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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	5231 byte(s)
Log Message:	updated copyright notices
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	898	*/
42
43			#include "applications/hydrodynamics/RoughShell.hpp"
44	tim	906	#include "applications/hydrodynamics/ShapeBuilder.hpp"
45			#include "brains/SimInfo.hpp"
46	gezelter	1562
47	gezelter	1390	namespace OpenMD {
48	gezelter	972
49			RoughShell::RoughShell(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info){
50	tim	906	shape_=ShapeBuilder::createShape(sd);
51			Globals* simParams = info->getSimParams();
52			if (simParams->haveBeadSize()) {
53	gezelter	972	sigma_ = simParams->getBeadSize();
54	tim	898	}else {
55	gezelter	972
56	tim	898	}
57	gezelter	972	}
58
59			struct BeadLattice {
60	tim	898	Vector3d origin;
61	gezelter	972	RealType radius;
62	tim	898	bool interior;
63	gezelter	972	};
64
65			struct ExteriorFunctor : public std::unary_function<BeadLattice, bool>{
66
67	tim	898	bool operator() (const BeadLattice& bead) {
68	gezelter	972	return !bead.interior;
69	tim	898	}
70	gezelter	972
71			};
72
73			struct InteriorFunctor : public std::unary_function<BeadLattice, bool>{
74
75	tim	898	bool operator() (const BeadLattice& bead) {
76	gezelter	972	return bead.interior;
77	tim	898	}
78	gezelter	972
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	tim	921	int numLattices = static_cast<int>(len/sigma_) + 2;
86	tim	898	Grid3D<BeadLattice> grid(numLattices, numLattices, numLattices);
87	gezelter	972
88	tim	898	//fill beads
89			for (int i = 0; i < numLattices; ++i) {
90	gezelter	972	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	xsun	1208	currentBead.radius = sigma_ / 2.0;
95	gezelter	972	currentBead.interior = shape_->isInterior(grid(i, j, k).origin);
96	tim	898	}
97	gezelter	972	}
98	tim	898	}
99	gezelter	972
100	tim	898	//remove embedded beads
101			for (int i = 0; i < numLattices; ++i) {
102	gezelter	972	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	tim	898	}
116	gezelter	972
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	tim	898	}
128	gezelter	972	}
129	tim	898	}
130	gezelter	972
131	tim	898	return true;
132	gezelter	972	}
133
134	tim	898	}