OpenMD 3.2
Molecular Dynamics in the Open
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CompositeVisitor.cpp
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 following paper when you publish your work:
33 *
34 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
35 *
36 * Good starting points for code and simulation methodology are:
37 *
38 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
39 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
40 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
41 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
42 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
43 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
44 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
45 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
46 */
47
48#include "visitors/CompositeVisitor.hpp"
49
50#include <cstring>
51
54
55namespace OpenMD {
56
57 CompositeVisitor::~CompositeVisitor() {
58 VisitorIterator i;
59 BaseVisitor* curVisitor;
60
61 for (curVisitor = beginVisitor(i); curVisitor; curVisitor = nextVisitor(i))
62 delete curVisitor;
63
64 visitorList.clear();
65 }
66 void CompositeVisitor::addVisitor(BaseVisitor* newVisitor, int priority) {
67 VisitorIterator i;
68 int curPriority;
69
70 for (i = visitorList.begin(); i != visitorList.end(); ++i) {
71 curPriority = (*i).second;
72 // if new visitor has higher priority, just insert it before current
73 // visitor
74 if (priority > curPriority) {
75 visitorList.insert(i, std::make_pair(newVisitor, priority));
76 }
77 }
78
79 // if new visitor has lowest priority, insert it at the end of the list
80 visitorList.insert(visitorList.end(), std::make_pair(newVisitor, priority));
81 }
82
83 BaseVisitor* CompositeVisitor::beginVisitor(VisitorIterator& i) {
84 i = visitorList.begin();
85 return i != visitorList.end() ? (*i).first : NULL;
86 }
87
88 BaseVisitor* CompositeVisitor::nextVisitor(VisitorIterator& i) {
89 ++i;
90 return i != visitorList.end() ? (*i).first : NULL;
91 }
92
93 void CompositeVisitor::visit(Atom* atom) {
94 VisitorIterator i;
95 BaseVisitor* curVisitor;
96
97 for (curVisitor = beginVisitor(i); curVisitor; curVisitor = nextVisitor(i))
98 atom->accept(curVisitor);
99 }
100
101 void CompositeVisitor::visit(DirectionalAtom* datom) {
102 VisitorIterator i;
103 BaseVisitor* curVisitor;
104
105 for (curVisitor = beginVisitor(i); curVisitor; curVisitor = nextVisitor(i))
106 datom->accept(curVisitor);
107 }
108 void CompositeVisitor::visit(RigidBody* rb) {
109 VisitorIterator i;
110 BaseVisitor* curVisitor;
111 std::vector<Atom*> myAtoms;
112 std::vector<Atom*>::iterator atomIter;
113
114 myAtoms = rb->getAtoms();
115
116 for (curVisitor = beginVisitor(i); curVisitor;
117 curVisitor = nextVisitor(i)) {
118 rb->accept(curVisitor);
119
120 for (atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
121 (*atomIter)->accept(curVisitor);
122 }
123 }
124
125 const std::string CompositeVisitor::toString() {
126 VisitorIterator i;
127 std::string result;
128 char buffer[65535];
129
130 snprintf(
131 buffer, 65535,
132 "******************************************************************\n");
133 result += buffer;
134
135 snprintf(buffer, 65535, "Visitor name: %s\n", visitorName.c_str());
136 result += buffer;
137
138 snprintf(
139 buffer, 65535,
140 "Visitor Description: visitor manager maintaining a priority list\n");
141 result += buffer;
142
143 snprintf(buffer, 65535, "visitors in current priority list:\n");
144 result += buffer;
145
146 for (i = visitorList.begin(); i != visitorList.end(); ++i) {
147 snprintf(buffer, 65535, "Priority = %d\tvisitor = %s\n", (*i).second,
148 ((*i).first->getVisitorName()).c_str());
149 result += buffer;
150 }
151
152 snprintf(buffer, 65535, "Detail information about every visitor:\n");
153
154 for (i = visitorList.begin(); i != visitorList.end(); ++i)
155 result += ((*i).first)->toString();
156
157 snprintf(
158 buffer, 65535,
159 "******************************************************************\n");
160 result += buffer;
161
162 return result;
163 }
164
165 void CompositeVisitor::update() {
166 VisitorIterator i;
167 BaseVisitor* curVisitor;
168
169 for (curVisitor = beginVisitor(i); curVisitor; curVisitor = nextVisitor(i))
170 curVisitor->update();
171 }
172
173} // namespace OpenMD
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.