src/io/BondTypesSectionParser.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/BondTypesSectionParser.hpp"
#include "types/FixedBondType.hpp"
#include "types/HarmonicBondType.hpp"
#include "types/CubicBondType.hpp"
#include "types/QuarticBondType.hpp"
#include "types/PolynomialBondType.hpp"
#include "UseTheForce/ForceField.hpp"
namespace oopse {

BondTypesSectionParser::BondTypesSectionParser() {
    setSectionName("BondTypes");

    stringToEnumMap_["Fixed"] =  btFixed;                
    stringToEnumMap_["Harmonic"] =  btHarmonic;                                
    stringToEnumMap_["Cubic"] = btCubic;
    stringToEnumMap_["Quartic"] = btQuartic;
    stringToEnumMap_["Polynomial"] = btPolynomial;
}

void BondTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
    StringTokenizer tokenizer(line);
    BondType* bondType = NULL;
    int nTokens = tokenizer.countTokens();

    if (nTokens < 4) {

        return;
    }
    
    std::string at1 = tokenizer.nextToken();
    std::string at2 = tokenizer.nextToken();
    BondTypeEnum bt = getBondTypeEnum(tokenizer.nextToken());
    double b0 = tokenizer.nextTokenAsDouble();
    nTokens -= 4;

    //switch is a maintain nightmare
    switch(bt) {
        case btFixed :
            bondType = new FixedBondType(b0);
            break;
            
        case btHarmonic :
            if (nTokens < 1) {

            } else {

                double kb = tokenizer.nextTokenAsDouble();
                bondType = new HarmonicBondType(b0, kb);
            }

            break;

        case btCubic :
            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 btQuartic :
            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 QuarticBondType(b0, k4, k3, k2, k1, k0);
            }
            break;

        case btPolynomial :
            if (nTokens < 2 || nTokens % 2 != 0) {

            } else {
                int nPairs = nTokens / 2;
                int power;
                double coefficient;
                PolynomialBondType* pbt = new PolynomialBondType(b0);
                
                for (int i = 0; i < nPairs; ++i) {
                    power = tokenizer.nextTokenAsInt();
                    coefficient = tokenizer.nextTokenAsDouble();
                    pbt->setCoefficient(power, coefficient);
                }
            }
            
            break;

        case btUnknown :
        default:
            break;
            
    }

    if (bondType != NULL) {
        ff.addBondType(at1, at2, bondType);
    }

}

BondTypesSectionParser::BondTypeEnum BondTypesSectionParser::getBondTypeEnum(const std::string& str) {
    std::map<std::string, BondTypeEnum>::iterator i;
    i = stringToEnumMap_.find(str);

    return i == stringToEnumMap_.end() ? btUnknown : i->second;
}

} //end namespace oopse

Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 6 months ago) by gezelter
File size:	5612 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	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/BondTypesSectionParser.hpp"
43			#include "types/FixedBondType.hpp"
44			#include "types/HarmonicBondType.hpp"
45			#include "types/CubicBondType.hpp"
46			#include "types/QuarticBondType.hpp"
47			#include "types/PolynomialBondType.hpp"
48			#include "UseTheForce/ForceField.hpp"
49			namespace oopse {
50
51			BondTypesSectionParser::BondTypesSectionParser() {
52			setSectionName("BondTypes");
53
54			stringToEnumMap_["Fixed"] = btFixed;
55			stringToEnumMap_["Harmonic"] = btHarmonic;
56			stringToEnumMap_["Cubic"] = btCubic;
57			stringToEnumMap_["Quartic"] = btQuartic;
58			stringToEnumMap_["Polynomial"] = btPolynomial;
59			}
60
61			void BondTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
62			StringTokenizer tokenizer(line);
63			BondType* bondType = NULL;
64			int nTokens = tokenizer.countTokens();
65
66			if (nTokens < 4) {
67
68			return;
69			}
70
71			std::string at1 = tokenizer.nextToken();
72			std::string at2 = tokenizer.nextToken();
73			BondTypeEnum bt = getBondTypeEnum(tokenizer.nextToken());
74			double b0 = tokenizer.nextTokenAsDouble();
75			nTokens -= 4;
76
77			//switch is a maintain nightmare
78			switch(bt) {
79			case btFixed :
80			bondType = new FixedBondType(b0);
81			break;
82
83			case btHarmonic :
84			if (nTokens < 1) {
85
86			} else {
87
88			double kb = tokenizer.nextTokenAsDouble();
89			bondType = new HarmonicBondType(b0, kb);
90			}
91
92			break;
93
94			case btCubic :
95			if (nTokens < 4) {
96
97			} else {
98
99			double k3 = tokenizer.nextTokenAsDouble();
100			double k2 = tokenizer.nextTokenAsDouble();
101			double k1 = tokenizer.nextTokenAsDouble();
102			double k0 = tokenizer.nextTokenAsDouble();
103
104			bondType = new CubicBondType(b0, k3, k2, k1, k0);
105			}
106			break;
107
108			case btQuartic :
109			if (nTokens < 5) {
110
111			} else {
112
113			b0 = tokenizer.nextTokenAsDouble();
114			double k4 = tokenizer.nextTokenAsDouble();
115			double k3 = tokenizer.nextTokenAsDouble();
116			double k2 = tokenizer.nextTokenAsDouble();
117			double k1 = tokenizer.nextTokenAsDouble();
118			double k0 = tokenizer.nextTokenAsDouble();
119
120			bondType = new QuarticBondType(b0, k4, k3, k2, k1, k0);
121			}
122			break;
123
124			case btPolynomial :
125			if (nTokens < 2 \|\| nTokens % 2 != 0) {
126
127			} else {
128			int nPairs = nTokens / 2;
129			int power;
130			double coefficient;
131			PolynomialBondType* pbt = new PolynomialBondType(b0);
132
133			for (int i = 0; i < nPairs; ++i) {
134			power = tokenizer.nextTokenAsInt();
135			coefficient = tokenizer.nextTokenAsDouble();
136			pbt->setCoefficient(power, coefficient);
137			}
138			}
139
140			break;
141
142			case btUnknown :
143			default:
144			break;
145
146			}
147
148			if (bondType != NULL) {
149			ff.addBondType(at1, at2, bondType);
150			}
151
152			}
153
154			BondTypesSectionParser::BondTypeEnum BondTypesSectionParser::getBondTypeEnum(const std::string& str) {
155			std::map<std::string, BondTypeEnum>::iterator i;
156			i = stringToEnumMap_.find(str);
157
158			return i == stringToEnumMap_.end() ? btUnknown : i->second;
159			}
160
161			} //end namespace oopse
162