OpenMD 3.0
Molecular Dynamics in the Open
Loading...
Searching...
No Matches
shapedLatticeRod.cpp
1/*
2 * Copyright (c) 2004-present, The University of Notre Dame. All rights
3 * reserved.
4 *
5 * Redistribution and use in source and binary forms, with or without
6 * modification, are permitted provided that the following conditions are met:
7 *
8 * 1. Redistributions of source code must retain the above copyright notice,
9 * this list of conditions and the following disclaimer.
10 *
11 * 2. Redistributions in binary form must reproduce the above copyright notice,
12 * this list of conditions and the following disclaimer in the documentation
13 * and/or other materials provided with the distribution.
14 *
15 * 3. Neither the name of the copyright holder nor the names of its
16 * contributors may be used to endorse or promote products derived from
17 * this software without specific prior written permission.
18 *
19 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
20 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
21 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
23 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
24 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
25 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
26 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
27 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
28 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
29 * POSSIBILITY OF SUCH DAMAGE.
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/*
46 * Created by Kelsey M. Stocker on 2/9/12.
47 * @author Kelsey M. Stocker
48 * @version $Id: shapedLatticeRod.cpp 1665 2011-11-22 20:38:56Z gezelter $
49 *
50 */
51
52#include "shapedLatticeRod.hpp"
53
54#include <cmath>
55
56#include "lattice/shapedLattice.hpp"
57
58using namespace std;
59namespace OpenMD {
60
61 shapedLatticeRod::shapedLatticeRod(RealType latticeConstant,
62 std::string latticeType, RealType radius,
63 RealType length) :
64 shapedLattice(latticeConstant, latticeType) {
65 rodRadius_ = radius;
66 rodLength_ = length;
67 Vector3d dimension;
68 dimension[0] = 3.0 * radius;
69 dimension[1] = 3.0 * radius;
70 dimension[2] = length + 3.0 * radius;
71 setGridDimension(dimension);
72 Vector3d origin;
73 origin[0] = 0;
74 origin[1] = 0;
75 origin[2] = 0;
76 setOrigin(origin);
77 }
78
79 /**
80 * Determines whether a point lies within a spherically-capped
81 * nanorod at origin (0,0,0)
82 *
83 */
84 bool shapedLatticeRod::isInterior(Vector3d point) {
85 RealType x, y, z, distance;
86
87 distance = 0;
88
89 x = point[0];
90 y = point[1];
91 z = point[2];
92
93 if (abs(z) >= rodLength_ / 2.0) {
94 RealType delta_z = abs(z) - rodLength_ / 2.0;
95 distance = sqrt((x * x) + (y * y) + (delta_z * delta_z));
96 } else {
97 distance = sqrt((x * x) + (y * y));
98 }
99
100 bool isIT = false;
101 if (distance <= rodRadius_) { isIT = true; }
102 return isIT;
103 }
104
105} // namespace OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.
Real distance(const DynamicVector< Real > &v1, const DynamicVector< Real > &v2)
Returns the distance between two DynamicVectors.