--- trunk/src/UseTheForce/ForceField.cpp 2008/09/10 19:40:06 1289 +++ branches/development/src/UseTheForce/ForceField.cpp 2010/12/31 18:31:56 1535 @@ -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; @@ -348,7 +357,7 @@ 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 { @@ -410,7 +419,7 @@ 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) ); } @@ -429,7 +438,7 @@ namespace oopse { int jklscore = foundInversions[0].second; std::vector theKeys = foundInversions[0].third; - InversionType* bestType = inversionTypeCont_.find(theKeys); + InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys); return bestType; } else { //if no exact match found, try wild card match @@ -442,14 +451,14 @@ namespace oopse { std::vector keys; keys.push_back(at1); keys.push_back(at2); - + //try exact match first NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys); if (nbiType) { return nbiType; } else { //if no exact match found, try wild card match - return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); + return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); } } @@ -506,12 +515,14 @@ 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); } @@ -586,13 +597,13 @@ 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(); } @@ -622,7 +633,7 @@ 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(); } @@ -630,9 +641,4 @@ namespace oopse { return ffStream; } - void ForceField::setFortranForceOptions(){ - ForceOptions theseFortranOptions; - forceFieldOptions_.makeFortranOptions(theseFortranOptions); - setfForceOptions(&theseFortranOptions); - } -} //end namespace oopse +} //end namespace OpenMD