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
#	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	#include "io/LennardJonesAtomTypesSectionParser.hpp"
43	#include "types/AtomType.hpp"
44	#include "UseTheForce/ForceField.hpp"
45	#include "utils/simError.h"
46	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	//in LennardJonesAtomTypesSectionParser, a line at least contains 3 tokens
57	//atomTypeName, epsilon and sigma
58	if (nTokens < 3) {
59	sprintf(painCave.errMsg, "LennardJonesAtomTypesSectionParser Error: Not enough tokens at line %d\n",
60	lineNo);
61	painCave.isFatal = 1;
62	simError();
63	} 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	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	atomType->addProperty(new LJParamGenericData("LennardJones", ljParam));
82	atomType->setLennardJones();
83	}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	}
88
89	}
90
91
92	}
93
94	} //end namespace oopse
95