Merge branch 'olaflow'

data/.gitignore

@@ -1 +1 @@
-/out
+/out*

data/config-of.ini

@@ -0,0 +1,26 @@
+[inp]
+root=data
+base=Database_20220224.xyz
+hires=bathyhires.dat
+hstru=Hstru.dat
+poro=Poro.dat
+psize=Psize.dat
+hires_step=0.5
+
+[out]
+#no_breakwater=True
+root=out_of
+sub=bathy_sub.npy
+out=bathy.npy
+step=0.5
+left=0
+right=-1000
+plot=True
+
+[artha]
+lat=43.398450
+lon=-1.673097
+
+[buoy]
+lat=43.408333
+lon=-1.681667

olaflow/config.ini

@@ -1,11 +1,10 @@
 [swash]
-npz_out=../swash/inp_post
+np_out=../swash/inp_post
 
 [bathy]
-bathy=../swash/data/bathyhires.dat
+bathy=../data/out_of/bathy.dat
-hstru=../swash/data/Hstru.dat
+hstru=../data/out_of/hstru.dat
 scale=[0.5,1,1]
-translate=[-149,0,0]
 out=out_bathy
 
 [olaflow]

olaflow/of/constant/polyMesh/boundary

@@ -0,0 +1,53 @@
+/*--------------------------------*- 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

@@ -0,0 +1,19 @@
+/*--------------------------------*- 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

@@ -0,0 +1,20 @@
+/*--------------------------------*- 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

@@ -0,0 +1,20 @@
+/*--------------------------------*- 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

@@ -0,0 +1,22 @@
+/*--------------------------------*- 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

@@ -0,0 +1,19 @@
+/*--------------------------------*- 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

@@ -0,0 +1,20 @@
+/*--------------------------------*- 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
+()
+
+// ************************************************************************* //

olaflow/of/constant/triSurface

@@ -0,0 +1 @@
+../../out_bathy/

olaflow/of/system/blockMeshDict

@@ -19,14 +19,14 @@ scale 1;
 
 vertices        
 (
+   (-150 0 -30)
    (0 0 -30)
-   (150 0 -30)
+   (0 0 30)
-   (150 0 20)
+   (-150 0 30)
-   (0 0 20)
+   (-150 1 -30)
    (0 1 -30)
-   (150 1 -30)
+   (0 1 30)
-   (150 1 20)
+   (-150 1 30)
-   (0 1 20)
 );
 
 blocks          

olaflow/of/system/setFieldsDict

@@ -25,7 +25,7 @@ regions
 (
     boxToCell
     {
-        box (-10 -10 -100) (500 10 5);
+        box (-200 -100 -100) (100 100 4.5);
 
         fieldValues
         (
@@ -34,8 +34,8 @@ regions
     }
     surfaceToCell
     {
-        file            "./constant/triSurface/rubble.stl";
+        file            "./constant/triSurface/poro.stl";
-        outsidePoints   ((0 0 0));    // definition of outside
+        outsidePoints   ((-100 0 0));    // definition of outside
         includeCut      true;              // cells cut by surface
         includeInside   true;              // cells not on outside of surf
         includeOutside  false;              // cells on outside of surf

olaflow/of/system/snappyHexMeshDict

@@ -29,16 +29,6 @@ addLayers       false;
 geometry
 {
 
-    bloc0.stl
-    {
-        type triSurfaceMesh;
-        name bloc0;
-    }
-    bloc1.stl
-    {
-        type triSurfaceMesh;
-        name bloc1;
-    }
 
 		bathy.stl
 		{
@@ -125,14 +115,6 @@ castellatedMeshControls
 				{
 					level ( 0 0 );
 				}
-				bloc0
-				{
-					level ( 0 0 );
-				}
-				bloc1
-				{
-					level ( 0 0 );
-				}
 
     }
 
@@ -172,7 +154,7 @@ castellatedMeshControls
     // section reachable from the locationInMesh is kept.
     // NOTE: This point should never be on a face, always inside a cell, even
     // after refinement.
-    locationInMesh (0.25 0.01 0.25);
+    locationInMesh (-100 0 0);
 
     // Whether any faceZones (as specified in the refinementSurfaces)
     // are only on the boundary of corresponding cellZones or also allow

olaflow/processing/bathy.py

@@ -20,8 +20,9 @@ log.info("Starting sws -> olaFlow converter")
 config = configparser.ConfigParser()
 config.read("config.ini")
 
-bathy = np.loadtxt(config.get("bathy", "bathy"))
+bathy = np.loadtxt(config.get("bathy", "bathy"))[::-1]
-poro = bathy + np.loadtxt(config.get("bathy", "hstru"))
+hstru = np.loadtxt(config.get("bathy", "hstru"))[::-1]
+poro = bathy + np.where(hstru == 0, -5, hstru)
 
 out = pathlib.Path(config.get("bathy", "out"))
 out.mkdir(exist_ok=True)

olaflow/processing/olaflow.py

@@ -25,6 +25,21 @@ class OFModel:
                 )
             )
 
+    def write_vector_field(self, field, values):
+        with open(self._root.joinpath("0", field), "r") as aw_file:
+            aw_raw = aw_file.read()
+
+        with open(self._root.joinpath("0", field), "w") as aw_file:
+            aw_file.write(
+                re.sub(
+                    r"(?<=\(\n).*?(?=\n\))",
+                    "\n".join(map(lambda x: f"({' '.join(x.astype('str'))})", values)),
+                    aw_raw,
+                    count=1,
+                    flags=re.S,
+                )
+            )
+
     @property
     def x(self):
         return self._x

olaflow/processing/stl.py

@@ -12,6 +12,7 @@ def stl_from_1d(data, output, scale=[1, 1, 1], translate=[0, 0, 0]):
         np.savetxt(tmpdir.joinpath("data.dat"), np.stack((data, data)))
         with open(tmpdir.joinpath("scad"), "wt") as scad:
             scad.write(
+                f"mirror([1, 0, 0])"
                 f"translate({translate})"
                 f"scale({scale})"
                 f"""surface("data.dat");"""

olaflow/processing/sws_ola.py

@@ -5,6 +5,7 @@ import pathlib
 
 import numpy as np
 from scipy import interpolate
+import matplotlib.pyplot as plt
 
 from .olaflow import OFModel
 
@@ -21,16 +22,39 @@ log.info("Starting sws -> olaFlow converter")
 config = configparser.ConfigParser()
 config.read("config.ini")
 
-sws_out = pathlib.Path(config.get("swash", "npz_out"))
+sws_out = pathlib.Path(config.get("swash", "np_out"))
-sws = np.load(sws_out.joinpath("sws.npz"))
+def data(var):
+    return np.load(sws_out.joinpath(f"{var}.npy"))
 
-x, t = sws["x"], sws["t"]
+x = data("xp")
+t = data("tsec")
+
+watl = data("watl")
+zk = data("zk")
+velk = data("velk")
+vz = data("vz")
 
 olaflow_root = pathlib.Path(config.get("olaflow", "root"))
 model = OFModel(olaflow_root)
 model.read_mesh()
 
-watl = interpolate.interp1d(x, sws["watl"][680])
+watl_t = interpolate.interp1d(x, watl[680])
-alpha_water = np.where(model.z < watl(model.x), 1, 0)
+alpha_water = np.where(model.z < watl_t(model.x), 1, 0)
 
+zk_t = interpolate.interp1d(x, zk[680])
+velk_t = interpolate.interp1d(x, velk[680,:,0,:])(model.x)
+vz_t = interpolate.interp1d(x, vz[680])(model.x)
+zk_tl = zk_t(model.x)
+
+print(velk.shape)
+ux = np.zeros(model.x.shape)
+uy = np.zeros(model.x.shape)
+uz = np.zeros(model.x.shape)
+print(zk_tl.shape, velk.shape, vz.shape)
+for zk_l, velk_l, vz_l in zip(zk_tl, velk_t, vz_t):
+    ux = np.where(model.z < zk_l, velk_l, ux)
+    uz = np.where(model.z < zk_l, vz_l, uz)
+
+print(np.stack((ux,uy,uz)).T)
 model.write_field("alpha.water", alpha_water)
+model.write_vector_field("U", np.stack((ux, uy, uz)).T)

swash/processing/animate.py

@@ -23,11 +23,9 @@ root = pathlib.Path(config.get("swash", "out"))
 out = pathlib.Path(config.get("plot", "out"))
 out.mkdir(exist_ok=True)
 
-
 def data(var):
     return np.load(inp.joinpath(f"{var}.npy"))
 
-
 x = data("xp")
 t = data("tsec")
 

swash/processing/layers.py

@@ -6,6 +6,10 @@ import pathlib
 import matplotlib.animation as animation
 import matplotlib.pyplot as plt
 import numpy as np
+<<<<<<< HEAD
+=======
+import pandas as pd
+>>>>>>> olaflow
 
 parser = argparse.ArgumentParser(description="Animate swash output")
 parser.add_argument("-v", "--verbose", action="count", default=0)
@@ -23,7 +27,6 @@ root = pathlib.Path(config.get("swash", "out"))
 out = pathlib.Path(config.get("plot", "out"))
 out.mkdir(exist_ok=True)
 
-
 def data(var):
     return np.load(inp.joinpath(f"{var}.npy"))
 

swash/sws/SPEC_buoy.sws

@@ -1,19 +1,19 @@
 $*************************    GENERAL   ***************************************
 PROJ 'GW' 'T1'
 SET NAUT
-SET LEVEL 4.5
+SET LEVEL 0.5
 SET MAXERR 1
 SET DEPMIN 0.001
 MODE DYN ONED 
 $************************     GRIDS     ***************************************
-CGRID REG -1250 0 0 1250 0 1250 0 
+CGRID REG -1450 0 0 1450 0 1450 0 
-INPGRID BOT REG -1250 0 0 1250 0 1 0   $x0 y0 theta nx-1 ny-1 dx dy  
+INPGRID BOT REG -1450 0 0 1450 0 1 0   $x0 y0 theta nx-1 ny-1 dx dy  
 VERT 10 $nb couches 
 READ BOTTOM -1 'bathy.dat' 3 0 FREE
 
-INPGRID PORO REG -1251 0 0 1250 0 1 0
+INPGRID PORO REG -1450 0 0 1450 0 1 0
-INPGRID PSIZ REG -1251 0 0 1250 0 1 0
+INPGRID PSIZ REG -1450 0 0 1450 0 1 0
-INPGRID HSTRUC REG  -1251 0 0 1250 0 1 0
+INPGRID HSTRUC REG  -1450 0 0 1450 0 1 0
 
 READINP PORO 1 'poro.dat' 3 0 FREE
 READINP PSIZ 1 'psize.dat' 3 0 FREE
@@ -47,6 +47,8 @@ BLOCK 'COMPGRID' NOHEAD 'dep.dat' DEP OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'botl.dat' BOTL OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'watl.dat' WATL OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'press.dat' PRESS OUTPUT 000000.00 0.25 SEC
+BLOCK 'COMPGRID' NOHEAD 'nhprsk.dat' NHPRSK OUTPUT 000000.00 0.25 SEC
+BLOCK 'COMPGRID' NOHEAD 'pressk.dat' PRESSK OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'disch.dat' DISCH OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'ustar.dat' USTAR OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'vel.dat' VEL OUTPUT 000000.00 0.25 SEC

swash/sws/SPEC_buoy_nb.sws

@@ -1,19 +1,19 @@
 $*************************    GENERAL   ***************************************
 PROJ 'GW' 'T1'
 SET NAUT
-SET LEVEL 4.5
+SET LEVEL 0.5
 SET MAXERR 1
 SET DEPMIN 0.001
 MODE DYN ONED 
 $************************     GRIDS     ***************************************
-CGRID REG -1250 0 0 1250 0 1250 0 
+CGRID REG -1450 0 0 1450 0 1450 0 
-INPGRID BOT REG -1250 0 0 1250 0 1 0   $x0 y0 theta nx-1 ny-1 dx dy  
+INPGRID BOT REG -1450 0 0 1450 0 1 0   $x0 y0 theta nx-1 ny-1 dx dy  
 VERT 10 $nb couches 
 READ BOTTOM -1 'bathy.dat' 3 0 FREE
 
-INPGRID PORO REG -1251 0 0 1250 0 1 0
+INPGRID PORO REG -1450 0 0 1450 0 1 0
-INPGRID PSIZ REG -1251 0 0 1250 0 1 0
+INPGRID PSIZ REG -1450 0 0 1450 0 1 0
-INPGRID HSTRUC REG  -1251 0 0 1250 0 1 0
+INPGRID HSTRUC REG  -1450 0 0 1450 0 1 0
 
 READINP PORO 1 'poro.dat' 3 0 FREE
 READINP PSIZ 1 'psize.dat' 3 0 FREE
@@ -48,6 +48,8 @@ BLOCK 'COMPGRID' NOHEAD 'dep.dat' DEP OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'botl.dat' BOTL OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'watl.dat' WATL OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'press.dat' PRESS OUTPUT 000000.00 0.25 SEC
+BLOCK 'COMPGRID' NOHEAD 'nhprsk.dat' NHPRSK OUTPUT 000000.00 0.25 SEC
+BLOCK 'COMPGRID' NOHEAD 'pressk.dat' PRESSK OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'disch.dat' DISCH OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'ustar.dat' USTAR OUTPUT 000000.00 0.25 SEC
 BLOCK 'COMPGRID' NOHEAD 'vel.dat' VEL OUTPUT 000000.00 0.25 SEC