src/io/LennardJonesAtomTypesSectionParser.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/LennardJonesAtomTypesSectionParser.hpp"
#include "io/ForceFieldOptions.hpp"
#include "types/AtomType.hpp"
#include "UseTheForce/ForceField.hpp"
#include "utils/simError.h"
namespace oopse {

  LennardJonesAtomTypesSectionParser::LennardJonesAtomTypesSectionParser(ForceFieldOptions& options) : options_(options) {
    setSectionName("LennardJonesAtomTypes");
  }

  void LennardJonesAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();    

    //in LennardJonesAtomTypesSectionParser, a line at least contains 3 tokens
    //atomTypeName, epsilon and sigma
    if (nTokens < 3)  {
      sprintf(painCave.errMsg, "LennardJonesAtomTypesSectionParser 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) {
        LJParam ljParam;                        
        ljParam.epsilon = tokenizer.nextTokenAsDouble();
        ljParam.sigma = tokenizer.nextTokenAsDouble();
        ljParam.soft_pot = 0;
  
  ljParam.epsilon *= options_.getEnergyUnitScaling();
  ljParam.sigma   *= options_.getDistanceUnitScaling();
  
        if (tokenizer.hasMoreTokens()) {
          std::string pot_type = tokenizer.nextToken();
          if (pot_type == "soft") {
            ljParam.soft_pot = 1;
          }
        }
            
        atomType->addProperty(new LJParamGenericData("LennardJones", ljParam));
        atomType->setLennardJones();
      }else {
        sprintf(painCave.errMsg, "LennardJonesAtomTypesSectionParser Error: Atom Type [%s] is not created yet\n", atomTypeName.c_str());
        painCave.isFatal = 1;
        simError();    
      }
                       
    }    


  }

} //end namespace oopse

Revision:	2498
Committed:	Wed Dec 7 23:00:26 2005 UTC (18 years, 7 months ago) by chuckv
File size:	3936 byte(s)
Log Message:	Added forceOptions to section parser
#	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/LennardJonesAtomTypesSectionParser.hpp"
43	chuckv	2498	#include "io/ForceFieldOptions.hpp"
44	gezelter	1930	#include "types/AtomType.hpp"
45			#include "UseTheForce/ForceField.hpp"
46	tim	1957	#include "utils/simError.h"
47	gezelter	1930	namespace oopse {
48
49	chuckv	2498	LennardJonesAtomTypesSectionParser::LennardJonesAtomTypesSectionParser(ForceFieldOptions& options) : options_(options) {
50	gezelter	1930	setSectionName("LennardJonesAtomTypes");
51	gezelter	2204	}
52	gezelter	1930
53	gezelter	2204	void LennardJonesAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
54	gezelter	1930	StringTokenizer tokenizer(line);
55			int nTokens = tokenizer.countTokens();
56
57	tim	2062	//in LennardJonesAtomTypesSectionParser, a line at least contains 3 tokens
58			//atomTypeName, epsilon and sigma
59	gezelter	1930	if (nTokens < 3) {
60	gezelter	2204	sprintf(painCave.errMsg, "LennardJonesAtomTypesSectionParser Error: Not enough tokens at line %d\n",
61			lineNo);
62			painCave.isFatal = 1;
63			simError();
64	gezelter	1930	} else {
65
66	gezelter	2204	std::string atomTypeName = tokenizer.nextToken();
67			AtomType* atomType = ff.getAtomType(atomTypeName);
68	gezelter	1930
69	gezelter	2204	if (atomType != NULL) {
70			LJParam ljParam;
71			ljParam.epsilon = tokenizer.nextTokenAsDouble();
72			ljParam.sigma = tokenizer.nextTokenAsDouble();
73			ljParam.soft_pot = 0;
74	chuckv	2498
75			ljParam.epsilon *= options_.getEnergyUnitScaling();
76			ljParam.sigma *= options_.getDistanceUnitScaling();
77
78	gezelter	2204	if (tokenizer.hasMoreTokens()) {
79			std::string pot_type = tokenizer.nextToken();
80			if (pot_type == "soft") {
81			ljParam.soft_pot = 1;
82			}
83			}
84	tim	2062
85	gezelter	2204	atomType->addProperty(new LJParamGenericData("LennardJones", ljParam));
86			atomType->setLennardJones();
87			}else {
88			sprintf(painCave.errMsg, "LennardJonesAtomTypesSectionParser Error: Atom Type [%s] is not created yet\n", atomTypeName.c_str());
89			painCave.isFatal = 1;
90			simError();
91			}
92	gezelter	1930
93			}
94
95
96	gezelter	2204	}
97	gezelter	1930
98			} //end namespace oopse
99