robocrys program

Robocrystallographer can be used on the command-line through the robocrys command. Most of the options provided in the Python API are also accessible on the command-line. This page details the basic usage of the program.

Usage

The full range of options supported by robocrys are detailed in the Command-line interface section, and be can be listed using:

robocrys -h

The package integrates with the Materials Project to for allow generation of structure descriptions directly from Materials Project ids. For example, to generate the description of SnO​​ 2 (mp-856), one can simply run:

robocrys mp-856

Alternatively, a structure file can be specified in place of a Materials Project id. Robocrystallographer supports the same file formats as pymatgen, including the Crystallographic Information Format (CIF), common electronic structure package formats such as POSCAR files, and JSON files containing pymatgen Structure objects. Gzipped files are also supported. For example, to generate the description of a CIF file:

robocrys MyStructure.cif

Basic options

Generating a structure description is split into two steps, the first is to condense the structure into an intermediate JSON representation, the second is to generate a description from the intermediate representation. The robocrys program contains options for controlling both steps of this process.

Condenser options

By default, robocrystallographer determines whether sites are equivalent using the site information (element, geometry, order parameter), nearest neighbor information (number and types of neighbors, bond lengths), and next nearest neighbor information (number and types of neighbors, connectivity, bond angles). To instead use symmetry to determine which sites are equivalent, the --symmetry option can be used. The symmetry tolerance is controlled using the --symprec option. Note that the symmetry information will always be used to determine the symmetry labels for the sites, even if the equivalent sites are determined through structural properties.

Robocrystallographer will produce a description for the structure provided as is. However, generally best results will be obtained when describing the conventional cell structure. The --conventional optional will automatically convert the structure into the standardized conventional cell representation.

For example, to generate the description for the conventional cell, with symmetry used to determine site inequivalence, and a symmetry tolerance of 0.001, the command would be:

robocrys MyStructure.cif --conventional --symmetry --symprec 0.001

Describer options

The robocrys program has many options to control the verbosity of the description. By default, oxidation states and symmetry labels are included in the description. These can be disabled using the --no-oxi and --no-symmetry--labels options, respectively.

By default, only the connectivity of cation-polyhedra is included. To also describe the connectivity anion polyhedra, the --anion-polyhedra option can be used.

Robocrystallographer also supports generating LaTeX ready descriptions through the --latexify option.

Command-line interface

robocrystallographer is a tool to generate crystal structure descriptions

usage: robocrys [-h] [-c] [-s] [--symprec SYMPREC] [--no-simplify]
                [--no-iupac] [--no-common-formulas] [--no-mineral]
                [--no-makeup] [--no-components] [--no-symmetry-labels]
                [--no-oxi] [--no-bond] [--precision P] [--distorted-tol T]
                [--anion-polyhedra] [--verbose-bonds] [--format FMT]
                [--api-key API_KEY]
                filename

Positional Arguments

filename structure file or mpid

Named Arguments

-c, --conventional
 

use the convention cell

Default: False

-s, --symmetry

use symmetry to determine inequivalent sites

Default: False

--symprec

symmetry tolerance

Default: 0.01

--no-simplify

don’t simplify molecules when mineral matching

Default: True

--no-iupac

don’t use IUPAC formula ordering

Default: True

--no-common-formulas
 

don’t use common formulas

Default: True

--no-mineral

don’t describe the mineral information

Default: True

--no-makeup

don’t describe the component makeup

Default: True

--no-components
 

don’t describe the components

Default: True

--no-symmetry-labels
 

don’t describe symmetry labels

Default: True

--no-oxi

don’t describe oxidation states

Default: True

--no-bond

don’t describe bond lengths

Default: True

--precision

decimal places for bond lengths

Default: 2

--distorted-tol
 

order parameter below which sites are distorted

Default: 0.6

--anion-polyhedra
 

describe anion polyhedra connectivity

Default: False

--verbose-bonds
 

describe bond lengths for each site

Default: True

--format

how to format the description (unicode [default], html, latex, raw)

Default: “unicode”

--api-key set the materials project API key. See: https://materialsproject.org/docs/api

Author: Alex Ganose, Version: 0.2.3, Last updated: December 17, 2018