# ClustIce
A tool to generate exotic ice clusters.
version 0.7.1
## Requirements
* python
* numpy
* networkx
* scikit-learn
* cycless
## Installation
ClustIce is registered to [PyPI (Python Package Index)](https://pypi.python.org/pypi/GenIce).
Install with pip3.
pip3 install clustice
## Uninstallation
pip3 uninstall clustice
## API
API manual is [here](https://clustice.github.io/ClustIce).
## Examples
Make an icosahedral ice cluster.
```python
import numpy as np
import networkx as nx
import genice_core
from clustice.geometry import make_layout
from clustice.gromacs import render
from clustice.water import tip4p
from clustice import graph
# O-O distance
L = 0.27
# note: g must be a graph whose labels start from 0.
# g = graph.great_icosahedron(12, separation=L)
g = graph.great_decahedron(12)
# g = graph.small_barrelan()
# g = graph.large_barrelan()
# g = graph.twistane()
# g = graph.adamantane()
# g = nx.cycle_graph(6) # hexagon
# g = nx.cycle_graph(7) # heptagon
# g = nx.cubical_graph() # cubic octamer
# g = nx.dodecahedral_graph()
if "pos" in g.nodes[0]:
# extract the embedded coords in g
layout = np.array([g.nodes[v]["pos"] for v in g])
else:
# estimate of the positions of the nodes
layout = make_layout(g, edgelen=L)
# set orientations of the hydrogen bonds.
# if vertexPositions is given, the net dipole moment is minimized.
dg = genice_core.ice_graph(g, vertexPositions=layout, dipoleOptimizationCycles=100)
# put water molecules
gro = render(dg, layout, watermodel=tip4p)
with open("sample.gro", "w") as f:
f.write(gro)
```
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"description": "# ClustIce\n\nA tool to generate exotic ice clusters.\n\nversion 0.7.1\n\n## Requirements\n\n* python\n* numpy\n* networkx\n* scikit-learn\n* cycless\n\n\n## Installation\n\nClustIce is registered to [PyPI (Python Package Index)](https://pypi.python.org/pypi/GenIce).\nInstall with pip3.\n\n pip3 install clustice\n\n## Uninstallation\n\n pip3 uninstall clustice\n\n## API\n\nAPI manual is [here](https://clustice.github.io/ClustIce).\n\n## Examples\n\nMake an icosahedral ice cluster.\n\n```python\nimport numpy as np\nimport networkx as nx\n\nimport genice_core\nfrom clustice.geometry import make_layout\nfrom clustice.gromacs import render\nfrom clustice.water import tip4p\nfrom clustice import graph\n\n# O-O distance\nL = 0.27\n\n# note: g must be a graph whose labels start from 0.\n# g = graph.great_icosahedron(12, separation=L)\ng = graph.great_decahedron(12)\n# g = graph.small_barrelan()\n# g = graph.large_barrelan()\n# g = graph.twistane()\n# g = graph.adamantane()\n# g = nx.cycle_graph(6) # hexagon\n# g = nx.cycle_graph(7) # heptagon\n# g = nx.cubical_graph() # cubic octamer\n# g = nx.dodecahedral_graph()\n\n\nif \"pos\" in g.nodes[0]:\n # extract the embedded coords in g\n layout = np.array([g.nodes[v][\"pos\"] for v in g])\nelse:\n # estimate of the positions of the nodes\n layout = make_layout(g, edgelen=L)\n\n# set orientations of the hydrogen bonds.\n# if vertexPositions is given, the net dipole moment is minimized.\ndg = genice_core.ice_graph(g, vertexPositions=layout, dipoleOptimizationCycles=100)\n\n# put water molecules\ngro = render(dg, layout, watermodel=tip4p)\nwith open(\"sample.gro\", \"w\") as f:\n f.write(gro)\n```\n",
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