Similar in spirit to the alumina example, here we create a single ice Ih crystal from the crystal information, and then replicate it to form a larger supercell. The crystal information used below is from Leadbetter et al., J. Chem. Phys., 82, 424 (1985), Table II (Structural parameters of ice at 5 K).
First, we create the unit cell, which from the paper is orthorhombic with side lengths A = 4.5019, B = 7.7978, and C = 7.328 Å. There are five symmetry-unique atoms to add into the cell. This might seem odd given that this doesn't add up to a whole number of water molecules, but one of the water molecules lays with its oxygen on a mirror plane, and so only needs one hydrogen to be specified. Atom positions in the paper are given in fractional coordinates - we will create the atoms using these coordinates which will be converted by Aten into their real (cell) coordinates automatically.
On the Build Panel change the drawing Element to oxygen, and then open the Add Atom tool. We will specify the new atoms in fractional cell coordinates, so make sure that the Fractional checkbox is ticked.
Add oxygen atoms at the following positions:
Change the Element to hydrogen and add hydrogen atoms at the following positions:
The cell should now look like this:
Back on the Cell Panel we now must set the correct spacegroup for the model, so that the full unit cell can be generated from the set of symmetry-unique atoms we have just entered. On the Define tool we can set the correct spacegroup (Cmc21) for the model - in the Set / Lookup section you can either choose the correct spacegroup from the drop-down list, or enter the name or number (36, in this case) for the spacegroup required. Once selected, press Set to assign it to the model, then press Pack to pack the unit cell with symmetry-generated atoms.
Finally, click Rebond on the Build Panel.
To complete the model the spacegroup of the crystal must be set so that generation of the symmetry-related atoms can be performed.
The basic cell of ice Ih isn’t particularly interesting by itself, so we will replicate the cell to create a larger supercell, and then calculate bonds in the new model so that the hexagonal structure is clear to see.
On the Build Panel long-press the Replicate tool and enter positive replication values of, say, 6 for x, 2 for y, and 2 for z. Close the tool, then single click the Replicate to create the supercell. The bonding will now not be pretty, so hit Rebond as well.
# Create periodic model newModel("ice"); cell(4.5019,7.7978,7.3280,90,90,90); # Add symmetry-unique atoms newAtomFrac(O,0,0.6648,0.0631); newAtomFrac(O,0.5,0.8255,-0.0631); newAtomFrac(H,0,0.6636,0.1963); newAtomFrac(H,0,0.5363,0.0183); newAtomFrac(H,0.6766,-0.2252,-0.0183); # Set spacegroup, pack, replicate, and rebond spacegroup("Cmc21"); pack(); replicate(0,0,0,6,2,2); rebond();