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"
#include "utils/simError.h"
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)  {
        sprintf(painCave.errMsg, "StickyAtomTypesSectionParser 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) {
            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 {
                sprintf(painCave.errMsg, "StickyAtomTypesSectionParser Error: Not enough tokens at line %d\n",
                        lineNo);
                painCave.isFatal = 1;
                simError();            
                std::cerr << "StickyAtomTypesSectionParser Warning:" << std::endl;
            }
        } else {
            sprintf(painCave.errMsg, "StickyAtomTypesSectionParser Error: Can not find matched AtomType %s\n",
                    atomTypeName.c_str());
            painCave.isFatal = 1;
            simError();    
        
        }
                       
    }    


}

} //end namespace oopse


Revision:	1957
Committed:	Tue Jan 25 17:45:23 2005 UTC (19 years, 5 months ago) by tim
File size:	4470 byte(s)
Log Message:	(1) complete section parser's error message (2) add GhostTorsion (3) accumulate inertial tensor from the directional atoms before calculate rigidbody's inertial tensor
#	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/StickyAtomTypesSectionParser.hpp"
43			#include "types/AtomType.hpp"
44			#include "types/DirectionalAtomType.hpp"
45			#include "UseTheForce/ForceField.hpp"
46	tim	1957	#include "utils/simError.h"
47	gezelter	1930	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	tim	1957	sprintf(painCave.errMsg, "StickyAtomTypesSectionParser Error: Not enough tokens at line %d\n",
61			lineNo);
62			painCave.isFatal = 1;
63			simError();
64	gezelter	1930	} else {
65
66			std::string atomTypeName = tokenizer.nextToken();
67			AtomType* atomType = ff.getAtomType(atomTypeName);
68
69			if (atomType != NULL) {
70			DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
71
72			if (dAtomType != NULL) {
73			StickyParam sticky;
74			sticky.w0 = tokenizer.nextTokenAsDouble();
75			sticky.v0 = tokenizer.nextTokenAsDouble();
76			sticky.v0p = tokenizer.nextTokenAsDouble();
77			sticky.rl = tokenizer.nextTokenAsDouble();
78			sticky.ru = tokenizer.nextTokenAsDouble();
79			sticky.rlp = tokenizer.nextTokenAsDouble();
80			sticky.rup = tokenizer.nextTokenAsDouble();
81
82			dAtomType->addProperty(new StickyParamGenericData("Sticky", sticky));
83			dAtomType->setSticky();
84			} else {
85	tim	1957	sprintf(painCave.errMsg, "StickyAtomTypesSectionParser Error: Not enough tokens at line %d\n",
86			lineNo);
87			painCave.isFatal = 1;
88			simError();
89	gezelter	1930	std::cerr << "StickyAtomTypesSectionParser Warning:" << std::endl;
90			}
91			} else {
92	tim	1957	sprintf(painCave.errMsg, "StickyAtomTypesSectionParser Error: Can not find matched AtomType %s\n",
93			atomTypeName.c_str());
94			painCave.isFatal = 1;
95			simError();
96
97	gezelter	1930	}
98
99			}
100
101
102			}
103
104			} //end namespace oopse
105
106
107