General Utility for crystals
Periodica performs a collection of different tasks for crystals.
Categories:
Here we provide some of the basic functionality for periodica. A crystal structure
file must be provided on the command line, either as a filename or as standard input.
The crystal structure is simply output if no other
commands are provided. Let us use pm-prototype to look at some examles.
# start with perovskite
pm-prototype-xtal --perovskite > xtal.yaml
pm-periodica xtal.yaml
# or we can simply do this
pm-prototype-xtal --perovskite | pm-periodica
In both cases, the output will be:
# Crystal
vec:
[[ 3.91300000, 0.00000000, 0.00000000],
[ 0.00000000, 3.91300000, 0.00000000],
[ 0.00000000, 0.00000000, 3.91300000]]
atoms:
- Sr:
[[ 0.50000000, 0.50000000, 0.50000000]]
- Ti:
[[ 0.00000000, 0.00000000, 0.00000000]]
- O:
[[ 0.50000000, 0.00000000, 0.00000000],
[ 0.00000000, 0.50000000, 0.00000000],
[ 0.00000000, 0.00000000, 0.50000000]]
Basic manipulations of the unit cell can be peformed, like shifting or permuting the atoms.
pm-periodica xtal.yaml --shift-origin 0.5,0.5,0.5 --shift-into-cell --permute-atoms 0,1,3,4,2
# Crystal
vec:
[[ 3.91300000, 0.00000000, 0.00000000],
[ 0.00000000, 3.91300000, 0.00000000],
[ 0.00000000, 0.00000000, 3.91300000]]
atoms:
- Sr:
[[ 0.00000000, 0.00000000, 0.00000000]]
- Ti:
[[ 0.50000000, 0.50000000, 0.50000000]]
- O:
[[ 0.50000000, 0.00000000, 0.50000000],
[ 0.50000000, 0.50000000, 0.00000000],
[ 0.00000000, 0.50000000, 0.50000000]]
Basic information about the lattice can be printed.
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