OpenMD 3.0
Molecular Dynamics in the Open
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AtomNameVisitor.cpp
1/*
2 * Copyright (c) 2004-present, The University of Notre Dame. All rights
3 * reserved.
4 *
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6 * modification, are permitted provided that the following conditions are met:
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9 * this list of conditions and the following disclaimer.
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11 * 2. Redistributions in binary form must reproduce the above copyright notice,
12 * this list of conditions and the following disclaimer in the documentation
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17 * this software without specific prior written permission.
18 *
19 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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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#include "visitors/AtomNameVisitor.hpp"
45
46#include <fstream>
47#include <memory>
48#include <sstream>
49
50#include "brains/SimInfo.hpp"
52
53namespace OpenMD {
54 AtomNameVisitor::AtomNameVisitor(SimInfo* info) : BaseVisitor(), info_(info) {
55 visitorName = "AtomNameVisitor";
56 ff_ = info_->getForceField();
57 }
58
59 void AtomNameVisitor::visitAtom(Atom* atom) {
60 std::shared_ptr<AtomData> atomData;
61 std::shared_ptr<GenericData> data = atom->getPropertyByName("ATOMDATA");
62
63 if (data != nullptr) {
64 atomData = std::dynamic_pointer_cast<AtomData>(data);
65 if (atomData == nullptr) {
66 std::cerr << "can not get Atom Data from " << atom->getType()
67 << std::endl;
68 atomData = std::make_shared<AtomData>();
69 }
70 } else {
71 atomData = std::make_shared<AtomData>();
72 }
73
74 std::vector<std::shared_ptr<AtomInfo>>::iterator i;
75 for (std::shared_ptr<AtomInfo> atomInfo = atomData->beginAtomInfo(i);
76 atomInfo != nullptr; atomInfo = atomData->nextAtomInfo(i)) {
77 // query the force field for the AtomType associated with this
78 // atomTypeName:
79 AtomType* at = ff_->getAtomType(atomInfo->atomTypeName);
80 // get the chain of base types for this atom type:
81 std::vector<AtomType*> ayb = at->allYourBase();
82 // use the last type in the chain of base types for the name:
83 std::string bn = ayb[ayb.size() - 1]->getName();
84
85 atomInfo->atomTypeName = bn;
86 }
87 }
88
89 void AtomNameVisitor::visit(RigidBody* rb) {
90 std::vector<Atom*>::iterator i;
91
92 for (Atom* atom = rb->beginAtom(i); atom != NULL; atom = rb->nextAtom(i)) {
93 visit(atom);
94 }
95 }
96
97 const std::string AtomNameVisitor::toString() {
98 char buffer[65535];
99 std::string result;
100
101 snprintf(
102 buffer, 65535,
103 "------------------------------------------------------------------\n");
104 result += buffer;
105
106 snprintf(buffer, 65535, "Visitor name: %s\n", visitorName.c_str());
107 result += buffer;
108
109 snprintf(buffer, 65535, "Visitor Description: print base atom types\n");
110 result += buffer;
111
112 snprintf(
113 buffer, 65535,
114 "------------------------------------------------------------------\n");
115 result += buffer;
116
117 return result;
118 }
119
120} // namespace OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.