src/io/EAMAtomTypesSectionParser.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 "io/EAMAtomTypesSectionParser.hpp"
#include "types/AtomType.hpp"
#include "UseTheForce/ForceField.hpp"
#include "utils/simError.h"
namespace oopse {

EAMAtomTypesSectionParser::EAMAtomTypesSectionParser() {
    setSectionName("EAMAtomTypes");
}

void EAMAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){

    StringTokenizer tokenizer(line);

    if (tokenizer.countTokens() >= 2) {
        std::string atomTypeName = tokenizer.nextToken();
        std::string potentialParamFile = tokenizer.nextToken();

        AtomType* atomType = ff.getAtomType(atomTypeName);
        if (atomType != NULL) {
            atomType->setEAM();                            
            parseEAMParamFile(ff, atomType, potentialParamFile, atomType->getIdent());                                                    
        } else {

        }
        
    } else {
      
    }
            

}

void EAMAtomTypesSectionParser::parseEAMParamFile(ForceField& ff, AtomType* atomType, 
    const std::string& potentialParamFile, int ident) {

    ifstrstream* ppfStream = ff.openForceFieldFile(potentialParamFile);
    const int bufferSize = 65535;
    char buffer[bufferSize];
    std::string line;

    //skip first line
    ppfStream->getline(buffer, bufferSize);


    //The Second line contains atomic number, atomic mass, a lattice constant and lattic type
    int junk;
    double mass;
    double latticeConstant; 
    std::string lattice;
    if (ppfStream->getline(buffer, bufferSize)) {       
        StringTokenizer tokenizer1(buffer);
        
        if (tokenizer1.countTokens() >= 4) {
            junk = tokenizer1.nextTokenAsInt();
            mass = tokenizer1.nextTokenAsDouble();
            latticeConstant = tokenizer1.nextTokenAsDouble();
            lattice = tokenizer1.nextToken();
        }else {
            std::cerr << "Not enought tokens" << std::endl;
        }
    } else {

    }
    
    // The third line is nrho, drho, nr, dr and rcut
    EAMParam eamParam;
    eamParam.latticeConstant = latticeConstant;
    
    if (ppfStream->getline(buffer, bufferSize)) {
        StringTokenizer tokenizer2(buffer);

        if (tokenizer2.countTokens() >= 5){
            eamParam.nrho = tokenizer2.nextTokenAsInt();
            eamParam.drho = tokenizer2.nextTokenAsDouble();
            eamParam.nr = tokenizer2.nextTokenAsInt();
            eamParam.dr = tokenizer2.nextTokenAsDouble();
            eamParam.rcut = tokenizer2.nextTokenAsDouble();
        }else {
            std::cerr << "Not enought tokens" << std::endl;
        }
    } else {

    }
    
    parseEAMArray(*ppfStream, eamParam.rvals, eamParam.nr);
    parseEAMArray(*ppfStream, eamParam.rhovals, eamParam.nr);
    parseEAMArray(*ppfStream, eamParam.Frhovals, eamParam.nrho);
    
    atomType->addProperty(new EAMParamGenericData("EAM", eamParam));
}

void EAMAtomTypesSectionParser::parseEAMArray(std::istream& input, 
    std::vector<double>& array, int num) {
    
    const int dataPerLine = 5;
    if (num % dataPerLine != 0) {

    }

    int nlinesToRead = num / dataPerLine;
    
    const int bufferSize = 65535;
    char buffer[bufferSize];
    std::string line;
    int readLines = num/dataPerLine;
    int lineCount = 0;

    while(lineCount < nlinesToRead && input.getline(buffer, bufferSize) ){

        StringTokenizer tokenizer(buffer);
        if (tokenizer.countTokens() >= dataPerLine) {
            for (int i = 0; i < dataPerLine; ++i) {
                array.push_back(tokenizer.nextTokenAsDouble());
            }
        } else {

        }
        ++lineCount;
    }

    if (lineCount < nlinesToRead) {
        
    }
    
}


} //end namespace oopse

Revision:	1892
Committed:	Thu Dec 16 17:27:47 2004 UTC (19 years, 9 months ago) by tim
File size:	4851 byte(s)
Log Message:	add getMaxRcutFromAtomType into EAM
#	User	Rev	Content
1	tim	1769	/*
2			* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3			*
4			* Contact: oopse@oopse.org
5			*
6			* This program is free software; you can redistribute it and/or
7			* modify it under the terms of the GNU Lesser General Public License
8			* as published by the Free Software Foundation; either version 2.1
9			* of the License, or (at your option) any later version.
10			* All we ask is that proper credit is given for our work, which includes
11			* - but is not limited to - adding the above copyright notice to the beginning
12			* of your source code files, and to any copyright notice that you may distribute
13			* with programs based on this work.
14			*
15			* This program is distributed in the hope that it will be useful,
16			* but WITHOUT ANY WARRANTY; without even the implied warranty of
17			* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18			* GNU Lesser General Public License for more details.
19			*
20			* You should have received a copy of the GNU Lesser General Public License
21			* along with this program; if not, write to the Free Software
22			* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23			*
24			*/
25
26			#include "io/EAMAtomTypesSectionParser.hpp"
27	tim	1784	#include "types/AtomType.hpp"
28	tim	1789	#include "UseTheForce/ForceField.hpp"
29			#include "utils/simError.h"
30	tim	1769	namespace oopse {
31
32			EAMAtomTypesSectionParser::EAMAtomTypesSectionParser() {
33			setSectionName("EAMAtomTypes");
34			}
35
36			void EAMAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
37
38	tim	1883	StringTokenizer tokenizer(line);
39	tim	1769
40	tim	1883	if (tokenizer.countTokens() >= 2) {
41			std::string atomTypeName = tokenizer.nextToken();
42			std::string potentialParamFile = tokenizer.nextToken();
43
44			AtomType* atomType = ff.getAtomType(atomTypeName);
45			if (atomType != NULL) {
46			atomType->setEAM();
47			parseEAMParamFile(ff, atomType, potentialParamFile, atomType->getIdent());
48			} else {
49
50			}
51
52			} else {
53
54			}
55	tim	1769
56
57			}
58
59	tim	1789	void EAMAtomTypesSectionParser::parseEAMParamFile(ForceField& ff, AtomType* atomType,
60	tim	1769	const std::string& potentialParamFile, int ident) {
61
62	tim	1789	ifstrstream* ppfStream = ff.openForceFieldFile(potentialParamFile);
63	tim	1769	const int bufferSize = 65535;
64			char buffer[bufferSize];
65			std::string line;
66
67			//skip first line
68			ppfStream->getline(buffer, bufferSize);
69
70
71			//The Second line contains atomic number, atomic mass, a lattice constant and lattic type
72			int junk;
73			double mass;
74			double latticeConstant;
75			std::string lattice;
76			if (ppfStream->getline(buffer, bufferSize)) {
77			StringTokenizer tokenizer1(buffer);
78
79			if (tokenizer1.countTokens() >= 4) {
80			junk = tokenizer1.nextTokenAsInt();
81			mass = tokenizer1.nextTokenAsDouble();
82			latticeConstant = tokenizer1.nextTokenAsDouble();
83			lattice = tokenizer1.nextToken();
84			}else {
85			std::cerr << "Not enought tokens" << std::endl;
86			}
87			} else {
88
89			}
90
91			// The third line is nrho, drho, nr, dr and rcut
92			EAMParam eamParam;
93			eamParam.latticeConstant = latticeConstant;
94
95			if (ppfStream->getline(buffer, bufferSize)) {
96			StringTokenizer tokenizer2(buffer);
97
98			if (tokenizer2.countTokens() >= 5){
99			eamParam.nrho = tokenizer2.nextTokenAsInt();
100			eamParam.drho = tokenizer2.nextTokenAsDouble();
101			eamParam.nr = tokenizer2.nextTokenAsInt();
102			eamParam.dr = tokenizer2.nextTokenAsDouble();
103			eamParam.rcut = tokenizer2.nextTokenAsDouble();
104			}else {
105			std::cerr << "Not enought tokens" << std::endl;
106			}
107			} else {
108
109			}
110
111	tim	1789	parseEAMArray(*ppfStream, eamParam.rvals, eamParam.nr);
112			parseEAMArray(*ppfStream, eamParam.rhovals, eamParam.nr);
113			parseEAMArray(*ppfStream, eamParam.Frhovals, eamParam.nrho);
114	tim	1769
115	tim	1789	atomType->addProperty(new EAMParamGenericData("EAM", eamParam));
116	tim	1769	}
117
118	tim	1789	void EAMAtomTypesSectionParser::parseEAMArray(std::istream& input,
119	tim	1769	std::vector<double>& array, int num) {
120
121			const int dataPerLine = 5;
122			if (num % dataPerLine != 0) {
123
124			}
125	tim	1892
126			int nlinesToRead = num / dataPerLine;
127	tim	1769
128			const int bufferSize = 65535;
129			char buffer[bufferSize];
130			std::string line;
131			int readLines = num/dataPerLine;
132			int lineCount = 0;
133
134	tim	1892	while(lineCount < nlinesToRead && input.getline(buffer, bufferSize) ){
135
136	tim	1769	StringTokenizer tokenizer(buffer);
137			if (tokenizer.countTokens() >= dataPerLine) {
138	tim	1770	for (int i = 0; i < dataPerLine; ++i) {
139	tim	1789	array.push_back(tokenizer.nextTokenAsDouble());
140	tim	1769	}
141			} else {
142
143			}
144			++lineCount;
145			}
146
147	tim	1892	if (lineCount < nlinesToRead) {
148	tim	1769
149			}
150
151			}
152
153
154			} //end namespace oopse
155