GenIce3

Reading from and writing to CIF files.

• cif/
  • Symlink to the project-root cif/ directory. Used so examples can refer to files such as cif/MEP.cif.
• 4_from_cif.py
  • Load an ice structure from a CIF file and use it as a GenIce3 UnitCell.
• 5_to_cif.py
  • Export a structure generated by GenIce3 in CIF format.

---

Sample code

4_from_cif

4_from_cif.py

4_from_cif.sh

4_from_cif.yaml

=== “4_from_cif.py”

```python
from genice3.genice import GenIce3
from genice3.plugin import Exporter
from logging import basicConfig, INFO

# corresponding command:
# genice3 'CIF[file=cif/MEP.cif, osite=T]' --exporter gromacs
basicConfig(level=INFO)
genice = GenIce3()
genice.set_unitcell("CIF", file="cif/MEP.cif", osite="T")
Exporter("gromacs").dump(genice)
```

=== “4_from_cif.sh”

```bash
#!/bin/bash
# Generated from 4_from_cif.yaml

python3 -m genice3.cli.genice CIF \
  --file cif/MEP.cif \
  --osite T
```

=== “4_from_cif.yaml”

```yaml
# Run with GenIce3: genice3 --config 4_from_cif.yaml
# Generated from 4_from_cif.sh

unitcell: CIF
file: cif/MEP.cif
osite: T
```

5_to_cif

5_to_cif.py

5_to_cif.sh

5_to_cif.yaml

=== “5_to_cif.py”

```python
from genice3.genice import GenIce3
from genice3.plugin import Exporter
from logging import basicConfig, INFO

# corresponding command:
# genice3 A15 -e cif
basicConfig(level=INFO)
genice = GenIce3()
genice.set_unitcell("A15")
Exporter("cif").dump(genice)
```

=== “5_to_cif.sh”

```bash
#!/bin/bash
# Generated from 5_to_cif.yaml

python3 -m genice3.cli.genice A15 \
  --exporter cif
```

=== “5_to_cif.yaml”

```yaml
# Run with GenIce3: genice3 --config 5_to_cif.yaml
# Generated from 5_to_cif.sh

unitcell: A15
exporter: cif
```

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