src/io/InversionTypesSectionParser.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/InversionTypesSectionParser.hpp"
#include "types/InversionType.hpp"
#include "types/ImproperCosineInversionType.hpp"
//#include "types/ImproperHarmonicInversionType.hpp"
//#include "types/CentralAtomHeightInversionType.hpp"
//#include "types/DreidingInversionType.hpp"
#include "UseTheForce/ForceField.hpp"

namespace oopse {
  
  InversionTypesSectionParser::InversionTypesSectionParser(ForceFieldOptions& options) : options_(options){
    
    stringToEnumMap_["ImproperCosine"] = itImproperCosine;
    stringToEnumMap_["ImproperHarmonic"] = itImproperHarmonic;
    stringToEnumMap_["CentralAtomHeight"] = itCentralAtomHeight;
    stringToEnumMap_["Dreiding"] = itDreiding;
  }
  
  void InversionTypesSectionParser::parseLine(ForceField& ff,
                                              const std::string& line, 
                                              int lineNo){
    StringTokenizer tokenizer(line);
    InversionType* inversionType = NULL;
    
    int nTokens = tokenizer.countTokens();
    
    if (nTokens < 5) {
      return;
    }
    
    std::string at1 = tokenizer.nextToken();
    std::string at2 = tokenizer.nextToken();
    std::string at3 = tokenizer.nextToken();
    std::string at4 = tokenizer.nextToken();
    InversionTypeEnum it = getInversionTypeEnum(tokenizer.nextToken());

    nTokens -= 5;

    switch(it) {
      
    case InversionTypesSectionParser::itImproperCosine :

      if (nTokens < 3) {

      } else {
          RealType kchi = tokenizer.nextTokenAsDouble();
          int n = tokenizer.nextTokenAsInt();
          RealType delta = tokenizer.nextTokenAsDouble();
          inversionType = new ImproperCosineInversionType(kchi, n, delta);
      }

      break;
      /*      
    case InversionTypesSectionParser::itImproperHarmonic :
      if (nTokens < 2) {
        
      } else {
        
        RealType k = tokenizer.nextTokenAsDouble();
        
        inversionType = new ImproperHarmonicInversionType(k);
      }
      break;
       
    case InversionTypesSectionParser::itCentralAtomHeight :
      if (nTokens < 1) {
        
      } else {
        
        RealType k = tokenizer.nextTokenAsDouble();
        
        inversionType = new CentralAtomHeightInversionType(k);
      }
      break;                 
    case InversionTypesSectionParser::itDreiding :
      if (nTokens < 3) {
        
      } else {
        
        RealType k = tokenizer.nextTokenAsDouble();
        
        inversionType = new CentralAtomHeightInversionType(k);
      }
      break;                 
      */
    case InversionTypesSectionParser::itUnknown :
    default:
      
      break;
      
    }
    
    if (inversionType != NULL) {
      ff.addInversionType(at1, at2, at3, at4, inversionType);
    }

  }
  
  InversionTypesSectionParser::InversionTypeEnum InversionTypesSectionParser::getInversionTypeEnum(const std::string& str) {
    std::map<std::string, InversionTypeEnum>::iterator i;
    i = stringToEnumMap_.find(str);
    
    return i == stringToEnumMap_.end() ? InversionTypesSectionParser::itUnknown : i->second;
  }
  
} //end namespace oopse


Revision:	3430
Committed:	Fri Jul 4 20:54:29 2008 UTC (15 years, 11 months ago) by cli2
File size:	5020 byte(s)
Log Message:	Changes required for Inversions and Base Atom types. This will break OOPSE badly for a few days or so...
#	User	Rev	Content
1	cli2	3430	/*
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/InversionTypesSectionParser.hpp"
43			#include "types/InversionType.hpp"
44			#include "types/ImproperCosineInversionType.hpp"
45			//#include "types/ImproperHarmonicInversionType.hpp"
46			//#include "types/CentralAtomHeightInversionType.hpp"
47			//#include "types/DreidingInversionType.hpp"
48			#include "UseTheForce/ForceField.hpp"
49
50			namespace oopse {
51
52			InversionTypesSectionParser::InversionTypesSectionParser(ForceFieldOptions& options) : options_(options){
53
54			stringToEnumMap_["ImproperCosine"] = itImproperCosine;
55			stringToEnumMap_["ImproperHarmonic"] = itImproperHarmonic;
56			stringToEnumMap_["CentralAtomHeight"] = itCentralAtomHeight;
57			stringToEnumMap_["Dreiding"] = itDreiding;
58			}
59
60			void InversionTypesSectionParser::parseLine(ForceField& ff,
61			const std::string& line,
62			int lineNo){
63			StringTokenizer tokenizer(line);
64			InversionType* inversionType = NULL;
65
66			int nTokens = tokenizer.countTokens();
67
68			if (nTokens < 5) {
69			return;
70			}
71
72			std::string at1 = tokenizer.nextToken();
73			std::string at2 = tokenizer.nextToken();
74			std::string at3 = tokenizer.nextToken();
75			std::string at4 = tokenizer.nextToken();
76			InversionTypeEnum it = getInversionTypeEnum(tokenizer.nextToken());
77
78			nTokens -= 5;
79
80			switch(it) {
81
82			case InversionTypesSectionParser::itImproperCosine :
83
84			if (nTokens < 3) {
85
86			} else {
87			RealType kchi = tokenizer.nextTokenAsDouble();
88			int n = tokenizer.nextTokenAsInt();
89			RealType delta = tokenizer.nextTokenAsDouble();
90			inversionType = new ImproperCosineInversionType(kchi, n, delta);
91			}
92
93			break;
94			/*
95			case InversionTypesSectionParser::itImproperHarmonic :
96			if (nTokens < 2) {
97
98			} else {
99
100			RealType k = tokenizer.nextTokenAsDouble();
101
102			inversionType = new ImproperHarmonicInversionType(k);
103			}
104			break;
105
106			case InversionTypesSectionParser::itCentralAtomHeight :
107			if (nTokens < 1) {
108
109			} else {
110
111			RealType k = tokenizer.nextTokenAsDouble();
112
113			inversionType = new CentralAtomHeightInversionType(k);
114			}
115			break;
116			case InversionTypesSectionParser::itDreiding :
117			if (nTokens < 3) {
118
119			} else {
120
121			RealType k = tokenizer.nextTokenAsDouble();
122
123			inversionType = new CentralAtomHeightInversionType(k);
124			}
125			break;
126			*/
127			case InversionTypesSectionParser::itUnknown :
128			default:
129
130			break;
131
132			}
133
134			if (inversionType != NULL) {
135			ff.addInversionType(at1, at2, at3, at4, inversionType);
136			}
137
138			}
139
140			InversionTypesSectionParser::InversionTypeEnum InversionTypesSectionParser::getInversionTypeEnum(const std::string& str) {
141			std::map<std::string, InversionTypeEnum>::iterator i;
142			i = stringToEnumMap_.find(str);
143
144			return i == stringToEnumMap_.end() ? InversionTypesSectionParser::itUnknown : i->second;
145			}
146
147			} //end namespace oopse
148
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150