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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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#include "UseTheForce/DUFF.hpp" |
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#include "UseTheForce/DarkSide/lj_interface.h" |
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|
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namespace oopse { |
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|
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//definition of createDUFF |
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ForceField* createDUFF() { |
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return new DUFF(); |
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} |
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|
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//register createDUFF to ForceFieldCreator |
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ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
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|
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|
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ParseState DUFF::getSection(const std::string& section) { |
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ParseState result; |
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|
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switch(section) { |
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case "AtomTypes" : |
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result = DUFF::AtomTypeSection; |
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break; |
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|
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case "BondTypes" : |
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result = DUFF::BondTypeSection; |
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break; |
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|
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case "BendTypes" : |
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result = DUFF::BendTypeSection; |
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break; |
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|
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case "TorsionTypes" : |
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result = DUFF::TorsionTypeSection; |
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break; |
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default: |
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result = DUFF::UnknownSection; |
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} |
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|
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return result; |
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} |
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|
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void DUFF::parse(const std::string& filename) { |
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ifstrstream* ffStream; |
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ffStream = openForceFiledFile(filename); |
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const int bufferSize = 65535; |
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std::string line; |
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char buffer[bufferSize]; |
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int lineNo = 0; |
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ParseState currentSection = DUFF::UnknownSection; |
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|
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while(ffStream.getline(buffer, bufferSize)){ |
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++lineNo; |
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|
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line = trimSpaces(buffer); |
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//a line begins with "//" is comment |
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if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) { |
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continue; |
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} else { |
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|
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switch(currentSection) { |
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case DUFF::AtomTypeSection : |
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parseAtomType(line, lineNo); |
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break; |
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|
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case DUFF::BondTypeSection : |
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parseBondType(line, lineNo); |
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break; |
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|
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case DUFF::BendTypeSection : |
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parseBendType(line, lineNo); |
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break; |
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|
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case DUFF::TorsionTypeSection : |
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parseTorsionType(line, lineNo); |
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break; |
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|
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case DUFF::UnknownSection: |
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StringTokenizer tokenizer(line); |
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|
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std::string keyword = tokenizer.nextToken(); |
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std::string section = tokenizer.nextToken(); |
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|
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ParseState newSection = getSection(section); |
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if (keyword != "begin" || keyword != "end") { |
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std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
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} else if (keyword == "begin") { |
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if (newSection == DUFF::UnknownSection) { |
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std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
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} else { |
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//enter a new section |
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currentSection = newSection; |
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} |
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|
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} else if (keyword == "end"){ |
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if (currentSection == newSection) ) { |
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//leave a section |
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currentSection = DUFF::UnknownSection; |
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} else { |
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std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
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} |
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|
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} |
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break; |
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default : |
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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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delete ffStream; |
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} |
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|
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|
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void DUFF::parseAtomType(const std::string& line, int lineNo){ |
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StringTokenizer tokenizer(line); |
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|
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if (tokenizer.countTokens() >= 4) { |
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atomTypeName = tokenizer.nextToken(); |
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mass = tokenizer.nextTokenAsFloat(); |
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epsilon = tokenizer.nextTokenAsFloat(); |
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sigma = tokenizer.nextTokenAsFloat(); |
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|
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atomType = new AtomType(); |
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atomType->setName(atomTypeName); |
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atomType->setMass(mass); |
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|
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//by default, all of the properties in AtomTypeProperties is set to 0 |
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//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true |
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atomType->setLennardJones(); |
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|
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atomType->setIdent(ident); |
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atomType->addProperty(new DoubleGenericData("Epsilon", epsilon)); |
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atomType->addProperty(new DoubleGenericData("Sigma", sigma)); |
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atomType->complete(); |
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//notify a new LJtype atom type is created |
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newLJtype(&ident, &sigma, &epsilon, &status); |
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|
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//add atom type to AtomTypeContainer |
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addAtomType(atomTypeName, atomType); |
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++ident; |
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|
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} else { |
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sprintf( painCave.errMsg, |
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"Not enough tokens when parsing Lennard-Jones Force Field : %s\n" |
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"in line %d : %s\n", |
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filename.c_str(), lineNo, line); |
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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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|
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void DUFF::parseBondType(const std::string& line, int lineNo){ |
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|
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StringTokenizer tokenizer(line); |
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std::string at1; |
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std::string at2; |
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std::string bt; |
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BondType* bondType = NULL; |
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double b0; |
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|
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int nTokens = tokenizer.countTokens(); |
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|
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if (nTokens < 4) { |
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|
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return; |
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} |
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|
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at1 = tokenizer.nextToken(); |
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at2 = tokenizer.nextToken(); |
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bt = tokenizer.nextToken(); |
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b0 = tokenizer.nextTokenAsDouble(); |
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nTokens -= 4; |
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|
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//switch is a maintain nightmare |
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switch(bt) { |
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case "FixedBondType" : |
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bondType = new FixedBondType(); |
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break; |
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|
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case "HarmonicBondType" : |
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if (nTokens < 1) { |
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|
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} else { |
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|
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double kb = tokenizer.nextTokenAsDouble(); |
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bondType = new HarmonicBondType(b0, kb); |
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} |
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|
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break; |
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|
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case "CubicBondType" : |
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if (nTokens < 4) { |
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|
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} else { |
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|
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double k3 = tokenizer.nextTokenAsDouble(); |
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double k2 = tokenizer.nextTokenAsDouble(); |
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double k1 = tokenizer.nextTokenAsDouble(); |
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double k0 = tokenizer.nextTokenAsDouble(); |
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|
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bondType = new CubicBondType(b0, k3, k2, k1, k0); |
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} |
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break; |
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|
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case "QuadraticBondType" : |
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if (nTokens < 5) { |
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|
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} else { |
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|
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b0 = tokenizer.nextTokenAsDouble(); |
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double k4 = tokenizer.nextTokenAsDouble(); |
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double k3 = tokenizer.nextTokenAsDouble(); |
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double k2 = tokenizer.nextTokenAsDouble(); |
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double k1 = tokenizer.nextTokenAsDouble(); |
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double k0 = tokenizer.nextTokenAsDouble(); |
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|
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bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0); |
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} |
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break; |
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|
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case "PolynomialBondType " : |
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if (nTokens < 2 || nTokens % 2 != 0) { |
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|
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} else { |
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int nPairs = nTokens / 2; |
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int power; |
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double coefficient; |
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PolynomialBondType pbt = new PolynomialBondType(); |
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|
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for (int i = 0; i < nPairs; ++i) { |
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power = tokenizer.nextTokenAsInt(); |
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coefficient = tokenizer.nextTokenAsDouble(); |
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|
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if (power < 0) { |
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|
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} else { |
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pbt->setCoefficient(power, coefficient); |
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} |
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} |
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} |
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|
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break; |
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|
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default: |
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|
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} |
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|
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if (bondType != NULL) { |
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addBondType(at1, at2, bondType); |
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} |
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} |
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|
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void DUFF::parseBendType(const std::string& line, int lineNo){ |
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StringTokenizer tokenizer(line); |
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std::string at1; |
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std::string at2; |
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std::string at3; |
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std::string bt; |
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double theta0; |
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BendType* bendType = NULL; |
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|
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int nTokens = tokenizer.countTokens(); |
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|
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if (nTokens < 5) { |
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|
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return; |
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} |
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|
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at1 = tokenizer.nextToken(); |
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at2 = tokenizer.nextToken(); |
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at3 = tokenizer.nextToken(); |
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bt = tokenizer.nextToken(); |
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theta0 = tokenizer.nextTokenAsDouble(); |
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nTokens -= 5; |
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|
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//switch is a maintain nightmare |
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switch(bt) { |
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|
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case "HarmonicBendType" : |
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|
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if (nTokens < 1) { |
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|
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} else { |
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|
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double ktheta = tokenizer.nextTokenAsDouble(); |
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bendType = new HarmonicBendType(theta0, ktheta); |
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} |
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break; |
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case "GhostBendType" : |
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if (nTokens < 1) { |
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|
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} else { |
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double ktheta = tokenizer.nextTokenAsDouble(); |
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bendType = new HarmonicBendType(theta0, ktheta); |
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} |
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break; |
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|
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case "UreyBradleyBendType" : |
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if (nTokens < 3) { |
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|
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} else { |
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double ktheta = tokenizer.nextTokenAsDouble(); |
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double s0 = tokenizer.nextTokenAsDouble(); |
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double kub = tokenizer.nextTokenAsDouble(); |
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bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub); |
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} |
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break; |
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|
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case "CubicBendType" : |
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if (nTokens < 4) { |
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|
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} else { |
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|
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double k3 = tokenizer.nextTokenAsDouble(); |
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double k2 = tokenizer.nextTokenAsDouble(); |
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double k1 = tokenizer.nextTokenAsDouble(); |
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double k0 = tokenizer.nextTokenAsDouble(); |
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|
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bendType = new CubicBendType(theta0, k3, k2, k1, k0); |
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} |
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break; |
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|
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case "QuadraticBendType" : |
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if (nTokens < 5) { |
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|
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} else { |
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|
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theta0 = tokenizer.nextTokenAsDouble(); |
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double k4 = tokenizer.nextTokenAsDouble(); |
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double k3 = tokenizer.nextTokenAsDouble(); |
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double k2 = tokenizer.nextTokenAsDouble(); |
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double k1 = tokenizer.nextTokenAsDouble(); |
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double k0 = tokenizer.nextTokenAsDouble(); |
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|
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bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0); |
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} |
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break; |
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|
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case "PolynomialBendType " : |
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if (nTokens < 2 || nTokens % 2 != 0) { |
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|
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} else { |
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int nPairs = nTokens / 2; |
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int power; |
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double coefficient; |
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PolynomialBendType* pbt = new PolynomialBendType(); |
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|
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for (int i = 0; i < nPairs; ++i) { |
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power = tokenizer.nextTokenAsInt(); |
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coefficient = tokenizer.nextTokenAsDouble(); |
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|
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if (power < 0) { |
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|
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} else { |
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pbt->setCoefficient(power, coefficient); |
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} |
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} |
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} |
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|
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break; |
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|
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default: |
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|
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} |
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|
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if (bendType != NULL) { |
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addBendType(at1, at2, at3, bendType); |
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} |
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|
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} |
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|
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void DUFF::parseTorsionType(const std::string& line, int lineNo){ |
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StringTokenizer tokenizer(line); |
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std::string at1; |
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std::string at2; |
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std::string at3; |
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std::string at4; |
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std::string tt; |
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TorsionType* bendType = NULL; |
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|
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int nTokens = tokenizer.countTokens(); |
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|
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if (nTokens < 5) { |
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|
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return; |
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} |
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|
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at1 = tokenizer.nextToken(); |
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at2 = tokenizer.nextToken(); |
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at3 = tokenizer.nextToken(); |
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at4 = tokenizer.nextToken(); |
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tt = tokenizer.nextToken(); |
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|
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nTokens -= 5; |
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|
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switch(tt) { |
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|
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case "CubicTorsionType" : |
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if (nTokens < 4) { |
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|
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} else { |
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|
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double k3 = tokenizer.nextTokenAsDouble(); |
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double k2 = tokenizer.nextTokenAsDouble(); |
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double k1 = tokenizer.nextTokenAsDouble(); |
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double k0 = tokenizer.nextTokenAsDouble(); |
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|
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bendType = new CubicTorsionType(k3, k2, k1, k0); |
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} |
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break; |
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|
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case "QuadraticTorsionType" : |
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if (nTokens < 5) { |
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|
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} else { |
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|
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theta0 = tokenizer.nextTokenAsDouble(); |
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double k4 = tokenizer.nextTokenAsDouble(); |
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double k3 = tokenizer.nextTokenAsDouble(); |
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double k2 = tokenizer.nextTokenAsDouble(); |
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double k1 = tokenizer.nextTokenAsDouble(); |
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double k0 = tokenizer.nextTokenAsDouble(); |
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|
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bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0); |
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} |
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break; |
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|
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case "PolynomialTorsionType " : |
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if (nTokens < 2 || nTokens % 2 != 0) { |
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|
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} else { |
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int nPairs = nTokens / 2; |
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int power; |
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double coefficient; |
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PolynomialTorsionType* pbt = new PolynomialTorsionType(); |
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|
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for (int i = 0; i < nPairs; ++i) { |
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power = tokenizer.nextTokenAsInt(); |
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coefficient = tokenizer.nextTokenAsDouble(); |
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|
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if (power < 0) { |
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|
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} else { |
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pbt->setCoefficient(power, coefficient); |
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} |
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} |
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} |
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|
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break; |
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case "CharmmTorsionType" : |
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|
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if (nTokens < 3 || nTokens % 3 != 0) { |
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|
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} else { |
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int nSets = nTokens / 3; |
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|
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double kchi; |
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int n; |
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double delta; |
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CharmmTorsionType* ctt = new CharmmTorsionType(); |
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|
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for (int i = 0; i < nSets; ++i) { |
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kchi = tokenizer.nextTokenAsDouble(); |
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n = tokenizer.nextTokenAsInt(); |
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delta = tokenizer.nextTokenAsDouble(); |
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|
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if (n < 0 || n > 6) { |
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|
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} else { |
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ctt->setCharmmTorsionParameter(kchi, n, delta); |
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} |
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} |
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} |
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default: |
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|
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} |
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|
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if (bendType != NULL) { |
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addTorsionType(at1, at2, at3, bendType); |
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} |
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} |
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|
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} //end namespace oopse |
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|