Update manual

data/band_structure.py

@@ -1,15 +1,24 @@
+from aiida import load_dbenv, is_dbenv_loaded
+if not is_dbenv_loaded():
+    load_dbenv()
+
 from aiida.orm import Data
 
 
 class BandStructureData(Data):
     """
-    Store the band structure.
+    Store the band structure data
+
     """
 
     def __init__(self, *args, **kwargs):
         super(BandStructureData, self).__init__(*args, **kwargs)
 
     def get_number_of_bands(self):
+        """
+
+        :return: Number of bands
+        """
 
         if 'nbands' in self.get_attrs():
             return self.get_attr('nbands')
@@ -25,6 +34,12 @@ def get_number_of_points(self):
 
 
     def set_bands(self, ranges):
+        """
+        Set the list of q-points the form the path in the reciprocal space
+
+        :param ranges: a 3D array that contains a list q-points in phonopy format: array[n_paths:n_qpoints:3]
+        :return:
+        """
 
         import tempfile
         import numpy
@@ -41,6 +56,12 @@ def set_bands(self, ranges):
         self._set_attr('npoints', len(ranges[0]))
 
     def set_labels(self, band_labels):
+        """
+        Set the labels of the high symmetry points in the reciprocal space that delimite the paths.
+
+        :param band_labels: Array (or list of lists) in seekpath format: array[n_paths:2]
+        :return:
+        """
 
         import tempfile
         import numpy
@@ -55,7 +76,7 @@ def set_labels(self, band_labels):
 
     def set_unitcell(self, unitcell):
         """
-        :param unitcell: Numpy Array that contains the unitcell matrix (Lattice vectors in columns)
+        :param unitcell: Numpy Array that contains the unitcell matrix (Lattice vectors in rows)
         :return:
         """
 
@@ -71,6 +92,14 @@ def set_unitcell(self, unitcell):
             self.add_path(f.name, 'unitcell.npy')
 
     def set_band_structure_phonopy(self, band_structure_phonopy):
+        """
+        Set the phonon band structure data obtained as output from phonopy. This includes the list of q-points,
+        q-points distances, and phonon frequencies. If q-points and distances are already set, this functions
+        checks consistency and stores only the phonon frequencies.
+
+        :param band_structure_phonopy: phonopy get_band_structure() function output.
+        :return:
+        """
 
         import tempfile
         import numpy
@@ -99,7 +128,15 @@ def set_band_structure_phonopy(self, band_structure_phonopy):
                 self.add_path(f.name, element[0])
 
     def set_band_structure_gruneisen(self, band_structure_gruneisen):
+        """
+        Set the mode Gruneisen band structure data obtained as output from phonopy. This includes the list of q-points,
+        q-points distances, and phonon frequencies and mode gruneisen parameter.
+        If q-points and distances are already set, this functions checks consistency and stores only
+        the phonon frequencies and mode Gruneisen parameters.
 
+        :param band_structure_phonopy: phonopy get_band_structure() function output.
+        :return:
+        """
         import tempfile
         import numpy
 
@@ -128,7 +165,9 @@ def set_band_structure_gruneisen(self, band_structure_gruneisen):
 
     def get_unitcell(self):
         """
-        Return the unitcell in the node as a numpy array
+        Returns the unitcell matrix as a numpy array (Lattice vectors in rows)
+
+        :return: numpy array containing the unit cell matrix
         """
         import numpy
 
@@ -141,7 +180,9 @@ def get_unitcell(self):
 
     def get_distances(self, band=None):
         """
-        Return the distances in the node as a numpy array
+        Returns the distances as a numpy array
+
+        :return: numpy array containing the q-point distances (in Angstroms^-1)
         """
         import numpy as np
 
@@ -173,7 +214,9 @@ def get_distances(self, band=None):
 
     def get_frequencies(self, band=None):
         """
-        Return the frequencies in the node as a numpy array
+        Return the frequencies as a numpy array
+
+        :return: numpy array containing the phonon frequencies
         """
         import numpy
 
@@ -189,7 +232,9 @@ def get_frequencies(self, band=None):
 
     def get_gamma(self, band=None):
         """
-        Return the frequencies in the node as a numpy array
+        Return the mode Gruneisen parameters as a numpy array
+
+        :return: numpy array containing the mode Gruneisen parameters
         """
         import numpy
 
@@ -206,7 +251,7 @@ def get_gamma(self, band=None):
 
     def get_eigenvalues(self, band=None):
         """
-        Return the frequencies in the node as a numpy array
+        Return the eigenvalues as a numpy array
         """
         import numpy
 
@@ -223,7 +268,9 @@ def get_eigenvalues(self, band=None):
 
     def get_bands(self, band=None):
         """
-        Return the bands in the node as a numpy array
+        Return the bands as a numpy array
+
+        :return: numpy array containing a list of q-points in phonopy format: array[n_paths:n_points:3]
         """
         import numpy
 
@@ -240,7 +287,10 @@ def get_bands(self, band=None):
 
     def get_band_ranges(self, band=None):
         """
-        Return the bands in the node as a numpy array
+        Return the band ranges (only the limiting q-points of each path). This is used in phonopy's
+        gruneisen  BandStructure class
+
+        :return: numpy array containing a list of 2 q-points for each path: array[n_paths:2:3]
         """
         import numpy
 
@@ -256,8 +306,11 @@ def get_band_ranges(self, band=None):
 
     def get_labels(self, band=None):
         """
-        Return the band labels in the node as a numpy array
+        Return the labels of the high symmetry points that limit each path as a numpy array
+
+        :return: numpy array containing a list of 2 labels for each path: array[n_paths:2]
         """
+
         import numpy
 
         fname = 'band_labels.npy'

data/force_constants.py

@@ -1,3 +1,7 @@
+from aiida import load_dbenv, is_dbenv_loaded
+if not is_dbenv_loaded():
+    load_dbenv()
+
 from aiida.orm import Data
 
 
@@ -12,15 +16,14 @@ def __init__(self, *args, **kwargs):
 
     def get_shape(self):
         """
-        Return the shape of an array (read from the value cached in the
-        properties for efficiency reasons).
+        Return the shape of the force constants. This correspond to the number of atoms
         :param name: The name of the array.
         """
         return self.get_attr("shape")
 
     def get_array(self):
         """
-        Return the force constants stored in the node as a numpy array
+        Return the force constants as a numpy array in phonopy format
         """
         import numpy
 
@@ -31,10 +34,10 @@ def get_array(self):
 
     def set_array(self, array):
         """
-        Store the force constants as a numpy array. Possibly overwrite the array
+        Store the force constants as a numpy array. Overwrites the array
         if it already existed.
         Internally, it is stored as a force_constants.npy file in numpy format.
-        :param array: The numpy array to store.
+        :param array: The numpy array containing the force constants to store.
         """
 
         import tempfile
@@ -59,7 +62,7 @@ def set_array(self, array):
 
     def get_epsilon(self):
         """
-        Return dielectric tensor stored in the node as a numpy array
+        Return dielectric tensor as a numpy array
         """
         import numpy
 
@@ -74,7 +77,7 @@ def get_epsilon(self):
 
     def get_born_charges(self):
         """
-        Return born charges stored in the node as a numpy array
+        Return born charges as a numpy array
         """
         import numpy
 
@@ -97,9 +100,9 @@ def epsilon_and_born_exist(self):
 
     def set_born_charges(self, array):
         """
-        Store Born charges as a numpy array. Possibly overwrite the array
+        Store Born charges as a numpy array. Overwrites the array
         if it already existed.
-        Internally, it is stored as a force_constants.npy file in numpy format.
+        Internally, it is stored as a born_charges.npy file in numpy format.
         :param array: The numpy array to store.
         """
 
@@ -118,9 +121,9 @@ def set_born_charges(self, array):
 
     def set_epsilon(self, array):
         """
-        Store the dielectric tensor as a numpy array. Possibly overwrite the array
+        Store the dielectric tensor as a numpy array. Overwrites the array
         if it already existed.
-        Internally, it is stored as a force_constants.npy file in numpy format.
+        Internally, it is stored as a epsilon.npy file in numpy format.
         :param array: The numpy array to store.
         """
 

data/force_sets.py

@@ -1,3 +1,7 @@
+from aiida import load_dbenv, is_dbenv_loaded
+if not is_dbenv_loaded():
+    load_dbenv()
+
 from aiida.orm import Data
 
 

data/phonon_dos.py

@@ -1,5 +1,8 @@
-from aiida.orm import Data
+from aiida import load_dbenv, is_dbenv_loaded
+if not is_dbenv_loaded():
+    load_dbenv()
 
+from aiida.orm import Data
 
 class PhononDosData(Data):
     """
@@ -30,7 +33,7 @@ def _get_equivalent_atom_list(self):
 
     def get_dos(self):
         """
-        Return the force constants stored in the node as a numpy array
+        Return the density of states stored as a numpy array
         """
         import numpy
 
@@ -41,7 +44,7 @@ def get_dos(self):
 
     def get_number_of_partial_dos(self, full=False):
         """
-        Return the force constants stored in the node as a numpy array
+        Return the number of partial density of states (corresponds to the number of atoms in the primitive cell)
         """
         import numpy
 
@@ -56,7 +59,7 @@ def get_number_of_partial_dos(self, full=False):
 
     def get_partial_dos(self, full=False):
         """
-        Return the force constants stored in the node as a numpy array
+        Return a numpy that contains the partial density of states of each atom in the primitive cell
         """
         import numpy
 
@@ -80,7 +83,6 @@ def get_frequencies(self):
 
         return array
 
-
     def get_atom_labels(self, full=False):
         """
         Store the phonon dos as a numpy array.

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = aiida-phonopy
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)