OpenMD 3.0
Molecular Dynamics in the Open
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SuttonChenAdapter.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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17 * this software without specific prior written permission.
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19 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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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 "types/SuttonChenAdapter.hpp"
46
47#include <cstdio>
48#include <memory>
49
50#include "utils/simError.h"
51
52namespace OpenMD {
53
54 bool SuttonChenAdapter::isSuttonChen() { return at_->hasProperty(SCtypeID); }
55
56 SCAtypeParameters SuttonChenAdapter::getSuttonChenParam() {
57 if (!isSuttonChen()) {
58 snprintf(
59 painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
60 "SuttonChenAdapter::getSuttonChenParam was passed an atomType (%s)\n"
61 "\tthat does not appear to be a Sutton-Chen atom.\n",
62 at_->getName().c_str());
63 painCave.severity = OPENMD_ERROR;
64 painCave.isFatal = 1;
65 simError();
66 }
67
68 std::shared_ptr<GenericData> data = at_->getPropertyByName(SCtypeID);
69 if (data == nullptr) {
70 snprintf(
71 painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
72 "SuttonChenAdapter::getSuttonChenParam could not find Sutton-Chen\n"
73 "\tparameters for atomType %s.\n",
74 at_->getName().c_str());
75 painCave.severity = OPENMD_ERROR;
76 painCave.isFatal = 1;
77 simError();
78 }
79
80 std::shared_ptr<SCAtypeData> scData =
81 std::dynamic_pointer_cast<SCAtypeData>(data);
82 if (scData == nullptr) {
83 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
84 "SuttonChenAdapter::getSuttonChenParam could not convert\n"
85 "\tGenericData to SCAtypeData for atom type %s\n",
86 at_->getName().c_str());
87 painCave.severity = OPENMD_ERROR;
88 painCave.isFatal = 1;
89 simError();
90 }
91
92 return scData->getData();
93 }
94
95 RealType SuttonChenAdapter::getC() {
96 SCAtypeParameters scParam = getSuttonChenParam();
97 return scParam.c;
98 }
99
100 RealType SuttonChenAdapter::getM() {
101 SCAtypeParameters scParam = getSuttonChenParam();
102 return scParam.m;
103 }
104
105 RealType SuttonChenAdapter::getN() {
106 SCAtypeParameters scParam = getSuttonChenParam();
107 return scParam.n;
108 }
109
110 RealType SuttonChenAdapter::getAlpha() {
111 SCAtypeParameters scParam = getSuttonChenParam();
112 return scParam.alpha;
113 }
114
115 RealType SuttonChenAdapter::getEpsilon() {
116 SCAtypeParameters scParam = getSuttonChenParam();
117 return scParam.epsilon;
118 }
119
120 void SuttonChenAdapter::makeSuttonChen(RealType c, RealType m, RealType n,
121 RealType alpha, RealType epsilon) {
122 if (isSuttonChen()) { at_->removeProperty(SCtypeID); }
123
124 SCAtypeParameters scParam {};
125 scParam.c = c;
126 scParam.m = m;
127 scParam.n = n;
128 scParam.alpha = alpha;
129 scParam.epsilon = epsilon;
130
131 at_->addProperty(std::make_shared<SCAtypeData>(SCtypeID, scParam));
132 }
133} // namespace OpenMD
std::shared_ptr< GenericData > getPropertyByName(const string &propName)
Returns property.
Definition AtomType.cpp:134
void removeProperty(const string &propName)
Removes property from PropertyMap by name.
Definition AtomType.cpp:114
bool hasProperty(const string &propName)
Checks if property is in this PropertyMap.
Definition AtomType.cpp:127
void addProperty(std::shared_ptr< GenericData > genData)
Adds property into property map.
Definition AtomType.cpp:109
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.