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 (12 years, 8 months ago) by gezelter
File size:	3576 byte(s)
Log Message:	MERGE OpenMD development branch 1465:1781 into trunk
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include "hydrodynamics/Sphere.hpp"
44	#include "utils/PhysicalConstants.hpp"
45	#include "math/LU.hpp"
46
47	namespace OpenMD {
48
49	Sphere::Sphere(Vector3d origin, RealType radius) : origin_(origin), radius_(radius){
50
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	HydroProp* Sphere::getHydroProp(RealType viscosity, RealType temperature) {
74
75	RealType Xitt = 6.0 * NumericConstant::PI * viscosity * radius_;
76	RealType Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_;
77
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
87	Xi *= PhysicalConstants::viscoConvert;
88	XiCopy = Xi;
89
90	invertMatrix(XiCopy, D);
91	RealType kt = PhysicalConstants::kb * temperature; // in kcal mol^-1
92	D *= kt; // now in angstroms^2 fs^-1 (at least for Trans-trans)
93
94	HydroProp* hprop = new HydroProp(V3Zero, Xi, D);
95
96	return hprop;
97	}
98
99	}