OpenMD 3.0
Molecular Dynamics in the Open
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ShapeAtomType.cpp
1/*
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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
46
47namespace OpenMD {
48
49 ShapeAtomType::~ShapeAtomType() {
50 std::vector<RealSphericalHarmonic*>::iterator iter;
51 for (iter = contactFuncs.begin(); iter != contactFuncs.end(); ++iter)
52 delete (*iter);
53 for (iter = rangeFuncs.begin(); iter != rangeFuncs.end(); ++iter)
54 delete (*iter);
55 for (iter = strengthFuncs.begin(); iter != strengthFuncs.end(); ++iter)
56 delete (*iter);
57 contactFuncs.clear();
58 rangeFuncs.clear();
59 strengthFuncs.clear();
60 }
61
62 RealType ShapeAtomType::getContactValueAt(RealType costheta, RealType phi) {
63 std::vector<RealSphericalHarmonic*>::iterator contactIter;
64 RealType contactVal;
65
66 contactVal = 0.0;
67
68 for (contactIter = contactFuncs.begin(); contactIter != contactFuncs.end();
69 ++contactIter)
70 contactVal += (*contactIter)->getValueAt(costheta, phi);
71
72 return contactVal;
73 }
74
75 RealType ShapeAtomType::getRangeValueAt(RealType costheta, RealType phi) {
76 std::vector<RealSphericalHarmonic*>::iterator rangeIter;
77 RealType rangeVal;
78
79 rangeVal = 0.0;
80
81 for (rangeIter = rangeFuncs.begin(); rangeIter != rangeFuncs.end();
82 ++rangeIter)
83 rangeVal += (*rangeIter)->getValueAt(costheta, phi);
84
85 return rangeVal;
86 }
87
88 RealType ShapeAtomType::getStrengthValueAt(RealType costheta, RealType phi) {
89 std::vector<RealSphericalHarmonic*>::iterator strengthIter;
90 RealType strengthVal;
91
92 strengthVal = 0.0;
93
94 for (strengthIter = strengthFuncs.begin();
95 strengthIter != strengthFuncs.end(); ++strengthIter)
96 strengthVal += (*strengthIter)->getValueAt(costheta, phi);
97
98 return strengthVal;
99 }
100} // namespace OpenMD
RealType getRangeValueAt(RealType costheta, RealType phi)
Gets the value of the range function at a particular orientation.
RealType getContactValueAt(RealType costheta, RealType phi)
Gets the value of the contact function at a particular orientation.
RealType getStrengthValueAt(RealType costheta, RealType phi)
Gets the value of the strength function at a particular orientation.
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.