| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* 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 |
|
* distribution. |
| 28 |
|
* 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 |
|
* 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, 24107 (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 |
|
/** |
| 60 |
|
#include "utils/simError.h" |
| 61 |
|
#include "utils/StringUtils.hpp" |
| 62 |
|
|
| 63 |
< |
namespace oopse { |
| 63 |
> |
namespace OpenMD { |
| 64 |
|
|
| 65 |
|
Molecule* MoleculeCreator::createMolecule(ForceField* ff, |
| 66 |
|
MoleculeStamp *molStamp, |
| 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 |
| 258 |
|
//The third part is the index of the rigidbody defined in meta-data file |
| 259 |
|
//For example, Butane_RB_0 is a valid rigid body name of butane molecule |
| 260 |
|
/**@todo replace itoa by lexi_cast */ |
| 261 |
< |
std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10); |
| 261 |
> |
std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10); |
| 262 |
|
rb->setType(mol->getType() + "_RB_" + s.c_str()); |
| 263 |
|
|
| 264 |
|
return rb; |
| 439 |
|
atomD->getType().c_str()); |
| 440 |
|
|
| 441 |
|
painCave.isFatal = 0; |
| 442 |
< |
painCave.severity = OOPSE_INFO; |
| 442 |
> |
painCave.severity = OPENMD_INFO; |
| 443 |
|
simError(); |
| 444 |
|
return NULL; |
| 445 |
|
} else { |
| 450 |
|
} |
| 451 |
|
|
| 452 |
|
|
| 453 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
| 453 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, |
| 454 |
> |
CutoffGroupStamp* stamp, |
| 455 |
> |
LocalIndexManager* localIndexMan) { |
| 456 |
|
int nAtoms; |
| 457 |
|
CutoffGroup* cg; |
| 458 |
|
Atom* atom; |
| 464 |
|
assert(atom); |
| 465 |
|
cg->addAtom(atom); |
| 466 |
|
} |
| 467 |
< |
|
| 467 |
> |
|
| 468 |
> |
//set the local index of this cutoffGroup, global index will be set later |
| 469 |
> |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 470 |
> |
|
| 471 |
|
return cg; |
| 472 |
|
} |
| 473 |
< |
|
| 474 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
| 473 |
> |
|
| 474 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom, |
| 475 |
> |
LocalIndexManager* localIndexMan) { |
| 476 |
|
CutoffGroup* cg; |
| 477 |
|
cg = new CutoffGroup(); |
| 478 |
|
cg->addAtom(atom); |
| 479 |
+ |
|
| 480 |
+ |
//set the local index of this cutoffGroup, global index will be set later |
| 481 |
+ |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 482 |
+ |
|
| 483 |
|
return cg; |
| 484 |
|
} |
| 485 |
|
|
