Skip to content

Commit 7a6cef9

Browse files
rperezsotorperezsoto
committed
Improved basic usage of potential, thermo and submit scripts and bumped to overall 0.0.1 version. Merge branch 'develop'
2 parents b217f4c + 34227f5 commit 7a6cef9

31 files changed

+11995
-1634
lines changed

‎Examples.rst

Lines changed: 42 additions & 22 deletions
Original file line numberDiff line numberDiff line change
@@ -40,18 +40,25 @@ As the -thermo and -inputHT scripts it has 3 general ways to specify inputs:
4040
Path/To/Files/File3.log -33333
4141
Path/To/Files/File2.log -22222
4242
43-
the *--quiet* or *-q* option is recommended when more than one file are fed
44-
otherwise if any calculation did not succeed it will raise an error and stop the
45-
execution of pyssian-potential.py (and similarly for pyssian-thermo.py)
43+
the *--verbose* or *-v* option is will raise an error for files that do not have
44+
a potential energy or thermochemistry and will stop the execution.
4645

4746
.. code:: shell-session
4847
49-
$ pyssian-potential.py -q Path/To/Files/File*.log Path/To/Error/Error.log
48+
$ pyssian-potential.py Path/To/Error/Error.log Path/To/Files/File*.log
5049
U
51-
Path/To/Files/File1.log -11111
52-
Path/To/Files/File2.log -22222
53-
Path/To/Files/File3.log -33333
54-
Path/To/Error/Error.log
50+
Path/To/Error/Error.log
51+
Traceback (most recent call last):
52+
File "/path/to/the/pyssianutils/installation/pyssian-thermo.py", line 7, in <module>
53+
exec(compile(f.read(), __file__, 'exec'))
54+
File "/path/to/the/pyssianutils/installation/pyssian-thermo.py", line 91, in <module>
55+
raise e
56+
File "/path/to/the/pyssianutils/installation/pyssian-thermo.py", line 88, in <module>
57+
Z,H,G = thermochemistry(GOF)
58+
File "/path/to/the/pyssianutils/installation/functions.py", line 33, in thermochemistry
59+
Link = GOF[-1].get_links(716)[-1]
60+
IndexError: list index out of range
61+
5562
5663
.. potential-end
5764
@@ -66,11 +73,12 @@ the value of the 'Done'
6673

6774
.. code:: shell-session
6875
69-
$ pyssian-thermo.py -L Files.txt -q
76+
$ pyssian-thermo.py -L Files.txt
7077
U Z H G
7178
Path/To/Files/File1.log -11111 -11111 -11111 -11111
7279
Path/To/Files/File3.log -33333 -33333 -33333 -33333
7380
Path/To/Files/File2.log -22222 -22222 -22222 -22222
81+
Path/To/Files/SPFile.log -22222
7482
7583
.. thermo-end
7684
@@ -79,18 +87,30 @@ pyssian-submit
7987

8088
.. submit-start
8189
82-
Checks all .in files in the current directory to generate a SubmitScript.sh
83-
that properly sends them to their queues (Files with a matching .out file
84-
are ignored as default). It checks in which queue they should go according
85-
to the values of nprocshared and %mem. To use the generated script run in
86-
the cluster: 'chmod +x SubmitScript.sh; ./SubmitScript;'
90+
Checks all .in files in the current directory or the provided folder
91+
to generate a SubmitScript.sh that properly sends them to their queues
92+
(Files with a matching .out file are ignored as default). It checks in which
93+
queue they should go according to the values of %nprocshared and %mem. To use
94+
the generated script run in the cluster:
95+
96+
.. code:: shell-session
97+
98+
chmod +x SubmitScript.sh
99+
./SubmitScript
100+
101+
or
102+
103+
.. code:: shell-session
104+
105+
bash SubmitScript.sh
106+
87107
88108
.. note::
89109

90110
This script is customized for the current Maseras' group needs and work
91111
environment. This script will nontheless end without any error upon execution
92-
but the generated submission script will be likely useless unless submission
93-
system is equal or similar to the Maseras' group.
112+
but the generated submission script will be likely useless unless the
113+
submission system is equal or similar to the Maseras' group.
94114

95115

96116
.. code:: shell-session
@@ -189,9 +209,9 @@ Lets assume the following project structure:
189209
project-folder
190210
$ ls project-folder/*/
191211
minima/ ts/
192-
$ls project-folder/minima/*
212+
$ ls project-folder/minima/*
193213
A.in A.out B.gjf B.log
194-
$ls project-folder/ts/*
214+
$ ls project-folder/ts/*
195215
TS1.in TS1.out
196216
197217
Lets assume that all were calculated with b3lyp in vacuum and we want to change
@@ -210,9 +230,9 @@ Now we check our directory
210230
project-folder project-folder-wb97xd SubmitScript.sh
211231
$ ls project-folder-wb97xd/*/
212232
minima/ ts/
213-
$ls project-folder-wb97xd/minima/*
233+
$ ls project-folder-wb97xd/minima/*
214234
A.in B.in
215-
$ls project-folder-wb97xd/ts/*
235+
$ ls project-folder-wb97xd/ts/*
216236
TS1.in
217237
218238
Now, lets assume that we run the calculations and all of them end without trouble.
@@ -231,9 +251,9 @@ Now our directory will look like this:
231251
project-folder project-folder-wb97xd SubmitScript.sh
232252
$ ls project-folder-wb97xd/*/
233253
minima/ ts/
234-
$ls project-folder-wb97xd/minima/*
254+
$ ls project-folder-wb97xd/minima/*
235255
A.in A.out A_SP.in B.in B.out B_SP.in
236-
$ls project-folder-wb97xd/ts/*
256+
$ ls project-folder-wb97xd/ts/*
237257
TS1.in TS1.out TS1_SP.in
238258
239259
If we check the contents of the SubmitScript we will see that it is completely

‎docs/.buildinfo

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
11
# Sphinx build info version 1
22
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
3-
config: 9f350a03b7220e63261badb8620d3dc0
3+
config: ed85d7e34a75853ca8f7ba35a18a8dfd
44
tags: 645f666f9bcd5a90fca523b33c5a78b7

‎docs/_modules/index.html

Lines changed: 20 additions & 123 deletions
Original file line numberDiff line numberDiff line change
@@ -1,199 +1,96 @@
1-
2-
31
<!DOCTYPE html>
42
<html class="writer-html5" lang="python" >
53
<head>
64
<meta charset="utf-8" />
7-
85
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
9-
10-
<title>Overview: module code &mdash; pyssianutils documentation</title>
11-
12-
13-
14-
<link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
15-
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
16-
17-
18-
19-
20-
21-
22-
23-
24-
25-
6+
<title>Overview: module code &mdash; pyssianutils documentation</title><link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
7+
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
268
<!--[if lt IE 9]>
279
<script src="../_static/js/html5shiv.min.js"></script>
2810
<![endif]-->
29-
30-
31-
<script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
32-
<script src="../_static/jquery.js"></script>
33-
<script src="../_static/underscore.js"></script>
34-
<script src="../_static/doctools.js"></script>
35-
36-
<script type="text/javascript" src="../_static/js/theme.js"></script>
37-
38-
11+
<script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
12+
<script type="text/javascript" src="../_static/jquery.js"></script>
13+
<script type="text/javascript" src="../_static/underscore.js"></script>
14+
<script type="text/javascript" src="../_static/doctools.js"></script>
15+
<script type="text/javascript" src="../_static/language_data.js"></script>
16+
<script src="../_static/js/theme.js"></script>
3917
<link rel="index" title="Index" href="../genindex.html" />
4018
<link rel="search" title="Search" href="../search.html" />
4119
</head>
4220

43-
<body class="wy-body-for-nav">
44-
45-
21+
<body class="wy-body-for-nav">
4622
<div class="wy-grid-for-nav">
47-
4823
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
4924
<div class="wy-side-scroll">
5025
<div class="wy-side-nav-search" >
51-
52-
53-
5426
<a href="../index.html" class="icon icon-home"> pyssianutils
55-
56-
57-
5827
</a>
59-
60-
61-
62-
63-
64-
65-
6628
<div role="search">
6729
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
6830
<input type="text" name="q" placeholder="Search docs" />
6931
<input type="hidden" name="check_keywords" value="yes" />
7032
<input type="hidden" name="area" value="default" />
7133
</form>
7234
</div>
73-
74-
75-
</div>
76-
77-
78-
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
79-
80-
81-
82-
83-
84-
35+
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
8536
<ul>
8637
<li class="toctree-l1"><a class="reference internal" href="../readme_link.html">Getting Started</a></li>
8738
<li class="toctree-l1"><a class="reference internal" href="../scripts.html">scripts</a></li>
8839
<li class="toctree-l1"><a class="reference internal" href="../pyssianutils.html">pyssianutils.functions</a></li>
8940
</ul>
9041

91-
92-
9342
</div>
94-
9543
</div>
9644
</nav>
9745

98-
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
99-
100-
101-
<nav class="wy-nav-top" aria-label="top navigation">
102-
46+
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
10347
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
10448
<a href="../index.html">pyssianutils</a>
105-
10649
</nav>
10750

108-
10951
<div class="wy-nav-content">
110-
11152
<div class="rst-content">
112-
113-
114-
115-
116-
117-
118-
119-
120-
121-
122-
123-
124-
125-
126-
127-
128-
129-
130-
131-
<div role="navigation" aria-label="breadcrumbs navigation">
132-
53+
<div role="navigation" aria-label="Page navigation">
13354
<ul class="wy-breadcrumbs">
134-
13555
<li><a href="../index.html" class="icon icon-home"></a> &raquo;</li>
136-
13756
<li>Overview: module code</li>
138-
139-
14057
<li class="wy-breadcrumbs-aside">
141-
14258
</li>
143-
14459
</ul>
145-
146-
14760
<hr/>
14861
</div>
14962
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
15063
<div itemprop="articleBody">
151-
64+
15265
<h1>All modules for which code is available</h1>
15366
<ul><li><a href="pyssianutils/functions.html">pyssianutils.functions</a></li>
15467
</ul>
15568

15669
</div>
157-
15870
</div>
15971
<footer>
16072

16173
<hr/>
16274

16375
<div role="contentinfo">
164-
<p>
165-
&#169; Copyright 2021, Pérez-Soto, R.; Besora, M.; Maseras, F..
166-
167-
</p>
76+
<p>&#169; Copyright 2021, Pérez-Soto, R.; Besora, M.; Maseras, F..</p>
16877
</div>
169-
170-
171-
172-
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
173-
78+
79+
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
17480
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
175-
176-
provided by <a href="https://readthedocs.org">Read the Docs</a>.
81+
provided by <a href="https://readthedocs.org">Read the Docs</a>.
82+
17783

17884
</footer>
17985
</div>
18086
</div>
181-
18287
</section>
183-
18488
</div>
185-
186-
187-
<script type="text/javascript">
89+
<script>
18890
jQuery(function () {
18991
SphinxRtdTheme.Navigation.enable(true);
19092
});
191-
</script>
192-
193-
194-
195-
196-
93+
</script>
19794

19895
</body>
19996
</html>

0 commit comments

Comments
 (0)