| 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
/** |
| 51 |
|
#include "UseTheForce/ForceField.hpp" |
| 52 |
|
#include "utils/simError.h" |
| 53 |
|
#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" |
| 57 |
< |
namespace oopse { |
| 54 |
> |
namespace OpenMD { |
| 55 |
|
|
| 56 |
|
ForceField::ForceField() { |
| 57 |
+ |
|
| 58 |
|
char* tempPath; |
| 59 |
|
tempPath = getenv("FORCE_PARAM_PATH"); |
| 60 |
< |
|
| 60 |
> |
|
| 61 |
|
if (tempPath == NULL) { |
| 62 |
|
//convert a macro from compiler to a string in c++ |
| 63 |
|
STR_DEFINE(ffPath_, FRC_PATH ); |
| 66 |
|
} |
| 67 |
|
} |
| 68 |
|
|
| 71 |
– |
|
| 72 |
– |
ForceField::~ForceField() { |
| 73 |
– |
deleteAtypes(); |
| 74 |
– |
deleteSwitch(); |
| 75 |
– |
} |
| 76 |
– |
|
| 69 |
|
AtomType* ForceField::getAtomType(const std::string &at) { |
| 70 |
|
std::vector<std::string> keys; |
| 71 |
|
keys.push_back(at); |
| 125 |
|
ii++; |
| 126 |
|
} |
| 127 |
|
|
| 136 |
– |
// sort the foundBonds by the score: |
| 128 |
|
|
| 129 |
< |
std::sort(foundBonds.begin(), foundBonds.end()); |
| 130 |
< |
|
| 131 |
< |
int bestScore = foundBonds[0].first; |
| 132 |
< |
std::vector<std::string> theKeys = foundBonds[0].second; |
| 133 |
< |
|
| 134 |
< |
std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1] << "\t(score = "<< bestScore << ")\n"; |
| 135 |
< |
BondType* bestType = bondTypeCont_.find(theKeys); |
| 136 |
< |
if (bestType) |
| 137 |
< |
return bestType; |
| 138 |
< |
else { |
| 139 |
< |
//if no exact match found, try wild card match |
| 140 |
< |
return bondTypeCont_.find(keys, wildCardAtomTypeName_); |
| 129 |
> |
if (foundBonds.size() > 0) { |
| 130 |
> |
// sort the foundBonds by the score: |
| 131 |
> |
std::sort(foundBonds.begin(), foundBonds.end()); |
| 132 |
> |
|
| 133 |
> |
int bestScore = foundBonds[0].first; |
| 134 |
> |
std::vector<std::string> theKeys = foundBonds[0].second; |
| 135 |
> |
|
| 136 |
> |
BondType* bestType = bondTypeCont_.find(theKeys); |
| 137 |
> |
|
| 138 |
> |
return bestType; |
| 139 |
> |
} else { |
| 140 |
> |
//if no exact match found, try wild card match |
| 141 |
> |
return bondTypeCont_.find(keys, wildCardAtomTypeName_); |
| 142 |
|
} |
| 143 |
|
} |
| 144 |
|
} |
| 212 |
|
jj++; |
| 213 |
|
} |
| 214 |
|
|
| 215 |
< |
std::sort(foundBends.begin(), foundBends.end()); |
| 216 |
< |
|
| 217 |
< |
int jscore = foundBends[0].first; |
| 218 |
< |
int ikscore = foundBends[0].second; |
| 219 |
< |
std::vector<std::string> theKeys = foundBends[0].third; |
| 220 |
< |
|
| 221 |
< |
std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n"; |
| 222 |
< |
|
| 223 |
< |
BendType* bestType = bendTypeCont_.find(theKeys); |
| 232 |
< |
if (bestType) |
| 233 |
< |
return bestType; |
| 234 |
< |
else { |
| 235 |
< |
|
| 215 |
> |
if (foundBends.size() > 0) { |
| 216 |
> |
std::sort(foundBends.begin(), foundBends.end()); |
| 217 |
> |
int jscore = foundBends[0].first; |
| 218 |
> |
int ikscore = foundBends[0].second; |
| 219 |
> |
std::vector<std::string> theKeys = foundBends[0].third; |
| 220 |
> |
|
| 221 |
> |
BendType* bestType = bendTypeCont_.find(theKeys); |
| 222 |
> |
return bestType; |
| 223 |
> |
} else { |
| 224 |
|
//if no exact match found, try wild card match |
| 225 |
|
return bendTypeCont_.find(keys, wildCardAtomTypeName_); |
| 226 |
|
} |
| 227 |
|
} |
| 228 |
|
} |
| 229 |
|
|
| 242 |
– |
|
| 230 |
|
TorsionType* ForceField::getTorsionType(const std::string &at1, |
| 231 |
|
const std::string &at2, |
| 232 |
|
const std::string &at3, |
| 314 |
|
jj++; |
| 315 |
|
} |
| 316 |
|
|
| 317 |
< |
std::sort(foundTorsions.begin(), foundTorsions.end()); |
| 317 |
> |
if (foundTorsions.size() > 0) { |
| 318 |
> |
std::sort(foundTorsions.begin(), foundTorsions.end()); |
| 319 |
> |
int jkscore = foundTorsions[0].first; |
| 320 |
> |
int ilscore = foundTorsions[0].second; |
| 321 |
> |
std::vector<std::string> theKeys = foundTorsions[0].third; |
| 322 |
> |
|
| 323 |
> |
TorsionType* bestType = torsionTypeCont_.find(theKeys); |
| 324 |
> |
return bestType; |
| 325 |
> |
} else { |
| 326 |
> |
//if no exact match found, try wild card match |
| 327 |
> |
return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 328 |
> |
} |
| 329 |
> |
} |
| 330 |
> |
} |
| 331 |
|
|
| 332 |
< |
int jkscore = foundTorsions[0].first; |
| 333 |
< |
int ilscore = foundTorsions[0].second; |
| 334 |
< |
std::vector<std::string> theKeys = foundTorsions[0].third; |
| 332 |
> |
InversionType* ForceField::getInversionType(const std::string &at1, |
| 333 |
> |
const std::string &at2, |
| 334 |
> |
const std::string &at3, |
| 335 |
> |
const std::string &at4) { |
| 336 |
> |
std::vector<std::string> keys; |
| 337 |
> |
keys.push_back(at1); |
| 338 |
> |
keys.push_back(at2); |
| 339 |
> |
keys.push_back(at3); |
| 340 |
> |
keys.push_back(at4); |
| 341 |
|
|
| 342 |
< |
std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n"; |
| 342 |
> |
//try exact match first |
| 343 |
> |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys); |
| 344 |
> |
if (inversionType) { |
| 345 |
> |
return inversionType; |
| 346 |
> |
} else { |
| 347 |
> |
|
| 348 |
> |
AtomType* atype1; |
| 349 |
> |
AtomType* atype2; |
| 350 |
> |
AtomType* atype3; |
| 351 |
> |
AtomType* atype4; |
| 352 |
> |
std::vector<std::string> at1key; |
| 353 |
> |
at1key.push_back(at1); |
| 354 |
> |
atype1 = atomTypeCont_.find(at1key); |
| 355 |
> |
|
| 356 |
> |
std::vector<std::string> at2key; |
| 357 |
> |
at2key.push_back(at2); |
| 358 |
> |
atype2 = atomTypeCont_.find(at2key); |
| 359 |
> |
|
| 360 |
> |
std::vector<std::string> at3key; |
| 361 |
> |
at3key.push_back(at3); |
| 362 |
> |
atype3 = atomTypeCont_.find(at3key); |
| 363 |
> |
|
| 364 |
> |
std::vector<std::string> at4key; |
| 365 |
> |
at4key.push_back(at4); |
| 366 |
> |
atype4 = atomTypeCont_.find(at4key); |
| 367 |
|
|
| 368 |
+ |
// query atom types for their chains of responsibility |
| 369 |
+ |
std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
| 370 |
+ |
std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
| 371 |
+ |
std::vector<AtomType*> at3Chain = atype3->allYourBase(); |
| 372 |
+ |
std::vector<AtomType*> at4Chain = atype4->allYourBase(); |
| 373 |
+ |
|
| 374 |
+ |
std::vector<AtomType*>::iterator i; |
| 375 |
+ |
std::vector<AtomType*>::iterator j; |
| 376 |
+ |
std::vector<AtomType*>::iterator k; |
| 377 |
+ |
std::vector<AtomType*>::iterator l; |
| 378 |
+ |
|
| 379 |
+ |
int ii = 0; |
| 380 |
+ |
int jj = 0; |
| 381 |
+ |
int kk = 0; |
| 382 |
+ |
int ll = 0; |
| 383 |
+ |
int Iscore; |
| 384 |
+ |
int JKLscore; |
| 385 |
|
|
| 386 |
< |
TorsionType* bestType = torsionTypeCont_.find(theKeys); |
| 387 |
< |
if (bestType) { |
| 388 |
< |
return bestType; |
| 386 |
> |
std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions; |
| 387 |
> |
|
| 388 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 389 |
> |
kk = 0; |
| 390 |
> |
for (k = at3Chain.begin(); k != at3Chain.end(); k++) { |
| 391 |
> |
ii = 0; |
| 392 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 393 |
> |
ll = 0; |
| 394 |
> |
for (l = at4Chain.begin(); l != at4Chain.end(); l++) { |
| 395 |
> |
|
| 396 |
> |
Iscore = ii; |
| 397 |
> |
JKLscore = jj + kk + ll; |
| 398 |
> |
|
| 399 |
> |
std::vector<std::string> myKeys; |
| 400 |
> |
myKeys.push_back((*i)->getName()); |
| 401 |
> |
myKeys.push_back((*j)->getName()); |
| 402 |
> |
myKeys.push_back((*k)->getName()); |
| 403 |
> |
myKeys.push_back((*l)->getName()); |
| 404 |
> |
|
| 405 |
> |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys); |
| 406 |
> |
if (inversionType) { |
| 407 |
> |
foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) ); |
| 408 |
> |
} |
| 409 |
> |
ll++; |
| 410 |
> |
} |
| 411 |
> |
ii++; |
| 412 |
> |
} |
| 413 |
> |
kk++; |
| 414 |
> |
} |
| 415 |
> |
jj++; |
| 416 |
> |
} |
| 417 |
> |
|
| 418 |
> |
if (foundInversions.size() > 0) { |
| 419 |
> |
std::sort(foundInversions.begin(), foundInversions.end()); |
| 420 |
> |
int iscore = foundInversions[0].first; |
| 421 |
> |
int jklscore = foundInversions[0].second; |
| 422 |
> |
std::vector<std::string> theKeys = foundInversions[0].third; |
| 423 |
> |
|
| 424 |
> |
InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys); |
| 425 |
> |
return bestType; |
| 426 |
|
} else { |
| 427 |
|
//if no exact match found, try wild card match |
| 428 |
< |
return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 428 |
> |
return inversionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 429 |
|
} |
| 430 |
|
} |
| 431 |
|
} |
| 432 |
< |
|
| 432 |
> |
|
| 433 |
|
NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) { |
| 434 |
|
std::vector<std::string> keys; |
| 435 |
|
keys.push_back(at1); |
| 474 |
|
keys.push_back(at4); |
| 475 |
|
return torsionTypeCont_.find(keys); |
| 476 |
|
} |
| 477 |
< |
|
| 477 |
> |
|
| 478 |
> |
InversionType* ForceField::getExactInversionType(const std::string &at1, |
| 479 |
> |
const std::string &at2, |
| 480 |
> |
const std::string &at3, |
| 481 |
> |
const std::string &at4){ |
| 482 |
> |
std::vector<std::string> keys; |
| 483 |
> |
keys.push_back(at1); |
| 484 |
> |
keys.push_back(at2); |
| 485 |
> |
keys.push_back(at3); |
| 486 |
> |
keys.push_back(at4); |
| 487 |
> |
return inversionTypeCont_.find(keys); |
| 488 |
> |
} |
| 489 |
> |
|
| 490 |
|
NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){ |
| 491 |
|
std::vector<std::string> keys; |
| 492 |
|
keys.push_back(at1); |
| 493 |
|
keys.push_back(at2); |
| 494 |
|
return nonBondedInteractionTypeCont_.find(keys); |
| 495 |
|
} |
| 496 |
+ |
|
| 497 |
|
|
| 401 |
– |
|
| 498 |
|
bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { |
| 499 |
|
std::vector<std::string> keys; |
| 500 |
|
keys.push_back(at); |
| 501 |
|
return atomTypeCont_.add(keys, atomType); |
| 502 |
|
} |
| 503 |
|
|
| 504 |
+ |
bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) { |
| 505 |
+ |
std::vector<std::string> keys; |
| 506 |
+ |
keys.push_back(at); |
| 507 |
+ |
return atomTypeCont_.replace(keys, atomType); |
| 508 |
+ |
} |
| 509 |
+ |
|
| 510 |
|
bool ForceField::addBondType(const std::string &at1, const std::string &at2, |
| 511 |
|
BondType* bondType) { |
| 512 |
|
std::vector<std::string> keys; |
| 537 |
|
return torsionTypeCont_.add(keys, torsionType); |
| 538 |
|
} |
| 539 |
|
|
| 540 |
+ |
bool ForceField::addInversionType(const std::string &at1, |
| 541 |
+ |
const std::string &at2, |
| 542 |
+ |
const std::string &at3, |
| 543 |
+ |
const std::string &at4, |
| 544 |
+ |
InversionType* inversionType) { |
| 545 |
+ |
std::vector<std::string> keys; |
| 546 |
+ |
keys.push_back(at1); |
| 547 |
+ |
keys.push_back(at2); |
| 548 |
+ |
keys.push_back(at3); |
| 549 |
+ |
keys.push_back(at4); |
| 550 |
+ |
return inversionTypeCont_.add(keys, inversionType); |
| 551 |
+ |
} |
| 552 |
+ |
|
| 553 |
|
bool ForceField::addNonBondedInteractionType(const std::string &at1, |
| 554 |
|
const std::string &at2, |
| 555 |
|
NonBondedInteractionType* nbiType) { |
| 578 |
|
} else { |
| 579 |
|
sprintf( painCave.errMsg, |
| 580 |
|
"Can not cast GenericData to LJParam\n"); |
| 581 |
< |
painCave.severity = OOPSE_ERROR; |
| 581 |
> |
painCave.severity = OPENMD_ERROR; |
| 582 |
|
painCave.isFatal = 1; |
| 583 |
|
simError(); |
| 584 |
|
} |
| 585 |
|
} else { |
| 586 |
|
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 587 |
< |
painCave.severity = OOPSE_ERROR; |
| 587 |
> |
painCave.severity = OPENMD_ERROR; |
| 588 |
|
painCave.isFatal = 1; |
| 589 |
|
simError(); |
| 590 |
|
} |
| 614 |
|
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 615 |
|
"variable?\n", |
| 616 |
|
forceFieldFilename.c_str() ); |
| 617 |
< |
painCave.severity = OOPSE_ERROR; |
| 617 |
> |
painCave.severity = OPENMD_ERROR; |
| 618 |
|
painCave.isFatal = 1; |
| 619 |
|
simError(); |
| 620 |
|
} |
| 622 |
|
return ffStream; |
| 623 |
|
} |
| 624 |
|
|
| 625 |
< |
void ForceField::setFortranForceOptions(){ |
| 511 |
< |
ForceOptions theseFortranOptions; |
| 512 |
< |
forceFieldOptions_.makeFortranOptions(theseFortranOptions); |
| 513 |
< |
setfForceOptions(&theseFortranOptions); |
| 514 |
< |
} |
| 515 |
< |
} //end namespace oopse |
| 625 |
> |
} //end namespace OpenMD |
