From 967cd26d82aa5c976dc18c570450b90e0aabd3a1 Mon Sep 17 00:00:00 2001
From: "Edgar P. Burkhart" <git@edgarpierre.fr>
Date: Tue, 29 Mar 2022 10:19:33 +0200
Subject: [PATCH 1/3] Updated README with info on processing steps

---
 README.md | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/README.md b/README.md
index bbf17eb..38c524d 100644
--- a/README.md
+++ b/README.md
@@ -5,3 +5,23 @@ displacement at the Artha breakwater on February 28, 2017"
 
 [Report](https://kalliope.edgarpierre.fr/latex/m2cce/internship/report.pdf)
 
+## Bathymetry
+
+* Insert database in `data/data`
+* Run `processing.subdomain` to generate 2D data in a smaller domain
+* Run `processing.projection` to generate a 1D bathymetry
+
+## Swash
+
+* Run `processing.swash` to run the Swash model
+* Run `processing.sws_npz` to convert Swash output to Numpy files
+* Run `processing.post` to plot wave height at a point, water level at an
+	instant, reflection coefficient at a point
+* Run `processing.animate` to plot an animation of water level
+* Run `processing.layers` to plot an animation of layers with flow velocity
+
+## OlaFlow
+
+* Run `processing.bathy` to generate stl input files
+* Run `blockMesh`, `snappyHexMesh -overwrite`, copy `0.org` to `0`, `setFields`
+* Run `processing.sws_ola` to convert Swash output to OlaFlow input

From 0a5596fe63a856b36be0e0bd608f298913324ef9 Mon Sep 17 00:00:00 2001
From: "Edgar P. Burkhart" <git@edgarpierre.fr>
Date: Tue, 29 Mar 2022 13:07:12 +0200
Subject: [PATCH 2/3] Updated README with help on running modules

---
 README.md | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/README.md b/README.md
index 38c524d..e299b6c 100644
--- a/README.md
+++ b/README.md
@@ -5,6 +5,21 @@ displacement at the Artha breakwater on February 28, 2017"
 
 [Report](https://kalliope.edgarpierre.fr/latex/m2cce/internship/report.pdf)
 
+## Configuration
+
+Each part can be run in their respective directories.
+```
+$  python -m processing.swash -h
+usage: swash.py [-h] [-v] [-c CONFIG]
+
+Run swash model
+
+options:
+  -h, --help            show this help message and exit
+  -v, --verbose
+  -c CONFIG, --config CONFIG
+```
+
 ## Bathymetry
 
 * Insert database in `data/data`

From 35ab13bea4456f0c6fba9542c1b9fa2f46a58361 Mon Sep 17 00:00:00 2001
From: "Edgar P. Burkhart" <git@edgarpierre.fr>
Date: Tue, 29 Mar 2022 15:24:17 +0200
Subject: [PATCH 3/3] Added margin option to subdomain config

---
 data/config.ini              | 1 +
 data/processing/subdomain.py | 5 +++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/data/config.ini b/data/config.ini
index 6fd5983..b9b2d50 100644
--- a/data/config.ini
+++ b/data/config.ini
@@ -8,6 +8,7 @@ psize=Psize.dat
 hires_step=0.5
 
 [out]
+margin=0.005
 #no_breakwater=True
 root=out
 sub=bathy_sub.npy
diff --git a/data/processing/subdomain.py b/data/processing/subdomain.py
index 06e3c16..8ccc6a4 100644
--- a/data/processing/subdomain.py
+++ b/data/processing/subdomain.py
@@ -26,8 +26,9 @@ domain = np.stack((artha, buoy))
 domain.sort(axis=0)
 log.debug(f"domain: {domain}")
 
-domain[0] -= 0.002
-domain[1] += 0.002
+margin = config.getfloat("out", "margin", default=0.002)
+domain[0] -= margin
+domain[1] += margin
 log.debug(f"domain: {domain}")
 
 inp_root = pathlib.Path(config.get("inp", "root"))