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root/OpenMD/trunk/src/lattice/Lattice.cpp

Comparing trunk/src/lattice/Lattice.cpp (file contents):
Revision 484 by tim, Tue Apr 12 21:58:09 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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 "lattice/Lattice.hpp"
43	–	#include "lattice/LatticeFactory.hpp"
44	–	#include "lattice/LatticeCreator.hpp"
44
45	<	namespace oopse {
45	>	namespace OpenMD{
46	>	void Lattice::getLatticePointsPos(std::vector<Vector3d>& latticePos, int nx, int ny, int nz){
47
48	<	CubicLattice::CubicLattice(){
49	<	latticeParam = 1.0;
50	<
51	<	cellLen[0] = latticeParam;
52	<	cellLen[1] = latticeParam;
53	<	cellLen[2] = latticeParam;
54	<
55	<	}
48	>	latticePos.resize(nCellSites);
49	>
50	>	for( int i=0;i < nCellSites;i++){
51
52	<	std::vector<double> CubicLattice::getLatticeConstant(){
53	<	std::vector<double> lc;
54	<
55	<	lc.push_back(cellLen.x());
61	<	return lc;
62	<	}
52	>	latticePos[i][0] = origin[0] + cellSitesPos[i][0] + cellLen[0] * (RealType(nx) - 0.5);
53	>	latticePos[i][1] = origin[1] + cellSitesPos[i][1] + cellLen[1] * (RealType(ny) - 0.5);
54	>	latticePos[i][2] = origin[2] + cellSitesPos[i][2] + cellLen[2] * (RealType(nz) - 0.5);
55	>	}
56
64	–	void CubicLattice::setLatticeConstant(const  std::vector<double>& lc){
65	–
66	–	if(lc.size() < 1){
67	–	std::cerr << "CubicLattice::setLatticeConstant Error: the size of lattice constant vector  is 0" << std::endl;
68	–	exit(1);
57		}
70	–	else if (lc.size() > 1){
71	–	std::cerr << "CubicLattice::setLatticeConstant Warning: the size of lattice constant vector  is " << lc.size() << std::endl;
72	–	}
73	–
74	–	latticeParam = lc[0];
75	–
76	–	cellLen[0] = latticeParam;
77	–	cellLen[1] = latticeParam;
78	–	cellLen[2] = latticeParam;
79	–
80	–	update();
81	–	}
58
83	–	FCCLattice::FCCLattice() : CubicLattice(){
84	–	nCellSites = 4;
85	–	cellSitesPos.resize(nCellSites);
86	–	cellSitesOrt.resize(nCellSites);
87	–	update();
88	–
59		}
90	–
91	–	void FCCLattice::update(){
92	–
93	–	double cellLenOver2;
94	–	double oneOverRoot3;
95	–
96	–	cellLenOver2  = 0.5 * latticeParam;
97	–	oneOverRoot3 = 1.0 / sqrt(3.0);
98	–
99	–	// Molecule 1
100	–	cellSitesPos[0][0] = 0.0;
101	–	cellSitesPos[0][1] = 0.0;
102	–	cellSitesPos[0][2] = 0.0;
103	–
104	–	cellSitesOrt[0][0] = oneOverRoot3;
105	–	cellSitesOrt[0][1] = oneOverRoot3;
106	–	cellSitesOrt[0][2] = oneOverRoot3;
107	–
108	–	// Molecule 2
109	–	cellSitesPos[1][0]   = 0.0;
110	–	cellSitesPos[1][1]   = cellLenOver2;
111	–	cellSitesPos[1][2]   = cellLenOver2;
112	–
113	–	cellSitesOrt[1][0] = -oneOverRoot3;
114	–	cellSitesOrt[1][1] = oneOverRoot3;
115	–	cellSitesOrt[1][2] = -oneOverRoot3;
116	–
117	–	// Molecule 3
118	–	cellSitesPos[2][0]   = cellLenOver2;
119	–	cellSitesPos[2][1]   = cellLenOver2;
120	–	cellSitesPos[2][2]   = 0.0;
121	–
122	–	cellSitesOrt[2][0] = oneOverRoot3;
123	–	cellSitesOrt[2][1] = -oneOverRoot3;
124	–	cellSitesOrt[2][2] = -oneOverRoot3;
125	–
126	–	// Molecule 4
127	–
128	–	cellSitesPos[3][0]   = cellLenOver2;
129	–	cellSitesPos[3][1]   = 0.0;
130	–	cellSitesPos[3][2]   = cellLenOver2;
131	–
132	–	cellSitesOrt[3][0] = -oneOverRoot3;
133	–	cellSitesOrt[3][1] = oneOverRoot3;
134	–	cellSitesOrt[3][2] = oneOverRoot3;
135	–	}
136	–
137	–	}

Comparing trunk/src/lattice/Lattice.cpp (property svn:keywords):
Revision 484 by tim, Tue Apr 12 21:58:09 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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