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tim |
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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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gezelter |
1490 |
|
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tim |
1741 |
#include "UseTheForce/DUFF.hpp" |
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gezelter |
1634 |
#include "UseTheForce/DarkSide/lj_interface.h" |
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gezelter |
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|
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tim |
1741 |
namespace oopse { |
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gezelter |
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|
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tim |
1741 |
//definition of createDUFF |
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ForceField* createDUFF() { |
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return new DUFF(); |
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} |
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gezelter |
1490 |
|
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tim |
1741 |
//register createDUFF to ForceFieldCreator |
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ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
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gezelter |
1490 |
|
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tim |
1757 |
|
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ParseState DUFF::getSection(const std::string& section) { |
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ParseState result; |
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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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case "BondTypes" : |
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result = DUFF::BondTypeSection; |
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break; |
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case "BendTypes" : |
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result = DUFF::BendTypeSection; |
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break; |
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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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return result; |
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} |
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tim |
1741 |
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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tim |
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std::string line; |
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char buffer[bufferSize]; |
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tim |
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int lineNo = 0; |
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tim |
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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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tim |
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++lineNo; |
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gezelter |
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|
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tim |
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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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gezelter |
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|
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tim |
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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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gezelter |
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|
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tim |
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case DUFF::BondTypeSection : |
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parseBondType(line, lineNo); |
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break; |
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gezelter |
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|
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tim |
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case DUFF::BendTypeSection : |
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parseBendType(line, lineNo); |
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break; |
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case DUFF::TorsionTypeSection : |
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parseTorsionType(line, lineNo); |
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break; |
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case DUFF::UnknownSection: |
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StringTokenizer tokenizer(line); |
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std::string keyword = tokenizer.nextToken(); |
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std::string section = tokenizer.nextToken(); |
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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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} 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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break; |
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default : |
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tim |
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|
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} |
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gezelter |
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|
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gezelter |
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} |
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gezelter |
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} |
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tim |
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delete ffStream; |
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gezelter |
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} |
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tim |
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void DUFF::parseAtomType(const std::string& line, int lineNo){ |
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StringTokenizer tokenizer(line); |
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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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atomType = new AtomType(); |
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atomType->setName(atomTypeName); |
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atomType->setMass(mass); |
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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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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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//add atom type to AtomTypeContainer |
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addAtomType(atomTypeName, atomType); |
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++ident; |
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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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gezelter |
1490 |
} |
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tim |
1757 |
void DUFF::parseBondType(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 bt; |
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BondType* bondType = NULL; |
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double b0; |
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int nTokens = tokenizer.countTokens(); |
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if (nTokens < 4) { |
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return; |
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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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//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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case "HarmonicBondType" : |
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if (nTokens < 1) { |
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} else { |
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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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break; |
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case "CubicBondType" : |
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if (nTokens < 4) { |
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} else { |
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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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bondType = new CubicBondType(b0, k3, k2, k1, k0); |
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} |
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break; |
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case "QuadraticBondType" : |
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if (nTokens < 5) { |
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} else { |
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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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bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0); |
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} |
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break; |
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case "PolynomialBondType " : |
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if (nTokens < 2 || nTokens % 2 != 0) { |
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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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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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if (power < 0) { |
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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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break; |
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default: |
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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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gezelter |
1490 |
} |
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279 |
tim |
1757 |
void DUFF::parseBendType(const std::string& line, int lineNo){ |
280 |
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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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288 |
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int nTokens = tokenizer.countTokens(); |
289 |
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290 |
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if (nTokens < 5) { |
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return; |
293 |
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} |
294 |
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295 |
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at1 = tokenizer.nextToken(); |
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at2 = tokenizer.nextToken(); |
297 |
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at3 = tokenizer.nextToken(); |
298 |
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bt = tokenizer.nextToken(); |
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theta0 = tokenizer.nextTokenAsDouble(); |
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nTokens -= 5; |
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302 |
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//switch is a maintain nightmare |
303 |
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switch(bt) { |
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305 |
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case "HarmonicBendType" : |
306 |
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307 |
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if (nTokens < 1) { |
308 |
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309 |
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} else { |
310 |
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311 |
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double ktheta = tokenizer.nextTokenAsDouble(); |
312 |
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bendType = new HarmonicBendType(theta0, ktheta); |
313 |
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} |
314 |
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break; |
315 |
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case "GhostBendType" : |
316 |
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if (nTokens < 1) { |
317 |
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318 |
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} else { |
319 |
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double ktheta = tokenizer.nextTokenAsDouble(); |
320 |
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bendType = new HarmonicBendType(theta0, ktheta); |
321 |
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} |
322 |
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break; |
323 |
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324 |
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case "UreyBradleyBendType" : |
325 |
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if (nTokens < 3) { |
326 |
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327 |
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} else { |
328 |
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double ktheta = tokenizer.nextTokenAsDouble(); |
329 |
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double s0 = tokenizer.nextTokenAsDouble(); |
330 |
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double kub = tokenizer.nextTokenAsDouble(); |
331 |
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bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub); |
332 |
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} |
333 |
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break; |
334 |
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335 |
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case "CubicBendType" : |
336 |
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if (nTokens < 4) { |
337 |
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338 |
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} else { |
339 |
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340 |
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double k3 = tokenizer.nextTokenAsDouble(); |
341 |
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double k2 = tokenizer.nextTokenAsDouble(); |
342 |
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double k1 = tokenizer.nextTokenAsDouble(); |
343 |
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double k0 = tokenizer.nextTokenAsDouble(); |
344 |
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345 |
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bendType = new CubicBendType(theta0, k3, k2, k1, k0); |
346 |
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} |
347 |
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break; |
348 |
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349 |
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case "QuadraticBendType" : |
350 |
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if (nTokens < 5) { |
351 |
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352 |
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} else { |
353 |
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354 |
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theta0 = tokenizer.nextTokenAsDouble(); |
355 |
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double k4 = tokenizer.nextTokenAsDouble(); |
356 |
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double k3 = tokenizer.nextTokenAsDouble(); |
357 |
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double k2 = tokenizer.nextTokenAsDouble(); |
358 |
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double k1 = tokenizer.nextTokenAsDouble(); |
359 |
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double k0 = tokenizer.nextTokenAsDouble(); |
360 |
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361 |
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bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0); |
362 |
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} |
363 |
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break; |
364 |
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365 |
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case "PolynomialBendType " : |
366 |
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if (nTokens < 2 || nTokens % 2 != 0) { |
367 |
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368 |
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} else { |
369 |
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int nPairs = nTokens / 2; |
370 |
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int power; |
371 |
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double coefficient; |
372 |
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PolynomialBendType* pbt = new PolynomialBendType(); |
373 |
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374 |
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for (int i = 0; i < nPairs; ++i) { |
375 |
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power = tokenizer.nextTokenAsInt(); |
376 |
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coefficient = tokenizer.nextTokenAsDouble(); |
377 |
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378 |
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if (power < 0) { |
379 |
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380 |
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} else { |
381 |
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pbt->setCoefficient(power, coefficient); |
382 |
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} |
383 |
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} |
384 |
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} |
385 |
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386 |
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break; |
387 |
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388 |
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default: |
389 |
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|
390 |
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} |
391 |
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392 |
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if (bendType != NULL) { |
393 |
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addBendType(at1, at2, at3, bendType); |
394 |
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} |
395 |
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|
396 |
gezelter |
1490 |
} |
397 |
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|
398 |
tim |
1757 |
void DUFF::parseTorsionType(const std::string& line, int lineNo){ |
399 |
|
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StringTokenizer tokenizer(line); |
400 |
|
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std::string at1; |
401 |
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std::string at2; |
402 |
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std::string at3; |
403 |
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std::string at4; |
404 |
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std::string tt; |
405 |
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TorsionType* bendType = NULL; |
406 |
gezelter |
1490 |
|
407 |
tim |
1757 |
int nTokens = tokenizer.countTokens(); |
408 |
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|
409 |
|
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if (nTokens < 5) { |
410 |
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|
411 |
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return; |
412 |
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} |
413 |
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|
414 |
|
|
at1 = tokenizer.nextToken(); |
415 |
|
|
at2 = tokenizer.nextToken(); |
416 |
|
|
at3 = tokenizer.nextToken(); |
417 |
|
|
at4 = tokenizer.nextToken(); |
418 |
|
|
tt = tokenizer.nextToken(); |
419 |
|
|
|
420 |
|
|
nTokens -= 5; |
421 |
|
|
|
422 |
|
|
switch(tt) { |
423 |
|
|
|
424 |
|
|
case "CubicTorsionType" : |
425 |
|
|
if (nTokens < 4) { |
426 |
|
|
|
427 |
|
|
} else { |
428 |
|
|
|
429 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
430 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
431 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
432 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
433 |
|
|
|
434 |
|
|
bendType = new CubicTorsionType(k3, k2, k1, k0); |
435 |
|
|
} |
436 |
|
|
break; |
437 |
|
|
|
438 |
|
|
case "QuadraticTorsionType" : |
439 |
|
|
if (nTokens < 5) { |
440 |
|
|
|
441 |
|
|
} else { |
442 |
|
|
|
443 |
|
|
theta0 = tokenizer.nextTokenAsDouble(); |
444 |
|
|
double k4 = tokenizer.nextTokenAsDouble(); |
445 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
446 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
447 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
448 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
449 |
|
|
|
450 |
|
|
bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0); |
451 |
|
|
} |
452 |
|
|
break; |
453 |
|
|
|
454 |
|
|
case "PolynomialTorsionType " : |
455 |
|
|
if (nTokens < 2 || nTokens % 2 != 0) { |
456 |
|
|
|
457 |
|
|
} else { |
458 |
|
|
int nPairs = nTokens / 2; |
459 |
|
|
int power; |
460 |
|
|
double coefficient; |
461 |
|
|
PolynomialTorsionType* pbt = new PolynomialTorsionType(); |
462 |
|
|
|
463 |
|
|
for (int i = 0; i < nPairs; ++i) { |
464 |
|
|
power = tokenizer.nextTokenAsInt(); |
465 |
|
|
coefficient = tokenizer.nextTokenAsDouble(); |
466 |
|
|
|
467 |
|
|
if (power < 0) { |
468 |
|
|
|
469 |
|
|
} else { |
470 |
|
|
pbt->setCoefficient(power, coefficient); |
471 |
|
|
} |
472 |
|
|
} |
473 |
|
|
} |
474 |
|
|
|
475 |
|
|
break; |
476 |
|
|
case "CharmmTorsionType" : |
477 |
|
|
|
478 |
|
|
if (nTokens < 3 || nTokens % 3 != 0) { |
479 |
|
|
|
480 |
|
|
} else { |
481 |
|
|
int nSets = nTokens / 3; |
482 |
|
|
|
483 |
|
|
double kchi; |
484 |
|
|
int n; |
485 |
|
|
double delta; |
486 |
|
|
CharmmTorsionType* ctt = new CharmmTorsionType(); |
487 |
|
|
|
488 |
|
|
for (int i = 0; i < nSets; ++i) { |
489 |
|
|
kchi = tokenizer.nextTokenAsDouble(); |
490 |
|
|
n = tokenizer.nextTokenAsInt(); |
491 |
|
|
delta = tokenizer.nextTokenAsDouble(); |
492 |
|
|
|
493 |
|
|
if (n < 0 || n > 6) { |
494 |
|
|
|
495 |
|
|
} else { |
496 |
|
|
ctt->setCharmmTorsionParameter(kchi, n, delta); |
497 |
|
|
} |
498 |
|
|
} |
499 |
|
|
} |
500 |
|
|
default: |
501 |
|
|
|
502 |
|
|
} |
503 |
|
|
|
504 |
|
|
if (bendType != NULL) { |
505 |
|
|
addTorsionType(at1, at2, at3, bendType); |
506 |
|
|
} |
507 |
gezelter |
1490 |
} |
508 |
|
|
|
509 |
tim |
1741 |
} //end namespace oopse |
510 |
gezelter |
1490 |
|