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root/OpenMD/trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp

Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp (file contents):
Revision 893 by tim, Fri Feb 24 21:17:05 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42	+	#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
43	+	#include "hydrodynamics/Shape.hpp"
44	+	#include "hydrodynamics/Sphere.hpp"
45	+	#include "hydrodynamics/Ellipsoid.hpp"
46	+	#include "applications/hydrodynamics/CompositeShape.hpp"
47
48	<	#include "applications/hydrodynamics/HydrodynamicsModel.hpp"
49	<	#include "math/LU.hpp"
50	<	#include "math/DynamicRectMatrix.hpp"
51	<	#include "math/SquareMatrix3.hpp"
52	<	#include "utils/OOPSEConstant.hpp"
53	<	namespace oopse {
54	<	/**
49	<	* Reference:
50	<	* Beatriz Carrasco and Jose Gracia de la Torre, Hydrodynamic Properties of Rigid Particles:
51	<	* Comparison of Different Modeling and Computational Procedures.
52	<	* Biophysical Journal, 75(6), 3044, 1999
53	<	*/
48	>	namespace OpenMD {
49	>
50	>	bool HydrodynamicsModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
51	>	return false;
52	>	}
53	>
54	>	void HydrodynamicsModel::writeHydroProps(std::ostream& os) {
55
56	<	HydrodynamicsModel::HydrodynamicsModel(StuntDouble* sd, const DynamicProperty& extraParams) : sd_(sd){
57	<	DynamicProperty::const_iterator iter;
57	<
58	<	iter = extraParams.find("Viscosity");
59	<	if (iter != extraParams.end()) {
60	<	boost::any param = iter->second;
61	<	viscosity_ = boost::any_cast<double>(param);
62	<	}else {
63	<	std::cout << "HydrodynamicsModel Error\n" ;
64	<	}
65	<
66	<	iter = extraParams.find("Temperature");
67	<	if (iter != extraParams.end()) {
68	<	boost::any param = iter->second;
69	<	temperature_ = boost::any_cast<double>(param);
70	<	}else {
71	<	std::cout << "HydrodynamicsModel Error\n" ;
72	<	}
73	<	}
74	<
75	<	bool HydrodynamicsModel::calcHydrodyanmicsProps() {
76	<	if (!createBeads(beads_)) {
77	<	std::cout << "can not create beads" << std::endl;
78	<	return false;
79	<	}
56	>	Vector3d center;
57	>	Mat6x6d Xi, D;
58
59	<	int nbeads = beads_.size();
82	<	DynamicRectMatrix<double> B(3*nbeads, 3*nbeads);
83	<	DynamicRectMatrix<double> C(3*nbeads, 3*nbeads);
84	<	Mat3x3d I;
85	<	I(0, 0) = 1.0;
86	<	I(1, 1) = 1.0;
87	<	I(2, 2) = 1.0;
59	>	os << sd_->getType() << "\t";
60
61	<	for (std::size_t i = 0; i < nbeads; ++i) {
90	<	for (std::size_t j = 0; j < nbeads; ++j) {
91	<	Mat3x3d Tij;
92	<	if (i != j ) {
93	<	Vector3d Rij = beads_[i].pos - beads_[j].pos;
94	<	double rij = Rij.length();
95	<	double rij2 = rij * rij;
96	<	double sumSigma2OverRij2 = ((beads_[i].radius*beads_[i].radius) + (beads_[i].radius*beads_[i].radius)) / rij2;
97	<	Mat3x3d tmpMat;
98	<	tmpMat = outProduct(Rij, Rij) / rij2;
99	<	double constant = 8.0 * NumericConstant::PI * viscosity_ * rij;
100	<	Tij = ((1.0 + sumSigma2OverRij2/3.0) * I + (1.0 - sumSigma2OverRij2) * tmpMat ) / constant;
101	<	}else {
102	<	double constant = 1.0 / (6.0 * NumericConstant::PI * viscosity_ * beads_[i].radius);
103	<	Tij(0, 0) = constant;
104	<	Tij(1, 1) = constant;
105	<	Tij(2, 2) = constant;
106	<	}
107	<	B.setSubMatrix(i*3, j*3, Tij);
108	<	std::cout << Tij << std::endl;
109	<	}
110	<	}
61	>	//center of resistance
62
63	<	std::cout << "B=\n"
113	<	<< B << std::endl;
114	<	//invert B Matrix
115	<	invertMatrix(B, C);
63	>	center = cr_->getCOR();
64
65	<	std::cout << "C=\n"
118	<	<< C << std::endl;
119	<
120	<	//prepare U Matrix relative to arbitrary origin O(0.0, 0.0, 0.0)
121	<	std::vector<Mat3x3d> U;
122	<	for (int i = 0; i < nbeads; ++i) {
123	<	Mat3x3d currU;
124	<	currU.setupSkewMat(beads_[i].pos);
125	<	U.push_back(currU);
126	<	}
65	>	os << center[0] <<  "\t" << center[1] <<  "\t" << center[2] <<  "\t";
66
67	<	//calculate Xi matrix at arbitrary origin O
68	<	Mat3x3d Xitt;
130	<	Mat3x3d Xirr;
131	<	Mat3x3d Xitr;
67	>	//resistance tensor at center of resistance
68	>	//translation
69
70	<	//calculate the total volume
70	>	Xi = cr_->getXi();
71
72	<	double volume = 0.0;
73	<	for (std::vector<BeadParam>::iterator iter = beads_.begin(); iter != beads_.end(); ++iter) {
74	<	volume = 4.0/3.0 * NumericConstant::PI * pow((*iter).radius,3);
75	<	}
76	<
77	<	for (std::size_t i = 0; i < nbeads; ++i) {
78	<	for (std::size_t j = 0; j < nbeads; ++j) {
79	<	Mat3x3d Cij;
80	<	C.getSubMatrix(i*3, j*3, Cij);
81	<
82	<	Xitt += Cij;
83	<	Xitr += U[i] * Cij;
84	<	Xirr += -U[i] * Cij * U[j];
85	<	//Xirr += -U[i] * Cij * U[j] + (0.166*6 * viscosity_ * volume) * I;
86	<	}
87	<	}
72	>	os << Xi(0, 0) <<  "\t" << Xi(0, 1) <<  "\t" << Xi(0, 2) <<  "\t"
73	>	<< Xi(1, 0) <<  "\t" << Xi(1, 1) <<  "\t" << Xi(1, 2) <<  "\t"
74	>	<< Xi(2, 0) <<  "\t" << Xi(2, 1) <<  "\t" << Xi(2, 2) <<  "\t";
75	>
76	>	//rotation-translation
77	>	os << Xi(0, 3) <<  "\t" << Xi(0, 4) <<  "\t" << Xi(0, 5) <<  "\t"
78	>	<< Xi(1, 3) <<  "\t" << Xi(1, 4) <<  "\t" << Xi(1, 5) <<  "\t"
79	>	<< Xi(2, 3) <<  "\t" << Xi(2, 4) <<  "\t" << Xi(2, 5) <<  "\t";
80	>
81	>	//translation-rotation
82	>	os << Xi(3, 0) <<  "\t" << Xi(3, 1) <<  "\t" << Xi(3, 2) <<  "\t"
83	>	<< Xi(4, 0) <<  "\t" << Xi(4, 1) <<  "\t" << Xi(4, 2) <<  "\t"
84	>	<< Xi(5, 0) <<  "\t" << Xi(5, 1) <<  "\t" << Xi(5, 2) <<  "\t";
85	>
86	>	//rotation
87	>	os << Xi(3, 3) <<  "\t" << Xi(3, 4) <<  "\t" << Xi(3, 5) <<  "\t"
88	>	<< Xi(4, 3) <<  "\t" << Xi(4, 4) <<  "\t" << Xi(4, 5) <<  "\t"
89	>	<< Xi(5, 3) <<  "\t" << Xi(5, 4) <<  "\t" << Xi(5, 5) <<  "\t";
90	>
91	>
92	>	//diffusion tensor at center of resistance
93	>	//translation
94
95	<	//invert Xi to get Diffusion Tensor at arbitrary origin O
153	<	RectMatrix<double, 6, 6> Xi;
154	<	RectMatrix<double, 6, 6> Do;
155	<	Xi.setSubMatrix(0, 0, Xitt);
156	<	Xi.setSubMatrix(0, 3, Xitr.transpose());
157	<	Xi.setSubMatrix(3, 0, Xitr);
158	<	Xi.setSubMatrix(3, 3, Xirr);
159	<	//invertMatrix(Xi, Do);
160	<	double kt = OOPSEConstant::kB * temperature_ * 1.66E-2;
161	<	//Do *= kt;
95	>	D = cr_->getD();
96
97	<
98	<	Mat3x3d Dott; //translational diffusion tensor at arbitrary origin O
99	<	Mat3x3d Dorr; //rotational diffusion tensor at arbitrary origin O
166	<	Mat3x3d Dotr; //translation-rotation couplingl diffusion tensor at arbitrary origin O
167	<
168	<	const static Mat3x3d zeroMat(0.0);
97	>	os << D(0, 0) <<  "\t" << D(0, 1) <<  "\t" << D(0, 2) <<  "\t"
98	>	<< D(1, 0) <<  "\t" << D(1, 1) <<  "\t" << D(1, 2) <<  "\t"
99	>	<< D(2, 0) <<  "\t" << D(2, 1) <<  "\t" << D(2, 2) <<  "\t";
100
101	<	Mat3x3d XittInv(0.0);
102	<	XittInv = Xitt.inverse();
101	>	//rotation-translation
102	>	os << D(0, 3) <<  "\t" << D(0, 4) <<  "\t" << D(0, 5) <<  "\t"
103	>	<< D(1, 3) <<  "\t" << D(1, 4) <<  "\t" << D(1, 5) <<  "\t"
104	>	<< D(2, 3) <<  "\t" << D(2, 4) <<  "\t" << D(2, 5) <<  "\t";
105
106	<	//Xirr may not be inverted,if it one of the diagonal element is zero, for example
107	<	//( a11 a12 0)
108	<	//( a21 a22 0)
109	<	//( 0    0    0)
110	<	Mat3x3d XirrInv;
111	<	XirrInv = Xirr.inverse();
106	>	//translation-rotation
107	>	os << D(3, 0) <<  "\t" << D(3, 1) <<  "\t" << D(3, 2) <<  "\t"
108	>	<< D(4, 0) <<  "\t" << D(4, 1) <<  "\t" << D(4, 2) <<  "\t"
109	>	<< D(5, 0) <<  "\t" << D(5, 1) <<  "\t" << D(5, 2) <<  "\t";
110	>
111	>	//rotation
112	>	os << D(3, 3) <<  "\t" << D(3, 4) <<  "\t" << D(3, 5) <<  "\t"
113	>	<< D(4, 3) <<  "\t" << D(4, 4) <<  "\t" << D(4, 5) <<  "\t"
114	>	<< D(5, 3) <<  "\t" << D(5, 4) <<  "\t" << D(5, 5) <<  "\t";
115	>
116	>	//---------------------------------------------------------------------
117	>
118	>	//center of diffusion
119
120	<	Mat3x3d tmp;
181	<	Mat3x3d tmpInv;
182	<	tmp = Xitt - Xitr.transpose() * XirrInv * Xitr;
183	<	tmpInv = tmp.inverse();
120	>	center = cd_->getCOR();
121
122	<	Dott = kt * tmpInv;
186	<	Dotr = -kt*XirrInv * Xitr * tmpInv* 1.0E8;
187	<
188	<	tmp = Xirr - Xitr * XittInv * Xitr.transpose();
189	<	tmpInv = tmp.inverse();
122	>	os << center[0] <<  "\t" << center[1] <<  "\t" << center[2] <<  "\t";
123
124	<	Dorr = kt * tmpInv*1.0E16;
124	>	//resistance tensor at center of diffusion
125	>	//translation
126
127	<	//Do.getSubMatrix(0, 0 , Dott);
194	<	//Do.getSubMatrix(3, 0, Dotr);
195	<	//Do.getSubMatrix(3, 3, Dorr);
127	>	Xi = cd_->getXi();
128
129	<	//calculate center of diffusion
130	<	tmp(0, 0) = Dorr(1, 1) + Dorr(2, 2);
131	<	tmp(0, 1) = - Dorr(0, 1);
200	<	tmp(0, 2) = -Dorr(0, 2);
201	<	tmp(1, 0) = -Dorr(0, 1);
202	<	tmp(1, 1) = Dorr(0, 0)  + Dorr(2, 2);
203	<	tmp(1, 2) = -Dorr(1, 2);
204	<	tmp(2, 0) = -Dorr(0, 2);
205	<	tmp(2, 1) = -Dorr(1, 2);
206	<	tmp(2, 2) = Dorr(1, 1) + Dorr(0, 0);
207	<
208	<	Vector3d tmpVec;
209	<	tmpVec[0] = Dotr(1, 2) - Dotr(2, 1);
210	<	tmpVec[1] = Dotr(2, 0) - Dotr(0, 2);
211	<	tmpVec[2] = Dotr(0, 1) - Dotr(1, 0);
212	<
213	<	tmpInv = tmp.inverse();
129	>	os << Xi(0, 0) <<  "\t" << Xi(0, 1) <<  "\t" << Xi(0, 2) <<  "\t"
130	>	<< Xi(1, 0) <<  "\t" << Xi(1, 1) <<  "\t" << Xi(1, 2) <<  "\t"
131	>	<< Xi(2, 0) <<  "\t" << Xi(2, 1) <<  "\t" << Xi(2, 2) <<  "\t";
132
133	<	Vector3d rod = tmpInv * tmpVec;
134	<
135	<	//calculate Diffusion Tensor at center of diffusion
136	<	Mat3x3d Uod;
219	<	Uod.setupSkewMat(rod);
133	>	//rotation-translation
134	>	os << Xi(0, 3) <<  "\t" << Xi(0, 4) <<  "\t" << Xi(0, 5) <<  "\t"
135	>	<< Xi(1, 3) <<  "\t" << Xi(1, 4) <<  "\t" << Xi(1, 5) <<  "\t"
136	>	<< Xi(2, 3) <<  "\t" << Xi(2, 4) <<  "\t" << Xi(2, 5) <<  "\t";
137
138	<	Mat3x3d Ddtt; //translational diffusion tensor at diffusion center
139	<	Mat3x3d Ddtr; //rotational diffusion tensor at diffusion center
140	<	Mat3x3d Ddrr; //translation-rotation couplingl diffusion tensor at diffusion tensor
138	>	//translation-rotation
139	>	os << Xi(3, 0) <<  "\t" << Xi(3, 1) <<  "\t" << Xi(3, 2) <<  "\t"
140	>	<< Xi(4, 0) <<  "\t" << Xi(4, 1) <<  "\t" << Xi(4, 2) <<  "\t"
141	>	<< Xi(5, 0) <<  "\t" << Xi(5, 1) <<  "\t" << Xi(5, 2) <<  "\t";
142
143	<	Ddtt = Dott - Uod * Dorr * Uod + Dotr.transpose() * Uod - Uod * Dotr;
144	<	Ddrr = Dorr;
145	<	Ddtr = Dotr + Dorr * Uod;
143	>	//rotation
144	>	os << Xi(3, 3) <<  "\t" << Xi(3, 4) <<  "\t" << Xi(3, 5) <<  "\t"
145	>	<< Xi(4, 3) <<  "\t" << Xi(4, 4) <<  "\t" << Xi(4, 5) <<  "\t"
146	>	<< Xi(5, 3) <<  "\t" << Xi(5, 4) <<  "\t" << Xi(5, 5) <<  "\t";
147
148	<	props_.diffCenter = rod;
149	<	props_.transDiff = Ddtt;
150	<	props_.transRotDiff = Ddtr;
232	<	props_.rotDiff = Ddrr;
148	>
149	>	//diffusion tensor at center of diffusion
150	>	//translation
151
152	<	return true;
235	<	}
152	>	D = cd_->getD();
153
154	<	void HydrodynamicsModel::writeBeads(std::ostream& os) {
155	<	std::vector<BeadParam>::iterator iter;
156	<	os << beads_.size() << std::endl;
240	<	os << "Generated by Hydro" << std::endl;
241	<	for (iter = beads_.begin(); iter != beads_.end(); ++iter) {
242	<	os << iter->atomName << "\t" << iter->pos[0] << "\t" << iter->pos[1] << "\t" << iter->pos[2] << std::endl;
243	<	}
244	<
245	<	}
246	<
247	<	void HydrodynamicsModel::writeDiffCenterAndDiffTensor(std::ostream& os) {
248	<	os << "//viscosity = " << viscosity_ << std::endl;
249	<	os << "//temperature = " << temperature_<< std::endl;
250	<	std::vector<BeadParam>::iterator iter;
251	<	os << sd_->getType() << "\n";
252	<
253	<	os << "//diffusion center" << std::endl;
254	<	os << props_.diffCenter << std::endl;
255	<
256	<	os << "//translational diffusion tensor" << std::endl;
257	<	os << props_.transDiff << std::endl;
258	<
259	<	os << "//translation-rotation coupling diffusion tensor" << std::endl;
260	<	os << props_.transRotDiff << std::endl;
261	<
262	<	os << "//rotational diffusion tensor" << std::endl;
263	<	os << props_.rotDiff << std::endl;
154	>	os << D(0, 0) <<  "\t" << D(0, 1) <<  "\t" << D(0, 2) <<  "\t"
155	>	<< D(1, 0) <<  "\t" << D(1, 1) <<  "\t" << D(1, 2) <<  "\t"
156	>	<< D(2, 0) <<  "\t" << D(2, 1) <<  "\t" << D(2, 2) <<  "\t";
157
158	<	/*
159	<	os << props_.diffCenter[0] << "\t" << props_.diffCenter[1] << "\t" << props_.diffCenter[2] << "\n"
160	<
161	<	os << props_.transDiff(0, 0) << "\t" << props_.transDiff(0, 1) << "\t" << props_.transDiff(0, 2) << "\t"
269	<	<< props_.transDiff(1, 0) << "\t" << props_.transDiff(1, 1) << "\t" << props_.transDiff(1, 2) << "\t"
270	<	<< props_.transDiff(2, 0) << "\t" << props_.transDiff(2, 1) << "\t" << props_.transDiff(2, 2) << "\n";
158	>	//rotation-translation
159	>	os << D(0, 3) <<  "\t" << D(0, 4) <<  "\t" << D(0, 5) <<  "\t"
160	>	<< D(1, 3) <<  "\t" << D(1, 4) <<  "\t" << D(1, 5) <<  "\t"
161	>	<< D(2, 3) <<  "\t" << D(2, 4) <<  "\t" << D(2, 5) <<  "\t";
162
163	<	os << props_.transRotDiff(0, 0) << "\t" << props_.transRotDiff(0, 1) << "\t" << props_.transRotDiff(0, 2) << "\t"
164	<	<< props_.transRotDiff(1, 0) << "\t" << props_.transRotDiff(1, 1) << "\t" << props_.transRotDiff(1, 2) << "\t"
165	<	<< props_.transRotDiff(2, 0) << "\t" << props_.transRotDiff(2, 1) << "\t" << props_.transRotDiff(2, 2) << "\t"
166	<
167	<	os << props_.rotDiff(0, 0) << "\t" << props_.rotDiff(0, 1) << "\t" << props_.rotDiff(0, 2) << "\t"
168	<	<< props_.rotDiff(1, 0) << "\t" << props_.rotDiff(1, 1) << "\t" << props_.rotDiff(1, 2) << "\t"
169	<	<< props_.rotDiff(2, 0) << "\t" << props_.rotDiff(2, 1) << "\t" << props_.rotDiff(2, 2) << ";"
170	<	<< std::endl;
171	<	*/
163	>	//translation-rotation
164	>	os << D(3, 0) <<  "\t" << D(3, 1) <<  "\t" << D(3, 2) <<  "\t"
165	>	<< D(4, 0) <<  "\t" << D(4, 1) <<  "\t" << D(4, 2) <<  "\t"
166	>	<< D(5, 0) <<  "\t" << D(5, 1) <<  "\t" << D(5, 2) <<  "\t";
167	>
168	>	//rotation
169	>	os << D(3, 3) <<  "\t" << D(3, 4) <<  "\t" << D(3, 5) <<  "\t"
170	>	<< D(4, 3) <<  "\t" << D(4, 4) <<  "\t" << D(4, 5) <<  "\t"
171	>	<< D(5, 3) <<  "\t" << D(5, 4) <<  "\t" << D(5, 5) <<  "\n";
172	>
173	>	}
174	>
175		}
282	–
283	–	}

Comparing trunk/src/applications/hydrodynamics/HydrodynamicsModel.cpp (property svn:keywords):
Revision 893 by tim, Fri Feb 24 21:17:05 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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