src/UseTheForce/DUFF.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

#include "UseTheForce/DUFF.hpp"
#include "UseTheForce/DarkSide/lj_interface.h"
#include "UseTheForce/DarkSide/charge_interface.h"
#include "UseTheForce/DarkSide/dipole_interface.h"
#include "UseTheForce/DarkSide/sticky_interface.h"
#include "UseTheForce/ForceFieldFactory.hpp"
#include "io/DirectionalAtomTypesSectionParser.hpp"
#include "io/AtomTypesSectionParser.hpp"
#include "io/LennardJonesAtomTypesSectionParser.hpp"
#include "io/ElectrostaticAtomTypesSectionParser.hpp"
#include "io/EAMAtomTypesSectionParser.hpp"
#include "io/StickyAtomTypesSectionParser.hpp"
#include "io/BondTypesSectionParser.hpp"
#include "io/BendTypesSectionParser.hpp"
#include "io/TorsionTypesSectionParser.hpp"

namespace oopse {

//definition of createDUFF
ForceField* createDUFF() {
    return new DUFF();
}

//register createDUFF to ForceFieldFactory
bool registerDUFFStatus = ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF);

DUFF::DUFF(){

    //the order of adding section parsers are important
    //DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
    //These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
    //AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
    //of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the 
    //"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
    //important. AtomTypesSectionParser should be added before other atom type section parsers.
    //Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. 
    //The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
    //not important.
    spMan_.push_back(new DirectionalAtomTypesSectionParser());
    spMan_.push_back(new AtomTypesSectionParser());
    spMan_.push_back(new LennardJonesAtomTypesSectionParser());
    spMan_.push_back(new ElectrostaticAtomTypesSectionParser());
    spMan_.push_back(new EAMAtomTypesSectionParser());
    spMan_.push_back(new StickyAtomTypesSectionParser());
    spMan_.push_back(new BondTypesSectionParser());
    spMan_.push_back(new BendTypesSectionParser());
    spMan_.push_back(new TorsionTypesSectionParser());
    
}

void DUFF::parse(const std::string& filename) {
    ifstrstream* ffStream;
    ffStream = openForceFieldFile(filename);

    spMan_.parse(*ffStream, *this);

    ForceField::AtomTypeContainer::MapTypeIterator i;
    AtomType* at;

    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
        at->makeFortranAtomType();
    }

    for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
        at->complete();
    }
    
}

/*
ParseState DUFF::getSection(const std::string& section) {
    ParseState result;
    
    switch(section) {
        case "AtomTypes" :
            result = DUFF::AtomTypeSection;
            break;
        case "DirectionalAtomTypes" :
            result = DUFF::DirectionalAtomTypeSection;
            break;

        case "BondTypes" :
            result = DUFF::BondTypeSection;
            break;

        case "BendTypes" :
            result = DUFF::BendTypeSection;
            break;

        case "TorsionTypes" :
            result = DUFF::TorsionTypeSection;
            break;
        default:
            result = DUFF::UnknownSection;
    }

    return result;
}

void DUFF::parse(const std::string& filename) {
    ifstrstream* ffStream;
    ffStream = openForceFieldFile(filename);
    const int bufferSize = 65535;
    std::string line;
    char buffer[bufferSize];
    int lineNo = 0;
    int atomIdent = getNAtomType() + 1;  //atom's indent begins from 1 (since only fortran's array begins from 1)
    ParseState currentSection = DUFF::UnknownSection;
    
    while(ffStream.getline(buffer, bufferSize)){
        ++lineNo;

        line = trimSpaces(buffer);
        //a line begins with "//" is comment
        if ( line.empty() || (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
            continue;
        } else {

            switch(currentSection) {
                case DUFF::AtomTypeSection :
                    parseAtomType(line, lineNo, atomIdent);
                    break;

                case DUFF::DirectionalAtomTypeSection :
                    parseDirectionalAtomType(line, lineNo);
                    break;
                    
                case DUFF::BondTypeSection :
                    parseBondType(line, lineNo);
                    break;

                case DUFF::BendTypeSection :
                    parseBendType(line, lineNo);
                    break;

                case DUFF::TorsionTypeSection :
                    parseTorsionType(line, lineNo);
                    break;
                    
                case DUFF::UnknownSection:
                    StringTokenizer tokenizer(line);
                    
                    std::string keyword = tokenizer.nextToken();
                    std::string section = tokenizer.nextToken();

                    ParseState newSection = getSection(section);
                    if (keyword != "begin" || keyword != "end") {
                            std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
                    } else if (keyword == "begin") {
                        if (newSection == DUFF::UnknownSection) {
                            std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
                        } else {
                            //enter a new section
                            currentSection = newSection;
                        }
                        
                    } else if (keyword == "end"){
                        if (currentSection == newSection) ) {
                            //leave a section
                            currentSection = DUFF::UnknownSection;
                        } else {                            
                            std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
                        }

                    }
                    break;
                default :
                
            }
            
        }
    }
    
    delete ffStream;
}

void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){ 
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();    

    //in AtomTypeSection, a line at least contains 5 tokens
    //atomTypeName, is Directional, isLJ, isCharge and mass
    if (nTokens < 5)  {
                      
    } else {

        std::string atomTypeName = tokenizer.nextToken();
        bool isDirectional = tokenizer.nextTokenAsBool();
        bool isLJ = tokenizer.nextTokenAsBool();
        bool isCharge = tokenizer.nextTokenAsBool();        
        double mass = tokenizer.nextTokenAsDouble();
        double epsilon;
        double sigma;
        double charge;
        nTokens -= 5;

        //parse epsilon and sigma
        if (isLJ) {
            if (nTokens >= 2) {
                epsilon = tokenizer.nextTokenAsDouble();
                sigma = tokenizer.nextTokenAsDouble();
                nTokens -= 2;
            } else {

            }
        }

        //parse charge 
        if (isCharge) {
            if (nTokens >= 1) {
                charge = tokenizer.nextTokenAsDouble();
                nTokens -= 1;
            } else {

            }
        }
        
        AtomType* atomType;
        if (isDirectional) {
            atomType = new DirectionalAtomType();        
        } else {
            atomType = new AtomType();
        }
        
        atomType->setName(atomTypeName);
        atomType->setMass(mass);
        
        if (isLJ) {
            atomType->setLennardJones();
        }

        if (isCharge) {
            atomType->setCharge();
        }
        
        atomType->setIdent(ident); 
        
        atomType->complete();

        int setLJStatus;
        
        //notify a new LJtype atom type is created
        if (isLJ) {
            newLJtype(&ident, &sigma, &epsilon, &setLJStatus);
        }

        int setChargeStatus;
        if (isCharge) {
            newChargeType(&ident, &charge, &setChargeStatus)
        }

        if (setLJStatus && setChargeStatus) {
            //add atom type to AtomTypeContainer
            addAtomType(atomTypeName, atomType);
            ++ident;
        } else {
            //error in notifying fortran
            delete atomType;
        }
    }    
    
}


void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) {
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();  
    
    //in DirectionalAtomTypeSection, a line at least contains 6 tokens
    //AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz
    if (nTokens < 6) {
        std::cerr << "Not enought tokens" << std::endl;
    } else {


        std::string atomTypeName = tokenizer.nextToken();
        bool isDipole = tokenizer.nextTokenAsBool();
        bool isSticky = tokenizer.nextTokenAsBool();
        double Ixx = tokenizer.nextTokenAsDouble();
        double Iyy = tokenizer.nextTokenAsDouble();
        double Izz = tokenizer.nextTokenAsDouble();
        nTokens -= 6;

        AtomType* atomType = getAtomType(atomTypeName);
        if (atomType == NULL) {

        }
        
        DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
        if (dAtomType == NULL) {


        }

        if (isDipole) {
            dAtomType->setDipole();
        }

        if (isSticky) {
            dAtomType->setSticky();
        }
        
        Mat3x3d inertialMat;
        inertialMat(0, 0) = Ixx;
        inertialMat(1, 1) = Iyy;
        inertialMat(2, 2) = Izz;        
        dAtomType->setI(inertialMat);

        //read dipole moment
        double dipole;
        if (isDipole) {
            if (nTokens >= 1) {
                dipole = tokenizer.nextTokenAsDouble();
                nTokens -= 1;
            } else {

            }
        }

        //read sticky parameters
        double w0;
        double v0;
        double v0p;
        double rl;
        double ru;
        double rlp;
        double rup;        
        if (isSticky) {
            if (nTokens >= 7) {
                w0 = tokenizer.nextTokenAsDouble();
                v0 = tokenizer.nextTokenAsDouble();
                v0p = tokenizer.nextTokenAsDouble();
                rl = tokenizer.nextTokenAsDouble();
                ru = tokenizer.nextTokenAsDouble();
                rlp = tokenizer.nextTokenAsDouble();
                rup = tokenizer.nextTokenAsDouble();     
                nTokens -= 7;
            } else {

            }
        }


        //notify fotran a newDipoleType is created
        int ident = dAtomType->getIdent();
        int setDipoleStatus;
        if (isDipole) {
            newDipoleType(&ident, &dipole, &setDipoleStatus);
        }               

        //notify fotran a StickyType is created
        int setStickyStatus;
        if (isSticky) {
            makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup);
        }


        if (!setDipoleStatus || !setStickyStatus) {

        }
        
    }
}

void DUFF::parseBondType(const std::string& line, int lineNo){ 

    StringTokenizer tokenizer(line);
    std::string at1;
    std::string at2;
    std::string bt;
    BondType* bondType = NULL;
    double b0;
    
    int nTokens = tokenizer.countTokens();

    if (nTokens < 4) {

        return;
    }
    
    at1 = tokenizer.nextToken();
    at2 = tokenizer.nextToken();
    bt = tokenizer.nextToken();
    b0 = tokenizer.nextTokenAsDouble();
    nTokens -= 4;

    //switch is a maintain nightmare
    switch(bt) {
        case "Fixed" :
            bondType = new FixedBondType();
            break;
            
        case "Harmonic" :
            if (nTokens < 1) {

            } else {

                double kb = tokenizer.nextTokenAsDouble();
                bondType = new HarmonicBondType(b0, kb);
            }

            break;

        case "Cubic" :
            if (nTokens < 4) {

            } else {

                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bondType = new CubicBondType(b0, k3, k2, k1, k0);
            }
            break;
            
        case "Quartic" :
            if (nTokens < 5) {

            } else {

                b0 = tokenizer.nextTokenAsDouble();
                double k4 = tokenizer.nextTokenAsDouble();
                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0);
            }
            break;

        case "Polynomial" :
            if (nTokens < 2 || nTokens % 2 != 0) {

            } else {
                int nPairs = nTokens / 2;
                int power;
                double coefficient;
                PolynomialBondType pbt = new PolynomialBondType();
                
                for (int i = 0; i < nPairs; ++i) {
                    power = tokenizer.nextTokenAsInt();
                    coefficient = tokenizer.nextTokenAsDouble();
                    pbt->setCoefficient(power, coefficient);
                }
            }
            
            break;

        default:
            
    }

    if (bondType != NULL) {
        addBondType(at1, at2, bondType);
    }
}

void DUFF::parseBendType(const std::string& line, int lineNo){ 
    StringTokenizer tokenizer(line);
    std::string at1;
    std::string at2;
    std::string at3;
    std::string bt;
    double theta0;
    BendType* bendType = NULL;

    int nTokens = tokenizer.countTokens();

    if (nTokens < 5) {

        return;
    }
    
    at1 = tokenizer.nextToken();
    at2 = tokenizer.nextToken();
    at3 = tokenizer.nextToken();
    bt = tokenizer.nextToken();
    theta0 = tokenizer.nextTokenAsDouble();
    nTokens -= 5;

    //switch is a maintain nightmare
    switch(bt) {
            
        case "Harmonic" :
            
            if (nTokens < 1) {

            } else {

                double ktheta = tokenizer.nextTokenAsDouble();
                bendType = new HarmonicBendType(theta0, ktheta);
            }
            break;
        case "GhostBend" :
            if (nTokens < 1) {

            } else {
                double ktheta = tokenizer.nextTokenAsDouble();
                bendType = new HarmonicBendType(theta0, ktheta);                
            }
            break;            

        case "UreyBradley" :
            if (nTokens < 3) {

            } else {
                double ktheta = tokenizer.nextTokenAsDouble();
                double s0 =  tokenizer.nextTokenAsDouble();
                double kub = tokenizer.nextTokenAsDouble();
                bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);                
            }
            break; 
            
        case "Cubic" :
            if (nTokens < 4) {

            } else {

                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bendType = new CubicBendType(theta0, k3, k2, k1, k0);
            }
            break;
            
        case "Quartic" :
            if (nTokens < 5) {

            } else {

                theta0 = tokenizer.nextTokenAsDouble();
                double k4 = tokenizer.nextTokenAsDouble();
                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0);
            }
            break;

        case "Polynomial" :
            if (nTokens < 2 || nTokens % 2 != 0) {

            } else {
                int nPairs = nTokens / 2;
                int power;
                double coefficient;
                PolynomialBendType* pbt = new PolynomialBendType();
                
                for (int i = 0; i < nPairs; ++i) {
                    power = tokenizer.nextTokenAsInt();
                    coefficient = tokenizer.nextTokenAsDouble();
                    pbt->setCoefficient(power, coefficient);
                }
            }
            
            break;

        default:
            
    }

    if (bendType != NULL) {
        addBendType(at1, at2, at3, bendType);
    }
    
}

void DUFF::parseTorsionType(const std::string& line, int lineNo){ 
    StringTokenizer tokenizer(line);
    std::string at1;
    std::string at2;
    std::string at3;
    std::string at4;
    std::string tt;
    TorsionType* torsionType = NULL;

    int nTokens = tokenizer.countTokens();

    if (nTokens < 5) {

        return;
    }
    
    at1 = tokenizer.nextToken();
    at2 = tokenizer.nextToken();
    at3 = tokenizer.nextToken();
    at4 = tokenizer.nextToken();
    tt = tokenizer.nextToken();

    nTokens -= 5;

    switch(tt) {
            
        case "Cubic" :
            if (nTokens < 4) {

            } else {

                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bendType = new CubicTorsionType(k3, k2, k1, k0);
            }
            break;
            
        case "Quartic" :
            if (nTokens < 5) {

            } else {

                theta0 = tokenizer.nextTokenAsDouble();
                double k4 = tokenizer.nextTokenAsDouble();
                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0);
            }
            break;

        case "Polynomial" :
            if (nTokens < 2 || nTokens % 2 != 0) {

            } else {
                int nPairs = nTokens / 2;
                int power;
                double coefficient;
                PolynomialTorsionType* pbt = new PolynomialTorsionType();
                
                for (int i = 0; i < nPairs; ++i) {
                    power = tokenizer.nextTokenAsInt();
                    coefficient = tokenizer.nextTokenAsDouble();
                    pbt->setCoefficient(power, coefficient);
                }
            }
            
            break;
        case "Charmm" :
            
            if (nTokens < 3 || nTokens % 3 != 0) {

            } else {
                int nSets = nTokens / 3;
  
                CharmmTorsionType* ctt = new CharmmTorsionType();
                
                for (int i = 0; i < nSets; ++i) {
                    double kchi = tokenizer.nextTokenAsDouble();
                    int n = tokenizer.nextTokenAsInt();
                    double delta = tokenizer.nextTokenAsDouble();
    
                    ctt->setCharmmTorsionParameter(kchi, n, delta);
                }
            }
        default:
            
    }

    if (torsionType != NULL) {
        addTorsionType(at1, at2, at3, at4, torsionType);
    }
}
*/
} //end namespace oopse
Revision:	1783
Committed:	Wed Nov 24 21:33:00 2004 UTC (19 years, 9 months ago) by tim
File size:	21250 byte(s)
Log Message:	UseTheForce get built
#	User	Rev	Content
1	tim	1741	/*
2			* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3			*
4			* Contact: oopse@oopse.org
5			*
6			* This program is free software; you can redistribute it and/or
7			* modify it under the terms of the GNU Lesser General Public License
8			* as published by the Free Software Foundation; either version 2.1
9			* of the License, or (at your option) any later version.
10			* All we ask is that proper credit is given for our work, which includes
11			* - but is not limited to - adding the above copyright notice to the beginning
12			* of your source code files, and to any copyright notice that you may distribute
13			* with programs based on this work.
14			*
15			* This program is distributed in the hope that it will be useful,
16			* but WITHOUT ANY WARRANTY; without even the implied warranty of
17			* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18			* GNU Lesser General Public License for more details.
19			*
20			* You should have received a copy of the GNU Lesser General Public License
21			* along with this program; if not, write to the Free Software
22			* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23			*
24			*/
25	gezelter	1490
26	tim	1741	#include "UseTheForce/DUFF.hpp"
27	gezelter	1634	#include "UseTheForce/DarkSide/lj_interface.h"
28	tim	1758	#include "UseTheForce/DarkSide/charge_interface.h"
29			#include "UseTheForce/DarkSide/dipole_interface.h"
30			#include "UseTheForce/DarkSide/sticky_interface.h"
31	tim	1783	#include "UseTheForce/ForceFieldFactory.hpp"
32			#include "io/DirectionalAtomTypesSectionParser.hpp"
33			#include "io/AtomTypesSectionParser.hpp"
34			#include "io/LennardJonesAtomTypesSectionParser.hpp"
35			#include "io/ElectrostaticAtomTypesSectionParser.hpp"
36			#include "io/EAMAtomTypesSectionParser.hpp"
37			#include "io/StickyAtomTypesSectionParser.hpp"
38			#include "io/BondTypesSectionParser.hpp"
39			#include "io/BendTypesSectionParser.hpp"
40			#include "io/TorsionTypesSectionParser.hpp"
41	gezelter	1490
42	tim	1741	namespace oopse {
43	gezelter	1490
44	tim	1741	//definition of createDUFF
45			ForceField* createDUFF() {
46			return new DUFF();
47			}
48	gezelter	1490
49	tim	1758	//register createDUFF to ForceFieldFactory
50	tim	1783	bool registerDUFFStatus = ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF);
51	gezelter	1490
52	tim	1770	DUFF::DUFF(){
53	tim	1757
54	tim	1770	//the order of adding section parsers are important
55			//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
56			//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
57			//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
58			//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
59			//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
60			//important. AtomTypesSectionParser should be added before other atom type section parsers.
61			//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
62			//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
63			//not important.
64			spMan_.push_back(new DirectionalAtomTypesSectionParser());
65			spMan_.push_back(new AtomTypesSectionParser());
66			spMan_.push_back(new LennardJonesAtomTypesSectionParser());
67			spMan_.push_back(new ElectrostaticAtomTypesSectionParser());
68			spMan_.push_back(new EAMAtomTypesSectionParser());
69			spMan_.push_back(new StickyAtomTypesSectionParser());
70			spMan_.push_back(new BondTypesSectionParser());
71			spMan_.push_back(new BendTypesSectionParser());
72			spMan_.push_back(new TorsionTypesSectionParser());
73
74			}
75
76			void DUFF::parse(const std::string& filename) {
77			ifstrstream* ffStream;
78	tim	1783	ffStream = openForceFieldFile(filename);
79	tim	1770
80			spMan_.parse(ffStream, this);
81
82	tim	1783	ForceField::AtomTypeContainer::MapTypeIterator i;
83	tim	1770	AtomType* at;
84
85			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
86			at->makeFortranAtomType();
87			}
88
89			for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
90			at->complete();
91			}
92
93			}
94
95			/*
96	tim	1757	ParseState DUFF::getSection(const std::string& section) {
97			ParseState result;
98
99			switch(section) {
100			case "AtomTypes" :
101			result = DUFF::AtomTypeSection;
102			break;
103	tim	1758	case "DirectionalAtomTypes" :
104			result = DUFF::DirectionalAtomTypeSection;
105			break;
106	tim	1757
107			case "BondTypes" :
108			result = DUFF::BondTypeSection;
109			break;
110
111			case "BendTypes" :
112			result = DUFF::BendTypeSection;
113			break;
114
115			case "TorsionTypes" :
116			result = DUFF::TorsionTypeSection;
117			break;
118			default:
119			result = DUFF::UnknownSection;
120			}
121
122			return result;
123			}
124
125	tim	1741	void DUFF::parse(const std::string& filename) {
126			ifstrstream* ffStream;
127	tim	1783	ffStream = openForceFieldFile(filename);
128	tim	1741	const int bufferSize = 65535;
129	tim	1757	std::string line;
130			char buffer[bufferSize];
131	tim	1741	int lineNo = 0;
132	tim	1760	int atomIdent = getNAtomType() + 1; //atom's indent begins from 1 (since only fortran's array begins from 1)
133	tim	1757	ParseState currentSection = DUFF::UnknownSection;
134
135			while(ffStream.getline(buffer, bufferSize)){
136	tim	1741	++lineNo;
137	gezelter	1490
138	tim	1757	line = trimSpaces(buffer);
139			//a line begins with "//" is comment
140			if ( line.empty() \|\| (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
141			continue;
142			} else {
143	gezelter	1490
144	tim	1757	switch(currentSection) {
145			case DUFF::AtomTypeSection :
146	tim	1759	parseAtomType(line, lineNo, atomIdent);
147	tim	1757	break;
148	gezelter	1490
149	tim	1759	case DUFF::DirectionalAtomTypeSection :
150			parseDirectionalAtomType(line, lineNo);
151			break;
152
153	tim	1757	case DUFF::BondTypeSection :
154			parseBondType(line, lineNo);
155			break;
156	gezelter	1490
157	tim	1757	case DUFF::BendTypeSection :
158			parseBendType(line, lineNo);
159			break;
160
161			case DUFF::TorsionTypeSection :
162			parseTorsionType(line, lineNo);
163			break;
164
165			case DUFF::UnknownSection:
166			StringTokenizer tokenizer(line);
167
168			std::string keyword = tokenizer.nextToken();
169			std::string section = tokenizer.nextToken();
170
171			ParseState newSection = getSection(section);
172			if (keyword != "begin" \|\| keyword != "end") {
173			std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
174			} else if (keyword == "begin") {
175			if (newSection == DUFF::UnknownSection) {
176			std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
177			} else {
178			//enter a new section
179			currentSection = newSection;
180			}
181
182			} else if (keyword == "end"){
183			if (currentSection == newSection) ) {
184			//leave a section
185			currentSection = DUFF::UnknownSection;
186			} else {
187			std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
188			}
189
190			}
191			break;
192			default :
193	tim	1741
194			}
195	gezelter	1653
196	gezelter	1634	}
197	gezelter	1490	}
198
199	tim	1741	delete ffStream;
200	gezelter	1490	}
201
202	tim	1758	void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){
203	tim	1757	StringTokenizer tokenizer(line);
204	tim	1758	int nTokens = tokenizer.countTokens();
205	tim	1757
206	tim	1758	//in AtomTypeSection, a line at least contains 5 tokens
207			//atomTypeName, is Directional, isLJ, isCharge and mass
208			if (nTokens < 5) {
209	tim	1759
210	tim	1758	} else {
211
212			std::string atomTypeName = tokenizer.nextToken();
213			bool isDirectional = tokenizer.nextTokenAsBool();
214			bool isLJ = tokenizer.nextTokenAsBool();
215			bool isCharge = tokenizer.nextTokenAsBool();
216			double mass = tokenizer.nextTokenAsDouble();
217			double epsilon;
218			double sigma;
219			double charge;
220			nTokens -= 5;
221
222			//parse epsilon and sigma
223			if (isLJ) {
224			if (nTokens >= 2) {
225			epsilon = tokenizer.nextTokenAsDouble();
226			sigma = tokenizer.nextTokenAsDouble();
227			nTokens -= 2;
228			} else {
229
230			}
231			}
232
233			//parse charge
234			if (isCharge) {
235			if (nTokens >= 1) {
236			charge = tokenizer.nextTokenAsDouble();
237			nTokens -= 1;
238			} else {
239
240			}
241			}
242
243			AtomType* atomType;
244			if (isDirectional) {
245			atomType = new DirectionalAtomType();
246			} else {
247			atomType = new AtomType();
248			}
249
250	tim	1757	atomType->setName(atomTypeName);
251			atomType->setMass(mass);
252
253	tim	1760	if (isLJ) {
254			atomType->setLennardJones();
255			}
256	tim	1757
257	tim	1760	if (isCharge) {
258			atomType->setCharge();
259			}
260
261	tim	1758	atomType->setIdent(ident);
262
263	tim	1757	atomType->complete();
264	tim	1758
265			int setLJStatus;
266
267	tim	1757	//notify a new LJtype atom type is created
268	tim	1758	if (isLJ) {
269			newLJtype(&ident, &sigma, &epsilon, &setLJStatus);
270			}
271	tim	1757
272	tim	1758	int setChargeStatus;
273			if (isCharge) {
274			newChargeType(&ident, &charge, &setChargeStatus)
275			}
276
277			if (setLJStatus && setChargeStatus) {
278			//add atom type to AtomTypeContainer
279			addAtomType(atomTypeName, atomType);
280			++ident;
281			} else {
282			//error in notifying fortran
283			delete atomType;
284			}
285	tim	1757	}
286	tim	1758
287	gezelter	1490	}
288
289	tim	1758
290			void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) {
291			StringTokenizer tokenizer(line);
292			int nTokens = tokenizer.countTokens();
293
294	tim	1765	//in DirectionalAtomTypeSection, a line at least contains 6 tokens
295	tim	1758	//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz
296			if (nTokens < 6) {
297	tim	1765	std::cerr << "Not enought tokens" << std::endl;
298	tim	1758	} else {
299
300
301			std::string atomTypeName = tokenizer.nextToken();
302			bool isDipole = tokenizer.nextTokenAsBool();
303			bool isSticky = tokenizer.nextTokenAsBool();
304			double Ixx = tokenizer.nextTokenAsDouble();
305			double Iyy = tokenizer.nextTokenAsDouble();
306			double Izz = tokenizer.nextTokenAsDouble();
307			nTokens -= 6;
308
309			AtomType* atomType = getAtomType(atomTypeName);
310			if (atomType == NULL) {
311
312			}
313
314			DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
315			if (dAtomType == NULL) {
316
317
318			}
319
320	tim	1760	if (isDipole) {
321			dAtomType->setDipole();
322			}
323	tim	1758
324	tim	1760	if (isSticky) {
325			dAtomType->setSticky();
326			}
327
328	tim	1758	Mat3x3d inertialMat;
329			inertialMat(0, 0) = Ixx;
330	tim	1765	inertialMat(1, 1) = Iyy;
331			inertialMat(2, 2) = Izz;
332	tim	1758	dAtomType->setI(inertialMat);
333
334			//read dipole moment
335			double dipole;
336			if (isDipole) {
337			if (nTokens >= 1) {
338			dipole = tokenizer.nextTokenAsDouble();
339			nTokens -= 1;
340			} else {
341
342			}
343			}
344
345			//read sticky parameters
346			double w0;
347			double v0;
348			double v0p;
349			double rl;
350			double ru;
351			double rlp;
352			double rup;
353			if (isSticky) {
354			if (nTokens >= 7) {
355			w0 = tokenizer.nextTokenAsDouble();
356			v0 = tokenizer.nextTokenAsDouble();
357			v0p = tokenizer.nextTokenAsDouble();
358			rl = tokenizer.nextTokenAsDouble();
359			ru = tokenizer.nextTokenAsDouble();
360			rlp = tokenizer.nextTokenAsDouble();
361			rup = tokenizer.nextTokenAsDouble();
362			nTokens -= 7;
363			} else {
364
365			}
366			}
367
368
369			//notify fotran a newDipoleType is created
370			int ident = dAtomType->getIdent();
371			int setDipoleStatus;
372			if (isDipole) {
373			newDipoleType(&ident, &dipole, &setDipoleStatus);
374			}
375
376			//notify fotran a StickyType is created
377			int setStickyStatus;
378			if (isSticky) {
379			makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup);
380			}
381
382
383			if (!setDipoleStatus \|\| !setStickyStatus) {
384
385			}
386
387			}
388			}
389
390	tim	1757	void DUFF::parseBondType(const std::string& line, int lineNo){
391
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