cellify

A user-friendly command-line interface (CLI) tool designed for DFT researchers to quickly generate supercells and prepare calculation-ready inputs (VASP, Quantum ESPRESSO, etc.) from unit cells.

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Features

• Format-Free Multi-Format Conversion: Supports VASP (POSCAR, CONTCAR), Quantum ESPRESSO (.in, .qe), CIF (.cif), XSF (.xsf), XYZ (.xyz), and FHI-aims (geometry.in).
• Flexible Cell Expansion (Supercell Generation):
  • Diagonal scaling (e.g., 2 2 2).
  • Arbitrary $3 \times 3$ transformation matrices (e.g., for orthogonalization).
  • Minimum periodic image distance scaling (calculates the smallest cell to keep periodic images $\ge d\ \text{Å}$ apart).
• Conventional Cell Auto-Conversion: Automatically transforms loaded primitive structures into their standard conventional representation using --conventional.
• Easy Defect & Doping Modeling: Supports atomic substitutions (absolute index or percentage) and vacancy creation.
• Surface Slab Generation: Cuts surface slabs by specifying Miller indices $(h, k, l)$, slab thickness, and vacuum thickness.
• Calculation-Ready Input Generation: Automatically updates coordinate-dependent variables (e.g., nat, ntyp in Quantum ESPRESSO) while preserving all original calculation parameters, namelists, and comments.

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Installation

1. Install via PyPI

To install the latest stable release of cellify directly using pip:

pip install cellify

2. Local Installation (Development)

To install from the source code for development or customization:

git clone https://github.com/ToAmano/cellify.git
cd cellify
pip install -e .

# Or install with test dependencies
pip install -e ".[test]"

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CLI Usage

cellify -i <input_file> -o <output_file> [options]

Arguments List

• -i, --input : Input structure file path (Required).
• -o, --output : Output structure file path (Default: <input_base>_supercell.<ext>).
• -d, --dim : Diagonal scaling factors. 3 integers separated by spaces (e.g., --dim 2 2 2).
• -m, --matrix : $3 \times 3$ transformation matrix. Specify row values separated by spaces, rows separated by slashes/commas/semicolons (e.g., --matrix "1 -1 0 / 1 1 0 / 0 0 2").
• --min-dist : Automatically generate a supercell with minimum periodic image distance $\ge$ specified distance (in $\text{Å}$).
• --conventional : Automatically convert the input structure to its standard conventional representation before applying other operations.
• --substitute : Substitution rule. Format: element:target_element:index_or_percentage (e.g., --substitute "Si:P:0" or --substitute "Si:Al:5%").
• --vacancy-index : Create a vacancy by removing an atom at a specific absolute index. Format: element:index (e.g., --vacancy-index "Si:0", --vacancy-index "C:33"). (Alias: --vacancy).
• --vacancy-count : Create vacancies by randomly removing a specified number of atoms of a given element. Format: element:count (e.g., --vacancy-count "O:2"_).
• --slab : Miller indices $h\ k\ l$ for surface slab model creation (e.g., --slab 1 1 1).
• --thick : Slab thickness in $\text{Å}$ or layers (e.g., --thick 15.0).
• --vacuum : Vacuum layer thickness in $\text{Å}$ (e.g., --vacuum 15.0).
• --template : Template QE input file to preserve computational parameters and comments when generating a new input file from a QE output log file.
• --calc, --calculation : Override the calculation parameter inside the QE input file namelist (e.g., scf, nscf, bands).
• -w, --view : Quickly visualize the final generated structure in 3D using ASE (requires GUI environment). If _tkinter is missing, it automatically falls back to a 2D matplotlib projection plot.

Note

3D Visualization (Tkinter / _tkinter error) If you run with -w/--view and see ModuleNotFoundError: No module named '_tkinter', your Python environment is missing Tcl/Tk support:

• macOS (Homebrew Python): Run brew install python-tk (or python-tk@3.9 matching your python version).
• macOS (Conda Python): Run conda install -c conda-forge tk python inside your active environment.
• Linux (Ubuntu/Debian): Run sudo apt-get install python3-tk.

If Tkinter is not available, cellify automatically falls back to rendering a 2D projection window using matplotlib.

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Examples

1. Create a simple $2 \times 2 \times 3$ supercell (VASP POSCAR)

cellify -i POSCAR -o POSCAR_223 --dim 2 2 3

➔

2. Convert primitive cell to conventional and scale to 2x2x2

cellify -i Si_primitive.POSCAR -o Si_conventional_222.POSCAR --conventional --dim 2 2 2

➔

3. Orthogonalize a hexagonal cell (Quantum ESPRESSO input)

# Preserves &CONTROL and &SYSTEM settings, and updates nat, CELL_PARAMETERS, and ATOMIC_POSITIONS
cellify -i qe.in -o qe_ortho.in --matrix "1 -1 0 / 1 1 0 / 0 0 1"

➔

4. Generate the smallest supercell keeping defect distance $\ge 15\ \text{Å}$

cellify -i POSCAR -o POSCAR_defect_bulk --min-dist 15.0

➔

5. Create a silicon supercell and replace 1 atom with Phosphorus (n-type doped model)

cellify -i Si_unit.cif -o Si_doped.POSCAR --dim 3 3 3 --substitute "Si:P:0"

➔

6. Introduce vacancies in a supercell (e.g., delete a specific Silicon atom, or randomly remove 2 Oxygen atoms)

# Deletes the Silicon atom at absolute index 0
cellify -i Si_supercell.POSCAR -o Si_vacancy.POSCAR --vacancy-index "Si:0"

# Randomly removes 2 Oxygen atoms from the structure
cellify -i STO_supercell.POSCAR -o STO_vacancies.POSCAR --vacancy-count "O:2"

➔

7. Generate a $\text{SrTiO}_3$ (100) surface slab model with $15\ \text{Å}$ vacuum

cellify -i STO_bulk.cif -o STO_100_slab.POSCAR --slab 1 0 0 --thick 12.0 --vacuum 15.0

➔

8. Extract relaxed structure from a Quantum ESPRESSO output log and generate an SCF input

# Reads the final relaxed structure from vc-relax.out,
# merges it with the computational settings in template.in,
# and writes scf.in with calculation = 'scf' and updated atom/type counts.
cellify -i vc-relax.out --template template.in -o scf.in --calc scf

graph TD
    subgraph Inputs ["Input Files"]
        A["vc-relax.out (QE Output Log)<br/>➔ Contains relaxed atomic coordinates"]
        B["template.in (Input Template)<br/>➔ Contains K-points, parameters, etc."]
    end

    C["cellify -i vc-relax.out --template template.in -o scf.in --calc scf"]

    subgraph Output ["Output File"]
        D["scf.in (Merged SCF Input)<br/>✓ Merged parameters & coordinates<br/>✓ Updated 'nat', 'ntyp' & calculation='scf'"]
    end

    A --> C
    B --> C
    C --> D

    style C fill:#238636,color:#fff,stroke:#2ea44f,stroke-width:2px;
    style D fill:#1f6feb,color:#fff,stroke:#58a6ff,stroke-width:2px;

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For more hands-on examples, check out the examples/ directory.

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Directory Structure

cellify/
├── pyproject.toml
├── README.md
├── examples/         # Runnable use cases for VASP and Quantum ESPRESSO
└── src/
    └── cellify/
        ├── __init__.py
        ├── cli.py            # CLI parser & execution flow
        ├── core.py           # Core structure modeling logic
        ├── viewer.py         # WebGL 3D structure viewer
        └── adapters/         # Formats and parameter preservation
            ├── __init__.py
            ├── base.py       # Base adapter interface
            ├── espresso.py   # Quantum ESPRESSO adapter
            └── standard.py   # Standard pymatgen/ASE adapter