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root/group/trunk/OOPSE-4/src/UseTheForce/SHAPES_FF.cpp
Revision: 2500
Committed: Wed Dec 7 23:10:53 2005 UTC (18 years, 7 months ago) by chuckv
File size: 5465 byte(s)
Log Message:
This should really break things.... Started adding support for ForceOptions to section parsers.

File Contents

# 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 "UseTheForce/DarkSide/shapes_interface.h"
43 #include "UseTheForce/DarkSide/lj_interface.h"
44 #include "UseTheForce/DarkSide/sticky_interface.h"
45 #include "UseTheForce/ForceFieldFactory.hpp"
46 #include "io/OptionSectionParser.hpp"
47 #include "io/DirectionalAtomTypesSectionParser.hpp"
48 #include "io/AtomTypesSectionParser.hpp"
49 #include "io/LennardJonesAtomTypesSectionParser.hpp"
50 #include "io/ChargeAtomTypesSectionParser.hpp"
51 #include "io/MultipoleAtomTypesSectionParser.hpp"
52 #include "io/ShapeAtomTypesSectionParser.hpp"
53 #include "io/StickyAtomTypesSectionParser.hpp"
54 #include "io/BondTypesSectionParser.hpp"
55 #include "io/BendTypesSectionParser.hpp"
56 #include "io/TorsionTypesSectionParser.hpp"
57 #include "UseTheForce/ForceFieldCreator.hpp"
58 #include "UseTheForce/SHAPES_FF.hpp"
59 #include "utils/simError.h"
60 namespace oopse {
61
62 SHAPES_FF::SHAPES_FF(){
63
64 //set default force field filename
65 setForceFieldFileName("Shapes.frc");
66
67 //The ordering of section parsers is important
68 //DirectionalAtomTypesSectionParser should be before
69 //AtomTypesSectionParser since these two section parsers will actually
70 //create "real" AtomTypes (AtomTypesSectionParser will create AtomType
71 //and DirectionalAtomTypesSectionParser will create DirectionalAtomType
72 //which is a subclass of AtomType, therefore it should come first). Other
73 //AtomTypes Section Parser will not create the "real" AtomType, they only
74 //add and set some attribute of the AtomType. Thus the ordering of these
75 //are not important. AtomTypesSectionParser should be added before other atom
76 //type section parsers. Make sure they are added after
77 //DirectionalAtomTypesSectionParser and AtomTypesSectionParser. The order
78 //of BondTypesSectionParser, BendTypesSectionParser and
79 //TorsionTypesSectionParser are not important.
80 spMan_.push_back(new OptionSectionParser(forceFieldOptions_));
81 spMan_.push_back(new ShapeAtomTypesSectionParser());
82 spMan_.push_back(new DirectionalAtomTypesSectionParser());
83 spMan_.push_back(new AtomTypesSectionParser());
84 spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_));
85 spMan_.push_back(new ChargeAtomTypesSectionParser());
86 spMan_.push_back(new MultipoleAtomTypesSectionParser());
87 spMan_.push_back(new StickyAtomTypesSectionParser());
88 spMan_.push_back(new BondTypesSectionParser());
89 spMan_.push_back(new BendTypesSectionParser());
90 spMan_.push_back(new TorsionTypesSectionParser());
91
92 }
93
94 SHAPES_FF::~SHAPES_FF(){
95 // We need to clean up the fortran side so we don't have bad things happen if
96 // we try to create a second EAM force field.
97 destroyShapeTypes();
98 }
99
100 void SHAPES_FF::parse(const std::string& filename) {
101 ifstrstream* ffStream;
102 ffStream = openForceFieldFile(filename);
103
104 spMan_.parse(*ffStream, *this);
105
106 ForceField::AtomTypeContainer::MapTypeIterator i;
107 AtomType* at;
108
109 for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
110 at->makeFortranAtomType();
111 }
112
113 for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) {
114 at->complete();
115 }
116
117 int isError = 0;
118 completeShapeFF(&isError);
119
120 delete ffStream;
121 }
122
123
124 // double SHAPES_FF::getRcutFromAtomType(AtomType* at){
125 // }
126 } //end namespace oopse
127