OpenMD 3.2
Molecular Dynamics in the Open
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MultipoleAdapter.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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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
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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 following paper when you publish your work:
33 *
34 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
35 *
36 * Good starting points for code and simulation methodology are:
37 *
38 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
39 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
40 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
41 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
42 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
43 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
44 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
45 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
46 */
47
48#include "types/MultipoleAdapter.hpp"
49
50#include <cstdio>
51#include <memory>
52
53#include "utils/simError.h"
54
55namespace OpenMD {
56
57 bool MultipoleAdapter::isMultipole() {
58 return at_->hasProperty(MultipoleTypeID);
59 }
60
61 MultipoleAtypeParameters MultipoleAdapter::getMultipoleParam() {
62 if (!isMultipole()) {
63 snprintf(
64 painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
65 "MultipoleAdapter::getMultipoleParam was passed an atomType (%s)\n"
66 "\tthat does not appear to be a Multipole atom.\n",
67 at_->getName().c_str());
68 painCave.severity = OPENMD_ERROR;
69 painCave.isFatal = 1;
70 simError();
71 }
72
73 std::shared_ptr<GenericData> data = at_->getPropertyByName(MultipoleTypeID);
74 if (data == nullptr) {
75 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
76 "MultipoleAdapter::getMultipoleParam could not find Multipole\n"
77 "\tparameters for atomType %s.\n",
78 at_->getName().c_str());
79 painCave.severity = OPENMD_ERROR;
80 painCave.isFatal = 1;
81 simError();
82 }
83
84 std::shared_ptr<MultipoleAtypeData> multipoleData =
85 std::dynamic_pointer_cast<MultipoleAtypeData>(data);
86 if (multipoleData == nullptr) {
87 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
88 "MultipoleAdapter::getMultipoleParam could not convert\n"
89 "\tGenericData to MultipoleAtypeData for atom type %s\n",
90 at_->getName().c_str());
91 painCave.severity = OPENMD_ERROR;
92 painCave.isFatal = 1;
93 simError();
94 }
95
96 return multipoleData->getData();
97 }
98
99 bool MultipoleAdapter::isDipole() {
100 if (isMultipole()) {
101 MultipoleAtypeParameters multipoleParam = getMultipoleParam();
102 return multipoleParam.isDipole;
103 } else
104 return false;
105 }
106 bool MultipoleAdapter::isQuadrupole() {
107 if (isMultipole()) {
108 MultipoleAtypeParameters multipoleParam = getMultipoleParam();
109 return multipoleParam.isQuadrupole;
110 } else
111 return false;
112 }
113
114 Vector3d MultipoleAdapter::getDipole() {
115 MultipoleAtypeParameters multipoleParam = getMultipoleParam();
116 return multipoleParam.dipole;
117 }
118
119 Mat3x3d MultipoleAdapter::getQuadrupole() {
120 MultipoleAtypeParameters multipoleParam = getMultipoleParam();
121 return multipoleParam.quadrupole;
122 }
123
124 void MultipoleAdapter::makeMultipole(Vector3d dipole, Mat3x3d quadrupole,
125 bool isDipole, bool isQuadrupole) {
126 if (isMultipole()) { at_->removeProperty(MultipoleTypeID); }
127
128 MultipoleAtypeParameters multipoleParam {};
129
130 multipoleParam.dipole = dipole;
131 multipoleParam.quadrupole = quadrupole;
132
133 multipoleParam.isDipole = isDipole;
134 multipoleParam.isQuadrupole = isQuadrupole;
135
136 at_->addProperty(
137 std::make_shared<MultipoleAtypeData>(MultipoleTypeID, multipoleParam));
138 }
139} // namespace OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.