Adds post-process cli guide, specifying vafs by element name

[harveydevereux]

I found I could not easily request partial VAFs on the CLI by element names (or StartStopStep likes). But instead would have to write all the indices down, which can be automated in shell but is quite unwieldy. So I implemented selecting vaf atoms by element name. Hopefully a useful addition.

Partial VAFs can be obtained in the CLI like so,

janus md --ensemble nve --struct tests/data/NaCl.cif --steps 100 --traj-every 10\
 --post-process-kwargs "{'vaf_compute': True, 'vaf_atoms': (('Na',), ('Cl',)), 'vaf_output_files': ('vaf_na.dat', 'vaf_cl.dat')}"

where 'Na' and 'Cl' are expanded to indices of those elements in the trajectory.

Also add some documentation for post-processing.

[ElliottKasoar]

Looks helpful, thanks! The documentation is great!

Added a few minor comments from a quick first look.

Quick question that's related, but not new to this: do you think we may want to rename filter_atoms to atoms_filter? To me, filter_atoms sounds more like a boolean.

[harveydevereux]

Looks helpful, thanks! The documentation is great!

Added a few minor comments from a quick first look.

Quick question that's related, but not new to this: do you think we may want to rename filter_atoms to atoms_filter? To me, filter_atoms sounds more like a boolean.

Looks helpful, thanks! The documentation is great!

Added a few minor comments from a quick first look.

Quick question that's related, but not new to this: do you think we may want to rename filter_atoms to atoms_filter? To me, filter_atoms sounds more like a boolean.

I can see that yes so might as well unless anyone can think of a better name

[ElliottKasoar]

I think we might want to handle invalid symbols more nicely. If I ask for "abc" instead of "Cl":

janus md --ensemble nve --struct tests/data/NaCl.cif --steps 100 --traj-every 10 --post-process-kwargs "{'vaf_compute': True, 'vaf_atoms': (('abc',), ('Cl',)), 'vaf_output_files': ('vaf_na.dat', 'vaf_cl.dat')}"

I get TypeError: 'numpy.float64' object is not iterable, which is quite strange.

[harveydevereux]

fix user guide typos

[harveydevereux]

I think we might want to handle invalid symbols more nicely. If I ask for "abc" instead of "Cl":

janus md --ensemble nve --struct tests/data/NaCl.cif --steps 100 --traj-every 10 --post-process-kwargs "{'vaf_compute': True, 'vaf_atoms': (('abc',), ('Cl',)), 'vaf_output_files': ('vaf_na.dat', 'vaf_cl.dat')}"

I get TypeError: 'numpy.float64' object is not iterable, which is quite strange.

now checked, and also in tests should recieve

ValueError: {'abc'} not allowed in VAF, allowed symbols are {'Cl', 'Na'}