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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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|
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#include "UseTheForce/DUFF.hpp" |
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#include "UseTheForce/DarkSide/lj_interface.h" |
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#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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|
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namespace oopse { |
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|
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//definition of createDUFF |
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ForceField* createDUFF() { |
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return new DUFF(); |
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} |
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|
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//register createDUFF to ForceFieldFactory |
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ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
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|
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|
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ParseState DUFF::getSection(const std::string& section) { |
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ParseState result; |
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|
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switch(section) { |
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case "AtomTypes" : |
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result = DUFF::AtomTypeSection; |
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break; |
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case "DirectionalAtomTypes" : |
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result = DUFF::DirectionalAtomTypeSection; |
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break; |
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|
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case "BondTypes" : |
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result = DUFF::BondTypeSection; |
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break; |
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|
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case "BendTypes" : |
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result = DUFF::BendTypeSection; |
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break; |
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|
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case "TorsionTypes" : |
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result = DUFF::TorsionTypeSection; |
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break; |
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default: |
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result = DUFF::UnknownSection; |
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} |
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|
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return result; |
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} |
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|
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void DUFF::parse(const std::string& filename) { |
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ifstrstream* ffStream; |
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ffStream = openForceFiledFile(filename); |
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const int bufferSize = 65535; |
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std::string line; |
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char buffer[bufferSize]; |
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int lineNo = 0; |
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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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|
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while(ffStream.getline(buffer, bufferSize)){ |
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++lineNo; |
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|
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line = trimSpaces(buffer); |
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//a line begins with "//" is comment |
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if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) { |
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continue; |
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} else { |
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|
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switch(currentSection) { |
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case DUFF::AtomTypeSection : |
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parseAtomType(line, lineNo, atomIdent); |
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break; |
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|
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case DUFF::DirectionalAtomTypeSection : |
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parseDirectionalAtomType(line, lineNo); |
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break; |
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|
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case DUFF::BondTypeSection : |
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parseBondType(line, lineNo); |
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break; |
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|
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case DUFF::BendTypeSection : |
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parseBendType(line, lineNo); |
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break; |
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|
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case DUFF::TorsionTypeSection : |
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parseTorsionType(line, lineNo); |
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break; |
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|
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case DUFF::UnknownSection: |
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StringTokenizer tokenizer(line); |
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|
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std::string keyword = tokenizer.nextToken(); |
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std::string section = tokenizer.nextToken(); |
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|
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ParseState newSection = getSection(section); |
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if (keyword != "begin" || keyword != "end") { |
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std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
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} else if (keyword == "begin") { |
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if (newSection == DUFF::UnknownSection) { |
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std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
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} else { |
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//enter a new section |
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currentSection = newSection; |
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} |
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|
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} else if (keyword == "end"){ |
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if (currentSection == newSection) ) { |
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//leave a section |
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currentSection = DUFF::UnknownSection; |
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} else { |
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std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
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} |
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|
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} |
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break; |
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default : |
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|
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} |
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|
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} |
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} |
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|
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delete ffStream; |
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} |
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|
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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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|
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} else { |
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|
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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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|
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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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} |
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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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} |
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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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|
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atomType->setName(atomTypeName); |
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atomType->setMass(mass); |
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|
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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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|
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atomType->setIdent(ident); |
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|
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atomType->complete(); |
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|
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int setLJStatus; |
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|
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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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|
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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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|
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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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} |
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|
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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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|
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//in DirectionalAtomTypeSection, 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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std::cerr << "Not enought tokens" << std::endl; |
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} else { |
246 |
|
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|
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std::string atomTypeName = tokenizer.nextToken(); |
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bool isDipole = tokenizer.nextTokenAsBool(); |
250 |
bool isSticky = tokenizer.nextTokenAsBool(); |
251 |
double Ixx = tokenizer.nextTokenAsDouble(); |
252 |
double Iyy = tokenizer.nextTokenAsDouble(); |
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double Izz = tokenizer.nextTokenAsDouble(); |
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nTokens -= 6; |
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|
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AtomType* atomType = getAtomType(atomTypeName); |
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if (atomType == NULL) { |
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|
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} |
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|
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DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
262 |
if (dAtomType == NULL) { |
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|
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|
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} |
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|
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if (isDipole) { |
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dAtomType->setDipole(); |
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} |
270 |
|
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if (isSticky) { |
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dAtomType->setSticky(); |
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} |
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|
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Mat3x3d inertialMat; |
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inertialMat(0, 0) = Ixx; |
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inertialMat(1, 1) = Iyy; |
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inertialMat(2, 2) = Izz; |
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dAtomType->setI(inertialMat); |
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|
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//read dipole moment |
282 |
double dipole; |
283 |
if (isDipole) { |
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if (nTokens >= 1) { |
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dipole = tokenizer.nextTokenAsDouble(); |
286 |
nTokens -= 1; |
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} else { |
288 |
|
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} |
290 |
} |
291 |
|
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//read sticky parameters |
293 |
double w0; |
294 |
double v0; |
295 |
double v0p; |
296 |
double rl; |
297 |
double ru; |
298 |
double rlp; |
299 |
double rup; |
300 |
if (isSticky) { |
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if (nTokens >= 7) { |
302 |
w0 = tokenizer.nextTokenAsDouble(); |
303 |
v0 = tokenizer.nextTokenAsDouble(); |
304 |
v0p = tokenizer.nextTokenAsDouble(); |
305 |
rl = tokenizer.nextTokenAsDouble(); |
306 |
ru = tokenizer.nextTokenAsDouble(); |
307 |
rlp = tokenizer.nextTokenAsDouble(); |
308 |
rup = tokenizer.nextTokenAsDouble(); |
309 |
nTokens -= 7; |
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} else { |
311 |
|
312 |
} |
313 |
} |
314 |
|
315 |
|
316 |
//notify fotran a newDipoleType is created |
317 |
int ident = dAtomType->getIdent(); |
318 |
int setDipoleStatus; |
319 |
if (isDipole) { |
320 |
newDipoleType(&ident, &dipole, &setDipoleStatus); |
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} |
322 |
|
323 |
//notify fotran a StickyType is created |
324 |
int setStickyStatus; |
325 |
if (isSticky) { |
326 |
makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup); |
327 |
} |
328 |
|
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|
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if (!setDipoleStatus || !setStickyStatus) { |
331 |
|
332 |
} |
333 |
|
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} |
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} |
336 |
|
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void DUFF::parseBondType(const std::string& line, int lineNo){ |
338 |
|
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StringTokenizer tokenizer(line); |
340 |
std::string at1; |
341 |
std::string at2; |
342 |
std::string bt; |
343 |
BondType* bondType = NULL; |
344 |
double b0; |
345 |
|
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int nTokens = tokenizer.countTokens(); |
347 |
|
348 |
if (nTokens < 4) { |
349 |
|
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return; |
351 |
} |
352 |
|
353 |
at1 = tokenizer.nextToken(); |
354 |
at2 = tokenizer.nextToken(); |
355 |
bt = tokenizer.nextToken(); |
356 |
b0 = tokenizer.nextTokenAsDouble(); |
357 |
nTokens -= 4; |
358 |
|
359 |
//switch is a maintain nightmare |
360 |
switch(bt) { |
361 |
case "Fixed" : |
362 |
bondType = new FixedBondType(); |
363 |
break; |
364 |
|
365 |
case "Harmonic" : |
366 |
if (nTokens < 1) { |
367 |
|
368 |
} else { |
369 |
|
370 |
double kb = tokenizer.nextTokenAsDouble(); |
371 |
bondType = new HarmonicBondType(b0, kb); |
372 |
} |
373 |
|
374 |
break; |
375 |
|
376 |
case "Cubic" : |
377 |
if (nTokens < 4) { |
378 |
|
379 |
} else { |
380 |
|
381 |
double k3 = tokenizer.nextTokenAsDouble(); |
382 |
double k2 = tokenizer.nextTokenAsDouble(); |
383 |
double k1 = tokenizer.nextTokenAsDouble(); |
384 |
double k0 = tokenizer.nextTokenAsDouble(); |
385 |
|
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bondType = new CubicBondType(b0, k3, k2, k1, k0); |
387 |
} |
388 |
break; |
389 |
|
390 |
case "Quartic" : |
391 |
if (nTokens < 5) { |
392 |
|
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} else { |
394 |
|
395 |
b0 = tokenizer.nextTokenAsDouble(); |
396 |
double k4 = tokenizer.nextTokenAsDouble(); |
397 |
double k3 = tokenizer.nextTokenAsDouble(); |
398 |
double k2 = tokenizer.nextTokenAsDouble(); |
399 |
double k1 = tokenizer.nextTokenAsDouble(); |
400 |
double k0 = tokenizer.nextTokenAsDouble(); |
401 |
|
402 |
bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0); |
403 |
} |
404 |
break; |
405 |
|
406 |
case "Polynomial" : |
407 |
if (nTokens < 2 || nTokens % 2 != 0) { |
408 |
|
409 |
} else { |
410 |
int nPairs = nTokens / 2; |
411 |
int power; |
412 |
double coefficient; |
413 |
PolynomialBondType pbt = new PolynomialBondType(); |
414 |
|
415 |
for (int i = 0; i < nPairs; ++i) { |
416 |
power = tokenizer.nextTokenAsInt(); |
417 |
coefficient = tokenizer.nextTokenAsDouble(); |
418 |
pbt->setCoefficient(power, coefficient); |
419 |
} |
420 |
} |
421 |
|
422 |
break; |
423 |
|
424 |
default: |
425 |
|
426 |
} |
427 |
|
428 |
if (bondType != NULL) { |
429 |
addBondType(at1, at2, bondType); |
430 |
} |
431 |
} |
432 |
|
433 |
void DUFF::parseBendType(const std::string& line, int lineNo){ |
434 |
StringTokenizer tokenizer(line); |
435 |
std::string at1; |
436 |
std::string at2; |
437 |
std::string at3; |
438 |
std::string bt; |
439 |
double theta0; |
440 |
BendType* bendType = NULL; |
441 |
|
442 |
int nTokens = tokenizer.countTokens(); |
443 |
|
444 |
if (nTokens < 5) { |
445 |
|
446 |
return; |
447 |
} |
448 |
|
449 |
at1 = tokenizer.nextToken(); |
450 |
at2 = tokenizer.nextToken(); |
451 |
at3 = tokenizer.nextToken(); |
452 |
bt = tokenizer.nextToken(); |
453 |
theta0 = tokenizer.nextTokenAsDouble(); |
454 |
nTokens -= 5; |
455 |
|
456 |
//switch is a maintain nightmare |
457 |
switch(bt) { |
458 |
|
459 |
case "Harmonic" : |
460 |
|
461 |
if (nTokens < 1) { |
462 |
|
463 |
} else { |
464 |
|
465 |
double ktheta = tokenizer.nextTokenAsDouble(); |
466 |
bendType = new HarmonicBendType(theta0, ktheta); |
467 |
} |
468 |
break; |
469 |
case "GhostBend" : |
470 |
if (nTokens < 1) { |
471 |
|
472 |
} else { |
473 |
double ktheta = tokenizer.nextTokenAsDouble(); |
474 |
bendType = new HarmonicBendType(theta0, ktheta); |
475 |
} |
476 |
break; |
477 |
|
478 |
case "UreyBradley" : |
479 |
if (nTokens < 3) { |
480 |
|
481 |
} else { |
482 |
double ktheta = tokenizer.nextTokenAsDouble(); |
483 |
double s0 = tokenizer.nextTokenAsDouble(); |
484 |
double kub = tokenizer.nextTokenAsDouble(); |
485 |
bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub); |
486 |
} |
487 |
break; |
488 |
|
489 |
case "Cubic" : |
490 |
if (nTokens < 4) { |
491 |
|
492 |
} else { |
493 |
|
494 |
double k3 = tokenizer.nextTokenAsDouble(); |
495 |
double k2 = tokenizer.nextTokenAsDouble(); |
496 |
double k1 = tokenizer.nextTokenAsDouble(); |
497 |
double k0 = tokenizer.nextTokenAsDouble(); |
498 |
|
499 |
bendType = new CubicBendType(theta0, k3, k2, k1, k0); |
500 |
} |
501 |
break; |
502 |
|
503 |
case "Quartic" : |
504 |
if (nTokens < 5) { |
505 |
|
506 |
} else { |
507 |
|
508 |
theta0 = tokenizer.nextTokenAsDouble(); |
509 |
double k4 = tokenizer.nextTokenAsDouble(); |
510 |
double k3 = tokenizer.nextTokenAsDouble(); |
511 |
double k2 = tokenizer.nextTokenAsDouble(); |
512 |
double k1 = tokenizer.nextTokenAsDouble(); |
513 |
double k0 = tokenizer.nextTokenAsDouble(); |
514 |
|
515 |
bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0); |
516 |
} |
517 |
break; |
518 |
|
519 |
case "Polynomial" : |
520 |
if (nTokens < 2 || nTokens % 2 != 0) { |
521 |
|
522 |
} else { |
523 |
int nPairs = nTokens / 2; |
524 |
int power; |
525 |
double coefficient; |
526 |
PolynomialBendType* pbt = new PolynomialBendType(); |
527 |
|
528 |
for (int i = 0; i < nPairs; ++i) { |
529 |
power = tokenizer.nextTokenAsInt(); |
530 |
coefficient = tokenizer.nextTokenAsDouble(); |
531 |
pbt->setCoefficient(power, coefficient); |
532 |
} |
533 |
} |
534 |
|
535 |
break; |
536 |
|
537 |
default: |
538 |
|
539 |
} |
540 |
|
541 |
if (bendType != NULL) { |
542 |
addBendType(at1, at2, at3, bendType); |
543 |
} |
544 |
|
545 |
} |
546 |
|
547 |
void DUFF::parseTorsionType(const std::string& line, int lineNo){ |
548 |
StringTokenizer tokenizer(line); |
549 |
std::string at1; |
550 |
std::string at2; |
551 |
std::string at3; |
552 |
std::string at4; |
553 |
std::string tt; |
554 |
TorsionType* torsionType = NULL; |
555 |
|
556 |
int nTokens = tokenizer.countTokens(); |
557 |
|
558 |
if (nTokens < 5) { |
559 |
|
560 |
return; |
561 |
} |
562 |
|
563 |
at1 = tokenizer.nextToken(); |
564 |
at2 = tokenizer.nextToken(); |
565 |
at3 = tokenizer.nextToken(); |
566 |
at4 = tokenizer.nextToken(); |
567 |
tt = tokenizer.nextToken(); |
568 |
|
569 |
nTokens -= 5; |
570 |
|
571 |
switch(tt) { |
572 |
|
573 |
case "Cubic" : |
574 |
if (nTokens < 4) { |
575 |
|
576 |
} else { |
577 |
|
578 |
double k3 = tokenizer.nextTokenAsDouble(); |
579 |
double k2 = tokenizer.nextTokenAsDouble(); |
580 |
double k1 = tokenizer.nextTokenAsDouble(); |
581 |
double k0 = tokenizer.nextTokenAsDouble(); |
582 |
|
583 |
bendType = new CubicTorsionType(k3, k2, k1, k0); |
584 |
} |
585 |
break; |
586 |
|
587 |
case "Quartic" : |
588 |
if (nTokens < 5) { |
589 |
|
590 |
} else { |
591 |
|
592 |
theta0 = tokenizer.nextTokenAsDouble(); |
593 |
double k4 = tokenizer.nextTokenAsDouble(); |
594 |
double k3 = tokenizer.nextTokenAsDouble(); |
595 |
double k2 = tokenizer.nextTokenAsDouble(); |
596 |
double k1 = tokenizer.nextTokenAsDouble(); |
597 |
double k0 = tokenizer.nextTokenAsDouble(); |
598 |
|
599 |
bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0); |
600 |
} |
601 |
break; |
602 |
|
603 |
case "Polynomial" : |
604 |
if (nTokens < 2 || nTokens % 2 != 0) { |
605 |
|
606 |
} else { |
607 |
int nPairs = nTokens / 2; |
608 |
int power; |
609 |
double coefficient; |
610 |
PolynomialTorsionType* pbt = new PolynomialTorsionType(); |
611 |
|
612 |
for (int i = 0; i < nPairs; ++i) { |
613 |
power = tokenizer.nextTokenAsInt(); |
614 |
coefficient = tokenizer.nextTokenAsDouble(); |
615 |
pbt->setCoefficient(power, coefficient); |
616 |
} |
617 |
} |
618 |
|
619 |
break; |
620 |
case "Charmm" : |
621 |
|
622 |
if (nTokens < 3 || nTokens % 3 != 0) { |
623 |
|
624 |
} else { |
625 |
int nSets = nTokens / 3; |
626 |
|
627 |
CharmmTorsionType* ctt = new CharmmTorsionType(); |
628 |
|
629 |
for (int i = 0; i < nSets; ++i) { |
630 |
double kchi = tokenizer.nextTokenAsDouble(); |
631 |
int n = tokenizer.nextTokenAsInt(); |
632 |
double delta = tokenizer.nextTokenAsDouble(); |
633 |
|
634 |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
635 |
} |
636 |
} |
637 |
default: |
638 |
|
639 |
} |
640 |
|
641 |
if (torsionType != NULL) { |
642 |
addTorsionType(at1, at2, at3, at4, torsionType); |
643 |
} |
644 |
} |
645 |
|
646 |
} //end namespace oopse |