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Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp (file contents):
Revision 891 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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]  Vardeman & Gezelter, in progress (2009).
40		*/
41	+	#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
42	+	#include "hydrodynamics/Shape.hpp"
43	+	#include "hydrodynamics/Sphere.hpp"
44	+	#include "hydrodynamics/Ellipsoid.hpp"
45	+	#include "applications/hydrodynamics/CompositeShape.hpp"
46
47	<	#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
48	<	#include "math/LU.hpp"
49	<	#include "math/DynamicRectMatrix.hpp"
50	<	#include "math/SquareMatrix3.hpp"
51	<	namespace oopse {
52	<	/**
53	<	* Reference:
49	<	* Beatriz Carrasco and Jose Gracia de la Torre, Hydrodynamic Properties of Rigid Particles:
50	<	* Comparison of Different Modeling and Computational Procedures.
51	<	* Biophysical Journal, 75(6), 3044, 1999
52	<	*/
53	<	bool HydrodynamicsModel::calcHydrodyanmicsProps(double eta) {
54	<	if (!createBeads(beads_)) {
55	<	std::cout << "can not create beads" << std::endl;
56	<	return false;
57	<	}
58	<
59	<	int nbeads = beads_.size();
60	<	DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
61	<	DynamicRectMatrix<double> C(3*nbeads, 3*nbeads);
62	<	Mat3x3d I;
63	<	for (std::size_t i = 0; i < nbeads; ++i) {
64	<	for (std::size_t j = 0; j < nbeads; ++j) {
65	<	Mat3x3d Tij;
66	<	if (i != j ) {
67	<	Vector3d Rij = beads_[i].pos - beads_[j].pos;
68	<	double rij = Rij.length();
69	<	double rij2 = rij * rij;
70	<	double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2;
71	<	Mat3x3d tmpMat;
72	<	tmpMat = outProduct(beads_[i].pos, beads_[j].pos) / rij2;
73	<	double constant = 8.0 * NumericConstant::PI * eta * rij;
74	<	Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
75	<	}else {
76	<	double constant = 1.0 / (6.0 * NumericConstant::PI * eta * beads_[i].radius);
77	<	Tij(0, 0) = constant;
78	<	Tij(1, 1) = constant;
79	<	Tij(2, 2) = constant;
80	<	}
81	<	B.setSubMatrix(i*3, j*3, Tij);
82	<	}
83	<	}
47	>	namespace OpenMD {
48	>
49	>	bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
50	>	return false;
51	>	}
52	>
53	>	void HydrodynamicsModel::writeHydroProps(std::ostream& os) {
54
55	<	//invert B Matrix
56	<	invertMatrix(B, C);
55	>	Vector3d center;
56	>	Mat6x6d Xi, D;
57
58	<	//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
89	<	std::vector<Mat3x3d> U;
90	<	for (int i = 0; i < nbeads; ++i) {
91	<	Mat3x3d currU;
92	<	currU.setupSkewMat(beads_[i].pos);
93	<	U.push_back(currU);
94	<	}
58	>	os << sd_->getType() << "\t";
59
60	<	//calculate Xi matrix at arbitrary origin O
97	<	Mat3x3d Xitt;
98	<	Mat3x3d Xirr;
99	<	Mat3x3d Xitr;
100	<
101	<	for (std::size_t i = 0; i < nbeads; ++i) {
102	<	for (std::size_t j = 0; j < nbeads; ++j) {
103	<	Mat3x3d Cij;
104	<	C.getSubMatrix(i*3, j*3, Cij);
105	<
106	<	Xitt += Cij;
107	<	Xirr += U[i] * Cij;
108	<	Xitr += U[i] * Cij * U[j];
109	<	}
110	<	}
60	>	//center of resistance
61
62	<	//invert Xi to get Diffusion Tensor at arbitrary origin O
113	<	RectMatrix<double, 6, 6> Xi;
114	<	RectMatrix<double, 6, 6> Do;
115	<	Xi.setSubMatrix(0, 0, Xitt);
116	<	Xi.setSubMatrix(0, 3, Xitr.transpose());
117	<	Xi.setSubMatrix(3, 0, Xitr);
118	<	Xi.setSubMatrix(3, 3, Xitt);
119	<	invertMatrix(Xi, Do);
62	>	center = cr_->getCOR();
63
64	<	Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O
65	<	Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O
66	<	Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O
67	<	Do.getSubMatrix(0, 0 , Dott);
125	<	Do.getSubMatrix(3, 0, Dotr);
126	<	Do.getSubMatrix(3, 3, Dorr);
64	>	os << center[0] <<  "\t" << center[1] <<  "\t" << center[2] <<  "\t";
65	>
66	>	//resistance tensor at center of resistance
67	>	//translation
68
69	<	//calculate center of diffusion
129	<	Mat3x3d tmpMat;
130	<	tmpMat(0, 0) = Dorr(1, 1) + Dorr(2, 2);
131	<	tmpMat(0, 1) = - Dorr(0, 1);
132	<	tmpMat(0, 2) = -Dorr(0, 2);
133	<	tmpMat(1, 0) = -Dorr(0, 1);
134	<	tmpMat(1, 1) = Dorr(0, 0)  + Dorr(2, 2);
135	<	tmpMat(1, 2) = -Dorr(1, 2);
136	<	tmpMat(2, 0) = -Dorr(0, 2);
137	<	tmpMat(2, 1) = -Dorr(1, 2);
138	<	tmpMat(2, 2) = Dorr(1, 1) + Dorr(0, 0);
69	>	Xi = cr_->getXi();
70
71	<	Vector3d tmpVec;
72	<	tmpVec[0] = Dotr(1, 2) - Dotr(2, 1);
73	<	tmpVec[1] = Dotr(2, 0) - Dotr(0, 2);
74	<	tmpVec[2] = Dotr(0, 1) - Dotr(1, 0);
75	<
76	<	Vector3d rod = tmpMat.inverse() * tmpVec;
71	>	os << Xi(0, 0) <<  "\t" << Xi(0, 1) <<  "\t" << Xi(0, 2) <<  "\t"
72	>	<< Xi(1, 0) <<  "\t" << Xi(1, 1) <<  "\t" << Xi(1, 2) <<  "\t"
73	>	<< Xi(2, 0) <<  "\t" << Xi(2, 1) <<  "\t" << Xi(2, 2) <<  "\t";
74	>
75	>	//rotation-translation
76	>	os << Xi(0, 3) <<  "\t" << Xi(0, 4) <<  "\t" << Xi(0, 5) <<  "\t"
77	>	<< Xi(1, 3) <<  "\t" << Xi(1, 4) <<  "\t" << Xi(1, 5) <<  "\t"
78	>	<< Xi(2, 3) <<  "\t" << Xi(2, 4) <<  "\t" << Xi(2, 5) <<  "\t";
79	>
80	>	//translation-rotation
81	>	os << Xi(3, 0) <<  "\t" << Xi(3, 1) <<  "\t" << Xi(3, 2) <<  "\t"
82	>	<< Xi(4, 0) <<  "\t" << Xi(4, 1) <<  "\t" << Xi(4, 2) <<  "\t"
83	>	<< Xi(5, 0) <<  "\t" << Xi(5, 1) <<  "\t" << Xi(5, 2) <<  "\t";
84	>
85	>	//rotation
86	>	os << Xi(3, 3) <<  "\t" << Xi(3, 4) <<  "\t" << Xi(3, 5) <<  "\t"
87	>	<< Xi(4, 3) <<  "\t" << Xi(4, 4) <<  "\t" << Xi(4, 5) <<  "\t"
88	>	<< Xi(5, 3) <<  "\t" << Xi(5, 4) <<  "\t" << Xi(5, 5) <<  "\t";
89	>
90	>
91	>	//diffusion tensor at center of resistance
92	>	//translation
93
94	<	//calculate Diffusion Tensor at center of diffusion
95	<	Mat3x3d Uod;
96	<	Uod.setupSkewMat(rod);
94	>	D = cr_->getD();
95	>
96	>	os << D(0, 0) <<  "\t" << D(0, 1) <<  "\t" << D(0, 2) <<  "\t"
97	>	<< D(1, 0) <<  "\t" << D(1, 1) <<  "\t" << D(1, 2) <<  "\t"
98	>	<< D(2, 0) <<  "\t" << D(2, 1) <<  "\t" << D(2, 2) <<  "\t";
99
100	<	Mat3x3d Ddtt; //translational diffusion tensor at diffusion center
101	<	Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center
102	<	Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor
100	>	//rotation-translation
101	>	os << D(0, 3) <<  "\t" << D(0, 4) <<  "\t" << D(0, 5) <<  "\t"
102	>	<< D(1, 3) <<  "\t" << D(1, 4) <<  "\t" << D(1, 5) <<  "\t"
103	>	<< D(2, 3) <<  "\t" << D(2, 4) <<  "\t" << D(2, 5) <<  "\t";
104
105	<	Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr;
106	<	Ddrr = Dorr;
107	<	Ddtr = Dotr + Dorr * Uod;
105	>	//translation-rotation
106	>	os << D(3, 0) <<  "\t" << D(3, 1) <<  "\t" << D(3, 2) <<  "\t"
107	>	<< D(4, 0) <<  "\t" << D(4, 1) <<  "\t" << D(4, 2) <<  "\t"
108	>	<< D(5, 0) <<  "\t" << D(5, 1) <<  "\t" << D(5, 2) <<  "\t";
109
110	<	props_.diffCenter = rod;
111	<	props_.transDiff = Ddtt;
112	<	props_.transRotDiff = Ddtr;
113	<	props_.rotDiff = Ddrr;
110	>	//rotation
111	>	os << D(3, 3) <<  "\t" << D(3, 4) <<  "\t" << D(3, 5) <<  "\t"
112	>	<< D(4, 3) <<  "\t" << D(4, 4) <<  "\t" << D(4, 5) <<  "\t"
113	>	<< D(5, 3) <<  "\t" << D(5, 4) <<  "\t" << D(5, 5) <<  "\t";
114	>
115	>	//---------------------------------------------------------------------
116	>
117	>	//center of diffusion
118
119	<	return true;
165	<	}
119	>	center = cd_->getCOR();
120
121	<	void HydrodynamicsModel::writeBeads(std::ostream& os) {
121	>	os << center[0] <<  "\t" << center[1] <<  "\t" << center[2] <<  "\t";
122	>
123	>	//resistance tensor at center of diffusion
124	>	//translation
125
126	<	}
126	>	Xi = cd_->getXi();
127
128	<	void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) {
128	>	os << Xi(0, 0) <<  "\t" << Xi(0, 1) <<  "\t" << Xi(0, 2) <<  "\t"
129	>	<< Xi(1, 0) <<  "\t" << Xi(1, 1) <<  "\t" << Xi(1, 2) <<  "\t"
130	>	<< Xi(2, 0) <<  "\t" << Xi(2, 1) <<  "\t" << Xi(2, 2) <<  "\t";
131	>
132	>	//rotation-translation
133	>	os << Xi(0, 3) <<  "\t" << Xi(0, 4) <<  "\t" << Xi(0, 5) <<  "\t"
134	>	<< Xi(1, 3) <<  "\t" << Xi(1, 4) <<  "\t" << Xi(1, 5) <<  "\t"
135	>	<< Xi(2, 3) <<  "\t" << Xi(2, 4) <<  "\t" << Xi(2, 5) <<  "\t";
136	>
137	>	//translation-rotation
138	>	os << Xi(3, 0) <<  "\t" << Xi(3, 1) <<  "\t" << Xi(3, 2) <<  "\t"
139	>	<< Xi(4, 0) <<  "\t" << Xi(4, 1) <<  "\t" << Xi(4, 2) <<  "\t"
140	>	<< Xi(5, 0) <<  "\t" << Xi(5, 1) <<  "\t" << Xi(5, 2) <<  "\t";
141	>
142	>	//rotation
143	>	os << Xi(3, 3) <<  "\t" << Xi(3, 4) <<  "\t" << Xi(3, 5) <<  "\t"
144	>	<< Xi(4, 3) <<  "\t" << Xi(4, 4) <<  "\t" << Xi(4, 5) <<  "\t"
145	>	<< Xi(5, 3) <<  "\t" << Xi(5, 4) <<  "\t" << Xi(5, 5) <<  "\t";
146	>
147	>
148	>	//diffusion tensor at center of diffusion
149	>	//translation
150
151	<	}
151	>	D = cd_->getD();
152
153	+	os << D(0, 0) <<  "\t" << D(0, 1) <<  "\t" << D(0, 2) <<  "\t"
154	+	<< D(1, 0) <<  "\t" << D(1, 1) <<  "\t" << D(1, 2) <<  "\t"
155	+	<< D(2, 0) <<  "\t" << D(2, 1) <<  "\t" << D(2, 2) <<  "\t";
156	+
157	+	//rotation-translation
158	+	os << D(0, 3) <<  "\t" << D(0, 4) <<  "\t" << D(0, 5) <<  "\t"
159	+	<< D(1, 3) <<  "\t" << D(1, 4) <<  "\t" << D(1, 5) <<  "\t"
160	+	<< D(2, 3) <<  "\t" << D(2, 4) <<  "\t" << D(2, 5) <<  "\t";
161	+
162	+	//translation-rotation
163	+	os << D(3, 0) <<  "\t" << D(3, 1) <<  "\t" << D(3, 2) <<  "\t"
164	+	<< D(4, 0) <<  "\t" << D(4, 1) <<  "\t" << D(4, 2) <<  "\t"
165	+	<< D(5, 0) <<  "\t" << D(5, 1) <<  "\t" << D(5, 2) <<  "\t";
166	+
167	+	//rotation
168	+	os << D(3, 3) <<  "\t" << D(3, 4) <<  "\t" << D(3, 5) <<  "\t"
169	+	<< D(4, 3) <<  "\t" << D(4, 4) <<  "\t" << D(4, 5) <<  "\t"
170	+	<< D(5, 3) <<  "\t" << D(5, 4) <<  "\t" << D(5, 5) <<  "\n";
171	+
172	+	}
173	+
174		}

Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp (property svn:keywords):
Revision 891 by tim, Wed Feb 22 20:35:16 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

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