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
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
|
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>MOLDEN — BAGEL Manual</title>
<link rel="stylesheet" href="../_static/override.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
<script type="text/javascript" src="../_static/jquery.js"></script>
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Printing orbital densities to cube files" href="moprint.html" />
<link rel="prev" title="Orbital localization" href="localization.html" />
</head><body>
<div class="related" role="navigation" aria-label="related navigation">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="moprint.html" title="Printing orbital densities to cube files"
accesskey="N">next</a></li>
<li class="right" >
<a href="localization.html" title="Orbital localization"
accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="../index.html">BAGEL Manual</a> »</li>
<li class="nav-item nav-item-1"><a href="../user-manual.html" ><strong>BAGEL user manual</strong></a> »</li>
<li class="nav-item nav-item-2"><a href="misc.html" accesskey="U">Miscellaneous features</a> »</li>
</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="molden">
<span id="id1"></span><h1>MOLDEN<a class="headerlink" href="#molden" title="Permalink to this headline">¶</a></h1>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>A molden file format can be generated as an output for orbitals, geometries, and vibrational frequencies. If a geometry optimization is performed, a molden file is generated that contains the geometry at each step in the optimization by default.</p>
<p>A molden file can also be read to restart calculations. See the molecule section for more information.</p>
</div>
<div class="section" id="keywords">
<h2>Keywords<a class="headerlink" href="#keywords" title="Permalink to this headline">¶</a></h2>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">file</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Name of the file to be generated</div>
<div class="line"><strong>Datatype:</strong> string</div>
</div>
</div>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">orbitals</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> Molecular orbitals are written to the molden file.</div>
<div class="line"><strong>Datatype:</strong> bool</div>
<div class="line"><strong>Default:</strong> false</div>
</div>
</div>
<div class="topic">
<p class="topic-title first"><code class="docutils literal notranslate"><span class="pre">vibration</span></code></p>
<div class="line-block">
<div class="line"><strong>Description:</strong> The vibrational frequencies, infrared intensities, and the cartesian eigenvectors of the normal modes are written to the molden file.</div>
<div class="line"><strong>Datatype:</strong> bool</div>
<div class="line"><strong>Default:</strong> false</div>
</div>
</div>
</div>
<div class="section" id="example">
<h2>Example<a class="headerlink" href="#example" title="Permalink to this headline">¶</a></h2>
<div class="section" id="sample-input">
<h3>Sample input<a class="headerlink" href="#sample-input" title="Permalink to this headline">¶</a></h3>
<p>Write molecular orbitals:</p>
<div class="highlight-javascript notranslate"><div class="highlight"><pre><span></span><span class="p">{</span> <span class="s2">"bagel"</span> <span class="o">:</span> <span class="p">[</span>
<span class="p">....</span> <span class="nx">energy</span> <span class="nx">calculation</span><span class="p">....</span>
<span class="p">{</span>
<span class="s2">"title"</span> <span class="o">:</span> <span class="s2">"print"</span><span class="p">,</span>
<span class="s2">"file"</span> <span class="o">:</span> <span class="s2">"orbitals.molden"</span><span class="p">,</span>
<span class="s2">"orbitals"</span> <span class="o">:</span> <span class="kc">true</span>
<span class="p">}</span>
<span class="p">]}</span>
</pre></div>
</div>
<p>Write results from a vibrational frequency calculation:</p>
<div class="highlight-javascript notranslate"><div class="highlight"><pre><span></span><span class="p">{</span> <span class="s2">"bagel"</span> <span class="o">:</span> <span class="p">[</span>
<span class="p">....</span> <span class="nx">energy</span> <span class="nx">and</span> <span class="nx">Hessian</span> <span class="nx">calculation</span> <span class="p">....</span>
<span class="p">{</span>
<span class="s2">"title"</span> <span class="o">:</span> <span class="s2">"print"</span><span class="p">,</span>
<span class="s2">"file"</span> <span class="o">:</span> <span class="s2">"freq.molden"</span><span class="p">,</span>
<span class="s2">"vibration"</span> <span class="o">:</span> <span class="kc">true</span>
<span class="p">}</span>
<span class="p">]}</span>
</pre></div>
</div>
<p>One can use a Molden file as an input as follows. Note that the Molden format does not specify the density fitting basis set,
and therefore, the molecule block does need to contain the df_basis keyword.</p>
<div class="highlight-javascript notranslate"><div class="highlight"><pre><span></span><span class="p">{</span> <span class="s2">"bagel"</span> <span class="o">:</span> <span class="p">[</span>
<span class="p">{</span>
<span class="s2">"title"</span> <span class="o">:</span> <span class="s2">"molecule"</span><span class="p">,</span>
<span class="s2">"basis"</span> <span class="o">:</span> <span class="s2">"molden"</span><span class="p">,</span>
<span class="s2">"df_basis"</span> <span class="o">:</span> <span class="s2">"svp-jkfit"</span><span class="p">,</span>
<span class="s2">"molden_file"</span> <span class="o">:</span> <span class="s2">"hf.molden"</span>
<span class="p">}</span>
<span class="p">]}</span>
</pre></div>
</div>
</div>
</div>
<div class="section" id="references">
<h2>References<a class="headerlink" href="#references" title="Permalink to this headline">¶</a></h2>
<table border="1" class="docutils">
<colgroup>
<col width="33%" />
<col width="67%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">Description of Reference</th>
<th class="head">Reference</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>Molden and the model file format</td>
<td>www.cmbi.ru.ml/molden</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul class="current">
<li class="toctree-l1 current"><a class="reference internal" href="../user-manual.html"><strong>BAGEL user manual</strong></a><ul class="current">
<li class="toctree-l2"><a class="reference internal" href="../quickstart/quickstart.html">First steps with BAGEL</a></li>
<li class="toctree-l2"><a class="reference internal" href="../molecule/molecule-toc.html">Molecule specification</a></li>
<li class="toctree-l2"><a class="reference internal" href="../scf/scf.html">Self-consistent field</a></li>
<li class="toctree-l2"><a class="reference internal" href="../ci/ci_methods.html">Configuration interaction</a></li>
<li class="toctree-l2"><a class="reference internal" href="../multi/multi.html">Multiconfiguration self-consistent field</a></li>
<li class="toctree-l2"><a class="reference internal" href="../pt2/pt2.html">Perturbation theory</a></li>
<li class="toctree-l2"><a class="reference internal" href="../smith/smith.html">SMITH3-generated code</a></li>
<li class="toctree-l2"><a class="reference internal" href="../grad/grad.html">Nuclear gradients and related functionalities</a></li>
<li class="toctree-l2"><a class="reference internal" href="../asd/asd.html">Active space decomposition method</a></li>
<li class="toctree-l2 current"><a class="reference internal" href="misc.html">Miscellaneous features</a></li>
<li class="toctree-l2"><a class="reference internal" href="../supp_info/supp_info.html">Supplementary information</a></li>
<li class="toctree-l2"><a class="reference internal" href="../author.html">Author contributions</a></li>
<li class="toctree-l2"><a class="reference internal" href="../funding.html">Funding and citation</a></li>
</ul>
</li>
</ul>
<h4>Previous topic</h4>
<p class="topless"><a href="localization.html"
title="previous chapter">Orbital localization</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="moprint.html"
title="next chapter">Printing orbital densities to cube files</a></p>
<div id="searchbox" style="display: none" role="search">
<h3>Quick search</h3>
<div class="searchformwrapper">
<form class="search" action="../search.html" method="get">
<input type="text" name="q" />
<input type="submit" value="Go" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<div class="related" role="navigation" aria-label="related navigation">
<h3>Navigation</h3>
<ul>
<li class="right" style="margin-right: 10px">
<a href="moprint.html" title="Printing orbital densities to cube files"
>next</a></li>
<li class="right" >
<a href="localization.html" title="Orbital localization"
>previous</a> |</li>
<li class="nav-item nav-item-0"><a href="../index.html">BAGEL Manual</a> »</li>
<li class="nav-item nav-item-1"><a href="../user-manual.html" ><strong>BAGEL user manual</strong></a> »</li>
<li class="nav-item nav-item-2"><a href="misc.html" >Miscellaneous features</a> »</li>
</ul>
</div>
<div class="footer" role="contentinfo">
© Copyright 2017, Shiozaki Group.
</div>
</body>
</html>
|
