src/io/EAMAtomTypesSectionParser.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#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 {
            sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Can not find AtomType [%s]\n",
                atomTypeName.c_str());
            painCave.isFatal = 1;
            simError();  
        }
        
    } else {
        sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens at line %d\n",
                lineNo);
        painCave.isFatal = 1;
        simError();    
    }
            
}

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 {
            sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens\n");
            painCave.isFatal = 1;
            simError();  
        }
    }
    
    // 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 {

            sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens\n");
            painCave.isFatal = 1;
            simError();            

        }
    } 
    
    parseEAMArray(*ppfStream, eamParam.Frhovals, eamParam.nrho);    
    parseEAMArray(*ppfStream, eamParam.rvals, eamParam.nr);
    parseEAMArray(*ppfStream, eamParam.rhovals, eamParam.nr);
    
    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 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 {
            sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens\n");
            painCave.isFatal = 1;
            simError();  
        }
        ++lineCount;
    }

    if (lineCount < nlinesToRead) {
        sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough lines to read\n");
        painCave.isFatal = 1;
        simError();          
    }
    
}


} //end namespace oopse

Revision:	1957
Committed:	Tue Jan 25 17:45:23 2005 UTC (19 years, 5 months ago) by tim
File size:	6592 byte(s)
Log Message:	(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
#	User	Rev	Content
1	gezelter	1930	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "io/EAMAtomTypesSectionParser.hpp"
43			#include "types/AtomType.hpp"
44			#include "UseTheForce/ForceField.hpp"
45			#include "utils/simError.h"
46			namespace oopse {
47
48			EAMAtomTypesSectionParser::EAMAtomTypesSectionParser() {
49			setSectionName("EAMAtomTypes");
50			}
51
52			void EAMAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
53
54			StringTokenizer tokenizer(line);
55
56			if (tokenizer.countTokens() >= 2) {
57			std::string atomTypeName = tokenizer.nextToken();
58			std::string potentialParamFile = tokenizer.nextToken();
59
60			AtomType* atomType = ff.getAtomType(atomTypeName);
61			if (atomType != NULL) {
62			atomType->setEAM();
63			parseEAMParamFile(ff, atomType, potentialParamFile, atomType->getIdent());
64			} else {
65	tim	1957	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Can not find AtomType [%s]\n",
66			atomTypeName.c_str());
67			painCave.isFatal = 1;
68			simError();
69	gezelter	1930	}
70
71			} else {
72	tim	1957	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens at line %d\n",
73			lineNo);
74			painCave.isFatal = 1;
75			simError();
76	gezelter	1930	}
77
78			}
79
80			void EAMAtomTypesSectionParser::parseEAMParamFile(ForceField& ff, AtomType* atomType,
81			const std::string& potentialParamFile, int ident) {
82
83			ifstrstream* ppfStream = ff.openForceFieldFile(potentialParamFile);
84			const int bufferSize = 65535;
85			char buffer[bufferSize];
86			std::string line;
87
88			//skip first line
89			ppfStream->getline(buffer, bufferSize);
90
91
92			//The Second line contains atomic number, atomic mass, a lattice constant and lattic type
93			int junk;
94			double mass;
95			double latticeConstant;
96			std::string lattice;
97			if (ppfStream->getline(buffer, bufferSize)) {
98			StringTokenizer tokenizer1(buffer);
99
100			if (tokenizer1.countTokens() >= 4) {
101			junk = tokenizer1.nextTokenAsInt();
102			mass = tokenizer1.nextTokenAsDouble();
103			latticeConstant = tokenizer1.nextTokenAsDouble();
104			lattice = tokenizer1.nextToken();
105			}else {
106	tim	1957	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens\n");
107			painCave.isFatal = 1;
108			simError();
109	gezelter	1930	}
110			}
111
112			// The third line is nrho, drho, nr, dr and rcut
113			EAMParam eamParam;
114			eamParam.latticeConstant = latticeConstant;
115
116			if (ppfStream->getline(buffer, bufferSize)) {
117			StringTokenizer tokenizer2(buffer);
118
119			if (tokenizer2.countTokens() >= 5){
120			eamParam.nrho = tokenizer2.nextTokenAsInt();
121			eamParam.drho = tokenizer2.nextTokenAsDouble();
122			eamParam.nr = tokenizer2.nextTokenAsInt();
123			eamParam.dr = tokenizer2.nextTokenAsDouble();
124			eamParam.rcut = tokenizer2.nextTokenAsDouble();
125			}else {
126
127	tim	1957	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens\n");
128			painCave.isFatal = 1;
129			simError();
130	gezelter	1930
131	tim	1957	}
132			}
133
134	gezelter	1930	parseEAMArray(*ppfStream, eamParam.Frhovals, eamParam.nrho);
135			parseEAMArray(*ppfStream, eamParam.rvals, eamParam.nr);
136			parseEAMArray(*ppfStream, eamParam.rhovals, eamParam.nr);
137
138			atomType->addProperty(new EAMParamGenericData("EAM", eamParam));
139			}
140
141			void EAMAtomTypesSectionParser::parseEAMArray(std::istream& input,
142			std::vector<double>& array, int num) {
143
144			const int dataPerLine = 5;
145			if (num % dataPerLine != 0) {
146
147			}
148
149			int nlinesToRead = num / dataPerLine;
150
151			const int bufferSize = 65535;
152			char buffer[bufferSize];
153			std::string line;
154			int lineCount = 0;
155
156			while(lineCount < nlinesToRead && input.getline(buffer, bufferSize) ){
157
158			StringTokenizer tokenizer(buffer);
159			if (tokenizer.countTokens() >= dataPerLine) {
160			for (int i = 0; i < dataPerLine; ++i) {
161			array.push_back(tokenizer.nextTokenAsDouble());
162			}
163			} else {
164	tim	1957	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens\n");
165			painCave.isFatal = 1;
166			simError();
167	gezelter	1930	}
168			++lineCount;
169			}
170
171			if (lineCount < nlinesToRead) {
172	tim	1957	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough lines to read\n");
173			painCave.isFatal = 1;
174			simError();
175	gezelter	1930	}
176
177			}
178
179
180			} //end namespace oopse
181