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);


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 = 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);
        
        //by default, all of the properties in AtomTypeProperties is set to 0
        //In  Lennard-Jones Force Field, we only need to set Lennard-Jones to true
        atomType->setLennardJones();

        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 irectionalAtomTypeSection, a line at least contains 6 tokens
    //AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz
    if (nTokens < 6) {

    } 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) {


        }

        dAtomType->setDipole(isDipole);
        dAtomType->setSticky(isSticky);

        Mat3x3d inertialMat;
        inertialMat(0, 0) = Ixx;
        inertialMat(1, 1) = Ixx;
        inertialMat(2, 2) = Ixx;        
        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 "FixedBondType" :
            bondType = new FixedBondType();
            break;
            
        case "HarmonicBondType" :
            if (nTokens < 1) {

            } else {

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

            break;

        case "CubicBondType" :
            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 "QuadraticBondType" :
            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 "PolynomialBondType " :
            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 "HarmonicBendType" :
            
            if (nTokens < 1) {

            } else {

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

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

        case "UreyBradleyBendType" :
            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 "CubicBendType" :
            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 "QuadraticBendType" :
            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 "PolynomialBendType " :
            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* bendType = 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 "CubicTorsionType" :
            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 "QuadraticTorsionType" :
            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 "PolynomialTorsionType " :
            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 "CharmmTorsionType" :
            
            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 (bendType != NULL) {
        addTorsionType(at1, at2, at3, bendType);
    }
}

} //end namespace oopse
Revision:	1759
Committed:	Fri Nov 19 18:02:33 2004 UTC (19 years, 9 months ago) by tim
File size:	18882 byte(s)
Log Message:	DUFF is almost done except error checking
#	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	gezelter	1490
32	tim	1741	namespace oopse {
33	gezelter	1490
34	tim	1741	//definition of createDUFF
35			ForceField* createDUFF() {
36			return new DUFF();
37			}
38	gezelter	1490
39	tim	1758	//register createDUFF to ForceFieldFactory
40	tim	1741	ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF);
41	gezelter	1490
42	tim	1757
43			ParseState DUFF::getSection(const std::string& section) {
44			ParseState result;
45
46			switch(section) {
47			case "AtomTypes" :
48			result = DUFF::AtomTypeSection;
49			break;
50	tim	1758	case "DirectionalAtomTypes" :
51			result = DUFF::DirectionalAtomTypeSection;
52			break;
53	tim	1757
54			case "BondTypes" :
55			result = DUFF::BondTypeSection;
56			break;
57
58			case "BendTypes" :
59			result = DUFF::BendTypeSection;
60			break;
61
62			case "TorsionTypes" :
63			result = DUFF::TorsionTypeSection;
64			break;
65			default:
66			result = DUFF::UnknownSection;
67			}
68
69			return result;
70			}
71
72	tim	1741	void DUFF::parse(const std::string& filename) {
73			ifstrstream* ffStream;
74			ffStream = openForceFiledFile(filename);
75			const int bufferSize = 65535;
76	tim	1757	std::string line;
77			char buffer[bufferSize];
78	tim	1741	int lineNo = 0;
79	tim	1759	int atomIdent = 1; //atom's indent begins from 1 (since only fortran's array begins from 1)
80	tim	1757	ParseState currentSection = DUFF::UnknownSection;
81
82			while(ffStream.getline(buffer, bufferSize)){
83	tim	1741	++lineNo;
84	gezelter	1490
85	tim	1757	line = trimSpaces(buffer);
86			//a line begins with "//" is comment
87			if ( line.empty() \|\| (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
88			continue;
89			} else {
90	gezelter	1490
91	tim	1757	switch(currentSection) {
92			case DUFF::AtomTypeSection :
93	tim	1759	parseAtomType(line, lineNo, atomIdent);
94	tim	1757	break;
95	gezelter	1490
96	tim	1759	case DUFF::DirectionalAtomTypeSection :
97			parseDirectionalAtomType(line, lineNo);
98			break;
99
100	tim	1757	case DUFF::BondTypeSection :
101			parseBondType(line, lineNo);
102			break;
103	gezelter	1490
104	tim	1757	case DUFF::BendTypeSection :
105			parseBendType(line, lineNo);
106			break;
107
108			case DUFF::TorsionTypeSection :
109			parseTorsionType(line, lineNo);
110			break;
111
112			case DUFF::UnknownSection:
113			StringTokenizer tokenizer(line);
114
115			std::string keyword = tokenizer.nextToken();
116			std::string section = tokenizer.nextToken();
117
118			ParseState newSection = getSection(section);
119			if (keyword != "begin" \|\| keyword != "end") {
120			std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
121			} else if (keyword == "begin") {
122			if (newSection == DUFF::UnknownSection) {
123			std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
124			} else {
125			//enter a new section
126			currentSection = newSection;
127			}
128
129			} else if (keyword == "end"){
130			if (currentSection == newSection) ) {
131			//leave a section
132			currentSection = DUFF::UnknownSection;
133			} else {
134			std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
135			}
136
137			}
138			break;
139			default :
140	tim	1741
141			}
142	gezelter	1653
143	gezelter	1634	}
144	gezelter	1490	}
145
146	tim	1741	delete ffStream;
147	gezelter	1490	}
148
149
150	tim	1758	void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){
151	tim	1757	StringTokenizer tokenizer(line);
152	tim	1758	int nTokens = tokenizer.countTokens();
153	tim	1757
154	tim	1758	//in AtomTypeSection, a line at least contains 5 tokens
155			//atomTypeName, is Directional, isLJ, isCharge and mass
156			if (nTokens < 5) {
157	tim	1759
158	tim	1758	} else {
159
160			std::string atomTypeName = tokenizer.nextToken();
161			bool isDirectional = tokenizer.nextTokenAsBool();
162			bool isLJ = tokenizer.nextTokenAsBool();
163			bool isCharge = tokenizer.nextTokenAsBool();
164			double mass = tokenizer.nextTokenAsDouble();
165			double epsilon;
166			double sigma;
167			double charge;
168			nTokens -= 5;
169
170			//parse epsilon and sigma
171			if (isLJ) {
172			if (nTokens >= 2) {
173			epsilon = tokenizer.nextTokenAsDouble();
174			sigma = tokenizer.nextTokenAsDouble();
175			nTokens -= 2;
176			} else {
177
178			}
179			}
180
181			//parse charge
182			if (isCharge) {
183			if (nTokens >= 1) {
184			charge = tokenizer.nextTokenAsDouble();
185			nTokens -= 1;
186			} else {
187
188			}
189			}
190
191			AtomType* atomType;
192			if (isDirectional) {
193			atomType = new DirectionalAtomType();
194			} else {
195			atomType = new AtomType();
196			}
197
198	tim	1757	atomType->setName(atomTypeName);
199			atomType->setMass(mass);
200
201			//by default, all of the properties in AtomTypeProperties is set to 0
202			//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true
203			atomType->setLennardJones();
204
205	tim	1758	atomType->setIdent(ident);
206
207	tim	1757	atomType->complete();
208	tim	1758
209			int setLJStatus;
210
211	tim	1757	//notify a new LJtype atom type is created
212	tim	1758	if (isLJ) {
213			newLJtype(&ident, &sigma, &epsilon, &setLJStatus);
214			}
215	tim	1757
216	tim	1758	int setChargeStatus;
217			if (isCharge) {
218			newChargeType(&ident, &charge, &setChargeStatus)
219			}
220
221			if (setLJStatus && setChargeStatus) {
222			//add atom type to AtomTypeContainer
223			addAtomType(atomTypeName, atomType);
224			++ident;
225			} else {
226			//error in notifying fortran
227			delete atomType;
228			}
229	tim	1757	}
230	tim	1758
231	gezelter	1490	}
232
233	tim	1758
234			void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) {
235			StringTokenizer tokenizer(line);
236			int nTokens = tokenizer.countTokens();
237
238			//in irectionalAtomTypeSection, a line at least contains 6 tokens
239			//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz
240			if (nTokens < 6) {
241
242			} else {
243
244
245			std::string atomTypeName = tokenizer.nextToken();
246			bool isDipole = tokenizer.nextTokenAsBool();
247			bool isSticky = tokenizer.nextTokenAsBool();
248			double Ixx = tokenizer.nextTokenAsDouble();
249			double Iyy = tokenizer.nextTokenAsDouble();
250			double Izz = tokenizer.nextTokenAsDouble();
251			nTokens -= 6;
252
253			AtomType* atomType = getAtomType(atomTypeName);
254			if (atomType == NULL) {
255
256			}
257
258			DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
259			if (dAtomType == NULL) {
260
261
262			}
263
264			dAtomType->setDipole(isDipole);
265			dAtomType->setSticky(isSticky);
266
267			Mat3x3d inertialMat;
268			inertialMat(0, 0) = Ixx;
269			inertialMat(1, 1) = Ixx;
270			inertialMat(2, 2) = Ixx;
271			dAtomType->setI(inertialMat);
272
273			//read dipole moment
274			double dipole;
275			if (isDipole) {
276			if (nTokens >= 1) {
277			dipole = tokenizer.nextTokenAsDouble();
278			nTokens -= 1;
279			} else {
280
281			}
282			}
283
284			//read sticky parameters
285			double w0;
286			double v0;
287			double v0p;
288			double rl;
289			double ru;
290			double rlp;
291			double rup;
292			if (isSticky) {
293			if (nTokens >= 7) {
294			w0 = tokenizer.nextTokenAsDouble();
295			v0 = tokenizer.nextTokenAsDouble();
296			v0p = tokenizer.nextTokenAsDouble();
297			rl = tokenizer.nextTokenAsDouble();
298			ru = tokenizer.nextTokenAsDouble();
299			rlp = tokenizer.nextTokenAsDouble();
300			rup = tokenizer.nextTokenAsDouble();
301			nTokens -= 7;
302			} else {
303
304			}
305			}
306
307
308			//notify fotran a newDipoleType is created
309			int ident = dAtomType->getIdent();
310			int setDipoleStatus;
311			if (isDipole) {
312			newDipoleType(&ident, &dipole, &setDipoleStatus);
313			}
314
315			//notify fotran a StickyType is created
316			int setStickyStatus;
317			if (isSticky) {
318			makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup);
319			}
320
321
322			if (!setDipoleStatus \|\| !setStickyStatus) {
323
324			}
325
326			}
327			}
328
329	tim	1757	void DUFF::parseBondType(const std::string& line, int lineNo){
330
331			StringTokenizer tokenizer(line);
332			std::string at1;
333			std::string at2;
334			std::string bt;
335			BondType* bondType = NULL;
336			double b0;
337
338			int nTokens = tokenizer.countTokens();
339
340			if (nTokens < 4) {
341
342			return;
343			}
344
345			at1 = tokenizer.nextToken();
346			at2 = tokenizer.nextToken();
347			bt = tokenizer.nextToken();
348			b0 = tokenizer.nextTokenAsDouble();
349			nTokens -= 4;
350
351			//switch is a maintain nightmare
352			switch(bt) {
353			case "FixedBondType" :
354			bondType = new FixedBondType();
355			break;
356
357			case "HarmonicBondType" :
358			if (nTokens < 1) {
359
360			} else {
361
362			double kb = tokenizer.nextTokenAsDouble();
363			bondType = new HarmonicBondType(b0, kb);
364			}
365
366			break;
367
368			case "CubicBondType" :
369			if (nTokens < 4) {
370
371			} else {
372
373			double k3 = tokenizer.nextTokenAsDouble();
374			double k2 = tokenizer.nextTokenAsDouble();
375			double k1 = tokenizer.nextTokenAsDouble();
376			double k0 = tokenizer.nextTokenAsDouble();
377
378			bondType = new CubicBondType(b0, k3, k2, k1, k0);
379			}
380			break;
381
382			case "QuadraticBondType" :
383			if (nTokens < 5) {
384
385			} else {
386
387			b0 = tokenizer.nextTokenAsDouble();
388			double k4 = tokenizer.nextTokenAsDouble();
389			double k3 = tokenizer.nextTokenAsDouble();
390			double k2 = tokenizer.nextTokenAsDouble();
391			double k1 = tokenizer.nextTokenAsDouble();
392			double k0 = tokenizer.nextTokenAsDouble();
393
394			bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0);
395			}
396			break;
397
398			case "PolynomialBondType " :
399			if (nTokens < 2 \|\| nTokens % 2 != 0) {
400
401			} else {
402			int nPairs = nTokens / 2;
403			int power;
404			double coefficient;
405			PolynomialBondType pbt = new PolynomialBondType();
406
407			for (int i = 0; i < nPairs; ++i) {
408			power = tokenizer.nextTokenAsInt();
409			coefficient = tokenizer.nextTokenAsDouble();
410	tim	1758	pbt->setCoefficient(power, coefficient);
411	tim	1757	}
412			}
413
414			break;
415
416			default:
417
418			}
419
420			if (bondType != NULL) {
421			addBondType(at1, at2, bondType);
422			}
423	gezelter	1490	}
424
425	tim	1757	void DUFF::parseBendType(const std::string& line, int lineNo){
426			StringTokenizer tokenizer(line);
427			std::string at1;
428			std::string at2;
429			std::string at3;
430			std::string bt;
431			double theta0;
432			BendType* bendType = NULL;
433
434			int nTokens = tokenizer.countTokens();
435
436			if (nTokens < 5) {
437
438			return;
439			}
440
441			at1 = tokenizer.nextToken();
442			at2 = tokenizer.nextToken();
443			at3 = tokenizer.nextToken();
444			bt = tokenizer.nextToken();
445			theta0 = tokenizer.nextTokenAsDouble();
446			nTokens -= 5;
447
448			//switch is a maintain nightmare
449			switch(bt) {
450
451			case "HarmonicBendType" :
452
453			if (nTokens < 1) {
454
455			} else {
456
457			double ktheta = tokenizer.nextTokenAsDouble();
458			bendType = new HarmonicBendType(theta0, ktheta);
459			}
460			break;
461			case "GhostBendType" :
462			if (nTokens < 1) {
463
464			} else {
465			double ktheta = tokenizer.nextTokenAsDouble();
466			bendType = new HarmonicBendType(theta0, ktheta);
467			}
468			break;
469
470			case "UreyBradleyBendType" :
471			if (nTokens < 3) {
472
473			} else {
474			double ktheta = tokenizer.nextTokenAsDouble();
475			double s0 = tokenizer.nextTokenAsDouble();
476			double kub = tokenizer.nextTokenAsDouble();
477			bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);
478			}
479			break;
480
481			case "CubicBendType" :
482			if (nTokens < 4) {
483
484			} else {
485
486			double k3 = tokenizer.nextTokenAsDouble();
487			double k2 = tokenizer.nextTokenAsDouble();
488			double k1 = tokenizer.nextTokenAsDouble();
489			double k0 = tokenizer.nextTokenAsDouble();
490
491			bendType = new CubicBendType(theta0, k3, k2, k1, k0);
492			}
493			break;
494
495			case "QuadraticBendType" :
496			if (nTokens < 5) {
497
498			} else {
499
500			theta0 = tokenizer.nextTokenAsDouble();
501			double k4 = tokenizer.nextTokenAsDouble();
502			double k3 = tokenizer.nextTokenAsDouble();
503			double k2 = tokenizer.nextTokenAsDouble();
504			double k1 = tokenizer.nextTokenAsDouble();
505			double k0 = tokenizer.nextTokenAsDouble();
506
507			bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0);
508			}
509			break;
510
511			case "PolynomialBendType " :
512			if (nTokens < 2 \|\| nTokens % 2 != 0) {
513
514			} else {
515			int nPairs = nTokens / 2;
516			int power;
517			double coefficient;
518			PolynomialBendType* pbt = new PolynomialBendType();
519
520			for (int i = 0; i < nPairs; ++i) {
521			power = tokenizer.nextTokenAsInt();
522			coefficient = tokenizer.nextTokenAsDouble();
523	tim	1758	pbt->setCoefficient(power, coefficient);
524	tim	1757	}
525			}
526
527			break;
528
529			default:
530
531			}
532
533			if (bendType != NULL) {
534			addBendType(at1, at2, at3, bendType);
535			}
536
537	gezelter	1490	}
538
539	tim	1757	void DUFF::parseTorsionType(const std::string& line, int lineNo){
540			StringTokenizer tokenizer(line);
541			std::string at1;
542			std::string at2;
543			std::string at3;
544			std::string at4;
545			std::string tt;
546			TorsionType* bendType = NULL;
547	gezelter	1490
548	tim	1757	int nTokens = tokenizer.countTokens();
549
550			if (nTokens < 5) {
551
552			return;
553			}
554
555			at1 = tokenizer.nextToken();
556			at2 = tokenizer.nextToken();
557			at3 = tokenizer.nextToken();
558			at4 = tokenizer.nextToken();
559			tt = tokenizer.nextToken();
560
561			nTokens -= 5;
562
563			switch(tt) {
564
565			case "CubicTorsionType" :
566			if (nTokens < 4) {
567
568			} else {
569
570			double k3 = tokenizer.nextTokenAsDouble();
571			double k2 = tokenizer.nextTokenAsDouble();
572			double k1 = tokenizer.nextTokenAsDouble();
573			double k0 = tokenizer.nextTokenAsDouble();
574
575			bendType = new CubicTorsionType(k3, k2, k1, k0);
576			}
577			break;
578
579			case "QuadraticTorsionType" :
580			if (nTokens < 5) {
581
582			} else {
583
584			theta0 = tokenizer.nextTokenAsDouble();
585			double k4 = tokenizer.nextTokenAsDouble();
586			double k3 = tokenizer.nextTokenAsDouble();
587			double k2 = tokenizer.nextTokenAsDouble();
588			double k1 = tokenizer.nextTokenAsDouble();
589			double k0 = tokenizer.nextTokenAsDouble();
590
591			bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0);
592			}
593			break;
594
595			case "PolynomialTorsionType " :
596			if (nTokens < 2 \|\| nTokens % 2 != 0) {
597
598			} else {
599			int nPairs = nTokens / 2;
600			int power;
601			double coefficient;
602			PolynomialTorsionType* pbt = new PolynomialTorsionType();
603
604			for (int i = 0; i < nPairs; ++i) {
605			power = tokenizer.nextTokenAsInt();
606			coefficient = tokenizer.nextTokenAsDouble();
607	tim	1758	pbt->setCoefficient(power, coefficient);
608	tim	1757	}
609			}
610
611			break;
612			case "CharmmTorsionType" :
613
614			if (nTokens < 3 \|\| nTokens % 3 != 0) {
615
616			} else {
617			int nSets = nTokens / 3;
618
619			CharmmTorsionType* ctt = new CharmmTorsionType();
620
621			for (int i = 0; i < nSets; ++i) {
622	tim	1758	double kchi = tokenizer.nextTokenAsDouble();
623			int n = tokenizer.nextTokenAsInt();
624			double delta = tokenizer.nextTokenAsDouble();
625	tim	1757
626	tim	1758	ctt->setCharmmTorsionParameter(kchi, n, delta);
627	tim	1757	}
628			}
629			default:
630
631			}
632
633			if (bendType != NULL) {
634			addTorsionType(at1, at2, at3, bendType);
635			}
636	gezelter	1490	}
637
638	tim	1741	} //end namespace oopse