| 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 |
|
/** |
| 54 |
|
#include "UseTheForce/DarkSide/atype_interface.h" |
| 55 |
|
#include "UseTheForce/DarkSide/fForceOptions_interface.h" |
| 56 |
|
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
| 57 |
< |
namespace oopse { |
| 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 ); |
| 72 |
|
|
| 73 |
|
ForceField::~ForceField() { |
| 74 |
|
deleteAtypes(); |
| 75 |
< |
deleteSwitch(); |
| 75 |
> |
deleteSwitch(); |
| 76 |
|
} |
| 77 |
|
|
| 78 |
|
AtomType* ForceField::getAtomType(const std::string &at) { |
| 134 |
|
ii++; |
| 135 |
|
} |
| 136 |
|
|
| 136 |
– |
// sort the foundBonds by the score: |
| 137 |
|
|
| 138 |
< |
std::sort(foundBonds.begin(), foundBonds.end()); |
| 139 |
< |
|
| 140 |
< |
int bestScore = foundBonds[0].first; |
| 141 |
< |
std::vector<std::string> theKeys = foundBonds[0].second; |
| 142 |
< |
|
| 143 |
< |
std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1] << "\t(score = "<< bestScore << ")\n"; |
| 144 |
< |
BondType* bestType = bondTypeCont_.find(theKeys); |
| 145 |
< |
if (bestType) |
| 146 |
< |
return bestType; |
| 147 |
< |
else { |
| 148 |
< |
//if no exact match found, try wild card match |
| 149 |
< |
return bondTypeCont_.find(keys, wildCardAtomTypeName_); |
| 138 |
> |
if (foundBonds.size() > 0) { |
| 139 |
> |
// sort the foundBonds by the score: |
| 140 |
> |
std::sort(foundBonds.begin(), foundBonds.end()); |
| 141 |
> |
|
| 142 |
> |
int bestScore = foundBonds[0].first; |
| 143 |
> |
std::vector<std::string> theKeys = foundBonds[0].second; |
| 144 |
> |
|
| 145 |
> |
BondType* bestType = bondTypeCont_.find(theKeys); |
| 146 |
> |
|
| 147 |
> |
return bestType; |
| 148 |
> |
} else { |
| 149 |
> |
//if no exact match found, try wild card match |
| 150 |
> |
return bondTypeCont_.find(keys, wildCardAtomTypeName_); |
| 151 |
|
} |
| 152 |
|
} |
| 153 |
|
} |
| 221 |
|
jj++; |
| 222 |
|
} |
| 223 |
|
|
| 224 |
< |
std::sort(foundBends.begin(), foundBends.end()); |
| 225 |
< |
|
| 226 |
< |
int jscore = foundBends[0].first; |
| 227 |
< |
int ikscore = foundBends[0].second; |
| 228 |
< |
std::vector<std::string> theKeys = foundBends[0].third; |
| 229 |
< |
|
| 230 |
< |
std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n"; |
| 231 |
< |
|
| 232 |
< |
BendType* bestType = bendTypeCont_.find(theKeys); |
| 232 |
< |
if (bestType) |
| 233 |
< |
return bestType; |
| 234 |
< |
else { |
| 235 |
< |
|
| 224 |
> |
if (foundBends.size() > 0) { |
| 225 |
> |
std::sort(foundBends.begin(), foundBends.end()); |
| 226 |
> |
int jscore = foundBends[0].first; |
| 227 |
> |
int ikscore = foundBends[0].second; |
| 228 |
> |
std::vector<std::string> theKeys = foundBends[0].third; |
| 229 |
> |
|
| 230 |
> |
BendType* bestType = bendTypeCont_.find(theKeys); |
| 231 |
> |
return bestType; |
| 232 |
> |
} else { |
| 233 |
|
//if no exact match found, try wild card match |
| 234 |
|
return bendTypeCont_.find(keys, wildCardAtomTypeName_); |
| 235 |
|
} |
| 236 |
|
} |
| 237 |
|
} |
| 238 |
|
|
| 242 |
– |
|
| 239 |
|
TorsionType* ForceField::getTorsionType(const std::string &at1, |
| 240 |
|
const std::string &at2, |
| 241 |
|
const std::string &at3, |
| 323 |
|
jj++; |
| 324 |
|
} |
| 325 |
|
|
| 326 |
< |
std::sort(foundTorsions.begin(), foundTorsions.end()); |
| 327 |
< |
|
| 328 |
< |
int jkscore = foundTorsions[0].first; |
| 329 |
< |
int ilscore = foundTorsions[0].second; |
| 330 |
< |
std::vector<std::string> theKeys = foundTorsions[0].third; |
| 331 |
< |
|
| 332 |
< |
std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n"; |
| 333 |
< |
|
| 338 |
< |
|
| 339 |
< |
TorsionType* bestType = torsionTypeCont_.find(theKeys); |
| 340 |
< |
if (bestType) { |
| 341 |
< |
return bestType; |
| 326 |
> |
if (foundTorsions.size() > 0) { |
| 327 |
> |
std::sort(foundTorsions.begin(), foundTorsions.end()); |
| 328 |
> |
int jkscore = foundTorsions[0].first; |
| 329 |
> |
int ilscore = foundTorsions[0].second; |
| 330 |
> |
std::vector<std::string> theKeys = foundTorsions[0].third; |
| 331 |
> |
|
| 332 |
> |
TorsionType* bestType = torsionTypeCont_.find(theKeys); |
| 333 |
> |
return bestType; |
| 334 |
|
} else { |
| 335 |
|
//if no exact match found, try wild card match |
| 336 |
|
return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 349 |
|
keys.push_back(at4); |
| 350 |
|
|
| 351 |
|
//try exact match first |
| 352 |
< |
InversionType* inversionType = inversionTypeCont_.find(keys); |
| 352 |
> |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys); |
| 353 |
|
if (inversionType) { |
| 354 |
|
return inversionType; |
| 355 |
|
} else { |
| 411 |
|
myKeys.push_back((*k)->getName()); |
| 412 |
|
myKeys.push_back((*l)->getName()); |
| 413 |
|
|
| 414 |
< |
InversionType* inversionType = inversionTypeCont_.find(myKeys); |
| 414 |
> |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys); |
| 415 |
|
if (inversionType) { |
| 416 |
|
foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) ); |
| 417 |
|
} |
| 423 |
|
} |
| 424 |
|
jj++; |
| 425 |
|
} |
| 426 |
< |
|
| 427 |
< |
std::sort(foundInversions.begin(), foundInversions.end()); |
| 428 |
< |
|
| 429 |
< |
int iscore = foundInversions[0].first; |
| 430 |
< |
int jklscore = foundInversions[0].second; |
| 431 |
< |
std::vector<std::string> theKeys = foundInversions[0].third; |
| 432 |
< |
|
| 433 |
< |
std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n"; |
| 434 |
< |
|
| 443 |
< |
|
| 444 |
< |
InversionType* bestType = inversionTypeCont_.find(theKeys); |
| 445 |
< |
if (bestType) { |
| 446 |
< |
return bestType; |
| 426 |
> |
|
| 427 |
> |
if (foundInversions.size() > 0) { |
| 428 |
> |
std::sort(foundInversions.begin(), foundInversions.end()); |
| 429 |
> |
int iscore = foundInversions[0].first; |
| 430 |
> |
int jklscore = foundInversions[0].second; |
| 431 |
> |
std::vector<std::string> theKeys = foundInversions[0].third; |
| 432 |
> |
|
| 433 |
> |
InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys); |
| 434 |
> |
return bestType; |
| 435 |
|
} else { |
| 436 |
|
//if no exact match found, try wild card match |
| 437 |
|
return inversionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 510 |
|
return atomTypeCont_.add(keys, atomType); |
| 511 |
|
} |
| 512 |
|
|
| 513 |
+ |
bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) { |
| 514 |
+ |
std::vector<std::string> keys; |
| 515 |
+ |
keys.push_back(at); |
| 516 |
+ |
return atomTypeCont_.replace(keys, atomType); |
| 517 |
+ |
} |
| 518 |
+ |
|
| 519 |
|
bool ForceField::addBondType(const std::string &at1, const std::string &at2, |
| 520 |
|
BondType* bondType) { |
| 521 |
|
std::vector<std::string> keys; |
| 587 |
|
} else { |
| 588 |
|
sprintf( painCave.errMsg, |
| 589 |
|
"Can not cast GenericData to LJParam\n"); |
| 590 |
< |
painCave.severity = OOPSE_ERROR; |
| 590 |
> |
painCave.severity = OPENMD_ERROR; |
| 591 |
|
painCave.isFatal = 1; |
| 592 |
|
simError(); |
| 593 |
|
} |
| 594 |
|
} else { |
| 595 |
|
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 596 |
< |
painCave.severity = OOPSE_ERROR; |
| 596 |
> |
painCave.severity = OPENMD_ERROR; |
| 597 |
|
painCave.isFatal = 1; |
| 598 |
|
simError(); |
| 599 |
|
} |
| 623 |
|
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 624 |
|
"variable?\n", |
| 625 |
|
forceFieldFilename.c_str() ); |
| 626 |
< |
painCave.severity = OOPSE_ERROR; |
| 626 |
> |
painCave.severity = OPENMD_ERROR; |
| 627 |
|
painCave.isFatal = 1; |
| 628 |
|
simError(); |
| 629 |
|
} |
| 636 |
|
forceFieldOptions_.makeFortranOptions(theseFortranOptions); |
| 637 |
|
setfForceOptions(&theseFortranOptions); |
| 638 |
|
} |
| 639 |
< |
} //end namespace oopse |
| 639 |
> |
} //end namespace OpenMD |
