src/io/StickyAtomTypesSectionParser.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/StickyAtomTypesSectionParser.hpp"
#include "types/AtomType.hpp"
#include "types/DirectionalAtomType.hpp"
#include "UseTheForce/ForceField.hpp"

namespace oopse {

StickyAtomTypesSectionParser::StickyAtomTypesSectionParser() {
    setSectionName("StickyAtomTypes");
}

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

    //in AtomTypeSection, a line at least contains 8 tokens
    //atomTypeName and 7 different sticky parameters
    if (nTokens < 8)  {
                      
    } else {

        std::string atomTypeName = tokenizer.nextToken();    
        AtomType* atomType = ff.getAtomType(atomTypeName);

        if (atomType != NULL) {
            DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
            
            if (dAtomType != NULL) {
                StickyParam sticky;
                sticky.w0 = tokenizer.nextTokenAsDouble();
                sticky.v0 = tokenizer.nextTokenAsDouble();
                sticky.v0p = tokenizer.nextTokenAsDouble();
                sticky.rl = tokenizer.nextTokenAsDouble();
                sticky.ru = tokenizer.nextTokenAsDouble();
                sticky.rlp = tokenizer.nextTokenAsDouble();
                sticky.rup = tokenizer.nextTokenAsDouble();   
                
                dAtomType->addProperty(new StickyParamGenericData("Sticky", sticky));
                dAtomType->setSticky();
            } else {
                std::cerr << "StickyAtomTypesSectionParser Warning:" << std::endl;
            }
        } else {
            std::cerr << "StickyAtomTypesSectionParser Error: Can not find matched AtomType " << atomTypeName << std::endl;
        }
                       
    }    


}

} //end namespace oopse


Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	3943 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	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/StickyAtomTypesSectionParser.hpp"
43	#include "types/AtomType.hpp"
44	#include "types/DirectionalAtomType.hpp"
45	#include "UseTheForce/ForceField.hpp"
46
47	namespace oopse {
48
49	StickyAtomTypesSectionParser::StickyAtomTypesSectionParser() {
50	setSectionName("StickyAtomTypes");
51	}
52
53	void StickyAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
54	StringTokenizer tokenizer(line);
55	int nTokens = tokenizer.countTokens();
56
57	//in AtomTypeSection, a line at least contains 8 tokens
58	//atomTypeName and 7 different sticky parameters
59	if (nTokens < 8) {
60
61	} else {
62
63	std::string atomTypeName = tokenizer.nextToken();
64	AtomType* atomType = ff.getAtomType(atomTypeName);
65
66	if (atomType != NULL) {
67	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
68
69	if (dAtomType != NULL) {
70	StickyParam sticky;
71	sticky.w0 = tokenizer.nextTokenAsDouble();
72	sticky.v0 = tokenizer.nextTokenAsDouble();
73	sticky.v0p = tokenizer.nextTokenAsDouble();
74	sticky.rl = tokenizer.nextTokenAsDouble();
75	sticky.ru = tokenizer.nextTokenAsDouble();
76	sticky.rlp = tokenizer.nextTokenAsDouble();
77	sticky.rup = tokenizer.nextTokenAsDouble();
78
79	dAtomType->addProperty(new StickyParamGenericData("Sticky", sticky));
80	dAtomType->setSticky();
81	} else {
82	std::cerr << "StickyAtomTypesSectionParser Warning:" << std::endl;
83	}
84	} else {
85	std::cerr << "StickyAtomTypesSectionParser Error: Can not find matched AtomType " << atomTypeName << std::endl;
86	}
87
88	}
89
90
91	}
92
93	} //end namespace oopse
94
95
96