From a21f4d813c9e525b7ca0d002faa7909ccc36eae9 Mon Sep 17 00:00:00 2001 From: Lars Pastewka Date: Sun, 14 Jan 2024 23:14:33 +0100 Subject: [PATCH] DOC: Added short description of commands --- docs/cli/diffusion.md | 5 +++++ docs/cli/electrochemistry.md | 30 +++++++++++++++--------------- docs/cli/glasses.md | 5 +++++ docs/cli/index.rst | 13 ++++++------- docs/cli/interatomic.md | 5 +++++ 5 files changed, 36 insertions(+), 22 deletions(-) create mode 100644 docs/cli/diffusion.md create mode 100644 docs/cli/glasses.md create mode 100644 docs/cli/interatomic.md diff --git a/docs/cli/diffusion.md b/docs/cli/diffusion.md new file mode 100644 index 00000000..3d26b347 --- /dev/null +++ b/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. diff --git a/docs/cli/electrochemistry.md b/docs/cli/electrochemistry.md index 40417291..262308da 100644 --- a/docs/cli/electrochemistry.md +++ b/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 diff --git a/docs/cli/glasses.md b/docs/cli/glasses.md new file mode 100644 index 00000000..0f9d7d2e --- /dev/null +++ b/docs/cli/glasses.md @@ -0,0 +1,5 @@ +# Glasses + +## Overview of commands + +* `matscipy_quench`: Liquid quench of a glassy structure. diff --git a/docs/cli/index.rst b/docs/cli/index.rst index ab3e1c27..7779c517 100644 --- a/docs/cli/index.rst +++ b/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 \ No newline at end of file + diffusion + electrochemistry + glasses + interatomic \ No newline at end of file diff --git a/docs/cli/interatomic.md b/docs/cli/interatomic.md new file mode 100644 index 00000000..1a99ab21 --- /dev/null +++ b/docs/cli/interatomic.md @@ -0,0 +1,5 @@ +# Interatomic potentials + +## Overview of commands + +* `matscipy_average_eam_potential`: Generate averaged EAM potential for an alloy. \ No newline at end of file