| 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 |
|
} |
| 211 |
|
} |
| 212 |
|
jj++; |
| 213 |
|
} |
| 222 |
– |
|
| 223 |
– |
std::sort(foundBends.begin(), foundBends.end()); |
| 224 |
– |
|
| 225 |
– |
int jscore = foundBends[0].first; |
| 226 |
– |
int ikscore = foundBends[0].second; |
| 227 |
– |
std::vector<std::string> theKeys = foundBends[0].third; |
| 228 |
– |
|
| 229 |
– |
std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n"; |
| 230 |
– |
|
| 231 |
– |
BendType* bestType = bendTypeCont_.find(theKeys); |
| 232 |
– |
if (bestType) |
| 233 |
– |
return bestType; |
| 234 |
– |
else { |
| 214 |
|
|
| 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()); |
| 318 |
< |
|
| 319 |
< |
int jkscore = foundTorsions[0].first; |
| 320 |
< |
int ilscore = foundTorsions[0].second; |
| 321 |
< |
std::vector<std::string> theKeys = foundTorsions[0].third; |
| 322 |
< |
|
| 323 |
< |
std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n"; |
| 324 |
< |
|
| 338 |
< |
|
| 339 |
< |
TorsionType* bestType = torsionTypeCont_.find(theKeys); |
| 340 |
< |
if (bestType) { |
| 341 |
< |
return bestType; |
| 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_); |
| 340 |
|
keys.push_back(at4); |
| 341 |
|
|
| 342 |
|
//try exact match first |
| 343 |
< |
InversionType* inversionType = inversionTypeCont_.find(keys); |
| 343 |
> |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys); |
| 344 |
|
if (inversionType) { |
| 345 |
|
return inversionType; |
| 346 |
|
} else { |
| 402 |
|
myKeys.push_back((*k)->getName()); |
| 403 |
|
myKeys.push_back((*l)->getName()); |
| 404 |
|
|
| 405 |
< |
InversionType* inversionType = inversionTypeCont_.find(myKeys); |
| 405 |
> |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys); |
| 406 |
|
if (inversionType) { |
| 407 |
|
foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) ); |
| 408 |
|
} |
| 414 |
|
} |
| 415 |
|
jj++; |
| 416 |
|
} |
| 417 |
< |
|
| 418 |
< |
std::sort(foundInversions.begin(), foundInversions.end()); |
| 419 |
< |
|
| 420 |
< |
int iscore = foundInversions[0].first; |
| 421 |
< |
int jklscore = foundInversions[0].second; |
| 422 |
< |
std::vector<std::string> theKeys = foundInversions[0].third; |
| 423 |
< |
|
| 424 |
< |
std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n"; |
| 425 |
< |
|
| 443 |
< |
|
| 444 |
< |
InversionType* bestType = inversionTypeCont_.find(theKeys); |
| 445 |
< |
if (bestType) { |
| 446 |
< |
return bestType; |
| 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 inversionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 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; |
| 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(){ |
| 641 |
< |
ForceOptions theseFortranOptions; |
| 642 |
< |
forceFieldOptions_.makeFortranOptions(theseFortranOptions); |
| 643 |
< |
setfForceOptions(&theseFortranOptions); |
| 644 |
< |
} |
| 645 |
< |
} //end namespace oopse |
| 625 |
> |
} //end namespace OpenMD |
