--- trunk/src/UseTheForce/ForceField.cpp 2008/07/14 12:35:58 1277 +++ branches/development/src/UseTheForce/ForceField.cpp 2011/09/14 21:15:17 1629 @@ -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). */ /** @@ -51,15 +51,13 @@ #include "UseTheForce/ForceField.hpp" #include "utils/simError.h" #include "utils/Tuple.hpp" -#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 ); @@ -68,18 +66,29 @@ namespace oopse { } } - - ForceField::~ForceField() { - deleteAtypes(); - deleteSwitch(); - } - + /** + * getAtomType by string + * + * finds the requested atom type in this force field using the string + * name of the atom type. + */ AtomType* ForceField::getAtomType(const std::string &at) { std::vector keys; keys.push_back(at); return atomTypeCont_.find(keys); } + /** + * getAtomType by ident + * + * finds the requested atom type in this force field using the + * integer ident instead of the string name of the atom type. + */ + AtomType* ForceField::getAtomType(int ident) { + std::string at = atypeIdentToName.find(ident)->second; + return getAtomType(at); + } + BondType* ForceField::getBondType(const std::string &at1, const std::string &at2) { std::vector keys; @@ -124,7 +133,6 @@ namespace oopse { myKeys.push_back((*i)->getName()); myKeys.push_back((*j)->getName()); - std::cerr << "looking for " << myKeys[0] << " " << myKeys[1] << "\n"; BondType* bondType = bondTypeCont_.find(myKeys); if (bondType) { foundBonds.push_back(std::make_pair(bondTypeScore, myKeys)); @@ -142,7 +150,6 @@ namespace oopse { 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); return bestType; @@ -226,9 +233,7 @@ namespace oopse { 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" < theKeys = foundBends[0].third; BendType* bestType = bendTypeCont_.find(theKeys); return bestType; @@ -332,8 +337,6 @@ namespace oopse { int ilscore = foundTorsions[0].second; std::vector theKeys = foundTorsions[0].third; - std::cout << "best matching torsion = " << theKeys[0] << "\t" <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) ); } @@ -435,9 +438,7 @@ namespace oopse { int jklscore = foundInversions[0].second; std::vector theKeys = foundInversions[0].third; - std::cout << "best matching inversion = " << theKeys[0] << "\t" < keys; keys.push_back(at1); keys.push_back(at2); @@ -456,9 +458,63 @@ namespace oopse { if (nbiType) { return nbiType; } else { - //if no exact match found, try wild card match - return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); - } + AtomType* atype1; + AtomType* atype2; + std::vector at1key; + at1key.push_back(at1); + atype1 = atomTypeCont_.find(at1key); + + std::vector at2key; + at2key.push_back(at2); + atype2 = atomTypeCont_.find(at2key); + + // query atom types for their chains of responsibility + std::vector at1Chain = atype1->allYourBase(); + std::vector at2Chain = atype2->allYourBase(); + + std::vector::iterator i; + std::vector::iterator j; + + int ii = 0; + int jj = 0; + int nbiTypeScore; + + std::vector > > foundNBI; + + for (i = at1Chain.begin(); i != at1Chain.end(); i++) { + jj = 0; + for (j = at2Chain.begin(); j != at2Chain.end(); j++) { + + nbiTypeScore = ii + jj; + + std::vector myKeys; + myKeys.push_back((*i)->getName()); + myKeys.push_back((*j)->getName()); + + NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys); + if (nbiType) { + foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys)); + } + jj++; + } + ii++; + } + + + if (foundNBI.size() > 0) { + // sort the foundNBI by the score: + std::sort(foundNBI.begin(), foundNBI.end()); + + int bestScore = foundNBI[0].first; + std::vector theKeys = foundNBI[0].second; + + NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys); + return bestType; + } else { + //if no exact match found, try wild card match + return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); + } + } } BondType* ForceField::getExactBondType(const std::string &at1, @@ -514,9 +570,17 @@ namespace oopse { bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { std::vector keys; keys.push_back(at); + atypeIdentToName[atomType->getIdent()] = at; return atomTypeCont_.add(keys, atomType); } + bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) { + std::vector keys; + keys.push_back(at); + atypeIdentToName[atomType->getIdent()] = at; + return atomTypeCont_.replace(keys, atomType); + } + bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) { std::vector keys; @@ -588,13 +652,13 @@ 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(); } @@ -624,7 +688,7 @@ 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(); } @@ -632,9 +696,4 @@ namespace oopse { return ffStream; } - void ForceField::setFortranForceOptions(){ - ForceOptions theseFortranOptions; - forceFieldOptions_.makeFortranOptions(theseFortranOptions); - setfForceOptions(&theseFortranOptions); - } -} //end namespace oopse +} //end namespace OpenMD