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/* |
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* Copyright (c) 2007 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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|
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#include "UseTheForce/MnM_FF.hpp" |
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#include "UseTheForce/DarkSide/lj_interface.h" |
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#include "UseTheForce/DarkSide/sticky_interface.h" |
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#include "UseTheForce/DarkSide/eam_interface.h" |
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#include "UseTheForce/DarkSide/suttonchen_interface.h" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "io/DirectionalAtomTypesSectionParser.hpp" |
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#include "io/BaseAtomTypesSectionParser.hpp" |
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#include "io/AtomTypesSectionParser.hpp" |
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#include "io/LennardJonesAtomTypesSectionParser.hpp" |
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#include "io/ChargeAtomTypesSectionParser.hpp" |
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#include "io/MultipoleAtomTypesSectionParser.hpp" |
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#include "io/StickyAtomTypesSectionParser.hpp" |
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#include "io/StickyPowerAtomTypesSectionParser.hpp" |
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#include "io/GayBerneAtomTypesSectionParser.hpp" |
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#include "io/BondTypesSectionParser.hpp" |
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#include "io/BendTypesSectionParser.hpp" |
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#include "io/TorsionTypesSectionParser.hpp" |
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#include "io/MetalNonMetalInteractionsSectionParser.hpp" |
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#include "io/EAMAtomTypesSectionParser.hpp" |
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#include "io/SCAtomTypesSectionParser.hpp" |
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#include "io/OptionSectionParser.hpp" |
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#include "UseTheForce/ForceFieldCreator.hpp" |
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|
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|
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namespace oopse { |
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|
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MnM_FF::MnM_FF() { |
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|
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//set default force field filename |
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setForceFieldFileName("MnM.frc"); |
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|
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//The order of adding section parsers is important. |
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//OptionSectionParser must come first to set options for other parsers |
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//DirectionalAtomTypesSectionParser should be added before |
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//AtomTypesSectionParser, and these two section parsers will actually |
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//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and |
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//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which |
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//is a subclass of AtomType and should come first). Other AtomTypes Section |
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//Parser will not create the "real" AtomType, they only add and set some |
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//attribute of the AtomType. Thus their order are not important. |
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//AtomTypesSectionParser should be added before other atom type section |
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//parsers. Make sure they are added after DirectionalAtomTypesSectionParser |
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//and AtomTypesSectionParser. The order of BondTypesSectionParser, |
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//BendTypesSectionParser and TorsionTypesSectionParser are not important. |
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spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new BaseAtomTypesSectionParser()); |
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spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new AtomTypesSectionParser()); |
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spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new MetalNonMetalInteractionsSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
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|
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} |
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|
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void MnM_FF::parse(const std::string& filename) { |
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ifstrstream* ffStream; |
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|
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ffStream = openForceFieldFile(filename); |
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|
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spMan_.parse(*ffStream, *this); |
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|
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ForceField::AtomTypeContainer::MapTypeIterator i; |
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AtomType* at; |
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ForceField::AtomTypeContainer::MapTypeIterator j; |
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AtomType* at2; |
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ForceField::NonBondedInteractionTypeContainer::MapTypeIterator k; |
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NonBondedInteractionType* nbit; |
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|
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for (at = atomTypeCont_.beginType(i); at != NULL; |
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at = atomTypeCont_.nextType(i)) { |
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// useBase sets the responsibilities, and these have to be done |
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// after the atomTypes and Base types have all been scanned: |
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|
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std::vector<AtomType*> ayb = at->allYourBase(); |
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if (ayb.size() > 1) { |
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for (int j = ayb.size()-1; j > 0; j--) { |
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|
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ayb[j-1]->useBase(ayb[j]); |
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|
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} |
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} |
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at->makeFortranAtomType(); |
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} |
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|
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for (at = atomTypeCont_.beginType(i); at != NULL; |
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at = atomTypeCont_.nextType(i)) { |
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at->complete(); |
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} |
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|
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hasSCtypes_ = false; |
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for (at = atomTypeCont_.beginType(i); at != NULL; |
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at = atomTypeCont_.nextType(i)) { |
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if (at->isSC()) |
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hasSCtypes_ = true; |
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} |
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|
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hasEAMtypes_ = false; |
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for (at = atomTypeCont_.beginType(i); at != NULL; |
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at = atomTypeCont_.nextType(i)) { |
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if (at->isEAM()) |
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hasEAMtypes_ = true; |
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} |
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|
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if (hasEAMtypes_ && hasSCtypes_) { |
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sprintf(painCave.errMsg, |
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"MnM_FF forcefield cannot use both EAM and Sutton-Chen at the same time\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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/* to handle metal-nonmetal interactions, first we loop over |
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all atom types: */ |
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|
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for (at = atomTypeCont_.beginType(i); at != NULL; |
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at = atomTypeCont_.nextType(i)) { |
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|
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/* if we find a metallic atom, we need to compare against |
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all other atom types */ |
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|
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if (at->isEAM() || at->isSC()) { |
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|
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/* loop over all other atom types */ |
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for (at2 = atomTypeCont_.beginType(j); at2 != NULL; |
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at2 = atomTypeCont_.nextType(j)) { |
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|
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/* if the other partner is not a metallic type, we need to |
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look for explicit non-bonded interactions */ |
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if (!at2->isEAM() && !at2->isSC()) { |
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|
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/* get the name and ident of the metallic atom type */ |
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std::string at1s = at->getName(); |
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int atid1 = at->getIdent(); |
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|
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/* get the name and ident of the nonmetallic atom type */ |
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std::string at2s = at2->getName(); |
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int atid2 = at2->getIdent(); |
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|
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/* look for a match in the non-bonded interactions parsed |
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from the force field file */ |
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nbit = getNonBondedInteractionType(at1s, at2s); |
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|
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/* if we found a match (even a partial match), punt to the |
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interaction to poke our info down to fortran. */ |
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if (nbit != NULL) nbit->tellFortran(atid1, atid2); |
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} |
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} |
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} |
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} |
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|
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delete ffStream; |
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|
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} |
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|
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|
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RealType MnM_FF::getRcutFromAtomType(AtomType* at) { |
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RealType rcut = 0.0; |
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if (at->isEAM()) { |
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GenericData* data = at->getPropertyByName("EAM"); |
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if (data != NULL) { |
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EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data); |
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|
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if (eamData != NULL) { |
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|
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EAMParam& eamParam = eamData->getData(); |
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rcut = eamParam.rcut; |
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} |
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else { |
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sprintf(painCave.errMsg, |
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"Can not cast GenericData to EAMParam\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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else { |
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sprintf(painCave.errMsg, "Can not find EAM Parameters\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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else { |
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rcut = ForceField::getRcutFromAtomType(at); |
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} |
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|
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return rcut; |
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} |
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|
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MnM_FF::~MnM_FF() { |
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destroyLJTypes(); |
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destroyStickyTypes(); |
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if (hasEAMtypes_) destroyEAMTypes(); |
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if (hasSCtypes_) destroySCTypes(); |
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} |
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} //end namespace oopse |
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|
