src/hydrodynamics/Sphere.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, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#include "hydrodynamics/Sphere.hpp"
#include "utils/PhysicalConstants.hpp"
#include "math/LU.hpp"

namespace OpenMD {
  
  Sphere::Sphere(Vector3d origin, RealType radius) : origin_(origin), radius_(radius){
    
  }
  
  bool Sphere::isInterior(Vector3d pos) {
    Vector3d r = pos - origin_;
    
    bool result;
    if (r.length() < radius_)
      result = true;
    else
      result = false;
    
    return result;
  }
  
  std::pair<Vector3d, Vector3d> Sphere::getBoundingBox() {
    std::pair<Vector3d, Vector3d>  boundary;
    Vector3d r(radius_, radius_, radius_);
    boundary.first = origin_ - r;
    boundary.second = origin_ + r;
    return boundary;
  }
  
  HydroProp* Sphere::getHydroProp(RealType viscosity, RealType temperature) {
    
    RealType Xitt  = 6.0 * NumericConstant::PI * viscosity * radius_;
    RealType Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_;

    Mat6x6d Xi, XiCopy, D;

    Xi(0, 0) = Xitt;
    Xi(1, 1) = Xitt;
    Xi(2, 2) = Xitt;
    Xi(3, 3) = Xirr;
    Xi(4, 4) = Xirr;
    Xi(5, 5) = Xirr;
    
    Xi *= PhysicalConstants::viscoConvert;
    XiCopy = Xi;

    invertMatrix(XiCopy, D);
    RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1
    D *= kt;  // now in angstroms^2 fs^-1  (at least for Trans-trans)

    HydroProp* hprop = new HydroProp(V3Zero, Xi, D);
    
    return hprop;
  }
  
}
Revision:	1782
Committed:	Wed Aug 22 02:28:28 2012 UTC (13 years, 2 months ago) by gezelter
File size:	3576 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	User	Rev	Content
1	gezelter	956	/*
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	956	* 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	956	* 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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	956	*/
42
43			#include "hydrodynamics/Sphere.hpp"
44	gezelter	1390	#include "utils/PhysicalConstants.hpp"
45	gezelter	956	#include "math/LU.hpp"
46
47	gezelter	1390	namespace OpenMD {
48	gezelter	956
49	tim	963	Sphere::Sphere(Vector3d origin, RealType radius) : origin_(origin), radius_(radius){
50	gezelter	956
51			}
52
53			bool Sphere::isInterior(Vector3d pos) {
54			Vector3d r = pos - origin_;
55
56			bool result;
57			if (r.length() < radius_)
58			result = true;
59			else
60			result = false;
61
62			return result;
63			}
64
65			std::pair<Vector3d, Vector3d> Sphere::getBoundingBox() {
66			std::pair<Vector3d, Vector3d> boundary;
67			Vector3d r(radius_, radius_, radius_);
68			boundary.first = origin_ - r;
69			boundary.second = origin_ + r;
70			return boundary;
71			}
72
73	gezelter	981	HydroProp* Sphere::getHydroProp(RealType viscosity, RealType temperature) {
74
75	tim	963	RealType Xitt = 6.0 * NumericConstant::PI * viscosity * radius_;
76			RealType Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_;
77	gezelter	981
78			Mat6x6d Xi, XiCopy, D;
79
80			Xi(0, 0) = Xitt;
81			Xi(1, 1) = Xitt;
82			Xi(2, 2) = Xitt;
83			Xi(3, 3) = Xirr;
84			Xi(4, 4) = Xirr;
85			Xi(5, 5) = Xirr;
86	gezelter	956
87	gezelter	1390	Xi *= PhysicalConstants::viscoConvert;
88	gezelter	981	XiCopy = Xi;
89
90			invertMatrix(XiCopy, D);
91	gezelter	1390	RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1
92	xsun	1184	D *= kt; // now in angstroms^2 fs^-1 (at least for Trans-trans)
93	gezelter	981
94			HydroProp* hprop = new HydroProp(V3Zero, Xi, D);
95	gezelter	956
96	gezelter	981	return hprop;
97	gezelter	956	}
98
99			}