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;
    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);
                    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)  {
        sprintf( painCave.errMsg,
               "Not enough tokens when parsing DUFF Force Field : %s\n"
               "in line %d : %s\n",
               filename.c_str(), lineNo, line);
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();                

        
    } 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:	1758
Committed:	Fri Nov 19 17:56:32 2004 UTC (19 years, 9 months ago) by tim
File size:	18894 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	1757	ParseState currentSection = DUFF::UnknownSection;
80
81			while(ffStream.getline(buffer, bufferSize)){
82	tim	1741	++lineNo;
83	gezelter	1490
84	tim	1757	line = trimSpaces(buffer);
85			//a line begins with "//" is comment
86			if ( line.empty() \|\| (line.size() >= 2 && line[0] == '/' && line[1] == '/')) {
87			continue;
88			} else {
89	gezelter	1490
90	tim	1757	switch(currentSection) {
91			case DUFF::AtomTypeSection :
92			parseAtomType(line, lineNo);
93			break;
94	gezelter	1490
95	tim	1757	case DUFF::BondTypeSection :
96			parseBondType(line, lineNo);
97			break;
98	gezelter	1490
99	tim	1757	case DUFF::BendTypeSection :
100			parseBendType(line, lineNo);
101			break;
102
103			case DUFF::TorsionTypeSection :
104			parseTorsionType(line, lineNo);
105			break;
106
107			case DUFF::UnknownSection:
108			StringTokenizer tokenizer(line);
109
110			std::string keyword = tokenizer.nextToken();
111			std::string section = tokenizer.nextToken();
112
113			ParseState newSection = getSection(section);
114			if (keyword != "begin" \|\| keyword != "end") {
115			std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
116			} else if (keyword == "begin") {
117			if (newSection == DUFF::UnknownSection) {
118			std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
119			} else {
120			//enter a new section
121			currentSection = newSection;
122			}
123
124			} else if (keyword == "end"){
125			if (currentSection == newSection) ) {
126			//leave a section
127			currentSection = DUFF::UnknownSection;
128			} else {
129			std::cerr << "DUFF Parsing Error at line " << lineNo << ": " << line << std::endl;
130			}
131
132			}
133			break;
134			default :
135	tim	1741
136			}
137	gezelter	1653
138	gezelter	1634	}
139	gezelter	1490	}
140
141	tim	1741	delete ffStream;
142	gezelter	1490	}
143
144
145	tim	1758	void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){
146	tim	1757	StringTokenizer tokenizer(line);
147	tim	1758	int nTokens = tokenizer.countTokens();
148	tim	1757
149	tim	1758	//in AtomTypeSection, a line at least contains 5 tokens
150			//atomTypeName, is Directional, isLJ, isCharge and mass
151			if (nTokens < 5) {
152			sprintf( painCave.errMsg,
153			"Not enough tokens when parsing DUFF Force Field : %s\n"
154			"in line %d : %s\n",
155			filename.c_str(), lineNo, line);
156			painCave.severity = OOPSE_ERROR;
157			painCave.isFatal = 1;
158			simError();
159
160
161			} else {
162
163			std::string atomTypeName = tokenizer.nextToken();
164			bool isDirectional = tokenizer.nextTokenAsBool();
165			bool isLJ = tokenizer.nextTokenAsBool();
166			bool isCharge = tokenizer.nextTokenAsBool();
167			double mass = tokenizer.nextTokenAsDouble();
168			double epsilon;
169			double sigma;
170			double charge;
171			nTokens -= 5;
172
173			//parse epsilon and sigma
174			if (isLJ) {
175			if (nTokens >= 2) {
176			epsilon = tokenizer.nextTokenAsDouble();
177			sigma = tokenizer.nextTokenAsDouble();
178			nTokens -= 2;
179			} else {
180
181			}
182			}
183
184			//parse charge
185			if (isCharge) {
186			if (nTokens >= 1) {
187			charge = tokenizer.nextTokenAsDouble();
188			nTokens -= 1;
189			} else {
190
191			}
192			}
193
194			AtomType* atomType;
195			if (isDirectional) {
196			atomType = new DirectionalAtomType();
197			} else {
198			atomType = new AtomType();
199			}
200
201	tim	1757	atomType->setName(atomTypeName);
202			atomType->setMass(mass);
203
204			//by default, all of the properties in AtomTypeProperties is set to 0
205			//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true
206			atomType->setLennardJones();
207
208	tim	1758	atomType->setIdent(ident);
209
210	tim	1757	atomType->complete();
211	tim	1758
212			int setLJStatus;
213
214	tim	1757	//notify a new LJtype atom type is created
215	tim	1758	if (isLJ) {
216			newLJtype(&ident, &sigma, &epsilon, &setLJStatus);
217			}
218	tim	1757
219	tim	1758	int setChargeStatus;
220			if (isCharge) {
221			newChargeType(&ident, &charge, &setChargeStatus)
222			}
223
224			if (setLJStatus && setChargeStatus) {
225			//add atom type to AtomTypeContainer
226			addAtomType(atomTypeName, atomType);
227			++ident;
228			} else {
229			//error in notifying fortran
230			delete atomType;
231			}
232	tim	1757	}
233	tim	1758
234	gezelter	1490	}
235
236	tim	1758
237			void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) {
238			StringTokenizer tokenizer(line);
239			int nTokens = tokenizer.countTokens();
240
241			//in irectionalAtomTypeSection, a line at least contains 6 tokens
242			//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz
243			if (nTokens < 6) {
244
245			} else {
246
247
248			std::string atomTypeName = tokenizer.nextToken();
249			bool isDipole = tokenizer.nextTokenAsBool();
250			bool isSticky = tokenizer.nextTokenAsBool();
251			double Ixx = tokenizer.nextTokenAsDouble();
252			double Iyy = tokenizer.nextTokenAsDouble();
253			double Izz = tokenizer.nextTokenAsDouble();
254			nTokens -= 6;
255
256			AtomType* atomType = getAtomType(atomTypeName);
257			if (atomType == NULL) {
258
259			}
260
261			DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
262			if (dAtomType == NULL) {
263
264
265			}
266
267			dAtomType->setDipole(isDipole);
268			dAtomType->setSticky(isSticky);
269
270			Mat3x3d inertialMat;
271			inertialMat(0, 0) = Ixx;
272			inertialMat(1, 1) = Ixx;
273			inertialMat(2, 2) = Ixx;
274			dAtomType->setI(inertialMat);
275
276			//read dipole moment
277			double dipole;
278			if (isDipole) {
279			if (nTokens >= 1) {
280			dipole = tokenizer.nextTokenAsDouble();
281			nTokens -= 1;
282			} else {
283
284			}
285			}
286
287			//read sticky parameters
288			double w0;
289			double v0;
290			double v0p;
291			double rl;
292			double ru;
293			double rlp;
294			double rup;
295			if (isSticky) {
296			if (nTokens >= 7) {
297			w0 = tokenizer.nextTokenAsDouble();
298			v0 = tokenizer.nextTokenAsDouble();
299			v0p = tokenizer.nextTokenAsDouble();
300			rl = tokenizer.nextTokenAsDouble();
301			ru = tokenizer.nextTokenAsDouble();
302			rlp = tokenizer.nextTokenAsDouble();
303			rup = tokenizer.nextTokenAsDouble();
304			nTokens -= 7;
305			} else {
306
307			}
308			}
309
310
311			//notify fotran a newDipoleType is created
312			int ident = dAtomType->getIdent();
313			int setDipoleStatus;
314			if (isDipole) {
315			newDipoleType(&ident, &dipole, &setDipoleStatus);
316			}
317
318			//notify fotran a StickyType is created
319			int setStickyStatus;
320			if (isSticky) {
321			makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup);
322			}
323
324
325			if (!setDipoleStatus \|\| !setStickyStatus) {
326
327			}
328
329			}
330			}
331
332	tim	1757	void DUFF::parseBondType(const std::string& line, int lineNo){
333
334			StringTokenizer tokenizer(line);
335			std::string at1;
336			std::string at2;
337			std::string bt;
338			BondType* bondType = NULL;
339			double b0;
340
341			int nTokens = tokenizer.countTokens();
342
343			if (nTokens < 4) {
344
345			return;
346			}
347
348			at1 = tokenizer.nextToken();
349			at2 = tokenizer.nextToken();
350			bt = tokenizer.nextToken();
351			b0 = tokenizer.nextTokenAsDouble();
352			nTokens -= 4;
353
354			//switch is a maintain nightmare
355			switch(bt) {
356			case "FixedBondType" :
357			bondType = new FixedBondType();
358			break;
359
360			case "HarmonicBondType" :
361			if (nTokens < 1) {
362
363			} else {
364
365			double kb = tokenizer.nextTokenAsDouble();
366			bondType = new HarmonicBondType(b0, kb);
367			}
368
369			break;
370
371			case "CubicBondType" :
372			if (nTokens < 4) {
373
374			} else {
375
376			double k3 = tokenizer.nextTokenAsDouble();
377			double k2 = tokenizer.nextTokenAsDouble();
378			double k1 = tokenizer.nextTokenAsDouble();
379			double k0 = tokenizer.nextTokenAsDouble();
380
381			bondType = new CubicBondType(b0, k3, k2, k1, k0);
382			}
383			break;
384
385			case "QuadraticBondType" :
386			if (nTokens < 5) {
387
388			} else {
389
390			b0 = tokenizer.nextTokenAsDouble();
391			double k4 = tokenizer.nextTokenAsDouble();
392			double k3 = tokenizer.nextTokenAsDouble();
393			double k2 = tokenizer.nextTokenAsDouble();
394			double k1 = tokenizer.nextTokenAsDouble();
395			double k0 = tokenizer.nextTokenAsDouble();
396
397			bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0);
398			}
399			break;
400
401			case "PolynomialBondType " :
402			if (nTokens < 2 \|\| nTokens % 2 != 0) {
403
404			} else {
405			int nPairs = nTokens / 2;
406			int power;
407			double coefficient;
408			PolynomialBondType pbt = new PolynomialBondType();
409
410			for (int i = 0; i < nPairs; ++i) {
411			power = tokenizer.nextTokenAsInt();
412			coefficient = tokenizer.nextTokenAsDouble();
413	tim	1758	pbt->setCoefficient(power, coefficient);
414	tim	1757	}
415			}
416
417			break;
418
419			default:
420
421			}
422
423			if (bondType != NULL) {
424			addBondType(at1, at2, bondType);
425			}
426	gezelter	1490	}
427
428	tim	1757	void DUFF::parseBendType(const std::string& line, int lineNo){
429			StringTokenizer tokenizer(line);
430			std::string at1;
431			std::string at2;
432			std::string at3;
433			std::string bt;
434			double theta0;
435			BendType* bendType = NULL;
436
437			int nTokens = tokenizer.countTokens();
438
439			if (nTokens < 5) {
440
441			return;
442			}
443
444			at1 = tokenizer.nextToken();
445			at2 = tokenizer.nextToken();
446			at3 = tokenizer.nextToken();
447			bt = tokenizer.nextToken();
448			theta0 = tokenizer.nextTokenAsDouble();
449			nTokens -= 5;
450
451			//switch is a maintain nightmare
452			switch(bt) {
453
454			case "HarmonicBendType" :
455
456			if (nTokens < 1) {
457
458			} else {
459
460			double ktheta = tokenizer.nextTokenAsDouble();
461			bendType = new HarmonicBendType(theta0, ktheta);
462			}
463			break;
464			case "GhostBendType" :
465			if (nTokens < 1) {
466
467			} else {
468			double ktheta = tokenizer.nextTokenAsDouble();
469			bendType = new HarmonicBendType(theta0, ktheta);
470			}
471			break;
472
473			case "UreyBradleyBendType" :
474			if (nTokens < 3) {
475
476			} else {
477			double ktheta = tokenizer.nextTokenAsDouble();
478			double s0 = tokenizer.nextTokenAsDouble();
479			double kub = tokenizer.nextTokenAsDouble();
480			bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);
481			}
482			break;
483
484			case "CubicBendType" :
485			if (nTokens < 4) {
486
487			} else {
488
489			double k3 = tokenizer.nextTokenAsDouble();
490			double k2 = tokenizer.nextTokenAsDouble();
491			double k1 = tokenizer.nextTokenAsDouble();
492			double k0 = tokenizer.nextTokenAsDouble();
493
494			bendType = new CubicBendType(theta0, k3, k2, k1, k0);
495			}
496			break;
497
498			case "QuadraticBendType" :
499			if (nTokens < 5) {
500
501			} else {
502
503			theta0 = tokenizer.nextTokenAsDouble();
504			double k4 = tokenizer.nextTokenAsDouble();
505			double k3 = tokenizer.nextTokenAsDouble();
506			double k2 = tokenizer.nextTokenAsDouble();
507			double k1 = tokenizer.nextTokenAsDouble();
508			double k0 = tokenizer.nextTokenAsDouble();
509
510			bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0);
511			}
512			break;
513
514			case "PolynomialBendType " :
515			if (nTokens < 2 \|\| nTokens % 2 != 0) {
516
517			} else {
518			int nPairs = nTokens / 2;
519			int power;
520			double coefficient;
521			PolynomialBendType* pbt = new PolynomialBendType();
522
523			for (int i = 0; i < nPairs; ++i) {
524			power = tokenizer.nextTokenAsInt();
525			coefficient = tokenizer.nextTokenAsDouble();
526	tim	1758	pbt->setCoefficient(power, coefficient);
527	tim	1757	}
528			}
529
530			break;
531
532			default:
533
534			}
535
536			if (bendType != NULL) {
537			addBendType(at1, at2, at3, bendType);
538			}
539
540	gezelter	1490	}
541
542	tim	1757	void DUFF::parseTorsionType(const std::string& line, int lineNo){
543			StringTokenizer tokenizer(line);
544			std::string at1;
545			std::string at2;
546			std::string at3;
547			std::string at4;
548			std::string tt;
549			TorsionType* bendType = NULL;
550	gezelter	1490
551	tim	1757	int nTokens = tokenizer.countTokens();
552
553			if (nTokens < 5) {
554
555			return;
556			}
557
558			at1 = tokenizer.nextToken();
559			at2 = tokenizer.nextToken();
560			at3 = tokenizer.nextToken();
561			at4 = tokenizer.nextToken();
562			tt = tokenizer.nextToken();
563
564			nTokens -= 5;
565
566			switch(tt) {
567
568			case "CubicTorsionType" :
569			if (nTokens < 4) {
570
571			} else {
572
573			double k3 = tokenizer.nextTokenAsDouble();
574			double k2 = tokenizer.nextTokenAsDouble();
575			double k1 = tokenizer.nextTokenAsDouble();
576			double k0 = tokenizer.nextTokenAsDouble();
577
578			bendType = new CubicTorsionType(k3, k2, k1, k0);
579			}
580			break;
581
582			case "QuadraticTorsionType" :
583			if (nTokens < 5) {
584
585			} else {
586
587			theta0 = tokenizer.nextTokenAsDouble();
588			double k4 = tokenizer.nextTokenAsDouble();
589			double k3 = tokenizer.nextTokenAsDouble();
590			double k2 = tokenizer.nextTokenAsDouble();
591			double k1 = tokenizer.nextTokenAsDouble();
592			double k0 = tokenizer.nextTokenAsDouble();
593
594			bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0);
595			}
596			break;
597
598			case "PolynomialTorsionType " :
599			if (nTokens < 2 \|\| nTokens % 2 != 0) {
600
601			} else {
602			int nPairs = nTokens / 2;
603			int power;
604			double coefficient;
605			PolynomialTorsionType* pbt = new PolynomialTorsionType();
606
607			for (int i = 0; i < nPairs; ++i) {
608			power = tokenizer.nextTokenAsInt();
609			coefficient = tokenizer.nextTokenAsDouble();
610	tim	1758	pbt->setCoefficient(power, coefficient);
611	tim	1757	}
612			}
613
614			break;
615			case "CharmmTorsionType" :
616
617			if (nTokens < 3 \|\| nTokens % 3 != 0) {
618
619			} else {
620			int nSets = nTokens / 3;
621
622			CharmmTorsionType* ctt = new CharmmTorsionType();
623
624			for (int i = 0; i < nSets; ++i) {
625	tim	1758	double kchi = tokenizer.nextTokenAsDouble();
626			int n = tokenizer.nextTokenAsInt();
627			double delta = tokenizer.nextTokenAsDouble();
628	tim	1757
629	tim	1758	ctt->setCharmmTorsionParameter(kchi, n, delta);
630	tim	1757	}
631			}
632			default:
633
634			}
635
636			if (bendType != NULL) {
637			addTorsionType(at1, at2, at3, bendType);
638			}
639	gezelter	1490	}
640
641	tim	1741	} //end namespace oopse