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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" |
| 30 |
#include "UseTheForce/DarkSide/sticky_interface.h" |
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|
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namespace oopse { |
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|
| 34 |
//definition of createDUFF |
| 35 |
ForceField* createDUFF() { |
| 36 |
return new DUFF(); |
| 37 |
} |
| 38 |
|
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//register createDUFF to ForceFieldFactory |
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ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF); |
| 41 |
|
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|
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ParseState DUFF::getSection(const std::string& section) { |
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ParseState result; |
| 45 |
|
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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 = 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; |
| 99 |
|
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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; |
| 107 |
|
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case DUFF::TorsionTypeSection : |
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parseTorsionType(line, lineNo); |
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break; |
| 111 |
|
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case DUFF::UnknownSection: |
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StringTokenizer tokenizer(line); |
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|
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std::string keyword = tokenizer.nextToken(); |
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std::string section = tokenizer.nextToken(); |
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|
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ParseState newSection = getSection(section); |
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if (keyword != "begin" || keyword != "end") { |
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std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
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} else if (keyword == "begin") { |
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if (newSection == DUFF::UnknownSection) { |
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std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
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} else { |
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//enter a new section |
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currentSection = newSection; |
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} |
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|
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} else if (keyword == "end"){ |
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if (currentSection == newSection) ) { |
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//leave a section |
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currentSection = DUFF::UnknownSection; |
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} else { |
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std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl; |
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} |
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|
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} |
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break; |
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default : |
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|
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} |
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|
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} |
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} |
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|
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delete ffStream; |
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} |
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|
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|
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void DUFF::parseAtomType(const std::string& line, int lineNo, 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 { |
| 159 |
|
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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; |
| 169 |
|
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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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//by default, all of the properties in AtomTypeProperties is set to 0 |
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//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true |
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atomType->setLennardJones(); |
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|
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atomType->setIdent(ident); |
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|
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atomType->complete(); |
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|
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int setLJStatus; |
| 210 |
|
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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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} |
| 215 |
|
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int setChargeStatus; |
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if (isCharge) { |
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newChargeType(&ident, &charge, &setChargeStatus) |
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} |
| 220 |
|
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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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} |
| 230 |
|
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} |
| 232 |
|
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|
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void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) { |
| 235 |
StringTokenizer tokenizer(line); |
| 236 |
int nTokens = tokenizer.countTokens(); |
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|
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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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|
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} else { |
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|
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|
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std::string atomTypeName = tokenizer.nextToken(); |
| 246 |
bool isDipole = tokenizer.nextTokenAsBool(); |
| 247 |
bool isSticky = tokenizer.nextTokenAsBool(); |
| 248 |
double Ixx = tokenizer.nextTokenAsDouble(); |
| 249 |
double Iyy = tokenizer.nextTokenAsDouble(); |
| 250 |
double Izz = tokenizer.nextTokenAsDouble(); |
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nTokens -= 6; |
| 252 |
|
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AtomType* atomType = getAtomType(atomTypeName); |
| 254 |
if (atomType == NULL) { |
| 255 |
|
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} |
| 257 |
|
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DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
| 259 |
if (dAtomType == NULL) { |
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|
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|
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} |
| 263 |
|
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dAtomType->setDipole(isDipole); |
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dAtomType->setSticky(isSticky); |
| 266 |
|
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Mat3x3d inertialMat; |
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inertialMat(0, 0) = Ixx; |
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inertialMat(1, 1) = Ixx; |
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inertialMat(2, 2) = Ixx; |
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dAtomType->setI(inertialMat); |
| 272 |
|
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//read dipole moment |
| 274 |
double dipole; |
| 275 |
if (isDipole) { |
| 276 |
if (nTokens >= 1) { |
| 277 |
dipole = tokenizer.nextTokenAsDouble(); |
| 278 |
nTokens -= 1; |
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} else { |
| 280 |
|
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} |
| 282 |
} |
| 283 |
|
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//read sticky parameters |
| 285 |
double w0; |
| 286 |
double v0; |
| 287 |
double v0p; |
| 288 |
double rl; |
| 289 |
double ru; |
| 290 |
double rlp; |
| 291 |
double rup; |
| 292 |
if (isSticky) { |
| 293 |
if (nTokens >= 7) { |
| 294 |
w0 = tokenizer.nextTokenAsDouble(); |
| 295 |
v0 = tokenizer.nextTokenAsDouble(); |
| 296 |
v0p = tokenizer.nextTokenAsDouble(); |
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rl = tokenizer.nextTokenAsDouble(); |
| 298 |
ru = tokenizer.nextTokenAsDouble(); |
| 299 |
rlp = tokenizer.nextTokenAsDouble(); |
| 300 |
rup = tokenizer.nextTokenAsDouble(); |
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nTokens -= 7; |
| 302 |
} else { |
| 303 |
|
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} |
| 305 |
} |
| 306 |
|
| 307 |
|
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//notify fotran a newDipoleType is created |
| 309 |
int ident = dAtomType->getIdent(); |
| 310 |
int setDipoleStatus; |
| 311 |
if (isDipole) { |
| 312 |
newDipoleType(&ident, &dipole, &setDipoleStatus); |
| 313 |
} |
| 314 |
|
| 315 |
//notify fotran a StickyType is created |
| 316 |
int setStickyStatus; |
| 317 |
if (isSticky) { |
| 318 |
makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup); |
| 319 |
} |
| 320 |
|
| 321 |
|
| 322 |
if (!setDipoleStatus || !setStickyStatus) { |
| 323 |
|
| 324 |
} |
| 325 |
|
| 326 |
} |
| 327 |
} |
| 328 |
|
| 329 |
void DUFF::parseBondType(const std::string& line, int lineNo){ |
| 330 |
|
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StringTokenizer tokenizer(line); |
| 332 |
std::string at1; |
| 333 |
std::string at2; |
| 334 |
std::string bt; |
| 335 |
BondType* bondType = NULL; |
| 336 |
double b0; |
| 337 |
|
| 338 |
int nTokens = tokenizer.countTokens(); |
| 339 |
|
| 340 |
if (nTokens < 4) { |
| 341 |
|
| 342 |
return; |
| 343 |
} |
| 344 |
|
| 345 |
at1 = tokenizer.nextToken(); |
| 346 |
at2 = tokenizer.nextToken(); |
| 347 |
bt = tokenizer.nextToken(); |
| 348 |
b0 = tokenizer.nextTokenAsDouble(); |
| 349 |
nTokens -= 4; |
| 350 |
|
| 351 |
//switch is a maintain nightmare |
| 352 |
switch(bt) { |
| 353 |
case "FixedBondType" : |
| 354 |
bondType = new FixedBondType(); |
| 355 |
break; |
| 356 |
|
| 357 |
case "HarmonicBondType" : |
| 358 |
if (nTokens < 1) { |
| 359 |
|
| 360 |
} else { |
| 361 |
|
| 362 |
double kb = tokenizer.nextTokenAsDouble(); |
| 363 |
bondType = new HarmonicBondType(b0, kb); |
| 364 |
} |
| 365 |
|
| 366 |
break; |
| 367 |
|
| 368 |
case "CubicBondType" : |
| 369 |
if (nTokens < 4) { |
| 370 |
|
| 371 |
} else { |
| 372 |
|
| 373 |
double k3 = tokenizer.nextTokenAsDouble(); |
| 374 |
double k2 = tokenizer.nextTokenAsDouble(); |
| 375 |
double k1 = tokenizer.nextTokenAsDouble(); |
| 376 |
double k0 = tokenizer.nextTokenAsDouble(); |
| 377 |
|
| 378 |
bondType = new CubicBondType(b0, k3, k2, k1, k0); |
| 379 |
} |
| 380 |
break; |
| 381 |
|
| 382 |
case "QuadraticBondType" : |
| 383 |
if (nTokens < 5) { |
| 384 |
|
| 385 |
} else { |
| 386 |
|
| 387 |
b0 = tokenizer.nextTokenAsDouble(); |
| 388 |
double k4 = tokenizer.nextTokenAsDouble(); |
| 389 |
double k3 = tokenizer.nextTokenAsDouble(); |
| 390 |
double k2 = tokenizer.nextTokenAsDouble(); |
| 391 |
double k1 = tokenizer.nextTokenAsDouble(); |
| 392 |
double k0 = tokenizer.nextTokenAsDouble(); |
| 393 |
|
| 394 |
bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0); |
| 395 |
} |
| 396 |
break; |
| 397 |
|
| 398 |
case "PolynomialBondType " : |
| 399 |
if (nTokens < 2 || nTokens % 2 != 0) { |
| 400 |
|
| 401 |
} else { |
| 402 |
int nPairs = nTokens / 2; |
| 403 |
int power; |
| 404 |
double coefficient; |
| 405 |
PolynomialBondType pbt = new PolynomialBondType(); |
| 406 |
|
| 407 |
for (int i = 0; i < nPairs; ++i) { |
| 408 |
power = tokenizer.nextTokenAsInt(); |
| 409 |
coefficient = tokenizer.nextTokenAsDouble(); |
| 410 |
pbt->setCoefficient(power, coefficient); |
| 411 |
} |
| 412 |
} |
| 413 |
|
| 414 |
break; |
| 415 |
|
| 416 |
default: |
| 417 |
|
| 418 |
} |
| 419 |
|
| 420 |
if (bondType != NULL) { |
| 421 |
addBondType(at1, at2, bondType); |
| 422 |
} |
| 423 |
} |
| 424 |
|
| 425 |
void DUFF::parseBendType(const std::string& line, int lineNo){ |
| 426 |
StringTokenizer tokenizer(line); |
| 427 |
std::string at1; |
| 428 |
std::string at2; |
| 429 |
std::string at3; |
| 430 |
std::string bt; |
| 431 |
double theta0; |
| 432 |
BendType* bendType = NULL; |
| 433 |
|
| 434 |
int nTokens = tokenizer.countTokens(); |
| 435 |
|
| 436 |
if (nTokens < 5) { |
| 437 |
|
| 438 |
return; |
| 439 |
} |
| 440 |
|
| 441 |
at1 = tokenizer.nextToken(); |
| 442 |
at2 = tokenizer.nextToken(); |
| 443 |
at3 = tokenizer.nextToken(); |
| 444 |
bt = tokenizer.nextToken(); |
| 445 |
theta0 = tokenizer.nextTokenAsDouble(); |
| 446 |
nTokens -= 5; |
| 447 |
|
| 448 |
//switch is a maintain nightmare |
| 449 |
switch(bt) { |
| 450 |
|
| 451 |
case "HarmonicBendType" : |
| 452 |
|
| 453 |
if (nTokens < 1) { |
| 454 |
|
| 455 |
} else { |
| 456 |
|
| 457 |
double ktheta = tokenizer.nextTokenAsDouble(); |
| 458 |
bendType = new HarmonicBendType(theta0, ktheta); |
| 459 |
} |
| 460 |
break; |
| 461 |
case "GhostBendType" : |
| 462 |
if (nTokens < 1) { |
| 463 |
|
| 464 |
} else { |
| 465 |
double ktheta = tokenizer.nextTokenAsDouble(); |
| 466 |
bendType = new HarmonicBendType(theta0, ktheta); |
| 467 |
} |
| 468 |
break; |
| 469 |
|
| 470 |
case "UreyBradleyBendType" : |
| 471 |
if (nTokens < 3) { |
| 472 |
|
| 473 |
} else { |
| 474 |
double ktheta = tokenizer.nextTokenAsDouble(); |
| 475 |
double s0 = tokenizer.nextTokenAsDouble(); |
| 476 |
double kub = tokenizer.nextTokenAsDouble(); |
| 477 |
bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub); |
| 478 |
} |
| 479 |
break; |
| 480 |
|
| 481 |
case "CubicBendType" : |
| 482 |
if (nTokens < 4) { |
| 483 |
|
| 484 |
} else { |
| 485 |
|
| 486 |
double k3 = tokenizer.nextTokenAsDouble(); |
| 487 |
double k2 = tokenizer.nextTokenAsDouble(); |
| 488 |
double k1 = tokenizer.nextTokenAsDouble(); |
| 489 |
double k0 = tokenizer.nextTokenAsDouble(); |
| 490 |
|
| 491 |
bendType = new CubicBendType(theta0, k3, k2, k1, k0); |
| 492 |
} |
| 493 |
break; |
| 494 |
|
| 495 |
case "QuadraticBendType" : |
| 496 |
if (nTokens < 5) { |
| 497 |
|
| 498 |
} else { |
| 499 |
|
| 500 |
theta0 = tokenizer.nextTokenAsDouble(); |
| 501 |
double k4 = tokenizer.nextTokenAsDouble(); |
| 502 |
double k3 = tokenizer.nextTokenAsDouble(); |
| 503 |
double k2 = tokenizer.nextTokenAsDouble(); |
| 504 |
double k1 = tokenizer.nextTokenAsDouble(); |
| 505 |
double k0 = tokenizer.nextTokenAsDouble(); |
| 506 |
|
| 507 |
bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0); |
| 508 |
} |
| 509 |
break; |
| 510 |
|
| 511 |
case "PolynomialBendType " : |
| 512 |
if (nTokens < 2 || nTokens % 2 != 0) { |
| 513 |
|
| 514 |
} else { |
| 515 |
int nPairs = nTokens / 2; |
| 516 |
int power; |
| 517 |
double coefficient; |
| 518 |
PolynomialBendType* pbt = new PolynomialBendType(); |
| 519 |
|
| 520 |
for (int i = 0; i < nPairs; ++i) { |
| 521 |
power = tokenizer.nextTokenAsInt(); |
| 522 |
coefficient = tokenizer.nextTokenAsDouble(); |
| 523 |
pbt->setCoefficient(power, coefficient); |
| 524 |
} |
| 525 |
} |
| 526 |
|
| 527 |
break; |
| 528 |
|
| 529 |
default: |
| 530 |
|
| 531 |
} |
| 532 |
|
| 533 |
if (bendType != NULL) { |
| 534 |
addBendType(at1, at2, at3, bendType); |
| 535 |
} |
| 536 |
|
| 537 |
} |
| 538 |
|
| 539 |
void DUFF::parseTorsionType(const std::string& line, int lineNo){ |
| 540 |
StringTokenizer tokenizer(line); |
| 541 |
std::string at1; |
| 542 |
std::string at2; |
| 543 |
std::string at3; |
| 544 |
std::string at4; |
| 545 |
std::string tt; |
| 546 |
TorsionType* bendType = NULL; |
| 547 |
|
| 548 |
int nTokens = tokenizer.countTokens(); |
| 549 |
|
| 550 |
if (nTokens < 5) { |
| 551 |
|
| 552 |
return; |
| 553 |
} |
| 554 |
|
| 555 |
at1 = tokenizer.nextToken(); |
| 556 |
at2 = tokenizer.nextToken(); |
| 557 |
at3 = tokenizer.nextToken(); |
| 558 |
at4 = tokenizer.nextToken(); |
| 559 |
tt = tokenizer.nextToken(); |
| 560 |
|
| 561 |
nTokens -= 5; |
| 562 |
|
| 563 |
switch(tt) { |
| 564 |
|
| 565 |
case "CubicTorsionType" : |
| 566 |
if (nTokens < 4) { |
| 567 |
|
| 568 |
} else { |
| 569 |
|
| 570 |
double k3 = tokenizer.nextTokenAsDouble(); |
| 571 |
double k2 = tokenizer.nextTokenAsDouble(); |
| 572 |
double k1 = tokenizer.nextTokenAsDouble(); |
| 573 |
double k0 = tokenizer.nextTokenAsDouble(); |
| 574 |
|
| 575 |
bendType = new CubicTorsionType(k3, k2, k1, k0); |
| 576 |
} |
| 577 |
break; |
| 578 |
|
| 579 |
case "QuadraticTorsionType" : |
| 580 |
if (nTokens < 5) { |
| 581 |
|
| 582 |
} else { |
| 583 |
|
| 584 |
theta0 = tokenizer.nextTokenAsDouble(); |
| 585 |
double k4 = tokenizer.nextTokenAsDouble(); |
| 586 |
double k3 = tokenizer.nextTokenAsDouble(); |
| 587 |
double k2 = tokenizer.nextTokenAsDouble(); |
| 588 |
double k1 = tokenizer.nextTokenAsDouble(); |
| 589 |
double k0 = tokenizer.nextTokenAsDouble(); |
| 590 |
|
| 591 |
bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0); |
| 592 |
} |
| 593 |
break; |
| 594 |
|
| 595 |
case "PolynomialTorsionType " : |
| 596 |
if (nTokens < 2 || nTokens % 2 != 0) { |
| 597 |
|
| 598 |
} else { |
| 599 |
int nPairs = nTokens / 2; |
| 600 |
int power; |
| 601 |
double coefficient; |
| 602 |
PolynomialTorsionType* pbt = new PolynomialTorsionType(); |
| 603 |
|
| 604 |
for (int i = 0; i < nPairs; ++i) { |
| 605 |
power = tokenizer.nextTokenAsInt(); |
| 606 |
coefficient = tokenizer.nextTokenAsDouble(); |
| 607 |
pbt->setCoefficient(power, coefficient); |
| 608 |
} |
| 609 |
} |
| 610 |
|
| 611 |
break; |
| 612 |
case "CharmmTorsionType" : |
| 613 |
|
| 614 |
if (nTokens < 3 || nTokens % 3 != 0) { |
| 615 |
|
| 616 |
} else { |
| 617 |
int nSets = nTokens / 3; |
| 618 |
|
| 619 |
CharmmTorsionType* ctt = new CharmmTorsionType(); |
| 620 |
|
| 621 |
for (int i = 0; i < nSets; ++i) { |
| 622 |
double kchi = tokenizer.nextTokenAsDouble(); |
| 623 |
int n = tokenizer.nextTokenAsInt(); |
| 624 |
double delta = tokenizer.nextTokenAsDouble(); |
| 625 |
|
| 626 |
ctt->setCharmmTorsionParameter(kchi, n, delta); |
| 627 |
} |
| 628 |
} |
| 629 |
default: |
| 630 |
|
| 631 |
} |
| 632 |
|
| 633 |
if (bendType != NULL) { |
| 634 |
addTorsionType(at1, at2, at3, bendType); |
| 635 |
} |
| 636 |
} |
| 637 |
|
| 638 |
} //end namespace oopse |
