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

Comparing trunk/src/applications/hydrodynamics/RoughShell.cpp (file contents):
Revision 898 by tim, Wed Mar 15 15:51:44 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
43		#include "applications/hydrodynamics/RoughShell.hpp"
44	+	#include "applications/hydrodynamics/ShapeBuilder.hpp"
45	+	#include "brains/SimInfo.hpp"
46
47	<	namespace oopse {
48	<
49	<	RoughShell::RoughShell(StuntDouble* sd, const DynamicProperty& extraParams) : HydrodynamicsModel(sd, extraParams), sdShape_(sd){
50	<	DynamicProperty::const_iterator iter = extraParams.find("Sigma");
51	<	if (iter != extraParams.end()) {
52	<	boost::any param = iter->second;
53	<	sigma_ = boost::any_cast<double>(param);
47	>	namespace OpenMD {
48	>
49	>	RoughShell::RoughShell(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info){
50	>	shape_=ShapeBuilder::createShape(sd);
51	>	Globals* simParams = info->getSimParams();
52	>	if (simParams->haveBeadSize()) {
53	>	sigma_ = simParams->getBeadSize();
54		}else {
55	<	std::cout << "RoughShell Model Error\n" ;
55	>
56		}
57	<	}
58	<
59	<	struct BeadLattice {
57	>	}
58	>
59	>	struct BeadLattice {
60		Vector3d origin;
61	<	double radius;
61	>	RealType radius;
62		bool interior;
63	<	};
64	<
65	<	struct ExteriorFunctor : public std::unary_function<BeadLattice, bool>{
66	<
63	>	};
64	>
65	>	struct ExteriorFunctor : public std::unary_function<BeadLattice, bool>{
66	>
67		bool operator() (const BeadLattice& bead) {
68	<	return !bead.interior;
68	>	return !bead.interior;
69		}
70	<
71	<	};
72	<
73	<	struct InteriorFunctor  : public std::unary_function<BeadLattice, bool>{
74	<
70	>
71	>	};
72	>
73	>	struct InteriorFunctor  : public std::unary_function<BeadLattice, bool>{
74	>
75		bool operator() (const BeadLattice& bead) {
76	<	return bead.interior;
76	>	return bead.interior;
77		}
78	<
79	<	};
80	<	bool RoughShell::createBeads(std::vector<BeadParam>& beads) {
81	<	std::pair<Vector3d, Vector3d> boxBoundary = sdShape_.getBox();
82	<	double len = boxBoundary.second[0] - boxBoundary.first[0];
83	<	int numLattices = static_cast<int>(len/sigma_) + 1;
78	>
79	>	};
80	>	bool RoughShell::createBeads(std::vector<BeadParam>& beads) {
81	>	std::pair<Vector3d, Vector3d> boxBoundary = shape_->getBoundingBox();
82	>	RealType firstMin = std::min(std::min(boxBoundary.first[0], boxBoundary.first[1]), boxBoundary.first[2]);
83	>	RealType secondMax = std::max(std::max(boxBoundary.second[0], boxBoundary.second[1]), boxBoundary.second[2]);
84	>	RealType len = secondMax - firstMin;
85	>	int numLattices = static_cast<int>(len/sigma_) + 2;
86		Grid3D<BeadLattice>  grid(numLattices, numLattices, numLattices);
87	<
87	>
88		//fill beads
89		for (int i = 0; i < numLattices; ++i) {
90	<	for (int j = 0; j < numLattices; ++j) {
91	<	for (int k = 0; k < numLattices; ++k) {
92	<	BeadLattice& currentBead = grid(i, j, k);
93	<	currentBead.origin = Vector3d(i*sigma_ + boxBoundary.first[0], j *sigma_ + boxBoundary.first[1], k*sigma_+ boxBoundary.first[2]);
94	<	currentBead.radius = sigma_;
95	<	currentBead.interior = sdShape_.isInterior(grid(i, j, k).origin);
91	<	}
90	>	for (int j = 0; j < numLattices; ++j) {
91	>	for (int k = 0; k < numLattices; ++k) {
92	>	BeadLattice& currentBead = grid(i, j, k);
93	>	currentBead.origin = Vector3d((i-1)*sigma_ + boxBoundary.first[0], (j-1) *sigma_ + boxBoundary.first[1], (k-1)*sigma_+ boxBoundary.first[2]);
94	>	currentBead.radius = sigma_ / 2.0;
95	>	currentBead.interior = shape_->isInterior(grid(i, j, k).origin);
96		}
97	+	}
98		}
99	<
99	>
100		//remove embedded beads
101		for (int i = 0; i < numLattices; ++i) {
102	<	for (int j = 0; j < numLattices; ++j) {
103	<	for (int k = 0; k < numLattices; ++k) {
104	<	std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k);
105	<	//if one of its neighbor cells is exterior, current cell is on the surface
106	<
107	<	std::vector<BeadLattice>::iterator ei = std::find_if(neighborCells.begin(), neighborCells.end(), ExteriorFunctor());
108	<	std::vector<BeadLattice>::iterator ii = std::find_if(neighborCells.begin(), neighborCells.end(), InteriorFunctor());
109	<
110	<	if (ei != neighborCells.end() && ii != neighborCells.end()) {
111	<	BeadParam surfaceBead;
112	<	surfaceBead.atomName = "Bead";
113	<	surfaceBead.pos = grid(i, j, k).origin;
114	<	surfaceBead.radius = grid(i, j, k).radius;
110	<	beads.push_back(surfaceBead);
111	<	}
112	<
102	>	for (int j = 0; j < numLattices; ++j) {
103	>	for (int k = 0; k < numLattices; ++k) {
104	>	std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k);
105	>	//if one of its neighbor cells is exterior, current cell is on the surface
106	>
107	>	if (grid(i, j, k).interior){
108	>
109	>	bool allNeighBorIsInterior = true;
110	>	for (std::vector<BeadLattice>::iterator l = neighborCells.begin(); l != neighborCells.end(); ++l) {
111	>	if (!l->interior) {
112	>	allNeighBorIsInterior = false;
113	>	break;
114	>	}
115		}
116	+
117	+	if (allNeighBorIsInterior)
118	+	continue;
119	+
120	+	BeadParam surfaceBead;
121	+	surfaceBead.atomName = "H";
122	+	surfaceBead.pos = grid(i, j, k).origin;
123	+	surfaceBead.radius = grid(i, j, k).radius;
124	+	beads.push_back(surfaceBead);
125	+
126	+	}
127		}
128	+	}
129		}
130	<
130	>
131		return true;
132	+	}
133	+
134		}
119	–
120	–	}

Comparing trunk/src/applications/hydrodynamics/RoughShell.cpp (property svn:keywords):
Revision 898 by tim, Wed Mar 15 15:51:44 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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