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

LennardJonesAtomTypesSectionParser::LennardJonesAtomTypesSectionParser() {
    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;

            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:	2062
Committed:	Fri Feb 25 21:22:00 2005 UTC (19 years, 4 months ago) by tim
File size:	3932 byte(s)
Log Message:	adding soft potential to LJ Module
#	User	Rev	Content
1	gezelter	1930	/*
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/LennardJonesAtomTypesSectionParser.hpp"
43			#include "types/AtomType.hpp"
44			#include "UseTheForce/ForceField.hpp"
45	tim	1957	#include "utils/simError.h"
46	gezelter	1930	namespace oopse {
47
48			LennardJonesAtomTypesSectionParser::LennardJonesAtomTypesSectionParser() {
49			setSectionName("LennardJonesAtomTypes");
50			}
51
52			void LennardJonesAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
53			StringTokenizer tokenizer(line);
54			int nTokens = tokenizer.countTokens();
55
56	tim	2062	//in LennardJonesAtomTypesSectionParser, a line at least contains 3 tokens
57			//atomTypeName, epsilon and sigma
58	gezelter	1930	if (nTokens < 3) {
59	tim	1957	sprintf(painCave.errMsg, "LennardJonesAtomTypesSectionParser Error: Not enough tokens at line %d\n",
60			lineNo);
61			painCave.isFatal = 1;
62			simError();
63	gezelter	1930	} else {
64
65			std::string atomTypeName = tokenizer.nextToken();
66			AtomType* atomType = ff.getAtomType(atomTypeName);
67
68			if (atomType != NULL) {
69			LJParam ljParam;
70			ljParam.epsilon = tokenizer.nextTokenAsDouble();
71			ljParam.sigma = tokenizer.nextTokenAsDouble();
72	tim	2062	ljParam.soft_pot = 0;
73
74			if (tokenizer.hasMoreTokens()) {
75			std::string pot_type = tokenizer.nextToken();
76			if (pot_type == "soft") {
77			ljParam.soft_pot = 1;
78			}
79			}
80
81	gezelter	1930	atomType->addProperty(new LJParamGenericData("LennardJones", ljParam));
82			atomType->setLennardJones();
83	tim	2008	}else {
84			sprintf(painCave.errMsg, "LennardJonesAtomTypesSectionParser Error: Atom Type [%s] is not created yet\n", atomTypeName.c_str());
85			painCave.isFatal = 1;
86			simError();
87	gezelter	1930	}
88
89			}
90
91
92			}
93
94			} //end namespace oopse
95