OpenMD 3.1
Molecular Dynamics in the Open
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AtomicBeadModel.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:
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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.
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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
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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/AtomicBeadModel.hpp"
46
47#include "hydrodynamics/CompositeShape.hpp"
48#include "hydrodynamics/Sphere.hpp"
49
50namespace OpenMD {
51
52 std::size_t AtomicBeadModel::assignElements() {
53 if (shape_ != NULL) {
54 if (shape_->isComposite()) {
55 createBeads(dynamic_cast<CompositeShape*>(shape_));
56 } else {
57 if (shape_->isSpherical()) {
58 createSingleBead(dynamic_cast<Sphere*>(shape_));
59 } else {
60 snprintf(
61 painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
62 "AtomicBeadModel::assignElements Error: GayBerne and other "
63 "non-spherical\n"
64 "\tatoms should use the RoughShell or BoundaryElement models\n");
65 painCave.severity = OPENMD_ERROR;
66 painCave.isFatal = 1;
67 simError();
68 }
69 }
70 return elements_.size();
71 }
72 return 0;
73 }
74
75 void AtomicBeadModel::createBeads(Shape* shape) {
76 if (shape != NULL) {
77 if (shape->isComposite()) {
78 std::vector<Shape*> shapes =
79 dynamic_cast<CompositeShape*>(shape)->getShapes();
80 for (std::vector<Shape*>::iterator i = shapes.begin();
81 i != shapes.end(); ++i) {
82 if ((*i)->isComposite()) {
83 createBeads(dynamic_cast<CompositeShape*>((*i)));
84 } else {
85 if ((*i)->isSpherical()) {
86 createSingleBead(dynamic_cast<Sphere*>((*i)));
87 } else {
88 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
89 "AtomicBeadModel::createBeads Error: GayBerne and other "
90 "non-spherical\n"
91 "\tatoms should use the RoughShell or BoundaryElement "
92 "models\n");
93 painCave.severity = OPENMD_ERROR;
94 painCave.isFatal = 1;
95 simError();
96 }
97 }
98 }
99 } else {
100 if (shape->isSpherical()) {
101 createSingleBead(dynamic_cast<Sphere*>(shape_));
102 } else {
103 snprintf(
104 painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
105 "AtomicBeadModel::createBeads Error: GayBerne and other "
106 "non-spherical\n"
107 "\tatoms should use the RoughShell or BoundaryElement models\n");
108 painCave.severity = OPENMD_ERROR;
109 painCave.isFatal = 1;
110 simError();
111 }
112 }
113 }
114 }
115
116 bool AtomicBeadModel::createSingleBead(Sphere* sphere) {
117 HydrodynamicsElement currBead;
118 currBead.name = sphere->getName();
119 currBead.pos = sphere->getOrigin();
120 currBead.radius = sphere->getRadius();
121 elements_.push_back(currBead);
122 return true;
123 }
124} // namespace OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.