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:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	6985 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	BendTypesSectionParser::BendTypesSectionParser() {
54	gezelter	1930	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	gezelter	2204	}
63	gezelter	1930
64	gezelter	2204	void BendTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
65	gezelter	1930	StringTokenizer tokenizer(line);
66			BendType* bendType = NULL;
67
68			int nTokens = tokenizer.countTokens();
69
70			if (nTokens < 5) {
71	gezelter	2204	sprintf(painCave.errMsg, "BendTypesSectionParser Error: Not enough tokens at line %d\n",
72			lineNo);
73			painCave.isFatal = 1;
74			simError();
75			return;
76	gezelter	1930	}
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	gezelter	2204	case btHarmonic :
89	gezelter	1930
90	gezelter	2204	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	gezelter	1930
97	gezelter	2204	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	gezelter	1930
113	gezelter	2204	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	gezelter	1930
127	gezelter	2204	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	gezelter	1930
135	gezelter	2204	double k3 = tokenizer.nextTokenAsDouble();
136			double k2 = tokenizer.nextTokenAsDouble();
137			double k1 = tokenizer.nextTokenAsDouble();
138			double k0 = tokenizer.nextTokenAsDouble();
139	gezelter	1930
140	gezelter	2204	bendType = new CubicBendType(theta0, k3, k2, k1, k0);
141			}
142			break;
143	gezelter	1930
144	gezelter	2204	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	gezelter	1930
152	gezelter	2204	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	gezelter	1930
159	gezelter	2204	bendType = new QuarticBendType(theta0, k4, k3, k2, k1, k0);
160			}
161			break;
162	gezelter	1930
163	gezelter	2204	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	gezelter	1930
175	gezelter	2204	for (int i = 0; i < nPairs; ++i) {
176			power = tokenizer.nextTokenAsInt();
177			coefficient = tokenizer.nextTokenAsDouble();
178			pbt->setCoefficient(power, coefficient);
179			}
180			}
181	gezelter	1930
182	gezelter	2204	break;
183	gezelter	1930
184	gezelter	2204	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	gezelter	1930
192			}
193
194			if (bendType != NULL) {
195	gezelter	2204	ff.addBendType(at1, at2, at3, bendType);
196	gezelter	1930	}
197	gezelter	2204	}
198	gezelter	1930
199	gezelter	2204	BendTypesSectionParser::BendTypeEnum BendTypesSectionParser::getBendTypeEnum(const std::string& str) {
200	gezelter	1930	std::map<std::string, BendTypeEnum>::iterator i;
201			i = stringToEnumMap_.find(str);
202
203			return i == stringToEnumMap_.end() ? btUnknown : i->second;
204	gezelter	2204	}
205	gezelter	1930
206			} //end namespace oopse
207
208