Add Bader analysis.

Former-commit-id: 30dd1d1c5aa5dd1a7070da41bc2adb9bdb927251 [formerly 0f0f4f3]
Former-commit-id: b7e11f702b83a9b020dff8fec20d35d590ebaaa5

circle.yml

@@ -11,4 +11,4 @@ test:
     - mv pymatgen pmg
     - nosetests:
         environment:
-            PATH: $PATH:`pwd`/cmd_line/enum/Linux_64bit
+            PATH: $PATH:`pwd`/cmd_line/enum/Linux_64bit:`pwd`/cmd_line/bader/Linux_64bit

pymatgen/command_line/bader_caller.py

@@ -0,0 +1,110 @@
+#!/usr/bin/env python
+
+"""
+This module implements an interface to the Henkelmann et al.'s excellent
+Fortran code for calculating a Bader charge analysis.
+
+This module depends on a compiled bader executable available in the path.
+Please download the library at http://theory.cm.utexas.edu/vasp/bader/ and
+follow the instructions to compile the executable.
+
+If you use this module, please cite the following:
+
+G. Henkelman, A. Arnaldsson, and H. Jonsson, "A fast and robust algorithm for
+Bader decomposition of charge density", Comput. Mater. Sci. 36, 254-360 (2006).
+"""
+
+from __future__ import division
+
+__author__ = "shyuepingong"
+__version__ = "0.1"
+__maintainer__ = "Shyue Ping Ong"
+__email__ = "[email protected]"
+__status__ = "Beta"
+__date__ = "4/5/13"
+
+import os
+import subprocess
+import tempfile
+import shutil
+
+
+class BaderAnalysis(object):
+    """
+    Bader analysis for a CHGCAR.
+
+    .. attribute: data
+
+        Atomic data parsed from bader analysis. Essentially a list of dicts
+        of the form::
+
+        [
+            {
+                "dist": 8.769,
+                "min": 0.8753,
+                "charge": 7.4168,
+                "y": 1.1598,
+                "x": 0.0079,
+                "z": 0.8348
+            },
+            ...
+        ]
+
+    .. attribute: vacuum_volume
+
+        Vacuum volume of the Bader analysis.
+
+    .. attribute: vacuum_charge
+
+        Vacuum charge of the Bader analysis.
+
+    .. attribute: nelectrons
+
+        Number of electrons of the Bader analysis.
+    """
+
+    def __init__(self, filename):
+        """
+        Args:
+            filename:
+                The filename of the CHGCAR.
+        """
+        temp_dir = tempfile.mkdtemp()
+        try:
+            shutil.copy(filename, os.path.join(temp_dir, "CHGCAR"))
+            current_dir = os.getcwd()
+            os.chdir(temp_dir)
+            rs = subprocess.Popen(["bader", "-p", "atom_index", "-p", "all_atom",
+                                   "CHGCAR"],
+                                  stdout=subprocess.PIPE,
+                                  stdin=subprocess.PIPE, close_fds=True)
+            rs.communicate()
+            data = []
+            with open("ACF.dat") as f:
+                raw = f.readlines()
+                headers = [s.lower() for s in raw.pop(0).split()]
+                raw.pop(0)
+                while True:
+                    l = raw.pop(0).strip()
+                    if l.startswith("-"):
+                        break
+                    vals = map(float, l.split()[1:])
+                    data.append(dict(zip(headers[1:], vals)))
+                for l in raw:
+                    toks = l.strip().split(":")
+                    if toks[0] == "VACUUM CHARGE":
+                        self.vacuum_charge = float(toks[1])
+                    elif toks[0] == "VACUUM VOLUME":
+                        self.vacuum_volume = float(toks[1])
+                    elif toks[0] == "NUMBER OF ELECTRONS":
+                        self.nelectrons = float(toks[1])
+            self.data = data
+            os.chdir(current_dir)
+        except Exception as ex:
+            print str(ex)
+        finally:
+            shutil.rmtree(temp_dir)
+
+
+if __name__ == "__main__":
+    a = BaderAnalysis("../../test_files/CHGCAR.noncubic")

pymatgen/command_line/tests/test_bader_caller.py

@@ -0,0 +1,43 @@
+#!/usr/bin/env python
+
+"""
+TODO: Change the module doc.
+"""
+
+from __future__ import division
+
+__author__ = "Shyue Ping Ong"
+__copyright__ = "Copyright 2012, The Materials Project"
+__version__ = "0.1"
+__maintainer__ = "Shyue Ping Ong"
+__email__ = "[email protected]"
+__date__ = "Jul 22, 2012"
+
+import unittest
+import os
+
+from nose.exc import SkipTest
+
+from pymatgen.command_line.bader_caller import BaderAnalysis
+from pymatgen.util.io_utils import which
+
+
+bader_present = which('bader')
+
+
+class BaderAnalysisTest(unittest.TestCase):
+
+    def test_init(self):
+        if not bader_present:
+            raise SkipTest("bader executable not present. Skipping...")
+        test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
+                                'test_files')
+        analysis = BaderAnalysis(os.path.join(test_dir, "CHGCAR.noncubic"))
+        self.assertEqual(len(analysis.data), 8)
+        self.assertAlmostEqual(analysis.data[0]["charge"], 7.4168)
+        self.assertAlmostEqual(analysis.nelectrons, 52)
+        self.assertAlmostEqual(analysis.vacuum_charge, 0)
+
+
+if __name__ == '__main__':
+    unittest.main()