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root/OpenMD/branches/development/src/UseTheForce/SC_FF.cpp
Revision: 1280
Committed: Wed Jul 16 02:07:09 2008 UTC (16 years, 9 months ago) by gezelter
Original Path: trunk/src/UseTheForce/SC_FF.cpp
File size: 5255 byte(s)
Log Message:
All your base are belong to us!

File Contents

# User Rev Content
1 chuckv 728 /*
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     * SC_FF.cpp
43     * OOPSE-2.0
44     *
45     * Created by Charles F. Vardeman II on 11/9/05.
46     * @author Charles F. Vardeman II
47 gezelter 1280 * @version $Id: SC_FF.cpp,v 1.10 2008-07-16 02:07:09 gezelter Exp $
48 chuckv 728 *
49     */
50    
51     #include "UseTheForce/SC_FF.hpp"
52     #include "UseTheForce/DarkSide/eam_interface.h"
53     #include "UseTheForce/DarkSide/lj_interface.h"
54     #include "UseTheForce/DarkSide/sticky_interface.h"
55     #include "UseTheForce/DarkSide/suttonchen_interface.h"
56     #include "UseTheForce/ForceFieldFactory.hpp"
57 gezelter 1280 #include "io/OptionSectionParser.hpp"
58     #include "io/BaseAtomTypesSectionParser.hpp"
59 chuckv 728 #include "io/AtomTypesSectionParser.hpp"
60     #include "io/SCAtomTypesSectionParser.hpp"
61     #include "UseTheForce/ForceFieldCreator.hpp"
62     #include "utils/simError.h"
63     namespace oopse {
64    
65     SC_FF::SC_FF(){
66    
67     //set default force field filename
68 chuckv 867 setForceFieldFileName("SuttonChen.frc");
69 chuckv 728
70     //the order of adding section parsers are important
71 chuckv 802 //OptionSectionParser must come first to set options for other parsers
72 chuckv 728 //DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since
73     //These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create
74     //AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass
75     //of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the
76     //"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not
77     //important. AtomTypesSectionParser should be added before other atom type section parsers.
78     //Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser.
79     //The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are
80     //not important.
81 tim 837 spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
82 gezelter 1280 spMan_.push_back(new BaseAtomTypesSectionParser());
83 chuckv 728 spMan_.push_back(new AtomTypesSectionParser());
84 tim 837 spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_));
85 chuckv 728
86     }
87    
88     void SC_FF::parse(const std::string& filename) {
89     ifstrstream* ffStream;
90     ffStream = openForceFieldFile(filename);
91    
92     spMan_.parse(*ffStream, *this);
93    
94     ForceField::AtomTypeContainer::MapTypeIterator i;
95     AtomType* at;
96    
97 chuckv 793 // Set forcefield options
98    
99 chuckv 728 for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
100 gezelter 1280 // useBase sets the responsibilities, and these have to be done
101     // after the atomTypes and Base types have all been scanned:
102    
103     std::vector<AtomType*> ayb = at->allYourBase();
104     if (ayb.size() > 1) {
105     for (int j = ayb.size()-1; j > 0; j--) {
106    
107     ayb[j-1]->useBase(ayb[j]);
108    
109     }
110     }
111 chuckv 728 at->makeFortranAtomType();
112     }
113    
114 chuckv 793
115 chuckv 728 for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
116     at->complete();
117     }
118    
119     delete ffStream;
120     }
121    
122    
123     SC_FF::~SC_FF(){
124     // We need to clean up the fortran side so we don't have bad things happen if
125 chuckv 735 // we try to create a second SC force field.
126 chuckv 728 destroySCTypes();
127     }
128     } //end namespace oopse
129