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root/OpenMD/trunk/src/hydrodynamics/HydroProp.cpp
Revision: 981
Committed: Mon Jun 5 18:24:45 2006 UTC (19 years, 5 months ago) by gezelter
File size: 5162 byte(s)
Log Message: 
Massive changes for GB code with multiple ellipsoid types (a la
Cleaver's paper).

Also, changes in hydrodynamics code to make HydroProp a somewhat
smarter class (rather than just a struct).

File Contents

# User Rev Content
1 gezelter 981 /*
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 "hydrodynamics/HydroProp.hpp"
43     #include "utils/StringTokenizer.hpp"
44     #include "math/CholeskyDecomposition.hpp"
45    
46     namespace oopse {
47    
48     HydroProp::HydroProp(){
49     hasCOR = false;
50     hasXi = false;
51     }
52    
53     HydroProp::HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D) : cor_(cor), Xi_(Xi), D_(D){
54     hasCOR = true;
55     hasXi = true;
56     }
57    
58     HydroProp::HydroProp(const std::string frictionLine) {
59    
60     StringTokenizer tokenizer(frictionLine);
61     if (tokenizer.countTokens() >= 40) {
62     name_ = tokenizer.nextToken();
63     cor_[0] = tokenizer.nextTokenAsDouble();
64     cor_[1] = tokenizer.nextTokenAsDouble();
65     cor_[2] = tokenizer.nextTokenAsDouble();
66    
67     Xitt_(0,0) = tokenizer.nextTokenAsDouble();
68     Xitt_(0,1) = tokenizer.nextTokenAsDouble();
69     Xitt_(0,2) = tokenizer.nextTokenAsDouble();
70     Xitt_(1,0) = tokenizer.nextTokenAsDouble();
71     Xitt_(1,1) = tokenizer.nextTokenAsDouble();
72     Xitt_(1,2) = tokenizer.nextTokenAsDouble();
73     Xitt_(2,0) = tokenizer.nextTokenAsDouble();
74     Xitt_(2,1) = tokenizer.nextTokenAsDouble();
75     Xitt_(2,2) = tokenizer.nextTokenAsDouble();
76    
77     Xirt_(0,0) = tokenizer.nextTokenAsDouble();
78     Xirt_(0,1) = tokenizer.nextTokenAsDouble();
79     Xirt_(0,2) = tokenizer.nextTokenAsDouble();
80     Xirt_(1,0) = tokenizer.nextTokenAsDouble();
81     Xirt_(1,1) = tokenizer.nextTokenAsDouble();
82     Xirt_(1,2) = tokenizer.nextTokenAsDouble();
83     Xirt_(2,0) = tokenizer.nextTokenAsDouble();
84     Xirt_(2,1) = tokenizer.nextTokenAsDouble();
85     Xirt_(2,2) = tokenizer.nextTokenAsDouble();
86    
87     Xitr_(0,0) = tokenizer.nextTokenAsDouble();
88     Xitr_(0,1) = tokenizer.nextTokenAsDouble();
89     Xitr_(0,2) = tokenizer.nextTokenAsDouble();
90     Xitr_(1,0) = tokenizer.nextTokenAsDouble();
91     Xitr_(1,1) = tokenizer.nextTokenAsDouble();
92     Xitr_(1,2) = tokenizer.nextTokenAsDouble();
93     Xitr_(2,0) = tokenizer.nextTokenAsDouble();
94     Xitr_(2,1) = tokenizer.nextTokenAsDouble();
95     Xitr_(2,2) = tokenizer.nextTokenAsDouble();
96    
97     Xirr_(0,0) = tokenizer.nextTokenAsDouble();
98     Xirr_(0,1) = tokenizer.nextTokenAsDouble();
99     Xirr_(0,2) = tokenizer.nextTokenAsDouble();
100     Xirr_(1,0) = tokenizer.nextTokenAsDouble();
101     Xirr_(1,1) = tokenizer.nextTokenAsDouble();
102     Xirr_(1,2) = tokenizer.nextTokenAsDouble();
103     Xirr_(2,0) = tokenizer.nextTokenAsDouble();
104     Xirr_(2,1) = tokenizer.nextTokenAsDouble();
105     Xirr_(2,2) = tokenizer.nextTokenAsDouble();
106    
107     Xi_.setSubMatrix(0, 0, Xitt_);
108     Xi_.setSubMatrix(0, 3, Xirt_);
109     Xi_.setSubMatrix(3, 0, Xitr_);
110     Xi_.setSubMatrix(3, 3, Xirr_);
111    
112     CholeskyDecomposition(Xi_, S_);
113    
114     }
115     }
116    
117     void HydroProp::complete() {
118    
119     if (hasXi) {
120     for (int i1 = 0; i1 < 3; i1++) {
121     for (int j1 = 0; j1 < 3; j1++) {
122     Xitt_(i1,j1) = Xi_(i1,j1);
123     Xirt_(i1,j1) = Xi_(i1,j1+3);
124     Xitr_(i1,j1) = Xi_(i1+3,j1);
125     Xirr_(i1,j1) = Xi_(i1+3,j1+3);
126     }
127     }
128     CholeskyDecomposition(Xi_, S_);
129     }
130     }
131    
132     }
133