src/io/SCAtomTypesSectionParser.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.
 *
 *
 *  SCAtomTypesSectionParser.cpp
 *  OOPSE-2.0
 *
 *  Created by Charles F. Vardeman II on 11/14/05.
 *  @author  Charles F. Vardeman II 
 *  @version $Id: SCAtomTypesSectionParser.cpp,v 1.1 2005-11-14 21:29:27 chuckv Exp $
 *
 */

#include "io/SCAtomTypesSectionParser.hpp"
#include "types/AtomType.hpp"
#include "UseTheForce/ForceField.hpp"
#include "utils/simError.h"
namespace oopse {
  
  SCAtomTypesSectionParser::SCAtomTypesSectionParser() {
    setSectionName("SCAtomTypes");
  }
  
  void SCAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();    
    
    //in SCAtomTypesSectionParser, a line at least contains 6 tokens
    //atomTypeName, epsilon,c,m,n and alpha
    if (nTokens < 6)  {
      sprintf(painCave.errMsg, "SCAtomTypesSectionParser Error: Not enough tokens at line %d\n",
              lineNo);
      painCave.isFatal = 1;
      simError();                    
    } else {
      
      std::string atomTypeName = tokenizer.nextToken();    
      AtomType* atomType = ff.getAtomType(atomTypeName);
      
      if (atomType != NULL) {
        SCParam scParam;                        
        scParam.epsilon = tokenizer.nextTokenAsDouble();
        scParam.c = tokenizer.nextTokenAsDouble();
        scParam.m = tokenizer.nextTokenAsDouble();
        scParam.n = tokenizer.nextTokenAsDouble();
        scParam.alpha = tokenizer.nextTokenAsDouble();
        
        
        
          
        atomType->addProperty(new SCParamGenericData("SC", scParam));
        atomType->setLennardJones();
      }else {
        sprintf(painCave.errMsg, "SCAtomTypesSectionParser Error: Atom Type [%s] is not created yet\n", atomTypeName.c_str());
        painCave.isFatal = 1;
        simError();    
      }
      
    }    
    
    
  }
  
} //end namespace oopse

Revision:	2427
Committed:	Mon Nov 14 21:29:36 2005 UTC (18 years, 7 months ago) by chuckv
File size:	3970 byte(s)
Log Message:	Sutton-Chen almost done. Just need to fix do_forces to use Sutton-Chen.
#	User	Rev	Content
1	chuckv	2427	/*
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			* SCAtomTypesSectionParser.cpp
43			* OOPSE-2.0
44			*
45			* Created by Charles F. Vardeman II on 11/14/05.
46			* @author Charles F. Vardeman II
47			* @version $Id: SCAtomTypesSectionParser.cpp,v 1.1 2005-11-14 21:29:27 chuckv Exp $
48			*
49			*/
50
51			#include "io/SCAtomTypesSectionParser.hpp"
52			#include "types/AtomType.hpp"
53			#include "UseTheForce/ForceField.hpp"
54			#include "utils/simError.h"
55			namespace oopse {
56
57			SCAtomTypesSectionParser::SCAtomTypesSectionParser() {
58			setSectionName("SCAtomTypes");
59			}
60
61			void SCAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
62			StringTokenizer tokenizer(line);
63			int nTokens = tokenizer.countTokens();
64
65			//in SCAtomTypesSectionParser, a line at least contains 6 tokens
66			//atomTypeName, epsilon,c,m,n and alpha
67			if (nTokens < 6) {
68			sprintf(painCave.errMsg, "SCAtomTypesSectionParser Error: Not enough tokens at line %d\n",
69			lineNo);
70			painCave.isFatal = 1;
71			simError();
72			} else {
73
74			std::string atomTypeName = tokenizer.nextToken();
75			AtomType* atomType = ff.getAtomType(atomTypeName);
76
77			if (atomType != NULL) {
78			SCParam scParam;
79			scParam.epsilon = tokenizer.nextTokenAsDouble();
80			scParam.c = tokenizer.nextTokenAsDouble();
81			scParam.m = tokenizer.nextTokenAsDouble();
82			scParam.n = tokenizer.nextTokenAsDouble();
83			scParam.alpha = tokenizer.nextTokenAsDouble();
84
85
86
87
88			atomType->addProperty(new SCParamGenericData("SC", scParam));
89			atomType->setLennardJones();
90			}else {
91			sprintf(painCave.errMsg, "SCAtomTypesSectionParser Error: Atom Type [%s] is not created yet\n", atomTypeName.c_str());
92			painCave.isFatal = 1;
93			simError();
94			}
95
96			}
97
98
99			}
100
101			} //end namespace oopse
102