src/hydrodynamics/HydroProp.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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include "hydrodynamics/HydroProp.hpp"
#include "utils/StringTokenizer.hpp"
#include "math/CholeskyDecomposition.hpp"

namespace OpenMD {
  
  HydroProp::HydroProp(){    
    hasCOR = false;
    hasXi = false;
  }
  
  HydroProp::HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D) : cor_(cor), Xi_(Xi), D_(D){
    hasCOR = true;
    hasXi = true;
  }
  
  HydroProp::HydroProp(const std::string frictionLine) {
    
    StringTokenizer tokenizer(frictionLine);
    if (tokenizer.countTokens() >= 40) {
      name_ = tokenizer.nextToken();
      cor_[0] = tokenizer.nextTokenAsDouble();
      cor_[1] = tokenizer.nextTokenAsDouble();
      cor_[2] = tokenizer.nextTokenAsDouble();
      
      Xitt_(0,0) = tokenizer.nextTokenAsDouble();
      Xitt_(0,1) = tokenizer.nextTokenAsDouble();
      Xitt_(0,2) = tokenizer.nextTokenAsDouble();
      Xitt_(1,0) = tokenizer.nextTokenAsDouble();
      Xitt_(1,1) = tokenizer.nextTokenAsDouble();
      Xitt_(1,2) = tokenizer.nextTokenAsDouble();
      Xitt_(2,0) = tokenizer.nextTokenAsDouble();
      Xitt_(2,1) = tokenizer.nextTokenAsDouble();
      Xitt_(2,2) = tokenizer.nextTokenAsDouble();
      
      Xirt_(0,0) = tokenizer.nextTokenAsDouble();
      Xirt_(0,1) = tokenizer.nextTokenAsDouble();
      Xirt_(0,2) = tokenizer.nextTokenAsDouble();
      Xirt_(1,0) = tokenizer.nextTokenAsDouble();
      Xirt_(1,1) = tokenizer.nextTokenAsDouble();
      Xirt_(1,2) = tokenizer.nextTokenAsDouble();
      Xirt_(2,0) = tokenizer.nextTokenAsDouble();
      Xirt_(2,1) = tokenizer.nextTokenAsDouble();
      Xirt_(2,2) = tokenizer.nextTokenAsDouble();
      
      Xitr_(0,0) = tokenizer.nextTokenAsDouble();
      Xitr_(0,1) = tokenizer.nextTokenAsDouble();
      Xitr_(0,2) = tokenizer.nextTokenAsDouble();
      Xitr_(1,0) = tokenizer.nextTokenAsDouble();
      Xitr_(1,1) = tokenizer.nextTokenAsDouble();
      Xitr_(1,2) = tokenizer.nextTokenAsDouble();
      Xitr_(2,0) = tokenizer.nextTokenAsDouble();
      Xitr_(2,1) = tokenizer.nextTokenAsDouble();
      Xitr_(2,2) = tokenizer.nextTokenAsDouble();
      
      Xirr_(0,0) = tokenizer.nextTokenAsDouble();
      Xirr_(0,1) = tokenizer.nextTokenAsDouble();
      Xirr_(0,2) = tokenizer.nextTokenAsDouble();
      Xirr_(1,0) = tokenizer.nextTokenAsDouble();
      Xirr_(1,1) = tokenizer.nextTokenAsDouble();
      Xirr_(1,2) = tokenizer.nextTokenAsDouble();
      Xirr_(2,0) = tokenizer.nextTokenAsDouble();
      Xirr_(2,1) = tokenizer.nextTokenAsDouble();
      Xirr_(2,2) = tokenizer.nextTokenAsDouble();     
  
      Xi_.setSubMatrix(0, 0, Xitt_);
      Xi_.setSubMatrix(0, 3, Xirt_);
      Xi_.setSubMatrix(3, 0, Xitr_);
      Xi_.setSubMatrix(3, 3, Xirr_);

      CholeskyDecomposition(Xi_, S_);            

    }
  }

  void HydroProp::complete() {
    
    if (hasXi) {
      for (int i1 = 0; i1 < 3; i1++) {
        for (int j1 = 0; j1 < 3; j1++) {
          Xitt_(i1,j1) = Xi_(i1,j1);
          Xirt_(i1,j1) = Xi_(i1,j1+3);
          Xitr_(i1,j1) = Xi_(i1+3,j1);
          Xirr_(i1,j1) = Xi_(i1+3,j1+3);
        }
      }
      CholeskyDecomposition(Xi_, S_);
    }      
  }

}

Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	5271 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	981	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	981	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	981	*/
42
43			#include "hydrodynamics/HydroProp.hpp"
44			#include "utils/StringTokenizer.hpp"
45			#include "math/CholeskyDecomposition.hpp"
46
47	gezelter	1390	namespace OpenMD {
48	gezelter	981
49			HydroProp::HydroProp(){
50			hasCOR = false;
51			hasXi = false;
52			}
53
54			HydroProp::HydroProp(Vector3d cor, Mat6x6d Xi, Mat6x6d D) : cor_(cor), Xi_(Xi), D_(D){
55			hasCOR = true;
56			hasXi = true;
57			}
58
59			HydroProp::HydroProp(const std::string frictionLine) {
60
61			StringTokenizer tokenizer(frictionLine);
62			if (tokenizer.countTokens() >= 40) {
63			name_ = tokenizer.nextToken();
64			cor_[0] = tokenizer.nextTokenAsDouble();
65			cor_[1] = tokenizer.nextTokenAsDouble();
66			cor_[2] = tokenizer.nextTokenAsDouble();
67
68			Xitt_(0,0) = tokenizer.nextTokenAsDouble();
69			Xitt_(0,1) = tokenizer.nextTokenAsDouble();
70			Xitt_(0,2) = tokenizer.nextTokenAsDouble();
71			Xitt_(1,0) = tokenizer.nextTokenAsDouble();
72			Xitt_(1,1) = tokenizer.nextTokenAsDouble();
73			Xitt_(1,2) = tokenizer.nextTokenAsDouble();
74			Xitt_(2,0) = tokenizer.nextTokenAsDouble();
75			Xitt_(2,1) = tokenizer.nextTokenAsDouble();
76			Xitt_(2,2) = tokenizer.nextTokenAsDouble();
77
78			Xirt_(0,0) = tokenizer.nextTokenAsDouble();
79			Xirt_(0,1) = tokenizer.nextTokenAsDouble();
80			Xirt_(0,2) = tokenizer.nextTokenAsDouble();
81			Xirt_(1,0) = tokenizer.nextTokenAsDouble();
82			Xirt_(1,1) = tokenizer.nextTokenAsDouble();
83			Xirt_(1,2) = tokenizer.nextTokenAsDouble();
84			Xirt_(2,0) = tokenizer.nextTokenAsDouble();
85			Xirt_(2,1) = tokenizer.nextTokenAsDouble();
86			Xirt_(2,2) = tokenizer.nextTokenAsDouble();
87
88			Xitr_(0,0) = tokenizer.nextTokenAsDouble();
89			Xitr_(0,1) = tokenizer.nextTokenAsDouble();
90			Xitr_(0,2) = tokenizer.nextTokenAsDouble();
91			Xitr_(1,0) = tokenizer.nextTokenAsDouble();
92			Xitr_(1,1) = tokenizer.nextTokenAsDouble();
93			Xitr_(1,2) = tokenizer.nextTokenAsDouble();
94			Xitr_(2,0) = tokenizer.nextTokenAsDouble();
95			Xitr_(2,1) = tokenizer.nextTokenAsDouble();
96			Xitr_(2,2) = tokenizer.nextTokenAsDouble();
97
98			Xirr_(0,0) = tokenizer.nextTokenAsDouble();
99			Xirr_(0,1) = tokenizer.nextTokenAsDouble();
100			Xirr_(0,2) = tokenizer.nextTokenAsDouble();
101			Xirr_(1,0) = tokenizer.nextTokenAsDouble();
102			Xirr_(1,1) = tokenizer.nextTokenAsDouble();
103			Xirr_(1,2) = tokenizer.nextTokenAsDouble();
104			Xirr_(2,0) = tokenizer.nextTokenAsDouble();
105			Xirr_(2,1) = tokenizer.nextTokenAsDouble();
106			Xirr_(2,2) = tokenizer.nextTokenAsDouble();
107
108			Xi_.setSubMatrix(0, 0, Xitt_);
109			Xi_.setSubMatrix(0, 3, Xirt_);
110			Xi_.setSubMatrix(3, 0, Xitr_);
111			Xi_.setSubMatrix(3, 3, Xirr_);
112
113			CholeskyDecomposition(Xi_, S_);
114
115			}
116			}
117
118			void HydroProp::complete() {
119
120			if (hasXi) {
121			for (int i1 = 0; i1 < 3; i1++) {
122			for (int j1 = 0; j1 < 3; j1++) {
123			Xitt_(i1,j1) = Xi_(i1,j1);
124			Xirt_(i1,j1) = Xi_(i1,j1+3);
125			Xitr_(i1,j1) = Xi_(i1+3,j1);
126			Xirr_(i1,j1) = Xi_(i1+3,j1+3);
127			}
128			}
129			CholeskyDecomposition(Xi_, S_);
130			}
131			}
132
133			}
134