src/io/TorsionTypesSectionParser.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/TorsionTypesSectionParser.hpp"
#include "types/TorsionType.hpp"
#include "types/CubicTorsionType.hpp"
#include "types/QuarticTorsionType.hpp"
#include "types/PolynomialTorsionType.hpp"
#include "types/CharmmTorsionType.hpp"
#include "UseTheForce/ForceField.hpp"

namespace oopse {

  TorsionTypesSectionParser::TorsionTypesSectionParser() {
    setSectionName("TorsionTypes");


    stringToEnumMap_["GhostTorsion"] == ttGhostTorsion;
    stringToEnumMap_["Cubic"] = ttCubic;
    stringToEnumMap_["Quartic"] = ttQuartic;
    stringToEnumMap_["Polynomial"] = ttPolynomial;
    stringToEnumMap_["Charmm"] =  ttCharmm;

  }

  void TorsionTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
    StringTokenizer tokenizer(line);
    TorsionType* torsionType = 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();
    TorsionTypeEnum tt = getTorsionTypeEnum(tokenizer.nextToken());

    nTokens -= 5;

    switch(tt) {

    case TorsionTypesSectionParser::ttGhostTorsion:
      if (nTokens < 4) {

      } else {

        double k3 = tokenizer.nextTokenAsDouble();
        double k2 = tokenizer.nextTokenAsDouble();
        double k1 = tokenizer.nextTokenAsDouble();
        double k0 = tokenizer.nextTokenAsDouble();
                
        torsionType = new CubicTorsionType(k3, k2, k1, k0);
      }
      break;
            
    case TorsionTypesSectionParser::ttCubic :
      if (nTokens < 4) {

      } else {

        double k3 = tokenizer.nextTokenAsDouble();
        double k2 = tokenizer.nextTokenAsDouble();
        double k1 = tokenizer.nextTokenAsDouble();
        double k0 = tokenizer.nextTokenAsDouble();
                
        torsionType = new CubicTorsionType(k3, k2, k1, k0);
      }
      break;
            
    case TorsionTypesSectionParser::ttQuartic:
      if (nTokens < 5) {

      } else {

        double k4 = tokenizer.nextTokenAsDouble();
        double k3 = tokenizer.nextTokenAsDouble();
        double k2 = tokenizer.nextTokenAsDouble();
        double k1 = tokenizer.nextTokenAsDouble();
        double k0 = tokenizer.nextTokenAsDouble();
                
        torsionType = new QuarticTorsionType( k4, k3, k2, k1, k0);
      }
      break;

        
    case TorsionTypesSectionParser::ttPolynomial:
      if (nTokens < 2 || nTokens % 2 != 0) {

      } else {
        int nPairs = nTokens / 2;
        int power;
        double coefficient;
        PolynomialTorsionType* ptt = new PolynomialTorsionType();
                
        for (int i = 0; i < nPairs; ++i) {
          power = tokenizer.nextTokenAsInt();
          coefficient = tokenizer.nextTokenAsDouble();
          ptt->setCoefficient(power, coefficient);
        }
      }
            
      break;
             
    case TorsionTypesSectionParser::ttCharmm:
            
      if (nTokens < 3 || nTokens % 3 != 0) {

      } else {
        int nSets = nTokens / 3;
  
        CharmmTorsionType* ctt = new CharmmTorsionType();
                
        for (int i = 0; i < nSets; ++i) {
          double kchi = tokenizer.nextTokenAsDouble();
          int n = tokenizer.nextTokenAsInt();
          double delta = tokenizer.nextTokenAsDouble();
    
          ctt->setCharmmTorsionParameter(kchi, n, delta);
        }
      }

      break;
            
    case TorsionTypesSectionParser::ttUnknown :
    default:

      break;
            
    }

    if (torsionType != NULL) {
      ff.addTorsionType(at1, at2, at3, at4, torsionType);
    }

  }

  TorsionTypesSectionParser::TorsionTypeEnum TorsionTypesSectionParser::getTorsionTypeEnum(const std::string& str) {
    std::map<std::string, TorsionTypeEnum>::iterator i;
    i = stringToEnumMap_.find(str);

    return i == stringToEnumMap_.end() ? TorsionTypesSectionParser::ttUnknown : 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:	5897 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/TorsionTypesSectionParser.hpp"
43			#include "types/TorsionType.hpp"
44			#include "types/CubicTorsionType.hpp"
45			#include "types/QuarticTorsionType.hpp"
46			#include "types/PolynomialTorsionType.hpp"
47			#include "types/CharmmTorsionType.hpp"
48			#include "UseTheForce/ForceField.hpp"
49
50			namespace oopse {
51
52	gezelter	2204	TorsionTypesSectionParser::TorsionTypesSectionParser() {
53	gezelter	1930	setSectionName("TorsionTypes");
54
55
56	tim	1957	stringToEnumMap_["GhostTorsion"] == ttGhostTorsion;
57	gezelter	1930	stringToEnumMap_["Cubic"] = ttCubic;
58			stringToEnumMap_["Quartic"] = ttQuartic;
59			stringToEnumMap_["Polynomial"] = ttPolynomial;
60			stringToEnumMap_["Charmm"] = ttCharmm;
61
62	gezelter	2204	}
63	gezelter	1930
64	gezelter	2204	void TorsionTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
65	gezelter	1930	StringTokenizer tokenizer(line);
66			TorsionType* torsionType = NULL;
67
68			int nTokens = tokenizer.countTokens();
69
70			if (nTokens < 5) {
71
72	gezelter	2204	return;
73	gezelter	1930	}
74
75			std::string at1 = tokenizer.nextToken();
76			std::string at2 = tokenizer.nextToken();
77			std::string at3 = tokenizer.nextToken();
78			std::string at4 = tokenizer.nextToken();
79			TorsionTypeEnum tt = getTorsionTypeEnum(tokenizer.nextToken());
80
81			nTokens -= 5;
82
83			switch(tt) {
84	tim	1957
85	gezelter	2204	case TorsionTypesSectionParser::ttGhostTorsion:
86			if (nTokens < 4) {
87	tim	1957
88	gezelter	2204	} else {
89	tim	1957
90	gezelter	2204	double k3 = tokenizer.nextTokenAsDouble();
91			double k2 = tokenizer.nextTokenAsDouble();
92			double k1 = tokenizer.nextTokenAsDouble();
93			double k0 = tokenizer.nextTokenAsDouble();
94	tim	1957
95	gezelter	2204	torsionType = new CubicTorsionType(k3, k2, k1, k0);
96			}
97			break;
98	gezelter	1930
99	gezelter	2204	case TorsionTypesSectionParser::ttCubic :
100			if (nTokens < 4) {
101	gezelter	1930
102	gezelter	2204	} else {
103	gezelter	1930
104	gezelter	2204	double k3 = tokenizer.nextTokenAsDouble();
105			double k2 = tokenizer.nextTokenAsDouble();
106			double k1 = tokenizer.nextTokenAsDouble();
107			double k0 = tokenizer.nextTokenAsDouble();
108	gezelter	1930
109	gezelter	2204	torsionType = new CubicTorsionType(k3, k2, k1, k0);
110			}
111			break;
112	gezelter	1930
113	gezelter	2204	case TorsionTypesSectionParser::ttQuartic:
114			if (nTokens < 5) {
115	gezelter	1930
116	gezelter	2204	} else {
117	gezelter	1930
118	gezelter	2204	double k4 = tokenizer.nextTokenAsDouble();
119			double k3 = tokenizer.nextTokenAsDouble();
120			double k2 = tokenizer.nextTokenAsDouble();
121			double k1 = tokenizer.nextTokenAsDouble();
122			double k0 = tokenizer.nextTokenAsDouble();
123	gezelter	1930
124	gezelter	2204	torsionType = new QuarticTorsionType( k4, k3, k2, k1, k0);
125			}
126			break;
127	gezelter	1930
128
129	gezelter	2204	case TorsionTypesSectionParser::ttPolynomial:
130			if (nTokens < 2 \|\| nTokens % 2 != 0) {
131	gezelter	1930
132	gezelter	2204	} else {
133			int nPairs = nTokens / 2;
134			int power;
135			double coefficient;
136			PolynomialTorsionType* ptt = new PolynomialTorsionType();
137	gezelter	1930
138	gezelter	2204	for (int i = 0; i < nPairs; ++i) {
139			power = tokenizer.nextTokenAsInt();
140			coefficient = tokenizer.nextTokenAsDouble();
141			ptt->setCoefficient(power, coefficient);
142			}
143			}
144	gezelter	1930
145	gezelter	2204	break;
146	gezelter	1930
147	gezelter	2204	case TorsionTypesSectionParser::ttCharmm:
148	gezelter	1930
149	gezelter	2204	if (nTokens < 3 \|\| nTokens % 3 != 0) {
150	gezelter	1930
151	gezelter	2204	} else {
152			int nSets = nTokens / 3;
153	gezelter	1930
154	gezelter	2204	CharmmTorsionType* ctt = new CharmmTorsionType();
155	gezelter	1930
156	gezelter	2204	for (int i = 0; i < nSets; ++i) {
157			double kchi = tokenizer.nextTokenAsDouble();
158			int n = tokenizer.nextTokenAsInt();
159			double delta = tokenizer.nextTokenAsDouble();
160	gezelter	1930
161	gezelter	2204	ctt->setCharmmTorsionParameter(kchi, n, delta);
162			}
163			}
164	gezelter	1930
165	gezelter	2204	break;
166	gezelter	1930
167	gezelter	2204	case TorsionTypesSectionParser::ttUnknown :
168			default:
169	gezelter	1930
170	gezelter	2204	break;
171	gezelter	1930
172			}
173
174			if (torsionType != NULL) {
175	gezelter	2204	ff.addTorsionType(at1, at2, at3, at4, torsionType);
176	gezelter	1930	}
177
178	gezelter	2204	}
179	gezelter	1930
180	gezelter	2204	TorsionTypesSectionParser::TorsionTypeEnum TorsionTypesSectionParser::getTorsionTypeEnum(const std::string& str) {
181	gezelter	1930	std::map<std::string, TorsionTypeEnum>::iterator i;
182			i = stringToEnumMap_.find(str);
183
184			return i == stringToEnumMap_.end() ? TorsionTypesSectionParser::ttUnknown : i->second;
185	gezelter	2204	}
186	gezelter	1930
187			} //end namespace oopse
188
189
190