| 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 |
|
/** |
| 52 |
|
#include "UseTheForce/ForceField.hpp" |
| 53 |
|
#include "utils/simError.h" |
| 54 |
|
#include "utils/Tuple.hpp" |
| 55 |
< |
#include "UseTheForce/DarkSide/atype_interface.h" |
| 55 |
< |
#include "UseTheForce/DarkSide/fForceOptions_interface.h" |
| 56 |
< |
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
| 57 |
< |
namespace oopse { |
| 55 |
> |
#include "types/LennardJonesAdapter.hpp" |
| 56 |
|
|
| 57 |
+ |
namespace OpenMD { |
| 58 |
+ |
|
| 59 |
|
ForceField::ForceField() { |
| 60 |
+ |
|
| 61 |
|
char* tempPath; |
| 62 |
|
tempPath = getenv("FORCE_PARAM_PATH"); |
| 63 |
< |
|
| 63 |
> |
|
| 64 |
|
if (tempPath == NULL) { |
| 65 |
|
//convert a macro from compiler to a string in c++ |
| 66 |
|
STR_DEFINE(ffPath_, FRC_PATH ); |
| 69 |
|
} |
| 70 |
|
} |
| 71 |
|
|
| 72 |
< |
|
| 73 |
< |
ForceField::~ForceField() { |
| 74 |
< |
deleteAtypes(); |
| 75 |
< |
deleteSwitch(); |
| 76 |
< |
} |
| 77 |
< |
|
| 72 |
> |
/** |
| 73 |
> |
* getAtomType by string |
| 74 |
> |
* |
| 75 |
> |
* finds the requested atom type in this force field using the string |
| 76 |
> |
* name of the atom type. |
| 77 |
> |
*/ |
| 78 |
|
AtomType* ForceField::getAtomType(const std::string &at) { |
| 79 |
|
std::vector<std::string> keys; |
| 80 |
|
keys.push_back(at); |
| 81 |
|
return atomTypeCont_.find(keys); |
| 82 |
|
} |
| 83 |
|
|
| 84 |
+ |
/** |
| 85 |
+ |
* getAtomType by ident |
| 86 |
+ |
* |
| 87 |
+ |
* finds the requested atom type in this force field using the |
| 88 |
+ |
* integer ident instead of the string name of the atom type. |
| 89 |
+ |
*/ |
| 90 |
+ |
AtomType* ForceField::getAtomType(int ident) { |
| 91 |
+ |
std::string at = atypeIdentToName.find(ident)->second; |
| 92 |
+ |
return getAtomType(at); |
| 93 |
+ |
} |
| 94 |
+ |
|
| 95 |
|
BondType* ForceField::getBondType(const std::string &at1, |
| 96 |
|
const std::string &at2) { |
| 97 |
|
std::vector<std::string> keys; |
| 145 |
|
ii++; |
| 146 |
|
} |
| 147 |
|
|
| 136 |
– |
// sort the foundBonds by the score: |
| 148 |
|
|
| 149 |
< |
std::sort(foundBonds.begin(), foundBonds.end()); |
| 150 |
< |
|
| 151 |
< |
int bestScore = foundBonds[0].first; |
| 152 |
< |
std::vector<std::string> theKeys = foundBonds[0].second; |
| 153 |
< |
|
| 154 |
< |
std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1] << "\t(score = "<< bestScore << ")\n"; |
| 155 |
< |
BondType* bestType = bondTypeCont_.find(theKeys); |
| 156 |
< |
if (bestType) |
| 157 |
< |
return bestType; |
| 158 |
< |
else { |
| 159 |
< |
//if no exact match found, try wild card match |
| 160 |
< |
return bondTypeCont_.find(keys, wildCardAtomTypeName_); |
| 149 |
> |
if (foundBonds.size() > 0) { |
| 150 |
> |
// sort the foundBonds by the score: |
| 151 |
> |
std::sort(foundBonds.begin(), foundBonds.end()); |
| 152 |
> |
|
| 153 |
> |
int bestScore = foundBonds[0].first; |
| 154 |
> |
std::vector<std::string> theKeys = foundBonds[0].second; |
| 155 |
> |
|
| 156 |
> |
BondType* bestType = bondTypeCont_.find(theKeys); |
| 157 |
> |
|
| 158 |
> |
return bestType; |
| 159 |
> |
} else { |
| 160 |
> |
//if no exact match found, try wild card match |
| 161 |
> |
return bondTypeCont_.find(keys, wildCardAtomTypeName_); |
| 162 |
|
} |
| 163 |
|
} |
| 164 |
|
} |
| 232 |
|
jj++; |
| 233 |
|
} |
| 234 |
|
|
| 235 |
< |
std::sort(foundBends.begin(), foundBends.end()); |
| 236 |
< |
|
| 237 |
< |
int jscore = foundBends[0].first; |
| 238 |
< |
int ikscore = foundBends[0].second; |
| 239 |
< |
std::vector<std::string> theKeys = foundBends[0].third; |
| 240 |
< |
|
| 241 |
< |
std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n"; |
| 242 |
< |
|
| 243 |
< |
BendType* bestType = bendTypeCont_.find(theKeys); |
| 232 |
< |
if (bestType) |
| 233 |
< |
return bestType; |
| 234 |
< |
else { |
| 235 |
< |
|
| 235 |
> |
if (foundBends.size() > 0) { |
| 236 |
> |
std::sort(foundBends.begin(), foundBends.end()); |
| 237 |
> |
int jscore = foundBends[0].first; |
| 238 |
> |
int ikscore = foundBends[0].second; |
| 239 |
> |
std::vector<std::string> theKeys = foundBends[0].third; |
| 240 |
> |
|
| 241 |
> |
BendType* bestType = bendTypeCont_.find(theKeys); |
| 242 |
> |
return bestType; |
| 243 |
> |
} else { |
| 244 |
|
//if no exact match found, try wild card match |
| 245 |
|
return bendTypeCont_.find(keys, wildCardAtomTypeName_); |
| 246 |
|
} |
| 247 |
|
} |
| 248 |
|
} |
| 249 |
|
|
| 242 |
– |
|
| 250 |
|
TorsionType* ForceField::getTorsionType(const std::string &at1, |
| 251 |
|
const std::string &at2, |
| 252 |
|
const std::string &at3, |
| 334 |
|
jj++; |
| 335 |
|
} |
| 336 |
|
|
| 337 |
< |
std::sort(foundTorsions.begin(), foundTorsions.end()); |
| 338 |
< |
|
| 339 |
< |
int jkscore = foundTorsions[0].first; |
| 340 |
< |
int ilscore = foundTorsions[0].second; |
| 341 |
< |
std::vector<std::string> theKeys = foundTorsions[0].third; |
| 342 |
< |
|
| 343 |
< |
std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n"; |
| 344 |
< |
|
| 338 |
< |
|
| 339 |
< |
TorsionType* bestType = torsionTypeCont_.find(theKeys); |
| 340 |
< |
if (bestType) { |
| 341 |
< |
return bestType; |
| 337 |
> |
if (foundTorsions.size() > 0) { |
| 338 |
> |
std::sort(foundTorsions.begin(), foundTorsions.end()); |
| 339 |
> |
int jkscore = foundTorsions[0].first; |
| 340 |
> |
int ilscore = foundTorsions[0].second; |
| 341 |
> |
std::vector<std::string> theKeys = foundTorsions[0].third; |
| 342 |
> |
|
| 343 |
> |
TorsionType* bestType = torsionTypeCont_.find(theKeys); |
| 344 |
> |
return bestType; |
| 345 |
|
} else { |
| 346 |
|
//if no exact match found, try wild card match |
| 347 |
|
return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 360 |
|
keys.push_back(at4); |
| 361 |
|
|
| 362 |
|
//try exact match first |
| 363 |
< |
InversionType* inversionType = inversionTypeCont_.find(keys); |
| 363 |
> |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys); |
| 364 |
|
if (inversionType) { |
| 365 |
|
return inversionType; |
| 366 |
|
} else { |
| 422 |
|
myKeys.push_back((*k)->getName()); |
| 423 |
|
myKeys.push_back((*l)->getName()); |
| 424 |
|
|
| 425 |
< |
InversionType* inversionType = inversionTypeCont_.find(myKeys); |
| 425 |
> |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys); |
| 426 |
|
if (inversionType) { |
| 427 |
|
foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) ); |
| 428 |
|
} |
| 434 |
|
} |
| 435 |
|
jj++; |
| 436 |
|
} |
| 437 |
< |
|
| 438 |
< |
std::sort(foundInversions.begin(), foundInversions.end()); |
| 439 |
< |
|
| 440 |
< |
int iscore = foundInversions[0].first; |
| 441 |
< |
int jklscore = foundInversions[0].second; |
| 442 |
< |
std::vector<std::string> theKeys = foundInversions[0].third; |
| 443 |
< |
|
| 444 |
< |
std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n"; |
| 445 |
< |
|
| 443 |
< |
|
| 444 |
< |
InversionType* bestType = inversionTypeCont_.find(theKeys); |
| 445 |
< |
if (bestType) { |
| 446 |
< |
return bestType; |
| 437 |
> |
|
| 438 |
> |
if (foundInversions.size() > 0) { |
| 439 |
> |
std::sort(foundInversions.begin(), foundInversions.end()); |
| 440 |
> |
int iscore = foundInversions[0].first; |
| 441 |
> |
int jklscore = foundInversions[0].second; |
| 442 |
> |
std::vector<std::string> theKeys = foundInversions[0].third; |
| 443 |
> |
|
| 444 |
> |
InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys); |
| 445 |
> |
return bestType; |
| 446 |
|
} else { |
| 447 |
|
//if no exact match found, try wild card match |
| 448 |
|
return inversionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 451 |
|
} |
| 452 |
|
|
| 453 |
|
NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) { |
| 454 |
+ |
|
| 455 |
|
std::vector<std::string> keys; |
| 456 |
|
keys.push_back(at1); |
| 457 |
|
keys.push_back(at2); |
| 461 |
|
if (nbiType) { |
| 462 |
|
return nbiType; |
| 463 |
|
} else { |
| 464 |
< |
//if no exact match found, try wild card match |
| 465 |
< |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 466 |
< |
} |
| 464 |
> |
AtomType* atype1; |
| 465 |
> |
AtomType* atype2; |
| 466 |
> |
std::vector<std::string> at1key; |
| 467 |
> |
at1key.push_back(at1); |
| 468 |
> |
atype1 = atomTypeCont_.find(at1key); |
| 469 |
> |
|
| 470 |
> |
std::vector<std::string> at2key; |
| 471 |
> |
at2key.push_back(at2); |
| 472 |
> |
atype2 = atomTypeCont_.find(at2key); |
| 473 |
> |
|
| 474 |
> |
// query atom types for their chains of responsibility |
| 475 |
> |
std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
| 476 |
> |
std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
| 477 |
> |
|
| 478 |
> |
std::vector<AtomType*>::iterator i; |
| 479 |
> |
std::vector<AtomType*>::iterator j; |
| 480 |
> |
|
| 481 |
> |
int ii = 0; |
| 482 |
> |
int jj = 0; |
| 483 |
> |
int nbiTypeScore; |
| 484 |
> |
|
| 485 |
> |
std::vector<std::pair<int, std::vector<std::string> > > foundNBI; |
| 486 |
> |
|
| 487 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 488 |
> |
jj = 0; |
| 489 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 490 |
> |
|
| 491 |
> |
nbiTypeScore = ii + jj; |
| 492 |
> |
|
| 493 |
> |
std::vector<std::string> myKeys; |
| 494 |
> |
myKeys.push_back((*i)->getName()); |
| 495 |
> |
myKeys.push_back((*j)->getName()); |
| 496 |
> |
|
| 497 |
> |
NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys); |
| 498 |
> |
if (nbiType) { |
| 499 |
> |
foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys)); |
| 500 |
> |
} |
| 501 |
> |
jj++; |
| 502 |
> |
} |
| 503 |
> |
ii++; |
| 504 |
> |
} |
| 505 |
> |
|
| 506 |
> |
|
| 507 |
> |
if (foundNBI.size() > 0) { |
| 508 |
> |
// sort the foundNBI by the score: |
| 509 |
> |
std::sort(foundNBI.begin(), foundNBI.end()); |
| 510 |
> |
|
| 511 |
> |
int bestScore = foundNBI[0].first; |
| 512 |
> |
std::vector<std::string> theKeys = foundNBI[0].second; |
| 513 |
> |
|
| 514 |
> |
NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys); |
| 515 |
> |
return bestType; |
| 516 |
> |
} else { |
| 517 |
> |
//if no exact match found, try wild card match |
| 518 |
> |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 519 |
> |
} |
| 520 |
> |
} |
| 521 |
|
} |
| 522 |
|
|
| 523 |
|
BondType* ForceField::getExactBondType(const std::string &at1, |
| 573 |
|
bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { |
| 574 |
|
std::vector<std::string> keys; |
| 575 |
|
keys.push_back(at); |
| 576 |
+ |
atypeIdentToName[atomType->getIdent()] = at; |
| 577 |
|
return atomTypeCont_.add(keys, atomType); |
| 578 |
|
} |
| 579 |
|
|
| 580 |
+ |
bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) { |
| 581 |
+ |
std::vector<std::string> keys; |
| 582 |
+ |
keys.push_back(at); |
| 583 |
+ |
atypeIdentToName[atomType->getIdent()] = at; |
| 584 |
+ |
return atomTypeCont_.replace(keys, atomType); |
| 585 |
+ |
} |
| 586 |
+ |
|
| 587 |
|
bool ForceField::addBondType(const std::string &at1, const std::string &at2, |
| 588 |
|
BondType* bondType) { |
| 589 |
|
std::vector<std::string> keys; |
| 637 |
|
} |
| 638 |
|
|
| 639 |
|
RealType ForceField::getRcutFromAtomType(AtomType* at) { |
| 578 |
– |
/**@todo */ |
| 579 |
– |
GenericData* data; |
| 640 |
|
RealType rcut = 0.0; |
| 641 |
|
|
| 642 |
< |
if (at->isLennardJones()) { |
| 643 |
< |
data = at->getPropertyByName("LennardJones"); |
| 644 |
< |
if (data != NULL) { |
| 585 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 586 |
< |
|
| 587 |
< |
if (ljData != NULL) { |
| 588 |
< |
LJParam ljParam = ljData->getData(); |
| 589 |
< |
|
| 590 |
< |
//by default use 2.5*sigma as cutoff radius |
| 591 |
< |
rcut = 2.5 * ljParam.sigma; |
| 592 |
< |
|
| 593 |
< |
} else { |
| 594 |
< |
sprintf( painCave.errMsg, |
| 595 |
< |
"Can not cast GenericData to LJParam\n"); |
| 596 |
< |
painCave.severity = OOPSE_ERROR; |
| 597 |
< |
painCave.isFatal = 1; |
| 598 |
< |
simError(); |
| 599 |
< |
} |
| 600 |
< |
} else { |
| 601 |
< |
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 602 |
< |
painCave.severity = OOPSE_ERROR; |
| 603 |
< |
painCave.isFatal = 1; |
| 604 |
< |
simError(); |
| 605 |
< |
} |
| 642 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(at); |
| 643 |
> |
if (lja.isLennardJones()) { |
| 644 |
> |
rcut = 2.5 * lja.getSigma(); |
| 645 |
|
} |
| 646 |
|
return rcut; |
| 647 |
|
} |
| 668 |
|
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 669 |
|
"variable?\n", |
| 670 |
|
forceFieldFilename.c_str() ); |
| 671 |
< |
painCave.severity = OOPSE_ERROR; |
| 671 |
> |
painCave.severity = OPENMD_ERROR; |
| 672 |
|
painCave.isFatal = 1; |
| 673 |
|
simError(); |
| 674 |
|
} |
| 676 |
|
return ffStream; |
| 677 |
|
} |
| 678 |
|
|
| 679 |
< |
void ForceField::setFortranForceOptions(){ |
| 641 |
< |
ForceOptions theseFortranOptions; |
| 642 |
< |
forceFieldOptions_.makeFortranOptions(theseFortranOptions); |
| 643 |
< |
setfForceOptions(&theseFortranOptions); |
| 644 |
< |
} |
| 645 |
< |
} //end namespace oopse |
| 679 |
> |
} //end namespace OpenMD |
