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.
#	Content
1	/*
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