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));

    delete ppfStream;
}

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:	2109
Committed:	Thu Mar 10 20:28:17 2005 UTC (19 years, 3 months ago) by tim
File size:	6615 byte(s)
Log Message:	using map to replace link list
#	Content
1	/*
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	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Can not find AtomType [%s]\n",
66	atomTypeName.c_str());
67	painCave.isFatal = 1;
68	simError();
69	}
70
71	} else {
72	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens at line %d\n",
73	lineNo);
74	painCave.isFatal = 1;
75	simError();
76	}
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	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens\n");
107	painCave.isFatal = 1;
108	simError();
109	}
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	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens\n");
128	painCave.isFatal = 1;
129	simError();
130
131	}
132	}
133
134	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	delete ppfStream;
141	}
142
143	void EAMAtomTypesSectionParser::parseEAMArray(std::istream& input,
144	std::vector<double>& array, int num) {
145
146	const int dataPerLine = 5;
147	if (num % dataPerLine != 0) {
148
149	}
150
151	int nlinesToRead = num / dataPerLine;
152
153	const int bufferSize = 65535;
154	char buffer[bufferSize];
155	std::string line;
156	int lineCount = 0;
157
158	while(lineCount < nlinesToRead && input.getline(buffer, bufferSize) ){
159
160	StringTokenizer tokenizer(buffer);
161	if (tokenizer.countTokens() >= dataPerLine) {
162	for (int i = 0; i < dataPerLine; ++i) {
163	array.push_back(tokenizer.nextTokenAsDouble());
164	}
165	} else {
166	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough tokens\n");
167	painCave.isFatal = 1;
168	simError();
169	}
170	++lineCount;
171	}
172
173	if (lineCount < nlinesToRead) {
174	sprintf(painCave.errMsg, "EAMAtomTypesSectionParser Error: Not enough lines to read\n");
175	painCave.isFatal = 1;
176	simError();
177	}
178
179	}
180
181
182	} //end namespace oopse
183