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]  Vardeman & Gezelter, in progress (2009).                        
 */

#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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	3510 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	956	*/
41
42			#include "hydrodynamics/Sphere.hpp"
43	gezelter	1390	#include "utils/PhysicalConstants.hpp"
44	gezelter	956	#include "math/LU.hpp"
45
46	gezelter	1390	namespace OpenMD {
47	gezelter	956
48	tim	963	Sphere::Sphere(Vector3d origin, RealType radius) : origin_(origin), radius_(radius){
49	gezelter	956
50			}
51
52			bool Sphere::isInterior(Vector3d pos) {
53			Vector3d r = pos - origin_;
54
55			bool result;
56			if (r.length() < radius_)
57			result = true;
58			else
59			result = false;
60
61			return result;
62			}
63
64			std::pair<Vector3d, Vector3d> Sphere::getBoundingBox() {
65			std::pair<Vector3d, Vector3d> boundary;
66			Vector3d r(radius_, radius_, radius_);
67			boundary.first = origin_ - r;
68			boundary.second = origin_ + r;
69			return boundary;
70			}
71
72	gezelter	981	HydroProp* Sphere::getHydroProp(RealType viscosity, RealType temperature) {
73
74	tim	963	RealType Xitt = 6.0 * NumericConstant::PI * viscosity * radius_;
75			RealType Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_;
76	gezelter	981
77			Mat6x6d Xi, XiCopy, D;
78
79			Xi(0, 0) = Xitt;
80			Xi(1, 1) = Xitt;
81			Xi(2, 2) = Xitt;
82			Xi(3, 3) = Xirr;
83			Xi(4, 4) = Xirr;
84			Xi(5, 5) = Xirr;
85	gezelter	956
86	gezelter	1390	Xi *= PhysicalConstants::viscoConvert;
87	gezelter	981	XiCopy = Xi;
88
89			invertMatrix(XiCopy, D);
90	gezelter	1390	RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1
91	xsun	1184	D *= kt; // now in angstroms^2 fs^-1 (at least for Trans-trans)
92	gezelter	981
93			HydroProp* hprop = new HydroProp(V3Zero, Xi, D);
94	gezelter	956
95	gezelter	981	return hprop;
96	gezelter	956	}
97
98			}