GenIce3

Guest occupancy and cage-related operations in clathrate hydrates.

• 6_with_guests.py
  • Place guest molecules with specified occupancy for each cage type.
• 8_cage_survey.py
  • Survey cage positions and types in the structure.

---

Sample code

6_with_guests

6_with_guests.py

6_with_guests.sh

6_with_guests.yaml

=== “6_with_guests.py”

```python
from logging import basicConfig, DEBUG, INFO
import numpy as np
from genice3.genice import GenIce3
from genice3.plugin import Exporter, Molecule
from genice3.cli.options import parse_guest_option, parse_spot_guest_option

# Corresponding CLI command (guest/spot_guest are base options, outside the exporter):
# genice3 "A15[shift=(0.1,0.1,0.1), anion.0=Cl, cation.6=Na, density=0.8]" \
#   --rep 2 2 2 \
#   --guest A12=me --guest A14=et --spot_guest 0=4site \
#   --exporter gromacs :water_model 4site \
#   --seed 42 --pol_loop_1 2000 -D

basicConfig(level=INFO)

# Create a GenIce3 instance.
# guests: guest molecules per cage type (raw dict is converted by parse_guest_option).
# spot_guests: guest molecules for specific cages (raw dict is converted by parse_spot_guest_option).
genice = GenIce3(
    seed=42,
    pol_loop_1=2000,
    replication_matrix=np.array([[2, 0, 0], [0, 2, 0], [0, 0, 2]]),
    guests=parse_guest_option({"A12": "me", "A14": "et"}),
    spot_guests=parse_spot_guest_option({0: "4site"}),
)

# Set the unit cell.
# shift: shift in fractional coordinates.
# anion / cation: replace lattice sites in the unit cell with ions (site index -> ion name). CLI: -a / --anion, -c / --cation
# density: density in g/cm³.
# If cage information is needed, you can use Exporter("cage_survey").dump(genice, file) to output JSON.
genice.set_unitcell("A15", shift=(0.1, 0.1, 0.1), density=0.8)


# Output using the exporter (guest/spot_guest are already set in the GenIce3 instance).
Exporter("gromacs").dump(
    genice,
    water_model="4site",
)
```

=== “6_with_guests.sh”

```bash
#!/bin/bash
# Generated from 6_with_guests.yaml

python3 -m genice3.cli.genice A15 \
  --shift 0.1 0.1 0.1 \
  --density 0.8 \
  --rep 2 2 2 \
  --guest A12=me A14=et \
  --spot_guest 0=4site \
  --exporter gromacs :water_model 4site \
  --seed 42 \
  --pol_loop_1 2000
```

=== “6_with_guests.yaml”

```yaml
# Run with GenIce3: genice3 --config 6_with_guests.yaml
# Generated from 6_with_guests.sh

unitcell: A15
shift:
- 0.1
- 0.1
- 0.1
density: 0.8
rep:
- 2
- 2
- 2
guest:
- A12=me
- A14=et
spot_guest: 0=4site
exporter:
  gromacs:
    water_model: 4site
seed: 42
pol_loop_1: 2000
```

8_cage_survey

8_cage_survey.py

8_cage_survey.sh

8_cage_survey.yaml

=== “8_cage_survey.py”

```python
"""Example of using ``cage_survey`` for the DOH structure (Python API)."""
from genice3.genice import GenIce3
from genice3.plugin import Exporter
from logging import basicConfig, INFO

# Corresponding CLI command:
#   genice3 DOH -e cage_survey
basicConfig(level=INFO)
genice = GenIce3()
genice.set_unitcell("DOH")
Exporter("cage_survey").dump(genice)
```

=== “8_cage_survey.sh”

```bash
#!/bin/bash
# Generated from 8_cage_survey.yaml

python3 -m genice3.cli.genice DOH \
  --exporter cage_survey
```

=== “8_cage_survey.yaml”

```yaml
# Run with GenIce3: genice3 --config 8_cage_survey.yaml
# Generated from 8_cage_survey.sh

unitcell: DOH
exporter: cage_survey
```

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