Final merge ICOGS3D branch

schism-dev · May 22, 2021 · 473827d · 473827d
2 parents 5fa3c83 + 858f460
commit 473827d
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diff --git a/pyschism/forcing/hycom/hycom2schism.py b/pyschism/forcing/hycom/hycom2schism.py
@@ -330,7 +330,11 @@ def fetch_data(self, outdir: Union[str, os.PathLike], hgrid, vgrid, start_date,
             dst['map_to_global_node'][:] = include+1
 
             dst.createVariable('tracer_concentration', 'f', ('time', 'node', 'nLevels', 'one'))
+<<<<<<< HEAD
             dst['tracer_concentration'][:, :, :, :] = timeseries_s
+=======
+            dst['tracer_concentration'][:,:,:,:] = timeseries_s
+>>>>>>> origin/ICOGS3D
 
         with Dataset(outdir / 'TEM_nu.nc', 'w', format='NETCDF4') as dst:
             # dimensions
@@ -346,9 +350,13 @@ def fetch_data(self, outdir: Union[str, os.PathLike], hgrid, vgrid, start_date,
             dst['map_to_global_node'][:] = include+1
 
             dst.createVariable('tracer_concentration', 'f', ('time', 'node', 'nLevels', 'one'))
+<<<<<<< HEAD
             dst['tracer_concentration'][:, :, :, :] = timeseries_t
 
         print(f'Writing *_nu.nc takes {time()-t0} seconds')
+=======
+            dst['tracer_concentration'][:,:,:,:] = timeseries_t
+>>>>>>> origin/ICOGS3D
 
 
 class InitialTS():

diff --git a/pyschism/mesh/fgrid.py b/pyschism/mesh/fgrid.py
@@ -141,6 +141,7 @@ def __init__(self, *argv, **kwargs):
     def linear_with_depth(
             cls,
             hgrid: Union[str, os.PathLike, Gr3],
+<<<<<<< HEAD
             depth1: float = -1.0,  # Are depth1 and depth2 positive up or positive down?
             depth2: float = -3.0,
             bfric_river: float = 0.0025,
@@ -151,6 +152,22 @@ def linear_with_depth(
 
         values = (bfric_river + (depth1 + hgrid.values) *
                   (bfric_land - bfric_river) / (depth1-depth2))
+=======
+            depth1: float = -1.0,
+            depth2: float = -3.0,
+            bfric_river: float = 0.0025,
+            bfric_land: float = 0.025):
+
+        obj = cls.constant(hgrid, np.nan)
+
+        '''
+        Note: pyschism treated bathymetry as negative in the water,
+             postive on the land. So here we have to negative the depth
+             value depth1 - (-hgrid.values)
+        ''' 
+        values = (bfric_river + (depth1+hgrid.values) \
+                * (bfric_land-bfric_river)/(depth1-depth2))
+>>>>>>> origin/ICOGS3D
 
         values[values > bfric_land] = bfric_land
         values[values < bfric_river] = bfric_river