OpenMD 3.0
Molecular Dynamics in the Open
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AtomStamp.cpp
1/*
2 * Copyright (c) 2004-present, The University of Notre Dame. All rights
3 * reserved.
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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
45#include "types/AtomStamp.hpp"
46
47#include <cstdio>
48#include <cstdlib>
49#include <cstring>
50#include <iostream>
51
52namespace OpenMD {
53 AtomStamp::AtomStamp(int index) :
54 havePos_(false), haveOrt_(false), hasOverride_(false), index_(index) {
55 DefineParameter(Type, "type");
56 }
57
58 bool AtomStamp::setPosition(const std::vector<RealType>& pos) {
59 bool ret = false;
60 if (pos.size() == 3) {
61 position_[0] = pos[0];
62 position_[1] = pos[1];
63 position_[2] = pos[2];
64 havePos_ = true;
65 } else {
66 std::ostringstream oss;
67 oss << "position" << containerToString(pos) << " is invalid" << std::endl;
68 throw OpenMDException(oss.str());
69 }
70 return ret;
71 }
72
73 bool AtomStamp::setOrientation(const std::vector<RealType>& ort) {
74 bool ret = false;
75 if (ort.size() == 3) {
76 orientation_[0] = ort[0];
77 orientation_[1] = ort[1];
78 orientation_[2] = ort[2];
79 haveOrt_ = true;
80 } else {
81 std::ostringstream oss;
82 oss << "orientation" << containerToString(ort) << " is invalid"
83 << std::endl;
84 throw OpenMDException(oss.str());
85 }
86
87 return ret;
88 }
89
90 void AtomStamp::validate() {
91 DataHolder::validate();
92 CheckParameter(Type, isNotEmpty());
93 }
94} // namespace OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.