Update to v1.0.2

atomate/__init__.py

@@ -1 +1 @@
-__version__ = "1.0.1"
+__version__ = "1.0.2"

docs/_sources/advanced_stores.rst.txt

@@ -6,7 +6,7 @@
 Advanced Storage Stratagies
 ==================
 
-Storing data greater than 16 Mb 
+Storing data greater than 16 Mb
 ============
 
 Introduction
@@ -56,7 +56,7 @@ Note, this AWS profile needs to be available anywhere the ``VaspCalcDb.insert_ta
 Usage
 -----------
 
-Example: store the charge density 
+Example: store the charge density
 
 To parse a completed calculation directory.  We need to instantiate the ``drone`` with the ``parse_aeccar`` or ``parse_chgcar`` flag.
 
@@ -72,7 +72,7 @@ Some workflows like the ``StaticWF`` will pass the parsing flags like ``parse_ch
 To access the data using the task_id we can call
 
 .. code-block:: python
-    
+
     chgcar = mmdb.get_chgcar(task_id)
 
 Similar functionalities exist for the band structure and DOS.

docs/_sources/atomate.qchem.workflows.base.rst.txt

@@ -28,6 +28,14 @@ atomate.qchem.workflows.base.fragmentation module
    :undoc-members:
    :show-inheritance:
 
+atomate.qchem.workflows.base.reaction\_path module
+--------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.base.reaction_path
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.qchem.workflows.base.torsion\_potential module
 ------------------------------------------------------
 

docs/_sources/atomate.qchem.workflows.tests.rst.txt

@@ -36,6 +36,14 @@ atomate.qchem.workflows.tests.test\_parse\_pass\_write module
    :undoc-members:
    :show-inheritance:
 
+atomate.qchem.workflows.tests.test\_reaction\_path module
+---------------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.tests.test_reaction_path
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.qchem.workflows.tests.test\_torsion\_potential module
 -------------------------------------------------------------
 

docs/_sources/atomate.vasp.analysis.rst.txt

@@ -4,6 +4,14 @@ atomate.vasp.analysis package
 Submodules
 ----------
 
+atomate.vasp.analysis.linear\_response module
+---------------------------------------------
+
+.. automodule:: atomate.vasp.analysis.linear_response
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.vasp.analysis.phonopy module
 ------------------------------------
 

docs/_sources/atomate.vasp.workflows.base.rst.txt

@@ -84,6 +84,14 @@ atomate.vasp.workflows.base.gibbs module
    :undoc-members:
    :show-inheritance:
 
+atomate.vasp.workflows.base.hubbard\_hund\_linresp module
+---------------------------------------------------------
+
+.. automodule:: atomate.vasp.workflows.base.hubbard_hund_linresp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.vasp.workflows.base.lobster module
 ------------------------------------------
 

docs/_sources/atomate.vasp.workflows.tests.rst.txt

@@ -52,6 +52,14 @@ atomate.vasp.workflows.tests.test\_ferroelectric\_workflow module
    :undoc-members:
    :show-inheritance:
 
+atomate.vasp.workflows.tests.test\_hubbard\_hund\_linresp module
+----------------------------------------------------------------
+
+.. automodule:: atomate.vasp.workflows.tests.test_hubbard_hund_linresp
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.vasp.workflows.tests.test\_insertion\_workflow module
 -------------------------------------------------------------
 

docs/_sources/builders.rst.txt

@@ -55,4 +55,4 @@ Running builders is simple. Note that running builders does not modify the sourc
 
 To try running builders, follow the example in ``atomate.vasp.builders.examples``. Afterwards, inspect your MongoDB database to find the new collections and data.
 
-Note that builders have a reset() function in case you want to start over.
+Note that builders have a reset() function in case you want to start over.

docs/_sources/changelog.rst.txt

@@ -366,4 +366,4 @@ atomate Changelog
 
 **v0.0.3**
 
-* initial release (A. Jain, S.P. Ong, K. Mathew, M. Aykol)
+* initial release (A. Jain, S.P. Ong, K. Mathew, M. Aykol)

docs/_sources/concepts.rst.txt

@@ -65,4 +65,4 @@ might come in handy when setting the NCORE parameter on NERSC machines:
 
 Thus, a good starting point is to set NCORE=4 for Matgen/Edison and NCORE=8 for
 Cori. Reduce NCORE if you want to try to increase speed at the risk of having
-lower memory available per orbital.
+lower memory available per orbital.

docs/_sources/creating_workflows.rst.txt

@@ -303,5 +303,3 @@ Understanding this guide has enabled you to create arbitrarily complex atomate w
 If any of this was unclear, or if you feel that useful documentation is missing, please leave us feedback on the `atomate Discourse forum`_! To see all of the different pieces you can control with Python, go to the :ref:`API documentation <modindex>`. Many customization options and features of interest are not in atomate alone, but in `FireWorks`_, `pymatgen`_, and `custodian`_. Mastering FireWorks will enable you to get the most out of executing and managing your workflows. Mastering pymatgen will help you write complex materials workflows and perform sophisticated analyses of results.
 
 .. _atomate Discourse forum:  https://discuss.matsci.org/c/atomate
-
-

docs/_sources/customizing_workflows.rst.txt

@@ -219,4 +219,3 @@ Which POTCAR file you want to use is controlled by the input set as well. The ea
 
 .. _pymatgen's vasp sets: http://pymatgen.org/pymatgen.io.vasp.sets.html
 .. _pymatgen.io.vasp.sets.MPHSERelaxSet: http://pymatgen.org/pymatgen.io.vasp.sets.html#pymatgen.io.vasp.sets.MPHSERelaxSet
-

docs/_sources/developer_installation.rst.txt

@@ -70,4 +70,4 @@ If you need to debug at a later point, this might be something to refer back to,
 Many tests have a DEBUG option that can sometimes help in finding problems.
 Sometimes you need to toggle DEBUG on/off a couple of times if you are doing this to make sure all the old data is actually cleared between debug runs.
 
-Run the tests by navigating to ``<<INSTALL_DIR>>/codes/atomate/`` and running ``python setup.py test`` or ``nosetests``.
+Run the tests by navigating to ``<<INSTALL_DIR>>/codes/atomate/`` and running ``python setup.py test`` or ``nosetests``.

docs/_sources/gibbs_workflow_tutorial.rst.txt

@@ -216,4 +216,3 @@ At this point, you might:
 
 * Explore using builders to generate metadata: :ref:`builders`.
 * Skip to learning how to create your own workflows that you can use and distribute: :ref:`creating workflows`.
-

docs/_sources/installation.rst.txt

@@ -626,4 +626,3 @@ Q: I honestly tried everything I can to solve my problem. I still need help!
 ----------------------------------------------------------------------------
 
 :A: There is a support forum for atomate: https://discuss.matsci.org/c/atomate
-

docs/_sources/running_workflows.rst.txt

@@ -232,4 +232,3 @@ At this point, you might:
 * Try another example: running a Gibbs free energy workflow: :ref:`running gibbs workflows`.
 * Skip to exploring how to use builders to generate metadata: :ref:`builders`.
 * Skip to learning how to create your own workflows that you can use and distribute: :ref:`creating workflows`.
-

docs/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.0.1',
+    VERSION: '1.0.2',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

docs/_static/nature.css

@@ -11,7 +11,7 @@
 
  @import url("basic.css");
 /* -- page layout ----------------------------------------------------------- */
- 
+
 body {
     font-family: "Lato", sans-serif;
     font-size: 100%;
@@ -33,18 +33,18 @@ div.bodywrapper {
 hr {
     border: 1px solid #B1B4B6;
 }
- 
+
 div.document {
     background-color: #eee;
 }
- 
+
 div.body {
     background-color: #ffffff;
     color: #3E4349;
     padding: 0 30px 30px 30px;
     font-size: 1.1em;
 }
- 
+
 div.footer {
 	background: none repeat scroll 0 0 #eeeeee;
     color: #555;
@@ -53,24 +53,24 @@ div.footer {
     text-align: center;
     font-size: 75%;
 }
- 
+
 div.footer a {
     color: #444;
     text-decoration: underline;
 }
- 
+
 div.related {
     background-color: #595959;
     line-height: 32px;
     color: #fff;
     text-shadow: 0px 1px 0 #444;
     font-size: 0.9em;
 }
- 
+
 div.related a {
     color: #fff;
 }
- 
+
 div.sphinxsidebar {
     font-size: 0.9em;
     line-height: 1.5em;
@@ -79,7 +79,7 @@ div.sphinxsidebar {
 div.sphinxsidebarwrapper{
     padding: 20px 0;
 }
- 
+
 div.sphinxsidebar h3,
 div.sphinxsidebar h4 {
     font-family: Arial, sans-serif;
@@ -95,30 +95,30 @@ div.sphinxsidebar h4 {
 div.sphinxsidebar h4{
     font-size: 1.1em;
 }
- 
+
 div.sphinxsidebar h3 a {
     color: #444;
 }
- 
- 
+
+
 div.sphinxsidebar p {
     color: #888;
     padding: 5px 20px;
 }
- 
+
 div.sphinxsidebar p.topless {
 }
- 
+
 div.sphinxsidebar ul {
     margin: 10px 20px;
     padding: 0;
     color: #000;
 }
- 
+
 div.sphinxsidebar a {
     color: #444;
 }
- 
+
 div.sphinxsidebar input {
     border: 1px solid #ccc;
     font-family: sans-serif;
@@ -128,19 +128,19 @@ div.sphinxsidebar input {
 div.sphinxsidebar input[type=text]{
     margin-left: 20px;
 }
- 
+
 /* -- body styles ----------------------------------------------------------- */
- 
+
 a {
     color: #0985b3;
     text-decoration: none;
 }
- 
+
 a:hover {
     color: #595959;
     text-decoration: underline;
 }
- 
+
 div.body h1,
 div.body h4,
 div.body h5,
@@ -153,30 +153,30 @@ div.body h6 {
     padding: 5px 0 5px 10px;
     text-shadow: 0px 1px 0 black
 }
- 
+
 div.body h1 { border-top: 20px solid white; margin-top: 0; font-size: 200%; }
 div.body h2 { font-size: 150%; color: #595959; font-family: "Palatino", serif}
 div.body h3 { font-size: 110%; color: #446; font-family: "Palatino", serif}
 div.body h4 { font-size: 110%; background-color: #595959; }
 div.body h5 { font-size: 100%; background-color: #595959; }
 div.body h6 { font-size: 100%; background-color: #595959; }
- 
+
 a.headerlink {
     color: #fff;
     font-size: 0.8em;
     padding: 0 4px 0 4px;
     text-decoration: none;
 }
- 
+
 a.headerlink:hover {
     background-color: #ffc000;
     color: white;
 }
- 
+
 div.body p, div.body dd, div.body li {
     line-height: 1.5em;
 }
- 
+
 div.admonition p.admonition-title + p {
     display: inline;
 }
@@ -189,29 +189,29 @@ div.note {
     background-color: #eee;
     border: 1px solid #ccc;
 }
- 
+
 div.seealso {
     background-color: #ffc;
     border: 1px solid #ff6;
 }
- 
+
 div.topic {
     background-color: #eee;
 }
- 
+
 div.warning {
     background-color: #ffe4e4;
     border: 1px solid #f66;
 }
- 
+
 p.admonition-title {
     display: inline;
 }
- 
+
 p.admonition-title:after {
     content: ":";
 }
- 
+
 pre {
     padding: 10px;
     background-color: White;
@@ -223,7 +223,7 @@ pre {
     -webkit-box-shadow: 1px 1px 1px #d8d8d8;
     -moz-box-shadow: 1px 1px 1px #d8d8d8;
 }
- 
+
 tt {
     background-color: #ecf0f3;
     color: #222;
@@ -258,4 +258,4 @@ p.caption {
     background-color: #eee;
     width: 65%;
     padding: 10px 10px;
-}
+}