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 = 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 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) {


        }

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

        if (isSticky) {
            dAtomType->setSticky();
        }
        
        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:	1760
Committed:	Fri Nov 19 20:23:26 2004 UTC (19 years, 9 months ago) by tim
File size:	18919 byte(s)
Log Message:	add EAM
#	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	1760	int atomIdent = getNAtomType() + 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	tim	1760	if (isLJ) {
202			atomType->setLennardJones();
203			}
204	tim	1757
205	tim	1760	if (isCharge) {
206			atomType->setCharge();
207			}
208
209	tim	1758	atomType->setIdent(ident);
210
211	tim	1757	atomType->complete();
212	tim	1758
213			int setLJStatus;
214
215	tim	1757	//notify a new LJtype atom type is created
216	tim	1758	if (isLJ) {
217			newLJtype(&ident, &sigma, &epsilon, &setLJStatus);
218			}
219	tim	1757
220	tim	1758	int setChargeStatus;
221			if (isCharge) {
222			newChargeType(&ident, &charge, &setChargeStatus)
223			}
224
225			if (setLJStatus && setChargeStatus) {
226			//add atom type to AtomTypeContainer
227			addAtomType(atomTypeName, atomType);
228			++ident;
229			} else {
230			//error in notifying fortran
231			delete atomType;
232			}
233	tim	1757	}
234	tim	1758
235	gezelter	1490	}
236
237	tim	1758
238			void DUFF::parseDirectionalAtomType(const std::string& line, int lineNo) {
239			StringTokenizer tokenizer(line);
240			int nTokens = tokenizer.countTokens();
241
242			//in irectionalAtomTypeSection, a line at least contains 6 tokens
243			//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz
244			if (nTokens < 6) {
245
246			} else {
247
248
249			std::string atomTypeName = tokenizer.nextToken();
250			bool isDipole = tokenizer.nextTokenAsBool();
251			bool isSticky = tokenizer.nextTokenAsBool();
252			double Ixx = tokenizer.nextTokenAsDouble();
253			double Iyy = tokenizer.nextTokenAsDouble();
254			double Izz = tokenizer.nextTokenAsDouble();
255			nTokens -= 6;
256
257			AtomType* atomType = getAtomType(atomTypeName);
258			if (atomType == NULL) {
259
260			}
261
262			DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
263			if (dAtomType == NULL) {
264
265
266			}
267
268	tim	1760	if (isDipole) {
269			dAtomType->setDipole();
270			}
271	tim	1758
272	tim	1760	if (isSticky) {
273			dAtomType->setSticky();
274			}
275
276	tim	1758	Mat3x3d inertialMat;
277			inertialMat(0, 0) = Ixx;
278			inertialMat(1, 1) = Ixx;
279			inertialMat(2, 2) = Ixx;
280			dAtomType->setI(inertialMat);
281
282			//read dipole moment
283			double dipole;
284			if (isDipole) {
285			if (nTokens >= 1) {
286			dipole = tokenizer.nextTokenAsDouble();
287			nTokens -= 1;
288			} else {
289
290			}
291			}
292
293			//read sticky parameters
294			double w0;
295			double v0;
296			double v0p;
297			double rl;
298			double ru;
299			double rlp;
300			double rup;
301			if (isSticky) {
302			if (nTokens >= 7) {
303			w0 = tokenizer.nextTokenAsDouble();
304			v0 = tokenizer.nextTokenAsDouble();
305			v0p = tokenizer.nextTokenAsDouble();
306			rl = tokenizer.nextTokenAsDouble();
307			ru = tokenizer.nextTokenAsDouble();
308			rlp = tokenizer.nextTokenAsDouble();
309			rup = tokenizer.nextTokenAsDouble();
310			nTokens -= 7;
311			} else {
312
313			}
314			}
315
316
317			//notify fotran a newDipoleType is created
318			int ident = dAtomType->getIdent();
319			int setDipoleStatus;
320			if (isDipole) {
321			newDipoleType(&ident, &dipole, &setDipoleStatus);
322			}
323
324			//notify fotran a StickyType is created
325			int setStickyStatus;
326			if (isSticky) {
327			makeStickyType( &w0, &v0, &v0p, &rl, &ru, &rlp, &rup);
328			}
329
330
331			if (!setDipoleStatus \|\| !setStickyStatus) {
332
333			}
334
335			}
336			}
337
338	tim	1757	void DUFF::parseBondType(const std::string& line, int lineNo){
339
340			StringTokenizer tokenizer(line);
341			std::string at1;
342			std::string at2;
343			std::string bt;
344			BondType* bondType = NULL;
345			double b0;
346
347			int nTokens = tokenizer.countTokens();
348
349			if (nTokens < 4) {
350
351			return;
352			}
353
354			at1 = tokenizer.nextToken();
355			at2 = tokenizer.nextToken();
356			bt = tokenizer.nextToken();
357			b0 = tokenizer.nextTokenAsDouble();
358			nTokens -= 4;
359
360			//switch is a maintain nightmare
361			switch(bt) {
362			case "FixedBondType" :
363			bondType = new FixedBondType();
364			break;
365
366			case "HarmonicBondType" :
367			if (nTokens < 1) {
368
369			} else {
370
371			double kb = tokenizer.nextTokenAsDouble();
372			bondType = new HarmonicBondType(b0, kb);
373			}
374
375			break;
376
377			case "CubicBondType" :
378			if (nTokens < 4) {
379
380			} else {
381
382			double k3 = tokenizer.nextTokenAsDouble();
383			double k2 = tokenizer.nextTokenAsDouble();
384			double k1 = tokenizer.nextTokenAsDouble();
385			double k0 = tokenizer.nextTokenAsDouble();
386
387			bondType = new CubicBondType(b0, k3, k2, k1, k0);
388			}
389			break;
390
391			case "QuadraticBondType" :
392			if (nTokens < 5) {
393
394			} else {
395
396			b0 = tokenizer.nextTokenAsDouble();
397			double k4 = tokenizer.nextTokenAsDouble();
398			double k3 = tokenizer.nextTokenAsDouble();
399			double k2 = tokenizer.nextTokenAsDouble();
400			double k1 = tokenizer.nextTokenAsDouble();
401			double k0 = tokenizer.nextTokenAsDouble();
402
403			bondType = new QuadraticBondType(b0, k4, k3, k2, k1, k0);
404			}
405			break;
406
407			case "PolynomialBondType " :
408			if (nTokens < 2 \|\| nTokens % 2 != 0) {
409
410			} else {
411			int nPairs = nTokens / 2;
412			int power;
413			double coefficient;
414			PolynomialBondType pbt = new PolynomialBondType();
415
416			for (int i = 0; i < nPairs; ++i) {
417			power = tokenizer.nextTokenAsInt();
418			coefficient = tokenizer.nextTokenAsDouble();
419	tim	1758	pbt->setCoefficient(power, coefficient);
420	tim	1757	}
421			}
422
423			break;
424
425			default:
426
427			}
428
429			if (bondType != NULL) {
430			addBondType(at1, at2, bondType);
431			}
432	gezelter	1490	}
433
434	tim	1757	void DUFF::parseBendType(const std::string& line, int lineNo){
435			StringTokenizer tokenizer(line);
436			std::string at1;
437			std::string at2;
438			std::string at3;
439			std::string bt;
440			double theta0;
441			BendType* bendType = NULL;
442
443			int nTokens = tokenizer.countTokens();
444
445			if (nTokens < 5) {
446
447			return;
448			}
449
450			at1 = tokenizer.nextToken();
451			at2 = tokenizer.nextToken();
452			at3 = tokenizer.nextToken();
453			bt = tokenizer.nextToken();
454			theta0 = tokenizer.nextTokenAsDouble();
455			nTokens -= 5;
456
457			//switch is a maintain nightmare
458			switch(bt) {
459
460			case "HarmonicBendType" :
461
462			if (nTokens < 1) {
463
464			} else {
465
466			double ktheta = tokenizer.nextTokenAsDouble();
467			bendType = new HarmonicBendType(theta0, ktheta);
468			}
469			break;
470			case "GhostBendType" :
471			if (nTokens < 1) {
472
473			} else {
474			double ktheta = tokenizer.nextTokenAsDouble();
475			bendType = new HarmonicBendType(theta0, ktheta);
476			}
477			break;
478
479			case "UreyBradleyBendType" :
480			if (nTokens < 3) {
481
482			} else {
483			double ktheta = tokenizer.nextTokenAsDouble();
484			double s0 = tokenizer.nextTokenAsDouble();
485			double kub = tokenizer.nextTokenAsDouble();
486			bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);
487			}
488			break;
489
490			case "CubicBendType" :
491			if (nTokens < 4) {
492
493			} else {
494
495			double k3 = tokenizer.nextTokenAsDouble();
496			double k2 = tokenizer.nextTokenAsDouble();
497			double k1 = tokenizer.nextTokenAsDouble();
498			double k0 = tokenizer.nextTokenAsDouble();
499
500			bendType = new CubicBendType(theta0, k3, k2, k1, k0);
501			}
502			break;
503
504			case "QuadraticBendType" :
505			if (nTokens < 5) {
506
507			} else {
508
509			theta0 = tokenizer.nextTokenAsDouble();
510			double k4 = tokenizer.nextTokenAsDouble();
511			double k3 = tokenizer.nextTokenAsDouble();
512			double k2 = tokenizer.nextTokenAsDouble();
513			double k1 = tokenizer.nextTokenAsDouble();
514			double k0 = tokenizer.nextTokenAsDouble();
515
516			bendType = new QuadraticBendType(theta0, k4, k3, k2, k1, k0);
517			}
518			break;
519
520			case "PolynomialBendType " :
521			if (nTokens < 2 \|\| nTokens % 2 != 0) {
522
523			} else {
524			int nPairs = nTokens / 2;
525			int power;
526			double coefficient;
527			PolynomialBendType* pbt = new PolynomialBendType();
528
529			for (int i = 0; i < nPairs; ++i) {
530			power = tokenizer.nextTokenAsInt();
531			coefficient = tokenizer.nextTokenAsDouble();
532	tim	1758	pbt->setCoefficient(power, coefficient);
533	tim	1757	}
534			}
535
536			break;
537
538			default:
539
540			}
541
542			if (bendType != NULL) {
543			addBendType(at1, at2, at3, bendType);
544			}
545
546	gezelter	1490	}
547
548	tim	1757	void DUFF::parseTorsionType(const std::string& line, int lineNo){
549			StringTokenizer tokenizer(line);
550			std::string at1;
551			std::string at2;
552			std::string at3;
553			std::string at4;
554			std::string tt;
555			TorsionType* bendType = NULL;
556	gezelter	1490
557	tim	1757	int nTokens = tokenizer.countTokens();
558
559			if (nTokens < 5) {
560
561			return;
562			}
563
564			at1 = tokenizer.nextToken();
565			at2 = tokenizer.nextToken();
566			at3 = tokenizer.nextToken();
567			at4 = tokenizer.nextToken();
568			tt = tokenizer.nextToken();
569
570			nTokens -= 5;
571
572			switch(tt) {
573
574			case "CubicTorsionType" :
575			if (nTokens < 4) {
576
577			} else {
578
579			double k3 = tokenizer.nextTokenAsDouble();
580			double k2 = tokenizer.nextTokenAsDouble();
581			double k1 = tokenizer.nextTokenAsDouble();
582			double k0 = tokenizer.nextTokenAsDouble();
583
584			bendType = new CubicTorsionType(k3, k2, k1, k0);
585			}
586			break;
587
588			case "QuadraticTorsionType" :
589			if (nTokens < 5) {
590
591			} else {
592
593			theta0 = tokenizer.nextTokenAsDouble();
594			double k4 = tokenizer.nextTokenAsDouble();
595			double k3 = tokenizer.nextTokenAsDouble();
596			double k2 = tokenizer.nextTokenAsDouble();
597			double k1 = tokenizer.nextTokenAsDouble();
598			double k0 = tokenizer.nextTokenAsDouble();
599
600			bendType = new QuadraticTorsionType( k4, k3, k2, k1, k0);
601			}
602			break;
603
604			case "PolynomialTorsionType " :
605			if (nTokens < 2 \|\| nTokens % 2 != 0) {
606
607			} else {
608			int nPairs = nTokens / 2;
609			int power;
610			double coefficient;
611			PolynomialTorsionType* pbt = new PolynomialTorsionType();
612
613			for (int i = 0; i < nPairs; ++i) {
614			power = tokenizer.nextTokenAsInt();
615			coefficient = tokenizer.nextTokenAsDouble();
616	tim	1758	pbt->setCoefficient(power, coefficient);
617	tim	1757	}
618			}
619
620			break;
621			case "CharmmTorsionType" :
622
623			if (nTokens < 3 \|\| nTokens % 3 != 0) {
624
625			} else {
626			int nSets = nTokens / 3;
627
628			CharmmTorsionType* ctt = new CharmmTorsionType();
629
630			for (int i = 0; i < nSets; ++i) {
631	tim	1758	double kchi = tokenizer.nextTokenAsDouble();
632			int n = tokenizer.nextTokenAsInt();
633			double delta = tokenizer.nextTokenAsDouble();
634	tim	1757
635	tim	1758	ctt->setCharmmTorsionParameter(kchi, n, delta);
636	tim	1757	}
637			}
638			default:
639
640			}
641
642			if (bendType != NULL) {
643			addTorsionType(at1, at2, at3, bendType);
644			}
645	gezelter	1490	}
646
647	tim	1741	} //end namespace oopse