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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 "io/LennardJonesAtomTypesSectionParser.hpp" |
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#include "io/ForceFieldOptions.hpp" |
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#include "types/AtomType.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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|
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LennardJonesAtomTypesSectionParser::LennardJonesAtomTypesSectionParser(ForceFieldOptions& options) : options_(options) { |
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setSectionName("LennardJonesAtomTypes"); |
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} |
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|
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void LennardJonesAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){ |
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StringTokenizer tokenizer(line); |
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int nTokens = tokenizer.countTokens(); |
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|
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//in LennardJonesAtomTypesSectionParser, a line at least contains 3 tokens |
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//atomTypeName, epsilon and sigma |
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if (nTokens < 3) { |
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sprintf(painCave.errMsg, "LennardJonesAtomTypesSectionParser Error: Not enough tokens at line %d\n", |
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lineNo); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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|
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std::string atomTypeName = tokenizer.nextToken(); |
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AtomType* atomType = ff.getAtomType(atomTypeName); |
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|
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if (atomType != NULL) { |
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LJParam ljParam; |
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ljParam.epsilon = tokenizer.nextTokenAsDouble(); |
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ljParam.sigma = tokenizer.nextTokenAsDouble(); |
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ljParam.soft_pot = 0; |
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|
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ljParam.epsilon *= options_.getEnergyUnitScaling(); |
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ljParam.sigma *= options_.getDistanceUnitScaling(); |
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|
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if (tokenizer.hasMoreTokens()) { |
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std::string pot_type = tokenizer.nextToken(); |
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if (pot_type == "soft") { |
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ljParam.soft_pot = 1; |
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} |
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} |
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|
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atomType->addProperty(new LJParamGenericData("LennardJones", ljParam)); |
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atomType->setLennardJones(); |
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}else { |
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sprintf(painCave.errMsg, "LennardJonesAtomTypesSectionParser Error: Atom Type [%s] is not created yet\n", atomTypeName.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} |
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|
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|
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} |
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|
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} //end namespace oopse |
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|
