diff --git a/README.md b/README.md
index 5279273..742507d 100644
--- a/README.md
+++ b/README.md
@@ -5,31 +5,101 @@ displacement at the Artha breakwater on February 28, 2017"
 
 [Report](https://kalliope.edgarpierre.fr/latex/m2cce/internship/report.pdf)
 
-## Structure
+## Configuration
 
-Le projet est séparé en dossiers pour chaque partie. Les dossiers sont les suivants:
+Each part can be run in their respective directories.
+```
+$  python -m processing.swash -h
+usage: swash.py [-h] [-v] [-c CONFIG]
 
-`data`
-: Données d'entrée et traitement (données bouée, bathymétrie)
+Run swash model
 
-`jngcgc`
-: Article pour la Journée Nationale Génie Côtier Génie Civil
+options:
+  -h, --help            show this help message and exit
+  -v, --verbose
+  -c CONFIG, --config CONFIG
+```
 
-`nature`
-: Article pour Nature Communications
+## Bathymetry
 
-`olaflow`
-: Modèle 2Dv VOF VARANS Olaflow
+Configuration:
+```
+[inp]
+root: input directory
+base: bathymetry database (.xyz) -- not provided in this repository
+hires: 1d hires smoothed breakwater profile (.dat)
+hstru: 1d hires smoothed breakwater porosity height (.dat)
+poro: 1d breakwater porosity (.dat)
+psize: 1d porosity size (.dat)
+hires_step: mesh sizing of 1d profile
 
-`report`
-: Résultats intermédiaires et bibliographie
+[out]
+margin: margin around the buoy and breakwater for subdomain
+no_breakwater: option to remove breakwater
+root: output directory
+sub: output file for subdomain
+out: output file for 1d projection
+step: mesh size
+left: margin for 1d projection (breakwater side)
+right: margin for 1d projection (buoy side)
 
-`swash`
-: Modèle 1D NLSW Swash
+[artha]
+lat: latitude of the breakwater
+lon: longitude of the breakwater
 
-## Fonctionnement
+[buoy]
+lat: latitude of the buoy
+lon: longitude of the buoy
+```
 
-Dans chaque dossier se trouve un fichier `README.md` détaillant son fonctionnement.
+* Insert database in `data/data`
+* Run `processing.subdomain` to generate 2D data in a smaller domain
+* Run `processing.projection` to generate a 1D bathymetry
 
-Les scripts Python sont regroupés dans un dossier `processing`, et généralement exécutables en fonctionnement module :
-`python -m processing.script`.
+## Swash
+
+Configuration:
+```
+[data]
+out: input directory (output of bathymetry)
+
+[swash]
+input: swash input file (.sws)
+path: path to swash directory (should contain swashrun and swash.exe)
+out: output directory for swash (created at the end of the computation)
+mpi: number of mpi threads (omit to use serial)
+
+[post]
+inp: input directory for post-processing (output of sws_npz)
+compare: input directory for post-processing comparison (omit to display results from single case)
+out: output directory for figures
+x0: position of reflection calculations
+t0: minimum time for reflection calculations (necessary because of boundary condition ramping)
+```
+
+* 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
+
+Configuration:
+```
+[swash]
+np_out: input of olaflow from swash (output of sws_npz)
+
+[bathy]
+bathy: bathymetry to be used by olaflow
+hstru: height of porous domain (see bathy)
+scale: openscad scaling (mesh sizing in [x,y,z])
+out: output folder for stl bathymetry
+
+[olaflow]
+root: olaflow computation directory
+```
+
+* Run `processing.bathy` to generate stl input files
+* Run `run_ola.sh` to run OlaFlow model
diff --git a/data/README.md b/data/README.md
deleted file mode 100644
index 427326a..0000000
--- a/data/README.md
+++ /dev/null
@@ -1,169 +0,0 @@
-# Data
-
-Ce dossier regroupe les données d'entrée et les scripts de pré-traitement des données.
-
-## Configuration initiale
-
-Afin de limiter l'espace utilisé, le fichier de bathymétrie n'est pas fourni. Il est recommandé d'utiliser la base de
-donnée construite par V. Roeber.
-
-Les scripts de ce dossier sont configurés à l'aide d'un fichier `config.ini`. Les options seront détaillées pour chaque
-script par la suite.
-
-## Scripts
-### Lambert
-`lambert.py` contient une classe permettant de réaliser la projection en coordonnées cartésiennes de la bathymétrie en
-coordonnées sphériques.
-
-### Nandasena
-`nandasena.py` permet de calculer le critère de déplacement de bloc de Nandasena (2011). Configuration dans le code
-directement en modifiant le contenu de la variable `const`.
-
-### Orbitals
-`orbitals.py` permet de tracer la trajectoire de la bouée lors du passage de la vague scélérate identifiée en 2 et 3
-dimensions.
-
-```python -m processing.orbitals [-c CONFIG] [-v]```
-
-* `-c CONFIG` : choix d'un fichier de configuration (`.ini`)
-* `-v` : verbose
-
-```
-[inp]
-root : racine des fichiers d'entrée
-raw_ts : liste des chemins vers les fichiers de données brutes de la bouée
-
-[out]
-root : racine des fichiers de sortie
-```
-
-### Plot
-`plot.py` permet de tracer la bathymétrie locale en 2 dimensions.
-
-```python -m processing.plot [-c CONFIG] [-v]```
-
-* `-c CONFIG` : choix d'un fichier de configuration (`.ini`)
-* `-v` : verbose
-
-```
-[inp]
-root : racine des fichiers d'entrée
-
-[out]
-root : racine des fichiers de sortie
-sub : sous-domaine de bathymétrie, doit être généré avec subdomain
-```
-
-### Projection
-`projection.py` utilise le module `lambert` afin de réaliser une projection 1D en coordonnées cartésiennes de la
-bathymétrie en coordonnées sphériques, en utilisant les données haute-résolution de PA Poncet pour la digue.
-
-```python -m processing.projection [-c CONFIG] [-v]```
-
-* `-c CONFIG` : choix d'un fichier de configuration (`.ini`)
-* `-v` : verbose
-
-```
-[inp]
-root : racine des fichiers d'entrée
-hires : bathymétrie haute-résolution (PA Poncet)
-hstru : hauteur de poreux (PA Poncet)
-poro : porosité (PA Poncet)
-psize : taille de porosité (PA Poncet)
-hires_step : résolution des données hires
-
-[out]
-root : racine des fichiers de sortie
-no_breakwater* : enlever la digue (défaut : False)
-sub : sous-domaine de bathymétrie, doit être généré avec subdomain
-step : résolution du domaine de sortie
-left : marge après la digue sur le domaine de sortie
-right : marge après la bouée sur le domaine de sortie
-
-[artha]
-lat : latitude de la digue
-lon : longitude de la digue
-
-[buoy]
-lat : latitude de la bouée
-lon : longitude de la bouée
-```
-
-### Spec
-`spec.py` permet de générer un spectre d'entrée de SWASH à partir du spectre mesuré par la bouée.
-
-```python -m processing.spec [-c CONFIG] [-v]```
-
-* `-c CONFIG` : choix d'un fichier de configuration (`.ini`)
-* `-v` : verbose
-
-```
-[inp]
-root : racine des fichiers d'entrée
-raw_spec : fichier de spectre à utiliser
-cycle : durée d'utilisation du spectre
-
-[out]
-root : racine des fichiers de sortie
-```
-
-### Subdomain
-`subdomain.py` permet de générer un sous-domaine de la bathymétrie pour utilisation avec `plot` et `projection`.
-
-```python -m processing.projection [-c CONFIG] [-v]```
-
-* `-c CONFIG` : choix d'un fichier de configuration (`.ini`)
-* `-v` : verbose
-
-```
-[inp]
-root : racine des fichiers d'entrée
-base : base de données de bathymétrie (V Roeber)
-
-[out]
-margin : marges (en degrés) autour des positions de la bouée et de la digue
-root : racine des fichiers de sortie
-sub : fichier de sortie du sous-domaine de bathymétrie
-
-[artha]
-lat : latitude de la digue
-lon : longitude de la digue
-
-[buoy]
-lat : latitude de la bouée
-lon : longitude de la bouée
-```
-
-### TS
-`ts.py` permet de générer une série temporelle pour SWASH à partir de plusieurs série temporelles brutes de la bouée.
-
-```python -m processing.ts [-c CONFIG] [-v]```
-
-* `-c CONFIG` : choix d'un fichier de configuration (`.ini`)
-* `-v` : verbose
-
-```
-[inp]
-root : racine des fichiers d'entrée
-raw_ts : liste des fichiers de données brutes de la bouée à utiliser
-
-[out]
-root : racine des fichiers de sortie
-```
-
-### Zero-cross
-`zero_cross.py` permet d'obtenir les vagues les plus grosses de toutes les séries temporelles et d'obtenir la
-transformée en ondelettes de la série.
-
-```python -m processing.zero_cross [-c CONFIG] [-v]```
-
-* `-c CONFIG` : choix d'un fichier de configuration (`.ini`)
-* `-v` : verbose
-
-```
-[inp]
-root : racine des fichiers d'entrée (les données brutes doivent être dans le sous-dossier `cerema/raw`)
-
-[out]
-root : racine des fichiers de sortie
-```
diff --git a/data/config2.ini b/data/config2.ini
deleted file mode 100644
index ebda150..0000000
--- a/data/config2.ini
+++ /dev/null
@@ -1,29 +0,0 @@
-[inp]
-root=data
-base=Database_20220224.xyz
-hires=bathyhires.dat
-hstru=Hstru.dat
-poro=Poro.dat
-psize=Psize.dat
-raw_ts=cerema/raw/201702281700.raw
-raw_spec=cerema/spt/201702281715.spt
-hires_step=0.5
-cycle=14400
-
-[out]
-margin=0.005
-#no_breakwater=True
-root=out2
-sub=bathy_sub.npy
-out=bathy.npy
-step=1
-left=-300
-right=150
-
-[artha]
-lat=43.398450
-lon=-1.673097
-
-[buoy]
-lat=43.408333
-lon=-1.681667
diff --git a/data/photos.md b/data/photos.md
deleted file mode 100644
index 5d33b18..0000000
--- a/data/photos.md
+++ /dev/null
@@ -1,65 +0,0 @@
-# Times
-## Block Displacement
-18:28:12
-## Previous
-18:27:39
-## Next
-18:28:28
-## Other Waves
-18:25:01
-18:23:13
-18:22:55
-18:22:00
-18:09:08
-18:08:43
-18:08:27
-18:07:18
-18:04:37
-17:59:08
-17:58:31
-17:54:15
-17:53:55
-17:53:39
-17:47:53
-17:39:40
-17:38:45
-17:38:28
-17:32:06
-17:31:46
-17:26:06
-17:25:12
-17:24:47
-17:23:55
-17:23:18
-
-# Periods
-## Block Displacement
-### Before
-33
-### After
-16
-## Other Waves
-
-18
-
-
-25
-16
-
-
-
-37
-
-20
-16
-
-
-
-17
-
-20
-
-
-25
-
-37
diff --git a/data/processing/nandasena.py b/data/processing/nandasena.py
deleted file mode 100644
index 298f20b..0000000
--- a/data/processing/nandasena.py
+++ /dev/null
@@ -1,27 +0,0 @@
-import numpy as np
-
-def u_nandasena(b, c, C_d, C_l, rho_s, rho_w=1e3, theta=0, g=9.81, **_):
-    return np.sqrt(
-        (2 * (rho_s/rho_w - 1) * g * c * np.cos(np.radians(theta)))
-        / C_l
-    )
-
-
-const = {
-    "a": 4,
-    "b": 2.5,
-    "c": 2,
-    "C_d": 1.95,
-    "C_l": 0.178,
-    "theta": 0,
-    "rho_s": 2.7e3,
-}
-
-u = u_nandasena(**const)
-u_ola = 14.5
-print(f"Nandasena: u={u:5.2f}m/s")
-print(f"Olaflow:   u={u_ola:5.2f}m/s")
-print(f"Gap:      du={abs(u_ola - u):5.2f}m/s")
-print(f"Gap:      du={abs(u_ola - u)/u:5.2%}")
-print(f"Gap:      du={abs(u_ola - u)/u_ola:5.2%}")
-
diff --git a/data/processing/orbitals.py b/data/processing/orbitals.py
index 6039d3c..884ecfa 100644
--- a/data/processing/orbitals.py
+++ b/data/processing/orbitals.py
@@ -4,7 +4,6 @@ import logging
 import pathlib
 
 import matplotlib.pyplot as plt
-from matplotlib.ticker import MultipleLocator
 import numpy as np
 
 parser = argparse.ArgumentParser(description="Plot orbitals")
@@ -22,6 +21,8 @@ config.read(args.config)
 inp_root = pathlib.Path(config.get("inp", "root"))
 out_root = pathlib.Path(config.get("out", "root"))
 
+out_ts = out_root.joinpath("ts.dat")
+
 raw_ts = []
 for tsi in config.get("inp", "raw_ts").split(","):
     raw_ts.append(
@@ -80,23 +81,18 @@ ax3d.quiver3D(
 ax3d.set(xlabel="x (cm)", ylabel="y (cm)", zlabel="z (cm)")
 
 theta = np.angle(raw_ts["x"] + 1j * raw_ts["y"]).mean()
-fig2dv, ax2dv = plt.subplots(figsize=(5/2.54, 2/3*10/2.54), dpi=200, constrained_layout=True)
+fig2dv, ax2dv = plt.subplots()
 x0 = ts_flt["x"] * np.cos(theta) + ts_flt["y"] * np.sin(theta)
-#ax2dv.plot(x0, z0, c="#0066ff", lw=1)
+ax2dv.plot(x0, z0, c="#0066ff", lw=1)
 ax2dv.quiver(
-    x0[:-1] * 1e-2,
-    z0[:-1] * 1e-2,
-    np.diff(x0)[:] * 1e-2,
-    np.diff(z0)[:] * 1e-2,
-    color="k",
-    scale_units="xy",
-    scale=1,
+    x0[:-1],
+    z0[:-1],
+    np.diff(x0)[:],
+    np.diff(z0)[:],
+    color="#0066ff",
 )
-ax2dv.grid(c="k", alpha=.2)
-ax2dv.set(aspect="equal", xlabel="x (m)", ylabel="z (m)")
-ax2dv.set(ylim=(-10, 10))
-ax2dv.yaxis.set_minor_locator(MultipleLocator(1))
-fig2dv.savefig(out_root.joinpath("orbitals.pdf"))
-fig2dv.savefig(out_root.joinpath("out_orbitals.jpg"))
+ax2dv.grid()
+ax2dv.set(aspect="equal")
+fig2dv.savefig("out_orbitals.pdf")
 
 plt.show()
diff --git a/data/processing/plot.py b/data/processing/plot.py
deleted file mode 100644
index 0ee1c12..0000000
--- a/data/processing/plot.py
+++ /dev/null
@@ -1,71 +0,0 @@
-import argparse
-import configparser
-import logging
-import pathlib
-
-import numpy as np
-from scipy import interpolate
-
-import matplotlib.pyplot as plt
-
-from .lambert import Lambert
-
-parser = argparse.ArgumentParser(description="Pre-process bathymetry")
-parser.add_argument("-v", "--verbose", action="count", default=0)
-parser.add_argument("-c", "--config", default="config.ini")
-args = parser.parse_args()
-
-logging.basicConfig(level=max((10, 20 - 10 * args.verbose)))
-log = logging.getLogger("bathy")
-
-log.info("Starting bathymetry pre-processing")
-config = configparser.ConfigParser()
-config.read(args.config)
-
-inp_root = pathlib.Path(config.get("inp", "root"))
-out_root = pathlib.Path(config.get("out", "root"))
-bathy_inp = out_root.joinpath(config.get("out", "sub"))
-
-log.info(f"Loading bathymetry from {bathy_inp}")
-bathy_curvi = np.load(bathy_inp)
-
-projection = Lambert()
-bathy = np.stack(
-    (
-        *projection.cartesian(bathy_curvi[:, 0], bathy_curvi[:, 1]),
-        bathy_curvi[:, 2],
-    ),
-    axis=1,
-)
-log.debug(f"Cartesian bathy: {bathy}")
-
-artha_curvi = np.array(
-    (config.getfloat("artha", "lon"), config.getfloat("artha", "lat"))
-)
-buoy_curvi = np.array((config.getfloat("buoy", "lon"), config.getfloat("buoy", "lat")))
-
-artha = np.asarray(projection.cartesian(*artha_curvi))
-buoy = np.asarray(projection.cartesian(*buoy_curvi))
-
-bathy[:, :2] = bathy[:, :2] - artha
-
-fig, ax = plt.subplots(figsize=(6 / 2.54, 5 / 2.54), constrained_layout=True, dpi=200)
-
-c = ax.tricontourf(
-    bathy[:, 0],
-    bathy[:, 1],
-    bathy[:, 2],
-    cmap="plasma",
-    levels=np.arange(-30, 10, 5),
-    extend="both",
-)
-ax.plot(*(np.stack((artha, buoy)) - artha).T, lw=1, ls="-.", c="k", marker="x")
-ax.set(xlim=(bathy[np.argmax(bathy[:, 1]), 0], bathy[np.argmin(bathy[:, 1]), 0]))
-ax.set(ylim=(bathy[np.argmin(bathy[:, 0]), 1], bathy[np.argmax(bathy[:, 0]), 1]))
-ax.set(xlabel="x (m)", ylabel="y (m)")
-fig.colorbar(c, label="z (m)")
-ax.set_aspect("equal")
-ax.set_rasterization_zorder(1.5)
-
-fig.savefig(out_root.joinpath("bathy2d.pdf"))
-plt.show()
diff --git a/data/processing/projection.py b/data/processing/projection.py
index 1afabf6..0aa1e16 100644
--- a/data/processing/projection.py
+++ b/data/processing/projection.py
@@ -60,12 +60,6 @@ x = np.arange(
 )
 theta = np.angle(D.dot((1, 1j)))
 
-log.info(f"N points: {bathy.size:e}")
-S = bathy[:, 0].ptp() * bathy[:, 1].ptp()
-log.info(f"Surface: {S*1e-6:.2f}km^2")
-res = np.sqrt(S / bathy.size)
-log.info(f"Resolution: {res:.2f}m")
-
 coords = artha + (x * np.stack((np.cos(theta), np.sin(theta)))).T
 
 log.info("Interpolating bathymetry in 1D")
@@ -137,12 +131,8 @@ np.savetxt(out_root.joinpath("hstru.dat"), hstru[::-1], newline=" ")
 np.savetxt(out_root.joinpath("poro.dat"), poro[::-1], newline=" ")
 np.savetxt(out_root.joinpath("psize.dat"), psize[::-1], newline=" ")
 
-fig, ax = plt.subplots(figsize=(16 / 2.54, 2 / 3 * 10 / 2.54), constrained_layout=True)
+fig, ax = plt.subplots()
 ax.plot(-x, z, color="k")
 ax.fill_between(-x, z + hstru, z, color="k", alpha=0.2)
-#ax.set_title(f"N={z.size-1}, x=[{-x.max()};{-x.min()}]")
-ax.set(ylim=(-40, 15))
-ax.set(xlabel="x (m)", ylabel="z (m)")
-ax.autoscale(True, "x", True)
-ax.grid()
+ax.set_title(f"N={z.size-1}, x=[{-x.max()};{-x.min()}]")
 fig.savefig(out_root.joinpath("bathy.pdf"))
diff --git a/data/processing/spec.py b/data/processing/spec.py
index 37665b9..b8a4b03 100644
--- a/data/processing/spec.py
+++ b/data/processing/spec.py
@@ -8,13 +8,14 @@ import numpy as np
 from scipy.interpolate import griddata
 
 parser = argparse.ArgumentParser(description="Pre-process time-series")
+parser.add_argument("-v", "--verbose", action="count", default=0)
 parser.add_argument("-c", "--config", default="config.ini")
 args = parser.parse_args()
 
 logging.basicConfig(level=max((10, 20 - 10 * args.verbose)))
 log = logging.getLogger("bathy")
 
-log.info("Starting pre-processing")
+log.info("Starting time-series pre-processing")
 config = configparser.ConfigParser()
 config.read(args.config)
 
@@ -44,7 +45,7 @@ if cycle is None:
     f = inp["f"]
     S = inp["S"] * Sm
 else:
-    f = np.arange(inp["f"].min(), inp["f"].max() + 1 / cycle, 1 / cycle)
+    f = np.arange(inp["f"].min(), inp["f"].max() + 1/cycle, 1/cycle)
     S = griddata(inp["f"], inp["S"] * Sm, f)
 
 with out_spec.open("w") as out:
diff --git a/data/processing/ts.py b/data/processing/ts.py
index aacbb81..1a9af04 100644
--- a/data/processing/ts.py
+++ b/data/processing/ts.py
@@ -4,7 +4,6 @@ import logging
 import pathlib
 
 import matplotlib.pyplot as plt
-from matplotlib.ticker import MultipleLocator
 import numpy as np
 
 parser = argparse.ArgumentParser(description="Pre-process time-series")
@@ -26,14 +25,12 @@ out_ts = out_root.joinpath("ts.dat")
 
 raw_ts = []
 for tsi in config.get("inp", "raw_ts").split(","):
-    raw_ts.append(
-        np.loadtxt(
-            inp_root.joinpath(tsi),
-            dtype=[("state", int), ("z", float), ("y", float), ("x", float)],
-            delimiter=",",
-            max_rows=2304,
-        )
-    )
+    raw_ts.append(np.loadtxt(
+        inp_root.joinpath(tsi),
+        dtype=[("state", int), ("z", float), ("y", float), ("x", float)],
+        delimiter=",",
+        max_rows=2304,
+    ))
 n = len(raw_ts)
 raw_ts = np.concatenate(raw_ts)
 log.debug(f"{raw_ts=}")
@@ -42,43 +39,13 @@ if (errs := np.count_nonzero(raw_ts["state"])) != 0:
     log.warning(f"{errs} transmission errors!")
     log.debug(f"{dict(zip(*np.unique(raw_ts['state'], return_counts=True)))}")
 
-t = np.linspace(0, 30 * 60 * n, 2304 * n + 1)[:-1]
+t = np.linspace(0, 30 * 60 * n, 2304*n+1)[:-1]
 log.debug(f"{t=}")
 
 log.info(f"Saving timeseries to '{out_ts}'")
-np.savetxt(out_ts, np.stack((t, raw_ts["z"] / 100), axis=1))
+np.savetxt(out_ts, np.stack((t, raw_ts["z"]/100), axis=1))
 
-fig, ax = plt.subplots(figsize=(8 / 2.54, 2 / 3 * 10 / 2.54), constrained_layout=True)
-tp = np.datetime64("2017-02-28T17:00:00") + t.astype(np.timedelta64)[-(t.size // 3) :]
-ax.plot(
-    tp,
-    raw_ts["z"][-(t.size // 3) :] * 1e-2,
-    color="k",
-    lw=1,
-)
-ax.axvline(
-    np.datetime64("2017-02-28T17:00:00") + np.timedelta64(23 * 60 + 8),
-    color="k",
-    alpha=0.1,
-    lw=20,
-)
-ax.autoscale(True, "x", True)
-ax.set(xlabel="t (s)", ylabel="z (m)")
-yabs_max = abs(max(ax.get_ylim(), key=abs))
-ax.set(ylim=(-10, 10))
-ax.set(
-    xticks=(
-        np.datetime64("2017-02-28T17:20:00"),
-        np.datetime64("2017-02-28T17:25:00"),
-        np.datetime64("2017-02-28T17:30:00"),
-    ),
-    xticklabels=(
-        "17:20",
-        "17:25",
-        "17:30",
-    ),
-)
-ax.yaxis.set_minor_locator(MultipleLocator(1))
-ax.grid(color="k", alpha=0.2)
+fig, ax = plt.subplots()
+ax.plot(t, raw_ts["z"])
+ax.set(xlabel="t (s)", ylabel="z (cm)")
 fig.savefig(out_root.joinpath("ts.pdf"))
-fig.savefig(out_root.joinpath("ts.jpg"), dpi=200)
diff --git a/data/processing/zero_cross.py b/data/processing/zero_cross.py
deleted file mode 100644
index 8e66ceb..0000000
--- a/data/processing/zero_cross.py
+++ /dev/null
@@ -1,181 +0,0 @@
-import argparse
-import configparser
-import logging
-import pathlib
-import sys
-
-import matplotlib.pyplot as plt
-import matplotlib.dates as mdates
-import numpy as np
-import scipy.signal as sgl
-from scipy import fft
-
-parser = argparse.ArgumentParser(description="Pre-process time-series")
-parser.add_argument("-v", "--verbose", action="count", default=0)
-parser.add_argument("-c", "--config", default="config.ini")
-args = parser.parse_args()
-
-logging.basicConfig()
-log = logging.getLogger("bathy")
-log.setLevel(max((10, 20 - 10 * args.verbose)))
-
-log.info("Starting time-series pre-processing")
-config = configparser.ConfigParser()
-config.read(args.config)
-
-inp_root = pathlib.Path(config.get("inp", "root"), "cerema/raw")
-out_root = pathlib.Path(config.get("out", "root"))
-out_root.mkdir(exist_ok=True)
-
-raw_ts = []
-#for tsi in sorted(inp_root.glob("2017022817*.raw")):
-for tsi in sorted(inp_root.glob("*.raw")):
-    raw_ts.append(
-        np.loadtxt(
-            tsi,
-            dtype=[("state", int), ("z", float), ("y", float), ("x", float)],
-            delimiter=",",
-            max_rows=2304,
-        )
-    )
-    log.debug(f"Loading <{tsi}>")
-n = len(raw_ts)
-raw_ts = np.concatenate(raw_ts)
-log.debug(f"{raw_ts=}")
-
-t0 = np.linspace(0, 30 * 60 * n, 2304 * n, endpoint=False)
-t = (t0 * 1e3).astype("timedelta64[ms]") + np.datetime64("2017-02-28T00:00")
-
-if (errs := np.count_nonzero(raw_ts["state"])) != 0:
-    log.warning(f"{errs} transmission errors!")
-    log.debug(f"{dict(zip(*np.unique(raw_ts['state'], return_counts=True)))}")
-    # log.debug(f"{t[raw_ts['state'] != 0]}")
-
-sos = sgl.butter(1, 0.2, btype="lowpass", fs=2305 / (30 * 60), output="sos")
-z = sgl.sosfiltfilt(sos, raw_ts["z"]*1e-2)
-cr0 = np.where(np.diff(np.sign(z)))[0]
-
-wave = np.fromiter(
-    (
-        np.max(np.abs(z[cr0[i - 1] : cr0[i]])) + np.max(np.abs(z[cr0[i] : cr0[i + 1]]))
-        #(np.max(np.abs(raw_ts["z"][cr0[i - 1] : cr0[i]])) + np.max(np.abs(raw_ts["z"][cr0[i] : cr0[i + 1]]))) * 1e-2
-        for i in range(1, len(cr0) - 1)
-    ),
-    dtype=np.single,
-)
-
-log.debug(f"{wave=}")
-log.debug(f"{t=}")
-
-# plt.plot(t[cr0[1:-1]], wave)
-
-
-dt = 30 * 60 / 2304
-# Mlims = (int(5 / dt), int(30 / dt))
-N = t.size // 24
-s0 = 2 * dt
-dj = 0.5
-J = 1 / dj * np.log2(N * dt / s0)
-j = np.arange(0, J)
-sj = s0 * 2 ** (j * dj)
-Tj = 2 * sj * np.pi / 5
-# sj = s0 * np.arange(1, 2 ** (J * dj))
-Mw = sj / dt
-Mlims = sj[[0, -1]]
-M = (np.abs(sgl.cwt(raw_ts["z"]*1e-2, sgl.morlet2, Mw))/np.std(raw_ts["z"]*1e-2))**2
-# M = np.abs(sgl.cwt(z, sgl.morlet, Mw))
-v = np.max(np.abs(M))
-
-fig, ax = plt.subplots()
-# ax2 = ax.twinx()
-# ax.plot(t0, raw_ts["z"], lw=.5, c="k", alpha=.2)
-# ax.plot(t0, z, ls="-.", lw=.25, alpha=.2, c="k")
-st = raw_ts["state"][raw_ts["state"] != 0]
-c = np.asarray(["g", "b", "r"])
-# ax.vlines(t0[raw_ts["state"] != 0], -20, 20, colors=c[np.where(st != 777, st, 0)])
-# ax.set(xlabel="t (s)", ylabel="z (cm)")
-# ax.set(xlim=(17 * 3600 + 20 * 60, 17 * 3600 + 30 * 60))
-ax.grid(c="k", alpha=0.2)
-ax.set(zorder=1, frame_on=False)
-ax.semilogy()
-a = [t0[0], t0[-1], *Mlims]
-# c = ax.imshow(M, extent=a, aspect="auto", cmap="plasma", vmin=0)
-c = ax.contourf(t, Tj, M, cmap="Greys", vmin=0, vmax=v)
-fig.colorbar(c)
-
-H13 = np.quantile(wave, 2 / 3)
-Hs = 4*np.std(raw_ts["z"]*1e-2)
-th = 2 * Hs
-log.info(f"Threshold: {th}m")
-bigw = np.where(wave > th)[0]
-ym = 1.1 * np.max(np.abs(z))
-nw = wave.size / 2
-nlw = bigw.size
-log.info(f"Number of waves: {nw}")
-log.info(f"Number of waves >m: {nlw}")
-log.info(f"Frequency: {nlw/nw:e}")
-log.info(f"Frequency: 1/{nw/nlw:.0f}")
-log.info(f"H1/3: {H13}m")
-log.info(f"Hs: {Hs}")
-
-if bigw.size > 32:
-    log.warning(f"Number of large waves: {bigw.size}")
-    sys.exit()
-
-fig, ax_ = plt.subplots(2 * (bigw.size // 2), 2, figsize=(15/2.54, 4/3*10/2.54), constrained_layout=True)
-for w, ax2, ax in zip(bigw, ax_[::2].flatten(), ax_[1::2].flatten()):
-    i0 = cr0[w] - int(400 / dt)
-    i1 = cr0[w + 2] + int(400 / dt)
-    # a = [t0[i0], t0[i1], *Mlims]
-    # c = ax2.imshow(M[:, i0:i1], extent=a, aspect="auto", cmap="Spectral", vmin=-v, vmax=+v)
-    ws = np.ptp(raw_ts["z"][cr0[w]:cr0[w+2]]) * 1e-2
-    log.info(f"Wave [{w}] size: {ws:.2f}m")
-    c = ax2.contourf(
-        t[i0:i1],
-        Tj,
-        M[:, i0:i1],
-        cmap="Greys",
-        vmin=0,
-        levels=[1, 2.5, 5, 10, 20, 40],
-        extend="both",
-    )
-    fig.colorbar(c, ax=ax2, label="NWPS")
-    ax.plot(t[i0:i1], (raw_ts["z"]*1e-2)[i0:i1], c="k", lw=1)
-    #ax.plot(t[i0:i1], z[i0:i1], c="k", lw=1, alpha=0.2, ls="-.")
-    # ax.vlines(t[raw_ts["state"] != 0], -20, 20, colors=c[np.where(st != 777, st, 0)])
-    ax.set(xlim=(t[i0], t[i1 - 1]), ylim=(-ym, ym))
-    ax2.set(ylim=(2, 200))
-    ax2.set(ylabel="T (s)")
-    ax2.grid(c="k", alpha=0.2)
-    ax2.semilogy()
-    ax.grid(c="k", alpha=.2)
-    #ax.axhline(0, c="k", alpha=0.2, lw=1, ls="-.")
-    #ax.set(zorder=1, frame_on=False)
-    ax.set_xlabel("t (s)", loc="left")
-    ax.set_ylabel("z (m)")
-    ax.axvspan(t[cr0[w]], t[cr0[w+2]], color="k", alpha=.1)
-
-    locator = mdates.AutoDateLocator(minticks=3, maxticks=7)
-    formatter = mdates.ConciseDateFormatter(locator)
-    ax.xaxis.set_major_locator(locator)
-    ax.xaxis.set_major_formatter(formatter)
-    ax2.xaxis.set_major_locator(locator)
-    ax2.xaxis.set_major_formatter(formatter)
-    ax2.axes.set_xticklabels([])
-
-    ax2.set_rasterization_zorder(1.5)
-
-fig.savefig(out_root.joinpath(f"wavelet.pdf"), dpi=300)
-fig.savefig(out_root.joinpath(f"wavelet.png"), dpi=200)
-
-#fig, ax = plt.subplots(constrained_layout=True)
-## ax.plot(fft.rfftfreq(raw_ts["z"].size, dt), np.abs(fft.rfft(raw_ts["z"])), c="k", alpha=.2, lw=1)
-#ax.plot(*sgl.welch(raw_ts["z"], 1 / dt), c="k", alpha=0.2, label="PSD")
-#ax.plot(1 / sj, N * np.mean(M, axis=1), c="k", label="CWT")
-## ax.grid(color="k", alpha=.2)
-#ax.set(xlabel="T (s)", ylabel="PSD")
-## ax2.set(ylabel="Average Wavelet Transform")
-#ax.set(xlim=1 / Mlims)
-#ax.legend()
-
-plt.show()
diff --git a/nature/fig/U.pdf b/defence/fig/U.pdf
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diff --git a/defence/library.bib b/defence/library.bib
new file mode 100644
index 0000000..7bddd1e
--- /dev/null
+++ b/defence/library.bib
@@ -0,0 +1,1203 @@
+@misc{olaFlow,
+	author={Higuera, P.},
+	title={olaFlow: {CFD} for waves [{S}oftware].},
+	year=2017,
+	doi={10.5281/zenodo.1297013},
+	url={https://doi.org/10.5281/zenodo.1297013}
+}
+
+@report{amir,
+	author={Amir Parvin},
+	title={Processes allowing large block displacement under wave action},
+	year={2020},
+}
+
+@article{cox2018extraordinary,
+	title={Extraordinary boulder transport by storm waves (west of Ireland, winter 2013--2014), and criteria for analysing coastal boulder deposits},
+	author={Cox, R{\'o}nadh and Jahn, Kalle L and Watkins, Oona G and Cox, Peter},
+	journal={Earth-Science Reviews},
+	volume={177},
+	pages={623--636},
+	year={2018},
+	publisher={Elsevier}
+}
+
+@article{shah2013coastal,
+	title={Coastal boulders in Martigues, French Mediterranean: evidence for extreme storm waves during the Little Ice Age},
+	author={Shah-Hosseini, M and Morhange, C and De Marco, A and Wante, J and Anthony, EJ and Sabatier, F and Mastronuzzi, G and Pignatelli, C and Piscitelli, A},
+	journal={Zeitschrift f{\"u}r Geomorphologie},
+	volume={57},
+	number={Suppl 4},
+	pages={181--199},
+	year={2013}
+}
+
+@conference{abadie,
+	title={Large concrete block displacement under extreme wave: analysis of the 2/28/2017 event},
+	author={Amir Parvin and Volker Roeber and Pierre-Antoine Poncet and D. Sous and M. Mengaillou and Stéphane Abadie},
+	booktitle={Seminaire technique EZPONDA},
+	year={2019},
+}
+
+@phdthesis{poncet2021characterization,
+	title={Characterization of wave impact loading on structures at full scale: field experiment, statistical analysis and 3D advanced numerical modeling},
+	author={Poncet, Pierre-Antoine},
+	year={2021},
+	school={Pau},
+	chapter={4},
+}
+
+@article{nott2003waves,
+	title={Waves, coastal boulder deposits and the importance of the pre-transport setting},
+	author={Nott, Jonathan},
+	journal={Earth and Planetary Science Letters},
+	volume={210},
+	number={1-2},
+	pages={269--276},
+	year={2003},
+	publisher={Elsevier}
+}
+
+@article{zijlema2011swash,
+	title={SWASH: An operational public domain code for simulating wave fields and rapidly varied flows in coastal waters},
+	author={Zijlema, Marcel and Stelling, Guus and Smit, Pieter},
+	journal={Coastal Engineering},
+	volume={58},
+	number={10},
+	pages={992--1012},
+	year={2011},
+	publisher={Elsevier}
+}
+
+@incollection{mansard1980measurement,
+	title={The measurement of incident and reflected spectra using a least squares method},
+	author={Mansard, Etienne PD and Funke, ER},
+	booktitle={Coastal Engineering 1980},
+	pages={154--172},
+	year={1980}
+}
+
+@article{suh2001separation,
+	title={Separation of incident and reflected waves in wave--current flumes},
+	author={Suh, Kyung Doug and Park, Woo Sun and Park, Beom Seok},
+	journal={Coastal Engineering},
+	volume={43},
+	number={3-4},
+	pages={149--159},
+	year={2001},
+	publisher={Elsevier}
+}
+
+@article{frigaard1995time,
+	title={A time-domain method for separating incident and reflected irregular waves},
+	author={Frigaard, Peter and Brorsen, Michael},
+	journal={Coastal engineering},
+	volume={24},
+	number={3-4},
+	pages={205--215},
+	year={1995},
+	publisher={Elsevier}
+}
+
+@article{baldock1999separation,
+	title={Separation of incident and reflected waves over sloping bathymetry},
+	author={Baldock, TE and Simmonds, DJ},
+	journal={Coastal Engineering},
+	volume={38},
+	number={3},
+	pages={167--176},
+	year={1999},
+	publisher={Elsevier}
+}
+
+@article{roge2019estimation,
+	title={Estimation of incident and reflected wave trains in highly nonlinear two-dimensional irregular waves},
+	author={R{\o}ge Eldrup, Mads and Lykke Andersen, Thomas},
+	journal={Journal of Waterway, Port, Coastal, and Ocean Engineering},
+	volume={145},
+	number={1},
+	pages={04018038},
+	year={2019},
+	publisher={American Society of Civil Engineers}
+}
+
+@article{andersen2017estimation,
+	title={Estimation of incident and reflected components in highly nonlinear regular waves},
+	author={Andersen, Thomas Lykke and Eldrup, Mads R{\o}ge and Frigaard, Peter},
+	journal={Coastal Engineering},
+	volume={119},
+	pages={51--64},
+	year={2017},
+	publisher={Elsevier}
+}
+
+@article{inch2016accurate,
+	title={Accurate estimation of wave reflection on a high energy, dissipative beach},
+	author={Inch, Kris and Davidson, Mark and Masselink, Gerd and Russell, Paul},
+	journal={Journal of Coastal Research},
+	number={75 (10075)},
+	pages={877--881},
+	year={2016},
+	publisher={Allen Press}
+}
+
+@incollection{pedersen2007resolving,
+	title={Resolving transformed wave directions near coastal structures},
+	author={Pedersen, Torstein and Goldberg, Judah and Lohrmann, Atle and Siegel, Eric},
+	booktitle={Coastal Engineering 2006: (In 5 Volumes)},
+	pages={4362--4373},
+	year={2007},
+	publisher={World Scientific}
+}
+
+@article{sobey1999locally,
+	title={A locally nonlinear interpretation of PUV measurements},
+	author={Sobey, Rodney J and Hughes, Steven A},
+	journal={Coastal engineering},
+	volume={36},
+	number={1},
+	pages={17--36},
+	year={1999},
+	publisher={Elsevier}
+}
+
+@article{davidson1996new,
+	title={A new non-dimensional number for the analysis of wave reflection from rubble mound breakwaters},
+	author={Davidson, MA and Bird, PAD and Bullock, GN and Huntley, DA},
+	journal={Coastal Engineering},
+	volume={28},
+	number={1-4},
+	pages={93--120},
+	year={1996},
+	publisher={Elsevier}
+}
+
+@article{poncet2020wave,
+	title={WAVE TRANSFORMATION OVER A STEEP COMPOSITE BREAKWATER, IN-SITU EXPERIMENT RESULTS},
+	author={Poncet, PIerre-Antoine and Sous, Damien and Abadie, Stephane},
+	journal={Coastal Engineering Proceedings},
+	number={36v},
+	pages={27--27},
+	year={2020}
+}
+
+@article{larroque2018situ,
+	title={In-situ measurements of wave impact pressure on a composite breakwater: preliminary results},
+	author={Larroque, Benoit and Arnould, Philippe and Luthon, Franck and Poncet, Pierre-Antoine and Rahali, A and Abadie, St{\'e}phane},
+	journal={Journal of Coastal Research},
+	number={85 (10085)},
+	pages={1086--1090},
+	year={2018},
+	publisher={Allen Press}
+}
+
+@article{sheremet2002observations,
+	title={Observations of nearshore infragravity waves: Seaward and shoreward propagating components},
+	author={Sheremet, A and Guza, RT and Elgar, Steve and Herbers, THC},
+	journal={Journal of Geophysical Research: Oceans},
+	volume={107},
+	number={C8},
+	pages={10--1},
+	year={2002},
+	publisher={Wiley Online Library}
+}
+
+@incollection{guza1977resonant,
+	title={Resonant interactions for waves breaking on a beach},
+	author={Guza, Robert T and Bowen, Anthony J},
+	booktitle={Coastal Engineering 1976},
+	pages={560--579},
+	year={1977}
+}
+
+@article{huntley1999use,
+	title={Use of collocated sensors to measure coastal wave reflection},
+	author={Huntley, David A and Simmonds, David and Tatavarti, Rao},
+	journal={Journal of waterway, port, coastal, and ocean engineering},
+	volume={125},
+	number={1},
+	pages={46--52},
+	year={1999},
+	publisher={American Society of Civil Engineers}
+}
+
+@incollection{tatavarti1989incoming,
+	title={Incoming and outgoing wave interactions on beaches},
+	author={Tatavarti, Rao VSN and Huntley, David A and Bowen, Anthony J},
+	booktitle={Coastal Engineering 1988},
+	pages={136--150},
+	year={1989}
+}
+
+@article{higuera2015application,
+	title={Application of computational fluid dynamics to wave action on structures},
+	author={Higuera, P},
+	journal={PhD. Universidade de Cantabria},
+	year={2015}
+}
+
+@inproceedings{bogdanov2011direct,
+	title={Direct pore-scale modeling of two-phase flow through natural media},
+	author={Bogdanov, II and Guerton, F and Kpahou, J and Kamp, AM},
+	booktitle={Proceedings of the 2011 COMSOL Conference in Stuttgart; http://www. comsol. com/paper/download/83497/bogdanov\_paper. pdf},
+	year={2011}
+}
+
+@article{del2011three,
+	title={Three-dimensional interaction of water waves with maritime structures},
+	author={del Jesus, M},
+	journal={University of Cantabria (Ph. D. thesis)},
+	year={2011}
+}
+
+@article{altomare2014numerical,
+	title={Numerical modelling of armour block sea breakwater with smoothed particle hydrodynamics},
+	author={Altomare, Corrado and Crespo, Alejandro JC and Rogers, BD and Dominguez, JM and Gironella, X and G{\'o}mez-Gesteira, M},
+	journal={Computers \& Structures},
+	volume={130},
+	pages={34--45},
+	year={2014},
+	publisher={Elsevier}
+}
+
+@article{vanneste20152d,
+	title={2D numerical simulation of large-scale physical model tests of wave interaction with a rubble-mound breakwater},
+	author={Vanneste, Dieter and Troch, Peter},
+	journal={Coastal Engineering},
+	volume={103},
+	pages={22--41},
+	year={2015},
+	publisher={Elsevier}
+}
+
+@article{sumer2000experimental,
+	title={Experimental study of 2D scour and its protection at a rubble-mound breakwater},
+	author={Sumer, B Mutlu and Freds{\o}e, J{\o}rgen},
+	journal={Coastal Engineering},
+	volume={40},
+	number={1},
+	pages={59--87},
+	year={2000},
+	publisher={Elsevier}
+}
+
+@article{kim2005neural,
+	title={Neural network for design and reliability analysis of rubble mound breakwaters},
+	author={Kim, Dong Hyawn and Park, Woo Sun},
+	journal={Ocean engineering},
+	volume={32},
+	number={11-12},
+	pages={1332--1349},
+	year={2005},
+	publisher={Elsevier}
+}
+
+@incollection{troch1999development,
+	title={Development of two-dimensional numerical wave flume for wave interaction with rubble mound breakwaters},
+	author={Troch, Peter and De Rouck, Julien},
+	booktitle={Coastal Engineering 1998},
+	pages={1638--1649},
+	year={1999}
+}
+
+@article{koley2020numerical,
+	title={Numerical and experimental modeling of water wave interaction with rubble mound offshore porous breakwaters},
+	author={Koley, Santanu and Panduranga, Kottala and Almashan, Nourah and Neelamani, Subramaniam and Al-Ragum, Alanoud},
+	journal={Ocean Engineering},
+	volume={218},
+	pages={108218},
+	year={2020},
+	publisher={Elsevier}
+}
+
+@article{losada1979joint,
+	title={The joint effect of the wave height and period on the stability of rubble mound breakwaters using Iribarren's number},
+	author={Losada, Miguel A and Gimenez-Curto, Luis A},
+	journal={Coastal Engineering},
+	volume={3},
+	pages={77--96},
+	year={1979},
+	publisher={Elsevier}
+}
+
+@article{lara2008wave,
+	title={Wave interaction with low-mound breakwaters using a RANS model},
+	author={Lara, JL and Losada, IJ and Guanche, R},
+	journal={Ocean engineering},
+	volume={35},
+	number={13},
+	pages={1388--1400},
+	year={2008},
+	publisher={Elsevier}
+}
+
+@inproceedings{troch1997vofbreak2,
+	title={VOFbreak2, a numerical model for simulation of wave interaction with rubble mound breakwater},
+	author={Troch, Peter},
+	booktitle={Proceedings of the 1997 27th Congress of the International Association of Hydraulic Research, IAHR. Part D},
+	year={1997}
+}
+
+@article{losada2008numerical,
+	title={Numerical analysis of wave overtopping of rubble mound breakwaters},
+	author={Losada, Inigo J and Lara, Javier L and Guanche, Raul and Gonzalez-Ondina, Jose M},
+	journal={Coastal engineering},
+	volume={55},
+	number={1},
+	pages={47--62},
+	year={2008},
+	publisher={Elsevier}
+}
+
+@article{erdmann2018boulder,
+	title={Boulder transport by storms--Extreme-waves in the coastal zone of the Irish west coast},
+	author={Erdmann, Wibke and Kelletat, Dieter and Scheffers, Anja},
+	journal={Marine Geology},
+	volume={399},
+	pages={1--13},
+	year={2018},
+	publisher={Elsevier}
+}
+
+@article{may2015block,
+	title={Block and boulder transport in eastern Samar (Philippines) during Supertyphoon Haiyan},
+	author={May, SM and Engel, M and Brill, D and Cuadra, C and Lagmay, AMF and Santiago, J and Suarez, JK and Reyes, M and Br{\"u}ckner, H},
+	journal={Earth Surface Dynamics},
+	volume={3},
+	number={4},
+	pages={543--558},
+	year={2015},
+	publisher={Copernicus GmbH}
+}
+
+@article{weiss2012mystery,
+	title={The mystery of boulders moved by tsunamis and storms},
+	author={Weiss, Robert},
+	journal={Marine Geology},
+	volume={295},
+	pages={28--33},
+	year={2012},
+	publisher={Elsevier}
+}
+
+@article{weiss2015untangling,
+	title={Untangling boulder dislodgement in storms and tsunamis: Is it possible with simple theories?},
+	author={Weiss, R and Diplas, P},
+	journal={Geochemistry, Geophysics, Geosystems},
+	volume={16},
+	number={3},
+	pages={890--898},
+	year={2015},
+	publisher={Wiley Online Library}
+}
+
+@article{zainali2015boulder,
+	title={Boulder dislodgement and transport by solitary waves: Insights from three-dimensional numerical simulations},
+	author={Zainali, Amir and Weiss, Robert},
+	journal={Geophysical Research Letters},
+	volume={42},
+	number={11},
+	pages={4490--4497},
+	year={2015},
+	publisher={Wiley Online Library}
+}
+
+@phdthesis{zainali2016high,
+	title={High-fidelity numerical simulation of shallow water waves},
+	author={Zainali, Amir},
+	year={2016},
+	school={Virginia Tech}
+}
+
+@article{nandasena2011reassessment,
+	title={Reassessment of hydrodynamic equations: Minimum flow velocity to initiate boulder transport by high energy events (storms, tsunamis)},
+	author={Nandasena, NAK and Paris, Rapha{\"e}l and Tanaka, Norio},
+	journal={Marine Geology},
+	volume={281},
+	number={1-4},
+	pages={70--84},
+	year={2011},
+	publisher={Elsevier}
+}
+
+@article{nandasena2013boulder,
+	title={Boulder transport by high energy: Numerical model-fitting experimental observations},
+	author={Nandasena, NAK and Tanaka, Norio},
+	journal={Ocean Engineering},
+	volume={57},
+	pages={163--179},
+	year={2013},
+	publisher={Elsevier}
+}
+
+@article{martinez2011quasi,
+	title={Quasi-three dimensional two-phase debris flow model accounting for boulder transport},
+	author={Martinez, CE and Miralles-Wilhelm, F and Garcia Martinez, R},
+	journal={Italian Journal of Engineering Geology and Environment-Book},
+	volume={3},
+	pages={457--466},
+	year={2011}
+}
+
+@article{kennedy2016observations,
+	title={Observations and modeling of coastal boulder transport and loading during Super Typhoon Haiyan},
+	author={Kennedy, Andrew B and Mori, Nobuhito and Zhang, Yao and Yasuda, Tomohiro and Chen, Shen-En and Tajima, Yoshimitsu and Pecor, William and Toride, Kinya},
+	journal={Coastal Engineering Journal},
+	volume={58},
+	number={01},
+	pages={1640004},
+	year={2016},
+	publisher={World Scientific}
+}
+
+@article{lodhi2020role,
+	title={The role of hydrodynamic impact force in subaerial boulder transport by tsunami—Experimental evidence and revision of boulder transport equation},
+	author={Lodhi, Hira A and Hasan, Haider and Nandasena, NAK},
+	journal={Sedimentary Geology},
+	volume={408},
+	pages={105745},
+	year={2020},
+	publisher={Elsevier}
+}
+
+@article{oetjen2021experiments,
+	title={Experiments on tsunami induced boulder transport--A review},
+	author={Oetjen, Jan and Engel, Max and Sch{\"u}ttrumpf, Holger},
+	journal={Earth-Science Reviews},
+	volume={220},
+	pages={103714},
+	year={2021},
+	publisher={Elsevier}
+}
+
+@article{oetjen2020significance,
+	title={Significance of boulder shape, shoreline configuration and pre-transport setting for the transport of boulders by tsunamis},
+	author={Oetjen, Jan and Engel, Max and Pudasaini, Shiva P and Schuettrumpf, Holger},
+	journal={Earth Surface Processes and Landforms},
+	volume={45},
+	number={9},
+	pages={2118--2133},
+	year={2020},
+	publisher={Wiley Online Library}
+}
+
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+	title={Numerical assessment of boulder transport by the 2004 Indian ocean tsunami in Lhok Nga, West Banda Aceh (Sumatra, Indonesia)},
+	author={Nandasena, NAK and Paris, Rapha{\"e}l and Tanaka, Norio},
+	journal={Computers \& geosciences},
+	volume={37},
+	number={9},
+	pages={1391--1399},
+	year={2011},
+	publisher={Elsevier}
+}
+
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+	author={Weiss, Robert and Sheremet, Alex},
+	journal={Geochemistry, Geophysics, Geosystems},
+	volume={18},
+	number={7},
+	pages={2717--2726},
+	year={2017},
+	publisher={Wiley Online Library}
+}
+
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+	author={Sheremet, Alex and Davis, Justin R and Tian, Miao and Hanson, Jeffrey L and Hathaway, Kent K},
+	journal={Ocean Modelling},
+	volume={99},
+	pages={60--74},
+	year={2016},
+	publisher={Elsevier}
+}
+
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+	title={A numerical model for the transport of a boulder by tsunami},
+	author={Imamura, Fumihiko and Goto, Kazuhisa and Ohkubo, Shigeki},
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+	volume={113},
+	number={C1},
+	year={2008},
+	publisher={Wiley Online Library}
+}
+
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+	author={Barbano, MS and Pirrotta, C and Gerardi, F},
+	journal={Marine Geology},
+	volume={275},
+	number={1-4},
+	pages={140--154},
+	year={2010},
+	publisher={Elsevier}
+}
+
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+	journal={Marine Geology},
+	volume={283},
+	number={1},
+	pages={1-11},
+	year={2011},
+	note={Special Issue on Boulders as a signature of storms on rock coasts},
+	issn={0025-3227},
+	doi={https://doi.org/10.1016/j.margeo.2011.03.016},
+	url={https://www.sciencedirect.com/science/article/pii/S002532271100079X},
+	author={Raphaël Paris and Larissa A. Naylor and Wayne J. Stephenson},
+}
+
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+	AUTHOR={Biolchi, S. and Furlani, S. and Antonioli, F. and Baldassini, N. and Causon Deguara, J. and Devoto, S. and Di Stefano, A. and Evans, J. and Gambin, T. and Gauci, R. and Mastronuzzi, G. and Monaco, C. and Scicchitano, G.},
+	TITLE={Boulder accumulations related to extreme wave events on the eastern coast of Malta},
+	JOURNAL={Natural Hazards and Earth System Sciences},
+	VOLUME={16},
+	YEAR={2016},
+	NUMBER={3},
+	PAGES={737--756},
+	URL={https://nhess.copernicus.org/articles/16/737/2016/},
+	DOI={10.5194/nhess-16-737-2016}
+}
+
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+	volume={57},
+	number={3},
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+	year={2010},
+	issn={0378-3839},
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+	url={https://www.sciencedirect.com/science/article/pii/S0378383909001628},
+	author={Songdong Shao},
+	keywords={ISPH, Porous flow, Wave damping, Breakwater},
+}
+
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+	year={2002},
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+	url={https://www.sciencedirect.com/science/article/pii/S0378383902000455},
+	author={Tian-Jian Hsu and Tsutomu Sakakiyama and Philip L.-F. Liu},
+	keywords={Composite breakwater, Wave forces, Breaking wave, Turbulence, Pore pressure, Porous media, Numerical modelling},
+}
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+	author={T. Justin Thomas and G.S. Dwarakish},
+	keywords={numerical wave modelling, ocean engineering, wave forecasting, wave hindcasting, physical oceanography},
+}
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+}
+
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+}
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+}
+
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+}
+
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+}
+
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+}
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+}
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+}
+
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+  publisher={Elsevier}
+}
+
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+}
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+}
+
+@article{menter1994two,
+  title={Two-Equation Eddy-Viscosity Turbulence Models for Engineering Applications},
+  author={Menter, FR},
+  journal={AIA A JOURNAL},
+  volume={32},
+  number={8},
+  year={1994}
+}
+
+@article{huang2003structural,
+  title={Structural permeability effects on the interaction of a solitary wave and a submerged breakwater},
+  author={Huang, Ching-Jer and Chang, Hsing-Han and Hwung, Hwung-Hweng},
+  journal={Coastal engineering},
+  volume={49},
+  number={1-2},
+  pages={1--24},
+  year={2003},
+  publisher={Elsevier}
+}
+
+@article{dalrymple2006numerical,
+  title={Numerical modeling of water waves with the SPH method},
+  author={Dalrymple, Robert Anthony and Rogers, BD},
+  journal={Coastal engineering},
+  volume={53},
+  number={2-3},
+  pages={141--147},
+  year={2006},
+  publisher={Elsevier}
+}
+
+@article{wen2016sph,
+  title={A SPH numerical wave basin for modeling wave-structure interactions},
+  author={Wen, Hongjie and Ren, Bing and Dong, Ping and Wang, Yongxue},
+  journal={Applied Ocean Research},
+  volume={59},
+  pages={366--377},
+  year={2016},
+  publisher={Elsevier}
+}
+
+@book{violeau2012fluid,
+  title={Fluid mechanics and the SPH method: theory and applications},
+  author={Violeau, Damien},
+  year={2012},
+  publisher={Oxford University Press}
+}
+
+@article{violeau2007numerical,
+  title={Numerical modelling of complex turbulent free-surface flows with the SPH method: an overview},
+  author={Violeau, Damien and Issa, Reza},
+  journal={International Journal for Numerical Methods in Fluids},
+  volume={53},
+  number={2},
+  pages={277--304},
+  year={2007},
+  publisher={Wiley Online Library}
+}
+
+@article{ren2014numerical,
+  title={Numerical simulation of wave interaction with porous structures using an improved smoothed particle hydrodynamic method},
+  author={Ren, Bing and Wen, Hongjie and Dong, Ping and Wang, Yongxue},
+  journal={Coastal Engineering},
+  volume={88},
+  pages={88--100},
+  year={2014},
+  publisher={Elsevier}
+}
+
+@article{liu2015isph,
+  title={ISPH wave simulation by using an internal wave maker},
+  author={Liu, Xin and Lin, Pengzhi and Shao, Songdong},
+  journal={Coastal Engineering},
+  volume={95},
+  pages={160--170},
+  year={2015},
+  publisher={Elsevier}
+}
+
+@article{zheng2010numerical,
+  title={Numerical wave flume with improved smoothed particle hydrodynamics},
+  author={Zheng, Jin-hai and Soe, Mee Mee and Zhang, Chi and Hsu, Tai-Wen},
+  journal={Journal of Hydrodynamics},
+  volume={22},
+  number={6},
+  pages={773--781},
+  year={2010},
+  publisher={Springer}
+}
+
+@article{nott1997extremely,
+  title={Extremely high-energy wave deposits inside the Great Barrier Reef, Australia: determining the cause—tsunami or tropical cyclone},
+  author={Nott, Jonathan},
+  journal={Marine Geology},
+  volume={141},
+  number={1-4},
+  pages={193--207},
+  year={1997},
+  publisher={Elsevier}
+}
+
+@article{buckley2012inverse,
+  title={Inverse modeling of velocities and inferred cause of overwash that emplaced inland fields of boulders at Anegada, British Virgin Islands},
+  author={Buckley, Mark L and Wei, Yong and Jaffe, Bruce E and Watt, Steve G},
+  journal={Natural Hazards},
+  volume={63},
+  number={1},
+  pages={133--149},
+  year={2012},
+  publisher={Springer}
+}
+
+@inproceedings{liu2014experimental,
+  title={An experimental study on the tsunami boulder movement},
+  author={Liu, Haijiang and Sakashita, Taiki and Sato, Shinji},
+  booktitle={Proceedings of the 34th International Conference on Coastal Engineering, ASCE, Seoul, Korea},
+  volume={16},
+  year={2014}
+}
+
+@article{kennedy2017extreme,
+  title={Extreme block and boulder transport along a cliffed coastline (Calicoan Island, Philippines) during Super Typhoon Haiyan},
+  author={Kennedy, Andrew B and Mori, Nobuhito and Yasuda, Tomohiro and Shimozono, Takenori and Tomiczek, Tori and Donahue, Aaron and Shimura, Tomoya and Imai, Yuki},
+  journal={Marine Geology},
+  volume={383},
+  pages={65--77},
+  year={2017},
+  publisher={Elsevier}
+}
+
+@article{bressan2018laboratory,
+  title={A laboratory experiment on the incipient motion of boulders by high-energy coastal flows},
+  author={Bressan, L and Guerrero, M and Antonini, A and Petruzzelli, V and Archetti, R and Lamberti, A and Tinti, S},
+  journal={Earth Surface Processes and Landforms},
+  volume={43},
+  number={14},
+  pages={2935--2947},
+  year={2018},
+  publisher={Wiley Online Library}
+}
+
+@article{cox2020systematic,
+  title={Systematic review shows that work done by storm waves can be misinterpreted as tsunami-related because commonly used hydrodynamic equations are flawed},
+  author={Cox, R{\'o}nadh and Ardhuin, Fabrice and Dias, Fr{\'e}d{\'e}ric and Autret, Ronan and Beisiegel, Nicole and Earlie, Claire S and Herterich, James G and Kennedy, Andrew and Paris, Rapha{\"e}l and Raby, Alison and others},
+  journal={Frontiers in Marine Science},
+  pages={4},
+  year={2020},
+  publisher={Frontiers}
+}
+
+@book{hudson1975reliability,
+  title={Reliability of rubble-mound breakwater stability models},
+  author={Hudson, Robert Y},
+  year={1975},
+  publisher={US Army Engineer Waterways Experiment Station}
+}
+
+@article{hudson1959laboratory,
+  title={Laboratory investigation of rubble-mound breakwaters},
+  author={Hudson, Robert Y},
+  journal={Journal of the waterways and Harbors division},
+  volume={85},
+  number={3},
+  pages={93--121},
+  year={1959},
+  publisher={American Society of Civil Engineers}
+}
+
+@article{van1987stability,
+  title={Stability of breakwater armour layers—design formulae},
+  author={Van der Meer, Jentsje W},
+  journal={Coastal engineering},
+  volume={11},
+  number={3},
+  pages={219--239},
+  year={1987},
+  publisher={Elsevier}
+}
+
+@incollection{galland1995rubble,
+  title={Rubble mound breakwater stability under oblique waves: an experimental study},
+  author={Galland, J-C},
+  booktitle={Coastal Engineering 1994},
+  pages={1061--1074},
+  year={1995}
+}
+
+@article{etemad2012stability,
+  title={Stability of rubble-mound breakwater using H50 wave height parameter},
+  author={Etemad-Shahidi, Amir and Bali, Meysam},
+  journal={Coastal Engineering},
+  volume={59},
+  number={1},
+  pages={38--45},
+  year={2012},
+  publisher={Elsevier}
+}
+
+@incollection{van1995conceptual,
+  title={Conceptual design of rubble mound breakwaters},
+  author={Van der Meer, Jentsje W},
+  booktitle={Advances In Coastal And Ocean Engineering: (Volume 1)},
+  pages={221--315},
+  year={1995},
+  publisher={World Scientific}
+}
+
+@article{van2014oblique,
+  title={Oblique wave attack on rubble mound breakwaters},
+  author={van Gent, Marcel RA},
+  journal={Coastal Engineering},
+  volume={88},
+  pages={43--54},
+  year={2014},
+  publisher={Elsevier}
+}
+
+@article{iglesias2008virtual,
+  title={A virtual laboratory for stability tests of rubble-mound breakwaters},
+  author={Iglesias, G and Rabu{\~n}al, J and Losada, MA and Pach{\'o}n, H and Castro, A and Carballo, R},
+  journal={Ocean engineering},
+  volume={35},
+  number={11-12},
+  pages={1113--1120},
+  year={2008},
+  publisher={Elsevier}
+}
+
+@inproceedings{suzuki2011applicability,
+  title={The applicability of SWASH model for wave transformation and wave overtopping: A case study for the Flemish coast},
+  author={Suzuki, Tomohiro and Verwaest, Toon and Hassan, Wael and Veale, William and Reyns, Johan and Trouw, Koen and Troch, Peter and Zijlema, M},
+  booktitle={Proc. 5th Int. Conf. Advanced Computational Methods Engineering (ACOMEN 2011), Li{\`e}ge, Belgium},
+  pages={14--17},
+  year={2011}
+}
+
+@article{zhang2020numerical,
+  title={Numerical simulation of wave overtopping on breakwater with an armor layer of accropode using SWASH model},
+  author={Zhang, Na and Zhang, Qinghe and Wang, Keh-Han and Zou, Guoliang and Jiang, Xuelian and Yang, Aiwu and Li, Yan},
+  journal={Water},
+  volume={12},
+  number={2},
+  pages={386},
+  year={2020},
+  publisher={Multidisciplinary Digital Publishing Institute}
+}
+
+@article{dysthe2008,
+  title={Oceanic rogue waves},
+  author={Dysthe, Kristian and Krogstad, Harald E and M{\"u}ller, Peter},
+  journal={Annu. Rev. Fluid Mech.},
+  volume={40},
+  pages={287--310},
+  year={2008},
+  publisher={Annual Reviews}
+}
diff --git a/defence/main.tex b/defence/main.tex
new file mode 100644
index 0000000..8769ead
--- /dev/null
+++ b/defence/main.tex
@@ -0,0 +1,270 @@
+\documentclass[english, 10pt, aspectratio=169]{beamer}
+\useoutertheme{infolines}
+\usecolortheme{whale}
+
+\usepackage{polyglossia}
+\setmainlanguage{english}
+
+\usepackage{inter}
+\usepackage{unicode-math}
+\setmathfont[mathrm=sym]{Fira Math}
+\setmonofont[Ligatures=TeX]{Fira Code}
+\usepackage{csquotes}
+\usepackage{siunitx}
+
+\usepackage[
+	backend=biber,
+	style=iso-authoryear,
+	sorting=nyt,
+]{biblatex}
+\bibliography{library}
+
+\title[50T block displacement]{Analysis of the displacement of a large concrete block under an extreme wave.}
+\author[Edgar P. Burkhart]{Edgar P. Burkhart \and Stéphane Abadie}
+\institute[SIAME]{Université de Pau et des Pays de l’Adour, E2S-UPPA,  SIAME, France}
+\date[2022]{2022}
+
+\begin{document}
+\maketitle
+
+\begin{frame}
+	\frametitle{Contents}
+	\tableofcontents
+\end{frame}
+
+\section{Contexte}
+\subsection{Block displacement}
+\begin{frame}
+	\frametitle{Context}
+	\framesubtitle{Block displacement}
+	
+	\begin{columns}
+		\column{.7\textwidth}
+			\begin{itemize}
+				\item \citetitle{cox2018extraordinary} \parencite{cox2018extraordinary}
+				\item \citetitle{shah2013coastal} \parencite{shah2013coastal}
+			\end{itemize}
+
+		\column{.3\textwidth}
+			\includegraphics[width=\textwidth]{fig/cox.png}
+			\includegraphics[width=\textwidth]{fig/shah.png}
+	\end{columns}
+\end{frame}
+
+\begin{frame}
+	\frametitle{Context}
+	\framesubtitle{Analytical equations of block displacement}
+
+	\begin{itemize}
+		\item \citetitle{nott2003waves} \parencite{nott2003waves}
+			\begin{equation}
+				u^2\geq\frac{2\left(\frac{\rho_s}{\rho_w}-1\right)ag}{C_d\frac{ac}{b^2}+C_l}
+			\end{equation}
+		\item \citetitle{nandasena2011reassessment} \parencite{nandasena2011reassessment}
+			\begin{equation}
+				u^2\geq\frac{2\left(\frac{\rho_s}{\rho_w}-1\right)ag\left(\cos\theta+\frac cb\sin\theta\right)}
+				{C_d\frac{c^2}{b^2}+C_l}
+			\end{equation}
+		\item \citetitle{weiss2015untangling} \parencite{weiss2015untangling}
+	\end{itemize}
+\end{frame}
+
+\subsection{28-02-2017 event}
+\begin{frame}
+	\frametitle{Context}
+	\framesubtitle{February 28, 2017 event}
+	
+	\begin{figure}
+		\centering
+		\includegraphics[width=.5\textwidth]{fig/artha.jpg}
+		\caption{\SI{50}{\tonne} concrete block displaced by a wave onto the crest of the Artha breakwater
+		($h=\SI{8}{\m}$).}
+	\end{figure}
+\end{frame}
+
+\begin{frame}
+	\frametitle{Context}
+	\framesubtitle{February 28, 2017 event}
+	
+	\begin{columns}
+		\column{.6\textwidth}
+			\begin{figure}
+				\centering
+				\includegraphics[scale=.75]{fig/ts.pdf}
+				\caption{Free surface measured during the extreme wave identified on February 28, 2017 at  17:23 UTC
+				($H=\SI{13.9}{\m}$).}
+			\end{figure}
+
+		\column{.4\textwidth}
+			\begin{figure}
+				\centering
+				\includegraphics[scale=.75]{fig/out_orbitals.pdf}
+				\caption{Trajectory of the wave buoy during this particular wave.}
+			\end{figure}
+	\end{columns}
+\end{frame}
+
+\section{Results}
+\subsection{Wavelet analysis}
+\begin{frame}
+	\frametitle{Wavelet analysis}
+	
+	\begin{figure}
+		\centering
+		\includegraphics[scale=.75]{fig/wavelet.pdf}
+		\caption{Normalized wavelet power spectrum of rogue waves on February 28, 2017.}
+	\end{figure}
+\end{frame}
+
+\subsection{1D SWASH model}
+\begin{frame}
+	\frametitle{1-dimensionnal SWASH model}
+	\framesubtitle{Reflection study}
+
+	\begin{figure}
+		\centering
+		\includegraphics[scale=.75]{fig/bathy.pdf}
+		\caption{Domain 1 studied with a SWASH model (real case).}
+	\end{figure}
+\end{frame}
+
+\begin{frame}
+	\frametitle{1-dimensionnal SWASH model}
+	\framesubtitle{Reflection study}
+
+	\begin{figure}
+		\centering
+		\includegraphics[scale=.75]{fig/bathy_nb.pdf}
+		\caption{Domain 2 studied with a SWASH model (without breakwater).}
+	\end{figure}
+\end{frame}
+
+\begin{frame}
+	\frametitle{1-dimensionnal SWASH model}
+	\framesubtitle{Reflection study}
+
+	\begin{itemize}
+		\item 1D model over 2 layers (instability with more layers)
+		\item Mesh with \SI{1}{\m} resolution
+		\item Spectral boundary condition with buoy spectrum
+		\item \SI{4}{\hour} model duration (around 1200 waves)
+		\item Model calibrated by \textcite{poncet2021characterization}
+	\end{itemize}
+\end{frame}
+
+\begin{frame}
+	\frametitle{1-dimensionnal SWASH model}
+	\framesubtitle{Reflection study}
+
+	\begin{figure}
+		\centering
+		\includegraphics[scale=.75]{fig/maxw.pdf}
+		\caption{Free surface calculated by swash with spectral boundary condition at the buoy location. The plot is
+		centered on the largest obtained wave.\newline {\itshape Case 1: Real bathymetry; Case 2: simplified bathymetry (no
+		breakwater).}}
+	\end{figure}
+\end{frame}
+
+\begin{frame}
+	\frametitle{1-dimensionnal SWASH model}
+	\framesubtitle{Wave propagation from the buoy to the breakwater}
+
+	\begin{itemize}
+		\item 1D model over 4 layers (instability with more layers)
+		\item Mesh with \SI{1}{\m} resolution
+		\item Free surface elevation boundary condition with raw buoy data
+	\end{itemize}
+\end{frame}
+
+\begin{frame}
+	\frametitle{1-dimensionnal SWASH model}
+	\framesubtitle{Wave propagation from the buoy to the breakwater}
+
+	\begin{figure}
+		\centering
+		\includegraphics[scale=.75]{fig/x.pdf}
+		\caption{Propagation of the studied wave from the buoy to the Artha breakwater.}
+	\end{figure}
+\end{frame}
+
+\begin{frame}
+	\frametitle{1-dimensionnal SWASH model}
+	\framesubtitle{Wavelet analysis}
+
+	\begin{figure}
+		\centering
+		\includegraphics[scale=.75]{fig/wavelet_sw.pdf}
+		\caption{Wavelet analysis from free surface elevation computed by SWASH along the SWASH domain.}
+	\end{figure}
+\end{frame}
+
+\subsection{2Dv Olaflow model}
+\begin{frame}
+	\frametitle{Olaflow model in 2 vertical dimensions}
+	\framesubtitle{Study of the hydrodynamic conditions on the breakwater armour}
+
+	\begin{figure}
+		\centering
+		\includegraphics[scale=.75]{fig/aw_t0.pdf}
+		\caption{Domain studied with a 2Dv Olaflow model.}
+	\end{figure}
+\end{frame}
+
+\begin{frame}
+	\frametitle{Olaflow model in 2 vertical dimensions}
+	\framesubtitle{Study of the hydrodynamic conditions on the breakwater armour}
+
+	\begin{itemize}
+		\item VOF model based on VARANS equations
+		\item 2Dv mesh with \SI{50}{\cm} resolution
+		\item $k-\omega$ SST turbulence model
+		\item Qualitative calibration using photographs
+	\end{itemize}
+\end{frame}
+
+\begin{frame}
+	\frametitle{Olaflow model in 2 vertical dimensions}
+	\framesubtitle{Study of the hydrodynamic conditions on the breakwater armour}
+
+	\begin{figure}
+		\centering
+		\includegraphics[scale=.75]{fig/U.pdf}
+		\caption{Flow velocity computed on the Artha breakwater ($x=\SI{-20}{\m}$); bottom: $z=\SI{5}{\m}$.}
+	\end{figure}
+\end{frame}
+
+\begin{frame}
+	\frametitle{Olaflow model in 2 vertical dimensions}
+	\framesubtitle{Study of the hydrodynamic conditions on the breakwater armour}
+
+	\begin{itemize}
+		\item Flow velocity computed with Olaflow:
+			\begin{equation}
+				U = \SI{14.5}{\m\per\s}
+			\end{equation}
+		\item Flow velocity calculated using \textcite{nandasena2011reassessment}:
+			\begin{equation}
+				U = \SI{19.4}{\m\per\s}
+			\end{equation}
+		\item \textcite{weiss2015untangling}: time dependency does matter.
+	\end{itemize}
+\end{frame}
+
+\section{Conclusion}
+\begin{frame}
+	\frametitle{Conclusion}
+
+	\begin{itemize}
+		\item Flow velocity lower than \textcite{nandasena2011reassessment}, in accordance with \textcite{lodhi2020role}
+		\item Time dependency matters, in accordance with \textcite{weiss2015untangling}
+	\end{itemize}
+\end{frame}
+
+\appendix
+\section{References}
+\begin{frame}[allowframebreaks]
+	\frametitle{References}
+
+	\printbibliography
+\end{frame}
+\end{document}
diff --git a/nature/README.md b/nature/README.md
deleted file mode 100644
index fd8cc76..0000000
--- a/nature/README.md
+++ /dev/null
@@ -1,12 +0,0 @@
-# Nature
-
-Article pour Nature Communications.
-
-* <https://www.nature.com/ncomms/submit/how-to-submit>
-* <https://www.nature.com/ncomms/submit/article>
-* 5000 mots
-* 10 figures
-
-## Compilation
-
-* Utiliser `xelatex` (`latexmk -xelatex main.tex`)
diff --git a/nature/fig/bathy2d.pdf b/nature/fig/bathy2d.pdf
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diff --git a/nature/fig/out_orbitals.pdf b/nature/fig/out_orbitals.pdf
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diff --git a/nature/fig/pic1.jpg b/nature/fig/pic1.jpg
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diff --git a/nature/fig/ts.pdf b/nature/fig/ts.pdf
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diff --git a/nature/fig/wavelet_sw.pdf b/nature/fig/wavelet_sw.pdf
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diff --git a/nature/library.bib b/nature/library.bib
index 0066c63..ee1285c 100644
--- a/nature/library.bib
+++ b/nature/library.bib
@@ -84,54 +84,15 @@
 	journal={PhD. Universidade de Cantabria},
 	year={2015}
 }
-@phdthesis{poncet2021,
-	title={Characterization of wave impact loading on structures at full scale: field experiment, statistical analysis and 3D advanced numerical modeling},
-	author={Poncet, Pierre-Antoine},
-	year={2021},
-	school={Université de Pau et des Pays de l'Adour},
-	chapter={4},
-}
-@article{torrence1998,
-  title={A practical guide to wavelet analysis},
-  author={Torrence, Christopher and Compo, Gilbert P},
-  journal={Bulletin of the American Meteorological society},
-  volume={79},
-  number={1},
-  pages={61--78},
-  year={1998},
-  publisher={American Meteorological Society}
-}
-@article{dysthe2008,
-  title={Oceanic rogue waves},
-  author={Dysthe, Kristian and Krogstad, Harald E and M{\"u}ller, Peter},
-  journal={Annu. Rev. Fluid Mech.},
-  volume={40},
-  pages={287--310},
-  year={2008},
-  publisher={Annual Reviews}
-}
-@article{lodhi2020,
-	title={The role of hydrodynamic impact force in subaerial boulder transport by tsunami—Experimental evidence and revision of boulder transport equation},
-	author={Lodhi, Hira A and Hasan, Haider and Nandasena, NAK},
-	journal={Sedimentary Geology},
-	volume={408},
-	pages={105745},
-	year={2020},
-	publisher={Elsevier}
-}
-@book{violeau2012,
-  title={Fluid mechanics and the SPH method: theory and applications},
-  author={Violeau, Damien},
-  year={2012},
-  publisher={Oxford University Press}
-}
-@article{violeau2007,
-  title={Numerical modelling of complex turbulent free-surface flows with the SPH method: an overview},
-  author={Violeau, Damien and Issa, Reza},
-  journal={International Journal for Numerical Methods in Fluids},
-  volume={53},
-  number={2},
-  pages={277--304},
-  year={2007},
-  publisher={Wiley Online Library}
+@article{poncet2022,
+	title = {In-situ measurements of energetic depth-limited wave loading},
+	journal = {Applied Ocean Research},
+	volume = {125},
+	pages = {103216},
+	year = {2022},
+	issn = {0141-1187},
+	doi = {https://doi.org/10.1016/j.apor.2022.103216},
+	url = {https://www.sciencedirect.com/science/article/pii/S0141118722001572},
+	author = {P.A. Poncet and B. Liquet and B. Larroque and D. D’Amico and D. Sous and S. Abadie},
+	keywords = {Wave impact, Breaking wave, Loading, Breakwater, Field measurement, Pressure impulse, Multiple linear regression, Wind, Water level},
 }
diff --git a/nature/main.tex b/nature/main.tex
index 7114d49..088c5e0 100644
--- a/nature/main.tex
+++ b/nature/main.tex
@@ -1,19 +1,7 @@
 \documentclass[a4paper, twocolumn]{article}
 \usepackage{polyglossia} \usepackage{authblk}
 \usepackage[sfdefault]{inter}
-\usepackage[math-style=french]{unicode-math}
-\setmathfont{Fira Math}
 \usepackage{graphicx}
-\usepackage[hmargin=2.1cm, vmargin=2.97cm]{geometry}
-\usepackage{hyperref}
-\usepackage{siunitx}
-\sisetup{
-	mode=text,
-	reset-text-family=false,
-	reset-text-series=false,
-	reset-text-shape=false,
-	propagate-math-font=true,
-}
 
 \setmainlanguage{english}
 
@@ -24,11 +12,6 @@
 ]{biblatex}
 \bibliography{library}
 
-\hypersetup{
-	pdftitle={Analysis of the displacement of a large concrete block under an extreme wave},
-	pdfauthor={Edgar P. Burkhart}
-}
-
 \title{Analysis of the displacement of a large concrete block under an extreme wave}
 \author[1]{Edgar P. Burkhart}
 \author[*,1]{Stéphane Abadie}
@@ -43,80 +26,65 @@
 % Displacement of blocks studies
 Displacement of large blocks or boulders by waves is an interesting phenomenon in the study of extreme historical
 coastal events. The existence of block deposits at unusual heights can be a clue to past events such as extreme storms
-or tsunamis. For instance, \textcite{cox2018} studied coastal deposits on the coast of Ireland in relation to the storms
-from winter 2013--2014, and extracted criteria for analysing such deposits. Similarly, \textcite{shah2013} found boulder
-deposits on the mediterranean coast to be evidence of extreme storms in the Little Ice Age.
+or tsunamis. For instance, \textcite{cox2018} studied coastal deposits on the coast of Ireland in relation to the
+storms from winter 2013--2014, and extracted criteria for analysing such deposits. Similarly, \textcite{shah2013}
+found boulder deposits on the mediterranean coast to be evidence of extreme storms in the Little Ice Age.
 
 % Need for analytical equations
 In order for those studies to be possible, analytical criterias are needed in order to ascertain the cause of the
 displacement of a block. \textcite{nott1997,nott2003} proposed a set of equations that have been widely used for that
 purpose. Those equations rely on an equilibrium relation between the lift force produced by a wave and restraining
-forces depending on the initial setting of the block, allowing to extract a minimal flow velocity necessary for movement
-initiation. A parametrisation of waves depending on their source is also used to provide minimal wave heights depending
-on the type of scenario --- wave or tsunami. Those equations were later revised by \textcite{nandasena2011}, as they
-were found to be partially incorrect. A revised formulation based on the same considerations was provided.
+forces depending on the initial setting of the block, allowing to extract a minimal flow velocity necessary for
+movement initiation. A parametrisation of waves depending on their source is also used to provide minimal wave heights
+depending on the type of scenario --- wave or tsunami. Those equations were later revised by \textcite{nandasena2011},
+as they were found to be partially incorrect. A revised formulation based on the same considerations was provided.
 
-The assumptions on which \textcite{nott2003, nandasena2011} are based were then critisized by \textcite{weiss2015}. In
-fact, according to them, the initiation of movement is not sufficient to guarantee block displacement.
+The assumptions on which \citeauthor{nott2003, nandasena2011} are based were then critisized by \textcite{weiss2015}.
+In fact, according to them, the initiation of movement is not sufficient to guarantee block displacement.
 \textcite{weiss2015} highlights the importance of the time dependency on block displacement. A method is proposed that
-allows to find the wave amplitude that lead to block displacement. Additionally, more recent research by
-\textcite{lodhi2020} has shown that the equations proposed by \textcite{nott2003, nandasena2011} tend to overestimate
-the minimum flow velocity needed to displace a block.
+allows to find the wave amplitude that lead to block displacement.
 
 % Lack of observations -> observation
 Whether it is \textcite{nott2003}, \textcite{nandasena2011} or \textcite{weiss2015}, all the proposed analytical
-equations suffer from a major flaw: they are all based on very simplified analytical models and statistical analysis.
-Unfortunately, no block displacement event seems to have been observed directly in the past, and those events are
-difficult to predict.
+equations suffer from a major flaw; they are all based on simplified analytical models and statistical analysis.
+Unfortunately, no block displacement event seems to have been observed directly in the past.
 
-In this paper, we study such an event. On February 28, 2017, a \SI{50}{\tonne} concrete block was dropped by a wave on
-the crest of the Artha breakwater (Figure~\ref{fig:photo}). Luckily, the event was captured by a photographer, and a
-wave buoy located \SI{1.2}{\km} offshore captured the seastate. Information from the photographer allowed to establish
-the approximate time at which the block displacement occured. The goal of this paper is to model the hydrodynamic
-conditions near the breakwater that lead to the displacement of the \SI{50}{\tonne} concrete block.
+In this paper, we study such an event. On February 28, 2017, a 50T concrete block was dropped by a wave on the crest of
+the Artha breakwater. Luckily, the event was captured by a photographer, and a wave buoy located 1.2km offshore
+captured the seastate. Information from the photographer allowed to establish the approximate time at which the block
+displacement occured. The goal of this paper is to model the hydrodynamic conditions near the breakwater that lead to
+the displacement of the 50T concrete block.
 
 % Modeling flow accounting for porous media
 Several approaches can be used when modelling flow near a breakwater. Depth-averaged models can be used to study the
 transformation of waves on complex bottoms. Studying the hydrodynamic conditions under the surface can be achieved
 using smoothed-particles hydrodynamics (SPH) or volume of fluid (VOF) models. SPH models rely on a Lagrangian
-representation of the fluid \parencite{violeau2012}, while VOF models rely on an Eulerian representation. VOF models
-are generally more mature for the study of multiphase incompressible flows, while SPH models generally require more
-processing power for similar results \parencite{violeau2007}.
+representation of the fluid, while VOF models rely on an Eulerian representation. VOF models are generally more mature
+for the study of multiphase incompressible flows.
 
 In this paper, we first use a one-dimensionnal depth-averaged non-linear non-hydrostatic model to verify that the
 signal measured by the wave buoy can be used as an incident wave input for the determination of hydrodynamic conditions
 near the breakwater. For this model, we use a SWASH model \parencite{zijlema2011} already calibrated by
-\textcite{poncet2021} on a domain reaching \SI{1450}{\m} offshore of the breakwater.
+\textcite{poncet2022} on a domain reaching 1450m offshore of the breakwater.
 
 Then, we use a nested VOF model in two vertical dimensions that uses the output from the larger scale SWASH model as
-initial and boundary conditions to obtain the hydrodynamic conditions on the breakwater. The model uses olaFlow
+initial and boundary conditions to obtain the hydrodynamic conditions on the breakwater. The models uses olaFlow
 \parencite{higuera2015}, a VOF model based on volume averaged Reynolds averaged Navier-Stokes (VARANS) equations, and
 which relies on a macroscopic representation of the porous armour of the breakwater. The model is qualitatively
 calibrated using photographs from the storm of February 28, 2017. Results from the nested models are finally compared
 to the analytical equations provided by \textcite{nandasena2011}.
 
-\begin{figure*}
-	\centering
-	\includegraphics[height=.4\textwidth]{fig/pic1.jpg}
-	\includegraphics[height=.4\textwidth]{fig/pic2.jpg}
-	\caption{Photographs taken during and after the wave that displaced a \SI{50}{\tonne} concrete block onto the Artha
-	breakwater.}\label{fig:photo}
-\end{figure*}
-
 \section{Results}
 \subsection{Identified wave}
 
 Preliminary work with the photographer allowed to identify the time at which the block displacement event happened.
-Using the data from the wave buoy located \SI{1250}{\m} offshore of the Artha breakwater, a seamingly abnormally large
-wave of \SI{14}{\m} amplitude was identified that is supposed to have led to the block displacement.
+Using the data from the wave buoy located 1250m offshore of the Artha breakwater, a seamingly abnormally large wave of
+14m amplitude was identified that is supposed to have lead to the block displacement.
 
 Initial analysis of the buoy data plotted in Figure~\ref{fig:wave} shows that the movement of the buoy follows two
 orbitals that correspond to an incident wave direction. These results would indicate that the identified wave is
 essentially an incident wave, with a minor reflected component.
 
-The wavelet power spectrum displayed in Figure~\ref{fig:wavelet} highlights a primary infragravity wave in the signal,
-with a period of over \SI{30}{\s}.
-
 \begin{figure*}
 	\centering
 	\includegraphics{fig/ts.pdf}
@@ -129,241 +97,22 @@ with a period of over \SI{30}{\s}.
 
 The results from the large scale SWASH model using two configurations --- one of them being the real bathymetry, and
 the other being a simplified bathymetry without the breakwater --- are compared in Figure~\ref{fig:swash}. The results
-obtained with both simulations show a maximum wave amplitude of \SI{13.9}{\m} for the real bathymetry, and
-\SI{12.1}{\m} in the case where the breakwater is removed.
-
-\begin{figure*}
-	\centering
-	\includegraphics{fig/maxw.pdf}
-	\caption{Free surface elevation obtained with the SWASH model in two configurations. \textit{Case 1}: With breakwater;
-	\textit{Case 2}: Without breakwater.}\label{fig:swash}
-\end{figure*}
-
-\subsection{Wave transformation}
-
-The free surface obtained with the SWASH model using raw buoy measurements as an elevation boundary condition is plotted
-in Figure~\ref{fig:swash_trans}. Those results display a strong transformation of the wave between the buoy and the
-breakwater. Not only the amplitude, but also the shape of the wave are strongly impacted by the propagation over the
-domain. While the amplitude of the wave is reduced as the wave propagates shorewards, the length of the trough and the
-crest increases, with a zone reaching \SI{400}{\m} long in front of the wave where the water level is below \SI{0}{\m}.
-
-\begin{figure*}
-	\centering
-	\includegraphics{fig/x.pdf}
-	\caption{Propagation of the wave supposed to be responsible for the block displacement; highlighted zone:
-	qualitatively estimated position of the wave front.}\label{fig:swash_trans}
-\end{figure*}
-
-In an attempt to understand the identified wave, a wavelet analysis is conducted on raw buoy data as well as at
-different points along the SWASH model using the method proposed by \textcite{torrence1998}. The results are displayed
-in Figure~\ref{fig:wavelet} and Figure~\ref{fig:wavelet_sw}. The wavelet power spectrum shows that the major component
-in identified rogue waves is a high energy infragravity wave, with a period of around \SI{60}{\s}. 
-
-The SWASH model seems to indicate that the observed transformation of the wave can be characterized by a transfer of
-energy from the infragravity band to shorter waves from around \SI{600}{\m} to \SI{300}{\m}, and returning to the
-infragravity band at \SI{200}{\m}.
-
-\begin{figure*}
-	\centering
-	\includegraphics{fig/wavelet.pdf}
-	\caption{Normalized wavelet power spectrum from the raw buoy timeseries for identified rogue waves on february 28,
-	2017.}\label{fig:wavelet}
-\end{figure*}
-\begin{figure*}
-	\centering
-	\includegraphics{fig/wavelet_sw.pdf}
-	\caption{Normalized wavelet power spectrum along the SWASH domain.}\label{fig:wavelet_sw}
-\end{figure*}
-
-\subsection{Hydrodynamic conditions on the breakwater}
-
-The two-dimensionnal olaFlow model near the breakwater allowed to compute the flow velocity near and on the breakwater
-during the passage of the identified wave. The results displayed in Figure~\ref{fig:U} show that the flow velocity
-reaches a maximum of \SI{14.5}{\m\per\s} towards the breakwater during the identified extreme wave. Although the
-maximum reached velocity is similar to earlier shorter waves, the flow velocity remains high for twice as long as
-during those earlier waves. The tail of the identified wave also exhibits a water level over \SI{5}{\m} for over
-\SI{40}{\s}.
-
-\begin{figure*}
-	\centering
-	\includegraphics{fig/U.pdf}
-	\caption{Horizontal flow velocity computed with the olaFlow model at $x=\SI{-20}{\m}$ on the breakwater armor.
-	Bottom: horizontal flow velocity at $z=\SI{5}{\m}$. The identified wave reaches this point around
-	$t=\SI{175}{\s}$.}\label{fig:U}
-\end{figure*}
-
-\section{Discussion}
-
-\subsection{Incident wave}
-
-According to the criteria proposed by \textcite{dysthe2008}, rogue waves can be defined as waves with an amplitude over
-twice the significant wave height over a given period. The identified wave fits this definition, as its amplitude is
-\SI{14.7}{\m}, over twice the significant wave height of \SI{6.3}{\m} on that day. According to \textcite{dysthe2008},
-rogue waves often occur from non-linear superposition of smaller waves. This seems to be what we observe on
-Figure~\ref{fig:wave}.
-
-As displayed in Figure~\ref{fig:wavelet}, a total of 4 rogue waves were identified on february 28, 2017 in the raw buoy
-timeseries using the wave height criteria proposed by \textcite{dysthe2008}. The wavelet power spectrum shows that a
-very prominent infragravity component is present, which usually corresponds to non-linear interactions of smaller
-waves. \textcite{dysthe2008} mentions that such waves in coastal waters are often the result of refractive focusing. On
-February 28, 2017, the frequency of rogue waves was found to be of 1 wave per 1627, which is considerably more than the
-excedance probability of 1 over 10\textsuperscript4 calculated by \textcite{dysthe2008}. Additionnal studies should be
-conducted to understand focusing and the formation of rogue waves in front of the Saint-Jean-de-Luz bay.
-
-An important point to note is that rogue waves are often short-lived: their nature means that they often separate into
-shorter waves shortly after appearing. A reason for which such rogue waves can be maintained over longer distances can
-be a change from a dispersive environment such as deep water to a non-dispersive environment. The bathymetry near the
-wave buoy (Figure~\ref{fig:bathy}) shows that this might be what we observe here, as the buoy is located near a step in
-the bathymetry, from around \SI{40}{\m} to \SI{20}{\m} depth.
-
-\subsection{Reflection analysis}
+obtained with both simulations show a maximum wave amplitude of 13.9m for the real bathymetry, and 12.1m in the case
+where the breakwater is removed.
 
 The 13\% difference between those values highlights the existence of a notable amount of reflection at the buoy.
 Nonetheless, the gap between the values is still fairly small and the extreme wave identified on February 28, 2017 at
 17:23:08 could still be considered as an incident wave.
 
-Unfortunately, the spectrum wave generation method used by SWASH could not reproduce simlar waves to the one observed
-at the buoy. As mentionned by \textcite{dysthe2008}, such rogue waves cannot be deterministicly from the wave spectrum.
-For this reason, this study only allows us to observe the influence of reflection on short waves, while mostly ignoring
-infragravity waves. Those results are only useful if we consider that infragravity waves behave similarly to shorter
-waves regarding reflection.
-
-\subsection{Wave transformation}
-
-The SWASH model yields a strongly changing wave over the domain, highlighting the highly complex composition of this
-wave. Although the peak of the amplitude of the wave is reduced as the wave propagates, the length of the wave is
-highlighted by the results. At $T+\SI{60}{\s}$ for instance, the water level is under \SI{0}{\m} for \SI{400}{\m}, and
-then over \SI{0}{\m} for around the same length, showing the main infragavity component of the studied wave.
-
-The wavelet analysis conducted at several points along the domain (Figure~\ref{fig:wavelet_sw}) show that the energy of
-the studied wave (slightly before $t=\SI{1500}{\s}$) initially displays a strong infragravity component. Energy is then
-transfered from the infragravity band towards shorter waves, and back to the infragravity band. This behavior is quite
-unexpected, and further investigations should be conducted to understand and validate those results.
-
-\subsection{Hydrodynamic conditions on the breakwater}
-
-The hydrodynamic conditions on the breakwater are the main focus of this study. Considering an initially submerged
-block, analytical equations proposed by \textcite{nandasena2011} yield a minimal flow velocity that would lead to block
-displacement by saltation of \SI{19.4}{\m\per\s} The results from the Olaflow model yield a maximal wave velocity during
-the displacement of the \SI{50}{\tonne} concrete block of \SI{14.5}{\m\per\s}. The results from the model are 25\% lower
-than the analytical value.
-
-Those results tend to confirm recent research by \textcite{lodhi2020}, where it was found that the block displacement
-threshold tend to overestimate the minimal flow velocity needed for block movement, although further validation of the
-model that is used would be needed to confirm those findings.
-
-Additionally, similar flow velocities are reached in the model. Other shorter waves yield similar flow velocities on
-the breakwater, but in a smaller timeframe. The importance of time dependency in studying block displacement would be
-in accordance with research from \textcite{weiss2015}, who suggested that the use of time-dependent equations for block
-displacement would lead to a better understanding of the phenomenon.
-
-Although those results are a major step in a better understanding of block displacement in coastal regions, further
-work is needed to understand in more depth the formation and propagation of infragravity waves in the near-shore
-region. Furthermore, this study was limited to a single block displacement event, and further work should be done to
-obtain more measurements and observations of such events, although their rarity and unpredictability makes this task
-difficult.
-
-\section{Methods}
-
-\subsection{Buoy data analysis}
-
-\subsubsection{Rogue wave identification}
-
-Identifying rogue waves requires two main steps: computing the significant wave height, and computing the height of
-individual waves. The first step is straightforward: $H_s=4\sigma$, where $\sigma$ is the standard deviation of the
-surface elevation. Computing the height of individual waves is conducted using the zero-crossing method: the time domain
-is split in sections where water level is strictly positive or negative, and wave size is computed according to the
-maxima and minima in each zone. This method can fail to identify some waves or wrongly identify waves in case of
-measurement errors or in the case where a small oscillation around 0 occurs in the middle of a larger wave. In order to
-account for those issues, the signal is first fed through a low-pass filter to prevent high frequency oscillations of
-over \SI{0.2}{\Hz}.
-
-\subsubsection{Wavelet analysis}
-
-All wavelet analysis in this study is conducted using a continuous wavelet transform over a Morlet window. The wavelet
-power spectrum is normalized by the variance of the timeseries, following the method proposed by
-\textcite{torrence1998}. This analysis extracts a time-dependent power spectrum and allows to identify the composition
-of waves in a time-series.
-
-\subsection{SWASH models}
-
-\subsubsection{Domain}
-
-\begin{figure}
-	\centering
-	\includegraphics{fig/bathy2d.pdf}
-	\caption{Bathymetry in front of the Artha breakwater. The extremities of the line are the buoy and the
-	breakwater.}\label{fig:bathy}
-\end{figure}
-
-A \SI{1750}{\m} long domain is constructed in order to study wave reflection and wave transformation over the bottom
-from the wave buoy to the breakwater. Bathymetry with a resolution of around \SI{1}{\m} was used for most of the domain
-(Figure~\ref{fig:bathy}).
-The breakwater model used in the study is taken from \textcite{poncet2021}. A smoothed section is created and considered
-as a porous media in the model.
-
-A second domain is constructed for reflection analysis. The second model is the same as the first, excepted that the
-breakwater is replaced by a smooth slope in order to remove the reflection generated by the structure.
-
-The reflection analysis is conducted over \SI{4}{\hour} in order to generate a fair range of conditions. The wave
-transformation study was conducted over a \SI{1}{\hour} timeframe in order to allow the model to reach steady-state
-before the studied wave was generated.
-
-\subsubsection{Model}
-
-A non-linear non-hydrostatic shallow water model (SWASH, \cite{zijlema2011}) is used to model wave reflection and
-transformation on the studied domain. The study is conducted using a layered one-dimensional model, that allows to
-consider porous media in the domain.
-
-The reflection analysis was conducted with 2 layers as to prevent model instability in overtopping conditions. The study
-of wave transformation and the generation of boundary conditions for the Olaflow model is done with 4 layers.
-
-\subsubsection{Porosity}
-
-In the SWASH model, the porous breakwater armour is represented using macroscale porosity. The porosity parameters were
-calibrated in \textcite{poncet2021}.
-
-\subsubsection{Boundary conditions}
-
-Two different sets of boundary conditions were used for both studies. In all cases, a sponge layer was added to the
-shorewards boundary to prevent wave reflection on the boundary. In the reflection analysis, offshore conditions were
-generated using the wave spectrum extracted from buoy data during the storm. The raw vertical surface elevation measured
-by the wave buoy was used in a second part.
-
-\subsection{Olaflow model}
-
 \begin{figure*}
 	\centering
-	\includegraphics{fig/aw_t0.pdf}
-	\caption{Domain studied with Olaflow. Initial configuration.}\label{fig:of}
+	\includegraphics{fig/maxw.pdf}
+	\caption{Free surface obtained with the SWASH model in two configurations. \textit{Case 1}: With breakwater;
+	\textit{Case 2}: Without breakwater.}\label{fig:swash}
 \end{figure*}
 
-\subsubsection{Domain}
-
-A \SI{150}{\m} long domain is built in order to obtain the hydrodynamic conditions on the Artha breakwater during the
-passage of the identified extreme wave. The bathymetry with \SI{50}{\cm} resolution from \textcite{poncet2021} is used.
-The domain extends \SI{30}{\m} up in order to be able to capture the largest waves hitting the breakwater. Measurements
-are extracted \SI{20}{\m} shorewards from the breakwater crest. The domain is displayed in Figure~\ref{fig:of}.
-
-A mesh in two-vertical dimensions with \SI{20}{\cm} resolution was generated using the interpolated bathymetry. As with
-the SWASH model, the porous armour was considered at a macroscopic scale.
-
-\subsubsection{Model}
-
-A volume-of-fluid (VOF) model in two-vertical dimensions based on volume-averaged Reynolds-averaged Navier-Stokes
-(VARANS) equations is used (olaFlow, \cite{higuera2015}). The model was initially setup using generic values for porous
-breakwater studies. A sensibility study conducted on the porosity parameters found the influence of these values on
-the final results to be very minor.
-
-The k-ω SST turbulence model was used, as it produced much more realistic results than the default k-ε model,
-especially compared to the photographs from the storm of February 28, 2017. The k-ε model yielded very high viscosity
-and thus strong dissipation in the entire domain, preventing an accurate wave breaking representation.
-
-\subsubsection{Boundary conditions}
-
-Initial and boundary conditions were generated using the output from the SWASH wave transformation model. The boundary
-condition is generated by a paddle-like wavemaker, using the water level and depth-averaged velocity computed by the
-SWASH model.
+\section{Discussion}
 
+\section{Methods}
 \printbibliography
 \end{document}
diff --git a/olaflow/README.md b/olaflow/README.md
deleted file mode 100644
index 836959b..0000000
--- a/olaflow/README.md
+++ /dev/null
@@ -1,131 +0,0 @@
-# Olaflow
-
-Ce dossier regroupe l'ensemble des scripts nécessaires à l'éxécution du modèle Olaflow ainsi qu'au post-traitement des
-données.
-
-## Scripts
-
-### Run Olaflow
-`run_ola.sh` permet de lancer les scripts Python et openfoam nécessaires au bon lancement du modèle Olaflow.
-
-```./run_ola.sh CASE```
-
-* `CASE` : choix du modèle Olaflow à utiliser
-
-Le cas de base utilisé est dans le dossier `of`. Les fichiers modifiés sont dans le dossier `of_$CASE`. Les sorties
-sont dans `out_of_$CASE` puis `out_post_$CASE`.
-
-### Animate
-`animate.py` permet d'obtenir une animation de `alpha.water` et `U` en sortie du modèle Olaflow.
-
-```python -m processing.animate -o OUTPUT [-v] [-m] [-i]```
-
-* `-o OUTPUT` : choix du dossier de sortie dans lequel travailler
-* `-v` : verbose
-* `-m` : au-lieu d'une animation, tracer le maximum de chaque grandeur dans le modèle
-* `-i` : au-lieu d'une animation, tracer la valeur initiale de chaque grandeur
-
-### Bathy
-
-`bathy.py` permet de générer la bathymétrie utilisée par Olaflow.
-
-```python -m processing.bathy [-c CONFIG] [-v]```
-
-* `-c CONFIG` : choix d'un fichier de configuration
-* `-v` : verbose
-
-```
-[bathy]
-bathy : bathymétrie générée dans data
-hstru : hauteur de poreux générée dans data
-scale* : échelle de la bathymétrie en [x,y,z]
-translate* : translation de la bathymétrie en [x,y,z]
-out : dossier de sortie de la bathymétrie
-```
-
-### Diff
-
-`diff.py` permet de comparer les sorties de plusieurs modèles Olaflow.
-
-```python -m processing.diff -o OUTPUT ... [-t TIMESTEP] [-f FUNCTION] [-y FIELD]```
-
-* `-o OUTPUT` : dossier des sorties de Olaflow à utiliser (répéter pour les modèles à comparer)
-* `-t TIMESTEP` : instant auquel comparer les modèles
-* `-f FUNCTION` : fonction de post-traitement à comparer (`graphUniform` ou `graphUniform2`)
-* `-y FIELD` : champs à comparer (`alpha.water` ou `U`)
-
-### Flow velocity
-
-`flow_velocity.py` permet de tracer la vitesse du courant pour un post-traitement du modèle Olaflow.
-
-```python -m processing.flow_velocity -o OUTPUT [-f FUNCTION]```
-
-* `-o OUTPUT` : dossier des sorties de Olaflow à utiliser
-* `-f FUNCTION` : fonction de post-traitement à comparer (`graphUniform` ou `graphUniform2`)
-
-### Olaflow
-
-`olaflow.py` définit la classe Python OFModel permettant de traiter les données de sortie de Olaflow.
-
-### Pickle
-
-`pickle.py` permet de lire les données de sortie d'un modèle Olaflow et de les convertir en objet `OFModel`, puis
-d'enregistrer cet objet pour une utilisation efficace avec Python.
-
-```python -m processing.pickle -i INPUT -o OUTPUT [-z]```
-
-* `-i INPUT` : dossier de sortie d'Olaflow
-* `-o OUTPUT` : dossier de sortie à utiliser
-* `-z` : activer la compression gzip (déconseillé)
-
-### STL
-
-`stl.py` définit une fonction permettant de convertir un tableau de bathymétrie en fichier STL. Nécessite Openscad.
-
-### SWS Olaflow
-
-`sws_ola.py` permet de convertir les données de sortie d'un modèle Swash en condition initiale d'un modèle Olaflow.
-
-```python -m processing.sws_ola -o OUTPUT [-c CONFIG]```
-
-* `-o OUTPUT` : dossier de sortie à utiliser
-* `-c CONFIG` : choix d'un fichier de configuration
-
-```
-[swash]
-np_out : dossier de sortie swash
-
-[bathy]
-level : niveau d'eau dans SWASH
-
-[olaflow]
-t0 : instant initial du modèle Olaflow
-```
-
-### SWS Wavedict Irregular
-
-`sws_wavedict_irregular.py` est une tentative de convertir les données de sortie d'un modèle SWASH en condition limite
-irrégulière de spectre d'un modèle Olaflow. Ne fonctionne pas.
-
-### SWS Wavedict Paddle
-
-`sws_wavedict_paddle.py` permet de convertir les données de sortie d'un modèle SWASH en condition limite en hauteur
-d'eau et vitesse d'un modèle Olaflow.
-
-```python -m processing.sws_wavedict_paddle -o OUTPUT [-c CONFIG]```
-
-* `-o OUTPUT` : dossier de sortie à utiliser
-* `-c CONFIG` : choix d'un fichier de configuration
-
-```
-[swash]
-np_out : dossier de sortie swash
-
-[bathy]
-level : niveau d'eau dans SWASH
-
-[olaflow]
-t0 : instant initial du modèle Olaflow
-tf : instant final du modèle Olaflow
-x0 : position de la limite du modèle Olaflow
-```
diff --git a/olaflow/of_ts_fine_1/constant/porosityDict b/olaflow/of_ts_fine_1/constant/porosityDict
deleted file mode 100644
index 1d10f00..0000000
--- a/olaflow/of_ts_fine_1/constant/porosityDict
+++ /dev/null
@@ -1,29 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  2.1.0                                 |
-|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "constant";
-    object      porosityDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-// Materials: clear region, core, secondary armour layer, primary armour layer
-// a,b,c: tuning parameters
-a               2(0 50);
-b               2(0 1.2);
-c               2(0 0.34);
-
-// D50: mean nominal diameter
-D50             2(1 4);
-// porosity (phi)
-porosity        2(1 0.4);
-
-// ************************************************************************* //
diff --git a/olaflow/of_ts_fine_1/constant/turbulenceProperties b/olaflow/of_ts_fine_1/constant/turbulenceProperties
deleted file mode 100644
index 187f845..0000000
--- a/olaflow/of_ts_fine_1/constant/turbulenceProperties
+++ /dev/null
@@ -1,29 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  2.1.0                                 |
-|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version     2.0;
-    format      ascii;
-    class       dictionary;
-    location    "constant";
-    object      turbulenceProperties;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-simulationType  RAS;
-
-RAS
-{
-    RASModel        kOmegaSST;
-
-    turbulence      on;
-
-    printCoeffs     on;
-}
-
-// ************************************************************************* //
diff --git a/olaflow/of_ts_fine_1/system/blockMeshDict b/olaflow/of_ts_fine_1/system/blockMeshDict
deleted file mode 100644
index c365fbc..0000000
--- a/olaflow/of_ts_fine_1/system/blockMeshDict
+++ /dev/null
@@ -1,81 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\ | =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.7.1                                 |
-|   \\  /    A nd           | Web:      www.OpenFOAM.com                      |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version         2.0;
-    format          ascii;
-    class           dictionary;
-    object          blockMeshDict;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-scale 1;
-
-vertices        
-(
-   (-150 0 -30)
-   (0 0 -30)
-   (0 0 30)
-   (-150 0 30)
-   (-150 1 -30)
-   (0 1 -30)
-   (0 1 30)
-   (-150 1 30)
-);
-
-blocks          
-(
-    hex (0 1 5 4 3 2 6 7)   (750 1 300) simpleGrading (1 1 1)
-);
-
-edges           
-(
-);
-
-boundary         
-(
-    inlet
-    {
-        type patch;
-        faces
-        (
-            (0 4 7 3)
-        );
-    }
-    /*outlet
-    {
-        type patch;
-        faces
-        (
-            (1 5 6 2)
-        );
-    }*/
-    wall1
-    {
-        type wall;
-        faces
-        (
-            (0 1 5 4)
-        );
-    }
-    atmosphere
-    {
-        type patch;
-        faces
-        (
-            (3 2 6 7)
-            (1 5 6 2)
-        );
-    }
-);
-
-mergePatchPairs
-(
-);
-
-// ************************************************************************* //
diff --git a/olaflow/of_ts_fine_1/system/controlDict b/olaflow/of_ts_fine_1/system/controlDict
deleted file mode 100644
index ca393bb..0000000
--- a/olaflow/of_ts_fine_1/system/controlDict
+++ /dev/null
@@ -1,138 +0,0 @@
-/*---------------------------------------------------------------------------*\
-| =========                 |                                                 |
-| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
-|  \\    /   O peration     | Version:  1.3                                   |
-|   \\  /    A nd           | Web:      http://www.openfoam.org               |
-|    \\/     M anipulation  |                                                 |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    version         2.0;
-    format          ascii;
-    location        "system";
-    class           dictionary;
-    object          controlDict;
-}
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-application     olaFlow;
-
-startFrom       latestTime;
-
-startTime       0;
-
-stopAt          endTime;
-
-endTime         400;
-
-deltaT          0.1;
-
-writeControl    adjustableRunTime;
-
-writeInterval   0.5;
-
-purgeWrite      0;
-
-writeFormat     ascii;
-
-writePrecision  6;
-
-compression     on;
-
-timeFormat      general;
-
-timePrecision   6;
-
-runTimeModifiable yes;
-
-adjustTimeStep  yes;
-
-maxCo           0.45;
-maxAlphaCo	    0.45;
-
-maxDeltaT       0.5;
-/*
-functions
-{
-    gaugesVOF
-    {
-        type    sets;
-        libs ("libsampling.so");
-        writeControl    outputTime;
-        writeInterval   1;
-        setFormat       raw;
-        surfaceFormat   raw;
-        interpolationScheme cell;
-        fields          ( alpha.water );
-        sets
-        (
-            GaugeVOF01
-            {
-                type    lineCellFace;
-                axis    xyz;
-                start   ( 0.5 0.001 0 );
-                end     ( 0.5 0.001 1.2 );
-            } 
-            GaugeVOF02
-            {
-                type    lineCellFace;
-                axis    xyz;
-                start   ( 9.25 0.001 0 );
-                end     ( 9.25 0.001 1.2 );
-            } 
-            GaugeVOF03
-            {
-                type    lineCellFace;
-                axis    xyz;
-                start   ( 15.75 0.001 0 );
-                end     ( 15.75 0.001 1.2 );
-            } 
-            GaugeVOF04
-            {
-                type    lineCellFace;
-                axis    xyz;
-                start   ( 17.75 0.001 0 );
-                end     ( 17.75 0.001 1.2 );
-            } 
-            GaugeVOF05
-            {
-                type    lineCellFace;
-                axis    xyz;
-                start   ( 21.1 0.001 0 );
-                end     ( 21.1 0.001 1.2 );
-            } 
-        );
-    }
-    gaugesP
-    {
-        type    sets;
-        libs ("libsampling.so");
-        writeControl    outputTime;
-        writeInterval   1;
-        setFormat       raw;
-        surfaceFormat   raw;
-        interpolationScheme cellPointFace;
-        fields          ( p );
-        sets
-        (
-            GaugesP
-            {
-                type    boundaryPoints;
-                axis    xyz;
-                patches 1(caisson);
-                points  ((18.0 0.01 0.75) 
-                        (18.00 0.01 0.80)
-                        (18.00 0.01 0.85)
-                        (18.00 0.01 0.95)
-                        (18.01 0.01 0.70)
-                        (18.25 0.01 0.70)
-                        (18.50 0.01 0.70)
-                        (18.75 0.01 0.70));
-                maxDistance 0.01;
-            }
-        );
-    }
-}
-*/
-// ************************************************************************* //
diff --git a/olaflow/of_ts_fine_1/system/graphUniform b/olaflow/of_ts_fine_1/system/graphUniform
deleted file mode 100644
index cb575db..0000000
--- a/olaflow/of_ts_fine_1/system/graphUniform
+++ /dev/null
@@ -1,25 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Version:  9
-     \\/     M anipulation  |
--------------------------------------------------------------------------------
-Description
-    Writes graph data for specified fields along a line, specified by start and
-    end points. A specified number of graph points are used, distributed
-    uniformly along the line.
-
-\*---------------------------------------------------------------------------*/
-
-start           (-50 0.5 -15);
-end             (-50 0.5 15);
-nPoints         100;
-
-fields          (alpha.water U);
-
-axis            z;
-
-#includeEtc "caseDicts/postProcessing/graphs/graphUniform.cfg"
-
-// ************************************************************************* //
diff --git a/olaflow/of_ts_fine_1/system/graphUniform2 b/olaflow/of_ts_fine_1/system/graphUniform2
deleted file mode 100644
index 185937c..0000000
--- a/olaflow/of_ts_fine_1/system/graphUniform2
+++ /dev/null
@@ -1,25 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Version:  9
-     \\/     M anipulation  |
--------------------------------------------------------------------------------
-Description
-    Writes graph data for specified fields along a line, specified by start and
-    end points. A specified number of graph points are used, distributed
-    uniformly along the line.
-
-\*---------------------------------------------------------------------------*/
-
-start           (-20 0.5 -15);
-end             (-20 0.5 15);
-nPoints         100;
-
-fields          (alpha.water U);
-
-axis            z;
-
-#includeEtc "caseDicts/postProcessing/graphs/graphUniform.cfg"
-
-// ************************************************************************* //
diff --git a/olaflow/processing/animate.py b/olaflow/processing/animate.py
index 165a8d0..bf89e4d 100644
--- a/olaflow/processing/animate.py
+++ b/olaflow/processing/animate.py
@@ -8,7 +8,6 @@ import pickle
 import matplotlib.pyplot as plt
 import matplotlib.animation as animation
 from matplotlib.gridspec import GridSpec
-from matplotlib.ticker import MultipleLocator
 import numpy as np
 from scipy import interpolate
 
@@ -29,12 +28,6 @@ parser.add_argument(
     help="Only compute maximum rather than animation",
     action="store_true",
 )
-parser.add_argument(
-    "-i",
-    "--initial",
-    help="Only compute initial domain",
-    action="store_true",
-)
 args = parser.parse_args()
 
 logging.basicConfig(level=max((10, 20 - 10 * args.verbose)))
@@ -68,19 +61,11 @@ AW[:, iz0[idz0], ix0[idx0]] = model.fields["alpha.water"]
 U = np.full((model.t.size, *X.shape), np.nan)
 U[:, iz0[idz0], ix0[idx0]] = np.linalg.norm(model.fields["U"], axis=1)
 
-fig = plt.figure(
-    figsize=(15 / 2.54, 4 / 2.54), dpi=200, constrained_layout=True
-)
-gs = GridSpec(
-    3 if not args.initial else 1,
-    1,
-    figure=fig,
-    height_ratios=[1, 0.1, 0.1] if not args.initial else [1],
-)
+fig = plt.figure()
+gs = GridSpec(3, 1, figure=fig, height_ratios=[1, 0.05, 0.05])
 ax = fig.add_subplot(gs[0])
-if not args.initial:
-    cax1 = fig.add_subplot(gs[1])
-    cax2 = fig.add_subplot(gs[2])
+cax1 = fig.add_subplot(gs[1])
+cax2 = fig.add_subplot(gs[2])
 aw_m = ax.imshow(
     AW[0],
     vmin=0,
@@ -101,15 +86,10 @@ p_m = ax.imshow(
 ax.axhline(4.5, ls="-.", lw=1, c="k", alpha=0.2, zorder=1.2)
 
 
-if not args.initial:
-    fig.colorbar(
-        aw_m, label=r"$\alpha_w$", cax=cax1, shrink=0.6, orientation="horizontal"
-    )
-    fig.colorbar(p_m, label=r"Porosity", cax=cax2, shrink=0.6, orientation="horizontal")
+fig.colorbar(aw_m, label=r"$\alpha_w$", cax=cax1, shrink=0.6, orientation="horizontal")
+fig.colorbar(p_m, label=r"Porosity", cax=cax2, shrink=0.6, orientation="horizontal")
 ax.set(xlabel="x (m)", ylabel="z (m)", aspect="equal", facecolor="#000000")
 ax.grid(c="k", alpha=0.2)
-ax.xaxis.set_minor_locator(MultipleLocator(5))
-ax.yaxis.set_minor_locator(MultipleLocator(5))
 
 
 figU = plt.figure()
@@ -157,13 +137,6 @@ if args.max:
 
     fig.savefig(out.joinpath("max_aw.pdf"))
     figU.savefig(out.joinpath("max_U.pdf"))
-elif args.initial:
-    aw_m.set_array(AW[0])
-    ax.vlines(-20, -15, 15, color="k", lw=1, ls="--", label="Measurements")
-    ax.text(-20, 15, "Measurements", ha="right", va="bottom")
-
-    fig.savefig(out.joinpath("aw_t0.pdf"))
-    fig.savefig(out.joinpath("aw_t0.jpg"), dpi=200)
 else:
     fig.set(figwidth=19.2, figheight=10.8, dpi=100)
     figU.set(figwidth=19.2, figheight=10.8, dpi=100)
diff --git a/olaflow/processing/animateU.py b/olaflow/processing/animateU.py
new file mode 100644
index 0000000..35a9eb5
--- /dev/null
+++ b/olaflow/processing/animateU.py
@@ -0,0 +1,104 @@
+import argparse
+import gzip
+import logging
+import multiprocessing as mp
+import pathlib
+import pickle
+
+import matplotlib.pyplot as plt
+import matplotlib.animation as animation
+from matplotlib.gridspec import GridSpec
+import numpy as np
+from scipy import interpolate
+
+from .olaflow import OFModel
+
+parser = argparse.ArgumentParser(description="Post-process olaflow results")
+parser.add_argument("-v", "--verbose", action="count", default=0)
+parser.add_argument(
+    "-o",
+    "--output",
+    type=pathlib.Path,
+    help="Output directory for pickled data",
+    required=True,
+)
+args = parser.parse_args()
+
+logging.basicConfig(level=max((10, 20 - 10 * args.verbose)))
+log = logging.getLogger("ola_post")
+
+log.info("Animating olaFlow output")
+out = args.output
+out.mkdir(parents=True, exist_ok=True)
+
+with (
+    path.open("rb")
+    if (path := out.joinpath("pickle")).exists()
+    else gzip.open(path.with_suffix(".gz"), "rb")
+) as f:
+    model = pickle.load(f)
+
+flt = np.where((model.x >= -60) & (model.x <= -20) & (model.z >= 0) & (model.z <= 10))[
+    0
+]
+x0, idx0 = np.unique(model.x[flt].astype(np.half), return_inverse=True)
+z0, idz0 = np.unique(model.z[flt].astype(np.half), return_inverse=True)
+
+X, Z = np.meshgrid(x0, z0)
+
+P = np.full((model.t.size, *X.shape), np.nan)
+P[:, idz0, idx0] = model.fields["porosity"][:, flt]
+
+AW = np.full((model.t.size, *X.shape), np.nan)
+AW[:, idz0, idx0] = model.fields["alpha.water"][:, flt]
+
+watl = z0[np.argmax((AW > 0.5)[:, ::-1, :], axis=1)]
+
+U = np.full((model.t.size, 2, *X.shape), np.nan)
+UU = np.full((model.t.size, *X.shape), np.nan)
+U[..., idz0, idx0] = model.fields["U"][..., flt][:, (0, 2)]
+UU[..., idz0, idx0] = np.linalg.norm(model.fields["U"][..., flt], axis=1)
+
+figU = plt.figure(figsize=(19.2, 10.8), dpi=100)
+gsU = GridSpec(2, 1, figure=figU, height_ratios=[1, 0.05])
+axU = figU.add_subplot(gsU[0])
+caxu1 = figU.add_subplot(gsU[1])
+# caxu2 = figU.add_subplot(gsU[2])
+
+alp = np.clip(np.nan_to_num(AW), 0, 1)
+axU.pcolormesh(X, Z, P[1], vmin=0, vmax=1, cmap="Greys_r")
+u_m = axU.quiver(
+    X,
+    Z,
+    *U[0],
+    UU[0],
+    alpha=alp[0],
+    cmap="inferno_r",
+    clim=(0, np.nanmax(UU)),
+)
+# (wat_p,) = axU.plot(x0, watl[0])
+
+axU.set(xlabel="x (m)", ylabel="z (m)", aspect="equal", facecolor="#bebebe")
+axU.grid(c="k", alpha=0.2)
+titU = axU.text(
+    0.5,
+    0.95,
+    f"t={model.t[0]}s",
+    horizontalalignment="center",
+    verticalalignment="top",
+    transform=axU.transAxes,
+)
+
+figU.colorbar(u_m, label=r"$U$", cax=caxu1, shrink=0.6, orientation="horizontal")
+
+
+def animU(i):
+    titU.set_text(f"t={model.t[i]}s")
+    u_m.set_UVC(*U[i], UU[i])
+    u_m.set_alpha(alp[i])
+    # wat_p.set_ydata(watl[i])
+
+
+aniU = animation.FuncAnimation(figU, animU, frames=model.t.size, interval=1 / 24)
+
+aniU.save(out.joinpath("animUzoom.mp4"), fps=24)
diff --git a/olaflow/processing/diff.py b/olaflow/processing/diff.py
index 321f264..6263143 100644
--- a/olaflow/processing/diff.py
+++ b/olaflow/processing/diff.py
@@ -9,7 +9,7 @@ import sys
 
 from cycler import cycler
 import matplotlib.pyplot as plt
-from matplotlib.ticker import MultipleLocator
+import matplotlib.gridspec as gridspec
 import numpy as np
 from scipy import interpolate
 
@@ -67,12 +67,11 @@ def get_pickle(out):
 
 models = list(map(get_pickle, args.output))
 
-figsize = 15 / 2.54, 4 / 2.54 * len(models)
 
 fig, ax_ = plt.subplots(
     len(models),
-    figsize=figsize,
-    dpi=200,
+    figsize=(6, 1.5 * len(models)),
+    dpi=100,
     constrained_layout=True,
     squeeze=False,
 )
@@ -91,71 +90,32 @@ if args.timestep is None:
                 )
         case "U":
             for i, (_ax, _model) in enumerate(zip(ax, models)):
-                v = np.nanmax(np.abs(np.where(
-                    _model.post_fields[args.func]["alpha.water"] > 0.5,
-                    #np.linalg.norm(_model.post_fields[args.func][args.field], axis=2),
-                    _model.post_fields[args.func][args.field][..., 0],
-                    np.nan,
-                )))
-                v150 = np.nanmax(np.abs(np.where(
-                    (_model.post_fields[args.func]["alpha.water"] > 0.5) & (_model.t[:, None] > 170) & (_model.t[:, None] < 200),
-                    #np.linalg.norm(_model.post_fields[args.func][args.field], axis=2),
-                    _model.post_fields[args.func][args.field][..., 0],
-                    np.nan,
-                )))
-                _data = _model.post_fields[args.func][args.field][..., 0].T
-                #_c = _ax.contourf(
-                #    _model.t,
-                #    _model.post_fields[args.func][f"x_{args.field}"],
-                #    _data,
-                #    cmap="PiYG",
-                #    #levels=[-15, -10, -5, -2, -1, 0, 1, 2, 5, 10, 15],
-                #    vmin=-np.nanmax(np.abs(_data)),
-                #    vmax=np.nanmax(np.abs(_data)),
-                #    extend="both",
-                #)
                 _c = _ax.imshow(
-                    _data[::-1],
-                    cmap="PiYG",
-                    alpha=np.clip(_model.post_fields[args.func]["alpha.water"], 0, 1).T[::-1],
+                    np.where(_model.post_fields[args.func]["alpha.water"] > 0.5, np.linalg.norm(_model.post_fields[args.func][args.field], axis=2), np.nan).T[::-1],
+                    vmin=0,
+                    vmax=20,
+                    cmap="inferno_r",
                     extent=(
                         _model.t.min(),
                         _model.t.max(),
                         _model.post_fields[args.func][f"x_{args.field}"].min(),
                         _model.post_fields[args.func][f"x_{args.field}"].max(),
                     ),
-                    vmin=-v150,
-                    vmax=v150,
-                    aspect="auto",
                 )
-                _ax.set(xlim=(100, 300))
-                _ax.set(facecolor="k")
-                _ax.xaxis.set_minor_locator(MultipleLocator(5))
-                _ax.yaxis.set_minor_locator(MultipleLocator(1))
                 fig.colorbar(_c, label=f"{args.field} (m/s)", ax=_ax)
-                log.info(f"Vitesse max: {v}m/s")
-                log.info(f"Vitesse max [170,200]: {v150}m/s")
-                log.info(f"Écart: {abs(np.nanmax(_data)-17.7)/17.7:%}")
         case _:
             log.error(f"Cannot plot field {args.field} from {args.func}")
             sys.exit(1)
 
     for i, (_ax, _model) in enumerate(zip(ax, models)):
-        _ax.set(xlabel="t (s)", ylabel="z (m)")
-        if len(models) > 1:
-            _ax.set(title=f"Case {i}")
-        #_ax.grid(color="#797979", alpha=0.5)
+        _ax.set(xlabel="t (s)", ylabel="z (m)", title=f"Case {i}")
+        _ax.grid(color="k", alpha=0.2)
 
     fig.savefig(
         args.output[0].joinpath(
             f"diff_{args.func}_{args.field}_{'_'.join([o.name for o in args.output])}.pdf"
         )
     )
-    fig.savefig(
-        args.output[0].joinpath(
-            f"diff_{args.func}_{args.field}_{'_'.join([o.name for o in args.output])}.jpg"
-        )
-    )
 else:
     match args.field:
         case "alpha.water":
@@ -163,9 +123,7 @@ else:
                 _ax.tricontour(
                     _model.x,
                     _model.z,
-                    _model.fields[args.field][np.where(_model.t == args.timestep)[0]][
-                        0
-                    ],
+                    _model.fields[args.field][np.where(_model.t == args.timestep)[0]][0],
                     levels=(0.5,),
                     colors="k",
                 )
diff --git a/olaflow/processing/flow_velocity.py b/olaflow/processing/flow_velocity.py
deleted file mode 100644
index cfd3133..0000000
--- a/olaflow/processing/flow_velocity.py
+++ /dev/null
@@ -1,137 +0,0 @@
-import argparse
-import gzip
-from itertools import starmap
-import logging
-from multiprocessing import pool
-import pathlib
-import pickle
-import sys
-
-from cycler import cycler
-import matplotlib.pyplot as plt
-from matplotlib.ticker import MultipleLocator
-import numpy as np
-from scipy import interpolate
-
-from .olaflow import OFModel
-
-parser = argparse.ArgumentParser(description="Post-process olaflow results")
-parser.add_argument("-v", "--verbose", action="count", default=0)
-parser.add_argument(
-    "-o",
-    "--output",
-    type=pathlib.Path,
-    help="Output directory for pickled data",
-    required=True,
-)
-parser.add_argument(
-    "-f",
-    "--func",
-    type=str,
-    help="Post-process function to compare",
-    default="graphUniform",
-    choices=("graphUniform", "graphUniform2"),
-)
-
-args = parser.parse_args()
-
-logging.basicConfig(level=max((10, 20 - 10 * args.verbose)))
-log = logging.getLogger("ola_post")
-
-log.info("Plotting comparison of model output")
-
-
-def get_pickle(out):
-    with (
-        path.open("rb")
-        if (path := out.joinpath("pickle")).exists()
-        else gzip.open(path.with_suffix(".gz"), "rb")
-    ) as f:
-        return pickle.load(f)
-
-
-model = get_pickle(args.output)
-
-figsize = 15 / 2.54, 6 / 2.54
-
-fig, ax_ = plt.subplots(
-    2,
-    figsize=figsize,
-    dpi=200,
-    constrained_layout=True,
-)
-
-_ax = ax_[0]
-v = np.nanmax(np.abs(np.where(
-    model.post_fields[args.func]["alpha.water"] > 0.5,
-    #np.linalg.norm(model.post_fields[args.func]["U"], axis=2),
-    model.post_fields[args.func]["U"][..., 0],
-    np.nan,
-)))
-v150 = np.nanmax(np.abs(np.where(
-    (model.post_fields[args.func]["alpha.water"] > 0.5) & (model.t[:, None] > 170) & (model.t[:, None] < 200),
-    #np.linalg.norm(model.post_fields[args.func]["U"], axis=2),
-    model.post_fields[args.func]["U"][..., 0],
-    np.nan,
-)))
-_data = model.post_fields[args.func]["U"][..., 0].T
-#_c = _ax.contourf(
-#    model.t,
-#    model.post_fields[args.func]["x_U"],
-#    _data,
-#    cmap="PiYG",
-#    #levels=[-15, -10, -5, -2, -1, 0, 1, 2, 5, 10, 15],
-#    vmin=-np.nanmax(np.abs(_data)),
-#    vmax=np.nanmax(np.abs(_data)),
-#    extend="both",
-#)
-_c = _ax.imshow(
-    _data[::-1],
-    cmap="PiYG",
-    alpha=np.clip(model.post_fields[args.func]["alpha.water"], 0, 1).T[::-1],
-    extent=(
-        model.t.min(),
-        model.t.max(),
-        model.post_fields[args.func]["x_U"].min(),
-        model.post_fields[args.func]["x_U"].max(),
-    ),
-    vmin=-v150,
-    vmax=v150,
-    aspect="auto",
-)
-_ax.set(xlim=(0, 400))
-_ax.set(facecolor="k")
-_ax.xaxis.set_minor_locator(MultipleLocator(10))
-_ax.yaxis.set_minor_locator(MultipleLocator(1))
-_ax.set(ylabel="z (m)")
-_ax.axes.set_xticklabels([])
-fig.colorbar(_c, label=f"U (m/s)", ax=_ax)
-log.info(f"Vitesse max: {v}m/s")
-log.info(f"Vitesse max [170,200]: {v150}m/s")
-log.info(f"Écart: {abs(np.nanmax(_data)-17.7)/17.7:%}")
-
-
-x = model.post_fields[args.func]["x_U"]
-i0 = np.argmin(np.abs(x - 5))
-_data = model.post_fields[args.func]["U"][..., i0, 0]
-_alpha = model.post_fields[args.func]["alpha.water"][..., i0]
-
-ax = ax_[1]
-ax.fill_between(model.t, np.where(_alpha > 0.5, _data, 0), lw=1, color="#898989", edgecolor="k")
-#ax.autoscale(True, "x", True)
-ax.set(xlim=(0, 400))
-ax.set(xlabel="t (s)", ylabel="U (m/s)")
-ax.grid(c="k", alpha=.2)
-ax.xaxis.set_minor_locator(MultipleLocator(10))
-ax.yaxis.set_minor_locator(MultipleLocator(2))
-
-fig.savefig(
-    args.output.joinpath(
-        f"U_{args.func}.pdf"
-    )
-)
-fig.savefig(
-    args.output.joinpath(
-        f"U_{args.func}.jpg"
-    )
-)
diff --git a/olaflow/processing/post.py b/olaflow/processing/post.py
new file mode 100644
index 0000000..36e4078
--- /dev/null
+++ b/olaflow/processing/post.py
@@ -0,0 +1,90 @@
+import argparse
+import configparser
+import gzip
+from itertools import starmap
+import logging
+import multiprocessing as mp
+import pathlib
+import pickle
+
+from cycler import cycler
+import matplotlib.pyplot as plt
+import matplotlib.gridspec as gridspec
+import numpy as np
+from scipy import interpolate
+
+from .olaflow import OFModel
+
+parser = argparse.ArgumentParser(description="Post-process olaflow results")
+parser.add_argument("-v", "--verbose", action="count", default=0)
+parser.add_argument("-c", "--config", default="config.ini")
+args = parser.parse_args()
+
+logging.basicConfig(level=max((10, 20 - 10 * args.verbose)))
+log = logging.getLogger("ola_post")
+
+log.info("Animating olaFlow output")
+config = configparser.ConfigParser()
+config.read(args.config)
+out = pathlib.Path(config.get("post", "out"))
+out.mkdir(parents=True, exist_ok=True)
+
+with (
+    path.open("rb")
+    if (path := out.joinpath("pickle")).exists()
+    else gzip.open(path.with_suffix(".gz"), "rb")
+) as f:
+    model = pickle.load(f)
+
+x0_conf = config.getfloat("post", "x")
+x0_val = model.x[np.argmin(np.abs(model.x - x0_conf))]
+# z0 = config.getfloat("post", "z")
+# z0 = np.linspace(-5, 5, 16)
+c0_ = ((model.x == x0_val)[None, :] & (model.fields["alpha.water"] > 0.95)).any(axis=0)
+c0 = model.coords[c0_][:: (c0_.sum() // 8 + 1)]
+
+i0 = np.argmin(
+    np.linalg.norm(model.coords[..., None] - c0.T[None, ...], axis=1),
+    axis=0,
+)
+
+aw = model.fields["alpha.water"][:, i0]
+
+U = np.where(aw > 0.95, np.linalg.norm(model.fields["U"][..., i0], axis=1), np.nan)
+P = np.where(aw > 0.95, model.fields["p"][..., i0], np.nan)
+P_rgh = np.where(aw > 0.95, model.fields["p_rgh"][..., i0], np.nan)
+
+with plt.rc_context(
+    {
+        "axes.prop_cycle": cycler(
+            color=np.linspace(0, 1, i0.size + 1)[:-1].astype("U")
+        ),
+        "axes.grid": True,
+        "axes.xmargin": 0,
+    }
+):
+    fig, ax = plt.subplots(3, constrained_layout=True)
+    ax1, ax2, ax3 = ax
+
+    ha = ax1.plot(model.t, U, lw=1)
+    ax1.set(xlabel="t (s)", ylabel="U (m/s)")
+
+    ax2.plot(model.t, P * 1e-3, lw=1)
+    ax2.set(xlabel="t (s)", ylabel="P (kPa)")
+
+    ax3.plot(model.t, P_rgh * 1e-3, lw=1)
+    ax3.set(xlabel="t (s)", ylabel="P_rgh (kPa)")
+
+    for a in ax:
+        a.set(ylim=0)
+
+    ax2.legend(
+        ha,
+        list(
+            starmap(lambda x, z: f"x={x:8}m; z={z:8}m", zip(model.x[i0], model.z[i0]))
+        ),
+        bbox_to_anchor=(1.05, 0.5),
+        loc="center left",
+    )
+
+    fig.savefig(out.joinpath("fig.pdf"))
diff --git a/openfoam_env.fish b/openfoam_env.fish
deleted file mode 100644
index 442317f..0000000
--- a/openfoam_env.fish
+++ /dev/null
@@ -1,4 +0,0 @@
-function openfoam_env
-	bash --rcfile /opt/openfoam9/etc/bashrc -ic "fish -C 'function fish_prompt; echo -s (set_color 66cc00) \"openfoam\" (set_color normal) \" \\\$ \"; end'"
-end
-
diff --git a/swash/README.md b/swash/README.md
deleted file mode 100644
index 58f9b68..0000000
--- a/swash/README.md
+++ /dev/null
@@ -1,36 +0,0 @@
-# SWASH
-
-Ce dossier regroupe l'ensemble des scripts nécessaires à l'éxécution du modèle SWASH ainsi qu'au post-traitement des
-données.
-
-## Scripts
-
-### Animate
-
-`animate.py` permet d'obtenir une animation des résultats de SWASH.
-
-```python -m processing.animate [-c CONFIG]```
-
-* `-c CONFIG` : choix du fichier de configuration
-
-```
-[post]
-inp : dossier contenant les données d'entrée
-out : dossier de sortie
-```
-
-### Mat Npz
-
-`mat_npz` permet de convertir les données de sortie de SWASH en données Numpy plus facile à exploiter en Python.
-
-```python -m processing.mat_npz [-c CONFIG]```
-
-* `-c CONFIG` : choix du fichier de configuration
-
-```
-[swash]
-out : dossier de sortie de swash
-
-[post]
-inp : dossier de sortie pour les données numpy
-```
diff --git a/swash/config-ts.ini b/swash/config-ts.ini
index 3371d49..f0a3752 100644
--- a/swash/config-ts.ini
+++ b/swash/config-ts.ini
@@ -10,5 +10,5 @@ mpi=8
 [post]
 inp=inp_post/ts_4lay_1h
 out=out_post/ts_4lay_1h
-x0=-50
+x0=-1250
 t0=180
diff --git a/swash/config.ini b/swash/config.ini
index 3e21397..647c623 100644
--- a/swash/config.ini
+++ b/swash/config.ini
@@ -9,7 +9,7 @@ mpi=8
 
 [post]
 inp=inp_post/real_spec_interp
-compare=inp_post/real_spec_interp_nb
+#compare=inp_post/real_spec_interp_nb
 out=out_post/real_spec_interp
 x0=-1250
 t0=180
diff --git a/swash/processing/animate.py b/swash/processing/animate.py
index 3fc19a3..33796ce 100644
--- a/swash/processing/animate.py
+++ b/swash/processing/animate.py
@@ -20,6 +20,7 @@ config = configparser.ConfigParser()
 config.read(args.config)
 
 inp = pathlib.Path(config.get("post", "inp"))
+root = pathlib.Path(config.get("swash", "out"))
 out = pathlib.Path(config.get("post", "out"))
 out.mkdir(parents=True, exist_ok=True)
 
diff --git a/swash/processing/layers.py b/swash/processing/layers.py
new file mode 100644
index 0000000..e1554ee
--- /dev/null
+++ b/swash/processing/layers.py
@@ -0,0 +1,90 @@
+import argparse
+import configparser
+import logging
+import pathlib
+
+import matplotlib.animation as animation
+import matplotlib.pyplot as plt
+import numpy as np
+
+parser = argparse.ArgumentParser(description="Animate swash output")
+parser.add_argument("-v", "--verbose", action="count", default=0)
+parser.add_argument("-c", "--config", default="config.ini")
+args = parser.parse_args()
+
+logging.basicConfig(level=max((10, 20 - 10 * args.verbose)))
+log = logging.getLogger("post")
+
+log.info("Starting post-processing")
+config = configparser.ConfigParser()
+config.read(args.config)
+
+inp = pathlib.Path(config.get("post", "inp"))
+root = pathlib.Path(config.get("swash", "out"))
+out = pathlib.Path(config.get("post", "out"))
+out.mkdir(parents=True, exist_ok=True)
+
+
+def data(var):
+    return np.load(inp.joinpath(f"{var}.npy"))
+
+
+x = data("xp")
+t = data("tsec")
+
+watl = data("watl")
+botl = data("botl")
+zk = data("zk")
+velk = data("velk")
+vz = data("vz")
+
+wl = np.maximum(watl, -botl)
+# print(x.size, -np.arange(0, 1 * bathy.hstru.size, 1)[::-1].size)
+
+fig, ax = plt.subplots()
+# ax.plot(x, -botl, c="k")
+# ax.fill_between(
+#    x, -botl, -data["botl"] + bathy.hstru, color="k", alpha=0.2
+# )
+
+n = 0
+vk = np.sqrt((velk[n] ** 2).sum(axis=1))
+# print(vk.shape)
+# plt.imshow(vk)
+# plt.colorbar()
+
+lines = ax.plot(x, zk[n].T, c="#0066cc")
+quiv = []
+for i in range(len(lines) - 1):
+    quiv.append(
+        ax.quiver(
+            x[::50],
+            (zk[n, i, ::50] + zk[n, i + 1, ::50]) / 2,
+            velk[n, i, 0, ::50],
+            vz[n, i, ::50],
+            units="dots",
+            width=2,
+            scale=0.05,
+        )
+    )
+
+ax.autoscale(True, "w", True)
+ax.set_ylim(top=15)
+
+
+def animate(k):
+    for i, q in enumerate(quiv):
+        q.set_UVC(
+            velk[k, i, 0, ::50],
+            vz[k, i, ::50],
+        )
+    for i, l in enumerate(lines):
+        l.set_ydata(zk[k, i])
+    return *quiv, *lines
+
+
+ani = animation.FuncAnimation(
+    fig, animate, frames=wl[:, 0].size, interval=20, blit=True
+)
+
+ani.save(out.joinpath("layers.mp4"))
diff --git a/swash/processing/post.py b/swash/processing/post.py
index cc24b73..92f31eb 100644
--- a/swash/processing/post.py
+++ b/swash/processing/post.py
@@ -7,6 +7,8 @@ import matplotlib.pyplot as plt
 import numpy as np
 import scipy.signal as sgl
 
+from .read_swash import *
+
 parser = argparse.ArgumentParser(description="Post-process swash output")
 parser.add_argument("-v", "--verbose", action="count", default=0)
 parser.add_argument("-c", "--config", default="config.ini")
@@ -28,8 +30,7 @@ t = np.load(inp.joinpath("t.npy"))
 
 botl = np.load(inp.joinpath("botl.npy"))
 watl = np.load(inp.joinpath("watl.npy"))
-#vel = np.load(inp.joinpath("vel_x.npy"))
-vel = np.load(inp.joinpath("vel.npy"))[0]
+vel = np.load(inp.joinpath("vel_x.npy"))
 
 # Cospectral calculations
 x0 = config.getint("post", "x0")
@@ -64,25 +65,22 @@ R = np.sqrt(
 
 if config.has_option("post", "compare"):
     inp_comp = pathlib.Path(config.get("post", "compare"))
-    x_ = np.load(inp_comp.joinpath("x.npy"))
-    t_ = np.load(inp_comp.joinpath("t.npy"))
+    x_ = np.load(inp_comp.joinpath("xp.npy"))
+    t_ = np.load(inp_comp.joinpath("tsec.npy"))
 
     botl_ = np.load(inp_comp.joinpath("botl.npy"))
     watl_ = np.load(inp_comp.joinpath("watl.npy"))
     vel_ = np.load(inp_comp.joinpath("vel_x.npy"))
 
-    # Cospectral calculations
     arg_x0_ = np.abs(x_ - x0).argmin()
     arg_t0_ = np.abs(t_ - t0).argmin()
-    dt_ = np.diff(t_).mean() * 1e-3
-    f_ = 1 / dt_
 
     eta_ = watl_[t_ > t0, arg_x0_]
     u_ = vel_[t_ > t0, arg_x0_]
 
-    phi_eta_ = sgl.welch(eta_, f_, nperseg=nperseg)
-    phi_u_ = sgl.welch(u_, f_, nperseg=nperseg)
-    phi_eta_u_ = sgl.csd(eta_, u_, f_, nperseg=nperseg)
+    phi_eta_ = sgl.welch(eta_, f, nperseg=nperseg)
+    phi_u_ = sgl.welch(u_, f, nperseg=nperseg)
+    phi_eta_u_ = sgl.csd(eta_, u_, f, nperseg=nperseg)
 
     H_ = np.sqrt(np.abs(phi_eta_[1]))
     U_ = np.sqrt(np.abs(phi_u_[1]))
@@ -93,6 +91,10 @@ if config.has_option("post", "compare"):
         (np.abs(phi_eta_[1]) + np.abs(phi_u_[1]) - 2 * phi_eta_u_[1].real)
         / (np.abs(phi_eta_[1]) + np.abs(phi_u_[1]) + 2 * phi_eta_u_[1].real)
     )
+    # R_ = np.sqrt(
+    #   (1 + G_**2 - 2 * G_ * np.cos(th_eta_u_))
+    #   / (1 + G_**2 + 2 * G_ * np.cos(th_eta_u_))
+    # )
 
 
 # Plotting
diff --git a/swash/processing/transmission.py b/swash/processing/transmission.py
index bbd47ba..b272a2d 100644
--- a/swash/processing/transmission.py
+++ b/swash/processing/transmission.py
@@ -30,7 +30,7 @@ botl = np.load(inp.joinpath("botl.npy"))
 watl = np.load(inp.joinpath("watl.npy"))
 vel = np.load(inp.joinpath("vel.npy"))[0]
 
-t0 = np.linspace(23 * 60 + 8, 23 * 60 + 8 + 100, 6)
+t0 = np.linspace(23 * 60 + 8, 23 * 60 + 8 + 100, 5)
 
 # Plotting
 log.info("Plotting results")
@@ -38,10 +38,10 @@ log.info("Plotting results")
 vlim = np.nanmin(np.maximum(watl, -botl)), np.nanmax(np.maximum(watl, -botl))
 
 fig_x, ax = plt.subplots(
-    3, 2, figsize=(15 / 2.54, 2 / 3 * 10 / 2.54), constrained_layout=True
+    len(t0), figsize=(10 / 2.54, 4 / 3 * 10 / 2.54), constrained_layout=True
 )
 i0 = np.argmin(np.abs(t * 1e-3 - t0[0]))
-for ax_x, t0_x in zip(ax.reshape(-1), t0):
+for ax_x, t0_x in zip(ax, t0):
     ax_x.plot(x, -botl, color="k")
     i = np.argmin(np.abs(t * 1e-3 - t0_x))
     ax_x.plot(
@@ -67,6 +67,5 @@ log.info(f"Saving plots in '{out}'")
 out.mkdir(parents=True, exist_ok=True)
 
 fig_x.savefig(out.joinpath("x.pdf"))
-fig_x.savefig(out.joinpath("x.jpg"), dpi=200)
 
 log.info("Finished post-processing")
diff --git a/swash/processing/wavelet.py b/swash/processing/wavelet.py
deleted file mode 100644
index 2cb55ab..0000000
--- a/swash/processing/wavelet.py
+++ /dev/null
@@ -1,93 +0,0 @@
-import argparse
-import configparser
-import logging
-import pathlib
-
-import matplotlib.pyplot as plt
-from matplotlib.ticker import MultipleLocator, LogLocator, NullFormatter
-import numpy as np
-import scipy.signal as sgl
-
-parser = argparse.ArgumentParser(description="Post-process swash output")
-parser.add_argument("-v", "--verbose", action="count", default=0)
-parser.add_argument("-c", "--config", default="config.ini")
-args = parser.parse_args()
-
-logging.basicConfig(level=max((10, 20 - 10 * args.verbose)))
-log = logging.getLogger("post")
-
-log.info("Starting post-processing")
-config = configparser.ConfigParser()
-config.read(args.config)
-
-inp = pathlib.Path(config.get("post", "inp"))
-root = pathlib.Path(config.get("swash", "out"))
-
-log.info(f"Reading data from '{inp}'")
-x = np.load(inp.joinpath("x.npy"))
-t = np.load(inp.joinpath("t.npy")) * 1e-3
-
-botl = np.load(inp.joinpath("botl.npy"))
-watl = np.load(inp.joinpath("watl.npy"))
-vel = np.load(inp.joinpath("vel.npy"))[0]
-
-# Plotting
-log.info("Plotting results")
-
-vlim = np.nanmin(np.maximum(watl, -botl)), np.nanmax(np.maximum(watl, -botl))
-
-x0 = np.linspace(-700, -200, 6)
-i0 = np.argmin(np.abs(x[:, None] - x0), axis=0)
-
-fig_x, ax = plt.subplots(
-    3, 2, figsize=(15 / 2.54, 7.5 / 2.54), constrained_layout=True
-)
-dt = np.mean(np.diff(t))
-N = t.size
-s0 = 2 * dt
-dj = 0.5
-J = 1 / dj * np.log2(N * dt / s0)
-j = np.arange(0, J)
-sj = s0 * 2 ** (j * dj)
-Mw = sj / dt
-sig = np.std(watl[:, i0])
-M = np.stack([(np.abs(sgl.cwt(watl[:, i], sgl.morlet2, Mw))/sig)**2 for i in i0])
-v = np.max(M)
-T = 2 * sj * np.pi / 5
-
-for ax_x, M_, x_ in zip(ax.flatten(), M, x[i0]):
-    c = ax_x.contourf(t, T, M_, cmap="Greys", vmin=0, levels=[1, 4, 16, 64], extend="both")
-    fig_x.colorbar(c, ax=ax_x, label="NWPS")
-    ax_x.grid(color="k", alpha=0.2)
-    ax_x.text(
-        0.95,
-        0.95,
-        f"x={x_:.0f}m",
-        horizontalalignment="right",
-        verticalalignment="top",
-        transform=ax_x.transAxes,
-        #c="w",
-    )
-    ax_x.semilogy()
-    ax_x.autoscale(True, "both", True)
-    ax_x.set_rasterization_zorder(1.5)
-    ax_x.set(ylabel="T (s)", ylim=(sj[0], sj[-1]))
-
-    ax_x.xaxis.set_minor_locator(MultipleLocator(100))
-    ax_x.yaxis.set_major_locator(LogLocator(10, numticks=2**10))
-    ax_x.yaxis.set_minor_locator(LogLocator(10, subs=np.arange(10), numticks=2**10))
-    ax_x.yaxis.set_minor_formatter(NullFormatter())
-    if ax_x not in ax[-1]:
-        ax_x.axes.set_xticklabels([])
-    else:
-        ax_x.set(xlabel="t (s)")
-
-out = pathlib.Path(config.get("post", "out")).joinpath(f"trans")
-log.info(f"Saving plots in '{out}'")
-out.mkdir(parents=True, exist_ok=True)
-
-fig_x.savefig(out.joinpath("wavelet.pdf"), dpi=300)
-fig_x.savefig(out.joinpath("wavelet.jpg"), dpi=200)
-fig_x.savefig(out.joinpath("wavelet.png"), dpi=200)
-
-log.info("Finished post-processing")
diff --git a/swash/processing/zero_cross.py b/swash/processing/zero_cross.py
index 6469641..5d5c0e5 100644
--- a/swash/processing/zero_cross.py
+++ b/swash/processing/zero_cross.py
@@ -38,9 +38,6 @@ w0_comp = watl_comp[:, arg_x0]
 cr0 = np.where(np.diff(np.sign(w0)))[0]
 cr0_comp = np.where(np.diff(np.sign(w0_comp)))[0]
 
-log.info(f"1: {cr0.size} waves")
-log.info(f"2: {cr0_comp.size} waves")
-
 wave = np.fromiter(
     (
         np.abs(
@@ -75,22 +72,9 @@ ax.autoscale(True, "x", True)
 ax.grid()
 fig.savefig(out.joinpath("wsize.pdf"))
 
-fig2, ax2 = plt.subplots(
-    figsize=(10 / 2.54, 4 / 2.54), constrained_layout=True
-)
-ax2.plot(
-    t[cr0[i0 - 5] : cr0[i0 + 7]] * 1e-3,
-    w0[cr0[i0 - 5] : cr0[i0 + 7]],
-    color="k",
-    label="Cas 1",
-)
-ax2.plot(
-    t[cr0[i0 - 5] : cr0[i0 + 7]] * 1e-3,
-    w0_comp[cr0[i0 - 5] : cr0[i0 + 7]],
-    color="k",
-    ls="-.",
-    label="Cas 2",
-)
+fig2, ax2 = plt.subplots(figsize=(10/2.54, 2/3*10/2.54), constrained_layout=True)
+ax2.plot(t[cr0[i0 - 5] : cr0[i0 + 7]] * 1e-3, w0[cr0[i0 - 5] : cr0[i0 + 7]], color="k", label="Case 1")
+ax2.plot(t[cr0[i0 - 5] : cr0[i0 + 7]] * 1e-3, w0_comp[cr0[i0 - 5] : cr0[i0 + 7]], color="k", ls="-.", label="Case 2")
 ax2.set(xlabel="t (s)", ylabel="z (m)")
 ax2.autoscale(True, "x", True)
 ax2.grid()
@@ -98,11 +82,7 @@ ax2.legend()
 fig2.savefig(out.joinpath("maxw.pdf"))
 fig2.savefig(out.joinpath("maxw.jpg"), dpi=200)
 
-log.info(
-    f"RMS difference: {np.sqrt(np.mean((w0_comp-w0)**2))}m ; {np.sqrt(np.mean((w0_comp-w0)**2))/(w0.max()-w0.min()):%}"
-)
+log.info(f"RMS difference: {np.sqrt(np.mean((w0_comp-w0)**2))}m ; {np.sqrt(np.mean((w0_comp-w0)**2))/(w0.max()-w0.min()):%}")
 log.info(f"Bias: {np.mean(w0_comp-w0)}m")
 log.info(f"Maximum wave size: {wave.max()}m ; {wave_comp.max()}m")
-log.info(
-    f"Maximum wave size difference: {abs(wave_comp.max()-wave.max())/wave.max():%}"
-)
+log.info(f"Maximum wave size difference: {abs(wave_comp.max()-wave.max())/wave.max():%}")
diff --git a/tasks.md b/tasks.md
index f5b8ceb..072cedf 100644
--- a/tasks.md
+++ b/tasks.md
@@ -18,18 +18,3 @@ Olaflow comparison with photos
 Comparison of olaflow output with block displacement theories
 
 Format rapport: Journal of Geophysical Research
-
-
-
-Ajouter Figures: photos: vague & bloc sur la digue, wavelet analysis bouée autres vagues,
-Snapshot vagues sortie olaflow
-
-Étoffer un peu contenu
-
-Figure 6: Line plot en 1 point de la vitesse du courant
-
-Faire lien entre photos et splashs dans swash
-
-Génération vague scélérate : combinaison + dispersion -> zone non dispersive : ajouter profil bathymétrie
-
-Tester bathy plane avec swash pour voir si transfert énergie IG -> G