--- trunk/src/UseTheForce/ForceField.cpp 2008/07/04 20:54:29 1275 +++ trunk/src/UseTheForce/ForceField.cpp 2010/07/07 15:04:32 1460 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,15 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). */ /** @@ -54,12 +54,13 @@ #include "UseTheForce/DarkSide/atype_interface.h" #include "UseTheForce/DarkSide/fForceOptions_interface.h" #include "UseTheForce/DarkSide/switcheroo_interface.h" -namespace oopse { +namespace OpenMD { ForceField::ForceField() { + char* tempPath; tempPath = getenv("FORCE_PARAM_PATH"); - + if (tempPath == NULL) { //convert a macro from compiler to a string in c++ STR_DEFINE(ffPath_, FRC_PATH ); @@ -133,20 +134,20 @@ namespace oopse { ii++; } - // sort the foundBonds by the score: - std::sort(foundBonds.begin(), foundBonds.end()); - - int bestScore = foundBonds[0].first; - std::vector theKeys = foundBonds[0].second; - - std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1] << "\t(score = "<< bestScore << ")\n"; - BondType* bestType = bondTypeCont_.find(theKeys); - if (bestType) - return bestType; - else { - //if no exact match found, try wild card match - return bondTypeCont_.find(keys, wildCardAtomTypeName_); + if (foundBonds.size() > 0) { + // sort the foundBonds by the score: + std::sort(foundBonds.begin(), foundBonds.end()); + + int bestScore = foundBonds[0].first; + std::vector theKeys = foundBonds[0].second; + + BondType* bestType = bondTypeCont_.find(theKeys); + + return bestType; + } else { + //if no exact match found, try wild card match + return bondTypeCont_.find(keys, wildCardAtomTypeName_); } } } @@ -220,26 +221,21 @@ namespace oopse { jj++; } - std::sort(foundBends.begin(), foundBends.end()); - - int jscore = foundBends[0].first; - int ikscore = foundBends[0].second; - std::vector theKeys = foundBends[0].third; - - std::cout << "best matching bend = " << theKeys[0] << "\t" < 0) { + std::sort(foundBends.begin(), foundBends.end()); + int jscore = foundBends[0].first; + int ikscore = foundBends[0].second; + std::vector theKeys = foundBends[0].third; + + BendType* bestType = bendTypeCont_.find(theKeys); + return bestType; + } else { //if no exact match found, try wild card match return bendTypeCont_.find(keys, wildCardAtomTypeName_); } } } - TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2, const std::string &at3, @@ -327,18 +323,14 @@ namespace oopse { jj++; } - std::sort(foundTorsions.begin(), foundTorsions.end()); - - int jkscore = foundTorsions[0].first; - int ilscore = foundTorsions[0].second; - std::vector theKeys = foundTorsions[0].third; - - std::cout << "best matching torsion = " << theKeys[0] << "\t" < 0) { + std::sort(foundTorsions.begin(), foundTorsions.end()); + int jkscore = foundTorsions[0].first; + int ilscore = foundTorsions[0].second; + std::vector theKeys = foundTorsions[0].third; + + TorsionType* bestType = torsionTypeCont_.find(theKeys); + return bestType; } else { //if no exact match found, try wild card match return torsionTypeCont_.find(keys, wildCardAtomTypeName_); @@ -357,7 +349,7 @@ namespace oopse { keys.push_back(at4); //try exact match first - InversionType* inversionType = inversionTypeCont_.find(keys); + InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys); if (inversionType) { return inversionType; } else { @@ -419,7 +411,7 @@ namespace oopse { myKeys.push_back((*k)->getName()); myKeys.push_back((*l)->getName()); - InversionType* inversionType = inversionTypeCont_.find(myKeys); + InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys); if (inversionType) { foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) ); } @@ -431,19 +423,15 @@ namespace oopse { } jj++; } - - std::sort(foundInversions.begin(), foundInversions.end()); - - int iscore = foundInversions[0].first; - int jklscore = foundInversions[0].second; - std::vector theKeys = foundInversions[0].third; - - std::cout << "best matching inversion = " << theKeys[0] << "\t" < 0) { + std::sort(foundInversions.begin(), foundInversions.end()); + int iscore = foundInversions[0].first; + int jklscore = foundInversions[0].second; + std::vector theKeys = foundInversions[0].third; + + InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys); + return bestType; } else { //if no exact match found, try wild card match return inversionTypeCont_.find(keys, wildCardAtomTypeName_); @@ -522,6 +510,12 @@ namespace oopse { return atomTypeCont_.add(keys, atomType); } + bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) { + std::vector keys; + keys.push_back(at); + return atomTypeCont_.replace(keys, atomType); + } + bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) { std::vector keys; @@ -593,13 +587,13 @@ namespace oopse { } else { sprintf( painCave.errMsg, "Can not cast GenericData to LJParam\n"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } } else { sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } @@ -629,7 +623,7 @@ namespace oopse { "\tHave you tried setting the FORCE_PARAM_PATH environment " "variable?\n", forceFieldFilename.c_str() ); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } @@ -642,4 +636,4 @@ namespace oopse { forceFieldOptions_.makeFortranOptions(theseFortranOptions); setfForceOptions(&theseFortranOptions); } -} //end namespace oopse +} //end namespace OpenMD