Updated Storm Model scripts

scripts/ampang.py

@@ -35,8 +35,8 @@ def __init__(self, reff=1.0, fig=None, rect=111, label='_', amprange=[0, 1.5],am
         self.reff = reff            # Reference standard deviation
         self.amprange = amprange    
         self.phsrange = phsrange    
-        idv = np.int( ( ampthck[1]+0.0000001 - ampthck[0] ) / ampthck[2] )+1
-        jdv = np.int( ( phsthck[1]+0.0000001 - phsthck[0] ) / phsthck[2] )+1
+        idv = np.int_( ( ampthck[1]+0.0000001 - ampthck[0] ) / ampthck[2] )+1
+        jdv = np.int_( ( phsthck[1]+0.0000001 - phsthck[0] ) / phsthck[2] )+1
 
         tr = PolarAxes.PolarTransform()
         degree_ticks = lambda d: (d*np.pi/180, "%d$^\\circ$"%(d))

scripts/analyse_tides.py

@@ -67,12 +67,12 @@
 
 ignore = []
 model_data = {}
-thetis_times = np.arange(params.spin_up, params.end_time, params.output_time)
+thetis_times = np.arange(params.spin_up, params.end_time+params.output_time, params.output_time)
 df = pd.read_csv(model_input, header=None)
 
 for name in tg_order:
     # pull amplitude
-    idx = tg_order.index(name)
+    idx = tg_order.index(name)+1
     # Subtract mean
     thetis_elev = df.iloc[:, idx]
     thetis_elev = thetis_elev - thetis_elev.mean()

scripts/create_rasters.sh

@@ -23,7 +23,7 @@ function process_file {
         # loop over variables with counter
         echo "   Rasterising ${var}"
         # create the raster ov the vtu
-        mpiexec -n ${ncore} python h5_2_raster.py --resolution ${resolution} ${file} ${mesh} temp --func ${var}
+        python h5_2_raster.py --resolution ${resolution} ${file} ${mesh} temp --func ${var}
         # create a filename
         filename="${directory}/${var}".nc
         #mask it

scripts/plot_tidal_gauges.py

@@ -40,7 +40,7 @@ def tex_escape(text):
 
 constituents = params.constituents
 tide = uptide.Tides(constituents)  # select which constituents to use
-tide.set_initial_time(params.start_datetime) 
+tide.set_initial_time(params.start_datetime + datetime.timedelta(hours=10)) 
 
 t_start = params.spin_up
 t_export = params.output_time
@@ -73,7 +73,7 @@ def tex_escape(text):
 tg_order = [] # we need to do things in order, so this helps keep track
 try:
     with open(tide_gauges, 'r') as csvfile:
-        # need to read in a couple of lines, rather thana set of bytes
+        # need to read in a couple of lines, rather than a set of bytes
         # for sniffer to work properly
         temp_lines = csvfile.readline() + '\n' + csvfile.readline()
         dialect = csv.Sniffer().sniff(temp_lines, delimiters=",\t")
@@ -95,15 +95,15 @@ def tex_escape(text):
     sys.exit(1)
 
 # list which gauges want plotting
-model_times = np.arange(t_start,t_end,t_export)
+model_times = np.arange(t_start,t_end+t_export,t_export)
 df = pd.read_csv(model_input, header=None)
 
 # now loop over tide gauges and plot them.
 for name in tg_order:
     # pull amplitude
     obs_amps = []
     obs_phases = []
-    idx = tg_order.index(name)
+    idx = tg_order.index(name) + 1
     for t in constituents:
         obs_amps.append(float(tide_gauge_data[name][t+" amp"]))
         obs_phases.append(np.radians(float(tide_gauge_data[name][t+" phase"])))

sims/base_case/tidal_forcing_tpxo.py

@@ -9,7 +9,7 @@
 constituents = params.constituents
 tide = uptide.Tides(constituents)
 # set your start date and time
-tide.set_initial_time(start_datetime)
+tide.set_initial_time(params.start_datetime)
 
 # point me at your TPXO files (grid and h_ data)
 grid_file_name = "../../data/grid_tpxo9.nc"

sims/base_case/tidal_model.py

@@ -15,9 +15,10 @@
 t_end = params.end_time
 output_dir = params.output_dir
 utm_zone = params.utm_zone
-utm_band=params.utm_band
+utm_band = params.utm_band
 cent_lat = params.cent_lat
 cent_lon = params.cent_lon
+t_start = 0
 
 # read bathymetry code
 chk = CheckpointFile('bathymetry.h5', 'r')
@@ -59,8 +60,8 @@ def coriolis(mesh, lat, lon):
 sim_tz = timezone.pytz.utc
 tau = Function(CG_2d_vec, name="tau")
 pressure = Function(CG_2d, name="pressure")
-tau_file = File(outputdir + '/tau.pvd')
-pressure_file = File(outputdir + '/pressure.pvd')
+tau_file = File(output_dir + '/Wind/tau.pvd')
+pressure_file = File(output_dir + '/Pressure/pressure.pvd')
 
 coord_system = coordsys.UTMCoordinateSystem(utm_zone=30, south=True)
 start_datetime = datetime.datetime(2020,2,14,0,0,0,tzinfo=sim_tz)