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v0.4.3 release.

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1 parent 8e0b8f2 commit 425ba7cd168d3ce233b778e2495842f453f58153 @shyuep shyuep committed Aug 27, 2013
Showing with 259 additions and 256 deletions.
  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
View
2 custodian/__init__.py
@@ -1,5 +1,5 @@
__author__ = "Shyue Ping Ong"
__date__ = "Jun 23 2013"
-__version__ = "0.4.2"
+__version__ = "0.4.3"
from custodian import Custodian
View
6 custodian/vasp/handlers.py
@@ -85,22 +85,28 @@ def correct(self):
if "tet" in self.errors or "dentet" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISMEAR": 0}}})
+
if "inv_rot_mat" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8}}})
+
if "brmix" in self.errors or "zpotrf" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISYM": 0}}})
+
if "subspacematrix" in self.errors or "rspher" in self.errors or \
"real_optlay" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"LREAL": False}}})
+
if "tetirr" in self.errors or "incorrect_shift" in self.errors:
actions.append({"dict": "KPOINTS",
"action": {"_set": {"generation_style": "Gamma"}}})
+
if "amin" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"AMIN": "0.01"}}})
+
if "too_few_bands" in self.errors:
if "NBANDS" in vi["INCAR"]:
nbands = int(vi["INCAR"]["NBANDS"])
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BIN docs/_build/doctrees/custodian.ansible.doctree
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BIN docs/_build/doctrees/custodian.doctree
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BIN docs/_build/doctrees/custodian.nwchem.doctree
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BIN docs/_build/doctrees/custodian.vasp.doctree
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BIN docs/_build/doctrees/environment.pickle
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BIN docs/_build/doctrees/index.doctree
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BIN docs/_build/doctrees/modules.doctree
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2 docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ed8b58475318735e2052586abcd2bbcc
+config: b27c9cbd993430d0bd16394c3878bcc4
tags: a205e9ed8462ae86fdd2f73488852ba9
View
10 docs/_build/html/_modules/custodian/ansible/actions.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>custodian.ansible.actions &mdash; custodian 0.4.2 documentation</title>
+ <title>custodian.ansible.actions &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
<link rel="up" title="Module code" href="../../index.html" />
<script type="text/javascript">
@@ -44,7 +44,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
</ul>
</div>
@@ -314,7 +314,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" >Module code</a> &raquo;</li>
</ul>
</div>
View
10 docs/_build/html/_modules/custodian/ansible/intepreter.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>custodian.ansible.intepreter &mdash; custodian 0.4.2 documentation</title>
+ <title>custodian.ansible.intepreter &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
<link rel="up" title="Module code" href="../../index.html" />
<script type="text/javascript">
@@ -44,7 +44,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
</ul>
</div>
@@ -191,7 +191,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" >Module code</a> &raquo;</li>
</ul>
</div>
View
10 docs/_build/html/_modules/custodian/custodian.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>custodian.custodian &mdash; custodian 0.4.2 documentation</title>
+ <title>custodian.custodian &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="../../_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../../_static/underscore.js"></script>
<script type="text/javascript" src="../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="../../index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="../../index.html" />
<link rel="up" title="Module code" href="../index.html" />
<script type="text/javascript">
@@ -44,7 +44,7 @@
<li class="right" >
<a href="../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../index.html" accesskey="U">Module code</a> &raquo;</li>
</ul>
</div>
@@ -376,7 +376,7 @@
<li class="right" >
<a href="../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../index.html" >Module code</a> &raquo;</li>
</ul>
</div>
View
10 docs/_build/html/_modules/custodian/nwchem/handlers.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>custodian.nwchem.handlers &mdash; custodian 0.4.2 documentation</title>
+ <title>custodian.nwchem.handlers &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
<link rel="up" title="Module code" href="../../index.html" />
<script type="text/javascript">
@@ -44,7 +44,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
</ul>
</div>
@@ -207,7 +207,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" >Module code</a> &raquo;</li>
</ul>
</div>
View
10 docs/_build/html/_modules/custodian/nwchem/jobs.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>custodian.nwchem.jobs &mdash; custodian 0.4.2 documentation</title>
+ <title>custodian.nwchem.jobs &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
<link rel="up" title="Module code" href="../../index.html" />
<script type="text/javascript">
@@ -44,7 +44,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
</ul>
</div>
@@ -206,7 +206,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" >Module code</a> &raquo;</li>
</ul>
</div>
View
10 docs/_build/html/_modules/custodian/vasp/handlers.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>custodian.vasp.handlers &mdash; custodian 0.4.2 documentation</title>
+ <title>custodian.vasp.handlers &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
<link rel="up" title="Module code" href="../../index.html" />
<script type="text/javascript">
@@ -44,7 +44,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
</ul>
</div>
@@ -466,7 +466,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" >Module code</a> &raquo;</li>
</ul>
</div>
View
10 docs/_build/html/_modules/custodian/vasp/jobs.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>custodian.vasp.jobs &mdash; custodian 0.4.2 documentation</title>
+ <title>custodian.vasp.jobs &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="../../../_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../../../',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../../../_static/underscore.js"></script>
<script type="text/javascript" src="../../../_static/doctools.js"></script>
<link rel="shortcut icon" href="../../../_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="../../../index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="../../../index.html" />
<link rel="up" title="Module code" href="../../index.html" />
<script type="text/javascript">
@@ -44,7 +44,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" accesskey="U">Module code</a> &raquo;</li>
</ul>
</div>
@@ -301,7 +301,7 @@
<li class="right" >
<a href="../../../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../../../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../../../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
<li><a href="../../index.html" >Module code</a> &raquo;</li>
</ul>
</div>
View
10 docs/_build/html/_modules/index.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Overview: module code &mdash; custodian 0.4.2 documentation</title>
+ <title>Overview: module code &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="../_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: '../',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="shortcut icon" href="../_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="../index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="../index.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
<li class="right" >
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -93,7 +93,7 @@
<li class="right" >
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="../index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="../index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
View
21 docs/_build/html/_sources/changelog.txt
@@ -1,6 +1,27 @@
Change Log
==========
+0.4.2
+-----
+1. Rudimentary support for Nwchem error handling (by Shyue Ping Ong).
+2. Improved VASP error handling (by Steve Dacek and Will Richards).
+
+0.4.1
+-----
+1. Added hanlding of PRICEL error in VASP.
+2. Speed and robustness improvements.
+3. BRIONS error now handled by changing ISYM.
+
+0.4.0
+-----
+1. Many VASP handlers are now consolidated into a single VaspErrorHandler.
+2. Many more fixes for VASP runs, including the "TOO FEW BANDS",
+ "TRIPLE PRODUCT", "DENTET" and "BRIONS" errors.
+3. VaspJob now includes the auto_npar and auto_gamma options, which
+ automatically optimizes the NPAR setting to be sqrt(number of cores) as
+ per the VASP recommendation for DFT runs and tries to search for a
+ gamma-only compiled version of VASP for gamma 1x1x1 runs.
+
0.3.5
-----
1. Bug fix for incorrect shift error handler in VASP.
View
24 docs/_build/html/_sources/index.txt
@@ -18,26 +18,10 @@ error, and potentially restart the job if necessary.
Change log
==========
-0.4.2
+0.4.3
-----
-1. Rudimentary support for Nwchem error handling (by Shyue Ping Ong).
-2. Improved VASP error handling (by Steve Dacek and Will Richards).
-
-0.4.1
------
-1. Added hanlding of PRICEL error in VASP.
-2. Speed and robustness improvements.
-3. BRIONS error now handled by changing ISYM.
-
-0.4.0
------
-1. Many VASP handlers are now consolidated into a single VaspErrorHandler.
-2. Many more fixes for VASP runs, including the "TOO FEW BANDS",
- "TRIPLE PRODUCT", "DENTET" and "BRIONS" errors.
-3. VaspJob now includes the auto_npar and auto_gamma options, which
- automatically optimizes the NPAR setting to be sqrt(number of cores) as
- per the VASP recommendation for DFT runs and tries to search for a
- gamma-only compiled version of VASP for gamma 1x1x1 runs.
+1. Added handling for ZBRENT error for VASP.
+2. Minor refactoring to consolidate backup and gzip directory methods.
:doc:`Older versions </changelog>`
@@ -377,6 +361,6 @@ follows::
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
-.. _`pymatgen's documentation`: http://pythonhosted.org/pymatgen
+.. _`pymatgen's documentation`: http://pymatgen.org
.. _`Materials Project`: https://www.materialsproject.org
.. _`pymatgen`: https://pypi.python.org/pypi/pymatgen
View
62 docs/_build/html/changelog.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Change Log &mdash; custodian 0.4.2 documentation</title>
+ <title>Change Log &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -55,30 +55,57 @@
<div class="section" id="change-log">
<h1>Change Log<a class="headerlink" href="#change-log" title="Permalink to this headline">¶</a></h1>
<div class="section" id="id1">
-<h2>0.3.5<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
+<h2>0.4.2<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
+<ol class="arabic simple">
+<li>Rudimentary support for Nwchem error handling (by Shyue Ping Ong).</li>
+<li>Improved VASP error handling (by Steve Dacek and Will Richards).</li>
+</ol>
+</div>
+<div class="section" id="id2">
+<h2>0.4.1<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h2>
+<ol class="arabic simple">
+<li>Added hanlding of PRICEL error in VASP.</li>
+<li>Speed and robustness improvements.</li>
+<li>BRIONS error now handled by changing ISYM.</li>
+</ol>
+</div>
+<div class="section" id="id3">
+<h2>0.4.0<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h2>
+<ol class="arabic simple">
+<li>Many VASP handlers are now consolidated into a single VaspErrorHandler.</li>
+<li>Many more fixes for VASP runs, including the &#8220;TOO FEW BANDS&#8221;,
+&#8220;TRIPLE PRODUCT&#8221;, &#8220;DENTET&#8221; and &#8220;BRIONS&#8221; errors.</li>
+<li>VaspJob now includes the auto_npar and auto_gamma options, which
+automatically optimizes the NPAR setting to be sqrt(number of cores) as
+per the VASP recommendation for DFT runs and tries to search for a
+gamma-only compiled version of VASP for gamma 1x1x1 runs.</li>
+</ol>
+</div>
+<div class="section" id="id4">
+<h2>0.3.5<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h2>
<ol class="arabic simple">
<li>Bug fix for incorrect shift error handler in VASP.</li>
<li>More robust fix for unconverged VASP runs (switching from ALGO fast to
normal).</li>
<li>Expanded documentation.</li>
</ol>
</div>
-<div class="section" id="id2">
-<h2>0.3.4<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="id5">
+<h2>0.3.4<a class="headerlink" href="#id5" title="Permalink to this headline">¶</a></h2>
<ol class="arabic simple">
<li>Added support for handlers that perform monitor a job as it is progressing
and terminates it if necessary. Useful for correcting errors that come up
by do not cause immediate job failures.</li>
</ol>
</div>
-<div class="section" id="id3">
-<h2>0.3.2<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="id6">
+<h2>0.3.2<a class="headerlink" href="#id6" title="Permalink to this headline">¶</a></h2>
<ol class="arabic simple">
<li>Important bug fix for VaspJob and converge_kpoints script.</li>
</ol>
</div>
-<div class="section" id="id4">
-<h2>0.3.0<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="id7">
+<h2>0.3.0<a class="headerlink" href="#id7" title="Permalink to this headline">¶</a></h2>
<ol class="arabic simple">
<li>Major update to custodian API. Custodian now perform more comprehensive
logging in a file called custodian.json, which logs all jobs and
@@ -118,10 +145,13 @@
<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Change Log</a><ul>
-<li><a class="reference internal" href="#id1">0.3.5</a></li>
-<li><a class="reference internal" href="#id2">0.3.4</a></li>
-<li><a class="reference internal" href="#id3">0.3.2</a></li>
-<li><a class="reference internal" href="#id4">0.3.0</a></li>
+<li><a class="reference internal" href="#id1">0.4.2</a></li>
+<li><a class="reference internal" href="#id2">0.4.1</a></li>
+<li><a class="reference internal" href="#id3">0.4.0</a></li>
+<li><a class="reference internal" href="#id4">0.3.5</a></li>
+<li><a class="reference internal" href="#id5">0.3.4</a></li>
+<li><a class="reference internal" href="#id6">0.3.2</a></li>
+<li><a class="reference internal" href="#id7">0.3.0</a></li>
<li><a class="reference internal" href="#version-0-2-6">Version 0.2.6</a></li>
<li><a class="reference internal" href="#version-0-2-5">Version 0.2.5</a></li>
<li><a class="reference internal" href="#version-0-2-4">Version 0.2.4</a></li>
@@ -160,7 +190,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
View
10 docs/_build/html/custodian.ansible.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>ansible Package &mdash; custodian 0.4.2 documentation</title>
+ <title>ansible Package &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -338,7 +338,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
View
48 docs/_build/html/custodian.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>custodian Package &mdash; custodian 0.4.2 documentation</title>
+ <title>custodian Package &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -60,8 +60,9 @@
<div class="section" id="module-custodian.custodian">
<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>
<p>This module implements the main Custodian class, which manages a list of jobs
-given a set of error handlers, and the abstract base classes for the
-ErrorHandlers and Jobs.</p>
+given a set of error handlers, the abstract base classes for the
+ErrorHandlers and Jobs, and some helper functions for backing up or
+compressing files in a directory.</p>
<dl class="class">
<dt id="custodian.custodian.Custodian">
<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 @@
</dd></dl>
+<dl class="function">
+<dt id="custodian.custodian.backup">
+<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>
+<dd><p>Backup files to a tar.gz file. Used, for example, in backing up the
+files of an errored run before performing corrections.</p>
+<dl class="docutils">
+<dt>Args:</dt>
+<dd><dl class="first last docutils">
+<dt>filenames:</dt>
+<dd>List of files to backup. Supports wildcards, e.g., <em>.</em>.</dd>
+<dt>prefix:</dt>
+<dd>prefix to the files. Defaults to error, which means a series of
+error.1.tar.gz, error.2.tar.gz, ... will be generated.</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="function">
+<dt id="custodian.custodian.gzip_dir">
+<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>
+<dd><p>Gzips all files in a directory. Used, for instance, to compress all
+files at the end of a run.</p>
+<dl class="docutils">
+<dt>Args:</dt>
+<dd><dl class="first last docutils">
+<dt>path:</dt>
+<dd>Path to directory.</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
</div>
<div class="section" id="subpackages">
<h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
@@ -302,7 +336,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
View
49 docs/_build/html/custodian.nwchem.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>nwchem Package &mdash; custodian 0.4.2 documentation</title>
+ <title>nwchem Package &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -56,7 +56,7 @@
<h1>nwchem Package<a class="headerlink" href="#nwchem-package" title="Permalink to this headline">¶</a></h1>
<div class="section" id="id1">
<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>
-<span class="target" id="module-custodian.nwchem"></span><p>TODO: Modify module doc.</p>
+<span class="target" id="module-custodian.nwchem"></span><p>This package implements various Nwchem Jobs and Error Handlers.</p>
</div>
<div class="section" id="module-custodian.nwchem.handlers">
<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 @@
</dd></dl>
-<dl class="function">
-<dt id="custodian.nwchem.handlers.backup">
-<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>
-<dd></dd></dl>
-
</div>
<div class="section" id="module-custodian.nwchem.jobs">
<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>
-<p>This module implements basic kinds of jobs for Gaussian runs.</p>
+<p>This module implements basic kinds of jobs for Nwchem runs.</p>
<dl class="class">
<dt id="custodian.nwchem.jobs.NwchemJob">
-<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>
+<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>
<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>
-<p>A basic Gaussian job. Just runs whatever is in the directory. But
-conceivably can be a complex processing of inputs etc. with initialization.</p>
-<p>This constructor is necessarily complex due to the need for
-flexibility. For standard kinds of runs, it&#8217;s often better to use one
-of the static constructors.</p>
+<p>A basic Nwchem job.</p>
<dl class="docutils">
<dt>Args:</dt>
<dd><dl class="first last docutils">
@@ -121,8 +112,6 @@
[&#8220;nwchem&#8221;].</dd>
<dt>output_file:</dt>
<dd>Name of file to direct standard out to.</dd>
-<dt>suffix:</dt>
-<dd>A suffix to be appended to the final output.</dd>
<dt>backup:</dt>
<dd>Boolean whether to backup the initial input files. If True,
the input files will be copied with a &#8221;.orig&#8221; appended.
@@ -131,13 +120,13 @@
<dd>Whether to gzip the final output. Defaults to False.</dd>
<dt>settings_override:</dt>
<dd>An ansible style list of dict to override changes.
-TODO: Not implemented yet.</dd>
+#TODO: Not implemented yet.</dd>
</dl>
</dd>
</dl>
-<dl class="staticmethod">
+<dl class="classmethod">
<dt id="custodian.nwchem.jobs.NwchemJob.from_dict">
-<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>
+<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>
<dd></dd></dl>
<dl class="attribute">
@@ -167,20 +156,6 @@
</dd></dl>
-<dl class="function">
-<dt id="custodian.nwchem.jobs.gzip_directory">
-<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>
-<dd><p>Gzips all files in a directory.</p>
-<dl class="docutils">
-<dt>Args:</dt>
-<dd><dl class="first last docutils">
-<dt>path:</dt>
-<dd>Path to directory.</dd>
-</dl>
-</dd>
-</dl>
-</dd></dl>
-
</div>
</div>
@@ -231,7 +206,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
View
46 docs/_build/html/custodian.vasp.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>vasp Package &mdash; custodian 0.4.2 documentation</title>
+ <title>vasp Package &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -56,7 +56,7 @@
<h1>vasp Package<a class="headerlink" href="#vasp-package" title="Permalink to this headline">¶</a></h1>
<div class="section" id="id1">
<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>
-<span class="target" id="module-custodian.vasp"></span><p>TODO: Change the module doc.</p>
+<span class="target" id="module-custodian.vasp"></span><p>This package implements various VASP Jobs and Error Handlers.</p>
</div>
<div class="section" id="module-custodian.vasp.handlers">
<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 @@
<dl class="class">
<dt id="custodian.vasp.handlers.NonConvergingErrorHandler">
-<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>
+<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>
<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>
<p>Check if a run is hitting the maximum number of electronic steps at the
-last 10 ionic steps. If so, kill the job.</p>
+last nionic_steps ionic steps (default=10). If so, change ALGO from Fast to
+Normal or kill the job.</p>
<dl class="method">
<dt id="custodian.vasp.handlers.NonConvergingErrorHandler.check">
<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 @@
<dt id="custodian.vasp.handlers.PotimErrorHandler">
<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>
<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>
-<p>Check if a run has excessively large positive energy changes.
-This is typically caused by too large a POTIM. Runs typically
+<p>Check if a run has excessively large positive energy changes.
+This is typically caused by too large a POTIM. Runs typically
end up crashing with some other error (e.g. BRMIX) as the geometry
gets progressively worse.</p>
<dl class="method">
@@ -248,7 +249,7 @@
<dl class="attribute">
<dt id="custodian.vasp.handlers.VaspErrorHandler.error_msgs">
-<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>
+<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>
<dd></dd></dl>
<dl class="classmethod">
@@ -268,11 +269,6 @@
</dd></dl>
-<dl class="function">
-<dt id="custodian.vasp.handlers.backup">
-<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>
-<dd></dd></dl>
-
</div>
<div class="section" id="module-custodian.vasp.jobs">
<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 @@
</dl>
</dd></dl>
-<dl class="staticmethod">
+<dl class="classmethod">
<dt id="custodian.vasp.jobs.VaspJob.from_dict">
-<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>
+<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>
<dd></dd></dl>
<dl class="attribute">
@@ -640,20 +636,6 @@
</dd></dl>
-<dl class="function">
-<dt id="custodian.vasp.jobs.gzip_directory">
-<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>
-<dd><p>Gzips all files in a directory.</p>
-<dl class="docutils">
-<dt>Args:</dt>
-<dd><dl class="first last docutils">
-<dt>path:</dt>
-<dd>Path to directory.</dd>
-</dl>
-</dd>
-</dl>
-</dd></dl>
-
</div>
</div>
@@ -704,7 +686,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
View
40 docs/_build/html/genindex.html
@@ -7,15 +7,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Index &mdash; custodian 0.4.2 documentation</title>
+ <title>Index &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -25,7 +25,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
@@ -44,7 +44,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -90,15 +90,9 @@ <h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="custodian.nwchem.html#custodian.nwchem.handlers.backup">backup() (in module custodian.nwchem.handlers)</a>
+ <dt><a href="custodian.html#custodian.custodian.backup">backup() (in module custodian.custodian)</a>
</dt>
- <dd><dl>
-
- <dt><a href="custodian.vasp.html#custodian.vasp.handlers.backup">(in module custodian.vasp.handlers)</a>
- </dt>
-
- </dl></dd>
</dl></td>
</tr></table>
@@ -285,19 +279,15 @@ <h2 id="F">F</h2>
<dd><dl>
- <dt><a href="custodian.nwchem.html#custodian.nwchem.jobs.NwchemJob.from_dict">(NwchemJob static method)</a>
- </dt>
-
-
- <dt><a href="custodian.vasp.html#custodian.vasp.jobs.VaspJob.from_dict">(VaspJob static method)</a>
+ <dt><a href="custodian.html#custodian.custodian.Job.from_dict">(custodian.custodian.Job class method)</a>
</dt>
- <dt><a href="custodian.html#custodian.custodian.Job.from_dict">(custodian.custodian.Job class method)</a>
+ <dt><a href="custodian.nwchem.html#custodian.nwchem.handlers.NwchemErrorHandler.from_dict">(custodian.nwchem.handlers.NwchemErrorHandler class method)</a>
</dt>
- <dt><a href="custodian.nwchem.html#custodian.nwchem.handlers.NwchemErrorHandler.from_dict">(custodian.nwchem.handlers.NwchemErrorHandler class method)</a>
+ <dt><a href="custodian.nwchem.html#custodian.nwchem.jobs.NwchemJob.from_dict">(custodian.nwchem.jobs.NwchemJob class method)</a>
</dt>
@@ -324,6 +314,10 @@ <h2 id="F">F</h2>
<dt><a href="custodian.vasp.html#custodian.vasp.handlers.VaspErrorHandler.from_dict">(custodian.vasp.handlers.VaspErrorHandler class method)</a>
</dt>
+
+ <dt><a href="custodian.vasp.html#custodian.vasp.jobs.VaspJob.from_dict">(custodian.vasp.jobs.VaspJob class method)</a>
+ </dt>
+
</dl></dd>
<dt><a href="custodian.vasp.html#custodian.vasp.handlers.FrozenJobErrorHandler">FrozenJobErrorHandler (class in custodian.vasp.handlers)</a>
@@ -342,15 +336,9 @@ <h2 id="G">G</h2>
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="custodian.nwchem.html#custodian.nwchem.jobs.gzip_directory">gzip_directory() (in module custodian.nwchem.jobs)</a>
+ <dt><a href="custodian.html#custodian.custodian.gzip_dir">gzip_dir() (in module custodian.custodian)</a>
</dt>
- <dd><dl>
-
- <dt><a href="custodian.vasp.html#custodian.vasp.jobs.gzip_directory">(in module custodian.vasp.jobs)</a>
- </dt>
-
- </dl></dd>
</dl></td>
</tr></table>
@@ -684,7 +672,7 @@ <h2 id="V">V</h2>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
View
46 docs/_build/html/index.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Change log &mdash; custodian 0.4.2 documentation</title>
+ <title>Change log &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="#" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="#" />
<script type="text/javascript">
var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="#">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="#">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -69,30 +69,10 @@
<div class="section" id="change-log">
<h1>Change log<a class="headerlink" href="#change-log" title="Permalink to this headline">¶</a></h1>
<div class="section" id="id1">
-<h2>0.4.2<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
+<h2>0.4.3<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
<ol class="arabic simple">
-<li>Rudimentary support for Nwchem error handling (by Shyue Ping Ong).</li>
-<li>Improved VASP error handling (by Steve Dacek and Will Richards).</li>
-</ol>
-</div>
-<div class="section" id="id2">
-<h2>0.4.1<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h2>
-<ol class="arabic simple">
-<li>Added hanlding of PRICEL error in VASP.</li>
-<li>Speed and robustness improvements.</li>
-<li>BRIONS error now handled by changing ISYM.</li>
-</ol>
-</div>
-<div class="section" id="id3">
-<h2>0.4.0<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h2>
-<ol class="arabic simple">
-<li>Many VASP handlers are now consolidated into a single VaspErrorHandler.</li>
-<li>Many more fixes for VASP runs, including the &#8220;TOO FEW BANDS&#8221;,
-&#8220;TRIPLE PRODUCT&#8221;, &#8220;DENTET&#8221; and &#8220;BRIONS&#8221; errors.</li>
-<li>VaspJob now includes the auto_npar and auto_gamma options, which
-automatically optimizes the NPAR setting to be sqrt(number of cores) as
-per the VASP recommendation for DFT runs and tries to search for a
-gamma-only compiled version of VASP for gamma 1x1x1 runs.</li>
+<li>Added handling for ZBRENT error for VASP.</li>
+<li>Minor refactoring to consolidate backup and gzip directory methods.</li>
</ol>
<p><a class="reference internal" href="changelog.html"><em>Older versions</em></a></p>
</div>
@@ -110,7 +90,7 @@
<div class="highlight-python"><pre>pip install custodian</pre>
</div>
<p>Some plugins (e.g., vasp management) require additional setup (please see
-<a class="reference external" href="http://pythonhosted.org/pymatgen">pymatgen&#8217;s documentation</a>).</p>
+<a class="reference external" href="http://pymatgen.org">pymatgen&#8217;s documentation</a>).</p>
</div>
<div class="section" id="developmental-version">
<h2>Developmental version<a class="headerlink" href="#developmental-version" title="Permalink to this headline">¶</a></h2>
@@ -136,7 +116,7 @@
Please install using:</p>
<div class="highlight-python"><pre>pip install pymatgen</pre>
</div>
-<p>For more information, please consult <a class="reference external" href="http://pythonhosted.org/pymatgen">pymatgen&#8217;s documentation</a>.</p>
+<p>For more information, please consult <a class="reference external" href="http://pymatgen.org">pymatgen&#8217;s documentation</a>.</p>
</li>
<li><p class="first">nose - For complete unittesting.</p>
</li>
@@ -148,7 +128,7 @@
<p>The main class in the workflow is known as Custodian, which manages a series
of jobs with a list of error handlers. The general workflow for Custodian is
presented in the figure below.</p>
-<div class="align-center figure align-center">
+<div class="align-center figure">
<a class="reference internal image-reference" href="_images/Custodian.png"><img alt="Custodian workflow" src="_images/Custodian.png" style="width: 500px;" /></a>
<p class="caption">Overview of the Custodian workflow.</p>
</div>
@@ -409,9 +389,7 @@
<h3><a href="#">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Change log</a><ul>
-<li><a class="reference internal" href="#id1">0.4.2</a></li>
-<li><a class="reference internal" href="#id2">0.4.1</a></li>
-<li><a class="reference internal" href="#id3">0.4.0</a></li>
+<li><a class="reference internal" href="#id1">0.4.3</a></li>
</ul>
</li>
<li><a class="reference internal" href="#getting-custodian">Getting custodian</a><ul>
@@ -464,7 +442,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="#">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="#">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
View
10 docs/_build/html/modules.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>custodian &mdash; custodian 0.4.2 documentation</title>
+ <title>custodian &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
<script type="text/javascript">
var _gaq = _gaq || [];
@@ -43,7 +43,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -122,7 +122,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
View
BIN docs/_build/html/objects.inv
Binary file not shown.
View
10 docs/_build/html/py-modindex.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Python Module Index &mdash; custodian 0.4.2 documentation</title>
+ <title>Python Module Index &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
- VERSION: '0.4.2',
+ VERSION: '0.4.3',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true
@@ -24,7 +24,7 @@
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
<script type="text/javascript">
@@ -46,7 +46,7 @@
<li class="right" >
<a href="#" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -156,7 +156,7 @@
<li class="right" >
<a href="#" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
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10 docs/_build/html/search.html
@@ -6,15 +6,15 @@
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Search &mdash; custodian 0.4.2 documentation</title>
+ <title>Search &mdash; custodian 0.4.3 documentation</title>
<link rel="stylesheet" href="_static/proBlue.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
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<script type="text/javascript" src="_static/doctools.js"></script>
<script type="text/javascript" src="_static/searchtools.js"></script>
<link rel="shortcut icon" href="_static/favicon.ico"/>
- <link rel="top" title="custodian 0.4.2 documentation" href="index.html" />
+ <link rel="top" title="custodian 0.4.3 documentation" href="index.html" />
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jQuery(function() { Search.loadIndex("searchindex.js"); });
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@@ -51,7 +51,7 @@
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
</div>
@@ -102,7 +102,7 @@ <h1 id="search-documentation">Search</h1>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li><a href="index.html">custodian 0.4.2 documentation</a> &raquo;</li>
+ <li><a href="index.html">custodian 0.4.3 documentation</a> &raquo;</li>
</ul>
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View
2 docs/_build/html/searchindex.js
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21 docs/changelog.rst
@@ -1,6 +1,27 @@
Change Log
==========
+0.4.2
+-----
+1. Rudimentary support for Nwchem error handling (by Shyue Ping Ong).
+2. Improved VASP error handling (by Steve Dacek and Will Richards).