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Comparing trunk/src/applications/hydrodynamics/AnalyticalModel.cpp (file contents):
Revision 915 by tim, Thu Mar 23 15:03:33 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/AnalyticalModel.hpp"
42	<	#include "applications/hydrodynamics/Spheric.hpp"
43	<	#include "applications/hydrodynamics/Ellipsoid.hpp"
42	>	#include "hydrodynamics/Sphere.hpp"
43	>	#include "hydrodynamics/Ellipsoid.hpp"
44		#include "applications/hydrodynamics/CompositeShape.hpp"
45		#include "math/LU.hpp"
46	<	namespace oopse {
47	<	bool AnalyticalModel::calcHydroProps(Spheric* spheric, double viscosity, double temperature) {
48	<
49	<	double radius = spheric->getRadius();
50	<	HydroProps props;
51	<	props.center =V3Zero;
52	<	double Xitt  = 6.0 * NumericConstant::PI * viscosity * radius;
53	<	double Xirr = 8.0 * NumericConstant::PI * viscosity * radius * radius * radius;
54	<	props.Xi(0, 0) = Xitt;
55	<	props.Xi(1, 1) = Xitt;
56	<	props.Xi(2, 2) = Xitt;
57	<	props.Xi(3, 3) = Xirr;
58	<	props.Xi(4, 4) = Xirr;
59	<	props.Xi(5, 5) = Xirr;
46	>	namespace OpenMD {
47	>
48	>	bool AnalyticalModel::calcHydroProps(Shape* shape, RealType viscosity, RealType temperature) {
49
50	<	const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
51	<	props.Xi *= convertConstant;
52	<	Mat6x6d XiCopy = props.Xi;
53	<	invertMatrix(XiCopy, props.D);
54	<	double kt = OOPSEConstant::kB * temperature;
55	<	props.D *= kt;
56	<	props.Xi *= OOPSEConstant::kb * temperature;
57	<
58	<	setCR(props);
59	<	setCD(props);
60	<
61	<	return true;
50	>	HydroProp* props;
51	>	Sphere* sphere = dynamic_cast<Sphere*>(shape);
52	>	if (sphere != NULL) {
53	>	props = sphere->getHydroProp(viscosity, temperature);
54	>	setCR(props);
55	>	setCD(props);
56	>	return true;
57	>	} else {
58	>	Ellipsoid* ellipsoid = dynamic_cast<Ellipsoid*>(shape);
59	>	if (ellipsoid != NULL) {
60	>	props = ellipsoid->getHydroProp(viscosity, temperature);
61	>	setCR(props);
62	>	setCD(props);
63	>	return true;
64	>	} else {
65	>	CompositeShape* composite = dynamic_cast<CompositeShape*>(shape);
66	>	if (composite != NULL) {
67	>	//           props = composite->getHydroProp(viscosity, temperature);
68	>	//           setCR(props);
69	>	//           setCD(props);
70	>	//           return true;
71	>	return false;
72	>	} else {
73	>	sprintf( painCave.errMsg,
74	>	"Could not figure out what kind of shape this is!\n");
75	>	painCave.severity = OPENMD_ERROR;
76	>	painCave.isFatal = 1;
77	>	simError();
78	>	return false;
79	>	}
80	>	}
81	>	}
82	>	}
83
84	<	}
75	<
76	<	/**
77	<	* Reference:
78	<	* (2) F. Perrin , J. Phys. Radium, [7] 5, 497-511, 1934
79	<	* (3) F. Perrin, J. Phys. Radium, [7] 7, 1-11, 1936
80	<	*/
81	<	bool AnalyticalModel::calcHydroProps(Ellipsoid* ellipsoid, double viscosity, double temperature) {
82	<
83	<	double rMajor = ellipsoid->getRMajor();
84	<	double rMinor = ellipsoid->getRMinor();
85	<
86	<	double a = rMinor;
87	<	double b = rMajor;
88	<	double a2 = a * a;
89	<	double b2 = b* b;
90	<
91	<	double p = a /b;
92	<	double S;
93	<	if (p > 1.0) { //prolate
94	<	S = 2.0/sqrt(a2 - b2) * log((a + sqrt(a2-b2))/b);
95	<	} else { //oblate
96	<	S = 2.0/sqrt(b2 - a2) * atan(sqrt(b2-a2)/a);
97	<	}
98	<
99	<	double P = 1.0/(a2 - b2) * (S - 2.0/a);
100	<	double Q = 0.5/(a2-b2) * (2.0*a/b2 - S);
101	<
102	<	double transMinor = 16.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-b2)*S -2.0*a);
103	<	double transMajor = 32.0 * NumericConstant::PI * viscosity * (a2 - b2) /((2.0*a2-3.0*b2)*S +2.0*a);
104	<	double rotMinor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2 - b2) * b2 /(2.0*a -b2*S);
105	<	double rotMajor = 32.0/3.0 * NumericConstant::PI * viscosity *(a2*a2 - b2*b2)/((2.0*a2-b2)*S-2.0*a);
106	<
107	<
108	<	HydroProps props;
109	<
110	<	props.Xi(0,0) = transMajor;
111	<	props.Xi(1,1) = transMajor;
112	<	props.Xi(2,2) = transMinor;
113	<	props.Xi(3,3) = rotMajor;
114	<	props.Xi(4,4) = rotMajor;
115	<	props.Xi(5,5) = rotMinor;
116	<
117	<	const double convertConstant = 6.023; //convert poise.angstrom to amu/fs
118	<	props.Xi *= convertConstant;
119	<
120	<	Mat6x6d XiCopy = props.Xi;
121	<	invertMatrix(XiCopy, props.D);
122	<	double kt = OOPSEConstant::kB * temperature;
123	<	props.D *= kt;
124	<	props.Xi *= OOPSEConstant::kb * temperature;
125	<
126	<	setCR(props);
127	<	setCD(props);
128	<
129	<	return true;
130	<	}
131	<
132	<	bool AnalyticalModel::calcHydroProps(CompositeShape* compositexShape, double viscosity, double temperature) {
133	<	return false;
134	<	}
135	<
136	<	void AnalyticalModel::writeBeads(std::ostream& os) {
84	>	void AnalyticalModel::writeBeads(std::ostream& os) {
85		os << "1\n";
86		os << "Generated by Hydro\n";
87		Vector3d pos = sd_->getPos();
88		os << sd_->getType() << "\t" << pos[0] << "\t" << pos[1] << "\t" << pos[2] << std::endl;
89	+	}
90		}
142	–
143	–
144	–	}

Comparing trunk/src/applications/hydrodynamics/AnalyticalModel.cpp (property svn:keywords):
Revision 915 by tim, Thu Mar 23 15:03:33 2006 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

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