Documentation, usability, consistency improvements for v1.0
As discussed in today's meeting we will focus on documentation, usability and consistency improvements for the v1.0 release and not on new features.
This is a sketchy list of some TODO's with some assignees. Feel free to adjust, extend and assign your self
README
say: Maicos doens't have an example section in each module of the documentation to keep our module without plenty of dublicated commands. Instead we refer to our tutorial. Once you understand the basic structure that will be teached there you can work with all modulessay: for the documentation of the main branch (the unstable development version) and older stable version please use our readthedocs documentaion.
@sgravelle
Tutorial sectionInstallationusage from the python interpreter, the current planar analysis notebook.Mention in the beginning that all maicos analysis module will follow the same structure (1. need an atomgroup and some parameters, use the run method for a trajectory analysis. All results are centrally stored in the results object). tell the user if he understands this workflow he can use all maicos modules even if they where not presented and discussed here.usage form the command line, the current entries frominstallation and usage
. maybe add plotting example with xmgrace or gnuplot? We should create a notebook for the cli and instead of python use bash commands. This is easily doable.
Mention in the end that of the command line tutorial that every example from now will be python only but can be equivilanlty used from the cli.
Philospopy
dielectric: as in a review paper @pstaerk @schlaichasaxs @PicoCentauri- 2d rdf general philosophy @kirafischer
how-to:
-
dielectric: deal with every problem that we faced in the last years @hejamu @pstaerk3d vs 2d electrostatics in simulation (see #79 (closed))virtual sitesnot unwrapped trajectories have to be rapaired otherwise you get wrong profiles
-
2d rdf @kirafischer -
saxs @PicoCentauri
@hejamu
Chemical potential doc:put equation and explanation in chemical potential docstringusually it the molecular density and add warning if people want to use atoms
@kirafischer
2D RDF doc:- improve description of mathematical formula
- fix mathematical formula (remove absolute of |z| or change heaviside function)
- maybe add derivation for clarity
@hejamu
Dielectric Modulesdisable zmin
, zmax
etc for dielectric and add a warning: currently
not supported because molecules might be cut in selection process which leads
to severe errors in the profile!
binxxx
paramaters and attributes to bin_xxx
@PicoCentauri
As for example the binmethod
parameter
Edited by Kira Fischer