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
#	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/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	tim	1957	#include "utils/simError.h"
50	gezelter	1930	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	tim	1957	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
69			lineNo);
70			painCave.isFatal = 1;
71			simError();
72	gezelter	1930	}
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	tim	1957	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
89			lineNo);
90			painCave.isFatal = 1;
91			simError();
92	gezelter	1930	} 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	tim	1957	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
103			lineNo);
104			painCave.isFatal = 1;
105			simError();
106	gezelter	1930	} 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	tim	1957	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
121			lineNo);
122			painCave.isFatal = 1;
123			simError();
124
125	gezelter	1930	} 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	tim	1957	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Not enough tokens at line %d\n",
141			lineNo);
142			painCave.isFatal = 1;
143			simError();
144	gezelter	1930
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	tim	1957	sprintf(painCave.errMsg, "BondTypesSectionParser Error: Unknown Bond Type at line %d\n",
163			lineNo);
164			painCave.isFatal = 1;
165			simError();
166
167	gezelter	1930	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