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"
#include "utils/simError.h"
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) {
        sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
                lineNo);
        painCave.isFatal = 1;
        simError();
    }
    
    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) {
                sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
                        lineNo);
                painCave.isFatal = 1;
                simError();
            } else {

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

            break;

        case btCubic :
            if (nTokens < 4) {
                sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
                        lineNo);
                painCave.isFatal = 1;
                simError();
            } 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) {

                sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
                        lineNo);
                painCave.isFatal = 1;
                simError();

            } 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) {
                sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
                        lineNo);
                painCave.isFatal = 1;
                simError();

            } 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:
                sprintf(painCave.errMsg, "BondTypesSectionParser Error: Unknown Bond Type at line %d\n",
                        lineNo);
                painCave.isFatal = 1;
                simError();

            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:	1957
Committed:	Tue Jan 25 17:45:23 2005 UTC (19 years, 5 months ago) by tim
File size:	6815 byte(s)
Log Message:	(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
#	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	#include "utils/simError.h"
50	namespace oopse {
51
52	BondTypesSectionParser::BondTypesSectionParser() {
53	setSectionName("BondTypes");
54
55	stringToEnumMap_["Fixed"] = btFixed;
56	stringToEnumMap_["Harmonic"] = btHarmonic;
57	stringToEnumMap_["Cubic"] = btCubic;
58	stringToEnumMap_["Quartic"] = btQuartic;
59	stringToEnumMap_["Polynomial"] = btPolynomial;
60	}
61
62	void BondTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
63	StringTokenizer tokenizer(line);
64	BondType* bondType = NULL;
65	int nTokens = tokenizer.countTokens();
66
67	if (nTokens < 4) {
68	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
69	lineNo);
70	painCave.isFatal = 1;
71	simError();
72	}
73
74	std::string at1 = tokenizer.nextToken();
75	std::string at2 = tokenizer.nextToken();
76	BondTypeEnum bt = getBondTypeEnum(tokenizer.nextToken());
77	double b0 = tokenizer.nextTokenAsDouble();
78	nTokens -= 4;
79
80	//switch is a maintain nightmare
81	switch(bt) {
82	case btFixed :
83	bondType = new FixedBondType(b0);
84	break;
85
86	case btHarmonic :
87	if (nTokens < 1) {
88	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
89	lineNo);
90	painCave.isFatal = 1;
91	simError();
92	} else {
93
94	double kb = tokenizer.nextTokenAsDouble();
95	bondType = new HarmonicBondType(b0, kb);
96	}
97
98	break;
99
100	case btCubic :
101	if (nTokens < 4) {
102	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
103	lineNo);
104	painCave.isFatal = 1;
105	simError();
106	} else {
107
108	double k3 = tokenizer.nextTokenAsDouble();
109	double k2 = tokenizer.nextTokenAsDouble();
110	double k1 = tokenizer.nextTokenAsDouble();
111	double k0 = tokenizer.nextTokenAsDouble();
112
113	bondType = new CubicBondType(b0, k3, k2, k1, k0);
114	}
115	break;
116
117	case btQuartic :
118	if (nTokens < 5) {
119
120	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
121	lineNo);
122	painCave.isFatal = 1;
123	simError();
124
125	} else {
126
127	b0 = tokenizer.nextTokenAsDouble();
128	double k4 = tokenizer.nextTokenAsDouble();
129	double k3 = tokenizer.nextTokenAsDouble();
130	double k2 = tokenizer.nextTokenAsDouble();
131	double k1 = tokenizer.nextTokenAsDouble();
132	double k0 = tokenizer.nextTokenAsDouble();
133
134	bondType = new QuarticBondType(b0, k4, k3, k2, k1, k0);
135	}
136	break;
137
138	case btPolynomial :
139	if (nTokens < 2 \|\| nTokens % 2 != 0) {
140	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
141	lineNo);
142	painCave.isFatal = 1;
143	simError();
144
145	} else {
146	int nPairs = nTokens / 2;
147	int power;
148	double coefficient;
149	PolynomialBondType* pbt = new PolynomialBondType(b0);
150
151	for (int i = 0; i < nPairs; ++i) {
152	power = tokenizer.nextTokenAsInt();
153	coefficient = tokenizer.nextTokenAsDouble();
154	pbt->setCoefficient(power, coefficient);
155	}
156	}
157
158	break;
159
160	case btUnknown :
161	default:
162	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Unknown Bond Type at line %d\n",
163	lineNo);
164	painCave.isFatal = 1;
165	simError();
166
167	break;
168
169	}
170
171	if (bondType != NULL) {
172	ff.addBondType(at1, at2, bondType);
173	}
174
175	}
176
177	BondTypesSectionParser::BondTypeEnum BondTypesSectionParser::getBondTypeEnum(const std::string& str) {
178	std::map<std::string, BondTypeEnum>::iterator i;
179	i = stringToEnumMap_.find(str);
180
181	return i == stringToEnumMap_.end() ? btUnknown : i->second;
182	}
183
184	} //end namespace oopse
185