| 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 |
|
/** |
| 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 { |
| 55 |
> |
namespace OpenMD { |
| 56 |
|
|
| 57 |
|
ForceField::ForceField() { |
| 58 |
+ |
|
| 59 |
|
char* tempPath; |
| 60 |
|
tempPath = getenv("FORCE_PARAM_PATH"); |
| 61 |
< |
|
| 61 |
> |
|
| 62 |
|
if (tempPath == NULL) { |
| 63 |
|
//convert a macro from compiler to a string in c++ |
| 64 |
|
STR_DEFINE(ffPath_, FRC_PATH ); |
| 70 |
|
|
| 71 |
|
ForceField::~ForceField() { |
| 72 |
|
deleteAtypes(); |
| 74 |
– |
deleteSwitch(); |
| 73 |
|
} |
| 74 |
|
|
| 75 |
|
AtomType* ForceField::getAtomType(const std::string &at) { |
| 122 |
|
myKeys.push_back((*i)->getName()); |
| 123 |
|
myKeys.push_back((*j)->getName()); |
| 124 |
|
|
| 127 |
– |
std::cerr << "looking for " << myKeys[0] << " " << myKeys[1] << "\n"; |
| 125 |
|
BondType* bondType = bondTypeCont_.find(myKeys); |
| 126 |
|
if (bondType) { |
| 127 |
|
foundBonds.push_back(std::make_pair(bondTypeScore, myKeys)); |
| 139 |
|
int bestScore = foundBonds[0].first; |
| 140 |
|
std::vector<std::string> theKeys = foundBonds[0].second; |
| 141 |
|
|
| 145 |
– |
std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1] << "\t(score = "<< bestScore << ")\n"; |
| 142 |
|
BondType* bestType = bondTypeCont_.find(theKeys); |
| 143 |
|
|
| 144 |
|
return bestType; |
| 222 |
|
std::sort(foundBends.begin(), foundBends.end()); |
| 223 |
|
int jscore = foundBends[0].first; |
| 224 |
|
int ikscore = foundBends[0].second; |
| 225 |
< |
std::vector<std::string> theKeys = foundBends[0].third; |
| 225 |
> |
std::vector<std::string> theKeys = foundBends[0].third; |
| 226 |
|
|
| 231 |
– |
std::cout << "best matching bend = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t(scores = "<< jscore << "\t" << ikscore << ")\n"; |
| 232 |
– |
|
| 227 |
|
BendType* bestType = bendTypeCont_.find(theKeys); |
| 228 |
|
return bestType; |
| 229 |
|
} else { |
| 326 |
|
int ilscore = foundTorsions[0].second; |
| 327 |
|
std::vector<std::string> theKeys = foundTorsions[0].third; |
| 328 |
|
|
| 335 |
– |
std::cout << "best matching torsion = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< jkscore << "\t" << ilscore << ")\n"; |
| 336 |
– |
|
| 329 |
|
TorsionType* bestType = torsionTypeCont_.find(theKeys); |
| 330 |
|
return bestType; |
| 331 |
|
} else { |
| 346 |
|
keys.push_back(at4); |
| 347 |
|
|
| 348 |
|
//try exact match first |
| 349 |
< |
InversionType* inversionType = inversionTypeCont_.find(keys); |
| 349 |
> |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys); |
| 350 |
|
if (inversionType) { |
| 351 |
|
return inversionType; |
| 352 |
|
} else { |
| 408 |
|
myKeys.push_back((*k)->getName()); |
| 409 |
|
myKeys.push_back((*l)->getName()); |
| 410 |
|
|
| 411 |
< |
InversionType* inversionType = inversionTypeCont_.find(myKeys); |
| 411 |
> |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys); |
| 412 |
|
if (inversionType) { |
| 413 |
|
foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) ); |
| 414 |
|
} |
| 427 |
|
int jklscore = foundInversions[0].second; |
| 428 |
|
std::vector<std::string> theKeys = foundInversions[0].third; |
| 429 |
|
|
| 430 |
< |
std::cout << "best matching inversion = " << theKeys[0] << "\t" <<theKeys[1] << "\t" << theKeys[2] << "\t" << theKeys[3] << "\t(scores = "<< iscore << "\t" << jklscore << ")\n"; |
| 439 |
< |
|
| 440 |
< |
InversionType* bestType = inversionTypeCont_.find(theKeys); |
| 430 |
> |
InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys); |
| 431 |
|
return bestType; |
| 432 |
|
} else { |
| 433 |
|
//if no exact match found, try wild card match |
| 584 |
|
} else { |
| 585 |
|
sprintf( painCave.errMsg, |
| 586 |
|
"Can not cast GenericData to LJParam\n"); |
| 587 |
< |
painCave.severity = OOPSE_ERROR; |
| 587 |
> |
painCave.severity = OPENMD_ERROR; |
| 588 |
|
painCave.isFatal = 1; |
| 589 |
|
simError(); |
| 590 |
|
} |
| 591 |
|
} else { |
| 592 |
|
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 593 |
< |
painCave.severity = OOPSE_ERROR; |
| 593 |
> |
painCave.severity = OPENMD_ERROR; |
| 594 |
|
painCave.isFatal = 1; |
| 595 |
|
simError(); |
| 596 |
|
} |
| 620 |
|
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 621 |
|
"variable?\n", |
| 622 |
|
forceFieldFilename.c_str() ); |
| 623 |
< |
painCave.severity = OOPSE_ERROR; |
| 623 |
> |
painCave.severity = OPENMD_ERROR; |
| 624 |
|
painCave.isFatal = 1; |
| 625 |
|
simError(); |
| 626 |
|
} |
| 628 |
|
return ffStream; |
| 629 |
|
} |
| 630 |
|
|
| 631 |
< |
void ForceField::setFortranForceOptions(){ |
| 642 |
< |
ForceOptions theseFortranOptions; |
| 643 |
< |
forceFieldOptions_.makeFortranOptions(theseFortranOptions); |
| 644 |
< |
setfForceOptions(&theseFortranOptions); |
| 645 |
< |
} |
| 646 |
< |
} //end namespace oopse |
| 631 |
> |
} //end namespace OpenMD |
