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, 5 months ago) by gezelter
File size:	5612 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/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