httk-atomistic¶

This site documents specifically the httk-atomistic module. For the full documentation of httk₂ as a whole, see docs.httk.org.

httk-atomistic is a httk₂ module providing crystal structure representations under the namespace httk.atomistic. It also carries the file input/output stack for atomistic data — the CIF/mCIF reader and writer, the VASP POSCAR/CONTCAR and output-file readers, the WAVECAR binary reader/writer, and the OPTIMADE trajectory JSON Lines holding format — registering these readers with httk-core through httk.registry.io.atomistic.

Quick links

API reference: Reference
Structures: Structures
Composition and formulas: Composition and formula families
Structure prototypes: Prototype families
Asymmetric units: Asymmetric units
Subgroups and pathfinding: Subgroups and pathfinding
Site moments (magnetism): Site moments
Integrations (ASE, pymatgen, VASP): Integrations
Data precision: Data precision
Periodicity (slabs, wires, molecules): Periodicity
Lattice reduction: Lattice reduction (Niggli)
Primitive cells: Primitive cells
Reading and writing CIF files: Reading and writing CIF files
Reading POSCAR/CONTCAR files: Reading VASP POSCAR / CONTCAR files
Reading VASP output files: Reading VASP output files
Reading and writing WAVECAR files: Reading and writing VASP WAVECAR files
Plane-wave wavefunctions: Plane-wave wavefunctions
Trajectory JSON Lines: Trajectory JSON Lines
Runnable examples: Examples
Examples notebook: Examples
Disorder walkthrough: Disorder, vacancies, and attached species

The topic pages above are short and practical; the ones with a full guide link onward to it in the Details section of the sidebar.

Install¶

Preferably work in a Python virtual environment, then do:

git clone https://github.com/httk/httk-atomistic
cd httk-atomistic
python -m pip install -e .

Usage example¶

from httk.atomistic import UnitcellStructure, PlainStructureView

structure = UnitcellStructure(
    cell=[[4.0, 0.0, 0.0], [0.0, 4.0, 0.0], [0.0, 0.0, 4.0]],
    sites=[[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]],
    species=[
        {"name": "Na", "chemical_symbols": ["Na"], "concentration": [1.0]},
        {"name": "Cl", "chemical_symbols": ["Cl"], "concentration": [1.0]},
    ],
    species_at_sites=["Na", "Cl"],
)

# Present the same structure as an spglib-like (lattice, positions, numbers) tuple.
lattice, positions, numbers = PlainStructureView(structure)

Documentation

Details