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v0.4.3 release.

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commit 425ba7cd168d3ce233b778e2495842f453f58153 1 parent 8e0b8f2
Shyue Ping Ong shyuep authored

Showing 36 changed files with 259 additions and 256 deletions. Show diff stats Hide diff stats

  1. +1 1  custodian/__init__.py
  2. +6 0 custodian/vasp/handlers.py
  3. BIN  docs/_build/doctrees/changelog.doctree
  4. BIN  docs/_build/doctrees/custodian.ansible.doctree
  5. BIN  docs/_build/doctrees/custodian.doctree
  6. BIN  docs/_build/doctrees/custodian.nwchem.doctree
  7. BIN  docs/_build/doctrees/custodian.vasp.doctree
  8. BIN  docs/_build/doctrees/environment.pickle
  9. BIN  docs/_build/doctrees/index.doctree
  10. BIN  docs/_build/doctrees/modules.doctree
  11. +1 1  docs/_build/html/.buildinfo
  12. +5 5 docs/_build/html/_modules/custodian/ansible/actions.html
  13. +5 5 docs/_build/html/_modules/custodian/ansible/intepreter.html
  14. +5 5 docs/_build/html/_modules/custodian/custodian.html
  15. +5 5 docs/_build/html/_modules/custodian/nwchem/handlers.html
  16. +5 5 docs/_build/html/_modules/custodian/nwchem/jobs.html
  17. +5 5 docs/_build/html/_modules/custodian/vasp/handlers.html
  18. +5 5 docs/_build/html/_modules/custodian/vasp/jobs.html
  19. +5 5 docs/_build/html/_modules/index.html
  20. +21 0 docs/_build/html/_sources/changelog.txt
  21. +4 20 docs/_build/html/_sources/index.txt
  22. +46 16 docs/_build/html/changelog.html
  23. +5 5 docs/_build/html/custodian.ansible.html
  24. +41 7 docs/_build/html/custodian.html
  25. +12 37 docs/_build/html/custodian.nwchem.html
  26. +14 32 docs/_build/html/custodian.vasp.html
  27. +14 26 docs/_build/html/genindex.html
  28. +12 34 docs/_build/html/index.html
  29. +5 5 docs/_build/html/modules.html
  30. BIN  docs/_build/html/objects.inv
  31. +5 5 docs/_build/html/py-modindex.html
  32. +5 5 docs/_build/html/search.html
  33. +1 1  docs/_build/html/searchindex.js
  34. +21 0 docs/changelog.rst
  35. +4 20 docs/index.rst
  36. +1 1  setup.py
2  custodian/__init__.py
... ... @@ -1,5 +1,5 @@
1 1 __author__ = "Shyue Ping Ong"
2 2 __date__ = "Jun 23 2013"
3   -__version__ = "0.4.2"
  3 +__version__ = "0.4.3"
4 4
5 5 from custodian import Custodian
6 custodian/vasp/handlers.py
@@ -85,22 +85,28 @@ def correct(self):
85 85 if "tet" in self.errors or "dentet" in self.errors:
86 86 actions.append({"dict": "INCAR",
87 87 "action": {"_set": {"ISMEAR": 0}}})
  88 +
88 89 if "inv_rot_mat" in self.errors:
89 90 actions.append({"dict": "INCAR",
90 91 "action": {"_set": {"SYMPREC": 1e-8}}})
  92 +
91 93 if "brmix" in self.errors or "zpotrf" in self.errors:
92 94 actions.append({"dict": "INCAR",
93 95 "action": {"_set": {"ISYM": 0}}})
  96 +
94 97 if "subspacematrix" in self.errors or "rspher" in self.errors or \
95 98 "real_optlay" in self.errors:
96 99 actions.append({"dict": "INCAR",
97 100 "action": {"_set": {"LREAL": False}}})
  101 +
98 102 if "tetirr" in self.errors or "incorrect_shift" in self.errors:
99 103 actions.append({"dict": "KPOINTS",
100 104 "action": {"_set": {"generation_style": "Gamma"}}})
  105 +
101 106 if "amin" in self.errors:
102 107 actions.append({"dict": "INCAR",
103 108 "action": {"_set": {"AMIN": "0.01"}}})
  109 +
104 110 if "too_few_bands" in self.errors:
105 111 if "NBANDS" in vi["INCAR"]:
106 112 nbands = int(vi["INCAR"]["NBANDS"])
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2  docs/_build/html/.buildinfo
... ... @@ -1,4 +1,4 @@
1 1 # Sphinx build info version 1
2 2 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
3   -config: ed8b58475318735e2052586abcd2bbcc
  3 +config: b27c9cbd993430d0bd16394c3878bcc4
4 4 tags: a205e9ed8462ae86fdd2f73488852ba9
10 docs/_build/html/_modules/custodian/ansible/actions.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>custodian.ansible.actions &mdash; custodian 0.4.2 documentation</title>
  9 + <title>custodian.ansible.actions &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: '../../../',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="../../../_static/underscore.js"></script>
25 25 <script type="text/javascript" src="../../../_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="../../../_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
28 28 <link rel="up" title="Module code" href="../../index.html" />
29 29
30 30 <script type="text/javascript">
@@ -44,7 +44,7 @@
44 44 <li class="right" >
45 45 <a href="../../../py-modindex.html" title="Python Module Index"
46 46 >modules</a> |</li>
47   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  47 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
48 48 <li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
49 49 </ul>
50 50 </div>
@@ -314,7 +314,7 @@
314 314 <li class="right" >
315 315 <a href="../../../py-modindex.html" title="Python Module Index"
316 316 >modules</a> |</li>
317   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  317 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
318 318 <li><a href="../../index.html" >Module code</a> &raquo;</li>
319 319 </ul>
320 320 </div>
10 docs/_build/html/_modules/custodian/ansible/intepreter.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>custodian.ansible.intepreter &mdash; custodian 0.4.2 documentation</title>
  9 + <title>custodian.ansible.intepreter &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: '../../../',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="../../../_static/underscore.js"></script>
25 25 <script type="text/javascript" src="../../../_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="../../../_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
28 28 <link rel="up" title="Module code" href="../../index.html" />
29 29
30 30 <script type="text/javascript">
@@ -44,7 +44,7 @@
44 44 <li class="right" >
45 45 <a href="../../../py-modindex.html" title="Python Module Index"
46 46 >modules</a> |</li>
47   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  47 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
48 48 <li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
49 49 </ul>
50 50 </div>
@@ -191,7 +191,7 @@
191 191 <li class="right" >
192 192 <a href="../../../py-modindex.html" title="Python Module Index"
193 193 >modules</a> |</li>
194   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  194 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
195 195 <li><a href="../../index.html" >Module code</a> &raquo;</li>
196 196 </ul>
197 197 </div>
10 docs/_build/html/_modules/custodian/custodian.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>custodian.custodian &mdash; custodian 0.4.2 documentation</title>
  9 + <title>custodian.custodian &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="../../_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: '../../',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="../../_static/underscore.js"></script>
25 25 <script type="text/javascript" src="../../_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="../../_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="../../index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="../../index.html" />
28 28 <link rel="up" title="Module code" href="../index.html" />
29 29
30 30 <script type="text/javascript">
@@ -44,7 +44,7 @@
44 44 <li class="right" >
45 45 <a href="../../py-modindex.html" title="Python Module Index"
46 46 >modules</a> |</li>
47   - <li><a href="../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  47 + <li><a href="../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
48 48 <li><a href="../index.html" accesskey="U">Module code</a> &raquo;</li>
49 49 </ul>
50 50 </div>
@@ -376,7 +376,7 @@
376 376 <li class="right" >
377 377 <a href="../../py-modindex.html" title="Python Module Index"
378 378 >modules</a> |</li>
379   - <li><a href="../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  379 + <li><a href="../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
380 380 <li><a href="../index.html" >Module code</a> &raquo;</li>
381 381 </ul>
382 382 </div>
10 docs/_build/html/_modules/custodian/nwchem/handlers.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>custodian.nwchem.handlers &mdash; custodian 0.4.2 documentation</title>
  9 + <title>custodian.nwchem.handlers &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: '../../../',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="../../../_static/underscore.js"></script>
25 25 <script type="text/javascript" src="../../../_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="../../../_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
28 28 <link rel="up" title="Module code" href="../../index.html" />
29 29
30 30 <script type="text/javascript">
@@ -44,7 +44,7 @@
44 44 <li class="right" >
45 45 <a href="../../../py-modindex.html" title="Python Module Index"
46 46 >modules</a> |</li>
47   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  47 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
48 48 <li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
49 49 </ul>
50 50 </div>
@@ -207,7 +207,7 @@
207 207 <li class="right" >
208 208 <a href="../../../py-modindex.html" title="Python Module Index"
209 209 >modules</a> |</li>
210   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  210 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
211 211 <li><a href="../../index.html" >Module code</a> &raquo;</li>
212 212 </ul>
213 213 </div>
10 docs/_build/html/_modules/custodian/nwchem/jobs.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>custodian.nwchem.jobs &mdash; custodian 0.4.2 documentation</title>
  9 + <title>custodian.nwchem.jobs &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: '../../../',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="../../../_static/underscore.js"></script>
25 25 <script type="text/javascript" src="../../../_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="../../../_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
28 28 <link rel="up" title="Module code" href="../../index.html" />
29 29
30 30 <script type="text/javascript">
@@ -44,7 +44,7 @@
44 44 <li class="right" >
45 45 <a href="../../../py-modindex.html" title="Python Module Index"
46 46 >modules</a> |</li>
47   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  47 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
48 48 <li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
49 49 </ul>
50 50 </div>
@@ -206,7 +206,7 @@
206 206 <li class="right" >
207 207 <a href="../../../py-modindex.html" title="Python Module Index"
208 208 >modules</a> |</li>
209   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  209 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
210 210 <li><a href="../../index.html" >Module code</a> &raquo;</li>
211 211 </ul>
212 212 </div>
10 docs/_build/html/_modules/custodian/vasp/handlers.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>custodian.vasp.handlers &mdash; custodian 0.4.2 documentation</title>
  9 + <title>custodian.vasp.handlers &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: '../../../',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="../../../_static/underscore.js"></script>
25 25 <script type="text/javascript" src="../../../_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="../../../_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
28 28 <link rel="up" title="Module code" href="../../index.html" />
29 29
30 30 <script type="text/javascript">
@@ -44,7 +44,7 @@
44 44 <li class="right" >
45 45 <a href="../../../py-modindex.html" title="Python Module Index"
46 46 >modules</a> |</li>
47   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  47 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
48 48 <li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
49 49 </ul>
50 50 </div>
@@ -466,7 +466,7 @@
466 466 <li class="right" >
467 467 <a href="../../../py-modindex.html" title="Python Module Index"
468 468 >modules</a> |</li>
469   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  469 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
470 470 <li><a href="../../index.html" >Module code</a> &raquo;</li>
471 471 </ul>
472 472 </div>
10 docs/_build/html/_modules/custodian/vasp/jobs.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>custodian.vasp.jobs &mdash; custodian 0.4.2 documentation</title>
  9 + <title>custodian.vasp.jobs &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: '../../../',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="../../../_static/underscore.js"></script>
25 25 <script type="text/javascript" src="../../../_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="../../../_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
28 28 <link rel="up" title="Module code" href="../../index.html" />
29 29
30 30 <script type="text/javascript">
@@ -44,7 +44,7 @@
44 44 <li class="right" >
45 45 <a href="../../../py-modindex.html" title="Python Module Index"
46 46 >modules</a> |</li>
47   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  47 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
48 48 <li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
49 49 </ul>
50 50 </div>
@@ -301,7 +301,7 @@
301 301 <li class="right" >
302 302 <a href="../../../py-modindex.html" title="Python Module Index"
303 303 >modules</a> |</li>
304   - <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  304 + <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
305 305 <li><a href="../../index.html" >Module code</a> &raquo;</li>
306 306 </ul>
307 307 </div>
10 docs/_build/html/_modules/index.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>Overview: module code &mdash; custodian 0.4.2 documentation</title>
  9 + <title>Overview: module code &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="../_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: '../',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="../_static/underscore.js"></script>
25 25 <script type="text/javascript" src="../_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="../_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="../index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="../index.html" />
28 28
29 29 <script type="text/javascript">
30 30 var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
43 43 <li class="right" >
44 44 <a href="../py-modindex.html" title="Python Module Index"
45 45 >modules</a> |</li>
46   - <li><a href="../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  46 + <li><a href="../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
47 47 </ul>
48 48 </div>
49 49
@@ -93,7 +93,7 @@
93 93 <li class="right" >
94 94 <a href="../py-modindex.html" title="Python Module Index"
95 95 >modules</a> |</li>
96   - <li><a href="../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  96 + <li><a href="../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
97 97 </ul>
98 98 </div>
99 99
21 docs/_build/html/_sources/changelog.txt
... ... @@ -1,6 +1,27 @@
1 1 Change Log
2 2 ==========
3 3
  4 +0.4.2
  5 +-----
  6 +1. Rudimentary support for Nwchem error handling (by Shyue Ping Ong).
  7 +2. Improved VASP error handling (by Steve Dacek and Will Richards).
  8 +
  9 +0.4.1
  10 +-----
  11 +1. Added hanlding of PRICEL error in VASP.
  12 +2. Speed and robustness improvements.
  13 +3. BRIONS error now handled by changing ISYM.
  14 +
  15 +0.4.0
  16 +-----
  17 +1. Many VASP handlers are now consolidated into a single VaspErrorHandler.
  18 +2. Many more fixes for VASP runs, including the "TOO FEW BANDS",
  19 + "TRIPLE PRODUCT", "DENTET" and "BRIONS" errors.
  20 +3. VaspJob now includes the auto_npar and auto_gamma options, which
  21 + automatically optimizes the NPAR setting to be sqrt(number of cores) as
  22 + per the VASP recommendation for DFT runs and tries to search for a
  23 + gamma-only compiled version of VASP for gamma 1x1x1 runs.
  24 +
4 25 0.3.5
5 26 -----
6 27 1. Bug fix for incorrect shift error handler in VASP.
24 docs/_build/html/_sources/index.txt
@@ -18,26 +18,10 @@ error, and potentially restart the job if necessary.
18 18 Change log
19 19 ==========
20 20
21   -0.4.2
  21 +0.4.3
22 22 -----
23   -1. Rudimentary support for Nwchem error handling (by Shyue Ping Ong).
24   -2. Improved VASP error handling (by Steve Dacek and Will Richards).
25   -
26   -0.4.1
27   ------
28   -1. Added hanlding of PRICEL error in VASP.
29   -2. Speed and robustness improvements.
30   -3. BRIONS error now handled by changing ISYM.
31   -
32   -0.4.0
33   ------
34   -1. Many VASP handlers are now consolidated into a single VaspErrorHandler.
35   -2. Many more fixes for VASP runs, including the "TOO FEW BANDS",
36   - "TRIPLE PRODUCT", "DENTET" and "BRIONS" errors.
37   -3. VaspJob now includes the auto_npar and auto_gamma options, which
38   - automatically optimizes the NPAR setting to be sqrt(number of cores) as
39   - per the VASP recommendation for DFT runs and tries to search for a
40   - gamma-only compiled version of VASP for gamma 1x1x1 runs.
  23 +1. Added handling for ZBRENT error for VASP.
  24 +2. Minor refactoring to consolidate backup and gzip directory methods.
41 25
42 26 :doc:`Older versions </changelog>`
43 27
@@ -377,6 +361,6 @@ follows::
377 361 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
378 362 DEALINGS IN THE SOFTWARE.
379 363
380   -.. _`pymatgen's documentation`: http://pythonhosted.org/pymatgen
  364 +.. _`pymatgen's documentation`: http://pymatgen.org
381 365 .. _`Materials Project`: https://www.materialsproject.org
382 366 .. _`pymatgen`: https://pypi.python.org/pypi/pymatgen
62 docs/_build/html/changelog.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>Change Log &mdash; custodian 0.4.2 documentation</title>
  9 + <title>Change Log &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: './',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="_static/underscore.js"></script>
25 25 <script type="text/javascript" src="_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
28 28
29 29 <script type="text/javascript">
30 30 var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
43 43 <li class="right" >
44 44 <a href="py-modindex.html" title="Python Module Index"
45 45 >modules</a> |</li>
46   - <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  46 + <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
47 47 </ul>
48 48 </div>
49 49
@@ -55,7 +55,34 @@
55 55 <div class="section" id="change-log">
56 56 <h1>Change Log<a class="headerlink" href="#change-log" title="Permalink to this headline">¶</a></h1>
57 57 <div class="section" id="id1">
58   -<h2>0.3.5<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
  58 +<h2>0.4.2<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
  59 +<ol class="arabic simple">
  60 +<li>Rudimentary support for Nwchem error handling (by Shyue Ping Ong).</li>
  61 +<li>Improved VASP error handling (by Steve Dacek and Will Richards).</li>
  62 +</ol>
  63 +</div>
  64 +<div class="section" id="id2">
  65 +<h2>0.4.1<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h2>
  66 +<ol class="arabic simple">
  67 +<li>Added hanlding of PRICEL error in VASP.</li>
  68 +<li>Speed and robustness improvements.</li>
  69 +<li>BRIONS error now handled by changing ISYM.</li>
  70 +</ol>
  71 +</div>
  72 +<div class="section" id="id3">
  73 +<h2>0.4.0<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h2>
  74 +<ol class="arabic simple">
  75 +<li>Many VASP handlers are now consolidated into a single VaspErrorHandler.</li>
  76 +<li>Many more fixes for VASP runs, including the &#8220;TOO FEW BANDS&#8221;,
  77 +&#8220;TRIPLE PRODUCT&#8221;, &#8220;DENTET&#8221; and &#8220;BRIONS&#8221; errors.</li>
  78 +<li>VaspJob now includes the auto_npar and auto_gamma options, which
  79 +automatically optimizes the NPAR setting to be sqrt(number of cores) as
  80 +per the VASP recommendation for DFT runs and tries to search for a
  81 +gamma-only compiled version of VASP for gamma 1x1x1 runs.</li>
  82 +</ol>
  83 +</div>
  84 +<div class="section" id="id4">
  85 +<h2>0.3.5<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h2>
59 86 <ol class="arabic simple">
60 87 <li>Bug fix for incorrect shift error handler in VASP.</li>
61 88 <li>More robust fix for unconverged VASP runs (switching from ALGO fast to
@@ -63,22 +90,22 @@
63 90 <li>Expanded documentation.</li>
64 91 </ol>
65 92 </div>
66   -<div class="section" id="id2">
67   -<h2>0.3.4<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h2>
  93 +<div class="section" id="id5">
  94 +<h2>0.3.4<a class="headerlink" href="#id5" title="Permalink to this headline">¶</a></h2>
68 95 <ol class="arabic simple">
69 96 <li>Added support for handlers that perform monitor a job as it is progressing
70 97 and terminates it if necessary. Useful for correcting errors that come up
71 98 by do not cause immediate job failures.</li>
72 99 </ol>
73 100 </div>
74   -<div class="section" id="id3">
75   -<h2>0.3.2<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h2>
  101 +<div class="section" id="id6">
  102 +<h2>0.3.2<a class="headerlink" href="#id6" title="Permalink to this headline">¶</a></h2>
76 103 <ol class="arabic simple">
77 104 <li>Important bug fix for VaspJob and converge_kpoints script.</li>
78 105 </ol>
79 106 </div>
80   -<div class="section" id="id4">
81   -<h2>0.3.0<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h2>
  107 +<div class="section" id="id7">
  108 +<h2>0.3.0<a class="headerlink" href="#id7" title="Permalink to this headline">¶</a></h2>
82 109 <ol class="arabic simple">
83 110 <li>Major update to custodian API. Custodian now perform more comprehensive
84 111 logging in a file called custodian.json, which logs all jobs and
@@ -118,10 +145,13 @@
118 145 <h3><a href="index.html">Table Of Contents</a></h3>
119 146 <ul>
120 147 <li><a class="reference internal" href="#">Change Log</a><ul>
121   -<li><a class="reference internal" href="#id1">0.3.5</a></li>
122   -<li><a class="reference internal" href="#id2">0.3.4</a></li>
123   -<li><a class="reference internal" href="#id3">0.3.2</a></li>
124   -<li><a class="reference internal" href="#id4">0.3.0</a></li>
  148 +<li><a class="reference internal" href="#id1">0.4.2</a></li>
  149 +<li><a class="reference internal" href="#id2">0.4.1</a></li>
  150 +<li><a class="reference internal" href="#id3">0.4.0</a></li>
  151 +<li><a class="reference internal" href="#id4">0.3.5</a></li>
  152 +<li><a class="reference internal" href="#id5">0.3.4</a></li>
  153 +<li><a class="reference internal" href="#id6">0.3.2</a></li>
  154 +<li><a class="reference internal" href="#id7">0.3.0</a></li>
125 155 <li><a class="reference internal" href="#version-0-2-6">Version 0.2.6</a></li>
126 156 <li><a class="reference internal" href="#version-0-2-5">Version 0.2.5</a></li>
127 157 <li><a class="reference internal" href="#version-0-2-4">Version 0.2.4</a></li>
@@ -160,7 +190,7 @@
160 190 <li class="right" >
161 191 <a href="py-modindex.html" title="Python Module Index"
162 192 >modules</a> |</li>
163   - <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  193 + <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
164 194 </ul>
165 195 </div>
166 196
10 docs/_build/html/custodian.ansible.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>ansible Package &mdash; custodian 0.4.2 documentation</title>
  9 + <title>ansible Package &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: './',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="_static/underscore.js"></script>
25 25 <script type="text/javascript" src="_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
28 28
29 29 <script type="text/javascript">
30 30 var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
43 43 <li class="right" >
44 44 <a href="py-modindex.html" title="Python Module Index"
45 45 >modules</a> |</li>
46   - <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  46 + <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
47 47 </ul>
48 48 </div>
49 49
@@ -338,7 +338,7 @@
338 338 <li class="right" >
339 339 <a href="py-modindex.html" title="Python Module Index"
340 340 >modules</a> |</li>
341   - <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  341 + <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
342 342 </ul>
343 343 </div>
344 344
48 docs/_build/html/custodian.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>custodian Package &mdash; custodian 0.4.2 documentation</title>
  9 + <title>custodian Package &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: './',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="_static/underscore.js"></script>
25 25 <script type="text/javascript" src="_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
28 28
29 29 <script type="text/javascript">
30 30 var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
43 43 <li class="right" >
44 44 <a href="py-modindex.html" title="Python Module Index"
45 45 >modules</a> |</li>
46   - <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  46 + <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
47 47 </ul>
48 48 </div>
49 49
@@ -60,8 +60,9 @@
60 60 <div class="section" id="module-custodian.custodian">
61 61 <span id="custodian-module"></span><h2><tt class="xref py py-mod docutils literal"><span class="pre">custodian</span></tt> Module<a class="headerlink" href="#module-custodian.custodian" title="Permalink to this headline">¶</a></h2>
62 62 <p>This module implements the main Custodian class, which manages a list of jobs
63   -given a set of error handlers, and the abstract base classes for the
64   -ErrorHandlers and Jobs.</p>
  63 +given a set of error handlers, the abstract base classes for the
  64 +ErrorHandlers and Jobs, and some helper functions for backing up or
  65 +compressing files in a directory.</p>
65 66 <dl class="class">
66 67 <dt id="custodian.custodian.Custodian">
67 68 <em class="property">class </em><tt class="descname">Custodian</tt><big>(</big><em>handlers</em>, <em>jobs</em>, <em>max_errors=1</em>, <em>polling_time_step=10</em>, <em>monitor_freq=30</em>, <em>log_file='custodian.json'</em>, <em>skip_over_errors=False</em><big>)</big><a class="reference internal" href="_modules/custodian/custodian.html#Custodian"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.custodian.Custodian" title="Permalink to this definition">¶</a></dt>
@@ -226,6 +227,39 @@
226 227
227 228 </dd></dl>
228 229
  230 +<dl class="function">
  231 +<dt id="custodian.custodian.backup">
  232 +<tt class="descname">backup</tt><big>(</big><em>filenames</em>, <em>prefix='error'</em><big>)</big><a class="headerlink" href="#custodian.custodian.backup" title="Permalink to this definition">¶</a></dt>
  233 +<dd><p>Backup files to a tar.gz file. Used, for example, in backing up the
  234 +files of an errored run before performing corrections.</p>
  235 +<dl class="docutils">
  236 +<dt>Args:</dt>
  237 +<dd><dl class="first last docutils">
  238 +<dt>filenames:</dt>
  239 +<dd>List of files to backup. Supports wildcards, e.g., <em>.</em>.</dd>
  240 +<dt>prefix:</dt>
  241 +<dd>prefix to the files. Defaults to error, which means a series of
  242 +error.1.tar.gz, error.2.tar.gz, ... will be generated.</dd>
  243 +</dl>
  244 +</dd>
  245 +</dl>
  246 +</dd></dl>
  247 +
  248 +<dl class="function">
  249 +<dt id="custodian.custodian.gzip_dir">
  250 +<tt class="descname">gzip_dir</tt><big>(</big><em>path</em><big>)</big><a class="headerlink" href="#custodian.custodian.gzip_dir" title="Permalink to this definition">¶</a></dt>
  251 +<dd><p>Gzips all files in a directory. Used, for instance, to compress all
  252 +files at the end of a run.</p>
  253 +<dl class="docutils">
  254 +<dt>Args:</dt>
  255 +<dd><dl class="first last docutils">
  256 +<dt>path:</dt>
  257 +<dd>Path to directory.</dd>
  258 +</dl>
  259 +</dd>
  260 +</dl>
  261 +</dd></dl>
  262 +
229 263 </div>
230 264 <div class="section" id="subpackages">
231 265 <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
@@ -302,7 +336,7 @@
302 336 <li class="right" >
303 337 <a href="py-modindex.html" title="Python Module Index"
304 338 >modules</a> |</li>
305   - <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  339 + <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
306 340 </ul>
307 341 </div>
308 342
49 docs/_build/html/custodian.nwchem.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>nwchem Package &mdash; custodian 0.4.2 documentation</title>
  9 + <title>nwchem Package &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: './',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="_static/underscore.js"></script>
25 25 <script type="text/javascript" src="_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
28 28
29 29 <script type="text/javascript">
30 30 var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
43 43 <li class="right" >
44 44 <a href="py-modindex.html" title="Python Module Index"
45 45 >modules</a> |</li>
46   - <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  46 + <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
47 47 </ul>
48 48 </div>
49 49
@@ -56,7 +56,7 @@
56 56 <h1>nwchem Package<a class="headerlink" href="#nwchem-package" title="Permalink to this headline">¶</a></h1>
57 57 <div class="section" id="id1">
58 58 <h2><tt class="xref py py-mod docutils literal"><span class="pre">nwchem</span></tt> Package<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
59   -<span class="target" id="module-custodian.nwchem"></span><p>TODO: Modify module doc.</p>
  59 +<span class="target" id="module-custodian.nwchem"></span><p>This package implements various Nwchem Jobs and Error Handlers.</p>
60 60 </div>
61 61 <div class="section" id="module-custodian.nwchem.handlers">
62 62 <span id="handlers-module"></span><h2><tt class="xref py py-mod docutils literal"><span class="pre">handlers</span></tt> Module<a class="headerlink" href="#module-custodian.nwchem.handlers" title="Permalink to this headline">¶</a></h2>
@@ -95,24 +95,15 @@
95 95
96 96 </dd></dl>
97 97
98   -<dl class="function">
99   -<dt id="custodian.nwchem.handlers.backup">
100   -<tt class="descname">backup</tt><big>(</big><big>)</big><a class="reference internal" href="_modules/custodian/nwchem/handlers.html#backup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.nwchem.handlers.backup" title="Permalink to this definition">¶</a></dt>
101   -<dd></dd></dl>
102   -
103 98 </div>
104 99 <div class="section" id="module-custodian.nwchem.jobs">
105 100 <span id="jobs-module"></span><h2><tt class="xref py py-mod docutils literal"><span class="pre">jobs</span></tt> Module<a class="headerlink" href="#module-custodian.nwchem.jobs" title="Permalink to this headline">¶</a></h2>
106   -<p>This module implements basic kinds of jobs for Gaussian runs.</p>
  101 +<p>This module implements basic kinds of jobs for Nwchem runs.</p>
107 102 <dl class="class">
108 103 <dt id="custodian.nwchem.jobs.NwchemJob">
109   -<em class="property">class </em><tt class="descname">NwchemJob</tt><big>(</big><em>nwchem_cmd</em>, <em>input_file='mol.nw'</em>, <em>output_file='mol.nwout'</em>, <em>suffix=''</em>, <em>gzipped=False</em>, <em>backup=True</em>, <em>settings_override=None</em><big>)</big><a class="reference internal" href="_modules/custodian/nwchem/jobs.html#NwchemJob"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.nwchem.jobs.NwchemJob" title="Permalink to this definition">¶</a></dt>
  104 +<em class="property">class </em><tt class="descname">NwchemJob</tt><big>(</big><em>nwchem_cmd</em>, <em>input_file='mol.nw'</em>, <em>output_file='mol.nwout'</em>, <em>gzipped=False</em>, <em>backup=True</em>, <em>settings_override=None</em><big>)</big><a class="reference internal" href="_modules/custodian/nwchem/jobs.html#NwchemJob"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.nwchem.jobs.NwchemJob" title="Permalink to this definition">¶</a></dt>
110 105 <dd><p>Bases: <a class="reference internal" href="custodian.html#custodian.custodian.Job" title="custodian.custodian.Job"><tt class="xref py py-class docutils literal"><span class="pre">custodian.custodian.Job</span></tt></a>, <tt class="xref py py-class docutils literal"><span class="pre">pymatgen.serializers.json_coders.MSONable</span></tt></p>
111   -<p>A basic Gaussian job. Just runs whatever is in the directory. But
112   -conceivably can be a complex processing of inputs etc. with initialization.</p>
113   -<p>This constructor is necessarily complex due to the need for
114   -flexibility. For standard kinds of runs, it&#8217;s often better to use one
115   -of the static constructors.</p>
  106 +<p>A basic Nwchem job.</p>
116 107 <dl class="docutils">
117 108 <dt>Args:</dt>
118 109 <dd><dl class="first last docutils">
@@ -121,8 +112,6 @@
121 112 [&#8220;nwchem&#8221;].</dd>
122 113 <dt>output_file:</dt>
123 114 <dd>Name of file to direct standard out to.</dd>
124   -<dt>suffix:</dt>
125   -<dd>A suffix to be appended to the final output.</dd>
126 115 <dt>backup:</dt>
127 116 <dd>Boolean whether to backup the initial input files. If True,
128 117 the input files will be copied with a &#8221;.orig&#8221; appended.
@@ -131,13 +120,13 @@
131 120 <dd>Whether to gzip the final output. Defaults to False.</dd>
132 121 <dt>settings_override:</dt>
133 122 <dd>An ansible style list of dict to override changes.
134   -TODO: Not implemented yet.</dd>
  123 +#TODO: Not implemented yet.</dd>
135 124 </dl>
136 125 </dd>
137 126 </dl>
138   -<dl class="staticmethod">
  127 +<dl class="classmethod">
139 128 <dt id="custodian.nwchem.jobs.NwchemJob.from_dict">
140   -<em class="property">static </em><tt class="descname">from_dict</tt><big>(</big><em>d</em><big>)</big><a class="reference internal" href="_modules/custodian/nwchem/jobs.html#NwchemJob.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.nwchem.jobs.NwchemJob.from_dict" title="Permalink to this definition">¶</a></dt>
  129 +<em class="property">classmethod </em><tt class="descname">from_dict</tt><big>(</big><em>d</em><big>)</big><a class="reference internal" href="_modules/custodian/nwchem/jobs.html#NwchemJob.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.nwchem.jobs.NwchemJob.from_dict" title="Permalink to this definition">¶</a></dt>
141 130 <dd></dd></dl>
142 131
143 132 <dl class="attribute">
@@ -167,20 +156,6 @@
167 156
168 157 </dd></dl>
169 158
170   -<dl class="function">
171   -<dt id="custodian.nwchem.jobs.gzip_directory">
172   -<tt class="descname">gzip_directory</tt><big>(</big><em>path</em><big>)</big><a class="reference internal" href="_modules/custodian/nwchem/jobs.html#gzip_directory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.nwchem.jobs.gzip_directory" title="Permalink to this definition">¶</a></dt>
173   -<dd><p>Gzips all files in a directory.</p>
174   -<dl class="docutils">
175   -<dt>Args:</dt>
176   -<dd><dl class="first last docutils">
177   -<dt>path:</dt>
178   -<dd>Path to directory.</dd>
179   -</dl>
180   -</dd>
181   -</dl>
182   -</dd></dl>
183   -
184 159 </div>
185 160 </div>
186 161
@@ -231,7 +206,7 @@
231 206 <li class="right" >
232 207 <a href="py-modindex.html" title="Python Module Index"
233 208 >modules</a> |</li>
234   - <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  209 + <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
235 210 </ul>
236 211 </div>
237 212
46 docs/_build/html/custodian.vasp.html
@@ -6,7 +6,7 @@
6 6 <head>
7 7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
8 8
9   - <title>vasp Package &mdash; custodian 0.4.2 documentation</title>
  9 + <title>vasp Package &mdash; custodian 0.4.3 documentation</title>
10 10
11 11 <link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
12 12 <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -14,7 +14,7 @@
14 14 <script type="text/javascript">
15 15 var DOCUMENTATION_OPTIONS = {
16 16 URL_ROOT: './',
17   - VERSION: '0.4.2',
  17 + VERSION: '0.4.3',
18 18 COLLAPSE_INDEX: false,
19 19 FILE_SUFFIX: '.html',
20 20 HAS_SOURCE: true
@@ -24,7 +24,7 @@
24 24 <script type="text/javascript" src="_static/underscore.js"></script>
25 25 <script type="text/javascript" src="_static/doctools.js"></script>
26 26 <link rel="shortcut icon" href="_static/favicon.ico"/>
27   - <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
  27 + <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
28 28
29 29 <script type="text/javascript">
30 30 var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
43 43 <li class="right" >
44 44 <a href="py-modindex.html" title="Python Module Index"
45 45 >modules</a> |</li>
46   - <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  46 + <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
47 47 </ul>
48 48 </div>
49 49
@@ -56,7 +56,7 @@
56 56 <h1>vasp Package<a class="headerlink" href="#vasp-package" title="Permalink to this headline">¶</a></h1>
57 57 <div class="section" id="id1">
58 58 <h2><tt class="xref py py-mod docutils literal"><span class="pre">vasp</span></tt> Package<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
59   -<span class="target" id="module-custodian.vasp"></span><p>TODO: Change the module doc.</p>
  59 +<span class="target" id="module-custodian.vasp"></span><p>This package implements various VASP Jobs and Error Handlers.</p>
60 60 </div>
61 61 <div class="section" id="module-custodian.vasp.handlers">
62 62 <span id="handlers-module"></span><h2><tt class="xref py py-mod docutils literal"><span class="pre">handlers</span></tt> Module<a class="headerlink" href="#module-custodian.vasp.handlers" title="Permalink to this headline">¶</a></h2>
@@ -132,10 +132,11 @@
132 132
133 133 <dl class="class">
134 134 <dt id="custodian.vasp.handlers.NonConvergingErrorHandler">
135   -<em class="property">class </em><tt class="descname">NonConvergingErrorHandler</tt><big>(</big><em>output_filename='OSZICAR'</em><big>)</big><a class="headerlink" href="#custodian.vasp.handlers.NonConvergingErrorHandler" title="Permalink to this definition">¶</a></dt>
  135 +<em class="property">class </em><tt class="descname">NonConvergingErrorHandler</tt><big>(</big><em>output_filename='OSZICAR'</em>, <em>nionic_steps=10</em>, <em>change_algo=False</em><big>)</big><a class="headerlink" href="#custodian.vasp.handlers.NonConvergingErrorHandler" title="Permalink to this definition">¶</a></dt>
136 136 <dd><p>Bases: <a class="reference internal" href="custodian.html#custodian.custodian.ErrorHandler" title="custodian.custodian.ErrorHandler"><tt class="xref py py-class docutils literal"><span class="pre">custodian.custodian.ErrorHandler</span></tt></a>, <tt class="xref py py-class docutils literal"><span class="pre">pymatgen.serializers.json_coders.MSONable</span></tt></p>
137 137 <p>Check if a run is hitting the maximum number of electronic steps at the
138   -last 10 ionic steps. If so, kill the job.</p>
  138 +last nionic_steps ionic steps (default=10). If so, change ALGO from Fast to
  139 +Normal or kill the job.</p>
139 140 <dl class="method">
140 141 <dt id="custodian.vasp.handlers.NonConvergingErrorHandler.check">
141 142 <tt class="descname">check</tt><big>(</big><big>)</big><a class="headerlink" href="#custodian.vasp.handlers.NonConvergingErrorHandler.check" title="Permalink to this definition">¶</a></dt>
@@ -167,8 +168,8 @@
167 168 <dt id="custodian.vasp.handlers.PotimErrorHandler">
168 169 <em class="property">class </em><tt class="descname">PotimErrorHandler</tt><big>(</big><em>input_filename='POSCAR'</em>, <em>output_filename='OSZICAR'</em>, <em>dE_threshold=1</em><big>)</big><a class="headerlink" href="#custodian.vasp.handlers.PotimErrorHandler" title="Permalink to this definition">¶</a></dt>
169 170 <dd><p>Bases: <a class="reference internal" href="custodian.html#custodian.custodian.ErrorHandler" title="custodian.custodian.ErrorHandler"><tt class="xref py py-class docutils literal"><span class="pre">custodian.custodian.ErrorHandler</span></tt></a>, <tt class="xref py py-class docutils literal"><span class="pre">pymatgen.serializers.json_coders.MSONable</span></tt></p>
170   -<p>Check if a run has excessively large positive energy changes.
171   -This is typically caused by too large a POTIM. Runs typically
  171 +<p>Check if a run has excessively large positive energy changes.
  172 +This is typically caused by too large a POTIM. Runs typically
172 173 end up crashing with some other error (e.g. BRMIX) as the geometry
173 174 gets progressively worse.</p>
174 175 <dl class="method">
@@ -248,7 +249,7 @@
248 249
249 250 <dl class="attribute">
250 251 <dt id="custodian.vasp.handlers.VaspErrorHandler.error_msgs">
251   -<tt class="descname">error_msgs</tt><em class="property"> = {'too_few_bands': ['TOO FEW BANDS'], 'triple_product': ['ERROR: the triple product of the basis vectors'], 'amin': ['One of the lattice vectors is very long (&gt;50 A), but AMIN'], 'pricel': ['internal error in subroutine PRICEL'], 'zpotrf': ['LAPACK: Routine ZPOTRF failed'], 'brmix': ['BRMIX: very serious problems'], 'real_optlay': ['REAL_OPTLAY: internal error'], 'inv_rot_mat': ['inverse of rotation matrix was not found (increase SYMPREC)'], 'dentet': ['DENTET'], 'incorrect_shift': ['Could not get correct shifts'], 'subspacematrix': ['WARNING: Sub-Space-Matrix is not hermitian in DAV'], 'rspher': ['ERROR RSPHER'], 'rot_matrix': ['Found some non-integer element in rotation matrix'], 'tet': ['Tetrahedron method fails for NKPT&lt;4', 'Fatal error detecting k-mesh', 'Fatal error: unable to match k-point', 'Routine TETIRR needs special values'], 'tetirr': ['Routine TETIRR needs special values'], 'brions': ['BRIONS problems: POTIM should be increased']}</em><a class="headerlink" href="#custodian.vasp.handlers.VaspErrorHandler.error_msgs" title="Permalink to this definition">¶</a></dt>
  252 +<tt class="descname">error_msgs</tt><em class="property"> = {'too_few_bands': ['TOO FEW BANDS'], 'triple_product': ['ERROR: the triple product of the basis vectors'], 'amin': ['One of the lattice vectors is very long (&gt;50 A), but AMIN'], 'pricel': ['internal error in subroutine PRICEL'], 'zpotrf': ['LAPACK: Routine ZPOTRF failed'], 'brmix': ['BRMIX: very serious problems'], 'real_optlay': ['REAL_OPTLAY: internal error'], 'inv_rot_mat': ['inverse of rotation matrix was not found (increase SYMPREC)'], 'dentet': ['DENTET'], 'incorrect_shift': ['Could not get correct shifts'], 'subspacematrix': ['WARNING: Sub-Space-Matrix is not hermitian in DAV'], 'rspher': ['ERROR RSPHER'], 'rot_matrix': ['Found some non-integer element in rotation matrix'], 'tet': ['Tetrahedron method fails for NKPT&lt;4', 'Fatal error detecting k-mesh', 'Fatal error: unable to match k-point', 'Routine TETIRR needs special values'], 'zbrent': ['ZBRENT: fatal internal in brackting'], 'tetirr': ['Routine TETIRR needs special values'], 'brions': ['BRIONS problems: POTIM should be increased']}</em><a class="headerlink" href="#custodian.vasp.handlers.VaspErrorHandler.error_msgs" title="Permalink to this definition">¶</a></dt>
252 253 <dd></dd></dl>
253 254
254 255 <dl class="classmethod">
@@ -268,11 +269,6 @@
268 269
269 270 </dd></dl>
270 271
271   -<dl class="function">
272   -<dt id="custodian.vasp.handlers.backup">
273   -<tt class="descname">backup</tt><big>(</big><em>outfile='vasp.out'</em><big>)</big><a class="reference internal" href="_modules/custodian/vasp/handlers.html#backup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.vasp.handlers.backup" title="Permalink to this definition">¶</a></dt>
274   -<dd></dd></dl>
275   -
276 272 </div>
277 273 <div class="section" id="module-custodian.vasp.jobs">
278 274 <span id="jobs-module"></span><h2><tt class="xref py py-mod docutils literal"><span class="pre">jobs</span></tt> Module<a class="headerlink" href="#module-custodian.vasp.jobs" title="Permalink to this headline">¶</a></h2>
@@ -608,9 +604,9 @@
608 604 </dl>
609 605 </dd></dl>
610 606
611   -<dl class="staticmethod">
  607 +<dl class="classmethod">
612 608 <dt id="custodian.vasp.jobs.VaspJob.from_dict">
613   -<em class="property">static </em><tt class="descclassname">VaspJob.</tt><tt class="descname">from_dict</tt><big>(</big><em>d</em><big>)</big><a class="reference internal" href="_modules/custodian/vasp/jobs.html#VaspJob.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.vasp.jobs.VaspJob.from_dict" title="Permalink to this definition">¶</a></dt>
  609 +<em class="property">classmethod </em><tt class="descclassname">VaspJob.</tt><tt class="descname">from_dict</tt><big>(</big><em>d</em><big>)</big><a class="reference internal" href="_modules/custodian/vasp/jobs.html#VaspJob.from_dict"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.vasp.jobs.VaspJob.from_dict" title="Permalink to this definition">¶</a></dt>
614 610 <dd></dd></dl>
615 611
616 612 <dl class="attribute">
@@ -640,20 +636,6 @@
640 636
641 637 </dd></dl>
642 638
643   -<dl class="function">
644   -<dt id="custodian.vasp.jobs.gzip_directory">
645   -<tt class="descname">gzip_directory</tt><big>(</big><em>path</em><big>)</big><a class="reference internal" href="_modules/custodian/vasp/jobs.html#gzip_directory"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#custodian.vasp.jobs.gzip_directory" title="Permalink to this definition">¶</a></dt>
646   -<dd><p>Gzips all files in a directory.</p>
647   -<dl class="docutils">
648   -<dt>Args:</dt>
649   -<dd><dl class="first last docutils">
650   -<dt>path:</dt>
651   -<dd>Path to directory.</dd>
652   -</dl>
653   -</dd>
654   -</dl>
655   -</dd></dl>
656   -
657 639 </div>
658 640 </div>
659 641
@@ -704,7 +686,7 @@
704 686 <li class="right" >
705 687 <a href="py-modindex.html" title="Python Module Index"
706 688 >modules</a> |</li>
707   - <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
  689 + <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
708 690 </ul>
709 691 </div>
710 692
40 docs/_build/html/genindex.html
@@ -7,7 +7,7 @@
7 7 <head>
8 8 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
9 9
10   - <title>Index &mdash; custodian 0.4.2 documentation</title>
  10 + <title>Index &mdash; custodian 0.4.3 documentation</title>
11 11
12 12 <link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
13 13 <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
@@ -15,7 +15,7 @@
15 15 <script type="text/javascript">
16