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/* |
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* Copyright (c) 2005 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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#include "UseTheForce/DarkSide/shapes_interface.h" |
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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/ForceFieldFactory.hpp" |
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#include "io/OptionSectionParser.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/ShapeAtomTypesSectionParser.hpp" |
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#include "io/StickyAtomTypesSectionParser.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 "UseTheForce/ForceFieldCreator.hpp" |
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#include "UseTheForce/SHAPES_FF.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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|
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SHAPES_FF::SHAPES_FF(){ |
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|
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//set default force field filename |
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setForceFieldFileName("Shapes.frc"); |
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|
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//The ordering of 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 before |
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//AtomTypesSectionParser since these two section parsers will actually |
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//create "real" AtomTypes (AtomTypesSectionParser will create AtomType |
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//and DirectionalAtomTypesSectionParser will create DirectionalAtomType |
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//which is a subclass of AtomType, therefore it should come first). Other |
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//AtomTypes Section Parser will not create the "real" AtomType, they only |
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//add and set some attribute of the AtomType. Thus the ordering of these |
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//are not important. AtomTypesSectionParser should be added before other atom |
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//type section parsers. Make sure they are added after |
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//DirectionalAtomTypesSectionParser and AtomTypesSectionParser. The order |
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//of BondTypesSectionParser, BendTypesSectionParser and |
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//TorsionTypesSectionParser are not important. |
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spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new BaseAtomTypesSectionParser()); |
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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 BondTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new BendTypesSectionParser(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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SHAPES_FF::~SHAPES_FF(){ |
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// We need to clean up the fortran side so we don't have bad things happen if |
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// we try to create a second EAM force field. |
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destroyShapeTypes(); |
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} |
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|
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void SHAPES_FF::parse(const std::string& filename) { |
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ifstrstream* ffStream; |
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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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|
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for (at = atomTypeCont_.beginType(i); at != NULL; 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; at = atomTypeCont_.nextType(i)) { |
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at->complete(); |
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} |
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|
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int isError = 0; |
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completeShapeFF(&isError); |
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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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// RealType SHAPES_FF::getRcutFromAtomType(AtomType* at){ |
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// } |
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} //end namespace oopse |
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|
