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, double 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;
  }
  
  HydroProps Sphere::getHydroProps(double viscosity, double temperature) {
    HydroProps props;
    props.center =V3Zero;
    double Xitt  = 6.0 * NumericConstant::PI * viscosity * radius_;
    double Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_;
    props.Xi(0, 0) = Xitt;
    props.Xi(1, 1) = Xitt;
    props.Xi(2, 2) = Xitt;
    props.Xi(3, 3) = Xirr;
    props.Xi(4, 4) = Xirr;
    props.Xi(5, 5) = Xirr;
    
    const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
    props.Xi *= convertConstant;
    Mat6x6d XiCopy = props.Xi;
    invertMatrix(XiCopy, props.D);
    double kt = OOPSEConstant::kB * temperature;
    props.D *= kt;
    props.Xi *= OOPSEConstant::kb * temperature;
    
    return props;
  }
  
}
Revision:	2752
Committed:	Tue May 16 02:06:37 2006 UTC (18 years, 1 month ago) by gezelter
File size:	3511 byte(s)
Log Message:	* empty log message *
#	User	Rev	Content
1	gezelter	2752	/*
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			Sphere::Sphere(Vector3d origin, double radius) : origin_(origin), radius_(radius){
49
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			HydroProps Sphere::getHydroProps(double viscosity, double temperature) {
73			HydroProps props;
74			props.center =V3Zero;
75			double Xitt = 6.0 * NumericConstant::PI * viscosity * radius_;
76			double Xirr = 8.0 * NumericConstant::PI * viscosity * radius_ * radius_ * radius_;
77			props.Xi(0, 0) = Xitt;
78			props.Xi(1, 1) = Xitt;
79			props.Xi(2, 2) = Xitt;
80			props.Xi(3, 3) = Xirr;
81			props.Xi(4, 4) = Xirr;
82			props.Xi(5, 5) = Xirr;
83
84			const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
85			props.Xi *= convertConstant;
86			Mat6x6d XiCopy = props.Xi;
87			invertMatrix(XiCopy, props.D);
88			double kt = OOPSEConstant::kB * temperature;
89			props.D *= kt;
90			props.Xi = OOPSEConstant::kb temperature;
91
92			return props;
93			}
94
95			}