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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

#include "applications/hydrodynamics/RoughShell.hpp"
#include "applications/hydrodynamics/ShapeBuilder.hpp"
#include "brains/SimInfo.hpp"
namespace OpenMD {
  
  RoughShell::RoughShell(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info){
    shape_=ShapeBuilder::createShape(sd);
    Globals* simParams = info->getSimParams();
    if (simParams->haveBeadSize()) {
      sigma_ = simParams->getBeadSize();
    }else {
      
    }
  }
  
  struct BeadLattice {
    Vector3d origin;
    RealType 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 = shape_->getBoundingBox();
    RealType firstMin = std::min(std::min(boxBoundary.first[0], boxBoundary.first[1]), boxBoundary.first[2]);
    RealType secondMax = std::max(std::max(boxBoundary.second[0], boxBoundary.second[1]), boxBoundary.second[2]);
    RealType len = secondMax - firstMin;
    int numLattices = static_cast<int>(len/sigma_) + 2;
    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-1)*sigma_ + boxBoundary.first[0], (j-1) *sigma_ + boxBoundary.first[1], (k-1)*sigma_+ boxBoundary.first[2]);
          currentBead.radius = sigma_ / 2.0;
          currentBead.interior = shape_->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
          
          if (grid(i, j, k).interior){
            
            bool allNeighBorIsInterior = true;
            for (std::vector<BeadLattice>::iterator l = neighborCells.begin(); l != neighborCells.end(); ++l) {
              if (!l->interior) {
                allNeighBorIsInterior = false;
                break;
              }
            }
            
            if (allNeighBorIsInterior)
              continue;
            
            BeadParam surfaceBead;
            surfaceBead.atomName = "H";
            surfaceBead.pos = grid(i, j, k).origin;
            surfaceBead.radius = grid(i, j, k).radius;
            beads.push_back(surfaceBead);                    
            
          }
        }
      }
    }
    
    return true;
  }
  
}
Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	5164 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	898	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	898	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
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	gezelter	1390	*
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	tim	898	*/
41
42			#include "applications/hydrodynamics/RoughShell.hpp"
43	tim	906	#include "applications/hydrodynamics/ShapeBuilder.hpp"
44			#include "brains/SimInfo.hpp"
45	gezelter	1390	namespace OpenMD {
46	gezelter	972
47			RoughShell::RoughShell(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info){
48	tim	906	shape_=ShapeBuilder::createShape(sd);
49			Globals* simParams = info->getSimParams();
50			if (simParams->haveBeadSize()) {
51	gezelter	972	sigma_ = simParams->getBeadSize();
52	tim	898	}else {
53	gezelter	972
54	tim	898	}
55	gezelter	972	}
56
57			struct BeadLattice {
58	tim	898	Vector3d origin;
59	gezelter	972	RealType radius;
60	tim	898	bool interior;
61	gezelter	972	};
62
63			struct ExteriorFunctor : public std::unary_function<BeadLattice, bool>{
64
65	tim	898	bool operator() (const BeadLattice& bead) {
66	gezelter	972	return !bead.interior;
67	tim	898	}
68	gezelter	972
69			};
70
71			struct InteriorFunctor : public std::unary_function<BeadLattice, bool>{
72
73	tim	898	bool operator() (const BeadLattice& bead) {
74	gezelter	972	return bead.interior;
75	tim	898	}
76	gezelter	972
77			};
78			bool RoughShell::createBeads(std::vector<BeadParam>& beads) {
79			std::pair<Vector3d, Vector3d> boxBoundary = shape_->getBoundingBox();
80			RealType firstMin = std::min(std::min(boxBoundary.first[0], boxBoundary.first[1]), boxBoundary.first[2]);
81			RealType secondMax = std::max(std::max(boxBoundary.second[0], boxBoundary.second[1]), boxBoundary.second[2]);
82			RealType len = secondMax - firstMin;
83	tim	921	int numLattices = static_cast<int>(len/sigma_) + 2;
84	tim	898	Grid3D<BeadLattice> grid(numLattices, numLattices, numLattices);
85	gezelter	972
86	tim	898	//fill beads
87			for (int i = 0; i < numLattices; ++i) {
88	gezelter	972	for (int j = 0; j < numLattices; ++j) {
89			for (int k = 0; k < numLattices; ++k) {
90			BeadLattice& currentBead = grid(i, j, k);
91			currentBead.origin = Vector3d((i-1)sigma_ + boxBoundary.first[0], (j-1) sigma_ + boxBoundary.first[1], (k-1)*sigma_+ boxBoundary.first[2]);
92	xsun	1208	currentBead.radius = sigma_ / 2.0;
93	gezelter	972	currentBead.interior = shape_->isInterior(grid(i, j, k).origin);
94	tim	898	}
95	gezelter	972	}
96	tim	898	}
97	gezelter	972
98	tim	898	//remove embedded beads
99			for (int i = 0; i < numLattices; ++i) {
100	gezelter	972	for (int j = 0; j < numLattices; ++j) {
101			for (int k = 0; k < numLattices; ++k) {
102			std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k);
103			//if one of its neighbor cells is exterior, current cell is on the surface
104
105			if (grid(i, j, k).interior){
106
107			bool allNeighBorIsInterior = true;
108			for (std::vector<BeadLattice>::iterator l = neighborCells.begin(); l != neighborCells.end(); ++l) {
109			if (!l->interior) {
110			allNeighBorIsInterior = false;
111			break;
112			}
113	tim	898	}
114	gezelter	972
115			if (allNeighBorIsInterior)
116			continue;
117
118			BeadParam surfaceBead;
119			surfaceBead.atomName = "H";
120			surfaceBead.pos = grid(i, j, k).origin;
121			surfaceBead.radius = grid(i, j, k).radius;
122			beads.push_back(surfaceBead);
123
124			}
125	tim	898	}
126	gezelter	972	}
127	tim	898	}
128	gezelter	972
129	tim	898	return true;
130	gezelter	972	}
131
132	tim	898	}