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"

namespace oopse {

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

//register createDUFF to ForceFieldFactory
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 = openForceFiledFile(filename);

    spMan_.parse(*ffStream, *this);

    typename 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 = openForceFiledFile(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:	1770
Committed:	Tue Nov 23 17:53:43 2004 UTC (19 years, 7 months ago) by tim
File size:	20771 byte(s)
Log Message:	add Electrostatic AtomType Section Parser
#	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
32	namespace oopse {
33
34	//definition of createDUFF
35	ForceField* createDUFF() {
36	return new DUFF();
37	}
38
39	//register createDUFF to ForceFieldFactory
40	ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF);
41
42	DUFF::DUFF(){
43
44	//the order of adding section parsers are important
45	//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
46	//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
47	//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
48	//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
49	//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
50	//important. AtomTypesSectionParser should be added before other atom type section parsers.
51	//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
52	//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
53	//not important.
54	spMan_.push_back(new DirectionalAtomTypesSectionParser());
55	spMan_.push_back(new AtomTypesSectionParser());
56	spMan_.push_back(new LennardJonesAtomTypesSectionParser());
57	spMan_.push_back(new ElectrostaticAtomTypesSectionParser());
58	spMan_.push_back(new EAMAtomTypesSectionParser());
59	spMan_.push_back(new StickyAtomTypesSectionParser());
60	spMan_.push_back(new BondTypesSectionParser());
61	spMan_.push_back(new BendTypesSectionParser());
62	spMan_.push_back(new TorsionTypesSectionParser());
63
64	}
65
66	void DUFF::parse(const std::string& filename) {
67	ifstrstream* ffStream;
68	ffStream = openForceFiledFile(filename);
69
70	spMan_.parse(ffStream, this);
71
72	typename ForceField::AtomTypeContainer::MapTypeIterator i;
73	AtomType* at;
74
75	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
76	at->makeFortranAtomType();
77	}
78
79	for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
80	at->complete();
81	}
82
83	}
84
85	/*
86	ParseState DUFF::getSection(const std::string& section) {
87	ParseState result;
88
89	switch(section) {
90	case "AtomTypes" :
91	result = DUFF::AtomTypeSection;
92	break;
93	case "DirectionalAtomTypes" :
94	result = DUFF::DirectionalAtomTypeSection;
95	break;
96
97	case "BondTypes" :
98	result = DUFF::BondTypeSection;
99	break;
100
101	case "BendTypes" :
102	result = DUFF::BendTypeSection;
103	break;
104
105	case "TorsionTypes" :
106	result = DUFF::TorsionTypeSection;
107	break;
108	default:
109	result = DUFF::UnknownSection;
110	}
111
112	return result;
113	}
114
115	void DUFF::parse(const std::string& filename) {
116	ifstrstream* ffStream;
117	ffStream = openForceFiledFile(filename);
118	const int bufferSize = 65535;
119	std::string line;
120	char buffer[bufferSize];
121	int lineNo = 0;
122	int atomIdent = getNAtomType() + 1; //atom's indent begins from 1 (since only fortran's array begins from 1)
123	ParseState currentSection = DUFF::UnknownSection;
124
125	while(ffStream.getline(buffer, bufferSize)){
126	++lineNo;
127
128	line = trimSpaces(buffer);
129	//a line begins with "//" is comment
130	if ( line.empty() \|\| (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
131	continue;
132	} else {
133
134	switch(currentSection) {
135	case DUFF::AtomTypeSection :
136	parseAtomType(line, lineNo, atomIdent);
137	break;
138
139	case DUFF::DirectionalAtomTypeSection :
140	parseDirectionalAtomType(line, lineNo);
141	break;
142
143	case DUFF::BondTypeSection :
144	parseBondType(line, lineNo);
145	break;
146
147	case DUFF::BendTypeSection :
148	parseBendType(line, lineNo);
149	break;
150
151	case DUFF::TorsionTypeSection :
152	parseTorsionType(line, lineNo);
153	break;
154
155	case DUFF::UnknownSection:
156	StringTokenizer tokenizer(line);
157
158	std::string keyword = tokenizer.nextToken();
159	std::string section = tokenizer.nextToken();
160
161	ParseState newSection = getSection(section);
162	if (keyword != "begin" \|\| keyword != "end") {
163	std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
164	} else if (keyword == "begin") {
165	if (newSection == DUFF::UnknownSection) {
166	std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
167	} else {
168	//enter a new section
169	currentSection = newSection;
170	}
171
172	} else if (keyword == "end"){
173	if (currentSection == newSection) ) {
174	//leave a section
175	currentSection = DUFF::UnknownSection;
176	} else {
177	std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
178	}
179
180	}
181	break;
182	default :
183
184	}
185
186	}
187	}
188
189	delete ffStream;
190	}
191
192	void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){
193	StringTokenizer tokenizer(line);
194	int nTokens = tokenizer.countTokens();
195
196	//in AtomTypeSection, a line at least contains 5 tokens
197	//atomTypeName, is Directional, isLJ, isCharge and mass
198	if (nTokens < 5) {
199
200	} else {
201
202	std::string atomTypeName = tokenizer.nextToken();
203	bool isDirectional = tokenizer.nextTokenAsBool();
204	bool isLJ = tokenizer.nextTokenAsBool();
205	bool isCharge = tokenizer.nextTokenAsBool();
206	double mass = tokenizer.nextTokenAsDouble();
207	double epsilon;
208	double sigma;
209	double charge;
210	nTokens -= 5;
211
212	//parse epsilon and sigma
213	if (isLJ) {
214	if (nTokens >= 2) {
215	epsilon = tokenizer.nextTokenAsDouble();
216	sigma = tokenizer.nextTokenAsDouble();
217	nTokens -= 2;
218	} else {
219
220	}
221	}
222
223	//parse charge
224	if (isCharge) {
225	if (nTokens >= 1) {
226	charge = tokenizer.nextTokenAsDouble();
227	nTokens -= 1;
228	} else {
229
230	}
231	}
232
233	AtomType* atomType;
234	if (isDirectional) {
235	atomType = new DirectionalAtomType();
236	} else {
237	atomType = new AtomType();
238	}
239
240	atomType->setName(atomTypeName);
241	atomType->setMass(mass);
242
243	if (isLJ) {
244	atomType->setLennardJones();
245	}
246
247	if (isCharge) {
248	atomType->setCharge();
249	}
250
251	atomType->setIdent(ident);
252
253	atomType->complete();
254
255	int setLJStatus;
256
257	//notify a new LJtype atom type is created
258	if (isLJ) {
259	newLJtype(&ident, &sigma, &epsilon, &setLJStatus);
260	}
261
262	int setChargeStatus;
263	if (isCharge) {
264	newChargeType(&ident, &charge, &setChargeStatus)
265	}
266
267	if (setLJStatus && setChargeStatus) {
268	//add atom type to AtomTypeContainer
269	addAtomType(atomTypeName, atomType);
270	++ident;
271	} else {
272	//error in notifying fortran
273	delete atomType;
274	}
275	}
276
277	}
278
279
280	void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) {
281	StringTokenizer tokenizer(line);
282	int nTokens = tokenizer.countTokens();
283
284	//in DirectionalAtomTypeSection, a line at least contains 6 tokens
285	//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz
286	if (nTokens < 6) {
287	std::cerr << "Not enought tokens" << std::endl;
288	} else {
289
290
291	std::string atomTypeName = tokenizer.nextToken();
292	bool isDipole = tokenizer.nextTokenAsBool();
293	bool isSticky = tokenizer.nextTokenAsBool();
294	double Ixx = tokenizer.nextTokenAsDouble();
295	double Iyy = tokenizer.nextTokenAsDouble();
296	double Izz = tokenizer.nextTokenAsDouble();
297	nTokens -= 6;
298
299	AtomType* atomType = getAtomType(atomTypeName);
300	if (atomType == NULL) {
301
302	}
303
304	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
305	if (dAtomType == NULL) {
306
307
308	}
309
310	if (isDipole) {
311	dAtomType->setDipole();
312	}
313
314	if (isSticky) {
315	dAtomType->setSticky();
316	}
317
318	Mat3x3d inertialMat;
319	inertialMat(0, 0) = Ixx;
320	inertialMat(1, 1) = Iyy;
321	inertialMat(2, 2) = Izz;
322	dAtomType->setI(inertialMat);
323
324	//read dipole moment
325	double dipole;
326	if (isDipole) {
327	if (nTokens >= 1) {
328	dipole = tokenizer.nextTokenAsDouble();
329	nTokens -= 1;
330	} else {
331
332	}
333	}
334
335	//read sticky parameters
336	double w0;
337	double v0;
338	double v0p;
339	double rl;
340	double ru;
341	double rlp;
342	double rup;
343	if (isSticky) {
344	if (nTokens >= 7) {
345	w0 = tokenizer.nextTokenAsDouble();
346	v0 = tokenizer.nextTokenAsDouble();
347	v0p = tokenizer.nextTokenAsDouble();
348	rl = tokenizer.nextTokenAsDouble();
349	ru = tokenizer.nextTokenAsDouble();
350	rlp = tokenizer.nextTokenAsDouble();
351	rup = tokenizer.nextTokenAsDouble();
352	nTokens -= 7;
353	} else {
354
355	}
356	}
357
358
359	//notify fotran a newDipoleType is created
360	int ident = dAtomType->getIdent();
361	int setDipoleStatus;
362	if (isDipole) {
363	newDipoleType(&ident, &dipole, &setDipoleStatus);
364	}
365
366	//notify fotran a StickyType is created
367	int setStickyStatus;
368	if (isSticky) {
369	makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup);
370	}
371
372
373	if (!setDipoleStatus \|\| !setStickyStatus) {
374
375	}
376
377	}
378	}
379
380	void DUFF::parseBondType(const std::string& line, int lineNo){
381
382	StringTokenizer tokenizer(line);
383	std::string at1;
384	std::string at2;
385	std::string bt;
386	BondType* bondType = NULL;
387	double b0;
388
389	int nTokens = tokenizer.countTokens();
390
391	if (nTokens < 4) {
392
393	return;
394	}
395
396	at1 = tokenizer.nextToken();
397	at2 = tokenizer.nextToken();
398	bt = tokenizer.nextToken();
399	b0 = tokenizer.nextTokenAsDouble();
400	nTokens -= 4;
401
402	//switch is a maintain nightmare
403	switch(bt) {
404	case "Fixed" :
405	bondType = new FixedBondType();
406	break;
407
408	case "Harmonic" :
409	if (nTokens < 1) {
410
411	} else {
412
413	double kb = tokenizer.nextTokenAsDouble();
414	bondType = new HarmonicBondType(b0, kb);
415	}
416
417	break;
418
419	case "Cubic" :
420	if (nTokens < 4) {
421
422	} else {
423
424	double k3 = tokenizer.nextTokenAsDouble();
425	double k2 = tokenizer.nextTokenAsDouble();
426	double k1 = tokenizer.nextTokenAsDouble();
427	double k0 = tokenizer.nextTokenAsDouble();
428
429	bondType = new CubicBondType(b0, k3, k2, k1, k0);
430	}
431	break;
432
433	case "Quartic" :
434	if (nTokens < 5) {
435
436	} else {
437
438	b0 = tokenizer.nextTokenAsDouble();
439	double k4 = tokenizer.nextTokenAsDouble();
440	double k3 = tokenizer.nextTokenAsDouble();
441	double k2 = tokenizer.nextTokenAsDouble();
442	double k1 = tokenizer.nextTokenAsDouble();
443	double k0 = tokenizer.nextTokenAsDouble();
444
445	bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0);
446	}
447	break;
448
449	case "Polynomial" :
450	if (nTokens < 2 \|\| nTokens % 2 != 0) {
451
452	} else {
453	int nPairs = nTokens / 2;
454	int power;
455	double coefficient;
456	PolynomialBondType pbt = new PolynomialBondType();
457
458	for (int i = 0; i < nPairs; ++i) {
459	power = tokenizer.nextTokenAsInt();
460	coefficient = tokenizer.nextTokenAsDouble();
461	pbt->setCoefficient(power, coefficient);
462	}
463	}
464
465	break;
466
467	default:
468
469	}
470
471	if (bondType != NULL) {
472	addBondType(at1, at2, bondType);
473	}
474	}
475
476	void DUFF::parseBendType(const std::string& line, int lineNo){
477	StringTokenizer tokenizer(line);
478	std::string at1;
479	std::string at2;
480	std::string at3;
481	std::string bt;
482	double theta0;
483	BendType* bendType = NULL;
484
485	int nTokens = tokenizer.countTokens();
486
487	if (nTokens < 5) {
488
489	return;
490	}
491
492	at1 = tokenizer.nextToken();
493	at2 = tokenizer.nextToken();
494	at3 = tokenizer.nextToken();
495	bt = tokenizer.nextToken();
496	theta0 = tokenizer.nextTokenAsDouble();
497	nTokens -= 5;
498
499	//switch is a maintain nightmare
500	switch(bt) {
501
502	case "Harmonic" :
503
504	if (nTokens < 1) {
505
506	} else {
507
508	double ktheta = tokenizer.nextTokenAsDouble();
509	bendType = new HarmonicBendType(theta0, ktheta);
510	}
511	break;
512	case "GhostBend" :
513	if (nTokens < 1) {
514
515	} else {
516	double ktheta = tokenizer.nextTokenAsDouble();
517	bendType = new HarmonicBendType(theta0, ktheta);
518	}
519	break;
520
521	case "UreyBradley" :
522	if (nTokens < 3) {
523
524	} else {
525	double ktheta = tokenizer.nextTokenAsDouble();
526	double s0 = tokenizer.nextTokenAsDouble();
527	double kub = tokenizer.nextTokenAsDouble();
528	bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);
529	}
530	break;
531
532	case "Cubic" :
533	if (nTokens < 4) {
534
535	} else {
536
537	double k3 = tokenizer.nextTokenAsDouble();
538	double k2 = tokenizer.nextTokenAsDouble();
539	double k1 = tokenizer.nextTokenAsDouble();
540	double k0 = tokenizer.nextTokenAsDouble();
541
542	bendType = new CubicBendType(theta0, k3, k2, k1, k0);
543	}
544	break;
545
546	case "Quartic" :
547	if (nTokens < 5) {
548
549	} else {
550
551	theta0 = tokenizer.nextTokenAsDouble();
552	double k4 = tokenizer.nextTokenAsDouble();
553	double k3 = tokenizer.nextTokenAsDouble();
554	double k2 = tokenizer.nextTokenAsDouble();
555	double k1 = tokenizer.nextTokenAsDouble();
556	double k0 = tokenizer.nextTokenAsDouble();
557
558	bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0);
559	}
560	break;
561
562	case "Polynomial" :
563	if (nTokens < 2 \|\| nTokens % 2 != 0) {
564
565	} else {
566	int nPairs = nTokens / 2;
567	int power;
568	double coefficient;
569	PolynomialBendType* pbt = new PolynomialBendType();
570
571	for (int i = 0; i < nPairs; ++i) {
572	power = tokenizer.nextTokenAsInt();
573	coefficient = tokenizer.nextTokenAsDouble();
574	pbt->setCoefficient(power, coefficient);
575	}
576	}
577
578	break;
579
580	default:
581
582	}
583
584	if (bendType != NULL) {
585	addBendType(at1, at2, at3, bendType);
586	}
587
588	}
589
590	void DUFF::parseTorsionType(const std::string& line, int lineNo){
591	StringTokenizer tokenizer(line);
592	std::string at1;
593	std::string at2;
594	std::string at3;
595	std::string at4;
596	std::string tt;
597	TorsionType* torsionType = NULL;
598
599	int nTokens = tokenizer.countTokens();
600
601	if (nTokens < 5) {
602
603	return;
604	}
605
606	at1 = tokenizer.nextToken();
607	at2 = tokenizer.nextToken();
608	at3 = tokenizer.nextToken();
609	at4 = tokenizer.nextToken();
610	tt = tokenizer.nextToken();
611
612	nTokens -= 5;
613
614	switch(tt) {
615
616	case "Cubic" :
617	if (nTokens < 4) {
618
619	} else {
620
621	double k3 = tokenizer.nextTokenAsDouble();
622	double k2 = tokenizer.nextTokenAsDouble();
623	double k1 = tokenizer.nextTokenAsDouble();
624	double k0 = tokenizer.nextTokenAsDouble();
625
626	bendType = new CubicTorsionType(k3, k2, k1, k0);
627	}
628	break;
629
630	case "Quartic" :
631	if (nTokens < 5) {
632
633	} else {
634
635	theta0 = tokenizer.nextTokenAsDouble();
636	double k4 = tokenizer.nextTokenAsDouble();
637	double k3 = tokenizer.nextTokenAsDouble();
638	double k2 = tokenizer.nextTokenAsDouble();
639	double k1 = tokenizer.nextTokenAsDouble();
640	double k0 = tokenizer.nextTokenAsDouble();
641
642	bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0);
643	}
644	break;
645
646	case "Polynomial" :
647	if (nTokens < 2 \|\| nTokens % 2 != 0) {
648
649	} else {
650	int nPairs = nTokens / 2;
651	int power;
652	double coefficient;
653	PolynomialTorsionType* pbt = new PolynomialTorsionType();
654
655	for (int i = 0; i < nPairs; ++i) {
656	power = tokenizer.nextTokenAsInt();
657	coefficient = tokenizer.nextTokenAsDouble();
658	pbt->setCoefficient(power, coefficient);
659	}
660	}
661
662	break;
663	case "Charmm" :
664
665	if (nTokens < 3 \|\| nTokens % 3 != 0) {
666
667	} else {
668	int nSets = nTokens / 3;
669
670	CharmmTorsionType* ctt = new CharmmTorsionType();
671
672	for (int i = 0; i < nSets; ++i) {
673	double kchi = tokenizer.nextTokenAsDouble();
674	int n = tokenizer.nextTokenAsInt();
675	double delta = tokenizer.nextTokenAsDouble();
676
677	ctt->setCharmmTorsionParameter(kchi, n, delta);
678	}
679	}
680	default:
681
682	}
683
684	if (torsionType != NULL) {
685	addTorsionType(at1, at2, at3, at4, torsionType);
686	}
687	}
688	*/
689	} //end namespace oopse