Further additions

.gitignore

@@ -0,0 +1,139 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+~.py
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

scripts/vasprun

@@ -43,6 +43,11 @@ if __name__ == "__main__":
                       help="figure' dpi, default: 300", metavar="dpi")
     parser.add_option("-S", "--save-bands", dest="saveBands", action='store_true',
                       help="saving of bands contributing to the plot, default: false", metavar="saveBands")
+    parser.add_option("-E", "--efermi", dest="fermiEnergy", default=None,
+                      help="fermi energy setting, default: read from vasprun.xml", metavar="fermiEnergy")
+    parser.add_option('--labels', default=None,
+                      help='Labels for each of high symmetry points. (e.g., \'$\Gamma$ X M\'; default None)')
+
 
     (options, args) = parser.parse_args()
     if options.vasprun is None:
@@ -102,14 +107,24 @@ if __name__ == "__main__":
     elif options.dosplot:
         lim = options.lim.split(',')
         lim = [float(i) for i in lim]
-        test.plot_dos(styles=options.dosplot, filename=options.figname, xlim=lim, smear=options.smear)
+        Ef  = None
+        if options.fermiEnergy is not None:
+            Ef = float(options.fermiEnergy)
+        test.plot_dos(styles=options.dosplot, filename=options.figname, xlim=lim, smear=options.smear, fermiEnergy=Ef)
     elif options.bandplot:
         lim = options.lim.split(',')
         lim = [float(i) for i in lim]
         pmaxmin = options.max.split(',')
         pmaxmin = [float(i) for i in pmaxmin]
         test.parse_bandpath()
-        test.plot_band(styles=options.bandplot, filename=options.figname, ylim=lim, plim=pmaxmin, saveBands=options.saveBands, dpi=options.dpi)
+        Ef = None
+        if options.labels:
+            kTags = options.labels.split()
+        else:
+            kTags = None
+        if options.fermiEnergy is not None:
+            Ef = float(options.fermiEnergy)
+        test.plot_band(styles=options.bandplot, filename=options.figname, ylim=lim, plim=pmaxmin, fermiEnergy=Ef, saveBands=options.saveBands, dpi=options.dpi, kTags=kTags)
     elif options.band:
         vb = test.values['bands']-1
         cb = vb + 1

vasprun/__init__.py

@@ -8,6 +8,7 @@
 import pandas as pd
 from tabulate import tabulate
 import warnings
+from scipy import constants
 
 import matplotlib as mpl
 mpl.use("Agg")
@@ -32,15 +33,15 @@ def smear_data(data, sigma):
     return data
 
 class units:
-    am2kg = 1.6605402e-27
-    ev2j = 1.60217733e-19
-    plank = 6.626075e-34
-    c = 2.99792458e+10
-    pi = 3.1415926
-    proton_mass = 1836
-    ev2hartree = 27.211386245988
-    a2bohr = 0.529
-    ev2cm = 8065.6
+    pi           =      constants.pi                                                                 #3.1415926
+    am2kg        =      constants.physical_constants['atomic mass constant'][0]                      #1.6605402e-27
+    ev2j         =      constants.physical_constants['electron volt-joule relationship'][0]          #1.60217733e-19
+    plank        =      constants.physical_constants['Planck constant'][0]                           #6.626075e-34
+    c            =  1e2*constants.physical_constants['speed of light in vacuum'][0]                  #2.99792458e+10 in cm/s?
+    proton_mass  =      constants.physical_constants['proton-electron mass ratio'][0]                #1836
+    ev2hartree   =      constants.physical_constants['Hartree energy in eV'][0]                      #27.211386245988
+    a2bohr       = 1e10*constants.physical_constants['Bohr radius'][0]                               #0.529
+    ev2cm        = 1e-2*constants.physical_constants['electron volt-inverse meter relationship'][0]  #8065.6
 
 class vasprun:
     """
@@ -686,7 +687,7 @@ def inline(kpt, path):
         self.values['band_paths'] = band_paths
         self.values['band_points'] = band_points
 
-    def plot_band(self, filename=None, styles='normal', ylim=[-20, 3], plim=[0.0,0.5], saveBands=False, dpi=300):
+    def plot_band(self, filename=None, styles='normal', ylim=[-20, 3], plim=[0.0,0.5], fermiEnergy=None, saveBands=False, dpi=300, kTags=None):
         """
         plot the bandstructure
 
@@ -695,17 +696,22 @@ def plot_band(self, filename=None, styles='normal', ylim=[-20, 3], plim=[0.0,0.5
             styles: string (`normal` or `projected`)
             ylim: list, the range of energy values on the y-axis, e.g. [-5, 3]
             p_max: float (the ratio of color plot in the `projected` mode)
+            fermiEnergy: Band Structure calculations do not contain the proper Fermi energy
+                         - it needs to be set by hand for precise calculations
 
         Returns:
             A figure with band structure
         """
         self.parse_bandpath()
-        efermi = self.values["calculation"]["efermi"]
-        eigens = np.array(self.values['calculation']['eband_eigenvalues'])
-        paths = self.values['band_paths']
-        band_pts = self.values['band_points']
-        proj = np.array(self.values["calculation"]["projected"]) #[N_kpts, N_band, Ions, 9]
-        cm = plt.cm.get_cmap('RdYlBu')
+        if fermiEnergy is None:
+            efermi = self.values["calculation"]["efermi"]
+        else:
+            efermi = fermiEnergy
+        eigens            = np.array(self.values['calculation']['eband_eigenvalues'])
+        paths             = self.values['band_paths']
+        band_pts          = self.values['band_points']
+        proj              = np.array(self.values["calculation"]["projected"]) #[N_kpts, N_band, Ions, 9]
+        cm                = plt.cm.get_cmap('RdYlBu')
         nkpt, nband, nocc = np.shape(eigens)
         for i in range(nband):
             band = eigens[:, i, 0] - efermi
@@ -755,8 +761,12 @@ def get_dos(self, rows, style='t'):
         N_atom = len(a_array)
         tdos = np.array(self.values['calculation']['tdos'])
         pdos = np.array(self.values['calculation']['pdos'])
-        a, b, c, d = np.shape(pdos)
-        pdos = np.reshape(pdos, [b, a, c, d])
+        try:
+            a, b, c, d = np.shape(pdos)
+            pdos = np.reshape(pdos, [b, a, c, d])
+        except ValueError as error:
+            if style != 't':
+                raise error
         if style == 't':
             for spin in tdos:
                 mydos.append(spin[rows, 1])
@@ -801,7 +811,7 @@ def get_dos(self, rows, style='t'):
             mydos[1] *= -1
         return mydos, labels
 
-    def plot_dos(self, filename=None, smear=None, styles='t', xlim=[-3, 3], dpi=300):
+    def plot_dos(self, filename=None, smear=None, fermiEnergy=None, styles='t', xlim=[-3, 3], dpi=300):
         """
         plot the DOS
 
@@ -810,11 +820,16 @@ def plot_dos(self, filename=None, smear=None, styles='t', xlim=[-3, 3], dpi=300)
             styles: string (`t` or `s` or `t+spd`)
             xlim: list, the range of energy values on the x-axis, e.g. [-5, 3]
             smear: float (the width of smearing, defult: None) 
+            fermiEnergy: Band Structure calculations do not contain the proper Fermi energy
+                         - it needs to be set by hand for precise calculations
 
         Returns:
             A figure with band structure
         """
-        efermi = self.values['calculation']['efermi']
+        if fermiEnergy is None:
+            efermi = self.values["calculation"]["efermi"]
+        else:
+            efermi = fermiEnergy
         tdos = np.array(self.values['calculation']['tdos'][0])
         tdos[:, 0] -= efermi
         e = tdos[:, 0]