From b2f33670dfdd1264e9e464077ad4a4a5ae6e3069 Mon Sep 17 00:00:00 2001
From: ElliottKasoar <ElliottKasoar@users.noreply.github.com>
Date: Fri, 15 Mar 2024 18:18:10 +0000
Subject: [PATCH] Add examples to README

---
 README.md | 36 +++++++++++++++++++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index b55575e1..1052c0ef 100644
--- a/README.md
+++ b/README.md
@@ -33,7 +33,6 @@ Tools for machine learnt interatomic potentials
 
 The code relies heavily on ASE, unless something else is mentioned.
 
-
 ## Development
 
 1. Install [poetry](https://python-poetry.org/docs/#installation)
@@ -61,6 +60,41 @@ To prevent poetry downgrading ASE when installing in future, add the commit to p
 poetry add git+https://gitlab.com:ase/ase.git#b31569210d739bd12c8ad2b6ec0290108e049eea
 ```
 
+## Examples
+
+Perform a single point calcuation:
+```shell
+janus singlepoint --struct tests/data/NaCl.cif
+```
+
+This will calculate the energy, stress and forces and save this in `NaCl-results.xyz`, in addition to generating a log file, `singlepoint.log`.
+
+Additional options may be specified. For example:
+
+```shell
+janus singlepoint --struct tests/data/NaCl.cif --property energy --arch mace_mp --calc-kwargs "{'model' : './tests/models/mace_mp_small.model'}" --log './example.log' --write-kwargs "{'filename': './example.xyz'}"
+```
+
+This defines the MLIP architecture and path to the saved model, as well as changing where the log and results files are saved.
+
+Note: the MACE calculator currently returns energy, forces and stress together, so in this case the choice of property will not change the output.
+
+
+Perform geometry optimization:
+```shell
+janus geomopt --struct tests/data/H2O.cif
+```
+
+This will calculate optimize the atomic positions and save the resulting structure in `H2O-opt.xyz`, in addition to generating a log file, `geomopt.log`.
+
+Additional options may be specified. This shares most options with `singlepoint`, as well as a few additional options, such as:
+
+```shell
+janus geomopt --struct tests/data/NaCl.cif --fully-opt --vectors-only --traj 'NaCl-traj.xyz'
+```
+
+This allows the cell to be optimised, allowing only hydrostatic deformation, and saves the optimization trajector in addition to the final structure and log.
+
 ## License
 
 [BSD 3-Clause License](LICENSE)