Usage

Installation

At release I’ll probably put this on pip, at which point you can do

pip install vestacrystparser

But that isn’t available yet. Until then, it lives on GitHub, at https://github.com/GriffinGroup/vestacrystparser.

Modifying VESTA files

You can load an existing VESTA file as so.

from vestacrystparser import VestaFile

vfile = VestaFile("file.vesta")

VestaFile holds all the data for a VESTA file and provides methods for inspecting and modifying that data. For example, you can change the view boundary and hide the compass with,

vfile.set_boundary(-0.5, 0.5, -0.5, 0.5, -0.5, 0.5)
vfile.set_compass_visibility(False)

The methods of VestaFile are not yet comprehensive. If you need to perform an action not covered by the high-level API, you can modify the sections directly (which are represented with VestaSection objects). Beware that no safety checks are performed here, so be careful not to leave the sections in a corrupt state.

section1 = vfile["BOUND"]
section1.data[0] = [-0.5, 0.5, -0.5, 0.5, -0.5, 0.5]
section2 = vfile["COMPS"]
section2.inline[0] = 0

For VESTA files with multiple phases, VestaFile.set_current_phase() should be used to change the phase referenced by default by the API. Alternatively, VestaFile.__getitem__() accepts a second argument, the index of the desired phase.

E.g. The following two code blocks both unset the compass visibility for Phase 1 (phase indices are 0-based).

vfile.set_current_phase(1)
vfile.set_compass_visibility(False)

section = vfile["COMPS", 1]
section.inline[0] = 0

Finally, the VestaFile may be written back to file with VestaFile.save().

Importing structure files to VESTA

Often, you may have structure data which you could open in VESTA, but not yet a VESTA file. In these cases, the convert module allows reading in structure data and outputing a VestaFile object (which can be written to a VESTA file). Currently, POSCAR files and generic pymatgen.core.Structure objects are supported.

The convert module requires pymatgen to be installed.

import vestacrystparser.convert

# Load directly from POSCAR file.
vfile = vestacrystparser.convert.vesta_from_poscar("POSCAR")

from pymatgen.core import Structure

# Create VestaFile from Structure object (which may be parsed from anything)
stru = Structure.from_file("POSCAR")
vfile = vestacrystparser.convert.vesta_from_structure(stru)