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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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tim |
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#include "UseTheForce/DarkSide/charge_interface.h" |
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#include "UseTheForce/DarkSide/dipole_interface.h" |
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#include "UseTheForce/DarkSide/sticky_interface.h" |
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gezelter |
1490 |
|
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tim |
1741 |
namespace oopse { |
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gezelter |
1490 |
|
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tim |
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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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gezelter |
1490 |
|
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tim |
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//register createDUFF to ForceFieldFactory |
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tim |
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ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
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gezelter |
1490 |
|
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tim |
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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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switch(section) { |
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case "AtomTypes" : |
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result = DUFF::AtomTypeSection; |
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break; |
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tim |
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case "DirectionalAtomTypes" : |
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result = DUFF::DirectionalAtomTypeSection; |
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break; |
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tim |
1757 |
|
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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 |
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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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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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int atomIdent = getNAtomType() + 1; //atom's indent begins from 1 (since only fortran's array begins from 1) |
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tim |
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ParseState currentSection = DUFF::UnknownSection; |
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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 |
1490 |
|
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tim |
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switch(currentSection) { |
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case DUFF::AtomTypeSection : |
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tim |
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parseAtomType(line, lineNo, atomIdent); |
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tim |
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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::DirectionalAtomTypeSection : |
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parseDirectionalAtomType(line, lineNo); |
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break; |
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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 |
1490 |
|
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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 |
1741 |
|
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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 |
1490 |
} |
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tim |
1741 |
delete ffStream; |
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gezelter |
1490 |
} |
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tim |
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void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){ |
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tim |
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StringTokenizer tokenizer(line); |
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tim |
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int nTokens = tokenizer.countTokens(); |
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tim |
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|
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tim |
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//in AtomTypeSection, a line at least contains 5 tokens |
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//atomTypeName, is Directional, isLJ, isCharge and mass |
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if (nTokens < 5) { |
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tim |
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|
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tim |
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} else { |
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std::string atomTypeName = tokenizer.nextToken(); |
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bool isDirectional = tokenizer.nextTokenAsBool(); |
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bool isLJ = tokenizer.nextTokenAsBool(); |
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bool isCharge = tokenizer.nextTokenAsBool(); |
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double mass = tokenizer.nextTokenAsDouble(); |
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double epsilon; |
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double sigma; |
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double charge; |
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nTokens -= 5; |
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//parse epsilon and sigma |
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if (isLJ) { |
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if (nTokens >= 2) { |
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epsilon = tokenizer.nextTokenAsDouble(); |
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sigma = tokenizer.nextTokenAsDouble(); |
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nTokens -= 2; |
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} else { |
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} |
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} |
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//parse charge |
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if (isCharge) { |
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if (nTokens >= 1) { |
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charge = tokenizer.nextTokenAsDouble(); |
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nTokens -= 1; |
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} else { |
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} |
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} |
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AtomType* atomType; |
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if (isDirectional) { |
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atomType = new DirectionalAtomType(); |
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} else { |
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atomType = new AtomType(); |
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} |
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tim |
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atomType->setName(atomTypeName); |
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atomType->setMass(mass); |
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tim |
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if (isLJ) { |
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atomType->setLennardJones(); |
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} |
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tim |
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|
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tim |
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if (isCharge) { |
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atomType->setCharge(); |
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} |
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tim |
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atomType->setIdent(ident); |
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tim |
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atomType->complete(); |
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tim |
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|
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int setLJStatus; |
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tim |
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//notify a new LJtype atom type is created |
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tim |
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if (isLJ) { |
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newLJtype(&ident, &sigma, &epsilon, &setLJStatus); |
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} |
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tim |
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|
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tim |
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int setChargeStatus; |
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if (isCharge) { |
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newChargeType(&ident, &charge, &setChargeStatus) |
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} |
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if (setLJStatus && setChargeStatus) { |
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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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//error in notifying fortran |
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delete atomType; |
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} |
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tim |
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} |
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tim |
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|
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gezelter |
1490 |
} |
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tim |
1758 |
|
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void DUFF::parseDirectionalAtomType(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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//in irectionalAtomTypeSection, a line at least contains 6 tokens |
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//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz |
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if (nTokens < 6) { |
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} else { |
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std::string atomTypeName = tokenizer.nextToken(); |
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bool isDipole = tokenizer.nextTokenAsBool(); |
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bool isSticky = tokenizer.nextTokenAsBool(); |
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double Ixx = tokenizer.nextTokenAsDouble(); |
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double Iyy = tokenizer.nextTokenAsDouble(); |
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double Izz = tokenizer.nextTokenAsDouble(); |
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nTokens -= 6; |
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AtomType* atomType = getAtomType(atomTypeName); |
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if (atomType == NULL) { |
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} |
261 |
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DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
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if (dAtomType == NULL) { |
264 |
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} |
267 |
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tim |
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if (isDipole) { |
269 |
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dAtomType->setDipole(); |
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} |
271 |
tim |
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|
272 |
tim |
1760 |
if (isSticky) { |
273 |
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dAtomType->setSticky(); |
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} |
275 |
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276 |
tim |
1758 |
Mat3x3d inertialMat; |
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inertialMat(0, 0) = Ixx; |
278 |
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inertialMat(1, 1) = Ixx; |
279 |
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inertialMat(2, 2) = Ixx; |
280 |
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dAtomType->setI(inertialMat); |
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//read dipole moment |
283 |
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double dipole; |
284 |
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if (isDipole) { |
285 |
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if (nTokens >= 1) { |
286 |
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dipole = tokenizer.nextTokenAsDouble(); |
287 |
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nTokens -= 1; |
288 |
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} else { |
289 |
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290 |
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} |
291 |
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} |
292 |
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293 |
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//read sticky parameters |
294 |
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double w0; |
295 |
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double v0; |
296 |
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double v0p; |
297 |
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double rl; |
298 |
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double ru; |
299 |
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double rlp; |
300 |
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double rup; |
301 |
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if (isSticky) { |
302 |
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if (nTokens >= 7) { |
303 |
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w0 = tokenizer.nextTokenAsDouble(); |
304 |
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v0 = tokenizer.nextTokenAsDouble(); |
305 |
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v0p = tokenizer.nextTokenAsDouble(); |
306 |
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rl = tokenizer.nextTokenAsDouble(); |
307 |
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ru = tokenizer.nextTokenAsDouble(); |
308 |
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rlp = tokenizer.nextTokenAsDouble(); |
309 |
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rup = tokenizer.nextTokenAsDouble(); |
310 |
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nTokens -= 7; |
311 |
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} else { |
312 |
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313 |
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} |
314 |
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} |
315 |
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316 |
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317 |
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//notify fotran a newDipoleType is created |
318 |
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int ident = dAtomType->getIdent(); |
319 |
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int setDipoleStatus; |
320 |
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if (isDipole) { |
321 |
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newDipoleType(&ident, &dipole, &setDipoleStatus); |
322 |
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} |
323 |
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324 |
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//notify fotran a StickyType is created |
325 |
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int setStickyStatus; |
326 |
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if (isSticky) { |
327 |
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makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup); |
328 |
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} |
329 |
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330 |
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331 |
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if (!setDipoleStatus || !setStickyStatus) { |
332 |
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333 |
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} |
334 |
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335 |
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} |
336 |
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} |
337 |
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338 |
tim |
1757 |
void DUFF::parseBondType(const std::string& line, int lineNo){ |
339 |
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|
340 |
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StringTokenizer tokenizer(line); |
341 |
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std::string at1; |
342 |
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std::string at2; |
343 |
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std::string bt; |
344 |
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BondType* bondType = NULL; |
345 |
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double b0; |
346 |
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|
347 |
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int nTokens = tokenizer.countTokens(); |
348 |
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349 |
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if (nTokens < 4) { |
350 |
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351 |
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return; |
352 |
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} |
353 |
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354 |
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at1 = tokenizer.nextToken(); |
355 |
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at2 = tokenizer.nextToken(); |
356 |
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bt = tokenizer.nextToken(); |
357 |
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b0 = tokenizer.nextTokenAsDouble(); |
358 |
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nTokens -= 4; |
359 |
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|
360 |
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//switch is a maintain nightmare |
361 |
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switch(bt) { |
362 |
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case "FixedBondType" : |
363 |
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bondType = new FixedBondType(); |
364 |
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break; |
365 |
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366 |
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case "HarmonicBondType" : |
367 |
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if (nTokens < 1) { |
368 |
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|
369 |
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} else { |
370 |
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371 |
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double kb = tokenizer.nextTokenAsDouble(); |
372 |
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bondType = new HarmonicBondType(b0, kb); |
373 |
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} |
374 |
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375 |
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break; |
376 |
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377 |
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case "CubicBondType" : |
378 |
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if (nTokens < 4) { |
379 |
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380 |
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} else { |
381 |
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382 |
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double k3 = tokenizer.nextTokenAsDouble(); |
383 |
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double k2 = tokenizer.nextTokenAsDouble(); |
384 |
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double k1 = tokenizer.nextTokenAsDouble(); |
385 |
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double k0 = tokenizer.nextTokenAsDouble(); |
386 |
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387 |
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bondType = new CubicBondType(b0, k3, k2, k1, k0); |
388 |
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} |
389 |
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break; |
390 |
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391 |
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case "QuadraticBondType" : |
392 |
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if (nTokens < 5) { |
393 |
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|
394 |
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} else { |
395 |
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396 |
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b0 = tokenizer.nextTokenAsDouble(); |
397 |
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double k4 = tokenizer.nextTokenAsDouble(); |
398 |
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double k3 = tokenizer.nextTokenAsDouble(); |
399 |
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double k2 = tokenizer.nextTokenAsDouble(); |
400 |
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double k1 = tokenizer.nextTokenAsDouble(); |
401 |
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double k0 = tokenizer.nextTokenAsDouble(); |
402 |
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403 |
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bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0); |
404 |
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} |
405 |
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break; |
406 |
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407 |
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case "PolynomialBondType " : |
408 |
|
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if (nTokens < 2 || nTokens % 2 != 0) { |
409 |
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|
410 |
|
|
} else { |
411 |
|
|
int nPairs = nTokens / 2; |
412 |
|
|
int power; |
413 |
|
|
double coefficient; |
414 |
|
|
PolynomialBondType pbt = new PolynomialBondType(); |
415 |
|
|
|
416 |
|
|
for (int i = 0; i < nPairs; ++i) { |
417 |
|
|
power = tokenizer.nextTokenAsInt(); |
418 |
|
|
coefficient = tokenizer.nextTokenAsDouble(); |
419 |
tim |
1758 |
pbt->setCoefficient(power, coefficient); |
420 |
tim |
1757 |
} |
421 |
|
|
} |
422 |
|
|
|
423 |
|
|
break; |
424 |
|
|
|
425 |
|
|
default: |
426 |
|
|
|
427 |
|
|
} |
428 |
|
|
|
429 |
|
|
if (bondType != NULL) { |
430 |
|
|
addBondType(at1, at2, bondType); |
431 |
|
|
} |
432 |
gezelter |
1490 |
} |
433 |
|
|
|
434 |
tim |
1757 |
void DUFF::parseBendType(const std::string& line, int lineNo){ |
435 |
|
|
StringTokenizer tokenizer(line); |
436 |
|
|
std::string at1; |
437 |
|
|
std::string at2; |
438 |
|
|
std::string at3; |
439 |
|
|
std::string bt; |
440 |
|
|
double theta0; |
441 |
|
|
BendType* bendType = NULL; |
442 |
|
|
|
443 |
|
|
int nTokens = tokenizer.countTokens(); |
444 |
|
|
|
445 |
|
|
if (nTokens < 5) { |
446 |
|
|
|
447 |
|
|
return; |
448 |
|
|
} |
449 |
|
|
|
450 |
|
|
at1 = tokenizer.nextToken(); |
451 |
|
|
at2 = tokenizer.nextToken(); |
452 |
|
|
at3 = tokenizer.nextToken(); |
453 |
|
|
bt = tokenizer.nextToken(); |
454 |
|
|
theta0 = tokenizer.nextTokenAsDouble(); |
455 |
|
|
nTokens -= 5; |
456 |
|
|
|
457 |
|
|
//switch is a maintain nightmare |
458 |
|
|
switch(bt) { |
459 |
|
|
|
460 |
|
|
case "HarmonicBendType" : |
461 |
|
|
|
462 |
|
|
if (nTokens < 1) { |
463 |
|
|
|
464 |
|
|
} else { |
465 |
|
|
|
466 |
|
|
double ktheta = tokenizer.nextTokenAsDouble(); |
467 |
|
|
bendType = new HarmonicBendType(theta0, ktheta); |
468 |
|
|
} |
469 |
|
|
break; |
470 |
|
|
case "GhostBendType" : |
471 |
|
|
if (nTokens < 1) { |
472 |
|
|
|
473 |
|
|
} else { |
474 |
|
|
double ktheta = tokenizer.nextTokenAsDouble(); |
475 |
|
|
bendType = new HarmonicBendType(theta0, ktheta); |
476 |
|
|
} |
477 |
|
|
break; |
478 |
|
|
|
479 |
|
|
case "UreyBradleyBendType" : |
480 |
|
|
if (nTokens < 3) { |
481 |
|
|
|
482 |
|
|
} else { |
483 |
|
|
double ktheta = tokenizer.nextTokenAsDouble(); |
484 |
|
|
double s0 = tokenizer.nextTokenAsDouble(); |
485 |
|
|
double kub = tokenizer.nextTokenAsDouble(); |
486 |
|
|
bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub); |
487 |
|
|
} |
488 |
|
|
break; |
489 |
|
|
|
490 |
|
|
case "CubicBendType" : |
491 |
|
|
if (nTokens < 4) { |
492 |
|
|
|
493 |
|
|
} else { |
494 |
|
|
|
495 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
496 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
497 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
498 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
499 |
|
|
|
500 |
|
|
bendType = new CubicBendType(theta0, k3, k2, k1, k0); |
501 |
|
|
} |
502 |
|
|
break; |
503 |
|
|
|
504 |
|
|
case "QuadraticBendType" : |
505 |
|
|
if (nTokens < 5) { |
506 |
|
|
|
507 |
|
|
} else { |
508 |
|
|
|
509 |
|
|
theta0 = tokenizer.nextTokenAsDouble(); |
510 |
|
|
double k4 = tokenizer.nextTokenAsDouble(); |
511 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
512 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
513 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
514 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
515 |
|
|
|
516 |
|
|
bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0); |
517 |
|
|
} |
518 |
|
|
break; |
519 |
|
|
|
520 |
|
|
case "PolynomialBendType " : |
521 |
|
|
if (nTokens < 2 || nTokens % 2 != 0) { |
522 |
|
|
|
523 |
|
|
} else { |
524 |
|
|
int nPairs = nTokens / 2; |
525 |
|
|
int power; |
526 |
|
|
double coefficient; |
527 |
|
|
PolynomialBendType* pbt = new PolynomialBendType(); |
528 |
|
|
|
529 |
|
|
for (int i = 0; i < nPairs; ++i) { |
530 |
|
|
power = tokenizer.nextTokenAsInt(); |
531 |
|
|
coefficient = tokenizer.nextTokenAsDouble(); |
532 |
tim |
1758 |
pbt->setCoefficient(power, coefficient); |
533 |
tim |
1757 |
} |
534 |
|
|
} |
535 |
|
|
|
536 |
|
|
break; |
537 |
|
|
|
538 |
|
|
default: |
539 |
|
|
|
540 |
|
|
} |
541 |
|
|
|
542 |
|
|
if (bendType != NULL) { |
543 |
|
|
addBendType(at1, at2, at3, bendType); |
544 |
|
|
} |
545 |
|
|
|
546 |
gezelter |
1490 |
} |
547 |
|
|
|
548 |
tim |
1757 |
void DUFF::parseTorsionType(const std::string& line, int lineNo){ |
549 |
|
|
StringTokenizer tokenizer(line); |
550 |
|
|
std::string at1; |
551 |
|
|
std::string at2; |
552 |
|
|
std::string at3; |
553 |
|
|
std::string at4; |
554 |
|
|
std::string tt; |
555 |
|
|
TorsionType* bendType = NULL; |
556 |
gezelter |
1490 |
|
557 |
tim |
1757 |
int nTokens = tokenizer.countTokens(); |
558 |
|
|
|
559 |
|
|
if (nTokens < 5) { |
560 |
|
|
|
561 |
|
|
return; |
562 |
|
|
} |
563 |
|
|
|
564 |
|
|
at1 = tokenizer.nextToken(); |
565 |
|
|
at2 = tokenizer.nextToken(); |
566 |
|
|
at3 = tokenizer.nextToken(); |
567 |
|
|
at4 = tokenizer.nextToken(); |
568 |
|
|
tt = tokenizer.nextToken(); |
569 |
|
|
|
570 |
|
|
nTokens -= 5; |
571 |
|
|
|
572 |
|
|
switch(tt) { |
573 |
|
|
|
574 |
|
|
case "CubicTorsionType" : |
575 |
|
|
if (nTokens < 4) { |
576 |
|
|
|
577 |
|
|
} else { |
578 |
|
|
|
579 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
580 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
581 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
582 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
583 |
|
|
|
584 |
|
|
bendType = new CubicTorsionType(k3, k2, k1, k0); |
585 |
|
|
} |
586 |
|
|
break; |
587 |
|
|
|
588 |
|
|
case "QuadraticTorsionType" : |
589 |
|
|
if (nTokens < 5) { |
590 |
|
|
|
591 |
|
|
} else { |
592 |
|
|
|
593 |
|
|
theta0 = tokenizer.nextTokenAsDouble(); |
594 |
|
|
double k4 = tokenizer.nextTokenAsDouble(); |
595 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
596 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
597 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
598 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
599 |
|
|
|
600 |
|
|
bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0); |
601 |
|
|
} |
602 |
|
|
break; |
603 |
|
|
|
604 |
|
|
case "PolynomialTorsionType " : |
605 |
|
|
if (nTokens < 2 || nTokens % 2 != 0) { |
606 |
|
|
|
607 |
|
|
} else { |
608 |
|
|
int nPairs = nTokens / 2; |
609 |
|
|
int power; |
610 |
|
|
double coefficient; |
611 |
|
|
PolynomialTorsionType* pbt = new PolynomialTorsionType(); |
612 |
|
|
|
613 |
|
|
for (int i = 0; i < nPairs; ++i) { |
614 |
|
|
power = tokenizer.nextTokenAsInt(); |
615 |
|
|
coefficient = tokenizer.nextTokenAsDouble(); |
616 |
tim |
1758 |
pbt->setCoefficient(power, coefficient); |
617 |
tim |
1757 |
} |
618 |
|
|
} |
619 |
|
|
|
620 |
|
|
break; |
621 |
|
|
case "CharmmTorsionType" : |
622 |
|
|
|
623 |
|
|
if (nTokens < 3 || nTokens % 3 != 0) { |
624 |
|
|
|
625 |
|
|
} else { |
626 |
|
|
int nSets = nTokens / 3; |
627 |
|
|
|
628 |
|
|
CharmmTorsionType* ctt = new CharmmTorsionType(); |
629 |
|
|
|
630 |
|
|
for (int i = 0; i < nSets; ++i) { |
631 |
tim |
1758 |
double kchi = tokenizer.nextTokenAsDouble(); |
632 |
|
|
int n = tokenizer.nextTokenAsInt(); |
633 |
|
|
double delta = tokenizer.nextTokenAsDouble(); |
634 |
tim |
1757 |
|
635 |
tim |
1758 |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
636 |
tim |
1757 |
} |
637 |
|
|
} |
638 |
|
|
default: |
639 |
|
|
|
640 |
|
|
} |
641 |
|
|
|
642 |
|
|
if (bendType != NULL) { |
643 |
|
|
addTorsionType(at1, at2, at3, bendType); |
644 |
|
|
} |
645 |
gezelter |
1490 |
} |
646 |
|
|
|
647 |
tim |
1741 |
} //end namespace oopse |