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/* |
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* Copyright (c) 2008 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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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|
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#include "UseTheForce/Amber_FF.hpp" |
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#include "UseTheForce/ForceFieldFactory.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/BondTypesSectionParser.hpp" |
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#include "io/BendTypesSectionParser.hpp" |
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#include "io/TorsionTypesSectionParser.hpp" |
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#include "io/InversionTypesSectionParser.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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namespace OpenMD { |
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|
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Amber_FF::Amber_FF(){ |
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|
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//set default force field filename |
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setForceFieldFileName("Amber.frc"); |
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|
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//The order of adding section parsers is important. |
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|
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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 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 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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spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_)); |
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} |
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|
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void Amber_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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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; |
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at = atomTypeCont_.nextType(i)) { |
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|
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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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} |
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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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} //end namespace OpenMD |
