1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
|
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en">
<head>
<title>GAMGI Interfaces: Group Create</title>
<link rel="icon" type="image/png" href="../../icon/gamgi16.png"/>
<link rel="stylesheet" type="text/css" href="../../css/base.css"/>
<link rel="stylesheet" type="text/css" href="../../css/notebook.css"/>
</head>
<body>
<h1>Group Create</h1>
<div id="notebook">
<ul>
<li><a href="create_type.html">Type</a></li>
<li><span>Scope</span></li>
<li><a href="create_view.html">View</a></li>
</ul>
</div>
<div class="contents">
Set here the atomic structure to include, and the coordination
neighbour atoms, for each coordination polytope.
<h3>Structure</h3>
It is often useful to recreate in a group the atomic
structure existing in the parent object. For each coordination
polyhedron, this includes all the atoms defining the polyhedron
vertices, plus the central atom.
<p/>
When <b>Structure</b> is set to <b>Copy</b>, atoms
are copied to the groups just created.
When <b>Structure</b> is set to <b>Link</b>, atoms
are linked to the groups just created.
When <b>Structure</b> is set to <b>None</b>, atoms
are ignored.
<h3>Filter</h3>
After collecting a list of atoms close enough to the group,
a filtering condition may be applied. This can be very useful
to avoid atom superposition, resulting for example from atoms
copied before to different groups.
<p/>
When <b>Filter</b> is set to <b>Class</b>,
atoms belonging to another groups are ignored.
When <b>Filter</b> is set to <b>Child</b>, atoms not
belonging directly to the group parent are ignored.
When <b>Filter</b> is set to <b>Identical</b>, atoms
closer than a given distance (currently <b>1.0E-2</b>,
as defined in <b>GAMGI_MATH_TOLERANCE_STRUCTURE</b>) to
a previous atom are ignored.
When <b>Filter</b> is set to <b>None</b>, no filtering
condition is applied.
<h3>Visible</h3>
When the mix product of four vertices (defining a face and a new vertex),
is larger than <b>Visible</b> the face is visible from the vertex and
must be replaced. Increasing <b>Visible</b> may reduce face reconstruction,
but may result in numerical inaccuracies. The whole calculation is very
sensitive to this parameter, so it should be handled carefully. Currently
the maximum allowed value is <b>1.0E-5</b>.
<p/>
For complex systems, where different faces have almost the same orientation,
forming curved surfaces, setting <b>Visible</b> to <b>0</b> might eliminate
numerical errors.
<h3>Coplanar</h3>
The initial triangle faces are merged when the mix product
of four vertices (belonging to both faces) is smaller than
<b>Coplanar</b>. Increasing <b>Coplanar</b> promotes face merging,
but may result in numerical inaccuracies. Currently the maximum
allowed value is <b>1.0E-1</b>.
<p/>
Setting <b>Coplanar</b> to <b>0</b> disables face merging,
so all faces will be triangles.
<h3>Neighbours</h3>
Set here the neighbour atoms that should be considered around each central atom.
The sampling universe is always the object currently selected. When the
central atom does not belong to the current object, an error is shown.
<p/>
<b>Element</b> defines the atomic element of the neighbours that should
be considered. When <b>Element</b> is empty (the default), all atomic
elements will be considered.
<p/>
Users can set the number of closest neighbours that should be considered
using <b>Number</b>, or the radius of the sphere around the central
atom that should be sampled, using <b>Radius</b>. When these are empty
(the default), all atoms in the sampling universe will be considered.
</div>
<div id="bottom">
<a href="../../index.shtml">Home</a>
</div>
</body>
</html>
|
