Merge branch 'master' into synthesis

.circleci/config.yml

@@ -4,6 +4,8 @@ jobs:
     working_directory: ~/pymatgen
     docker:
       - image: materialsvirtuallab/circle-ci-pmg-py3:0.0.2
+        environment:
+          PMG_MAPI_ENDPOINT: https://zola.lbl.gov/rest/v2
     parallelism: 4
     steps:
       - checkout
@@ -37,6 +39,10 @@ jobs:
             export PATH=$HOME/miniconda3/bin:$PATH
             export GULP_LIB=`pwd`/cmd_line/gulp/Libraries
             export MPLBACKEND=Agg
+            # Only do matproj and other ext API tests once every five random runs or so.
+            # The parallelism is 4. If 1/20 we have to run, that measn the probability of a matproj test running is 1-(1-0.05)**4 = 0.18.
+            if [ "$(( RANDOM % 20 ))" -ne "0" ]; then export NOSE_EXCLUDE_TESTS="pymatgen.ext.tests.test_matproj.MPResterTest;pymatgen.analysis.tests.test_pourbaix_diagram.PourbaixDiagramTest;pymatgen.tests.test_init.SettingsTestCase"; fi
+            echo "NOSE_EXCLUDE_TESTS=$NOSE_EXCLUDE_TESTS"
             source activate test_env
             pip install --quiet -e .
             nosetests --config=nose.cfg --processes=4 --process-timeout=600 --cover-html --cover-html-dir=coverage_reports --with-timer --timer-top-n 30

.travis.yml

@@ -9,6 +9,8 @@ env:
     - PATH=$PATH:`pwd`/cmd_line/bader/Linux_64bit:`pwd`/cmd_line/aconvasp/Linux_64bit:`pwd`/cmd_line/boltztrap/Linux_64bit
     - GULP_LIB=`pwd`/cmd_line/gulp/Libraries
     - MPLBACKEND=Agg
+    - PMG_MAPI_ENDPOINT=https://zola.lbl.gov/rest/v2
+    - NOSE_EXCLUDE_TESTS="pymatgen.ext.tests.test_matproj.MPResterTest;pymatgen.analysis.tests.test_pourbaix_diagram.PourbaixDiagramTest;pymatgen.tests.test_init.SettingsTestCase"
 # command to install dependencies
 sudo: false
 install:
@@ -25,7 +27,8 @@ install:
 before_script:
   - python setup.py --quiet develop
 # command to run tests, e.g. python setup.py test
-script: travis_wait 28800 nosetests --with-timer --timer-top-n 30 pymatgen
+script:
+  - travis_wait 28800 nosetests --with-timer --timer-top-n 30 pymatgen
 notifications:
   email:
     recipients:

CHANGES.rst

@@ -1,6 +1,23 @@
 Change log
 ==========
 
+v2018.12.12
+-----------
+* Support for IUPAC ordering of elements in Composition formulae (@utf)
+* Various bug fixes including returning integer miller indices, catching negative values in Composition and fixes to graph analysis (@utf), fix to Composition serialization (@jmmshen), defect analysis (@HanmeiTang), removing sites in surfaces (@yiming-xu), and fix to support the new PROCAR format in VASP (@dkorotin)
+* `PMG_MAPI_ENDPOINT` environment variable added to support different endpoints for the Materials Project REST interface (@mkhorton)
+
+v2018.11.30
+-----------
+* MPRester.query now supports bulk queries for large scale requests. 
+  (@dwinston)
+* MVLRelax52Set which uses VASP 52 pseudopotentials. (@HanmeiTang)
+* EPH calculations in ABINIT (@gmatteo)
+* New ScaleToRelaxedTransformation (@richardtran415)
+* New dimensionality finder, and consolidation of existing algorithms (@utf)
+* New dopant predictor built on structure predictor (@utf)
+* Misc bug fixes (@HanmeiTang, @utf, @tamuhey, @mkhorton, @yiming-xu, @richardtran415)
+
 v2018.11.6
 ----------
 * Ionic radius based CrystalNN (@computron)

appveyor.yml

@@ -13,11 +13,14 @@ environment:
       SPLIT_RUN: "FALSE"
   PMG_MAPI_KEY:
     secure: XIbk1W27nucVUHTVpIL2B+FodL9w2Efyw5PqTdnfbHg=
+  PMG_MAPI_ENDPOINT: https://zola.lbl.gov/rest/v2
   PYPIPWD:
     secure: QPpXonUAeLJ8p3f936jh7g==
 install:
   # Add the paths
   - 'set PATH=%PYTHON%;%PYTHON%\Library\bin;%PYTHON%\Scripts;%PATH%'
+  - 'set MPLBACKEND=Agg'
+  - 'set NOSE_EXCLUDE_TESTS="pymatgen.ext.tests.test_matproj.MPResterTest;pymatgen.analysis.tests.test_pourbaix_diagram.PourbaixDiagramTest;pymatgen.tests.test_init.SettingsTestCase"'
   # Check that we have the expected version and architecture for Python
   # - 'python --version'
   # - 'python -c "import struct; print(struct.calcsize(''P'') * 8)"'

dev_scripts/update_pt_data.py

@@ -7,9 +7,16 @@
 
 from __future__ import division
 import json
+from itertools import product
+
 import ruamel.yaml as yaml
 import re
 
+from monty.serialization import loadfn
+
+from pymatgen import Element
+from pymatgen.core.periodic_table import get_el_sp
+
 __author__ = "Shyue Ping Ong"
 __copyright__ = "Copyright 2011, The Materials Project"
 __version__ = "0.1"
@@ -216,6 +223,48 @@ def gen_periodic_table():
         json.dump(data, f)
 
 
+def gen_iupac_ordering():
+    periodic_table = loadfn("periodic_table.json")
+    order = [([18], range(6, 0, -1)),  # noble gasses
+             ([1], range(7, 1, -1)),  # alkali metals
+             ([2], range(7, 1, -1)),  # alkali earth metals
+             (range(17, 2, -1), [9]),  # actinides
+             (range(17, 2, -1), [8]),  # lanthanides
+             ([3], (5, 4)),  # Y, Sc
+             ([4], (6, 5, 4)),  # Hf -> Ti
+             ([5], (6, 5, 4)),  # Ta -> V
+             ([6], (6, 5, 4)),  # W -> Cr
+             ([7], (6, 5, 4)),  # Re -> Mn
+             ([8], (6, 5, 4)),  # Os -> Fe
+             ([9], (6, 5, 4)),  # Ir -> Co
+             ([10], (6, 5, 4)),  # Pt -> Ni
+             ([11], (6, 5, 4)),  # Au -> Cu
+             ([12], (6, 5, 4)),  # Hg -> Zn
+             ([13], range(6, 1, -1)),  # Tl -> B
+             ([14], range(6, 1, -1)),  # Pb -> C
+             ([15], range(6, 1, -1)),  # Bi -> N
+             ([1], [1]),  # Hydrogen
+             ([16], range(6, 1, -1)),  # Po -> O
+             ([17], range(6, 1, -1))]  # At -> F
+
+    order = sum([list(product(x, y)) for x, y in order], [])
+    iupac_ordering_dict = dict(zip(
+        [Element.from_row_and_group(row, group) for group, row in order],
+        range(len(order))))
+
+    # first clean periodic table of any IUPAC ordering
+    for el in periodic_table:
+        periodic_table[el].pop('IUPAC ordering', None)
+
+    # now add iupac ordering
+    for el in periodic_table:
+        if 'IUPAC ordering' in periodic_table[el]:
+            # sanity check that we don't cover the same element twice
+            raise KeyError("IUPAC ordering already exists for {}".format(el))
+
+        periodic_table[el]['IUPAC ordering'] = iupac_ordering_dict[get_el_sp(el)]
+
+
 if __name__ == "__main__":
     parse_shannon_radii()
     #gen_periodic_table()

docs/_modules/collections.html

@@ -4,27 +4,16 @@
 
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
-    <title>collections &#8212; pymatgen 2018.11.6 documentation</title>
-
+    <title>collections &#8212; pymatgen 2018.12.12 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:     '2018.11.6',
-        COLLAPSE_INDEX: false,
-        FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true,
-        SOURCELINK_SUFFIX: '.txt'
-      };
-    </script>
+    <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
     <script type="text/javascript" src="../_static/jquery.js"></script>
     <script type="text/javascript" src="../_static/underscore.js"></script>
     <script type="text/javascript" src="../_static/doctools.js"></script>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -35,8 +24,7 @@
   _gaq.push(['_trackPageview']);
 </script>
 
-  </head>
-  <body>
+  </head><body>
     <div class="related" role="navigation" aria-label="related navigation">
       <h3>Navigation</h3>
       <ul>
@@ -46,7 +34,7 @@ <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">pymatgen 2018.11.6 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">pymatgen 2018.12.12 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="index.html" accesskey="U">Module code</a> &#187;</li> 
       </ul>
     </div>  
@@ -808,12 +796,14 @@ <h1>Source code for collections</h1><div class="highlight"><pre>
         <div class="sphinxsidebarwrapper">
 <div id="searchbox" style="display: none" role="search">
   <h3>Quick search</h3>
+    <div class="searchformwrapper">
     <form class="search" action="../search.html" method="get">
-      <div><input type="text" name="q" /></div>
-      <div><input type="submit" value="Go" /></div>
+      <input type="text" name="q" />
+      <input type="submit" value="Go" />
       <input type="hidden" name="check_keywords" value="yes" />
       <input type="hidden" name="area" value="default" />
     </form>
+    </div>
 </div>
 <script type="text/javascript">$('#searchbox').show(0);</script>
         </div>
@@ -829,14 +819,14 @@ <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">pymatgen 2018.11.6 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">pymatgen 2018.12.12 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="index.html" >Module code</a> &#187;</li> 
       </ul>
     </div>
 
     <div class="footer" role="contentinfo">
         &#169; Copyright 2011, Pymatgen Development Team.
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.6.2.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.1.
     </div>
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