src/io/BendTypesSectionParser.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/BendTypesSectionParser.hpp"
#include "types/HarmonicBendType.hpp"
#include "types/UreyBradleyBendType.hpp"
#include "types/CubicBendType.hpp"
#include "types/QuarticBendType.hpp"
#include "types/PolynomialBendType.hpp"
#include "UseTheForce/ForceField.hpp"
#include "utils/NumericConstant.hpp"
namespace oopse {

BendTypesSectionParser::BendTypesSectionParser() {
    setSectionName("BendTypes");

    stringToEnumMap_["Harmonic"] =  btHarmonic;       
    stringToEnumMap_["GhostBend"] =  btGhostBend;                
    stringToEnumMap_["UreyBradley"] =  btUreyBradley;                    
    stringToEnumMap_["Cubic"] = btCubic;
    stringToEnumMap_["Quartic"] = btQuartic;
    stringToEnumMap_["Polynomial"] = btPolynomial;    
}

void BendTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
    StringTokenizer tokenizer(line);
    BendType* bendType = NULL;

    int nTokens = tokenizer.countTokens();

    if (nTokens < 5) {

        return;
    }
    
    std::string at1 = tokenizer.nextToken();
    std::string at2 = tokenizer.nextToken();
    std::string at3 = tokenizer.nextToken();
    BendTypeEnum bt = getBendTypeEnum(tokenizer.nextToken());
    double theta0 = tokenizer.nextTokenAsDouble() / 180.0 * NumericConstant::PI; //convert to rad
    nTokens -= 5;

    //switch is a maintain nightmare
    switch(bt) {
            
        case btHarmonic :
            
            if (nTokens < 1) {

            } else {

                double ktheta = tokenizer.nextTokenAsDouble();
                bendType = new HarmonicBendType(theta0, ktheta);
            }
            break;
        case btGhostBend :
            if (nTokens < 1) {

            } else {
                double ktheta = tokenizer.nextTokenAsDouble();
                bendType = new HarmonicBendType(theta0, ktheta);                
            }
            break;            

        case btUreyBradley :
            if (nTokens < 3) {

            } else {
                double ktheta = tokenizer.nextTokenAsDouble();
                double s0 =  tokenizer.nextTokenAsDouble();
                double kub = tokenizer.nextTokenAsDouble();
                bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);                
            }
            break; 
            
        case btCubic :
            if (nTokens < 4) {

            } else {

                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bendType = new CubicBendType(theta0, k3, k2, k1, k0);
            }
            break;
            
        case btQuartic :
            if (nTokens < 5) {

            } else {

                theta0 = tokenizer.nextTokenAsDouble();
                double k4 = tokenizer.nextTokenAsDouble();
                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                bendType = new QuarticBendType(theta0, k4, k3, k2, k1, k0);
            }
            break;

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

            } else {
                int nPairs = nTokens / 2;
                int power;
                double coefficient;
                PolynomialBendType* pbt = new PolynomialBendType(theta0);
                
                for (int i = 0; i < nPairs; ++i) {
                    power = tokenizer.nextTokenAsInt();
                    coefficient = tokenizer.nextTokenAsDouble();
                    pbt->setCoefficient(power, coefficient);
                }
            }
            
            break;

        case btUnknown :
        default:
            break;
            
    }

    if (bendType != NULL) {
        ff.addBendType(at1, at2, at3, bendType);
    }
}

BendTypesSectionParser::BendTypeEnum BendTypesSectionParser::getBendTypeEnum(const std::string& str) {
    std::map<std::string, BendTypeEnum>::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:	6444 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/BendTypesSectionParser.hpp"
43			#include "types/HarmonicBendType.hpp"
44			#include "types/UreyBradleyBendType.hpp"
45			#include "types/CubicBendType.hpp"
46			#include "types/QuarticBendType.hpp"
47			#include "types/PolynomialBendType.hpp"
48			#include "UseTheForce/ForceField.hpp"
49			#include "utils/NumericConstant.hpp"
50			namespace oopse {
51
52			BendTypesSectionParser::BendTypesSectionParser() {
53			setSectionName("BendTypes");
54
55			stringToEnumMap_["Harmonic"] = btHarmonic;
56			stringToEnumMap_["GhostBend"] = btGhostBend;
57			stringToEnumMap_["UreyBradley"] = btUreyBradley;
58			stringToEnumMap_["Cubic"] = btCubic;
59			stringToEnumMap_["Quartic"] = btQuartic;
60			stringToEnumMap_["Polynomial"] = btPolynomial;
61			}
62
63			void BendTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
64			StringTokenizer tokenizer(line);
65			BendType* bendType = NULL;
66
67			int nTokens = tokenizer.countTokens();
68
69			if (nTokens < 5) {
70
71			return;
72			}
73
74			std::string at1 = tokenizer.nextToken();
75			std::string at2 = tokenizer.nextToken();
76			std::string at3 = tokenizer.nextToken();
77			BendTypeEnum bt = getBendTypeEnum(tokenizer.nextToken());
78			double theta0 = tokenizer.nextTokenAsDouble() / 180.0 * NumericConstant::PI; //convert to rad
79			nTokens -= 5;
80
81			//switch is a maintain nightmare
82			switch(bt) {
83
84			case btHarmonic :
85
86			if (nTokens < 1) {
87
88			} else {
89
90			double ktheta = tokenizer.nextTokenAsDouble();
91			bendType = new HarmonicBendType(theta0, ktheta);
92			}
93			break;
94			case btGhostBend :
95			if (nTokens < 1) {
96
97			} else {
98			double ktheta = tokenizer.nextTokenAsDouble();
99			bendType = new HarmonicBendType(theta0, ktheta);
100			}
101			break;
102
103			case btUreyBradley :
104			if (nTokens < 3) {
105
106			} else {
107			double ktheta = tokenizer.nextTokenAsDouble();
108			double s0 = tokenizer.nextTokenAsDouble();
109			double kub = tokenizer.nextTokenAsDouble();
110			bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);
111			}
112			break;
113
114			case btCubic :
115			if (nTokens < 4) {
116
117			} else {
118
119			double k3 = tokenizer.nextTokenAsDouble();
120			double k2 = tokenizer.nextTokenAsDouble();
121			double k1 = tokenizer.nextTokenAsDouble();
122			double k0 = tokenizer.nextTokenAsDouble();
123
124			bendType = new CubicBendType(theta0, k3, k2, k1, k0);
125			}
126			break;
127
128			case btQuartic :
129			if (nTokens < 5) {
130
131			} else {
132
133			theta0 = tokenizer.nextTokenAsDouble();
134			double k4 = tokenizer.nextTokenAsDouble();
135			double k3 = tokenizer.nextTokenAsDouble();
136			double k2 = tokenizer.nextTokenAsDouble();
137			double k1 = tokenizer.nextTokenAsDouble();
138			double k0 = tokenizer.nextTokenAsDouble();
139
140			bendType = new QuarticBendType(theta0, k4, k3, k2, k1, k0);
141			}
142			break;
143
144			case btPolynomial :
145			if (nTokens < 2 \|\| nTokens % 2 != 0) {
146
147			} else {
148			int nPairs = nTokens / 2;
149			int power;
150			double coefficient;
151			PolynomialBendType* pbt = new PolynomialBendType(theta0);
152
153			for (int i = 0; i < nPairs; ++i) {
154			power = tokenizer.nextTokenAsInt();
155			coefficient = tokenizer.nextTokenAsDouble();
156			pbt->setCoefficient(power, coefficient);
157			}
158			}
159
160			break;
161
162			case btUnknown :
163			default:
164			break;
165
166			}
167
168			if (bendType != NULL) {
169			ff.addBendType(at1, at2, at3, bendType);
170			}
171			}
172
173			BendTypesSectionParser::BendTypeEnum BendTypesSectionParser::getBendTypeEnum(const std::string& str) {
174			std::map<std::string, BendTypeEnum>::iterator i;
175			i = stringToEnumMap_.find(str);
176
177			return i == stringToEnumMap_.end() ? btUnknown : i->second;
178			}
179
180			} //end namespace oopse
181
182