OpenMD 3.1
Molecular Dynamics in the Open
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Icosahedron.cpp
1/*
2 * Copyright (c) 2004-present, The University of Notre Dame. All rights
3 * reserved.
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9 * this list of conditions and the following disclaimer.
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19 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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28 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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30 *
31 * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32 * research, please cite the appropriate papers when you publish your
33 * work. Good starting points are:
34 *
35 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45#include "clusters/Icosahedron.hpp"
46
47#include <tuple>
48
49namespace OpenMD {
50
51 Icosahedron::Icosahedron() {
52 Basis.clear();
53 Edges.clear();
54 Facets.clear();
55 Points.clear();
56
57 //
58 // Initialize Basis vectors.
59 //
60 const RealType HGR = (sqrt(5.0) + 1.0) / 4.0; // half of the golden ratio
61
62 Basis.push_back(Vector3d(HGR, 0.0, 0.5));
63 Basis.push_back(Vector3d(HGR, 0.0, -0.5));
64 Basis.push_back(Vector3d(0.5, HGR, 0.0));
65 Basis.push_back(Vector3d(-0.5, HGR, 0.0));
66 Basis.push_back(Vector3d(0.0, 0.5, HGR));
67 Basis.push_back(Vector3d(0.0, -0.5, HGR));
68 Basis.push_back(Vector3d(0.5, -HGR, 0.0));
69 Basis.push_back(Vector3d(0.0, 0.5, -HGR));
70 Basis.push_back(Vector3d(-HGR, 0.0, 0.5));
71 Basis.push_back(Vector3d(0.0, -0.5, -HGR));
72 Basis.push_back(Vector3d(-HGR, 0.0, -0.5));
73 Basis.push_back(Vector3d(-0.5, -HGR, 0.0));
74
75 //
76 // Initialize 30 edges
77 //
78
79 Edges.push_back(std::make_pair(0, 1));
80 Edges.push_back(std::make_pair(0, 2));
81 Edges.push_back(std::make_pair(0, 4));
82 Edges.push_back(std::make_pair(0, 5));
83 Edges.push_back(std::make_pair(0, 6));
84
85 Edges.push_back(std::make_pair(10, 3));
86 Edges.push_back(std::make_pair(10, 7));
87 Edges.push_back(std::make_pair(10, 8));
88 Edges.push_back(std::make_pair(10, 9));
89 Edges.push_back(std::make_pair(10, 11));
90
91 Edges.push_back(std::make_pair(1, 2));
92 Edges.push_back(std::make_pair(1, 6));
93 Edges.push_back(std::make_pair(1, 7));
94 Edges.push_back(std::make_pair(1, 9));
95
96 Edges.push_back(std::make_pair(8, 3));
97 Edges.push_back(std::make_pair(8, 4));
98 Edges.push_back(std::make_pair(8, 5));
99 Edges.push_back(std::make_pair(8, 11));
100
101 Edges.push_back(std::make_pair(2, 3));
102 Edges.push_back(std::make_pair(2, 4));
103 Edges.push_back(std::make_pair(2, 7));
104
105 Edges.push_back(std::make_pair(11, 5));
106 Edges.push_back(std::make_pair(11, 6));
107 Edges.push_back(std::make_pair(11, 9));
108
109 Edges.push_back(std::make_pair(6, 5));
110 Edges.push_back(std::make_pair(6, 9));
111
112 Edges.push_back(std::make_pair(3, 4));
113 Edges.push_back(std::make_pair(3, 7));
114
115 Edges.push_back(std::make_pair(7, 9));
116
117 Edges.push_back(std::make_pair(5, 4));
118
119 //
120 // Initialize 20 facets
121 //
122 Facets.push_back(std::make_tuple(0, 1, 2));
123 Facets.push_back(std::make_tuple(0, 2, 4));
124 Facets.push_back(std::make_tuple(0, 4, 5));
125 Facets.push_back(std::make_tuple(0, 5, 6));
126 Facets.push_back(std::make_tuple(0, 1, 6));
127
128 Facets.push_back(std::make_tuple(10, 3, 7));
129 Facets.push_back(std::make_tuple(10, 3, 8));
130 Facets.push_back(std::make_tuple(10, 8, 11));
131 Facets.push_back(std::make_tuple(10, 9, 11));
132 Facets.push_back(std::make_tuple(10, 7, 9));
133
134 Facets.push_back(std::make_tuple(1, 2, 7));
135 Facets.push_back(std::make_tuple(1, 7, 9));
136 Facets.push_back(std::make_tuple(1, 6, 9));
137
138 Facets.push_back(std::make_tuple(8, 5, 11));
139 Facets.push_back(std::make_tuple(8, 4, 5));
140 Facets.push_back(std::make_tuple(8, 3, 4));
141
142 Facets.push_back(std::make_tuple(2, 3, 7));
143 Facets.push_back(std::make_tuple(2, 3, 4));
144
145 Facets.push_back(std::make_tuple(11, 5, 6));
146 Facets.push_back(std::make_tuple(11, 6, 9));
147 }
148
149 int Icosahedron::getNpoints(int n) {
150 int count = 0;
151 for (int i = 0; i <= n; i++)
152 count += np(i);
153 return count;
154 }
155
156 int Icosahedron::np(int n) {
157 if (n < 0)
158 return -1;
159 else if (n == 0)
160 return 1;
161 else if (n == 1)
162 return 12;
163 else if (n == 2)
164 return 42;
165 else {
166 int count = 0;
167 count += 12; // edge particles
168 count += (n - 1) * 30; // side particles
169 for (int i = 1; i <= n - 2; i++)
170 count += i * 20; // body particles
171 return count;
172 }
173 }
174
175 std::vector<Vector3d> Icosahedron::ih(int n) {
176 if (n < 0) return Points;
177
178 if (n == 0) {
179 // center particle only
180
181 Points.push_back(Vector3d(0.0, 0.0, 0.0));
182 return Points;
183 }
184
185 //
186 // Generate edge particles
187 //
188 for (std::vector<Vector3d>::iterator i = Basis.begin(); i != Basis.end();
189 ++i) {
190 Points.push_back((*i) * RealType(n));
191 }
192
193 //
194 // Generate side particles
195 //
196 if (n < 2) return Points;
197
198 for (std::vector<std::pair<int, int>>::iterator i = Edges.begin();
199 i != Edges.end(); ++i) {
200 Vector3d e1 = Basis[(*i).first] * RealType(n);
201 Vector3d e2 = Basis[(*i).second] * RealType(n);
202
203 for (int j = 1; j <= n - 1; j++) {
204 Points.push_back(e1 + (e2 - e1) * RealType(j) / RealType(n));
205 }
206 }
207
208 //
209 // Generate body particles
210 //
211 if (n < 3) return Points;
212
213 for (const auto& [first, second, third] : Facets) {
214 Vector3d e1 = Basis[first] * RealType(n);
215 Vector3d e2 = Basis[second] * RealType(n);
216 Vector3d e3 = Basis[third] * RealType(n);
217
218 for (int j = 1; j <= n - 2; j++) {
219 Vector3d v1 = e1 + (e2 - e1) * RealType(j + 1) / RealType(n);
220 Vector3d v2 = e1 + (e3 - e1) * RealType(j + 1) / RealType(n);
221
222 for (int k = 1; k <= j; k++) {
223 Points.push_back(v1 + (v2 - v1) * RealType(k) / RealType(j + 1));
224 }
225 }
226 }
227
228 return Points;
229 }
230
231 std::vector<Vector3d> Icosahedron::getPoints(int nshells) {
232 // generate the coordinates
233 for (int i = 0; i <= nshells; i++)
234 ih(i);
235 return Points;
236 }
237} // namespace OpenMD
Icosahedron.hpp
Icosahedron cluster structure generator.
OpenMD::Icosahedron::np
int np(int n)
Calculate number of particles on the nth layer.
Definition Icosahedron.cpp:156
OpenMD::Icosahedron::Icosahedron
Icosahedron()
Default constructor.
Definition Icosahedron.cpp:51
OpenMD::Icosahedron::getNpoints
int getNpoints(int nShells)
Calculate number of particles in an icosahedron with nShells shells.
Definition Icosahedron.cpp:149
OpenMD::Icosahedron::getPoints
std::vector< Vector3d > getPoints(int nShells)
Get the generated points in an icosahedron with nShells shells.
Definition Icosahedron.cpp:231
OpenMD::Icosahedron::ih
std::vector< Vector3d > ih(int n)
Create nth layer particles.
Definition Icosahedron.cpp:175
OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
Definition ActionCorrFunc.cpp:60