OpenMD 3.1
Molecular Dynamics in the Open
Loading...
Searching...
No Matches
Atom.hpp
Go to the documentation of this file.
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:
7 *
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.
14 *
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
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/**
46 * @file Atom.hpp
47 * @author tlin
48 * @date 10/22/2004
49 * @version 1.0
50 */
51
52#ifndef PRIMITIVES_ATOM_HPP
53#define PRIMITIVES_ATOM_HPP
54
56#include "types/AtomType.hpp"
57
58namespace OpenMD {
59 class Atom : public StuntDouble {
60 public:
61 Atom(AtomType* at);
62
63 virtual std::string getType() { return atomType_->getName(); }
64
65 /**
66 * Returns the inertia tensor of this stuntdouble
67 * @return the inertia tensor of this stuntdouble
68 */
69 virtual Mat3x3d getI();
70
71 /**
72 * Returns the gradient of this stuntdouble
73 * @return the inertia tensor of this stuntdouble
74 */
75 virtual std::vector<RealType> getGrad();
76
77 virtual void accept(BaseVisitor* v);
78
79 /**
80 * Returns the AtomType of this Atom.
81 * @return the atom type of this atom
82 */
83 AtomType* getAtomType() { return atomType_; }
84
85 // forward functions of AtomType class
86 bool isCharge() { return atomType_->isCharge(); }
87
88 bool isDirectional() { return atomType_->isDirectional(); }
89
90 bool isDipole() { return atomType_->isDipole(); }
91
92 bool isMultipole() { return atomType_->isMultipole(); }
93
94 bool isGayBerne() { return atomType_->isGayBerne(); }
95
96 bool isSticky() { return atomType_->isSticky(); }
97
98 bool isShape() { return atomType_->isShape(); }
99
100 bool isMetal() { return atomType_->isMetal(); }
101
102 bool isFluctuatingCharge() { return atomType_->isFluctuatingCharge(); }
103
104 int getIdent() { return atomType_->getIdent(); }
105
106 RealType getChargeMass() { return chargeMass_; }
107
108 void setChargeMass(RealType cm) { chargeMass_ = cm; }
109
110 protected:
111 AtomType* atomType_;
112 RealType chargeMass_;
113 };
114} // namespace OpenMD
115
116#endif // PRIMITIVES_ATOM_HPP
virtual std::string getType()
Returns the name of this stuntDouble.
Definition Atom.hpp:63
virtual std::vector< RealType > getGrad()
Returns the gradient of this stuntdouble.
virtual Mat3x3d getI()
Returns the inertia tensor of this stuntdouble.
virtual void accept(BaseVisitor *v)
AtomType * getAtomType()
Returns the AtomType of this Atom.
Definition Atom.hpp:83
AtomType is what OpenMD looks to for unchanging data about an atom.
Definition AtomType.hpp:66
"Don't move, or you're dead! Stand up! Captain, we've got them!"
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.