From d19d17fdf703dcf9c1299ee99a724bcb43d07c65 Mon Sep 17 00:00:00 2001
From: Chazeon <chenxing.luo@gmail.com>
Date: Sat, 2 Jan 2021 11:56:00 -0500
Subject: [PATCH] Update README

---
 README.md | 71 ++++++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 52 insertions(+), 19 deletions(-)

diff --git a/README.md b/README.md
index fe855cd..193166c 100644
--- a/README.md
+++ b/README.md
@@ -4,45 +4,78 @@ Calculate high temperature thermal elasticity in Python.
 
 ## Installation
 
-### Additional information
-
-Pint need to be updated to the GitHub master branch for the code to work with atomic units, so it is installed from GitHub.
+The package can be installed with `pip` package manager.
 
 ## Usage
 
-### Configuration file
+### Command-line programs
+
+The packge is shipped with the following command-line programs:
+
+- **`qha-cij`**         - Perform SAM-Cij calculation.
+- **`qha-cij-static`** - Calculate elastic moduli and acoustic velocities.
+- **`qha-cij-extract`**     - Extract the value and create table for multiple variables at spcific P or T.
+- **`qha-cij-fill`**        - Fill non-zero Cij terms based on symmetry.
+- **`qha-cij-modes`**       - Plot interpolated mode frequency vs volume.
+- **`qha-cij-plot`**        - Plot SAM-Cij calculation results.
+
+And is avaliable as sub-commands of the `cij` program:
+
+
+```
+Usage: cij [OPTIONS] COMMAND [ARGS]...
+
+Options:
+  --version  Show the version and exit.
+  --help     Show this message and exit.
+
+Commands:
+  extract     Extract the value and create table for multiple variables at...
+  fill        Fill non-zero Cij terms based on symmetry.
+  modes       Plot interpolated mode frequency vs volume.
+  plot        Plot SAM-Cij calculation results.
+  run         Perform SAM-Cij calculation.
+  run-static  Calculate elastic moduli and acoustic velocities.
+```
+
+### SAM-Cij calculations with `qha-cij` or `cij run`
+
+#### Configuration file
 
 ```yml
 qha:
   input: input01
   settings:
-    # QHA INPUT FILE HERE ...
+    # QHA settings here ...
 elast:
   input: elast.dat
-settings:
-  mode_gamma:
-    # Refer to cij.core.mode_gamma
-    interpolator: spline
-    order: 5
-  cij_keys: [11, 22, 33, 12, 13, 23, 44, 55, 66]
-  disable_phonon_contribution: False
+  settings:
+    mode_gamma:
+      interpolator: spline
+      order: 5
+    symmetry: cubic
 ```
 
-### Command line arguments
+#### Command line arguments
 
 ```txt
-usage: qha-cij [-h] [-V] CONF.yml
+Usage: cij run [OPTIONS] SETTINGS_FILENAME
 
-positional arguments:
-  CONF.yml       name of the configuration file
+  Perform SAM-Cij calculation.
 
-optional arguments:
-  -h, --help     show this help message and exit
-  -V, --version  show program's version number and exit
+Options:
+  --version                       Show the version and exit.
+  --debug [CRITICAL|ERROR|WARNING|INFO|DEBUG|NOTSET]
+                                  Logging level
+  --help                          Show this message and exit.
 ```
 
 ## Documentation
 
+See [GitHub pages][1].
+
+[1]: https://mineralscloud.github.io/qha-cij
+
 ## Author
 
 The code in this repo is initially authored by Chenxing Luo.