OpenMD 3.0
Molecular Dynamics in the Open
Loading...
Searching...
No Matches
Sphere.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#include "hydrodynamics/Sphere.hpp"
46
47#include "math/LU.hpp"
48#include "utils/Constants.hpp"
49
50namespace OpenMD {
51
52 Sphere::Sphere(Vector3d origin, RealType radius) :
53 origin_(origin), radius_(radius) {}
54
55 bool Sphere::isInterior(Vector3d pos) {
56 Vector3d r = pos - origin_;
57
58 bool result;
59 if (r.length() < radius_)
60 result = true;
61 else
62 result = false;
63
64 return result;
65 }
66
67 std::pair<Vector3d, Vector3d> Sphere::getBoundingBox() {
68 std::pair<Vector3d, Vector3d> boundary;
69 Vector3d r(radius_, radius_, radius_);
70 boundary.first = origin_ - r;
71 boundary.second = origin_ + r;
72 return boundary;
73 }
74
75 HydroProp* Sphere::getHydroProp(RealType viscosity) {
76 RealType Xitt = 6.0 * Constants::PI * viscosity * radius_;
77 RealType Xirr = 8.0 * Constants::PI * viscosity * pow(radius_, 3);
78
79 Mat6x6d Xi;
80
81 Xi(0, 0) = Xitt;
82 Xi(1, 1) = Xitt;
83 Xi(2, 2) = Xitt;
84 Xi(3, 3) = Xirr;
85 Xi(4, 4) = Xirr;
86 Xi(5, 5) = Xirr;
87
88 Xi *= Constants::viscoConvert;
89
90 HydroProp* hprop = new HydroProp(V3Zero, Xi);
91 hprop->setName(getName());
92 return hprop;
93 }
94
95} // namespace OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.