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;

    const RealType convertConstant = 1.439326479e4; // converts Poise angstroms
                                                    // to kcal fs mol^-1 Angstrom^-1

    Xi *= convertConstant;    
    
    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:	1184
Committed:	Fri Oct 5 19:01:12 2007 UTC (18 years, 1 month ago) by xsun
File size:	4729 byte(s)
Log Message:	Fixed some temperature and conversion constant bugs in Sphere and Ellipsoid
#	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/Ellipsoid.hpp"
43			#include "utils/OOPSEConstant.hpp"
44			#include "math/LU.hpp"
45
46			namespace oopse {
47
48	xsun	1184	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	gezelter	956	}
60	xsun	1184
61	gezelter	956	bool Ellipsoid::isInterior(Vector3d pos) {
62			Vector3d r = pos - origin_;
63			Vector3d rbody = rotMat_ * r;
64	xsun	1184
65			RealType xoverb = rbody[0]/rEquatorial_;
66			RealType yoverb = rbody[1]/rEquatorial_;
67			RealType zovera = rbody[2]/rAxial_;
68	gezelter	956
69			bool result;
70	xsun	1184	if (xoverbxoverb + yoverbyoverb + zovera*zovera < 1)
71	gezelter	956	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	xsun	1184	RealType rad = rAxial_ > rEquatorial_ ? rAxial_ : rEquatorial_;
83	gezelter	956	Vector3d r(rad, rad, rad);
84			boundary.first = origin_ - r;
85			boundary.second = origin_ + r;
86			return boundary;
87			}
88
89	xsun	1184	HydroProp* Ellipsoid::getHydroProp(RealType viscosity,
90			RealType temperature) {
91	gezelter	956
92	xsun	1184	RealType a = rAxial_;
93			RealType b = rEquatorial_;
94	tim	963	RealType a2 = a * a;
95	xsun	1184	RealType b2 = b * b;
96	gezelter	956
97	xsun	1184	RealType p = a / b;
98	tim	963	RealType S;
99	xsun	1184	if (p > 1.0) {
100			// Ellipsoid is prolate:
101	gezelter	956	S = 2.0/sqrt(a2 - b2) * log((a + sqrt(a2-b2))/b);
102	xsun	1184	} else {
103			// Ellipsoid is oblate:
104	gezelter	956	S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a);
105			}
106
107	xsun	1184	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	gezelter	956
113
114	gezelter	981	Mat6x6d Xi, XiCopy, D;
115	gezelter	956
116	xsun	1184	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			const RealType convertConstant = 1.439326479e4; // converts Poise angstroms
124			// to kcal fs mol^-1 Angstrom^-1
125
126	gezelter	981	Xi *= convertConstant;
127	gezelter	956
128	gezelter	981	XiCopy = Xi;
129			invertMatrix(XiCopy, D);
130	xsun	1184	RealType kt = OOPSEConstant::kb * temperature; // in kcal mol^-1
131	gezelter	981	D *= kt;
132	gezelter	956
133	gezelter	981	HydroProp* hprop = new HydroProp(V3Zero, Xi, D);
134	gezelter	956
135	gezelter	981	return hprop;
136
137	gezelter	956	}
138			}