How to Use CIF2Cell — Quick Guide and ExamplesCIF2Cell is a command-line utility designed to convert crystallographic information files (CIF) into input files for common electronic-structure codes (VASP, Quantum ESPRESSO, ABINIT, CP2K, SIESTA, and others). It streamlines the process of preparing crystal structures for density functional theory (DFT) and other atomistic simulations by parsing CIF symmetry and atomic positions, generating conventional or primitive cells, and exporting files in formats accepted by target codes. This guide explains installation, typical workflows, useful options, and concrete examples for common use cases.
Why use CIF2Cell?
- Interoperability: Quickly convert standardized CIF data into input files for many simulation packages.
- Symmetry handling: CIF2Cell reads symmetry information in CIFs and can expand asymmetric units into full unit cells.
- Format options: Supports POSCAR/VASP, PWscf/Quantum ESPRESSO, ABINIT, CP2K (XYZ/INPUT), and more.
- Automation-friendly: Command-line interface suitable for scripting and high-throughput workflows.
Installation
CIF2Cell is a Python package typically installed via pip. Recommended steps:
- Ensure you have Python 3.7+ and pip installed.
- Install with pip:
pip install cif2cell - (Optional) Install additional dependencies for specific formats if prompted (some features may require ASE — Atomic Simulation Environment — or other packages).
Confirm installation:
cif2cell --version If you prefer, install in a virtual environment:
python -m venv venv source venv/bin/activate pip install cif2cell Basic usage and common options
The basic command structure:
cif2cell input.cif --<format> [options] Common format flags:
- –vasp : generate POSCAR for VASP
- –espresso or –pwscf : generate Quantum ESPRESSO input
- –abinit : generate ABINIT input
- –cp2k : generate CP2K input
- –xyz : export standard XYZ
Useful options:
- –primitive : convert to primitive cell
- –conventional : generate a conventional cell
- –supercell a b c : build a supercell with integer multipliers
- –no_symmetry : ignore CIF symmetry; use coordinates as-is
- –species-mapping : remap element names if CIF uses nonstandard labels
- –positions fractional|cartesian : specify coordinate type for output
- –element-sort : enforce element ordering in output
- –cell-format fractional|cartesian : how cell vectors are printed
Example:
cif2cell Fe2O3.cif --vasp --primitive --supercell 2 2 1 -o POSCAR This reads Fe2O3.cif, converts to the primitive cell, builds a 2x2x1 supercell, and writes a VASP POSCAR file.
Handling CIF quirks
CIF files can vary in quality; common issues and fixes:
- Missing or nonstandard element labels: use –species-mapping to rename labels (e.g., map “Fe1” → Fe).
- Partial occupancies and disorder: CIF2Cell typically cannot resolve fractional occupancies into explicit atomic positions. Preprocess the CIF to choose one configuration or use tools that sample disorder.
- Incorrect symmetry or conflicting fractional coordinates: try –no_symmetry to avoid expanding incomplete symmetry definitions.
- Units and scale factors: ensure the CIF contains lattice parameters in Å. If scale mismatches occur, manually check cell vectors.
Examples
1) Convert CIF to a VASP POSCAR (primitive cell)
cif2cell Si.cif --vasp --primitive -o POSCAR Result: POSCAR with primitive lattice vectors and atomic positions suitable for VASP.
2) Generate Quantum ESPRESSO input with a 2x2x2 supercell
cif2cell material.cif --pwscf --supercell 2 2 2 --positions cartesian -o qe.in Result: Quantum ESPRESSO input file with atomic positions in Cartesian coordinates.
3) Create CP2K input and an XYZ for visualization
cif2cell structure.cif --cp2k -o cp2k.in cif2cell structure.cif --xyz -o structure.xyz 4) Ignore CIF symmetry and keep coordinates as provided
cif2cell messy.cif --vasp --no_symmetry -o POSCAR_messy 5) Map nonstandard species labels
If the CIF uses labels like “Cu1” and “Cu2” that the converter misinterprets, provide a mapping file or pass mappings on the command line (syntax may vary by version):
cif2cell weird.cif --vasp --species-mapping "Cu1:Cu,Cu2:Cu" -o POSCAR_fixed Integrating into workflows
- Batch conversion: Use shell loops to convert multiple CIFs:
for f in *.cif; do cif2cell "$f" --vasp -o "${f%.cif}.POSCAR" done - High-throughput pipelines: Combine CIF2Cell with tools like pymatgen, ASE, or FireWorks. Example: parse CIFs with pymatgen to validate, then call cif2cell for format-specific outputs.
- Version control: Keep a copy of the original CIFs and generated inputs; record conversion flags in a small metadata file for reproducibility.
Tips and best practices
- Validate outputs visually with a viewer (VESTA, VMD, OVITO) or programmatically using ASE/pymatgen.
- Check element ordering and counts in generated files; mismatches indicate mapping or symmetry issues.
- Prefer primitive cells for computational efficiency; choose conventional cells when comparing with experimental lattice parameters.
- When working with DFT codes, follow code-specific conventions for lattice vectors, atomic ordering, and pseudopotential selections after conversion.
Troubleshooting checklist
- Wrong atomic species: verify CIF labels and use species mapping.
- Unexpected cell vectors or scales: confirm CIF units and check for apparent scale factors in the CIF header.
- Missing atoms after symmetry expansion: try –no_symmetry and compare results.
- Errors running target code after conversion: compare with a minimal example POSCAR/input to ensure formatting and ordering are correct.
Further resources
- CIF2Cell documentation (installed package often includes man pages or –help text). Run:
cif2cell --help - ASE and pymatgen for additional structure manipulation and file format conversions.
- Visualization tools: VESTA, VMD, OVITO — useful for quick checks.
CIF2Cell is a compact, effective tool for quickly translating experimental CIFs into simulation-ready inputs. Start by validating a single conversion manually, then incorporate it into scripts for batch processing.