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

                double ktheta = tokenizer.nextTokenAsDouble();
                bendType = new HarmonicBendType(theta0, ktheta);
            }
            break;
        case btGhostBend :
            if (nTokens < 1) {
                sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
                        lineNo);
                painCave.isFatal = 1;
                simError();
            } else {
                double ktheta = tokenizer.nextTokenAsDouble();
                bendType = new HarmonicBendType(theta0, ktheta);                
            }
            break;            

        case btUreyBradley :
            if (nTokens < 3) {
                sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
                        lineNo);
                painCave.isFatal = 1;
                simError();
            } 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) {
                sprintf(painCave.errMsg, "BendTypesSectionParser 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();
                
                bendType = new CubicBendType(theta0, k3, k2, k1, k0);
            }
            break;
            
        case btQuartic :
            if (nTokens < 5) {
                sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
                        lineNo);
                painCave.isFatal = 1;
                simError();
            } 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) {
                sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
                        lineNo);
                painCave.isFatal = 1;
                simError();
            } 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:
            sprintf(painCave.errMsg, "BendTypesSectionParser Error: Unknown Bond Type at line %d\n",
                    lineNo);
            painCave.isFatal = 1;
            simError();
            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:	1957
Committed:	Tue Jan 25 17:45:23 2005 UTC (19 years, 5 months ago) by tim
File size:	8049 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/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	#include "utils/simError.h"
51	namespace oopse {
52
53	BendTypesSectionParser::BendTypesSectionParser() {
54	setSectionName("BendTypes");
55
56	stringToEnumMap_["Harmonic"] = btHarmonic;
57	stringToEnumMap_["GhostBend"] = btGhostBend;
58	stringToEnumMap_["UreyBradley"] = btUreyBradley;
59	stringToEnumMap_["Cubic"] = btCubic;
60	stringToEnumMap_["Quartic"] = btQuartic;
61	stringToEnumMap_["Polynomial"] = btPolynomial;
62	}
63
64	void BendTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
65	StringTokenizer tokenizer(line);
66	BendType* bendType = NULL;
67
68	int nTokens = tokenizer.countTokens();
69
70	if (nTokens < 5) {
71	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
72	lineNo);
73	painCave.isFatal = 1;
74	simError();
75	return;
76	}
77
78	std::string at1 = tokenizer.nextToken();
79	std::string at2 = tokenizer.nextToken();
80	std::string at3 = tokenizer.nextToken();
81	BendTypeEnum bt = getBendTypeEnum(tokenizer.nextToken());
82	double theta0 = tokenizer.nextTokenAsDouble() / 180.0 * NumericConstant::PI; //convert to rad
83	nTokens -= 5;
84
85	//switch is a maintain nightmare
86	switch(bt) {
87
88	case btHarmonic :
89
90	if (nTokens < 1) {
91	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
92	lineNo);
93	painCave.isFatal = 1;
94	simError();
95	} else {
96
97	double ktheta = tokenizer.nextTokenAsDouble();
98	bendType = new HarmonicBendType(theta0, ktheta);
99	}
100	break;
101	case btGhostBend :
102	if (nTokens < 1) {
103	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
104	lineNo);
105	painCave.isFatal = 1;
106	simError();
107	} else {
108	double ktheta = tokenizer.nextTokenAsDouble();
109	bendType = new HarmonicBendType(theta0, ktheta);
110	}
111	break;
112
113	case btUreyBradley :
114	if (nTokens < 3) {
115	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
116	lineNo);
117	painCave.isFatal = 1;
118	simError();
119	} else {
120	double ktheta = tokenizer.nextTokenAsDouble();
121	double s0 = tokenizer.nextTokenAsDouble();
122	double kub = tokenizer.nextTokenAsDouble();
123	bendType = new UreyBradleyBendType(theta0, ktheta, s0, kub);
124	}
125	break;
126
127	case btCubic :
128	if (nTokens < 4) {
129	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
130	lineNo);
131	painCave.isFatal = 1;
132	simError();
133	} else {
134
135	double k3 = tokenizer.nextTokenAsDouble();
136	double k2 = tokenizer.nextTokenAsDouble();
137	double k1 = tokenizer.nextTokenAsDouble();
138	double k0 = tokenizer.nextTokenAsDouble();
139
140	bendType = new CubicBendType(theta0, k3, k2, k1, k0);
141	}
142	break;
143
144	case btQuartic :
145	if (nTokens < 5) {
146	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
147	lineNo);
148	painCave.isFatal = 1;
149	simError();
150	} else {
151
152	theta0 = tokenizer.nextTokenAsDouble();
153	double k4 = tokenizer.nextTokenAsDouble();
154	double k3 = tokenizer.nextTokenAsDouble();
155	double k2 = tokenizer.nextTokenAsDouble();
156	double k1 = tokenizer.nextTokenAsDouble();
157	double k0 = tokenizer.nextTokenAsDouble();
158
159	bendType = new QuarticBendType(theta0, k4, k3, k2, k1, k0);
160	}
161	break;
162
163	case btPolynomial :
164	if (nTokens < 2 \|\| nTokens % 2 != 0) {
165	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
166	lineNo);
167	painCave.isFatal = 1;
168	simError();
169	} else {
170	int nPairs = nTokens / 2;
171	int power;
172	double coefficient;
173	PolynomialBendType* pbt = new PolynomialBendType(theta0);
174
175	for (int i = 0; i < nPairs; ++i) {
176	power = tokenizer.nextTokenAsInt();
177	coefficient = tokenizer.nextTokenAsDouble();
178	pbt->setCoefficient(power, coefficient);
179	}
180	}
181
182	break;
183
184	case btUnknown :
185	default:
186	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Unknown Bond Type at line %d\n",
187	lineNo);
188	painCave.isFatal = 1;
189	simError();
190	break;
191
192	}
193
194	if (bendType != NULL) {
195	ff.addBendType(at1, at2, at3, bendType);
196	}
197	}
198
199	BendTypesSectionParser::BendTypeEnum BendTypesSectionParser::getBendTypeEnum(const std::string& str) {
200	std::map<std::string, BendTypeEnum>::iterator i;
201	i = stringToEnumMap_.find(str);
202
203	return i == stringToEnumMap_.end() ? btUnknown : i->second;
204	}
205
206	} //end namespace oopse
207
208