Merge branch 'master' of ssh://git.edgarpierre.fr:39529/m2cce/internship

README.md

@@ -22,12 +22,61 @@ options:
 
 ## Bathymetry
 
+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
+
+[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)
+
+[artha]
+lat: latitude of the breakwater
+lon: longitude of the breakwater
+
+[buoy]
+lat: latitude of the buoy
+lon: longitude of the buoy
+```
+
 * Insert database in `data/data`
 * Run `processing.subdomain` to generate 2D data in a smaller domain
 * Run `processing.projection` to generate a 1D bathymetry
 
 ## Swash
 
+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
@@ -37,6 +86,21 @@ options:
 
 ## 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 `blockMesh`, `snappyHexMesh -overwrite`, copy `0.org` to `0`, `setFields`
 * Run `processing.sws_ola` to convert Swash output to OlaFlow input

data/config-nb.ini

@@ -8,12 +8,13 @@ psize=Psize.dat
 hires_step=0.5
 
 [out]
+margin=0.005
 no_breakwater=True
 root=out_nb
 sub=bathy_sub.npy
 out=bathy.npy
 step=1
-left=0
+left=-300
 right=150
 
 [artha]

data/config.ini

@@ -14,7 +14,7 @@ root=out
 sub=bathy_sub.npy
 out=bathy.npy
 step=1
-left=0
+left=-300
 right=150
 
 [artha]

data/processing/projection.py

@@ -91,13 +91,14 @@ x_min_hires = x[z_crossing] + (bathy_hires[:, 0].min() - bathy_hires[hires_cross
 x_max_hires = x[z_crossing] + (bathy_hires[:, 0].max() - bathy_hires[hires_crossing, 0])
 log.debug(f"Replacing range: [{x_min_hires},{x_max_hires}]")
 
-flt_x = (x > x_min_hires) & (x < x_max_hires)
 hstru = np.zeros(z.shape)
 poro = np.zeros(z.shape)
 psize = np.zeros(z.shape)
 if config.getboolean("out", "no_breakwater", fallback=False):
-    z[flt_x] = z[flt_x][-1]
+    flt_x = np.abs(x) < 250
+    z[flt_x] = np.linspace(z[flt_x][0], z[flt_x][-1], flt_x.sum())
 else:
+    flt_x = (x > x_min_hires) & (x < x_max_hires)
     z[flt_x] = interpolate.griddata(
         (bathy_hires[:, 0],),
         bathy_hires[:, 1],
@@ -133,4 +134,5 @@ np.savetxt(out_root.joinpath("psize.dat"), psize[::-1], newline=" ")
 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()}]")
 fig.savefig(out_root.joinpath("bathy.pdf"))

olaflow/of/constant/polyMesh/boundary

@@ -1,53 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Version:  9
-     \\/     M anipulation  |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    format      ascii;
-    class       polyBoundaryMesh;
-    location    "constant/polyMesh";
-    object      boundary;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-5
-(
-    inlet
-    {
-        type            patch;
-        nFaces          77;
-        startFace       38318;
-    }
-    outlet
-    {
-        type            patch;
-        nFaces          34;
-        startFace       38395;
-    }
-    atmosphere
-    {
-        type            patch;
-        nFaces          300;
-        startFace       38429;
-    }
-    defaultFaces
-    {
-        type            empty;
-        inGroups        List<word> 1(empty);
-        nFaces          38698;
-        startFace       38729;
-    }
-    bathy
-    {
-        type            wall;
-        inGroups        List<word> 1(wall);
-        nFaces          349;
-        startFace       77427;
-    }
-)
-
-// ************************************************************************* //

olaflow/of/constant/polyMesh/cellLevel

@@ -1,19 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Version:  9
-     \\/     M anipulation  |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    format      ascii;
-    class       labelList;
-    location    "constant/polyMesh";
-    object      cellLevel;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-19349{0}
-
-// ************************************************************************* //

olaflow/of/constant/polyMesh/cellZones

@@ -1,20 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Version:  9
-     \\/     M anipulation  |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    format      ascii;
-    class       regIOobject;
-    location    "constant/polyMesh";
-    object      cellZones;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-0
-()
-
-// ************************************************************************* //

olaflow/of/constant/polyMesh/faceZones

@@ -1,20 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Version:  9
-     \\/     M anipulation  |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    format      ascii;
-    class       regIOobject;
-    location    "constant/polyMesh";
-    object      faceZones;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-0
-()
-
-// ************************************************************************* //

olaflow/of/constant/polyMesh/level0Edge

@@ -1,22 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Version:  9
-     \\/     M anipulation  |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    format      ascii;
-    class       uniformDimensionedScalarField;
-    location    "constant/polyMesh";
-    object      level0Edge;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-dimensions      [0 1 0 0 0 0 0];
-value           0.5;
-
-
-
-// ************************************************************************* //

olaflow/of/constant/polyMesh/pointLevel

@@ -1,19 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Version:  9
-     \\/     M anipulation  |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    format      ascii;
-    class       labelList;
-    location    "constant/polyMesh";
-    object      pointLevel;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-39460{0}
-
-// ************************************************************************* //

olaflow/of/constant/polyMesh/pointZones

@@ -1,20 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-  =========                 |
-  \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
-   \\    /   O peration     | Website:  https://openfoam.org
-    \\  /    A nd           | Version:  9
-     \\/     M anipulation  |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
-    format      ascii;
-    class       regIOobject;
-    location    "constant/polyMesh";
-    object      pointZones;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-0
-()
-
-// ************************************************************************* //

swash/config-nb.ini

@@ -2,16 +2,14 @@
 out=../data/out_nb
 
 [swash]
-input=sws/SPEC_buoy_nb.sws
+input=sws/SPEC_buoy.sws
 path=/data/code/swash
-out=out/spec_nb
+out=out/spec_nb_2lay
 mpi=8
 
 [post]
-inp=inp_post/spec_nb
+inp=inp_post/spec_nb_2lay
-compare=inp_post_nb
+#compare=
-out=out_post
+out=out_post/spec_nb_2lay
-#nperseg=1024
-dt=0.25
 x0=-1250
 t0=180

swash/config.ini

@@ -4,14 +4,12 @@ out=../data/out
 [swash]
 input=sws/SPEC_buoy.sws
 path=/data/code/swash
-out=out/spec
+out=out/spec_2lay
 mpi=8
 
 [post]
-inp=inp_post/spec
+inp=inp_post/spec_2lay
-compare=inp_post_nb
+compare=inp_post/spec_nb_2lay
-out=out_post
+out=out_post/spec_2lay_bvsnb
-#nperseg=1024
-dt=0.25
 x0=-1250
 t0=180

swash/processing/layers.py

@@ -55,7 +55,7 @@ vk = np.sqrt((velk[n] ** 2).sum(axis=1))
 
 lines = ax.plot(x, zk[n].T, c="#0066cc")
 quiv = []
-for i in range(10):
+for i in range(len(lines)-1):
     quiv.append(
         ax.quiver(
             x[::50],
@@ -87,4 +87,4 @@ ani = animation.FuncAnimation(
     fig, animate, frames=wl[:, 0].size, interval=20, blit=True
 )
 
-ani.save(out.joinpath("layers.mp4", codec="h265"))
+ani.save(out.joinpath("layers.mp4"))

swash/processing/post.py

@@ -38,7 +38,7 @@ x0 = config.getint("post", "x0")
 arg_x0 = np.abs(x - x0).argmin()
 t0 = config.getfloat("post", "t0")
 arg_t0 = np.abs(t - t0).argmin()
-dt = config.getfloat("post", "dt")
+dt = np.diff(t).mean()
 f = 1 / dt
 nperseg = config.getint("post", "nperseg", fallback=None)
 log.info(f"Computing reflection coefficient at x={x0}")
@@ -59,10 +59,10 @@ R = np.sqrt(
     (np.abs(phi_eta[1]) + np.abs(phi_u[1]) - 2 * np.abs(phi_eta_u[1]))
     / (np.abs(phi_eta[1]) + np.abs(phi_u[1]) + 2 * np.abs(phi_eta_u[1]))
 )
-# R = np.sqrt(
+#R = np.sqrt(
-#    (1 + G**2 - 2 * G * np.cos(th_eta_u))
+#   (1 + G**2 - 2 * G * np.cos(th_eta_u))
-#    / (1 + G**2 + 2 * G * np.cos(th_eta_u))
+#   / (1 + G**2 + 2 * G * np.cos(th_eta_u))
-# )
+#)
 
 if config.has_option("post", "compare"):
     inp_comp = pathlib.Path(config.get("post", "compare"))
@@ -92,10 +92,10 @@ if config.has_option("post", "compare"):
         (np.abs(phi_eta_[1]) + np.abs(phi_u_[1]) - 2 * np.abs(phi_eta_u_[1]))
         / (np.abs(phi_eta_[1]) + np.abs(phi_u_[1]) + 2 * np.abs(phi_eta_u_[1]))
     )
-    # R_ = np.sqrt(
+    #R_ = np.sqrt(
-    #    (1 + G_**2 - 2 * G_ * np.cos(th_eta_u_))
+    #   (1 + G_**2 - 2 * G_ * np.cos(th_eta_u_))
-    #    / (1 + G_**2 + 2 * G_ * np.cos(th_eta_u_))
+    #   / (1 + G_**2 + 2 * G_ * np.cos(th_eta_u_))
-    # )
+    #)
 
 
 # Plotting
@@ -166,8 +166,8 @@ out = pathlib.Path(config.get("post", "out")).joinpath(f"t{t0}x{x0}")
 log.info(f"Saving plots in '{out}'")
 out.mkdir(parents=True, exist_ok=True)
 
-fig.savefig(out.joinpath("t.png"))
+fig.savefig(out.joinpath("t.pdf"))
-fig_r.savefig(out.joinpath("R.png"))
+fig_r.savefig(out.joinpath("R.pdf"))
-fig_x.savefig(out.joinpath("x.png"))
+fig_x.savefig(out.joinpath("x.pdf"))
 
 log.info("Finished post-processing")

swash/processing/read_swash.py

@@ -1,9 +1,12 @@
+import logging
 import subprocess
 import tempfile
 
 import numpy as np
 
 
+log = logging.getLogger("read_swash")
+
 class ReadSwash:
     def __init__(self):
         self._n_x = None
@@ -13,7 +16,9 @@ class ReadSwash:
 
     @classmethod
     def read_nohead(cls, path):
+        log.info(f"Replacing \\s with \\n in '{path}'")
         subprocess.run(("sed", "-i", r"s/\s\+/\n/g", path))
+        log.info(f"Loading '{path}'")
         return np.loadtxt(path)
 
     def read_time(self, path):

swash/processing/sws_npz.py

@@ -30,7 +30,7 @@ np.save(inp.joinpath("tsec"), rsws.read_time(sws_out.joinpath("tsec.dat")))
 np.save(inp.joinpath("xp"), rsws.read_x(sws_out.joinpath("xp.dat")))
 
 var = {
-    "dep": rsws.read_scalar,
+    #"dep": rsws.read_scalar,
     "botl": rsws.read_const,
     "watl": rsws.read_scalar,
     "pressk": rsws.read_scalar_lay,
@@ -38,6 +38,7 @@ var = {
     "zk": rsws.read_scalar_lay,
     "velk": rsws.read_vector_lay,
     "vz": rsws.read_scalar_lay,
+    "vel": rsws.read_vector,
 }
 
 with ThreadPool(len(var)) as pool:

swash/sws/SPEC_buoy.sws

@@ -1,19 +1,19 @@
 $*************************    GENERAL   ***************************************
 PROJ 'GW' 'T1'
 SET NAUT
-SET LEVEL 0.5
+SET LEVEL 4.5
 SET MAXERR 1
-SET DEPMIN 0.001
+$SET DEPMIN 0.001
-MODE DYN ONED 
+MODE NONST ONED 
 $************************     GRIDS     ***************************************
-CGRID REG -1450 0 0 1450 0 1450 0 
+CGRID REG -1450 0 0 1750 0 1750 0 
-INPGRID BOT REG -1450 0 0 1450 0 1 0   $x0 y0 theta nx-1 ny-1 dx dy  
+INPGRID BOT REG -1450 0 0 1750 0 1 0   $x0 y0 theta nx-1 ny-1 dx dy  
-VERT 10 $nb couches 
+VERT 2
 READ BOTTOM -1 'bathy.dat' 3 0 FREE
 
-INPGRID PORO REG -1450 0 0 1450 0 1 0
+INPGRID PORO REG -1450 0 0 1750 0 1 0
-INPGRID PSIZ REG -1450 0 0 1450 0 1 0
+INPGRID PSIZ REG -1450 0 0 1750 0 1 0
-INPGRID HSTRUC REG  -1450 0 0 1450 0 1 0
+INPGRID HSTRUC REG  -1450 0 0 1750 0 1 0
 
 READINP PORO 1 'poro.dat' 3 0 FREE
 READINP PSIZ 1 'psize.dat' 3 0 FREE
@@ -24,7 +24,7 @@ $***********************   BOUNDARIES  ****************************************
 INIT ZERO  
 BOUN SHAP JON SIG PEAK DSPR DEGR
 BOUN SIDE W BTYPE WEAK SMOOT 10 SEC ADDBOUNDWAVE CON SPECT 7.31 16.9 0 0 CYCLE 20 MIN
-BOUN SIDE E BTYPE SOMMERFELD
+SPON E 250
 
 
 $***********************   PHYSICS  *******************************************