--- trunk/src/UseTheForce/ForceField.cpp 2004/11/04 20:51:23 206 +++ trunk/src/UseTheForce/ForceField.cpp 2008/07/30 18:11:19 1282 @@ -1,96 +1,646 @@ +/* + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. + * + * The University of Notre Dame grants you ("Licensee") a + * non-exclusive, royalty free, license to use, modify and + * 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 + * notice, this list of conditions and the following disclaimer. + * + * 3. 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. + * + * This software is provided "AS IS," without a warranty of any + * kind. All express or implied conditions, representations and + * warranties, including any implied warranty of merchantability, + * fitness for a particular purpose or non-infringement, are hereby + * excluded. The University of Notre Dame and its licensors shall not + * be liable for any damages suffered by licensee as a result of + * using, modifying or distributing the software or its + * derivatives. In no event will the University of Notre Dame or its + * licensors be liable for any lost revenue, profit or data, or for + * direct, indirect, special, consequential, incidental or punitive + * damages, however caused and regardless of the theory of liability, + * 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. + */ + +/** + * @file ForceField.cpp + * @author tlin + * @date 11/04/2004 + * @time 22:51am + * @version 1.0 + */ + +#include #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 { -AtomType* ForceField::getMatchingAtomType(const string &at) { + ForceField::ForceField() { + char* tempPath; + tempPath = getenv("FORCE_PARAM_PATH"); - map::iterator iter; - - iter = atomTypeMap.find(at); - if (iter != atomTypeMap.end()) { - return iter->second; - } else { - return NULL; + if (tempPath == NULL) { + //convert a macro from compiler to a string in c++ + STR_DEFINE(ffPath_, FRC_PATH ); + } else { + ffPath_ = tempPath; + } } -} -BondType* ForceField::getMatchingBondType(const string &at1, - const string &at2) { - map, BondType*>::iterator iter; - vector foundTypes; + ForceField::~ForceField() { + deleteAtypes(); + deleteSwitch(); + } - iter = bondTypeMap.find(pair); - if (iter != bondTypeMap.end()) { - // exact match, so just return it - return iter->second; - } + AtomType* ForceField::getAtomType(const std::string &at) { + std::vector keys; + keys.push_back(at); + return atomTypeCont_.find(keys); + } - iter = bondTypeMap.find(pair); - if (iter != bondTypeMap.end()) { - // exact match in reverse order, so just return it - return iter->second; - } + BondType* ForceField::getBondType(const std::string &at1, + const std::string &at2) { + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); - iter = bondTypeMap.find(pair); - if (iter != bondTypeMap.end()) { - foundTypes.push_back(iter->second); - } + //try exact match first + BondType* bondType = bondTypeCont_.find(keys); + if (bondType) { + return bondType; + } else { + 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); - iter = bondTypeMap.find(pair); - if (iter != bondTypeMap.end()) { - foundTypes.push_back(iter->second); - } + // query atom types for their chains of responsibility + std::vector at1Chain = atype1->allYourBase(); + std::vector at2Chain = atype2->allYourBase(); - iter = bondTypeMap.find(pair); - if (iter != bondTypeMap.end()) { - foundTypes.push_back(iter->second); - } + std::vector::iterator i; + std::vector::iterator j; - iter = bondTypeMap.find(pair); - if (iter != bondTypeMap.end()) { - foundTypes.push_back(iter->second); + int ii = 0; + int jj = 0; + int bondTypeScore; + + std::vector > > foundBonds; + + for (i = at1Chain.begin(); i != at1Chain.end(); i++) { + jj = 0; + for (j = at2Chain.begin(); j != at2Chain.end(); j++) { + + bondTypeScore = ii + jj; + + std::vector myKeys; + 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)); + } + jj++; + } + ii++; + } + + + 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; + + std::cout << "best matching bond = " << theKeys[0] << "\t" << theKeys[1] << "\t(score = "<< bestScore << ")\n"; + BondType* bestType = bondTypeCont_.find(theKeys); + + return bestType; + } else { + //if no exact match found, try wild card match + return bondTypeCont_.find(keys, wildCardAtomTypeName_); + } + } } - if (foundTypes.empty()) { - return NULL; - } else { - + BendType* ForceField::getBendType(const std::string &at1, + const std::string &at2, + const std::string &at3) { + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); + keys.push_back(at3); - + //try exact match first + BendType* bendType = bendTypeCont_.find(keys); + if (bendType) { + return bendType; + } else { + AtomType* atype1; + AtomType* atype2; + AtomType* atype3; + std::vector at1key; + at1key.push_back(at1); + atype1 = atomTypeCont_.find(at1key); + + std::vector at2key; + at2key.push_back(at2); + atype2 = atomTypeCont_.find(at2key); + std::vector at3key; + at3key.push_back(at3); + atype3 = atomTypeCont_.find(at3key); - + // query atom types for their chains of responsibility + std::vector at1Chain = atype1->allYourBase(); + std::vector at2Chain = atype2->allYourBase(); + std::vector at3Chain = atype3->allYourBase(); + std::vector::iterator i; + std::vector::iterator j; + std::vector::iterator k; -BendType* ForceField::getMatchingBendType(const string &at1, const string &at2, - const string &at3); -TorsionType* ForceField::getMatchingTorsionType(const string &at1, const string &at2, - const string &at3, const string &at4); + int ii = 0; + int jj = 0; + int kk = 0; + int IKscore; -double ForceField::getRcutForAtomType(AtomType* at); + std::vector > > foundBends; + for (j = at2Chain.begin(); j != at2Chain.end(); j++) { + ii = 0; + for (i = at1Chain.begin(); i != at1Chain.end(); i++) { + kk = 0; + for (k = at3Chain.begin(); k != at3Chain.end(); k++) { + + IKscore = ii + kk; - vector > generateWildcardSequence(const vector atomTypes) { - - vector > results; + std::vector myKeys; + myKeys.push_back((*i)->getName()); + myKeys.push_back((*j)->getName()); + myKeys.push_back((*k)->getName()); - + BendType* bendType = bendTypeCont_.find(myKeys); + if (bendType) { + foundBends.push_back( make_tuple3(jj, IKscore, myKeys) ); + } + kk++; + } + ii++; + } + jj++; + } + + if (foundBends.size() > 0) { + 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" < keys; + keys.push_back(at1); + keys.push_back(at2); + keys.push_back(at3); + keys.push_back(at4); - vector > getAllWildcardPermutations(const vector myAts) { - - int nStrings; - vector oneResult; - vector > allResults; - nStrings = myAts.size(); + //try exact match first + TorsionType* torsionType = torsionTypeCont_.find(keys); + if (torsionType) { + return torsionType; + } else { - if (nStrings == 1) { - oneResult.push_back(wildcardCharacter); - allResults.push_back(oneResult); - return allResults; - } else { - - for (i=0; i < nStrings; i++) { - oneResult = myAts; - replace(oneResult.begin(), oneResult.end(), + AtomType* atype1; + AtomType* atype2; + AtomType* atype3; + AtomType* atype4; + std::vector at1key; + at1key.push_back(at1); + atype1 = atomTypeCont_.find(at1key); + + std::vector at2key; + at2key.push_back(at2); + atype2 = atomTypeCont_.find(at2key); + + std::vector at3key; + at3key.push_back(at3); + atype3 = atomTypeCont_.find(at3key); + + std::vector at4key; + at4key.push_back(at4); + atype4 = atomTypeCont_.find(at4key); + + // query atom types for their chains of responsibility + std::vector at1Chain = atype1->allYourBase(); + std::vector at2Chain = atype2->allYourBase(); + std::vector at3Chain = atype3->allYourBase(); + std::vector at4Chain = atype4->allYourBase(); + + std::vector::iterator i; + std::vector::iterator j; + std::vector::iterator k; + std::vector::iterator l; + + int ii = 0; + int jj = 0; + int kk = 0; + int ll = 0; + int ILscore; + int JKscore; + + std::vector > > foundTorsions; + + for (j = at2Chain.begin(); j != at2Chain.end(); j++) { + kk = 0; + for (k = at3Chain.begin(); k != at3Chain.end(); k++) { + ii = 0; + for (i = at1Chain.begin(); i != at1Chain.end(); i++) { + ll = 0; + for (l = at4Chain.begin(); l != at4Chain.end(); l++) { + + ILscore = ii + ll; + JKscore = jj + kk; + + std::vector myKeys; + myKeys.push_back((*i)->getName()); + myKeys.push_back((*j)->getName()); + myKeys.push_back((*k)->getName()); + myKeys.push_back((*l)->getName()); + + TorsionType* torsionType = torsionTypeCont_.find(myKeys); + if (torsionType) { + foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) ); + } + ll++; + } + ii++; + } + kk++; + } + jj++; + } + + if (foundTorsions.size() > 0) { + 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" < keys; + keys.push_back(at1); + keys.push_back(at2); + keys.push_back(at3); + keys.push_back(at4); + + //try exact match first + InversionType* inversionType = inversionTypeCont_.find(keys); + if (inversionType) { + return inversionType; + } else { + + AtomType* atype1; + AtomType* atype2; + AtomType* atype3; + AtomType* atype4; + std::vector at1key; + at1key.push_back(at1); + atype1 = atomTypeCont_.find(at1key); + + std::vector at2key; + at2key.push_back(at2); + atype2 = atomTypeCont_.find(at2key); + + std::vector at3key; + at3key.push_back(at3); + atype3 = atomTypeCont_.find(at3key); + + std::vector at4key; + at4key.push_back(at4); + atype4 = atomTypeCont_.find(at4key); + + // query atom types for their chains of responsibility + std::vector at1Chain = atype1->allYourBase(); + std::vector at2Chain = atype2->allYourBase(); + std::vector at3Chain = atype3->allYourBase(); + std::vector at4Chain = atype4->allYourBase(); + + std::vector::iterator i; + std::vector::iterator j; + std::vector::iterator k; + std::vector::iterator l; + + int ii = 0; + int jj = 0; + int kk = 0; + int ll = 0; + int Iscore; + int JKLscore; + + std::vector > > foundInversions; + + for (j = at2Chain.begin(); j != at2Chain.end(); j++) { + kk = 0; + for (k = at3Chain.begin(); k != at3Chain.end(); k++) { + ii = 0; + for (i = at1Chain.begin(); i != at1Chain.end(); i++) { + ll = 0; + for (l = at4Chain.begin(); l != at4Chain.end(); l++) { + + Iscore = ii; + JKLscore = jj + kk + ll; + + std::vector myKeys; + myKeys.push_back((*i)->getName()); + myKeys.push_back((*j)->getName()); + myKeys.push_back((*k)->getName()); + myKeys.push_back((*l)->getName()); + + InversionType* inversionType = inversionTypeCont_.find(myKeys); + if (inversionType) { + foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) ); + } + ll++; + } + ii++; + } + kk++; + } + jj++; + } + + if (foundInversions.size() > 0) { + 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" < 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_); + } + } + + BondType* ForceField::getExactBondType(const std::string &at1, + const std::string &at2){ + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); + return bondTypeCont_.find(keys); + } + + BendType* ForceField::getExactBendType(const std::string &at1, + const std::string &at2, + const std::string &at3){ + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); + keys.push_back(at3); + return bendTypeCont_.find(keys); + } + + TorsionType* ForceField::getExactTorsionType(const std::string &at1, + const std::string &at2, + const std::string &at3, + const std::string &at4){ + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); + keys.push_back(at3); + keys.push_back(at4); + return torsionTypeCont_.find(keys); + } + + InversionType* ForceField::getExactInversionType(const std::string &at1, + const std::string &at2, + const std::string &at3, + const std::string &at4){ + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); + keys.push_back(at3); + keys.push_back(at4); + return inversionTypeCont_.find(keys); + } + + NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){ + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); + return nonBondedInteractionTypeCont_.find(keys); + } + + + bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { + std::vector keys; + keys.push_back(at); + 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; + keys.push_back(at1); + keys.push_back(at2); + return bondTypeCont_.add(keys, bondType); + } + + bool ForceField::addBendType(const std::string &at1, const std::string &at2, + const std::string &at3, BendType* bendType) { + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); + keys.push_back(at3); + return bendTypeCont_.add(keys, bendType); + } + + bool ForceField::addTorsionType(const std::string &at1, + const std::string &at2, + const std::string &at3, + const std::string &at4, + TorsionType* torsionType) { + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); + keys.push_back(at3); + keys.push_back(at4); + return torsionTypeCont_.add(keys, torsionType); + } + + bool ForceField::addInversionType(const std::string &at1, + const std::string &at2, + const std::string &at3, + const std::string &at4, + InversionType* inversionType) { + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); + keys.push_back(at3); + keys.push_back(at4); + return inversionTypeCont_.add(keys, inversionType); + } + + bool ForceField::addNonBondedInteractionType(const std::string &at1, + const std::string &at2, + NonBondedInteractionType* nbiType) { + std::vector keys; + keys.push_back(at1); + keys.push_back(at2); + return nonBondedInteractionTypeCont_.add(keys, nbiType); + } + + RealType ForceField::getRcutFromAtomType(AtomType* at) { + /**@todo */ + GenericData* data; + RealType rcut = 0.0; + + if (at->isLennardJones()) { + data = at->getPropertyByName("LennardJones"); + if (data != NULL) { + LJParamGenericData* ljData = dynamic_cast(data); + + if (ljData != NULL) { + LJParam ljParam = ljData->getData(); + + //by default use 2.5*sigma as cutoff radius + rcut = 2.5 * ljParam.sigma; + + } else { + sprintf( painCave.errMsg, + "Can not cast GenericData to LJParam\n"); + painCave.severity = OOPSE_ERROR; + painCave.isFatal = 1; + simError(); + } + } else { + sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); + painCave.severity = OOPSE_ERROR; + painCave.isFatal = 1; + simError(); + } + } + return rcut; + } + + + ifstrstream* ForceField::openForceFieldFile(const std::string& filename) { + std::string forceFieldFilename(filename); + ifstrstream* ffStream = new ifstrstream(); + + //try to open the force filed file in current directory first + ffStream->open(forceFieldFilename.c_str()); + if(!ffStream->is_open()){ + + forceFieldFilename = ffPath_ + "/" + forceFieldFilename; + ffStream->open( forceFieldFilename.c_str() ); + + //if current directory does not contain the force field file, + //try to open it in the path + if(!ffStream->is_open()){ + + sprintf( painCave.errMsg, + "Error opening the force field parameter file:\n" + "\t%s\n" + "\tHave you tried setting the FORCE_PARAM_PATH environment " + "variable?\n", + forceFieldFilename.c_str() ); + painCave.severity = OOPSE_ERROR; + painCave.isFatal = 1; + simError(); + } + } + return ffStream; + } + + void ForceField::setFortranForceOptions(){ + ForceOptions theseFortranOptions; + forceFieldOptions_.makeFortranOptions(theseFortranOptions); + setfForceOptions(&theseFortranOptions); + } +} //end namespace oopse