OpenMD 3.0
Molecular Dynamics in the Open
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DirectionalAdapter.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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28 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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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/DirectionalAdapter.hpp"
46
47#include <cstdio>
48#include <memory>
49
50#include "utils/simError.h"
51
52namespace OpenMD {
53
54 bool DirectionalAdapter::isDirectional() {
55 return at_->hasProperty(DirectionalTypeID);
56 }
57
58 DirectionalAtypeParameters DirectionalAdapter::getDirectionalParam() {
59 if (!isDirectional()) {
60 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
61 "DirectionalAdapter::getDirectionalParam was passed an atomType "
62 "(%s)\n"
63 "\tthat does not appear to be a Directional atom.\n",
64 at_->getName().c_str());
65 painCave.severity = OPENMD_ERROR;
66 painCave.isFatal = 1;
67 simError();
68 }
69
70 std::shared_ptr<GenericData> data =
71 at_->getPropertyByName(DirectionalTypeID);
72 if (data == nullptr) {
73 snprintf(
74 painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
75 "DirectionalAdapter::getDirectionalParam could not find Directional\n"
76 "\tparameters for atomType %s.\n",
77 at_->getName().c_str());
78 painCave.severity = OPENMD_ERROR;
79 painCave.isFatal = 1;
80 simError();
81 }
82
83 std::shared_ptr<DirectionalAtypeData> directionalData =
84 std::dynamic_pointer_cast<DirectionalAtypeData>(data);
85 if (directionalData == nullptr) {
86 snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
87 "DirectionalAdapter::getDirectionalParam could not convert\n"
88 "\tGenericData to DirectionalAtypeData for atom type %s\n",
89 at_->getName().c_str());
90 painCave.severity = OPENMD_ERROR;
91 painCave.isFatal = 1;
92 simError();
93 }
94
95 return directionalData->getData();
96 }
97
98 Mat3x3d DirectionalAdapter::getI() {
99 DirectionalAtypeParameters directionalParam = getDirectionalParam();
100 return directionalParam.I;
101 }
102
103 void DirectionalAdapter::makeDirectional(Mat3x3d I) {
104 if (isDirectional()) { at_->removeProperty(DirectionalTypeID); }
105
106 DirectionalAtypeParameters directionalParam {};
107
108 directionalParam.I = I;
109
110 at_->addProperty(std::make_shared<DirectionalAtypeData>(DirectionalTypeID,
111 directionalParam));
112 }
113} // 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.