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"

namespace oopse {

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

//register createDUFF to ForceFieldCreator
ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF);

void DUFF::parse(const std::string& filename) {
    ifstrstream* ffStream;
    ffStream = openForceFiledFile(filename);
    const int bufferSize = 65535;
    char line[bufferSize];
    AtomType* atomType;
    std::string atomTypeName;
    double mass;
    double epsilon;
    double sigma;
    int status;
    int ident = 1; //ident begins from 1 (fortran's index begins from 1)
    int lineNo = 0;

    while(ffStream.getline(line, bufferSize)){
        ++lineNo;

        //a line begins with '#' or '!' is comment which is skipped
        if (line[0] != '#' ||line[0] != '!') {
            StringTokenizer tokenizer(line);
            
            if (tokenizer.countTokens() >= 4) {
                atomTypeName = tokenizer.nextToken();
                mass = tokenizer.nextTokenAsFloat();
                epsilon = tokenizer.nextTokenAsFloat();
                sigma = tokenizer.nextTokenAsFloat();

                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->addProperty(new DoubleGenericData("Epsilon", epsilon));                                
                atomType->addProperty(new DoubleGenericData("Sigma", sigma));                                
                atomType->complete();
                //notify a new LJtype atom type is created
                newLJtype(&ident, &sigma, &epsilon, &status);

                //add atom type to AtomTypeContainer
                addAtomType(atomTypeName, atomType);
                ++ident;
                
            } else {
                sprintf( painCave.errMsg,
                       "Not enough tokens when parsing Lennard-Jones Force Field : %s\n"
                       "in line %d : %s\n",
                       filename.c_str(), lineNo, line);
                painCave.severity = OOPSE_ERROR;
                painCave.isFatal = 1;
                simError();                
            }
            
        }
    }
    
    delete ffStream;
}


void DUFF::parseAtomType(){ 
}

void DUFF::parseBondType(){ 
}

void DUFF::parseBendType(){ 
}

void DUFF::parseTorsionType(){ 

}

} //end namespace oopse

Revision:	1741
Committed:	Tue Nov 16 02:07:14 2004 UTC (21 years, 6 months ago) by tim
File size:	3910 byte(s)
Log Message:	adding DUFF class; adding checking statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer
#	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	gezelter	1490
29	tim	1741	namespace oopse {
30	gezelter	1490
31	tim	1741	//definition of createDUFF
32			ForceField* createDUFF() {
33			return new DUFF();
34			}
35	gezelter	1490
36	tim	1741	//register createDUFF to ForceFieldCreator
37			ForceFieldFactory::getInstance()->registerForceField("DUFF", createDUFF);
38	gezelter	1490
39	tim	1741	void DUFF::parse(const std::string& filename) {
40			ifstrstream* ffStream;
41			ffStream = openForceFiledFile(filename);
42			const int bufferSize = 65535;
43			char line[bufferSize];
44			AtomType* atomType;
45			std::string atomTypeName;
46	gezelter	1490	double mass;
47	tim	1741	double epsilon;
48	gezelter	1490	double sigma;
49	tim	1741	int status;
50			int ident = 1; //ident begins from 1 (fortran's index begins from 1)
51			int lineNo = 0;
52	gezelter	1490
53	tim	1741	while(ffStream.getline(line, bufferSize)){
54			++lineNo;
55	gezelter	1490
56	tim	1741	//a line begins with '#' or '!' is comment which is skipped
57			if (line[0] != '#' \|\|line[0] != '!') {
58			StringTokenizer tokenizer(line);
59
60			if (tokenizer.countTokens() >= 4) {
61			atomTypeName = tokenizer.nextToken();
62			mass = tokenizer.nextTokenAsFloat();
63			epsilon = tokenizer.nextTokenAsFloat();
64			sigma = tokenizer.nextTokenAsFloat();
65	gezelter	1490
66	tim	1741	atomType = new AtomType();
67			atomType->setName(atomTypeName);
68			atomType->setMass(mass);
69
70			//by default, all of the properties in AtomTypeProperties is set to 0
71			//In Lennard-Jones Force Field, we only need to set Lennard-Jones to true
72			atomType->setLennardJones();
73	gezelter	1490
74	tim	1741	atomType->setIdent(ident);
75			atomType->addProperty(new DoubleGenericData("Epsilon", epsilon));
76			atomType->addProperty(new DoubleGenericData("Sigma", sigma));
77			atomType->complete();
78			//notify a new LJtype atom type is created
79			newLJtype(&ident, &sigma, &epsilon, &status);
80	gezelter	1490
81	tim	1741	//add atom type to AtomTypeContainer
82			addAtomType(atomTypeName, atomType);
83			++ident;
84
85			} else {
86			sprintf( painCave.errMsg,
87			"Not enough tokens when parsing Lennard-Jones Force Field : %s\n"
88			"in line %d : %s\n",
89			filename.c_str(), lineNo, line);
90			painCave.severity = OOPSE_ERROR;
91			painCave.isFatal = 1;
92			simError();
93			}
94	gezelter	1653
95	gezelter	1634	}
96	gezelter	1490	}
97
98	tim	1741	delete ffStream;
99	gezelter	1490	}
100
101
102	tim	1741	void DUFF::parseAtomType(){
103	gezelter	1490	}
104
105	tim	1741	void DUFF::parseBondType(){
106	gezelter	1490	}
107
108	tim	1741	void DUFF::parseBendType(){
109	gezelter	1490	}
110
111	tim	1741	void DUFF::parseTorsionType(){
112	gezelter	1490
113			}
114
115	tim	1741	} //end namespace oopse
116	gezelter	1490