| 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 |
|
/** |
| 52 |
|
#include "UseTheForce/ForceField.hpp" |
| 53 |
|
#include "utils/simError.h" |
| 54 |
|
#include "utils/Tuple.hpp" |
| 54 |
– |
#include "UseTheForce/DarkSide/atype_interface.h" |
| 55 |
– |
#include "UseTheForce/DarkSide/fForceOptions_interface.h" |
| 56 |
– |
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
| 55 |
|
namespace OpenMD { |
| 56 |
|
|
| 57 |
|
ForceField::ForceField() { |
| 67 |
|
} |
| 68 |
|
} |
| 69 |
|
|
| 70 |
< |
|
| 71 |
< |
ForceField::~ForceField() { |
| 72 |
< |
deleteAtypes(); |
| 73 |
< |
deleteSwitch(); |
| 74 |
< |
} |
| 75 |
< |
|
| 70 |
> |
/** |
| 71 |
> |
* getAtomType by string |
| 72 |
> |
* |
| 73 |
> |
* finds the requested atom type in this force field using the string |
| 74 |
> |
* name of the atom type. |
| 75 |
> |
*/ |
| 76 |
|
AtomType* ForceField::getAtomType(const std::string &at) { |
| 77 |
|
std::vector<std::string> keys; |
| 78 |
|
keys.push_back(at); |
| 79 |
|
return atomTypeCont_.find(keys); |
| 80 |
+ |
} |
| 81 |
+ |
|
| 82 |
+ |
/** |
| 83 |
+ |
* getAtomType by ident |
| 84 |
+ |
* |
| 85 |
+ |
* finds the requested atom type in this force field using the |
| 86 |
+ |
* integer ident instead of the string name of the atom type. |
| 87 |
+ |
*/ |
| 88 |
+ |
AtomType* ForceField::getAtomType(int ident) { |
| 89 |
+ |
std::string at = atypeIdentToName.find(ident)->second; |
| 90 |
+ |
return getAtomType(at); |
| 91 |
|
} |
| 92 |
|
|
| 93 |
|
BondType* ForceField::getBondType(const std::string &at1, |
| 449 |
|
} |
| 450 |
|
|
| 451 |
|
NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) { |
| 452 |
+ |
|
| 453 |
|
std::vector<std::string> keys; |
| 454 |
|
keys.push_back(at1); |
| 455 |
|
keys.push_back(at2); |
| 459 |
|
if (nbiType) { |
| 460 |
|
return nbiType; |
| 461 |
|
} else { |
| 462 |
< |
//if no exact match found, try wild card match |
| 463 |
< |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 464 |
< |
} |
| 462 |
> |
AtomType* atype1; |
| 463 |
> |
AtomType* atype2; |
| 464 |
> |
std::vector<std::string> at1key; |
| 465 |
> |
at1key.push_back(at1); |
| 466 |
> |
atype1 = atomTypeCont_.find(at1key); |
| 467 |
> |
|
| 468 |
> |
std::vector<std::string> at2key; |
| 469 |
> |
at2key.push_back(at2); |
| 470 |
> |
atype2 = atomTypeCont_.find(at2key); |
| 471 |
> |
|
| 472 |
> |
// query atom types for their chains of responsibility |
| 473 |
> |
std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
| 474 |
> |
std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
| 475 |
> |
|
| 476 |
> |
std::vector<AtomType*>::iterator i; |
| 477 |
> |
std::vector<AtomType*>::iterator j; |
| 478 |
> |
|
| 479 |
> |
int ii = 0; |
| 480 |
> |
int jj = 0; |
| 481 |
> |
int nbiTypeScore; |
| 482 |
> |
|
| 483 |
> |
std::vector<std::pair<int, std::vector<std::string> > > foundNBI; |
| 484 |
> |
|
| 485 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 486 |
> |
jj = 0; |
| 487 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 488 |
> |
|
| 489 |
> |
nbiTypeScore = ii + jj; |
| 490 |
> |
|
| 491 |
> |
std::vector<std::string> myKeys; |
| 492 |
> |
myKeys.push_back((*i)->getName()); |
| 493 |
> |
myKeys.push_back((*j)->getName()); |
| 494 |
> |
|
| 495 |
> |
NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys); |
| 496 |
> |
if (nbiType) { |
| 497 |
> |
foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys)); |
| 498 |
> |
} |
| 499 |
> |
jj++; |
| 500 |
> |
} |
| 501 |
> |
ii++; |
| 502 |
> |
} |
| 503 |
> |
|
| 504 |
> |
|
| 505 |
> |
if (foundNBI.size() > 0) { |
| 506 |
> |
// sort the foundNBI by the score: |
| 507 |
> |
std::sort(foundNBI.begin(), foundNBI.end()); |
| 508 |
> |
|
| 509 |
> |
int bestScore = foundNBI[0].first; |
| 510 |
> |
std::vector<std::string> theKeys = foundNBI[0].second; |
| 511 |
> |
|
| 512 |
> |
NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys); |
| 513 |
> |
return bestType; |
| 514 |
> |
} else { |
| 515 |
> |
//if no exact match found, try wild card match |
| 516 |
> |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 517 |
> |
} |
| 518 |
> |
} |
| 519 |
|
} |
| 520 |
|
|
| 521 |
|
BondType* ForceField::getExactBondType(const std::string &at1, |
| 571 |
|
bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { |
| 572 |
|
std::vector<std::string> keys; |
| 573 |
|
keys.push_back(at); |
| 574 |
+ |
atypeIdentToName[atomType->getIdent()] = at; |
| 575 |
|
return atomTypeCont_.add(keys, atomType); |
| 576 |
|
} |
| 577 |
|
|
| 578 |
|
bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) { |
| 579 |
|
std::vector<std::string> keys; |
| 580 |
|
keys.push_back(at); |
| 581 |
+ |
atypeIdentToName[atomType->getIdent()] = at; |
| 582 |
|
return atomTypeCont_.replace(keys, atomType); |
| 583 |
|
} |
| 584 |
|
|
| 697 |
|
return ffStream; |
| 698 |
|
} |
| 699 |
|
|
| 634 |
– |
void ForceField::setFortranForceOptions(){ |
| 635 |
– |
ForceOptions theseFortranOptions; |
| 636 |
– |
forceFieldOptions_.makeFortranOptions(theseFortranOptions); |
| 637 |
– |
setfForceOptions(&theseFortranOptions); |
| 638 |
– |
} |
| 700 |
|
} //end namespace OpenMD |
