applications/hydrodynamics/RoughShell.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 "applications/hydrodynamics/RoughShell.hpp"

namespace oopse {

RoughShell::RoughShell(StuntDouble* sd, const DynamicProperty& extraParams) : HydrodynamicsModel(sd, extraParams), sdShape_(sd){
    DynamicProperty::const_iterator iter = extraParams.find("Sigma");
    if (iter != extraParams.end()) {
        boost::any param = iter->second;
        sigma_ = boost::any_cast<double>(param);
    }else {
        std::cout << "RoughShell Model Error\n" ;
    }
}

struct BeadLattice {
    Vector3d origin;
    double radius;
    bool interior;
};

struct ExteriorFunctor : public std::unary_function<BeadLattice, bool>{

    bool operator() (const BeadLattice& bead) {
        return !bead.interior;
    }

};

struct InteriorFunctor  : public std::unary_function<BeadLattice, bool>{

    bool operator() (const BeadLattice& bead) {
        return bead.interior;
    }

};
bool RoughShell::createBeads(std::vector<BeadParam>& beads) {
    std::pair<Vector3d, Vector3d> boxBoundary = sdShape_.getBox();
    double len = boxBoundary.second[0] - boxBoundary.first[0];
    int numLattices = static_cast<int>(len/sigma_) + 1;
    Grid3D<BeadLattice>  grid(numLattices, numLattices, numLattices);

    //fill beads
    for (int i = 0; i < numLattices; ++i) {
        for (int j = 0; j < numLattices; ++j) {
            for (int k = 0; k < numLattices; ++k) {
                BeadLattice& currentBead = grid(i, j, k);
                currentBead.origin = Vector3d(i*sigma_ + boxBoundary.first[0], j *sigma_ + boxBoundary.first[1], k*sigma_+ boxBoundary.first[2]);
                currentBead.radius = sigma_;
                currentBead.interior = sdShape_.isInterior(grid(i, j, k).origin);                
            }
        }
    }

    //remove embedded beads 
    for (int i = 0; i < numLattices; ++i) {
        for (int j = 0; j < numLattices; ++j) {
            for (int k = 0; k < numLattices; ++k) {
                 std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k);
                 //if one of its neighbor cells is exterior, current cell is on the surface

                 std::vector<BeadLattice>::iterator ei = std::find_if(neighborCells.begin(), neighborCells.end(), ExteriorFunctor());                
                 std::vector<BeadLattice>::iterator ii = std::find_if(neighborCells.begin(), neighborCells.end(), InteriorFunctor());                
                 
                  if (ei != neighborCells.end() && ii != neighborCells.end()) {
                      BeadParam surfaceBead;
                      surfaceBead.atomName = "Bead";
                      surfaceBead.pos = grid(i, j, k).origin;
                      surfaceBead.radius = grid(i, j, k).radius;
                      beads.push_back(surfaceBead);
                  }

            }
        }
    }
     
    return true;
}

}
Revision:	898
Committed:	Wed Mar 15 15:51:44 2006 UTC (19 years, 1 month ago) by tim
Original Path:	*trunk/src/applications/hydrodynamics/RoughShell.cpp*
File size:	4921 byte(s)
Log Message:	Adding RoughShell and BeadModel
#	User	Rev	Content
1	tim	898	/*
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 "applications/hydrodynamics/RoughShell.hpp"
43
44			namespace oopse {
45
46			RoughShell::RoughShell(StuntDouble* sd, const DynamicProperty& extraParams) : HydrodynamicsModel(sd, extraParams), sdShape_(sd){
47			DynamicProperty::const_iterator iter = extraParams.find("Sigma");
48			if (iter != extraParams.end()) {
49			boost::any param = iter->second;
50			sigma_ = boost::any_cast<double>(param);
51			}else {
52			std::cout << "RoughShell Model Error\n" ;
53			}
54			}
55
56			struct BeadLattice {
57			Vector3d origin;
58			double radius;
59			bool interior;
60			};
61
62			struct ExteriorFunctor : public std::unary_function<BeadLattice, bool>{
63
64			bool operator() (const BeadLattice& bead) {
65			return !bead.interior;
66			}
67
68			};
69
70			struct InteriorFunctor : public std::unary_function<BeadLattice, bool>{
71
72			bool operator() (const BeadLattice& bead) {
73			return bead.interior;
74			}
75
76			};
77			bool RoughShell::createBeads(std::vector<BeadParam>& beads) {
78			std::pair<Vector3d, Vector3d> boxBoundary = sdShape_.getBox();
79			double len = boxBoundary.second[0] - boxBoundary.first[0];
80			int numLattices = static_cast<int>(len/sigma_) + 1;
81			Grid3D<BeadLattice> grid(numLattices, numLattices, numLattices);
82
83			//fill beads
84			for (int i = 0; i < numLattices; ++i) {
85			for (int j = 0; j < numLattices; ++j) {
86			for (int k = 0; k < numLattices; ++k) {
87			BeadLattice& currentBead = grid(i, j, k);
88			currentBead.origin = Vector3d(isigma_ + boxBoundary.first[0], j sigma_ + boxBoundary.first[1], k*sigma_+ boxBoundary.first[2]);
89			currentBead.radius = sigma_;
90			currentBead.interior = sdShape_.isInterior(grid(i, j, k).origin);
91			}
92			}
93			}
94
95			//remove embedded beads
96			for (int i = 0; i < numLattices; ++i) {
97			for (int j = 0; j < numLattices; ++j) {
98			for (int k = 0; k < numLattices; ++k) {
99			std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k);
100			//if one of its neighbor cells is exterior, current cell is on the surface
101
102			std::vector<BeadLattice>::iterator ei = std::find_if(neighborCells.begin(), neighborCells.end(), ExteriorFunctor());
103			std::vector<BeadLattice>::iterator ii = std::find_if(neighborCells.begin(), neighborCells.end(), InteriorFunctor());
104
105			if (ei != neighborCells.end() && ii != neighborCells.end()) {
106			BeadParam surfaceBead;
107			surfaceBead.atomName = "Bead";
108			surfaceBead.pos = grid(i, j, k).origin;
109			surfaceBead.radius = grid(i, j, k).radius;
110			beads.push_back(surfaceBead);
111			}
112
113			}
114			}
115			}
116
117			return true;
118			}
119
120			}