abio Package ¶

Contents

abio Package

`abio` Package ¶

This sub-package provides objects and methods to generate Input files.

`abivars` Module ¶

This module contains lookup table with the name of the ABINIT variables.

abipy.abio.abivars.is_abivar(varname)[source]¶: True if s is an ABINIT variable.

abipy.abio.abivars.is_abiunit(s)[source]¶: True if string is one of the units supported by the ABINIT parser

class abipy.abio.abivars.AbinitInputFile(filepath)[source]¶

Bases: abipy.core.mixins.TextFile, abipy.core.mixins.Has_Structure, abipy.core.mixins.NotebookWriter

This object parses the Abinit input file, stores the variables in dict-like objects (Datasets) and build Structure objects from the input variables. Mainly used for inspecting the structure declared in the Abinit input file.

classmethod from_string(string)[source]¶: Build the object from string.

to_string(verbose=0)[source]¶: String representation.

has_multi_structures()[source]¶: True if input defines multiple structures.

close()[source]¶: NOP, required by ABC.

structure()[source]¶

The structure defined in the input file.

If the input file contains multiple datasets AND the datasets have different structures, this property returns None. In this case, one has to access the structure of the individual datasets. For example:

input.datasets[0].structure

gives the structure of the first dataset.

yield_figs(**kwargs)[source]¶: This function generates a predefined list of matplotlib figures with minimal input from the user.

write_notebook(nbpath=None)[source]¶: Write an ipython notebook to nbpath. If nbpath is None, a temporay file in the current working directory is created. Return path to the notebook.

class abipy.abio.abivars.AbinitInputParser[source]¶

Bases: object

verbose = 0¶

parse(s)[source]¶: This function receives a string s with the Abinit input and return a list of Dataset objects.

static eval_abinit_operators(tokens)[source]¶

static varname_dtindex(tok)[source]¶

>>> p = AbinitInputParser()
>>> assert p.varname_dtindex("acell1") == ("acell", 1)
>>> assert p.varname_dtindex("fa1k2") == ("fa1k", 2)

abipy.abio.abivars.structure_from_abistruct_fmt(string)[source]¶

Parse geometrical information given in the structure:abivars format return Structure object

A typical input file in “structure:abivars” format looks like:

# MgB2 lattice structure.
natom   3
acell   2*3.086  3.523 Angstrom
rprim   0.866025403784439  0.5  0.0
       -0.866025403784439  0.5  0.0
        0.0                0.0  1.0

# Atomic positions
xred_symbols
    0.0  0.0  0.0 Mg
    1/3  2/3  0.5 B
    2/3  1/3  0.5 B

i.e. the zcucl, typat and ntypat vars are implicitly defined via the xred_symbols table.

`abivars_db` Module ¶

Database with the names of the input variables used in Abinit and in other main programs.

abipy.abio.abivars_db.get_abinit_variables()[source]¶: Returns the database with the description of the ABINIT variables.

abipy.abio.abivars_db.get_anaddb_variables()[source]¶: Returns the database with the description of the ANADDB variables.

abipy.abio.abivars_db.docvar(varname, executable='abinit')[source]¶: Return the Variable object associated to this name.

abipy.abio.abivars_db.abinit_help(varname, info=True, stream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>)[source]¶: Print the abinit documentation on the ABINIT input variable varname

abipy.abio.abivars_db.repr_html_from_abinit_string(text)[source]¶: Given a string text with an Abinit input file, replace all variables with HTML links pointing to the official documentation. Return new string.

`decorators` Module ¶

Decorators for AbinitInput or MultiDataset objects.

exception abipy.abio.decorators.InputDecoratorError[source]¶

Bases: Exception

Error class raised by AbinitInputDecorator.

class abipy.abio.decorators.AbinitInputDecorator[source]¶

Bases: monty.json.MSONable

An AbinitInputDecorator adds new options to an existing AbinitInput or an existing MultiDataset without altering its structure. This is an abstract Base class.

Example

decorator = MyDecorator(arguments)

new_abinit_input = decorator(abinit_input) new_multidataset = decorator(multidataset)

Note that a decorator does not modify the object on which it acts.

Warning

Please avoid introducing decorators acting on the structure (in particular the lattice) since the initial input may use the initial structure to compute important variables. For instance, the list of k-points for band structure calculation depend on the bravais lattice and a decorator that changes it should recompute the path. This should not represent a serious limitation because it’s always possible to change the structure with its methods and then call the factory function without having to decorate an already existing object.

Error¶: alias of abipy.abio.decorators.InputDecoratorError

class abipy.abio.decorators.SpinDecorator(spinmode, kptopt_ifspinor=4)[source]¶

Bases: abipy.abio.decorators.AbinitInputDecorator

This decorator changes the spin polarization.

as_dict()[source]¶: A JSON serializable dict representation of an object.