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
#	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	tim	1957	#include "utils/simError.h"
51	gezelter	1930	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	tim	1957	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
72			lineNo);
73			painCave.isFatal = 1;
74			simError();
75	gezelter	1930	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	tim	1957	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
92			lineNo);
93			painCave.isFatal = 1;
94			simError();
95	gezelter	1930	} else {
96
97			double ktheta = tokenizer.nextTokenAsDouble();
98			bendType = new HarmonicBendType(theta0, ktheta);
99			}
100			break;
101			case btGhostBend :
102			if (nTokens < 1) {
103	tim	1957	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
104			lineNo);
105			painCave.isFatal = 1;
106			simError();
107	gezelter	1930	} else {
108			double ktheta = tokenizer.nextTokenAsDouble();
109			bendType = new HarmonicBendType(theta0, ktheta);
110			}
111			break;
112
113			case btUreyBradley :
114			if (nTokens < 3) {
115	tim	1957	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
116			lineNo);
117			painCave.isFatal = 1;
118			simError();
119	gezelter	1930	} 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	tim	1957	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
130			lineNo);
131			painCave.isFatal = 1;
132			simError();
133	gezelter	1930	} 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	tim	1957	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
147			lineNo);
148			painCave.isFatal = 1;
149			simError();
150	gezelter	1930	} 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	tim	1957	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
166			lineNo);
167			painCave.isFatal = 1;
168			simError();
169	gezelter	1930	} 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	tim	1957	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Unknown Bond Type at line %d\n",
187			lineNo);
188			painCave.isFatal = 1;
189			simError();
190	gezelter	1930	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