Merge branch 'main' of https://github.com/openearth/xbeach-toolbox

.gitignore

@@ -0,0 +1,6 @@
+/xbTools/__pycache__
+/xbTools/general/__pycache__
+/xbTools/grid/__pycache__
+/.idea
+/examples/xb-2D/
+

examples/xbeach-setup-1D.ipynb

@@ -306,7 +306,7 @@
     "xb_setup.set_waves('parametric',{'Hm0':2, 'Tp':5, 'mainang':270, 'gammajsp':3.3, 's' : 10000, 'fnyq':1})\n",
     "#xb_setup.set_waves('jonstable',{'Hm0':[1.5, 2, 1.5],'Tp':[4, 5, 4],'gammajsp':[3.3, 3.3, 3.3], 's' : [20,20,20], 'mainang':[270,280, 290],'duration':[3600, 3600, 3600],'dtbc':[1,1,1]})\n",
     "\n",
-    "xb_setup.set_params({'Wavemodel':'surfbeat',\n",
+    "xb_setup.set_params({'wavemodel':'surfbeat',\n",
     "                     'morphology':0,\n",
     "                     'befriccoef':0.01,\n",
     "                     'tstop':3600,\n",

xbTools/general/executing_runs.py

@@ -2,7 +2,6 @@
 """
 Created on Wed May 5 10:04:00 2023
 
-@author: Cas van Bemmelen
 collection containing executing run functionalities
 """
 # import python modules
@@ -38,7 +37,7 @@ def xb_run_script_win(xb, N, maindir, xbeach_exe):
             for item in xb:
                 path_sims.append(item.model_path)
         elif isinstance(xb[0],str):
-            path_sims = [xb]
+            path_sims = xb
         else:
             print('Unvalid path')
     else:
@@ -64,4 +63,5 @@ def xb_run_script_win(xb, N, maindir, xbeach_exe):
         print(os.path.join(maindir,'run{}.bat'.format(run_number)))
         with open(os.path.join(maindir,'run{}.bat'.format(run_number)), 'w') as f:
             f.write(string)
+
 

xbTools/general/visualize_mesh.py

@@ -40,7 +40,9 @@ def plot_mesh(mesh_x,mesh_y,thinning=1,ax=None,**kwargs):
     # thin on y axis and then on x axis if value > 1
     ax.plot(mesh_x[:,::thinning], mesh_y[:,::thinning], **kwargs)
     ax.plot(mesh_x[::thinning,:].T, mesh_y[::thinning,:].T, **kwargs)
-
+    ax.plot(mesh_x[:,-1], mesh_y[:,-1], **kwargs)
+    ax.plot(mesh_x[-1,:].T, mesh_y[-1,:].T, **kwargs)
+
 def write_mesh_to_shp(mesh_x,mesh_y,file_name,modelnr,EPSG=3844):
     '''
     Function to write mesh to shapefile

xbTools/grid/extension.py

@@ -103,11 +103,16 @@ def seaward_extend(x,y,z,slope=1/20,depth=-20):
 
     ## maximum distance
     distance    = (z0max - depth)/slope
+
     ## prevent very small grid sizes!
     distance    = np.ceil(distance/dx_grid) * dx_grid
+
     ## dummy array
     x_dummy     = np.arange(x[0, 0]-distance, x[0, 0], dx_grid)
-
+    # prevent very small grid sizes when floating point zero goes wrong for computing var distance!
+    if (x_dummy[-1]-x[0, 0])< 0.01:
+        x_dummy = x_dummy[:-1]  
+
     x_extend    = np.ones((x.shape[0], len(x_dummy) ))
     x_extend    = x_extend * x_dummy
     z_extend    = np.ones_like(x_extend)

xbTools/par.json

@@ -1,21 +1,159 @@
-{"Physical processes":["wavemodel","sedtrans","morphology","vegetation","spongelength","ships","wind","viscosity","swrunup","swave","snells","single_dir","setbathy","gwflow","avalanching","nonhq3d"],
-"Initial conditions":["zs0","zsinitfile","hotstartflow"],
-"Model time":["tstop","CFL"],
-"Grid parameters":["thetamin","thetamax","dtheta","dtheta_s","thetanaut","posdwn"],
-"Flow boundary condition parameters":["front","back","left","right"],
-"Flow parameters":["tidetype","epsi","bedfriction","bedfriccoef","nuhfac","bedfricfile"],
-"Flow numerics parameters" : ["eps","eps_sd"],
-"Tide boundary conditions":["zs0file","tideloc","paulrevere"],
-"Wave boundary condition parameters":["Hrms","Tlong","Trep","dir0","m","taper","Tm01"],
-"Wave-spectrum boundary condition parameters":["wbctype","rt","Tm01switch","correctHm0","dtbc","dthetaS_XB","fcutoff","nonhspectrum","nspectrumloc","nspr","random","sprdthr","trepfac","wbcEvarreduce","wbcScaleEnergy","wbcRemoveStokes","wbcversion"],
-"Wave breaking parameters":["break","gamma","gamma2","alpha","deltahmin","fwfile"],
-"Roller parameters":["beta"],
-"Morphology parameters":["morstart","morfac","wetslp","struct","ne_layer","Hswitch"],
-"Sediment input":["por","ws","rhos","ngd"],
-"Bed composition parameters":["D50","D90"],
-"Bed update numerics parameters":["nTrepavaltime"],
-"Sediment transport parameters":["form","waveform","facSk","facAs","bulk","alfaD50","oldTsmin","oldhmin","bulk"],
-"Sediment transport numerics parameters":["dtlimTs"],
-"Avalanching":["wetslp","dryslp","fixedavaltime"],
-"Output":["outputformat","tintg","tintm","tstart","tintp","tintc","nrugdepth","outputprecision","timings"],
-"_Output": ["nglobalvar","nmeanvar","npointvar","npoints"]}
+{
+    "_General": [
+        "wavemodel",
+        "wbctype"
+    ],
+    "Physical processes": [
+        "sedtrans",
+        "morphology",
+        "vegetation",
+        "spongelength",
+        "ships",
+        "wind",
+        "viscosity",
+        "swrunup",
+        "swave",
+        "snells",
+        "single_dir",
+        "setbathy",
+        "gwflow",
+        "avalanching",
+        "cyclic",
+        "nonhq3d"
+    ],
+    "Initial conditions": [
+        "zs0",
+        "zsinitfile",
+        "hotstartflow"
+    ],
+    "Model time": [
+        "tstop",
+        "CFL"
+    ],
+    "Grid parameters": [
+        "thetamin",
+        "thetamax",
+        "dtheta",
+        "dtheta_s",
+        "thetanaut",
+        "posdwn"
+    ],
+    "Flow boundary condition parameters": [
+        "front",
+        "back",
+        "left",
+        "right"
+    ],
+    "Flow parameters": [
+        "tidetype",
+        "epsi",
+        "bedfriction",
+        "bedfriccoef",
+        "nuhfac",
+        "bedfricfile"
+    ],
+    "Flow numerics parameters": [
+        "eps",
+        "eps_sd"
+    ],
+    "Tide boundary conditions": [
+        "zs0file",
+        "tideloc",
+        "paulrevere"
+    ],
+    "Wave boundary condition parameters": [
+        "Hrms",
+        "Tlong",
+        "Trep",
+        "dir0",
+        "m",
+        "taper",
+        "Tm01"
+    ],
+    "Wave-spectrum boundary condition parameters": [
+        "rt",
+        "Tm01switch",
+        "correctHm0",
+        "dtbc",
+        "dthetaS_XB",
+        "fcutoff",
+        "nonhspectrum",
+        "nspectrumloc",
+        "nspr",
+        "random",
+        "sprdthr",
+        "trepfac",
+        "wbcEvarreduce",
+        "wbcScaleEnergy",
+        "wbcRemoveStokes",
+        "wbcversion"
+    ],
+    "Wave breaking parameters": [
+        "break",
+        "gamma",
+        "gamma2",
+        "alpha",
+        "deltahmin",
+        "fwfile"
+    ],
+    "Roller parameters": [
+        "beta"
+    ],
+    "Morphology parameters": [
+        "morstart",
+        "morfac",
+        "wetslp",
+        "struct",
+        "ne_layer",
+        "Hswitch"
+    ],
+    "Sediment input": [
+        "por",
+        "ws",
+        "rhos",
+        "ngd"
+    ],
+    "Bed composition parameters": [
+        "D50",
+        "D90"
+    ],
+    "Bed update numerics parameters": [
+        "nTrepavaltime"
+    ],
+    "Sediment transport parameters": [
+        "form",
+        "waveform",
+        "facSk",
+        "facAs",
+        "bulk",
+        "alfaD50",
+        "oldTsmin",
+        "oldhmin",
+        "bulk"
+    ],
+    "Sediment transport numerics parameters": [
+        "dtlimTs"
+    ],
+    "Avalanching": [
+        "wetslp",
+        "dryslp",
+        "fixedavaltime"
+    ],
+    "Output": [
+        "outputformat",
+        "tintg",
+        "tintm",
+        "tstart",
+        "tintp",
+        "tintc",
+        "nrugdepth",
+        "outputprecision",
+        "timings"
+    ],
+    "_Output": [
+        "nglobalvar",
+        "nmeanvar",
+        "npointvar",
+        "npoints"
+    ]
+}

xbTools/xbeachpost.py

@@ -2,7 +2,7 @@
 """
 Created on Fri Aug 11 14:10:02 2023
 
-@author: MarliesA
+@author: Marlies van der Lugt
 main collection for the postprocessing of XBeach models
 module contains class for analysis of 2D XBeach models 
 note that output and input must be available in directory
@@ -52,7 +52,7 @@ def __init__(self, fname, model_path):
         self.plot_km_coords = False
         self.AOI = []
         self.globalstarttime = None
-        self.unitdict = {'Hm0': ' [m]', 'H': ' [m]', 'zs': ' [m+NAP]', 'u': ' [m/s]', 'v': ' [m/s]',
+        self.unitdict = {'Hm0': ' [m]', 'H': ' [m]', 'zs': ' [m]', 'u': ' [m/s]', 'v': ' [m/s]',
                          'zb': ' [m]', 'thetamean': ' [deg]', 'beta': '[-]'}
 
     def get_metadata(self):
@@ -312,7 +312,7 @@ def load_output_coordinates(self):
         x = ds.variables['globalx'][:]
         y = ds.variables['globaly'][:]
         if len(self.AOI) > 0:
-            assert len(self.AOI) == 4, 'AOI should be specified as [x0, xend, y0, yend]'
+            assert len(self.AOI) == 4, 'AOI should be specified as [i_y0, i_yend, i_x0, i_xend]'
 
             x = x[self.AOI[0]:self.AOI[1], self.AOI[2]:self.AOI[3]]
             y = y[self.AOI[0]:self.AOI[1], self.AOI[2]:self.AOI[3]]
@@ -426,6 +426,8 @@ def load_modeloutput(self, var):
 
         if '_mean' in var:
             assert sum([var[:-5] in x for x in self.params['meanvar']]) > 0, '{} not in xb output'
+        elif '_var' in var:
+            assert sum([var[:-4] in x for x in self.params['meanvar']]) > 0, '{} not in xb output'
         elif '_min' in var:
             assert sum([var[:-4] in x for x in self.params['meanvar']]) > 0, '{} not in xb output'
         elif '_max' in var:
@@ -540,8 +542,8 @@ def fig_check_tide_bc(self):
         assert 'zs0file' in self.params, 'No tidal signal available'
 
         # get model output
-        self.load_modeloutput('zs')
-        zs = self.var['zs']
+        self.load_modeloutput('zs_mean')
+        zs = self.var['zs_mean']
 
         # get model input
         if self.tide == {}:
@@ -624,7 +626,7 @@ def _fig_map_var(self, dat, label, figsize=None, **kwargs):
         divider = make_axes_locatable(ax)
         cax = divider.append_axes('right', size='5%', pad=0.05)
 
-        if np.max(np.abs(dat))<0.001:
+        if np.max(np.abs(dat))<0.01:
             fmt = lambda x, pos: '{:.1e}'.format(x)
         else:
             fmt = lambda x, pos: '{:.1f}'.format(x)
@@ -656,7 +658,7 @@ def _fig_map_var(self, dat, label, figsize=None, **kwargs):
 
         return fig, ax
 
-    def fig_map_var(self, var, label, it=np.inf, figsize=None, **kwargs):
+    def fig_map_var(self, var, label=None, it=np.inf, figsize=None, **kwargs):
         """_summary_
 
         Args:
@@ -675,6 +677,8 @@ def fig_map_var(self, var, label, it=np.inf, figsize=None, **kwargs):
         assert it <= len(self.var['globaltime']) - 1, 'it should be <= {}'.format(len(self.var['globaltime']) - 1)
 
         data = self.var[var][it, :, :]
+        if label is None:
+            label = str(var)
         fig, ax = self._fig_map_var(data, label, figsize, **kwargs)
 
         if self.globalstarttime is None:
@@ -758,7 +762,7 @@ def fig_cross_var(self,var, it, iy=None, coord=None, plot_ref_bathy=True, zmin=-
             self.load_modeloutput(var)
         except:
             print('var not found as output specified in params. Will try to continue to see if computed earlier')
-        self.load_modeloutput('zb')
+
 
         x = self.var['globalx']
         y = self.var['globaly']
@@ -768,7 +772,6 @@ def fig_cross_var(self,var, it, iy=None, coord=None, plot_ref_bathy=True, zmin=-
             iy, _ = np.unravel_index(((x - coord[0]) ** 2 + (y - coord[1]) ** 2).argmin(), x.shape)
 
         data = self.var[var][it, iy, :]
-        z = self.var['zb'][it, iy, :]
         cross = self.var['cross']
 
         fig, ax1 = plt.subplots(figsize=[5, 3])
@@ -781,6 +784,9 @@ def fig_cross_var(self,var, it, iy=None, coord=None, plot_ref_bathy=True, zmin=-
             ax1.set_xlabel('cross shore [m]')
 
         if plot_ref_bathy:
+            self.load_modeloutput('zb')
+            z = self.var['zb'][it, iy, :]
+
             ax2 = ax1.twinx()
             ax1.set_zorder(ax2.get_zorder() + 1)  # move ax in front
             ax1.patch.set_visible(False)