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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */

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

namespace oopse {
  
  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;
    
    const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs
    Xi *= convertConstant;
    XiCopy = Xi;

    invertMatrix(XiCopy, D);
    RealType kt = OOPSEConstant::kB * temperature;
    D *= kt;
    Xi *= OOPSEConstant::kb * temperature;

    HydroProp* hprop = new HydroProp(V3Zero, Xi, D);
    
    return hprop;
  }
  
}
Revision:	981
Committed:	Mon Jun 5 18:24:45 2006 UTC (18 years, 11 months ago) by gezelter
File size:	3491 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).
#	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			* 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/Sphere.hpp"
43			#include "utils/OOPSEConstant.hpp"
44			#include "math/LU.hpp"
45
46			namespace oopse {
47
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	tim	963	const RealType convertConstant = 6.023; //convert poise.angstrom to amu/fs
87	gezelter	981	Xi *= convertConstant;
88			XiCopy = Xi;
89
90			invertMatrix(XiCopy, D);
91	tim	963	RealType kt = OOPSEConstant::kB * temperature;
92	gezelter	981	D *= kt;
93			Xi = OOPSEConstant::kb temperature;
94
95			HydroProp* hprop = new HydroProp(V3Zero, Xi, D);
96	gezelter	956
97	gezelter	981	return hprop;
98	gezelter	956	}
99
100			}