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Crystals

Atomic crystal structures for Julia

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Crystals

The audience for this package should have a need or a want to play with relatively small (DFT/GW scale) crystalline structure from an atomistic point of view. Its purpose is to allow users to build and investigate crystal structures programmatically.

A Crystal declares an atomic crystalline structure, e.g an inifinite periodic arrangement of atoms. The constructor takes at the very least an n by n array defining the periodicity of the crystal, i.e. the crystal cell. The cell must have physical units attached to it.

using Crystals
crystal = Crystal(eye(3)u"nm")
@assert crystal.cell === [1 0 0; 0 1 0; 0 0 1]

However, it can also accept atomic positions and any other array of atomic properties:

using Crystals
crystal = Crystal(eye(2)u"km",
                  position=transpose([1 1; 2 3; 4 5])u"m",
                  species=["Al", "O", "O"],
                  label=[:+, :-, :-])
@assert crystal[:position] == transpose([1 1; 2 3; 4 5])u"m"
@assert crystal[:label] == [:+, :-, :-]

Note that the positions form an n by N array where N is the number of atoms. This is the logical mathematical format when performing matrix operations on the positions. However, from an input point of view, it is easier to think one atom at at time, rather than one coordinate (and all atoms) at a time. Hence the transpose.Similarly, the input-cell is given in matrix format, not in the vector column format of many DFT codes. Do look at the tests and at the sample Lattices for other input formats.

Access to the crystal cell happens via . call, crystal.cell. Atomic properties can be accessed and modified through the square bracket operator.

Several methods are available to manipulate the crystal more extensively (supercell, primitive, space_group, hart_forcade, etc..).

First Commit

05/26/2016

Last Touched

4 days ago

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69 commits

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