src/hydrodynamics/Ellipsoid.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/Ellipsoid.hpp"
#include "utils/OOPSEConstant.hpp"
#include "math/LU.hpp"

namespace oopse {
  
  Ellipsoid::Ellipsoid(Vector3d origin, RealType rAxial, RealType rEquatorial,
                       Mat3x3d rotMat) : origin_(origin), rAxial_(rAxial), 
                                         rEquatorial_(rEquatorial), 
                                         rotMat_(rotMat) {
    if (rAxial_ > rEquatorial_) {
      rMajor_ = rAxial_;
      rMinor_ = rEquatorial_;
    } else {
      rMajor_ = rEquatorial_;
      rMinor_ = rAxial_;
    }          
  }

  bool Ellipsoid::isInterior(Vector3d pos) {
    Vector3d r = pos - origin_;
    Vector3d rbody = rotMat_ * r;

    RealType xoverb = rbody[0]/rEquatorial_;
    RealType yoverb = rbody[1]/rEquatorial_;
    RealType zovera = rbody[2]/rAxial_;
    
    bool result;
    if (xoverb*xoverb + yoverb*yoverb + zovera*zovera < 1)
      result = true;
    else
      result = false;
    
    return result;    
  }
  
  std::pair<Vector3d, Vector3d> Ellipsoid::getBoundingBox() {
    
    std::pair<Vector3d, Vector3d>  boundary;
    //make a cubic box
    RealType rad  = rAxial_ > rEquatorial_ ? rAxial_ : rEquatorial_; 
    Vector3d r(rad, rad, rad);
    boundary.first = origin_ - r;
    boundary.second = origin_ + r;
    return boundary;
  }
  
  HydroProp* Ellipsoid::getHydroProp(RealType viscosity, 
                                     RealType temperature) {
    
    RealType a = rAxial_;
    RealType b = rEquatorial_;
    RealType a2 = a * a;
    RealType b2 = b * b;
    
    RealType p = a / b;
    RealType S;
    if (p > 1.0) {  
      // Ellipsoid is prolate:
      S = 2.0/sqrt(a2 - b2) * log((a + sqrt(a2-b2))/b);
    } else { 
      // Ellipsoid is oblate:
      S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a);
    }
    
    RealType pi = NumericConstant::PI;
    RealType XittA = 16.0 * pi * viscosity * (a2 - b2) /((2.0*a2-b2)*S -2.0*a);
    RealType XittB = 32.0 * pi * viscosity * (a2 - b2) /((2.0*a2-3.0*b2)*S +2.0*a);
    RealType XirrA = 32.0/3.0 * pi * viscosity *(a2 - b2) * b2 /(2.0*a -b2*S);
    RealType XirrB = 32.0/3.0 * pi * viscosity *(a2*a2 - b2*b2)/((2.0*a2-b2)*S-2.0*a);
    
    
    Mat6x6d Xi, XiCopy, D;
    
    Xi(0,0) = XittB;
    Xi(1,1) = XittB;
    Xi(2,2) = XittA;
    Xi(3,3) = XirrB;
    Xi(4,4) = XirrB;
    Xi(5,5) = XirrA;

    Xi *= OOPSEConstant::viscoConvert;    
    
    XiCopy = Xi;
    invertMatrix(XiCopy, D);
    RealType kt = OOPSEConstant::kb * temperature; // in kcal mol^-1
    D *= kt;
   
    HydroProp* hprop = new HydroProp(V3Zero, Xi, D);

    return hprop;

  }  
}
Revision:	3479
Committed:	Mon Nov 24 22:01:56 2008 UTC (16 years, 5 months ago) by gezelter
File size:	4575 byte(s)
Log Message:	use the viscoConvert in OOPSEConstant
#	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. 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/Ellipsoid.hpp"
43	#include "utils/OOPSEConstant.hpp"
44	#include "math/LU.hpp"
45
46	namespace oopse {
47
48	Ellipsoid::Ellipsoid(Vector3d origin, RealType rAxial, RealType rEquatorial,
49	Mat3x3d rotMat) : origin_(origin), rAxial_(rAxial),
50	rEquatorial_(rEquatorial),
51	rotMat_(rotMat) {
52	if (rAxial_ > rEquatorial_) {
53	rMajor_ = rAxial_;
54	rMinor_ = rEquatorial_;
55	} else {
56	rMajor_ = rEquatorial_;
57	rMinor_ = rAxial_;
58	}
59	}
60
61	bool Ellipsoid::isInterior(Vector3d pos) {
62	Vector3d r = pos - origin_;
63	Vector3d rbody = rotMat_ * r;
64
65	RealType xoverb = rbody[0]/rEquatorial_;
66	RealType yoverb = rbody[1]/rEquatorial_;
67	RealType zovera = rbody[2]/rAxial_;
68
69	bool result;
70	if (xoverbxoverb + yoverbyoverb + zovera*zovera < 1)
71	result = true;
72	else
73	result = false;
74
75	return result;
76	}
77
78	std::pair<Vector3d, Vector3d> Ellipsoid::getBoundingBox() {
79
80	std::pair<Vector3d, Vector3d> boundary;
81	//make a cubic box
82	RealType rad = rAxial_ > rEquatorial_ ? rAxial_ : rEquatorial_;
83	Vector3d r(rad, rad, rad);
84	boundary.first = origin_ - r;
85	boundary.second = origin_ + r;
86	return boundary;
87	}
88
89	HydroProp* Ellipsoid::getHydroProp(RealType viscosity,
90	RealType temperature) {
91
92	RealType a = rAxial_;
93	RealType b = rEquatorial_;
94	RealType a2 = a * a;
95	RealType b2 = b * b;
96
97	RealType p = a / b;
98	RealType S;
99	if (p > 1.0) {
100	// Ellipsoid is prolate:
101	S = 2.0/sqrt(a2 - b2) * log((a + sqrt(a2-b2))/b);
102	} else {
103	// Ellipsoid is oblate:
104	S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a);
105	}
106
107	RealType pi = NumericConstant::PI;
108	RealType XittA = 16.0 * pi * viscosity * (a2 - b2) /((2.0a2-b2)S -2.0*a);
109	RealType XittB = 32.0 * pi * viscosity * (a2 - b2) /((2.0a2-3.0b2)S +2.0a);
110	RealType XirrA = 32.0/3.0 * pi * viscosity (a2 - b2) b2 /(2.0a -b2S);
111	RealType XirrB = 32.0/3.0 * pi * viscosity (a2a2 - b2b2)/((2.0a2-b2)S-2.0a);
112
113
114	Mat6x6d Xi, XiCopy, D;
115
116	Xi(0,0) = XittB;
117	Xi(1,1) = XittB;
118	Xi(2,2) = XittA;
119	Xi(3,3) = XirrB;
120	Xi(4,4) = XirrB;
121	Xi(5,5) = XirrA;
122
123	Xi *= OOPSEConstant::viscoConvert;
124
125	XiCopy = Xi;
126	invertMatrix(XiCopy, D);
127	RealType kt = OOPSEConstant::kb * temperature; // in kcal mol^-1
128	D *= kt;
129
130	HydroProp* hprop = new HydroProp(V3Zero, Xi, D);
131
132	return hprop;
133
134	}
135	}