GenIce3

Extending or transforming the unit cell

• 10_extend_unitcell.py
  • Use replication_matrix to extend the unit cell and build a larger supercell, then export it as a standalone unitcell plugin (Python file) via the python exporter.
• 14_use_reshaped_unitcell.py
  • Use genice3.exporter.python.supercell_as_unitcell to turn the current supercell into an in‑memory UnitCell object (no file output), then run cage_survey on the reshaped unit cell to analyse cage positions and types.

---

Sample code

10_extend_unitcell

10_extend_unitcell.py

10_extend_unitcell.sh

10_extend_unitcell.yaml

=== “10_extend_unitcell.py”

```python
#!/usr/bin/env python3
"""
Example that outputs a unitcell plugin whose unit cell is a reshaped supercell.

Corresponding CLI: examples/api/10_extend_unitcell.sh
Corresponding YAML: examples/api/10_extend_unitcell.yaml

The generated ``A15e.py`` is a unitcell plugin that reproduces the same structure
with ``rep=1 1 1``.
"""

from pathlib import Path

from genice3.genice import GenIce3
from genice3.plugin import safe_import

# Start from the A15 unit cell and enlarge it using a replication matrix.
unitcell = safe_import("unitcell", "A15").UnitCell()
genice = GenIce3(unitcell=unitcell)
genice.set_replication_matrix([[1, 1, 0], [-1, 1, 0], [0, 0, 1]])

# Use the python exporter to obtain the source code of a unitcell plugin.
exporter = safe_import("exporter", "python")
exporter.dump(genice)
```

=== “10_extend_unitcell.sh”

```bash
#!/bin/bash
# Generated from 10_extend_unitcell.yaml

python3 -m genice3.cli.genice A15 \
  --replication_matrix 1 1 0 -1 1 0 0 0 1 \
  --exporter python
```

=== “10_extend_unitcell.yaml”

```yaml
# Run with GenIce3: genice3 --config 10_extend_unitcell.yaml
# Generated from 10_extend_unitcell.sh

unitcell: A15
replication_matrix:
- 1
- 1
- 0
- -1
- 1
- 0
- 0
- 0
- 1
exporter: python
```

14_use_reshaped_unitcell

14_use_reshaped_unitcell.py

#!/usr/bin/env python3
"""
Example that outputs a unitcell plugin whose unit cell is a reshaped supercell.

Corresponding CLI: examples/api/10_extend_unitcell.sh
Corresponding YAML: examples/api/10_extend_unitcell.yaml

The generated ``A15e.py`` is a unitcell plugin that reproduces the same structure
with ``rep=1 1 1``.
"""

from genice3.genice import GenIce3
from genice3.unitcell import ice1c
from genice3.exporter import python as py_exporter, cage_survey

# Start from the ice1c unit cell and enlarge it using a replication matrix.
unitcell = ice1c.UnitCell()
genice = GenIce3(unitcell=unitcell)
genice.set_replication_matrix([[2, 2, 0], [-2, 2, 0], [0, 0, 2]])

reshaped = py_exporter.supercell_as_unitcell(genice, name="ice1c_reshaped")

genice2 = GenIce3(unitcell=reshaped)
print(cage_survey.dumps(genice2))

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