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, 234107 (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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (11 years, 10 months ago) by gezelter
File size:	5232 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	Content
1	/*
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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
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	*
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 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
56	}
57	}
58
59	struct BeadLattice {
60	Vector3d origin;
61	RealType radius;
62	bool interior;
63	};
64
65	struct ExteriorFunctor : public std::unary_function<BeadLattice, bool>{
66
67	bool operator() (const BeadLattice& bead) {
68	return !bead.interior;
69	}
70
71	};
72
73	struct InteriorFunctor : public std::unary_function<BeadLattice, bool>{
74
75	bool operator() (const BeadLattice& bead) {
76	return bead.interior;
77	}
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
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-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
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	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
131	return true;
132	}
133
134	}