Update to v0.9.5

atomate/__init__.py

@@ -1 +1 @@
-__version__ = "0.9.4"
+__version__ = "0.9.5"

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

@@ -11,6 +11,14 @@ Subpackages
 Submodules
 ----------
 
+atomate.vasp.firetasks.exchange module
+--------------------------------------
+
+.. automodule:: atomate.vasp.firetasks.exchange
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.vasp.firetasks.glue\_tasks module
 -----------------------------------------
 

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

@@ -12,6 +12,14 @@ atomate.vasp.firetasks.tests.test\_copy module
    :undoc-members:
    :show-inheritance:
 
+atomate.vasp.firetasks.tests.test\_exchange module
+--------------------------------------------------
+
+.. automodule:: atomate.vasp.firetasks.tests.test_exchange
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.vasp.firetasks.tests.test\_get\_interpolated\_poscar module
 -------------------------------------------------------------------
 

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

@@ -12,6 +12,14 @@ atomate.vasp.fireworks.core module
    :undoc-members:
    :show-inheritance:
 
+atomate.vasp.fireworks.exchange module
+--------------------------------------
+
+.. automodule:: atomate.vasp.fireworks.exchange
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.vasp.fireworks.nmr module
 ---------------------------------
 

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

@@ -44,6 +44,14 @@ atomate.vasp.workflows.base.elastic module
    :undoc-members:
    :show-inheritance:
 
+atomate.vasp.workflows.base.exchange module
+-------------------------------------------
+
+.. automodule:: atomate.vasp.workflows.base.exchange
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.vasp.workflows.base.ferroelectric module
 ------------------------------------------------
 

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

@@ -28,6 +28,14 @@ atomate.vasp.workflows.tests.test\_elastic\_workflow module
    :undoc-members:
    :show-inheritance:
 
+atomate.vasp.workflows.tests.test\_exchange\_workflow module
+------------------------------------------------------------
+
+.. automodule:: atomate.vasp.workflows.tests.test_exchange_workflow
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 atomate.vasp.workflows.tests.test\_ferroelectric\_workflow module
 -----------------------------------------------------------------
 

docs/_sources/changelog.rst.txt

@@ -2,6 +2,14 @@
 atomate Changelog
 =================
 
+**v0.9.5**
+
+* Add magnetism workflow (M. Horton, N. Frey)
+* Overhaul SCAN workflow (R. Kingsbury)
+* Move help to Discourse (A. Ganose)
+* add ModifyKPoints Firetask (M. Siron)
+* Misc fixes, dependency updates, and improvements (M. Horton, N. Frey, A. Jain, M. Siron, A. Ganose)
+
 **v0.9.4**
 
 * Fixes for new pymatgen (S. Blau, S.P. Ong)

docs/_sources/contributors.rst.txt

@@ -7,9 +7,9 @@ atomate development is led by the Hacking Materials research group led by Anubha
 Contributions are provided by:
 
 * Alireza Faghaninia, Alex Dunn, Alex Ganose, and Evan Spotte-Smith through the research group of A. Jain at LBNL.
-* Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Patrick Huck, Brandon Wood, Sam Blau, Jimmy Shen, Anne Rutt, Eric Sivonxay, and Martin Siron through the research group of Prof. Kristin Persson at UC Berkeley.
+* Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Matt Horton, Patrick Huck, Brandon Wood, Sam Blau, Jimmy Shen, Ryan Kingsbury, Anne Rutt, Eric Sivonxay, and Martin Siron through the research group of Prof. Kristin Persson at UC Berkeley.
 * Hanmei Tang, Prof. Shyue Ping Ong, and the Materials Virtual Lab research group at UC San Diego.
 * Brandon Bocklund, who led the atomate documentation effort, through the research group of Prof. Zi-Kiu Liu at Penn State.
 * Tess Smidt through the research group of Prof. Jeff Neaton at UC Berkeley.
 * Danny Broberg through the research group of Prof. Mark Asta at UC Berkeley.
-* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla, Marnik Bercx, Tara Maria Boland
+* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla, Marnik Bercx, Tara Maria Boland, Nathan Frey, Martin Siron

docs/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.9.4',
+    VERSION: '0.9.5',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

docs/atomate.common.firetasks.html

@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.common.firetasks package &#8212; atomate 0.9.4 documentation</title>
+    <title>atomate.common.firetasks package &#8212; atomate 0.9.5 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -63,12 +63,20 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">fireworks.core.firework.FiretaskBase</span></code></p>
 <p>Task to copy the given list of files from the given directory to the destination directory.
 To customize override the setup_copy and copy_files methods.</p>
-<dl class="simple">
-<dt>Optional params:</dt><dd><p>from_dir (str): path to the directory containing the files to be copied.
-to_dir (str): path to the destination directory
+<dl>
+<dt>Optional params:</dt><dd><p>from_dir (str): path to the directory containing the files to be copied. Supports env_chk.
+to_dir (str): path to the destination directory. Supports env_chk.
 filesystem (str)
-files_to_copy (list): list of file names.
-exclude_files (list): list of file names to be excluded.</p>
+files_to_copy (list): list of file names. Defaults to copying everything in from_dir.
+exclude_files (list): list of file names to be excluded.
+suffix (str): suffix to append to each filename when copying</p>
+<blockquote>
+<div><p>(e.g., rename ‘INCAR’ to ‘INCAR.precondition’)</p>
+</div></blockquote>
+<dl class="simple">
+<dt>continue_on_missing(bool): Whether to continue copying when a file</dt><dd><p>in filenames is missing. Defaults to False.</p>
+</dd>
+</dl>
 </dd>
 </dl>
 <dl class="method">
@@ -79,7 +87,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 <dl class="attribute">
 <dt id="atomate.common.firetasks.glue_tasks.CopyFiles.optional_params">
-<code class="sig-name descname">optional_params</code><em class="property"> = ['from_dir', 'to_dir', 'filesystem', 'files_to_copy', 'exclude_files']</em><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.CopyFiles.optional_params" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">optional_params</code><em class="property"> = ['from_dir', 'to_dir', 'filesystem', 'files_to_copy', 'exclude_files', 'suffix', 'continue_on_missing']</em><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.CopyFiles.optional_params" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="method">
@@ -109,18 +117,24 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 <dl class="method">
 <dt id="atomate.common.firetasks.glue_tasks.CopyFiles.setup_copy">
-<code class="sig-name descname">setup_copy</code><span class="sig-paren">(</span><em class="sig-param">from_dir</em>, <em class="sig-param">to_dir=None</em>, <em class="sig-param">filesystem=None</em>, <em class="sig-param">files_to_copy=None</em>, <em class="sig-param">exclude_files=None</em>, <em class="sig-param">from_path_dict=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.CopyFiles.setup_copy" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">setup_copy</code><span class="sig-paren">(</span><em class="sig-param">from_dir</em>, <em class="sig-param">to_dir=None</em>, <em class="sig-param">filesystem=None</em>, <em class="sig-param">files_to_copy=None</em>, <em class="sig-param">exclude_files=None</em>, <em class="sig-param">from_path_dict=None</em>, <em class="sig-param">suffix=None</em>, <em class="sig-param">fw_spec=None</em>, <em class="sig-param">continue_on_missing=False</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.CopyFiles.setup_copy" title="Permalink to this definition">¶</a></dt>
 <dd><p>setup the copy i.e setup the from directory, filesystem, destination directory etc.</p>
 <dl>
 <dt>Args:</dt><dd><p>from_dir (str)
 to_dir (str)
 filesystem (str)
 files_to_copy (list): if None all the files in the from_dir will be copied
-exclude_files (list)
-from_path_dict (dict): dict specification of the path. If specified must contain atleast</p>
+exclude_files (list): list of file names to be excluded.
+suffix (str): suffix to append to each filename when copying</p>
 <blockquote>
-<div><p>the key “path” that specifies the path to the from_dir.</p>
+<div><p>(e.g., rename ‘INCAR’ to ‘INCAR.precondition’)</p>
 </div></blockquote>
+<dl class="simple">
+<dt>continue_on_missing(bool): Whether to continue copying when a file</dt><dd><p>in filenames is missing. Defaults to False.</p>
+</dd>
+<dt>from_path_dict (dict): dict specification of the path. If specified must contain atleast</dt><dd><p>the key “path” that specifies the path to the from_dir.</p>
+</dd>
+</dl>
 </dd>
 </dl>
 </dd></dl>
@@ -131,7 +145,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dt id="atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc">
 <em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.glue_tasks.</code><code class="sig-name descname">CopyFilesFromCalcLoc</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">fireworks.core.firework.FiretaskBase</span></code></p>
-<p>Based on CopyVaspOutputs but for general file copying. Note that “calc_locs”
+<p>Based on CopyVaspOutputs but for general file copying. Note “calc_locs”
 must be set in the fw_spec. Files are copied to the current folder.</p>
 <dl>
 <dt>Required params:</dt><dd><p>calc_loc: name of target fw to get location for within the calc_locs.</p>
@@ -141,17 +155,23 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 ‘$ALL_NO_SUBDIRS’ in filenames: similar to filenames is None
 ‘$ALL’ in filenames: all files and subfolders copied, name_prepend</p>
 <blockquote>
-<div><p>and name_append cannot be set in this case</p>
+<div><p>and name_append cannot be set in this case.</p>
 </div></blockquote>
+<p>Accepts glob patterns.</p>
+</dd>
+<dt>name_prepend (str): string to prepend filenames, e.g. can be a </dt><dd><p>directory.</p>
 </dd>
 </dl>
-<p>name_prepend (str): string to prepend filenames, e.g. can be a directory.
-name_append (str): string to append to destination filenames.</p>
+<p>name_append (str): string to append to destination filenames.
+exclude_files (list): list of file names to be excluded. Accepts glob</p>
+<blockquote>
+<div><p>patterns.</p>
+</div></blockquote>
 </dd>
 </dl>
 <dl class="attribute">
 <dt id="atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc.optional_params">
-<code class="sig-name descname">optional_params</code><em class="property"> = ['filenames', 'name_prepend', 'name_append']</em><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc.optional_params" title="Permalink to this definition">¶</a></dt>
+<code class="sig-name descname">optional_params</code><em class="property"> = ['filenames', 'name_prepend', 'name_append', 'exclude_files']</em><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.CopyFilesFromCalcLoc.optional_params" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>
 
 <dl class="attribute">
@@ -281,6 +301,48 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 </dd></dl>
 
+<dl class="class">
+<dt id="atomate.common.firetasks.glue_tasks.GzipDir">
+<em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.glue_tasks.</code><code class="sig-name descname">GzipDir</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.GzipDir" title="Permalink to this definition">¶</a></dt>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">fireworks.core.firework.FiretaskBase</span></code></p>
+<p>Task to gzip the current directory.</p>
+<dl class="attribute">
+<dt id="atomate.common.firetasks.glue_tasks.GzipDir.optional_params">
+<code class="sig-name descname">optional_params</code><em class="property"> = []</em><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.GzipDir.optional_params" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="atomate.common.firetasks.glue_tasks.GzipDir.required_params">
+<code class="sig-name descname">required_params</code><em class="property"> = []</em><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.GzipDir.required_params" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="method">
+<dt id="atomate.common.firetasks.glue_tasks.GzipDir.run_task">
+<code class="sig-name descname">run_task</code><span class="sig-paren">(</span><em class="sig-param">fw_spec=None</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.GzipDir.run_task" title="Permalink to this definition">¶</a></dt>
+<dd><p>This method gets called when the Firetask is run. It can take in a
+Firework spec, perform some task using that data, and then return an
+output in the form of a FWAction.</p>
+<dl class="simple">
+<dt>Args:</dt><dd><dl class="simple">
+<dt>fw_spec (dict): A Firework spec. This comes from the master spec.</dt><dd><p>In addition, this spec contains a special “_fw_env” key that
+contains the env settings of the FWorker calling this method.
+This provides for abstracting out certain commands or
+settings. For example, “foo” may be named “foo1” in resource
+1 and “foo2” in resource 2. The FWorker env can specify {
+“foo”: “foo1”}, which maps an abstract variable “foo” to the
+relevant “foo1” or “foo2”. You can then write a task that
+uses fw_spec[“_fw_env”][“foo”] that will work across all
+these multiple resources.</p>
+</dd>
+</dl>
+</dd>
+<dt>Returns:</dt><dd><p>(FWAction)</p>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
 <dl class="class">
 <dt id="atomate.common.firetasks.glue_tasks.PassCalcLocs">
 <em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.glue_tasks.</code><code class="sig-name descname">PassCalcLocs</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.glue_tasks.PassCalcLocs" title="Permalink to this definition">¶</a></dt>
@@ -658,7 +720,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

docs/atomate.common.firetasks.tests.html

@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.common.firetasks.tests package &#8212; atomate 0.9.4 documentation</title>
+    <title>atomate.common.firetasks.tests package &#8212; atomate 0.9.5 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -207,7 +207,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

docs/atomate.common.html

@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.common package &#8212; atomate 0.9.4 documentation</title>
+    <title>atomate.common package &#8212; atomate 0.9.5 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -113,7 +113,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

docs/atomate.feff.firetasks.html

@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.feff.firetasks package &#8212; atomate 0.9.4 documentation</title>
+    <title>atomate.feff.firetasks package &#8212; atomate 0.9.5 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -444,7 +444,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>