); |
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< |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp); |
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> |
cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan); |
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mol->addCutoffGroup(cutoffGroup); |
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} |
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|
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// every single free atom |
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|
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for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
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< |
cutoffGroup = createCutoffGroup(mol, *fai); |
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> |
cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan); |
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mol->addCutoffGroup(cutoffGroup); |
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} |
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//create constraints |
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createConstraintPair(mol); |
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createConstraintElem(mol); |
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|
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+ |
// Does this molecule stamp define a total constrained charge value? |
| 181 |
+ |
// If so, let the created molecule know about it. |
| 182 |
+ |
|
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+ |
if (molStamp->haveConstrainTotalCharge() ) { |
| 184 |
+ |
mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() ); |
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+ |
} |
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+ |
|
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//the construction of this molecule is finished |
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mol->complete(); |
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|
| 206 |
|
painCave.isFatal = 1; |
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|
simError(); |
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|
} |
| 209 |
< |
|
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> |
|
| 210 |
|
//below code still have some kind of hard-coding smell |
| 211 |
|
if (atomType->isDirectional()){ |
| 204 |
– |
|
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– |
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 |
|
} |
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else{ |
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//The third part is the index of the rigidbody defined in meta-data file |
| 257 |
|
//For example, Butane_RB_0 is a valid rigid body name of butane molecule |
| 258 |
|
/**@todo replace itoa by lexi_cast */ |
| 259 |
< |
std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10); |
| 259 |
> |
std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10); |
| 260 |
|
rb->setType(mol->getType() + "_RB_" + s.c_str()); |
| 261 |
|
|
| 262 |
|
return rb; |
| 364 |
|
atomB->getType(), |
| 365 |
|
atomC->getType(), |
| 366 |
|
atomD->getType()); |
| 368 |
– |
|
| 367 |
|
if (torsionType == NULL) { |
| 368 |
|
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 369 |
|
atomA->getType().c_str(), |
| 437 |
|
atomD->getType().c_str()); |
| 438 |
|
|
| 439 |
|
painCave.isFatal = 0; |
| 440 |
< |
painCave.severity = OOPSE_INFO; |
| 440 |
> |
painCave.severity = OPENMD_INFO; |
| 441 |
|
simError(); |
| 442 |
|
return NULL; |
| 443 |
|
} 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 |
|
|
