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(){

    //set default force field filename
    setForceFieldFileName("DUFF.frc");

    //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:	1807
Committed:	Tue Nov 30 22:43:51 2004 UTC (19 years, 8 months ago) by tim
File size:	21329 byte(s)
Log Message:	brains get built
#	Content
1	/*
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
26	#include "UseTheForce/DUFF.hpp"
27	#include "UseTheForce/DarkSide/lj_interface.h"
28	#include "UseTheForce/DarkSide/charge_interface.h"
29	#include "UseTheForce/DarkSide/dipole_interface.h"
30	#include "UseTheForce/DarkSide/sticky_interface.h"
31	#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
42	namespace oopse {
43
44	//definition of createDUFF
45	ForceField* createDUFF() {
46	return new DUFF();
47	}
48
49	//register createDUFF to ForceFieldFactory
50	bool registerDUFFStatus = ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF);
51
52	DUFF::DUFF(){
53
54	//set default force field filename
55	setForceFieldFileName("DUFF.frc");
56
57	//the order of adding section parsers are important
58	//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
59	//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
60	//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
61	//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
62	//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
63	//important. AtomTypesSectionParser should be added before other atom type section parsers.
64	//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
65	//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
66	//not important.
67	spMan_.push_back(new DirectionalAtomTypesSectionParser());
68	spMan_.push_back(new AtomTypesSectionParser());
69	spMan_.push_back(new LennardJonesAtomTypesSectionParser());
70	spMan_.push_back(new ElectrostaticAtomTypesSectionParser());
71	spMan_.push_back(new EAMAtomTypesSectionParser());
72	spMan_.push_back(new StickyAtomTypesSectionParser());
73	spMan_.push_back(new BondTypesSectionParser());
74	spMan_.push_back(new BendTypesSectionParser());
75	spMan_.push_back(new TorsionTypesSectionParser());
76
77	}
78
79	void DUFF::parse(const std::string& filename) {
80	ifstrstream* ffStream;
81	ffStream = openForceFieldFile(filename);
82
83	spMan_.parse(ffStream, this);
84
85	ForceField::AtomTypeContainer::MapTypeIterator i;
86	AtomType* at;
87
88	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
89	at->makeFortranAtomType();
90	}
91
92	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
93	at->complete();
94	}
95
96	}
97
98	/*
99	ParseState DUFF::getSection(const std::string& section) {
100	ParseState result;
101
102	switch(section) {
103	case "AtomTypes" :
104	result = DUFF::AtomTypeSection;
105	break;
106	case "DirectionalAtomTypes" :
107	result = DUFF::DirectionalAtomTypeSection;
108	break;
109
110	case "BondTypes" :
111	result = DUFF::BondTypeSection;
112	break;
113
114	case "BendTypes" :
115	result = DUFF::BendTypeSection;
116	break;
117
118	case "TorsionTypes" :
119	result = DUFF::TorsionTypeSection;
120	break;
121	default:
122	result = DUFF::UnknownSection;
123	}
124
125	return result;
126	}
127
128	void DUFF::parse(const std::string& filename) {
129	ifstrstream* ffStream;
130	ffStream = openForceFieldFile(filename);
131	const int bufferSize = 65535;
132	std::string line;
133	char buffer[bufferSize];
134	int lineNo = 0;
135	int atomIdent = getNAtomType() + 1; //atom's indent begins from 1 (since only fortran's array begins from 1)
136	ParseState currentSection = DUFF::UnknownSection;
137
138	while(ffStream.getline(buffer, bufferSize)){
139	++lineNo;
140
141	line = trimSpaces(buffer);
142	//a line begins with "//" is comment
143	if ( line.empty() \|\| (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
144	continue;
145	} else {
146
147	switch(currentSection) {
148	case DUFF::AtomTypeSection :
149	parseAtomType(line, lineNo, atomIdent);
150	break;
151
152	case DUFF::DirectionalAtomTypeSection :
153	parseDirectionalAtomType(line, lineNo);
154	break;
155
156	case DUFF::BondTypeSection :
157	parseBondType(line, lineNo);
158	break;
159
160	case DUFF::BendTypeSection :
161	parseBendType(line, lineNo);
162	break;
163
164	case DUFF::TorsionTypeSection :
165	parseTorsionType(line, lineNo);
166	break;
167
168	case DUFF::UnknownSection:
169	StringTokenizer tokenizer(line);
170
171	std::string keyword = tokenizer.nextToken();
172	std::string section = tokenizer.nextToken();
173
174	ParseState newSection = getSection(section);
175	if (keyword != "begin" \|\| keyword != "end") {
176	std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
177	} else if (keyword == "begin") {
178	if (newSection == DUFF::UnknownSection) {
179	std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
180	} else {
181	//enter a new section
182	currentSection = newSection;
183	}
184
185	} else if (keyword == "end"){
186	if (currentSection == newSection) ) {
187	//leave a section
188	currentSection = DUFF::UnknownSection;
189	} else {
190	std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
191	}
192
193	}
194	break;
195	default :
196
197	}
198
199	}
200	}
201
202	delete ffStream;
203	}
204
205	void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){
206	StringTokenizer tokenizer(line);
207	int nTokens = tokenizer.countTokens();
208
209	//in AtomTypeSection, a line at least contains 5 tokens
210	//atomTypeName, is Directional, isLJ, isCharge and mass
211	if (nTokens < 5) {
212
213	} else {
214
215	std::string atomTypeName = tokenizer.nextToken();
216	bool isDirectional = tokenizer.nextTokenAsBool();
217	bool isLJ = tokenizer.nextTokenAsBool();
218	bool isCharge = tokenizer.nextTokenAsBool();
219	double mass = tokenizer.nextTokenAsDouble();
220	double epsilon;
221	double sigma;
222	double charge;
223	nTokens -= 5;
224
225	//parse epsilon and sigma
226	if (isLJ) {
227	if (nTokens >= 2) {
228	epsilon = tokenizer.nextTokenAsDouble();
229	sigma = tokenizer.nextTokenAsDouble();
230	nTokens -= 2;
231	} else {
232
233	}
234	}
235
236	//parse charge
237	if (isCharge) {
238	if (nTokens >= 1) {
239	charge = tokenizer.nextTokenAsDouble();
240	nTokens -= 1;
241	} else {
242
243	}
244	}
245
246	AtomType* atomType;
247	if (isDirectional) {
248	atomType = new DirectionalAtomType();
249	} else {
250	atomType = new AtomType();
251	}
252
253	atomType->setName(atomTypeName);
254	atomType->setMass(mass);
255
256	if (isLJ) {
257	atomType->setLennardJones();
258	}
259
260	if (isCharge) {
261	atomType->setCharge();
262	}
263
264	atomType->setIdent(ident);
265
266	atomType->complete();
267
268	int setLJStatus;
269
270	//notify a new LJtype atom type is created
271	if (isLJ) {
272	newLJtype(&ident, &sigma, &epsilon, &setLJStatus);
273	}
274
275	int setChargeStatus;
276	if (isCharge) {
277	newChargeType(&ident, &charge, &setChargeStatus)
278	}
279
280	if (setLJStatus && setChargeStatus) {
281	//add atom type to AtomTypeContainer
282	addAtomType(atomTypeName, atomType);
283	++ident;
284	} else {
285	//error in notifying fortran
286	delete atomType;
287	}
288	}
289
290	}
291
292
293	void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) {
294	StringTokenizer tokenizer(line);
295	int nTokens = tokenizer.countTokens();
296
297	//in DirectionalAtomTypeSection, a line at least contains 6 tokens
298	//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz
299	if (nTokens < 6) {
300	std::cerr << "Not enought tokens" << std::endl;
301	} else {
302
303
304	std::string atomTypeName = tokenizer.nextToken();
305	bool isDipole = tokenizer.nextTokenAsBool();
306	bool isSticky = tokenizer.nextTokenAsBool();
307	double Ixx = tokenizer.nextTokenAsDouble();
308	double Iyy = tokenizer.nextTokenAsDouble();
309	double Izz = tokenizer.nextTokenAsDouble();
310	nTokens -= 6;
311
312	AtomType* atomType = getAtomType(atomTypeName);
313	if (atomType == NULL) {
314
315	}
316
317	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
318	if (dAtomType == NULL) {
319
320
321	}
322
323	if (isDipole) {
324	dAtomType->setDipole();
325	}
326
327	if (isSticky) {
328	dAtomType->setSticky();
329	}
330
331	Mat3x3d inertialMat;
332	inertialMat(0, 0) = Ixx;
333	inertialMat(1, 1) = Iyy;
334	inertialMat(2, 2) = Izz;
335	dAtomType->setI(inertialMat);
336
337	//read dipole moment
338	double dipole;
339	if (isDipole) {
340	if (nTokens >= 1) {
341	dipole = tokenizer.nextTokenAsDouble();
342	nTokens -= 1;
343	} else {
344
345	}
346	}
347
348	//read sticky parameters
349	double w0;
350	double v0;
351	double v0p;
352	double rl;
353	double ru;
354	double rlp;
355	double rup;
356	if (isSticky) {
357	if (nTokens >= 7) {
358	w0 = tokenizer.nextTokenAsDouble();
359	v0 = tokenizer.nextTokenAsDouble();
360	v0p = tokenizer.nextTokenAsDouble();
361	rl = tokenizer.nextTokenAsDouble();
362	ru = tokenizer.nextTokenAsDouble();
363	rlp = tokenizer.nextTokenAsDouble();
364	rup = tokenizer.nextTokenAsDouble();
365	nTokens -= 7;
366	} else {
367
368	}
369	}
370
371
372	//notify fotran a newDipoleType is created
373	int ident = dAtomType->getIdent();
374	int setDipoleStatus;
375	if (isDipole) {
376	newDipoleType(&ident, &dipole, &setDipoleStatus);
377	}
378
379	//notify fotran a StickyType is created
380	int setStickyStatus;
381	if (isSticky) {
382	makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup);
383	}
384
385
386	if (!setDipoleStatus \|\| !setStickyStatus) {
387
388	}
389
390	}
391	}
392
393	void DUFF::parseBondType(const std::string& line, int lineNo){
394
395	StringTokenizer tokenizer(line);
396	std::string at1;
397	std::string at2;
398	std::string bt;
399	BondType* bondType = NULL;
400	double b0;
401
402	int nTokens = tokenizer.countTokens();
403
404	if (nTokens < 4) {
405
406	return;
407	}
408
409	at1 = tokenizer.nextToken();
410	at2 = tokenizer.nextToken();
411	bt = tokenizer.nextToken();
412	b0 = tokenizer.nextTokenAsDouble();
413	nTokens -= 4;
414
415	//switch is a maintain nightmare
416	switch(bt) {
417	case "Fixed" :
418	bondType = new FixedBondType();
419	break;
420
421	case "Harmonic" :
422	if (nTokens < 1) {
423
424	} else {
425
426	double kb = tokenizer.nextTokenAsDouble();
427	bondType = new HarmonicBondType(b0, kb);
428	}
429
430	break;
431
432	case "Cubic" :
433	if (nTokens < 4) {
434
435	} else {
436
437	double k3 = tokenizer.nextTokenAsDouble();
438	double k2 = tokenizer.nextTokenAsDouble();
439	double k1 = tokenizer.nextTokenAsDouble();
440	double k0 = tokenizer.nextTokenAsDouble();
441
442	bondType = new CubicBondType(b0, k3, k2, k1, k0);
443	}
444	break;
445
446	case "Quartic" :
447	if (nTokens < 5) {
448
449	} else {
450
451	b0 = tokenizer.nextTokenAsDouble();
452	double k4 = tokenizer.nextTokenAsDouble();
453	double k3 = tokenizer.nextTokenAsDouble();
454	double k2 = tokenizer.nextTokenAsDouble();
455	double k1 = tokenizer.nextTokenAsDouble();
456	double k0 = tokenizer.nextTokenAsDouble();
457
458	bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0);
459	}
460	break;
461
462	case "Polynomial" :
463	if (nTokens < 2 \|\| nTokens % 2 != 0) {
464
465	} else {
466	int nPairs = nTokens / 2;
467	int power;
468	double coefficient;
469	PolynomialBondType pbt = new PolynomialBondType();
470
471	for (int i = 0; i < nPairs; ++i) {
472	power = tokenizer.nextTokenAsInt();
473	coefficient = tokenizer.nextTokenAsDouble();
474	pbt->setCoefficient(power, coefficient);
475	}
476	}
477
478	break;
479
480	default:
481
482	}
483
484	if (bondType != NULL) {
485	addBondType(at1, at2, bondType);
486	}
487	}
488
489	void DUFF::parseBendType(const std::string& line, int lineNo){
490	StringTokenizer tokenizer(line);
491	std::string at1;
492	std::string at2;
493	std::string at3;
494	std::string bt;
495	double theta0;
496	BendType* bendType = NULL;
497
498	int nTokens = tokenizer.countTokens();
499
500	if (nTokens < 5) {
501
502	return;
503	}
504
505	at1 = tokenizer.nextToken();
506	at2 = tokenizer.nextToken();
507	at3 = tokenizer.nextToken();
508	bt = tokenizer.nextToken();
509	theta0 = tokenizer.nextTokenAsDouble();
510	nTokens -= 5;
511
512	//switch is a maintain nightmare
513	switch(bt) {
514
515	case "Harmonic" :
516
517	if (nTokens < 1) {
518
519	} else {
520
521	double ktheta = tokenizer.nextTokenAsDouble();
522	bendType = new HarmonicBendType(theta0, ktheta);
523	}
524	break;
525	case "GhostBend" :
526	if (nTokens < 1) {
527
528	} else {
529	double ktheta = tokenizer.nextTokenAsDouble();
530	bendType = new HarmonicBendType(theta0, ktheta);
531	}
532	break;
533
534	case "UreyBradley" :
535	if (nTokens < 3) {
536
537	} else {
538	double ktheta = tokenizer.nextTokenAsDouble();
539	double s0 = tokenizer.nextTokenAsDouble();
540	double kub = tokenizer.nextTokenAsDouble();
541	bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);
542	}
543	break;
544
545	case "Cubic" :
546	if (nTokens < 4) {
547
548	} else {
549
550	double k3 = tokenizer.nextTokenAsDouble();
551	double k2 = tokenizer.nextTokenAsDouble();
552	double k1 = tokenizer.nextTokenAsDouble();
553	double k0 = tokenizer.nextTokenAsDouble();
554
555	bendType = new CubicBendType(theta0, k3, k2, k1, k0);
556	}
557	break;
558
559	case "Quartic" :
560	if (nTokens < 5) {
561
562	} else {
563
564	theta0 = tokenizer.nextTokenAsDouble();
565	double k4 = tokenizer.nextTokenAsDouble();
566	double k3 = tokenizer.nextTokenAsDouble();
567	double k2 = tokenizer.nextTokenAsDouble();
568	double k1 = tokenizer.nextTokenAsDouble();
569	double k0 = tokenizer.nextTokenAsDouble();
570
571	bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0);
572	}
573	break;
574
575	case "Polynomial" :
576	if (nTokens < 2 \|\| nTokens % 2 != 0) {
577
578	} else {
579	int nPairs = nTokens / 2;
580	int power;
581	double coefficient;
582	PolynomialBendType* pbt = new PolynomialBendType();
583
584	for (int i = 0; i < nPairs; ++i) {
585	power = tokenizer.nextTokenAsInt();
586	coefficient = tokenizer.nextTokenAsDouble();
587	pbt->setCoefficient(power, coefficient);
588	}
589	}
590
591	break;
592
593	default:
594
595	}
596
597	if (bendType != NULL) {
598	addBendType(at1, at2, at3, bendType);
599	}
600
601	}
602
603	void DUFF::parseTorsionType(const std::string& line, int lineNo){
604	StringTokenizer tokenizer(line);
605	std::string at1;
606	std::string at2;
607	std::string at3;
608	std::string at4;
609	std::string tt;
610	TorsionType* torsionType = NULL;
611
612	int nTokens = tokenizer.countTokens();
613
614	if (nTokens < 5) {
615
616	return;
617	}
618
619	at1 = tokenizer.nextToken();
620	at2 = tokenizer.nextToken();
621	at3 = tokenizer.nextToken();
622	at4 = tokenizer.nextToken();
623	tt = tokenizer.nextToken();
624
625	nTokens -= 5;
626
627	switch(tt) {
628
629	case "Cubic" :
630	if (nTokens < 4) {
631
632	} else {
633
634	double k3 = tokenizer.nextTokenAsDouble();
635	double k2 = tokenizer.nextTokenAsDouble();
636	double k1 = tokenizer.nextTokenAsDouble();
637	double k0 = tokenizer.nextTokenAsDouble();
638
639	bendType = new CubicTorsionType(k3, k2, k1, k0);
640	}
641	break;
642
643	case "Quartic" :
644	if (nTokens < 5) {
645
646	} else {
647
648	theta0 = tokenizer.nextTokenAsDouble();
649	double k4 = tokenizer.nextTokenAsDouble();
650	double k3 = tokenizer.nextTokenAsDouble();
651	double k2 = tokenizer.nextTokenAsDouble();
652	double k1 = tokenizer.nextTokenAsDouble();
653	double k0 = tokenizer.nextTokenAsDouble();
654
655	bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0);
656	}
657	break;
658
659	case "Polynomial" :
660	if (nTokens < 2 \|\| nTokens % 2 != 0) {
661
662	} else {
663	int nPairs = nTokens / 2;
664	int power;
665	double coefficient;
666	PolynomialTorsionType* pbt = new PolynomialTorsionType();
667
668	for (int i = 0; i < nPairs; ++i) {
669	power = tokenizer.nextTokenAsInt();
670	coefficient = tokenizer.nextTokenAsDouble();
671	pbt->setCoefficient(power, coefficient);
672	}
673	}
674
675	break;
676	case "Charmm" :
677
678	if (nTokens < 3 \|\| nTokens % 3 != 0) {
679
680	} else {
681	int nSets = nTokens / 3;
682
683	CharmmTorsionType* ctt = new CharmmTorsionType();
684
685	for (int i = 0; i < nSets; ++i) {
686	double kchi = tokenizer.nextTokenAsDouble();
687	int n = tokenizer.nextTokenAsInt();
688	double delta = tokenizer.nextTokenAsDouble();
689
690	ctt->setCharmmTorsionParameter(kchi, n, delta);
691	}
692	}
693	default:
694
695	}
696
697	if (torsionType != NULL) {
698	addTorsionType(at1, at2, at3, at4, torsionType);
699	}
700	}
701	*/
702	} //end namespace oopse