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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/EAMAtomTypesSectionParser.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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EAMAtomTypesSectionParser::EAMAtomTypesSectionParser() { |
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setSectionName("EAMAtomTypes"); |
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} |
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|
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void EAMAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){ |
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|
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StringTokenizer tokenizer(line); |
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|
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if (tokenizer.countTokens() >= 2) { |
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std::string atomTypeName = tokenizer.nextToken(); |
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std::string potentialParamFile = tokenizer.nextToken(); |
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|
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AtomType* atomType = ff.getAtomType(atomTypeName); |
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if (atomType != NULL) { |
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atomType->setEAM(); |
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parseEAMParamFile(ff, atomType, potentialParamFile, atomType->getIdent()); |
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} else { |
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|
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} |
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|
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} else { |
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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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void EAMAtomTypesSectionParser::parseEAMParamFile(ForceField& ff, AtomType* atomType, |
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const std::string& potentialParamFile, int ident) { |
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|
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ifstrstream* ppfStream = ff.openForceFieldFile(potentialParamFile); |
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const int bufferSize = 65535; |
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char buffer[bufferSize]; |
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std::string line; |
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|
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//skip first line |
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ppfStream->getline(buffer, bufferSize); |
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|
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|
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//The Second line contains atomic number, atomic mass, a lattice constant and lattic type |
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int junk; |
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double mass; |
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double latticeConstant; |
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std::string lattice; |
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if (ppfStream->getline(buffer, bufferSize)) { |
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StringTokenizer tokenizer1(buffer); |
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|
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if (tokenizer1.countTokens() >= 4) { |
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junk = tokenizer1.nextTokenAsInt(); |
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mass = tokenizer1.nextTokenAsDouble(); |
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latticeConstant = tokenizer1.nextTokenAsDouble(); |
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lattice = tokenizer1.nextToken(); |
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}else { |
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std::cerr << "Not enought tokens" << std::endl; |
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} |
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} else { |
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|
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} |
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|
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// The third line is nrho, drho, nr, dr and rcut |
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EAMParam eamParam; |
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eamParam.latticeConstant = latticeConstant; |
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|
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if (ppfStream->getline(buffer, bufferSize)) { |
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StringTokenizer tokenizer2(buffer); |
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|
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if (tokenizer2.countTokens() >= 5){ |
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eamParam.nrho = tokenizer2.nextTokenAsInt(); |
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eamParam.drho = tokenizer2.nextTokenAsDouble(); |
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eamParam.nr = tokenizer2.nextTokenAsInt(); |
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eamParam.dr = tokenizer2.nextTokenAsDouble(); |
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eamParam.rcut = tokenizer2.nextTokenAsDouble(); |
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}else { |
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std::cerr << "Not enought tokens" << std::endl; |
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} |
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} else { |
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|
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} |
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|
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parseEAMArray(*ppfStream, eamParam.Frhovals, eamParam.nrho); |
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parseEAMArray(*ppfStream, eamParam.rvals, eamParam.nr); |
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parseEAMArray(*ppfStream, eamParam.rhovals, eamParam.nr); |
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|
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atomType->addProperty(new EAMParamGenericData("EAM", eamParam)); |
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} |
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|
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void EAMAtomTypesSectionParser::parseEAMArray(std::istream& input, |
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std::vector<double>& array, int num) { |
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|
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const int dataPerLine = 5; |
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if (num % dataPerLine != 0) { |
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|
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} |
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|
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int nlinesToRead = num / dataPerLine; |
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|
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const int bufferSize = 65535; |
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char buffer[bufferSize]; |
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std::string line; |
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int readLines = num/dataPerLine; |
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int lineCount = 0; |
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|
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while(lineCount < nlinesToRead && input.getline(buffer, bufferSize) ){ |
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|
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StringTokenizer tokenizer(buffer); |
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if (tokenizer.countTokens() >= dataPerLine) { |
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for (int i = 0; i < dataPerLine; ++i) { |
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array.push_back(tokenizer.nextTokenAsDouble()); |
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} |
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} else { |
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|
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} |
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++lineCount; |
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} |
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|
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if (lineCount < nlinesToRead) { |
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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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