trunk/nanorodBuilder/Lattice.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/simpleBuilder/Lattice.hpp"
#include "applications/simpleBuilder/LatticeFactory.hpp"
#include "applications/simpleBuilder/LatticeCreator.hpp"

namespace oopse {

static LatticeCreator<FCCLattice> *FCCLatticeCreator = new LatticeCreator<FCCLattice>(FCCLatticeType);

CubicLattice::CubicLattice(){
  latticeParam = 1.0;
  
  cellLen[0] = latticeParam;
  cellLen[1] = latticeParam;
  cellLen[2] = latticeParam;
  
}

 std::vector<double> CubicLattice::getLatticeConstant(){
   std::vector<double> lc;
  
  lc.push_back(cellLen.x());
  return lc;
}

void CubicLattice::setLatticeConstant(const  std::vector<double>& lc){
  
  if(lc.size() < 1){
    std::cerr << "CubicLattice::setLatticeConstant Error: the size of lattice constant vector  is 0" << std::endl;
    exit(1);
  }
  else if (lc.size() > 1){
    std::cerr << "CubicLattice::setLatticeConstant Warning: the size of lattice constant vector  is " << lc.size() << std::endl;
  }
  
  latticeParam = lc[0];
  
  cellLen[0] = latticeParam;
  cellLen[1] = latticeParam;
  cellLen[2] = latticeParam;
  
  update();
}

FCCLattice::FCCLattice() : CubicLattice(){
  nCellSites = 4;
  cellSitesPos.resize(nCellSites);
  cellSitesOrt.resize(nCellSites);
  update();

}

void FCCLattice::update(){

  double cellLenOver2;
  double oneOverRoot3;

  cellLenOver2  = 0.5 * latticeParam;
  oneOverRoot3 = 1.0 / sqrt(3.0);

  // Molecule 1
  cellSitesPos[0][0] = 0.0; 
  cellSitesPos[0][1] = 0.0;
  cellSitesPos[0][2] = 0.0;
  
   cellSitesOrt[0][0] = oneOverRoot3;
   cellSitesOrt[0][1] = oneOverRoot3;
   cellSitesOrt[0][2] = oneOverRoot3;

  // Molecule 2  
  cellSitesPos[1][0]   = 0.0;
  cellSitesPos[1][1]   = cellLenOver2;
  cellSitesPos[1][2]   = cellLenOver2;

  cellSitesOrt[1][0] = -oneOverRoot3;
  cellSitesOrt[1][1] = oneOverRoot3;
  cellSitesOrt[1][2] = -oneOverRoot3;
   
  // Molecule 3
  cellSitesPos[2][0]   = cellLenOver2;
  cellSitesPos[2][1]   = cellLenOver2;
  cellSitesPos[2][2]   = 0.0;

  cellSitesOrt[2][0] = oneOverRoot3;
  cellSitesOrt[2][1] = -oneOverRoot3;
  cellSitesOrt[2][2] = -oneOverRoot3;

  // Molecule 4

  cellSitesPos[3][0]   = cellLenOver2;
  cellSitesPos[3][1]   = 0.0;
  cellSitesPos[3][2]   = cellLenOver2;

  cellSitesOrt[3][0] = -oneOverRoot3;
  cellSitesOrt[3][1] = oneOverRoot3;
  cellSitesOrt[3][2] = oneOverRoot3;
}

}
Revision:	2148
Committed:	Wed Apr 6 16:34:09 2005 UTC (19 years, 3 months ago) by chuckv
File size:	4407 byte(s)
Log Message:	Initial import of nanorod builder.
#	User	Rev	Content
1	chuckv	2148	/*
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/simpleBuilder/Lattice.hpp"
43			#include "applications/simpleBuilder/LatticeFactory.hpp"
44			#include "applications/simpleBuilder/LatticeCreator.hpp"
45
46			namespace oopse {
47
48			static LatticeCreator<FCCLattice> *FCCLatticeCreator = new LatticeCreator<FCCLattice>(FCCLatticeType);
49
50			CubicLattice::CubicLattice(){
51			latticeParam = 1.0;
52
53			cellLen[0] = latticeParam;
54			cellLen[1] = latticeParam;
55			cellLen[2] = latticeParam;
56
57			}
58
59			std::vector<double> CubicLattice::getLatticeConstant(){
60			std::vector<double> lc;
61
62			lc.push_back(cellLen.x());
63			return lc;
64			}
65
66			void CubicLattice::setLatticeConstant(const std::vector<double>& lc){
67
68			if(lc.size() < 1){
69			std::cerr << "CubicLattice::setLatticeConstant Error: the size of lattice constant vector is 0" << std::endl;
70			exit(1);
71			}
72			else if (lc.size() > 1){
73			std::cerr << "CubicLattice::setLatticeConstant Warning: the size of lattice constant vector is " << lc.size() << std::endl;
74			}
75
76			latticeParam = lc[0];
77
78			cellLen[0] = latticeParam;
79			cellLen[1] = latticeParam;
80			cellLen[2] = latticeParam;
81
82			update();
83			}
84
85			FCCLattice::FCCLattice() : CubicLattice(){
86			nCellSites = 4;
87			cellSitesPos.resize(nCellSites);
88			cellSitesOrt.resize(nCellSites);
89			update();
90
91			}
92
93			void FCCLattice::update(){
94
95			double cellLenOver2;
96			double oneOverRoot3;
97
98			cellLenOver2 = 0.5 * latticeParam;
99			oneOverRoot3 = 1.0 / sqrt(3.0);
100
101			// Molecule 1
102			cellSitesPos[0][0] = 0.0;
103			cellSitesPos[0][1] = 0.0;
104			cellSitesPos[0][2] = 0.0;
105
106			cellSitesOrt[0][0] = oneOverRoot3;
107			cellSitesOrt[0][1] = oneOverRoot3;
108			cellSitesOrt[0][2] = oneOverRoot3;
109
110			// Molecule 2
111			cellSitesPos[1][0] = 0.0;
112			cellSitesPos[1][1] = cellLenOver2;
113			cellSitesPos[1][2] = cellLenOver2;
114
115			cellSitesOrt[1][0] = -oneOverRoot3;
116			cellSitesOrt[1][1] = oneOverRoot3;
117			cellSitesOrt[1][2] = -oneOverRoot3;
118
119			// Molecule 3
120			cellSitesPos[2][0] = cellLenOver2;
121			cellSitesPos[2][1] = cellLenOver2;
122			cellSitesPos[2][2] = 0.0;
123
124			cellSitesOrt[2][0] = oneOverRoot3;
125			cellSitesOrt[2][1] = -oneOverRoot3;
126			cellSitesOrt[2][2] = -oneOverRoot3;
127
128			// Molecule 4
129
130			cellSitesPos[3][0] = cellLenOver2;
131			cellSitesPos[3][1] = 0.0;
132			cellSitesPos[3][2] = cellLenOver2;
133
134			cellSitesOrt[3][0] = -oneOverRoot3;
135			cellSitesOrt[3][1] = oneOverRoot3;
136			cellSitesOrt[3][2] = oneOverRoot3;
137			}
138
139			}