Software for generating a lattice from a unit cell for molecular crystals?

Question

I am looking for a software package which can take a unit cell (and lattice parameters, etc.) and from that generate a crystal lattice. Ideally it will have functionality for orthorhombic, hexagonal, and other types of unit cells which are slightly less trivial than a cubic lattice.

Finally, it should work for molecular crystals.

I have seen the ASE lattice class (https://wiki.fysik.dtu.dk/ase/ase/lattice.html), but it isn't so clear to me how to define a lattice for a system when the unit cell is quite large.

As an example, I have a unit cell for a clathrate hydrate which contains 68 water molecules and I want to generate a lattice from this unit cell. How would one usually go about doing this?

My guess is that one way around this is to use some kind of MD package and just give the unit cell along with the lattice parameters and the type of lattice. Then, after applying periodic boundary conditions, somehow get the package to print out the coordinates of atoms beyond just the original unit cell. This feels a bit hacky to me, but if this is normal and someone knows a relatively simple way to do this, then let me know. Answers involving either open-source or purchasable software are acceptable, although open-source is always preferred :)

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As an aside, it seems to me that it may not be too hard to just write code to do this for my specific cases, so if anyone has a good reference for generating the lattice given the type of unit cell, lattice parameters, and a set of Cartesian coordinates, that would also be helpful.

Answer 1

In addition to the presentations about CCDC Mercury and Vesta by @andselisk here and later mine about Avogadro could be extended. As described earlier, Avogadro's capability to read .cif files about crystallographic models allows you to extend these via the slab builder to any extent you need (GUI entry Crystallography -> Build -> Slab) and to export them either as normal .xyz file, or (via the extension tab, template assisted) in one of multiple formats recognized by quantum chemical programs (e.g., Gaussian, GAMESS-UK, MOPAC).

It equally is possible to start from scratch with a cubic unit cell of 3 Å. Subsequently, you would alter the lattice parameters ($a, b, c; \alpha, \beta, \gamma$) and enter atoms one, after the other, either in cartesian coordinates (either Angstrom, Bohr, nm or pm), or in fractional atomic coordinates as typically in .cif files. You may wrap the atoms into the cell, and of course impose one of the space group symmetries to fill your cell, too. You may symmetrize your constructed unit cell and reset (within tolerances you determine) into a standard setting, too. Equally than just reading a .cif,.pdb, or .xyz, these constructed unit cells may be extended with the slab builder, and equally may be exported in one of the computer chemistry formats mentioned earlier, too.

Answer 2

You might also look into Force Field X 'Crystal' module (https://ffx.biochem.uiowa.edu/modules/crystal/index.html), unit conventions can be found here (https://ffx.biochem.uiowa.edu/properties-spacegroup.html).

Also, I feel it's important to mention that the code is open source and freely available, useful if you're interested in exactly how the calculations are performed: the procedure outlined by https://chemistry.stackexchange.com/users/1782/buttonwood is very similar, if not identical, to the implementation, IIRC.

Cheers!