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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 |
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#include "UseTheForce/DUFF.hpp" |
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gezelter |
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#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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tim |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "io/DirectionalAtomTypesSectionParser.hpp" |
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#include "io/AtomTypesSectionParser.hpp" |
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#include "io/LennardJonesAtomTypesSectionParser.hpp" |
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#include "io/ElectrostaticAtomTypesSectionParser.hpp" |
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#include "io/EAMAtomTypesSectionParser.hpp" |
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#include "io/StickyAtomTypesSectionParser.hpp" |
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#include "io/BondTypesSectionParser.hpp" |
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#include "io/BendTypesSectionParser.hpp" |
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#include "io/TorsionTypesSectionParser.hpp" |
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gezelter |
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|
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tim |
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namespace oopse { |
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gezelter |
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|
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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 |
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|
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tim |
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//register createDUFF to ForceFieldFactory |
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bool registerDUFFStatus = ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
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gezelter |
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|
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tim |
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DUFF::DUFF(){ |
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|
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//the order of adding section parsers are important |
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//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since |
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//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create |
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//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass |
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//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the |
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//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not |
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//important. AtomTypesSectionParser should be added before other atom type section parsers. |
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//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. |
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//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are |
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//not important. |
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spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
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spMan_.push_back(new AtomTypesSectionParser()); |
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spMan_.push_back(new LennardJonesAtomTypesSectionParser()); |
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spMan_.push_back(new ElectrostaticAtomTypesSectionParser()); |
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spMan_.push_back(new EAMAtomTypesSectionParser()); |
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spMan_.push_back(new StickyAtomTypesSectionParser()); |
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spMan_.push_back(new BondTypesSectionParser()); |
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spMan_.push_back(new BendTypesSectionParser()); |
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spMan_.push_back(new TorsionTypesSectionParser()); |
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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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tim |
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ffStream = openForceFieldFile(filename); |
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|
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spMan_.parse(*ffStream, *this); |
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ForceField::AtomTypeContainer::MapTypeIterator i; |
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AtomType* at; |
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for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
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at->makeFortranAtomType(); |
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} |
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for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
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at->complete(); |
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} |
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} |
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/* |
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tim |
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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 |
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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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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 = openForceFieldFile(filename); |
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tim |
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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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int atomIdent = getNAtomType() + 1; //atom's indent begins from 1 (since only fortran's array begins from 1) |
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ParseState currentSection = DUFF::UnknownSection; |
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while(ffStream.getline(buffer, bufferSize)){ |
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++lineNo; |
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gezelter |
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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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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, atomIdent); |
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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 |
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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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void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){ |
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StringTokenizer tokenizer(line); |
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int nTokens = tokenizer.countTokens(); |
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|
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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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} 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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atomType->setName(atomTypeName); |
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atomType->setMass(mass); |
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if (isLJ) { |
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atomType->setLennardJones(); |
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} |
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|
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if (isCharge) { |
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atomType->setCharge(); |
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} |
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atomType->setIdent(ident); |
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atomType->complete(); |
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|
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int setLJStatus; |
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//notify a new LJtype atom type is created |
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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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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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} |
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|
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gezelter |
1490 |
} |
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tim |
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|
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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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tim |
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//in DirectionalAtomTypeSection, a line at least contains 6 tokens |
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tim |
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//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz |
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if (nTokens < 6) { |
297 |
tim |
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std::cerr << "Not enought tokens" << std::endl; |
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tim |
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} else { |
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300 |
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301 |
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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(); |
307 |
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nTokens -= 6; |
308 |
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309 |
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AtomType* atomType = getAtomType(atomTypeName); |
310 |
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if (atomType == NULL) { |
311 |
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312 |
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} |
313 |
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314 |
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DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
315 |
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if (dAtomType == NULL) { |
316 |
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318 |
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} |
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tim |
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if (isDipole) { |
321 |
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dAtomType->setDipole(); |
322 |
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} |
323 |
tim |
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|
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tim |
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if (isSticky) { |
325 |
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dAtomType->setSticky(); |
326 |
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} |
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328 |
tim |
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Mat3x3d inertialMat; |
329 |
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inertialMat(0, 0) = Ixx; |
330 |
tim |
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inertialMat(1, 1) = Iyy; |
331 |
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inertialMat(2, 2) = Izz; |
332 |
tim |
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dAtomType->setI(inertialMat); |
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//read dipole moment |
335 |
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double dipole; |
336 |
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if (isDipole) { |
337 |
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if (nTokens >= 1) { |
338 |
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dipole = tokenizer.nextTokenAsDouble(); |
339 |
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nTokens -= 1; |
340 |
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} else { |
341 |
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342 |
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} |
343 |
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} |
344 |
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345 |
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//read sticky parameters |
346 |
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double w0; |
347 |
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double v0; |
348 |
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double v0p; |
349 |
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double rl; |
350 |
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double ru; |
351 |
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double rlp; |
352 |
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double rup; |
353 |
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if (isSticky) { |
354 |
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if (nTokens >= 7) { |
355 |
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w0 = tokenizer.nextTokenAsDouble(); |
356 |
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v0 = tokenizer.nextTokenAsDouble(); |
357 |
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v0p = tokenizer.nextTokenAsDouble(); |
358 |
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rl = tokenizer.nextTokenAsDouble(); |
359 |
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ru = tokenizer.nextTokenAsDouble(); |
360 |
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rlp = tokenizer.nextTokenAsDouble(); |
361 |
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rup = tokenizer.nextTokenAsDouble(); |
362 |
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nTokens -= 7; |
363 |
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} else { |
364 |
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365 |
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} |
366 |
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} |
367 |
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368 |
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369 |
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//notify fotran a newDipoleType is created |
370 |
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int ident = dAtomType->getIdent(); |
371 |
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int setDipoleStatus; |
372 |
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if (isDipole) { |
373 |
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newDipoleType(&ident, &dipole, &setDipoleStatus); |
374 |
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} |
375 |
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376 |
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//notify fotran a StickyType is created |
377 |
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int setStickyStatus; |
378 |
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if (isSticky) { |
379 |
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makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup); |
380 |
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} |
381 |
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382 |
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383 |
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if (!setDipoleStatus || !setStickyStatus) { |
384 |
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385 |
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} |
386 |
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387 |
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} |
388 |
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} |
389 |
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|
390 |
tim |
1757 |
void DUFF::parseBondType(const std::string& line, int lineNo){ |
391 |
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|
392 |
|
|
StringTokenizer tokenizer(line); |
393 |
|
|
std::string at1; |
394 |
|
|
std::string at2; |
395 |
|
|
std::string bt; |
396 |
|
|
BondType* bondType = NULL; |
397 |
|
|
double b0; |
398 |
|
|
|
399 |
|
|
int nTokens = tokenizer.countTokens(); |
400 |
|
|
|
401 |
|
|
if (nTokens < 4) { |
402 |
|
|
|
403 |
|
|
return; |
404 |
|
|
} |
405 |
|
|
|
406 |
|
|
at1 = tokenizer.nextToken(); |
407 |
|
|
at2 = tokenizer.nextToken(); |
408 |
|
|
bt = tokenizer.nextToken(); |
409 |
|
|
b0 = tokenizer.nextTokenAsDouble(); |
410 |
|
|
nTokens -= 4; |
411 |
|
|
|
412 |
|
|
//switch is a maintain nightmare |
413 |
|
|
switch(bt) { |
414 |
tim |
1767 |
case "Fixed" : |
415 |
tim |
1757 |
bondType = new FixedBondType(); |
416 |
|
|
break; |
417 |
|
|
|
418 |
tim |
1767 |
case "Harmonic" : |
419 |
tim |
1757 |
if (nTokens < 1) { |
420 |
|
|
|
421 |
|
|
} else { |
422 |
|
|
|
423 |
|
|
double kb = tokenizer.nextTokenAsDouble(); |
424 |
|
|
bondType = new HarmonicBondType(b0, kb); |
425 |
|
|
} |
426 |
|
|
|
427 |
|
|
break; |
428 |
|
|
|
429 |
tim |
1767 |
case "Cubic" : |
430 |
tim |
1757 |
if (nTokens < 4) { |
431 |
|
|
|
432 |
|
|
} else { |
433 |
|
|
|
434 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
435 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
436 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
437 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
438 |
|
|
|
439 |
|
|
bondType = new CubicBondType(b0, k3, k2, k1, k0); |
440 |
|
|
} |
441 |
|
|
break; |
442 |
|
|
|
443 |
tim |
1767 |
case "Quartic" : |
444 |
tim |
1757 |
if (nTokens < 5) { |
445 |
|
|
|
446 |
|
|
} else { |
447 |
|
|
|
448 |
|
|
b0 = tokenizer.nextTokenAsDouble(); |
449 |
|
|
double k4 = tokenizer.nextTokenAsDouble(); |
450 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
451 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
452 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
453 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
454 |
|
|
|
455 |
|
|
bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0); |
456 |
|
|
} |
457 |
|
|
break; |
458 |
|
|
|
459 |
tim |
1767 |
case "Polynomial" : |
460 |
tim |
1757 |
if (nTokens < 2 || nTokens % 2 != 0) { |
461 |
|
|
|
462 |
|
|
} else { |
463 |
|
|
int nPairs = nTokens / 2; |
464 |
|
|
int power; |
465 |
|
|
double coefficient; |
466 |
|
|
PolynomialBondType pbt = new PolynomialBondType(); |
467 |
|
|
|
468 |
|
|
for (int i = 0; i < nPairs; ++i) { |
469 |
|
|
power = tokenizer.nextTokenAsInt(); |
470 |
|
|
coefficient = tokenizer.nextTokenAsDouble(); |
471 |
tim |
1758 |
pbt->setCoefficient(power, coefficient); |
472 |
tim |
1757 |
} |
473 |
|
|
} |
474 |
|
|
|
475 |
|
|
break; |
476 |
|
|
|
477 |
|
|
default: |
478 |
|
|
|
479 |
|
|
} |
480 |
|
|
|
481 |
|
|
if (bondType != NULL) { |
482 |
|
|
addBondType(at1, at2, bondType); |
483 |
|
|
} |
484 |
gezelter |
1490 |
} |
485 |
|
|
|
486 |
tim |
1757 |
void DUFF::parseBendType(const std::string& line, int lineNo){ |
487 |
|
|
StringTokenizer tokenizer(line); |
488 |
|
|
std::string at1; |
489 |
|
|
std::string at2; |
490 |
|
|
std::string at3; |
491 |
|
|
std::string bt; |
492 |
|
|
double theta0; |
493 |
|
|
BendType* bendType = NULL; |
494 |
|
|
|
495 |
|
|
int nTokens = tokenizer.countTokens(); |
496 |
|
|
|
497 |
|
|
if (nTokens < 5) { |
498 |
|
|
|
499 |
|
|
return; |
500 |
|
|
} |
501 |
|
|
|
502 |
|
|
at1 = tokenizer.nextToken(); |
503 |
|
|
at2 = tokenizer.nextToken(); |
504 |
|
|
at3 = tokenizer.nextToken(); |
505 |
|
|
bt = tokenizer.nextToken(); |
506 |
|
|
theta0 = tokenizer.nextTokenAsDouble(); |
507 |
|
|
nTokens -= 5; |
508 |
|
|
|
509 |
|
|
//switch is a maintain nightmare |
510 |
|
|
switch(bt) { |
511 |
|
|
|
512 |
tim |
1767 |
case "Harmonic" : |
513 |
tim |
1757 |
|
514 |
|
|
if (nTokens < 1) { |
515 |
|
|
|
516 |
|
|
} else { |
517 |
|
|
|
518 |
|
|
double ktheta = tokenizer.nextTokenAsDouble(); |
519 |
|
|
bendType = new HarmonicBendType(theta0, ktheta); |
520 |
|
|
} |
521 |
|
|
break; |
522 |
tim |
1767 |
case "GhostBend" : |
523 |
tim |
1757 |
if (nTokens < 1) { |
524 |
|
|
|
525 |
|
|
} else { |
526 |
|
|
double ktheta = tokenizer.nextTokenAsDouble(); |
527 |
|
|
bendType = new HarmonicBendType(theta0, ktheta); |
528 |
|
|
} |
529 |
|
|
break; |
530 |
|
|
|
531 |
tim |
1767 |
case "UreyBradley" : |
532 |
tim |
1757 |
if (nTokens < 3) { |
533 |
|
|
|
534 |
|
|
} else { |
535 |
|
|
double ktheta = tokenizer.nextTokenAsDouble(); |
536 |
|
|
double s0 = tokenizer.nextTokenAsDouble(); |
537 |
|
|
double kub = tokenizer.nextTokenAsDouble(); |
538 |
|
|
bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub); |
539 |
|
|
} |
540 |
|
|
break; |
541 |
|
|
|
542 |
tim |
1767 |
case "Cubic" : |
543 |
tim |
1757 |
if (nTokens < 4) { |
544 |
|
|
|
545 |
|
|
} else { |
546 |
|
|
|
547 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
548 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
549 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
550 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
551 |
|
|
|
552 |
|
|
bendType = new CubicBendType(theta0, k3, k2, k1, k0); |
553 |
|
|
} |
554 |
|
|
break; |
555 |
|
|
|
556 |
tim |
1767 |
case "Quartic" : |
557 |
tim |
1757 |
if (nTokens < 5) { |
558 |
|
|
|
559 |
|
|
} else { |
560 |
|
|
|
561 |
|
|
theta0 = tokenizer.nextTokenAsDouble(); |
562 |
|
|
double k4 = tokenizer.nextTokenAsDouble(); |
563 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
564 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
565 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
566 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
567 |
|
|
|
568 |
|
|
bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0); |
569 |
|
|
} |
570 |
|
|
break; |
571 |
|
|
|
572 |
tim |
1767 |
case "Polynomial" : |
573 |
tim |
1757 |
if (nTokens < 2 || nTokens % 2 != 0) { |
574 |
|
|
|
575 |
|
|
} else { |
576 |
|
|
int nPairs = nTokens / 2; |
577 |
|
|
int power; |
578 |
|
|
double coefficient; |
579 |
|
|
PolynomialBendType* pbt = new PolynomialBendType(); |
580 |
|
|
|
581 |
|
|
for (int i = 0; i < nPairs; ++i) { |
582 |
|
|
power = tokenizer.nextTokenAsInt(); |
583 |
|
|
coefficient = tokenizer.nextTokenAsDouble(); |
584 |
tim |
1758 |
pbt->setCoefficient(power, coefficient); |
585 |
tim |
1757 |
} |
586 |
|
|
} |
587 |
|
|
|
588 |
|
|
break; |
589 |
|
|
|
590 |
|
|
default: |
591 |
|
|
|
592 |
|
|
} |
593 |
|
|
|
594 |
|
|
if (bendType != NULL) { |
595 |
|
|
addBendType(at1, at2, at3, bendType); |
596 |
|
|
} |
597 |
|
|
|
598 |
gezelter |
1490 |
} |
599 |
|
|
|
600 |
tim |
1757 |
void DUFF::parseTorsionType(const std::string& line, int lineNo){ |
601 |
|
|
StringTokenizer tokenizer(line); |
602 |
|
|
std::string at1; |
603 |
|
|
std::string at2; |
604 |
|
|
std::string at3; |
605 |
|
|
std::string at4; |
606 |
|
|
std::string tt; |
607 |
tim |
1767 |
TorsionType* torsionType = NULL; |
608 |
gezelter |
1490 |
|
609 |
tim |
1757 |
int nTokens = tokenizer.countTokens(); |
610 |
|
|
|
611 |
|
|
if (nTokens < 5) { |
612 |
|
|
|
613 |
|
|
return; |
614 |
|
|
} |
615 |
|
|
|
616 |
|
|
at1 = tokenizer.nextToken(); |
617 |
|
|
at2 = tokenizer.nextToken(); |
618 |
|
|
at3 = tokenizer.nextToken(); |
619 |
|
|
at4 = tokenizer.nextToken(); |
620 |
|
|
tt = tokenizer.nextToken(); |
621 |
|
|
|
622 |
|
|
nTokens -= 5; |
623 |
|
|
|
624 |
|
|
switch(tt) { |
625 |
|
|
|
626 |
tim |
1767 |
case "Cubic" : |
627 |
tim |
1757 |
if (nTokens < 4) { |
628 |
|
|
|
629 |
|
|
} else { |
630 |
|
|
|
631 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
632 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
633 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
634 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
635 |
|
|
|
636 |
|
|
bendType = new CubicTorsionType(k3, k2, k1, k0); |
637 |
|
|
} |
638 |
|
|
break; |
639 |
|
|
|
640 |
tim |
1767 |
case "Quartic" : |
641 |
tim |
1757 |
if (nTokens < 5) { |
642 |
|
|
|
643 |
|
|
} else { |
644 |
|
|
|
645 |
|
|
theta0 = tokenizer.nextTokenAsDouble(); |
646 |
|
|
double k4 = tokenizer.nextTokenAsDouble(); |
647 |
|
|
double k3 = tokenizer.nextTokenAsDouble(); |
648 |
|
|
double k2 = tokenizer.nextTokenAsDouble(); |
649 |
|
|
double k1 = tokenizer.nextTokenAsDouble(); |
650 |
|
|
double k0 = tokenizer.nextTokenAsDouble(); |
651 |
|
|
|
652 |
|
|
bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0); |
653 |
|
|
} |
654 |
|
|
break; |
655 |
|
|
|
656 |
tim |
1767 |
case "Polynomial" : |
657 |
tim |
1757 |
if (nTokens < 2 || nTokens % 2 != 0) { |
658 |
|
|
|
659 |
|
|
} else { |
660 |
|
|
int nPairs = nTokens / 2; |
661 |
|
|
int power; |
662 |
|
|
double coefficient; |
663 |
|
|
PolynomialTorsionType* pbt = new PolynomialTorsionType(); |
664 |
|
|
|
665 |
|
|
for (int i = 0; i < nPairs; ++i) { |
666 |
|
|
power = tokenizer.nextTokenAsInt(); |
667 |
|
|
coefficient = tokenizer.nextTokenAsDouble(); |
668 |
tim |
1758 |
pbt->setCoefficient(power, coefficient); |
669 |
tim |
1757 |
} |
670 |
|
|
} |
671 |
|
|
|
672 |
|
|
break; |
673 |
tim |
1767 |
case "Charmm" : |
674 |
tim |
1757 |
|
675 |
|
|
if (nTokens < 3 || nTokens % 3 != 0) { |
676 |
|
|
|
677 |
|
|
} else { |
678 |
|
|
int nSets = nTokens / 3; |
679 |
|
|
|
680 |
|
|
CharmmTorsionType* ctt = new CharmmTorsionType(); |
681 |
|
|
|
682 |
|
|
for (int i = 0; i < nSets; ++i) { |
683 |
tim |
1758 |
double kchi = tokenizer.nextTokenAsDouble(); |
684 |
|
|
int n = tokenizer.nextTokenAsInt(); |
685 |
|
|
double delta = tokenizer.nextTokenAsDouble(); |
686 |
tim |
1757 |
|
687 |
tim |
1758 |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
688 |
tim |
1757 |
} |
689 |
|
|
} |
690 |
|
|
default: |
691 |
|
|
|
692 |
|
|
} |
693 |
|
|
|
694 |
tim |
1767 |
if (torsionType != NULL) { |
695 |
|
|
addTorsionType(at1, at2, at3, at4, torsionType); |
696 |
tim |
1757 |
} |
697 |
gezelter |
1490 |
} |
698 |
tim |
1770 |
*/ |
699 |
tim |
1741 |
} //end namespace oopse |