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Structure object¶
The AbiPy structure inherits from the pymatgen structure.
One has therefore access to all the methods and tools already available in pymatgen.
In this notebook, we mainly focus on the extensions added by AbiPy.
For the features provided by pymatgen, please consult the
official pymatgen documentation
Table of Contents¶
from __future__ import division, print_function, unicode_literals
import warnings
warnings.filterwarnings("ignore") # to get rid of deprecation warnings
# Import abipy modules
from abipy import abilab
from abipy.abilab import Structure
import abipy.data as abidata
# Useful tools we'll need later on.
from pprint import pprint
import numpy as np
# This line configures matplotlib to show figures embedded in the notebook.
# Replace `inline` with `notebook` in classic notebook
%matplotlib inline
# Option available in jupyterlab. See https://github.com/matplotlib/jupyter-matplotlib
#%matplotlib widget
Reading a structure from file¶
It is possible to initialize a crystalline structure from different file formats:
- CIF
- POSCAR/CONTCAR
- CHGCAR
- LOCPOT,
- vasprun.xml
- CSSR
- ABINIT Netcdf files
- pymatgen's JSON serialized structures
Note, in particular, that one can initialize the structure from the netcdf files
produced by Abinit (GSR.nc, WFK.nc, etc) as well as output files in text format
such as the Abinit input/output files or even the DDB file.
To initialize the structure from a CIF file use the from_file method:
# abidata.cif_file returns one of the CIF files shipped with AbiPy.
structure = Structure.from_file(abidata.cif_file("si.cif"))
print(structure)
To read the structure from a netcdf file:
structure = Structure.from_file(abidata.ref_file("si_nscf_GSR.nc"))
# Use to_string with verbose > 0 to get more info
print(structure.to_string(verbose=1))
Use to_abivars to get the list of Abinit variables in a python dictionary:
structure.to_abivars()
and abi_string to get a string that can be used directly in the input file:
print(structure.abi_string)
To visualize the structure with matplotlib, use:
structure.plot();
The matplotlib version is minimalistic but it plays well with jupyter notebooks. For a more advanced visualization we suggest using a specialized graphical applications. Fortunately, one can invoke (already installed) external applications directly from AbiPy with e.g.
# structure.visualize("vesta")
To get a structure from the materials project database (https://www.materialsproject.org ), use:
# You can pass the api_key or set the env variable PMG_MAPI_KEY in your ~/.pmgrc.yaml files.
si2_mp = Structure.from_mpid("mp-149", api_key=None)
print(si2_mp)
In some cases, we have multiple structures and we need to compare the lattice parameters.
Use dataframes_from_structures to build a pandas DataFrame:
dfs = abilab.dataframes_from_structures([structure, si2_mp], index=["CIF", "MP"])
then we can compare the lattice parameters with:
dfs.lattice
Note that all AbiPy robots have this feature built-in.
Sometimes it is much easier to build a robot directly from files
and then compare the structures with e.g. robot.get_lattice_dataframe().
Converting to other formats¶
Use structure.convert(format) to get the string representation in the new format:
for fmt in ["cif", "POSCAR", "qe"]:
print((" Abinit --> %s " % fmt).center(80, "*"))
print(structure.convert(fmt=fmt))
Getting information on the structure¶
print(structure.reciprocal_lattice)
structure.reciprocal_lattice.matrix.T @ structure.lattice.matrix / (2 * np.pi)
# List of high-symmetry k-points.
print(structure.hsym_kpoints)
The method calc_ksampling allows one to get an efficient sampling of the Brillouin zone
by just specifying the number of divisions to be used for the smallest lattice vector of the reciprocal lattice:
pprint(structure.calc_ksampling(nksmall=10))
To get the recommended high symmetry $k$-path in reduced coordinates:
structure.calc_kptbounds()
The high-symmetry q-path is automatically selected assuming the structure fulfills the convention described in Setyawan2010
To visualize the Brillouin zone with matplotlib:
structure.plot_bz();
To get the number of valence electrons for a given set of pseudopotentials:
structure.num_valence_electrons(pseudos=abidata.pseudos("14si.pspnc"))
To visualize the X-ray diffraction plot with pymatgen XRDCalculator
structure.plot_xrd();
abistruct.py¶
abistruct.py provides a handy command line interface to operate on structure objects
constructed from external files.
There are several options available as well an interface to the materials project
and the COD database.
!abistruct.py --help
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