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, 5 months ago) by gezelter
File size:	6444 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	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/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