Compound flooding scripts: updated some regions in Bathy_loading/ and…

… other minor changes.

.gitignore

@@ -30,3 +30,8 @@ site/
 
 src/Core/_version
 .DS_Store
+
+# Files related to Python scripts #
+#############
+*.egg*
+__pycache__

src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/minas_inlet_2m.reg

@@ -0,0 +1,12 @@
+Region written by ACE/gredit
+1
+9 1
+-64.443032 45.318950
+-64.511029 45.314985
+-64.534135 45.351003
+-64.493865 45.397595
+-64.391538 45.398586
+-64.310337 45.390986
+-64.295483 45.355959
+-64.335424 45.299124
+-64.401771 45.298463

src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence1.reg

@@ -0,0 +1,48 @@
+Region written by ACE/gredit
+1
+45 1
+-60.483012 45.719008
+-60.114531 45.733735
+-60.026095 45.969367
+-60.085052 46.293361
+-60.114531 46.661536
+-60.247184 46.926622
+-60.615666 47.073892
+-61.205236 46.676263
+-61.647414 46.146091
+-61.942199 45.998821
+-62.236985 45.925186
+-62.384377 45.895732
+-62.679163 45.881005
+-63.136080 45.910459
+-63.460344 45.998821
+-63.740390 46.190272
+-63.932000 46.278634
+-64.226785 46.322815
+-64.388917 46.455358
+-64.668963 46.852987
+-64.683702 47.176981
+-64.551049 47.648245
+-64.374178 47.824969
+-64.256264 48.252052
+-64.020436 48.399322
+-64.035175 48.841132
+-64.271003 49.076764
+-64.713181 49.297669
+-65.759669 49.371304
+-66.599807 49.282942
+-67.145159 49.194580
+-67.425205 49.165126
+-68.058994 49.474393
+-68.810696 49.312396
+-70.151969 48.576046
+-71.493242 47.338978
+-71.124760 46.484812
+-69.179178 46.543720
+-67.572598 46.617355
+-65.450144 46.087183
+-64.565788 45.984094
+-63.607736 45.586465
+-62.384377 45.424468
+-61.603196 45.468649
+-60.939930 45.748462

src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence2.reg

@@ -0,0 +1,27 @@
+Region written by ACE/gredit
+1
+24 1
+-68.176908 49.459666
+-68.073733 49.047310
+-67.646294 49.076764
+-67.233595 49.253488
+-66.865113 49.651117
+-66.319761 49.975111
+-65.229055 50.092927
+-63.740390 50.137108
+-62.752859 49.960384
+-61.470543 49.842568
+-60.556709 49.872022
+-59.392307 50.196016
+-58.168948 50.726188
+-56.945589 51.256361
+-56.356019 51.609809
+-55.589577 51.830714
+-55.368488 52.125254
+-56.061234 52.360886
+-57.903641 51.771806
+-60.541969 50.961821
+-63.239255 50.785096
+-65.951279 50.755642
+-67.631555 50.092927
+-67.970558 49.665844

src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Bathy_loading/regions/st_lawrence3.reg

@@ -0,0 +1,27 @@
+Region written by ACE/gredit
+1
+24 1
+-55.397967 51.948530
+-55.854884 51.786533
+-56.341280 51.595082
+-56.842414 51.315269
+-57.476203 50.932366
+-58.404776 49.754206
+-59.392307 48.826405
+-59.657614 48.325687
+-59.598657 47.633518
+-59.171218 47.338978
+-58.198427 47.324251
+-57.446724 47.250616
+-56.827675 47.103346
+-56.429715 46.823533
+-55.958059 46.632082
+-55.545359 46.440631
+-54.867353 46.352269
+-53.997737 46.293361
+-53.319731 46.337542
+-52.848074 46.646809
+-52.892292 47.103346
+-53.452384 47.957512
+-54.454654 50.402194
+-55.132660 51.698171

src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Gr3/Nudge_gr3/gen_nudge_gr3.py

@@ -0,0 +1,83 @@
+from pylib_essentials.schism_file import schism_grid
+
+def gen_nudge(hgrid:schism_grid, outdir, rlmax = 1.5, rnu_day=0.25):
+        """
+        schism_grid (from pylib) must be in lon/lat coordinates
+        set up nudge zone within rlmax distance from the ocean boundary;
+        modify the nudging zone width rlmax.
+        rlmax can be a uniform value, e.g., rl_max = 1.5,
+        or a 2D array of the same size as the hgrid's number of nodes,
+        e.g., rl_max = np.zeros(NP) with further tuning of the nudging zone width.
+        """
+
+        rnu_max = 1.0 / rnu_day / 86400.0
+
+        #get nudge zone
+        lon = hgrid.x
+        lat = hgrid.y
+        nudge_coeff = np.zeros(hgrid.x.shape, dtype=float)
+
+        global_idxs = {}
+
+        t0 = time()
+
+        nudge_coeff = np.array([0.0]*NP, dtype=float)
+
+        for i in self.ocean_bnd_ids:
+            print(f'boundary {i}')
+            bnd_idxs = gdf.iloc[i].indexes
+
+            dis = abs((lon + 1j*lat)[:, None] - (lon[bnd_idxs] + 1j*lat[bnd_idxs])[None, :]).min(axis=1)
+
+            out = (1-dis/rlmax)*rnu_max
+            out[out<0] = 0
+            out[out>rnu_max] = rnu_max
+            fp = out>0
+            nudge_coeff[fp] = np.maximum(out[fp], nudge_coeff[fp])
+
+            idxs_nudge=np.zeros(NP, dtype=int)
+            idxs=np.where(out > 0)[0]
+            idxs_nudge[idxs]=1
+
+            #expand nudging marker to neighbor nodes
+            i34 = self.hgrid.elements.i34
+            fp = i34==3
+            idxs=np.where(np.max(out[elnode[fp, 0:3]], axis=1) > 0)[0]
+            idxs_nudge[elnode[fp,0:3][idxs,:]]=1
+            idxs=np.where(np.max(out[elnode[~fp, :]], axis=1) > 0)[0]
+            idxs_nudge[elnode[~fp,:][idxs,:]]=1
+
+            idxs=np.where(idxs_nudge == 1)[0]
+            global_idxs[i] = idxs
+
+
+        #logger.info(f'len of nudge idxs is {len(idxs)}')
+        logger.info(f'It took {time() -t0} sencods to calcuate nudge coefficient')
+
+        nudge = [f"rlmax={rlmax}, rnu_day={rnu_day}"]
+        nudge.extend("\n")
+        nudge.append(f"{NE} {NP}")
+        nudge.extend("\n")
+        hgrid = self.hgrid.to_dict()
+        nodes = hgrid['nodes']
+        elements = hgrid['elements']
+        for idn, (coords, values) in nodes.items():
+            line = [f"{idn}"]
+            line.extend([f"{x:<.7e}" for x in coords])
+            line.extend([f"{nudge_coeff[int(idn)-1]:<.7e}"])
+            line.extend("\n")
+            nudge.append(" ".join(line))
+
+        for id, element in elements.items():
+            line = [f"{id}"]
+            line.append(f"{len(element)}")
+            line.extend([f"{e}" for e in element])
+            line.extend("\n")
+            nudge.append(" ".join(line))
+
+        with open(outdir / 'TEM_nudge.gr3','w+') as fid:
+            fid.writelines(nudge)
+
+        shutil.copy2(outdir / 'TEM_nudge.gr3', outdir / 'SAL_nudge.gr3')
+
+        return global_idxs

src/Utility/Pre-Processing/STOFS-3D-Atl-shadow-VIMS/Pre_processing/Nudge/gen_nudge2.py

@@ -0,0 +1,21 @@
+#! /usr/bin/env python
+from datetime import datetime, timedelta
+import logging
+
+from pyschism.mesh import Hgrid, Vgrid
+from pyschism.forcing.hycom.hycom2schism import Nudge
+
+
+logging.basicConfig(level=logging.INFO, force=True)
+
+
+if __name__ == '__main__':
+
+    hgrid=Hgrid.open('./hgrid.gr3', crs='epsg:4326')
+    vgrid='./vgrid.in'
+    outdir='./'
+    start_date = datetime(2022, 1, 1)
+    rnday=171
+
+    nudge=Nudge()
+    nudge.fetch_data(outdir, hgrid, vgrid, start_date, rnday)