Merge remote-tracking branch 'origin/master'

Former-commit-id: e29697270585fb64ccab0363309be78fd2284f77 [formerly a1c0313]
Former-commit-id: e70be79bb9d9900a54bd00bc5444f99f4cb938b0

docs/changelog.rst

@@ -1,6 +1,29 @@
 Change log
 ==========
 
+v2.9.14
+-------
+1. Implements Structure.sort method. Both Structure.sort and the
+   get_sorted_structure methods now supports all arguments supported by list
+   .sort().
+2. VaspInputSets configs, as well as several other configs now uses yaml. Note
+   the new dependency on pyyaml. It is highly recommended that you install
+   pyyaml with the libyaml C bindings.
+3. Fix missing spglib dependency.
+4. Use monty.serialization for transparent handling of JSON vs YAML.
+   Requirements updated to monty>=0.3.1.
+
+v2.9.13
+-------
+1. Urgent bug fix for missing compatibility yamls.
+
+v2.9.12
+-------
+1. Defect transformations (Bharat).
+2. Support for optical properties (Geoffroy Hautier and David Waroquiers).
+3. Improved support for some VASP output files (XDATCAR and OSZICAR).
+4. Refactored compatibilities now uses YAML for ease of reading.
+
 v2.9.11
 -------
 1. Bug fix for get_xrd_plot.

docs/index.rst

@@ -72,35 +72,24 @@ several advantages over other codes out there:
 Latest Change Log
 =================
 
-v2.9.15
+v2.10.1
 -------
-1. Major update: MPRester now uses Materials API v2! Also major refactoring
-   of MPRester.
-2. Bug fix for XYZ parsing for scientific notation.
-3. Update numpy requirements to 1.8+. Fixes memory leak.
+1. Minor fix for monty requirements in setup.py.
 
-v2.9.14
+v2.10.0
 -------
-1. Implements Structure.sort method. Both Structure.sort and the
-   get_sorted_structure methods now supports all arguments supported by list
-   .sort().
-2. VaspInputSets configs, as well as several other configs now uses yaml. Note
-   the new dependency on pyyaml. It is highly recommended that you install
-   pyyaml with the libyaml C bindings.
-3. Fix missing spglib dependency.
-4. Use monty.serialization for transparent handling of JSON vs YAML.
-   Requirements updated to monty>=0.3.1.
-
-v2.9.13
--------
-1. Urgent bug fix for missing compatibility yamls.
-
-v2.9.12
--------
-1. Defect transformations (Bharat).
-2. Support for optical properties (Geoffroy Hautier and David Waroquiers).
-3. Improved support for some VASP output files (XDATCAR and OSZICAR).
-4. Refactored compatibilities now uses YAML for ease of reading.
+1. Major update: MPRester now uses Materials API v2! Also major refactoring
+   of MPRester.
+2. Vastly improved Vasprun parser using cElementTree. Twice as fast,
+   half as much code and easier to maintain.
+3. Vast improvements to Qchem functionality (Xiaohui Qu).
+4. Improved handling of Structure manipulations for extremely large
+   structures (particularly in terms of memory consumption).
+5. Bug fix for XYZ parsing for scientific notation.
+6. Improve monty.serialization for transparent handling of JSON vs YAML.
+   Requirements updated to monty>=0.3.3.
+7. Update numpy requirements to 1.8+. Fixes memory leak.
+8. Other minor bug fixes.
 
 :doc:`Older versions </changelog>`
 

examples/Explanation of Corrections.ipynb

@@ -0,0 +1,115 @@
+{
+ "metadata": {
+  "name": "",
+  "signature": "sha256:1b0762dea41bd3b1b6224430bfd0661f6a71ee0df8e3f375cec94e2e5dacbca3"
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": [
+  {
+   "cells": [
+    {
+     "cell_type": "markdown",
+     "metadata": {},
+     "source": [
+      "This notebook illustrates how to obtain an explaination of the different corrections being applied in the Materials Project."
+     ]
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "import re\n",
+      "from pymatgen.entries.computed_entries import ComputedEntry\n",
+      "from pymatgen.entries.compatibility import MaterialsProjectCompatibility"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 1
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "from pymatgen import MPRester\n",
+      "\n",
+      "#To do our testing, let's use the MPRester to get a sample computed entry from the Materials Project.\n",
+      "m = MPRester()\n",
+      "entries = m.get_entries(\"LiFePO4\")\n",
+      "entry = entries[0]"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 2
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "compat = MaterialsProjectCompatibility()"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [],
+     "prompt_number": 3
+    },
+    {
+     "cell_type": "code",
+     "collapsed": false,
+     "input": [
+      "compat.explain(entry)"
+     ],
+     "language": "python",
+     "metadata": {},
+     "outputs": [
+      {
+       "output_type": "stream",
+       "stream": "stdout",
+       "text": [
+        "The uncorrected value of the energy of P4 Fe4 O16 Li4 is -191.338121 eV\n",
+        "The following corrections / screening are applied for MaterialsProjectCompatibility:\n",
+        "\n",
+        "MP Potcar Correction correction: Checks that POTCARs are valid within a pre-defined input set. This\n",
+        "    ensures that calculations performed using different InputSets are not\n",
+        "    compared against each other.\n",
+        "\n",
+        "    Entry.parameters must contain a \"potcar_symbols\" key that is a list of\n",
+        "    all POTCARs used in the run. Again, using the example of an Fe2O3 run\n",
+        "    using Materials Project parameters, this would look like\n",
+        "    entry.parameters[\"potcar_symbols\"] = ['PAW_PBE Fe_pv 06Sep2000',\n",
+        "    'PAW_PBE O 08Apr2002'].\n",
+        "\n",
+        "This correction does not make any changes to the energy.\n",
+        "------------------------------\n",
+        "MP Gas Correction correction: Correct gas energies to obtain the right formation energies. Note that\n",
+        "    this depends on calculations being run within the same input set.\n",
+        "\n",
+        "For the entry, this correction has the value -11.236640 eV.\n",
+        "------------------------------\n",
+        "MP Advanced Correction correction: This class implements the GGA/GGA+U mixing scheme, which allows mixing of\n",
+        "    entries. Entry.parameters must contain a \"hubbards\" key which is a dict\n",
+        "    of all non-zero Hubbard U values used in the calculation. For example,\n",
+        "    if you ran a Fe2O3 calculation with Materials Project parameters,\n",
+        "    this would look like entry.parameters[\"hubbards\"] = {\"Fe\": 5.3}\n",
+        "    If the \"hubbards\" key is missing, a GGA run is assumed.\n",
+        "\n",
+        "    It should be noted that ComputedEntries assimilated using the\n",
+        "    pymatgen.apps.borg package and obtained via the MaterialsProject REST\n",
+        "    interface using the pymatgen.matproj.rest package will automatically have\n",
+        "    these fields populated.\n",
+        "\n",
+        "For the entry, this correction has the value -10.932000 eV.\n",
+        "------------------------------\n",
+        "The final energy after corrections is -213.506761\n"
+       ]
+      }
+     ],
+     "prompt_number": 4
+    }
+   ],
+   "metadata": {}
+  }
+ ]
+}

pymatgen/__init__.py

@@ -3,8 +3,8 @@
                         "Sai Jayaraman", "Michael Kocher", "Dan Gunter",
                         "Shreyas Cholia", "Vincent L Chevrier",
                         "Rickard Armiento"])
-__date__ = "Aug 5 2014"
-__version__ = "2.9.14"
+__date__ = "Aug 15 2014"
+__version__ = "2.10.1"
 
 #Useful aliases for commonly used objects and modules.
 

pymatgen/entries/compatibility.py

@@ -366,6 +366,33 @@ def process_entries(self, entries):
         """
         return filter(None, map(self.process_entry, entries))
 
+    def explain(self, entry):
+        """
+        Prints an explanation of the corrections that are being applied for a
+        given compatibility scheme. Inspired by the "explain" methods in many
+        database methodologies.
+
+        Args:
+            entry: A ComputedEntry.
+        """
+        entry = self.process_entry(entry)
+        print "The uncorrected value of the energy of %s is %f eV" % (
+            entry.composition, entry.uncorrected_energy)
+        print "The following corrections / screening are applied for %s:\n" %\
+            self.__class__.__name__
+        corr_dict = self.get_corrections_dict(entry)
+        for c in self.corrections:
+            desc = c.__doc__.split("Args")[0].strip()
+            print "%s correction: %s\n" % (str(c), desc.strip())
+            if str(c) in corr_dict:
+                print "For the entry, this correction has the value %f eV." % \
+                      corr_dict[str(c)]
+            else:
+                print "This correction does not make any changes to the energy."
+            print "-" * 30
+
+        print "The final energy after corrections is %f" % entry.energy
+
 
 @cached_class
 class MaterialsProjectCompatibility(Compatibility):

pymatgen/io/vaspio/tests/test_vasp_output.py

@@ -30,6 +30,13 @@ class VasprunTest(unittest.TestCase):
     def test_properties(self):
         filepath = os.path.join(test_dir, 'vasprun.xml')
         vasprun = Vasprun(filepath)
+
+        #test pdos parsing
+        pdos0 = vasprun.complete_dos.pdos[vasprun.final_structure[0]]
+        self.assertAlmostEqual(pdos0[Orbital.s][1][16], 0.0026)
+        self.assertAlmostEqual(pdos0[Orbital.pz][-1][16], 0.0012)
+        self.assertEqual(pdos0[Orbital.s][1].shape, (301, ))
+
         filepath2 = os.path.join(test_dir, 'lifepo4.xml')
         vasprun_ggau = Vasprun(filepath2, parse_projected_eigen=True)
         totalscsteps = sum([len(i['electronic_steps'])

pymatgen/io/vaspio/vasp_output.py

@@ -820,7 +820,7 @@ def _parse_dos(self, elem):
                 data = np.array(_parse_varray(ss))
                 nrow, ncol = data.shape
                 for j in xrange(1, ncol):
-                    pdos[Orbital.from_vasp_index(j - 1)][spin] = data
+                    pdos[Orbital.from_vasp_index(j - 1)][spin] = data[:, j]
             pdoss.append(pdos)
         elem.clear()
         return Dos(efermi, energies, tdensities), \

pymatgen/vis/structure_vtk.py

@@ -832,17 +832,17 @@ def keyPressEvent(self, obj, event):
 
 
 def make_movie(structures, output_filename="movie.mp4", zoom=1.0, fps=20,
-               bitrate=10000, quality=5):
+               bitrate="10000k", quality=1):
     """
     Generate a movie from a sequence of structures using vtk and ffmpeg.
 
     Args:
         structures: sequence of structures
         output_filename: filename for structure output. defaults to movie.mp4
-        zoom: A zoom to be applied to the visulizer. Defaults to 1.0
+        zoom: A zoom to be applied to the visualizer. Defaults to 1.0.
         fps: Frames per second for the movie. Defaults to 20.
-        bitrate: Video bitate.  Defaults to 10000 (fairly high quality).
-        quality: A quality scale. Defaults to 5.
+        bitrate: Video bitate.  Defaults to 10000k (fairly high quality).
+        quality: A quality scale. Defaults to 1.
     """
     vis = StructureVis()
     vis.show_help = False
@@ -854,6 +854,7 @@ def make_movie(structures, output_filename="movie.mp4", zoom=1.0, fps=20,
         vis.set_structure(s)
         vis.write_image(filename.format(i), 3)
     filename = "image%0" + str(sigfig) + "d.png"
-    args = ["ffmpeg", "-y", "-qscale", str(quality), "-r", str(fps), "-b",
-            str(bitrate), "-i", filename, output_filename]
+    args = ["ffmpeg", "-y", "-i", filename,
+            "-qscale", str(quality), "-r", str(fps), "-b", str(bitrate),
+            output_filename]
     subprocess.Popen(args)

setup.py

@@ -42,10 +42,10 @@ def get_spglib_ext():
 setup(
     name="pymatgen",
     packages=find_packages(),
-    version="2.9.14",
+    version="2.10.1",
     install_requires=["numpy>=1.8", "pyhull>=1.4.3", "PyCifRW>=3.3",
                       "requests>=1.0", "pybtex>=0.16", "pyyaml>=3.0",
-                      "monty>=0.3.1"],
+                      "monty>=0.3.3"],
     extras_require={"electronic_structure": ["scipy>=0.10"],
                     "plotting": ["matplotlib>=1.1"],
                     "ase_adaptor": ["ase>=3.3"],