DOC: Added short description of commands

docs/cli/diffusion.md

@@ -0,0 +1,5 @@
+# Diffusion
+
+## Overview of commands
+
+* `matscipy_rms`: Compute the root-mean-square (rms) displacement on a trajectory file.

docs/cli/electrochemistry.md

@@ -1,46 +1,46 @@
-# Command line interface for the electrochemistry module
+# Electrochemistry
 
 ## Overview of commands
 
-* `poisson-nernst-planck`: Command line interface to the functionality of
+* `matscipy_poisson-nernst-planck`: Command line interface to the functionality of
   `matscipy.electrochemistry.posson_nernst_planck_solver` and
   `matscipy.electrochemistry.posson_nernst_planck_solver_fenics`.
   If available `poisson-nernst-planck` will make use of the third-party
   `FEniCS` finite elements solver, but fall back to our own controlled-volumes
   solver otherwise.
-* `continuous2discrete`: Command line interface to the functionality of
+* `matscipy_continuous2discrete`: Command line interface to the functionality of
   `matscipy.electrochemistry.continuous2discrete`.
-* `stericify`: Command line interface to the functionality of 
+* `matscipy_stericify`: Command line interface to the functionality of 
   `matscipy.electrochemistry.steric_correction`.
 
 ## Usage
 
-`poisson-nernst-planck`, `continuous2discrete` and
-`stericify` executable scripts offer simple command line interfaces
+`matscipy_poisson-nernst-planck`, `matscipy_continuous2discrete` and
+`matscipy_stericify` executable scripts offer simple command line interfaces
 to solve arbitrary (1D) Poisson-Nernst-Planck systems, to sample
 discrete coordinate sets from continuous distributions, and to
 assure steric radii for all coordinate points in a sample.
-Type `poisson-nernst-planck --help`, `continuous2discrete --help`, and 
-`stericify --help` for usage information.
+Type `matscipy_poisson-nernst-planck --help`, `matscipy_continuous2discrete --help`, and 
+`matscipy_stericify --help` for usage information.
 
 A simple sample usage to generate a discrete coordinate set from
 the continuous solution of Poisson-Nernst-Planck equations for
 0.1 mM NaCl aqueous solution across a 100 nm gap and a 0.05 V potential drop
 would look like this
 
-    poisson-nernst-planck -c 0.1 0.1 -u 0.05 -l 1.0e-7 -bc cell --verbose NaCl.txt
-    continuous2discrete --verbose NaCl.txt NaCl.lammps
+    matscipy_poisson-nernst-planck -c 0.1 0.1 -u 0.05 -l 1.0e-7 -bc cell --verbose NaCl.txt
+    matscipy_continuous2discrete --verbose NaCl.txt NaCl.lammps
 
 for PNP solution in plain text file and according coordinate samples LAMMPS
 data file, or like this
 
-    poisson-nernst-planck -c 0.1 0.1 -u 0.05 -l 1.0e-7 -bc cell --verbose NaCl.npz
-    continuous2discrete --verbose NaCl.npz NaCl.xyz
+    matscipy_poisson-nernst-planck -c 0.1 0.1 -u 0.05 -l 1.0e-7 -bc cell --verbose NaCl.npz
+    matscipy_continuous2discrete --verbose NaCl.npz NaCl.xyz
 
 for PNP solution in binary numpy .npz file and coordinate samples in generic
 xyz file, or as a pipeline
 
-    poisson-nernst-planck -c 0.1 0.1 -u 0.05 -l 1.0e-7 -bc cell --verbose | continuous2discrete --verbose > NaCl.xyz
+    matscipy_poisson-nernst-planck -c 0.1 0.1 -u 0.05 -l 1.0e-7 -bc cell --verbose | continuous2discrete --verbose > NaCl.xyz
 
 for text and xyz format streams.
 
@@ -50,8 +50,8 @@ layer region, or implicitly by excluding the compact layer region from the
 computation domain and applying Robin boundary conditions. Latter is the default
 via command line interface.
 
-    poisson-nernst-planck -c 0.1 0.1 -u 0.05 -l 1.0e-7 --lambda-s 5.0e-10 -bc cell-robin --verbose NaCl.npz
+    matscipy_poisson-nernst-planck -c 0.1 0.1 -u 0.05 -l 1.0e-7 --lambda-s 5.0e-10 -bc cell-robin --verbose NaCl.npz
 
 In order to impose a steric radius to the coordinates in some data file, use
 
-    stericify --verbose -r 2.0 -- NaCl.lammps stericNaCl.lammps
+    matscipy_stericify --verbose -r 2.0 -- NaCl.lammps stericNaCl.lammps

docs/cli/glasses.md

@@ -0,0 +1,5 @@
+# Glasses
+
+## Overview of commands
+
+* `matscipy_quench`: Liquid quench of a glassy structure.

docs/cli/index.rst

@@ -1,13 +1,12 @@
 Command line interface
 ======================
 
-`matscipy` provides command line interfaces (CLI) for selected functionality.
-These CLI are not installed per default. Install with the `[cli]` extra, e.g.
-
-  pip install matscipy[cli]
-
-to create all provided CLI scripts.
+`matscipy` provides command line interfaces (CLIs) for selected functionality.
+These CLIs are installed per default and are prefixed with `matscipy_`.
 
 .. toctree::
 
-   electrochemistry
+   diffusion
+   electrochemistry
+   glasses
+   interatomic

docs/cli/interatomic.md

@@ -0,0 +1,5 @@
+# Interatomic potentials
+
+## Overview of commands
+
+* `matscipy_average_eam_potential`: Generate averaged EAM potential for an alloy.