def test_point_source_1d():
"""
Create a 1D water column, with a point source at the bed.
Verifies that all cells with valid thickness (dzz>0.001m)
have near unity salinity.
"""
g=unstructured_grid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0,0],[10,10],2,2)
g.add_cell_field('depth',-6*np.ones(g.Ncells()))
model=sun_driver.SuntansModel()
model.load_template('point_source_test.dat')
model.set_grid(g)
model.run_start=np.datetime64("2018-01-01 00:00")
model.run_stop =np.datetime64("2018-01-01 10:00")
source=sun_driver.SourceSinkBC(name='inflow',geom=np.array([5,5]),
z=-10,Q=1.0)
model.add_bcs(source)
model.add_bcs( [sun_driver.ScalarBC(parent=source,scalar="S",value=1),
sun_driver.ScalarBC(parent=source,scalar="T",value=1)] )
model.set_run_dir('rundata_point_1d', mode='pristine')
model.projection='EPSG:26910'
model.config['dt']=2.5
model.config['ntout']=1
model.config['Cmax']=30
model.config['Nkmax']=10
model.config['stairstep']=0
model.config['mergeArrays']=0
model.write()
model.ic_ds.eta.values[:]=-5.999
model.ic_ds.salt.values[:]=1.0
model.ic_ds.temp.values[:]=1.0
model.write_ic_ds()
model.partition()
model.sun_verbose_flag='-v'
model.run_simulation()
ds=xr.open_dataset(model.map_outputs()[0])
dzz=ds.dzz.values
dzz_thresh=0.001
salt=ds.salt.values
salt_errors=salt[dzz>=dzz_thresh] - 1.0
assert np.max( np.abs(salt_errors) )<0.001
def base_model():
"""
Channel
"""
g=unstructured_grid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0,0],[1000,100],21,3)
g.add_cell_field('depth',-6*np.ones(g.Ncells()))
model=sun_driver.SuntansModel()
model.load_template('point_source_test.dat')
model.set_grid(g)
model.run_start=np.datetime64("2018-01-01 00:00")
model.run_stop =np.datetime64("2018-01-05 00:00")
dt=np.timedelta64(600,'s')
times=np.arange(model.run_start-dt,model.run_stop+2*dt,dt)
secs=(times-times[0])/np.timedelta64(1,'s')
eta0=-1
eta_bc=sun_driver.StageBC(name="eta_bc",
geom=np.array([ [0,0],
[0,100]]),
z=eta0)
model.add_bcs(eta_bc)
model.add_bcs( [sun_driver.ScalarBC(parent=eta_bc,scalar="S",value=34),
sun_driver.ScalarBC(parent=eta_bc,scalar="T",value=15)] )
model.set_run_dir('rundata_met_3d', mode='pristine')
model.projection='EPSG:26910'
model.num_procs=1 # test single first
model.config['dt']=120
model.config['ntout']=5
model.config['Cmax']=30
model.config['Nkmax']=10
model.config['stairstep']=0
model.config['mergeArrays']=0
return model
def base_model_setup(L=100, dx=10):
g = unstructured_grid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0, 0], [L, 10], 1 + int(L / dx), 2)
g.add_cell_field('depth', -6 * np.ones(g.Ncells()))
model = sun_driver.SuntansModel()
model.num_procs = 1
model.load_template('point_source_test.dat')
model.set_grid(g)
model.run_start = np.datetime64("2018-01-01 00:00")
model.run_stop = np.datetime64("2018-01-02 00:00")
# 50m2, 5.0 m3/s, 0.1m/s
source = sun_driver.FlowBC(name='inflow',
geom=np.array([[0, 0], [0, 10]]),
Q=10.0)
outlet = sun_driver.StageBC(name='outflow',
geom=np.array([[100, 0], [100, 10]]),
z=-1)
model.add_bcs([source, outlet])
model.set_run_dir('rundata_2d_average', mode='pristine')
model.projection = 'EPSG:26910'
model.config['dt'] = 2.5
model.config['ntout'] = 100
model.config['ntaverage'] = 100
model.config['calcaverage'] = 1
model.config['averageNetcdfFile'] = "average.nc"
model.config['thetaramptime'] = 100
model.config['Cmax'] = 2
model.config['Nkmax'] = 1
model.config['stairstep'] = 0
model.config['mergeArrays'] = 0
return model
import numpy as np
import xarray as xr
import pandas as pd
from stompy import filters, utils
from stompy.spatial import wkb2shp
from stompy.grid import unstructured_grid
from stompy.model.suntans import sun_driver as drv
import stompy.model.delft.dflow_model as dfm
six.moves.reload_module(utils)
six.moves.reload_module(dfm)
six.moves.reload_module(unstructured_grid)
six.moves.reload_module(drv)
model=drv.SuntansModel()
model.projection="EPSG:26910"
model.num_procs=1
model.sun_bin_dir="/home/rusty/src/suntans/main"
model.mpi_bin_dir="/usr/bin"
model.load_template("sun-template.dat")
# backstep_00: initial... clobbered.
# 01: nu_H 0.0 => 0.25
model.set_run_dir(os.path.join('runs',"backstep_01"),
mode='pristine')
model.run_start=np.datetime64('2017-03-01 00:00:00')
model.run_stop=np.datetime64('2017-03-01 04:00:00')
cc = g.cells_center()
cell_depth = -6 + np.cos(cc[:, 0] * np.pi / half_wave) * np.cos(
cc[:, 1] * np.pi / half_wave)
g.add_cell_field('depth', cell_depth)
#plt.clf()
#g.plot_cells(values=cell_depth,cmap='jet')
#plt.axis('equal')
##
n1 = g.select_nodes_nearest([300, 0])
n2 = g.select_nodes_nearest([300, 500])
model = sun_driver.SuntansModel()
model.load_template('sun-template.dat')
model.set_grid(g)
model.run_start = np.datetime64("2018-01-01 00:00")
model.run_stop = np.datetime64("2018-01-01 10:00")
dt = np.timedelta64(600, 's')
times = np.arange(model.run_start - dt, model.run_stop + 2 * dt, dt)
secs = (times - times[0]) / np.timedelta64(1, 's')
eta_values = -6 + 0.75 * np.cos(secs * np.pi / 7200)
eta_da = xr.DataArray(eta_values, coords=[('time', times)])
eta_bc = sun_driver.StageBC(name="eta_bc",
geom=np.array([[0, 0], [0, 500]]),
z=eta_da)
model.add_bcs(eta_bc)
def test_point_source_3d():
"""
A square 3D grid with wetting and drying.
the bathymetry is a wavy cos(x)*cos(y) function.
two point sources and an oscillating freesurface.
one point source at a saddle point, and the other
on top of a bump which goes dry.
This currently does pretty well, but it could be
better -- see the test thresholds near the end which
have been relaxed somewhat.
"""
g=unstructured_grid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0,0],[500,500],50,50)
# wavy bed
half_wave=150
cc=g.cells_center()
cell_depth=-6 + np.cos(cc[:,0]*np.pi/half_wave) * np.cos(cc[:,1]*np.pi/half_wave)
g.add_cell_field('depth',cell_depth)
model=sun_driver.SuntansModel()
model.load_template('point_source_test.dat')
model.set_grid(g)
model.run_start=np.datetime64("2018-01-01 00:00")
model.run_stop =np.datetime64("2018-01-01 10:00")
dt=np.timedelta64(600,'s')
times=np.arange(model.run_start-dt,model.run_stop+2*dt,dt)
secs=(times-times[0])/np.timedelta64(1,'s')
eta_values=-6 + 0.75*np.cos(secs*np.pi/7200)
eta_da=xr.DataArray(eta_values,coords=[ ('time',times) ])
eta_bc=sun_driver.StageBC(name="eta_bc",geom=np.array([ [0,0],
[0,500]]),
z=eta_da)
model.add_bcs(eta_bc)
model.add_bcs( [sun_driver.ScalarBC(parent=eta_bc,scalar="S",value=1),
sun_driver.ScalarBC(parent=eta_bc,scalar="T",value=1)] )
# point source that is typically dry
hill_source=sun_driver.SourceSinkBC(name='inflow',geom=np.array([150,150]),
z=-10,Q=1.0)
# on a saddle
saddle_source=sun_driver.SourceSinkBC(name='inflow',geom=np.array([220,225]),
z=-10,Q=1.0)
model.add_bcs(hill_source)
model.add_bcs(saddle_source)
model.add_bcs( [sun_driver.ScalarBC(parent=hill_source,scalar="S",value=1),
sun_driver.ScalarBC(parent=hill_source,scalar="T",value=1)] )
model.add_bcs( [sun_driver.ScalarBC(parent=saddle_source,scalar="S",value=1),
sun_driver.ScalarBC(parent=saddle_source,scalar="T",value=1)] )
model.set_run_dir('rundata_point_3d', mode='pristine')
model.projection='EPSG:26910'
model.num_procs=4
model.config['dt']=2.5
model.config['ntout']=5
model.config['Cmax']=30
model.config['Nkmax']=10
model.config['stairstep']=0
model.config['mergeArrays']=0
model.write()
model.ic_ds.eta.values[:]=eta_da.values[1]
model.ic_ds.salt.values[:]=1.0
model.ic_ds.temp.values[:]=1.0
model.write_ic_ds()
model.partition()
model.sun_verbose_flag='-v'
model.run_simulation()
for map_fn in model.map_outputs():
ds=xr.open_dataset(map_fn)
dzz=ds.dzz.values
# This is not as strict as it should be.
# should be 0.001 or less.
dzz_thresh=0.05
salt=ds.salt.values
valid=np.isfinite(dzz) & (dzz>=dzz_thresh)
salt_errors=salt[valid] - 1.0
# This is not as strict as it should be.
# we should be able to get this down to 1e-4 or
# better.
assert np.max( np.abs(salt_errors) )<0.01
ds.close()
six.moves.reload_module(local_config)
local_config.install()
##
# fabricate grid:
g = unstructured_grid.UnstructuredGrid(max_sides=4)
L = 10000
W = 75
g.add_rectilinear([0, 0], [L, W], 101, 6)
g.add_node_field('z_bed', -(10 - 8 * (2 * g.nodes['x'][:, 1] / W - 1)**2))
#model=dfm.DFlowModel()
six.moves.reload_module(dfm)
six.moves.reload_module(sun)
local_config.install()
model = sun.SuntansModel()
model.set_grid(g)
model.run_start = np.datetime64("2010-01-01 00:00")
model.run_stop = np.datetime64("2010-01-05 00:00")
ds = xr.Dataset()
ds['time'] = ('time', ), np.arange(model.run_start, model.run_stop,
np.timedelta64(15, 'm'))
t_sec = (ds.time - ds.time[0]) / np.timedelta64(1, 's')
ds['eta'] = ('time', ), np.cos(2 * np.pi * t_sec / (12 * 3600.))
model.add_bcs(
dfm.StageBC(name='tide', z=ds.eta, geom=np.array([[0, 0], [0, W]])))
dt_secs = 30
def base_model():
"""
A channel, uniform bathy.
"""
g=unstructured_grid.UnstructuredGrid(max_sides=4)
g.add_rectilinear([0,0],[1000,100],21,3)
g.add_cell_field('depth',-6*np.ones(g.Ncells()))
model=sun_driver.SuntansModel()
model.load_template('point_source_test.dat')
model.set_grid(g)
model.run_start=np.datetime64("2018-01-01 00:00")
model.run_stop =np.datetime64("2018-01-01 10:00")
dt=np.timedelta64(600,'s')
times=np.arange(model.run_start-dt,model.run_stop+2*dt,dt)
secs=(times-times[0])/np.timedelta64(1,'s')
eta0=-2
eta_bc=sun_driver.StageBC(name="eta_bc",
geom=np.array([ [0,0],
[0,100]]),
z=eta0)
model.add_bcs(eta_bc)
model.add_bcs( [sun_driver.ScalarBC(parent=eta_bc,scalar="S",value=1),
sun_driver.ScalarBC(parent=eta_bc,scalar="T",value=1)] )
model.set_run_dir('rundata_sedi_3d', mode='pristine')
model.projection='EPSG:26910'
model.num_procs=1 # test single first
model.config['dt']=30
model.config['ntout']=5
model.config['Cmax']=30
model.config['Nkmax']=10
model.config['stairstep']=0
model.config['mergeArrays']=0
# Sediment:
model.config['computeSediments']=1 # whether include sediment model
model.config['Nlayer']=0 # Number of bed layers (MAX = 5)
model.config['Nsize']=3 # Number of sediment fractions (Max = 3)
model.config['TBMAX']=1 # whether to output tb for each cell
model.config['SETsediment']=0 # When Nlayer>5 or Nsize>3, SETsediment=1 to use SetSediment
model.config['WSconstant']=1 # if 1, ws for sediment = ws0
model.config['readSediment']=0 # if 1, read sediment concentration data as IC. only work with Nsize==1
model.config['bedInterval']=150 # the interval steps to update bed change
model.config['bedComplex']=0 # whether to consider the possibility to flush away a whole layer
model.config['ParabolKappa']=0 # whether to use parabolic tubulent diffusivity
model.config['Ds90']=0.000008 # ds90 for calculation of erosion taub
model.config['Ds1']=0.00000057 # sediment diameter for fraction No.1 (m)
model.config['Ds2']=0.0002 # sediment diameter for fraction No.2
model.config['Ds3']=0.0002 # sediment diameter for fraction No.3
model.config['Ws01']= 0.0001 # constant settling velocity for fraction No.1 (m/s)
model.config['Ws02']= 0.01 # constant settling velocity for fraction No.2
model.config['Ws03']=-0.01 # constant settling velocity for fraction No.3
model.config['Gsedi1']=2.65 # relative density for fraction No.1
model.config['Gsedi2']=2.65 # relative density for fraction No.2
model.config['Gsedi3']=2.65 # relative density for fraction No.3
model.config['Prt1']=1 # Prandtl Number for fraction No.1
model.config['Prt2']=1 # Prandtl Number for fraction No.2
model.config['Prt3']=1 # Prandtl Number for fraction No.3
model.config['Consolid1']=0.00 # Consolidation rate (g/m^2/s) for layer No.1
model.config['E01']=0.1 # Basic Erosion Rate Constant (g/m^2/s) for layer No.1
model.config['Taue1']=0.0 # Erosion Critical Shear Stress (N/m^2) for layer No.1
# Taud1 isn't actually used in current code. Deposition always occurs at the rate
# of w_s.
model.config['Taud1']=0.0 # Deposition Critical Shear Stress (N/m^2) for layer No.1
model.config['Drydensity1']=530000 # Dry density (g/m^3) for layer No.1
model.config['Thickness1']=0.0 # Thickness (m) for layer No.1
model.config['softhard1']=1 # 0 soft or hard for layer No.1 to decide how to calculate erosion
model.config['Bedmudratio1']=0.8 # Bed mud ratio for layer No.1
model.config['Chind']=1000000 # Concentration (in volumetric fraction) criterion for hindered settling velocity
model.config['Cfloc']=500000 # Concentration (in volumetric fraction) criterion for flocculated settling velcoity
model.config['k']=0.0002 # Constant coefficient for settling velocity as a function of conc.
model.config['Sediment1File']='sedi1.dat'
model.config['Sediment2File']='sedi2.dat'
model.config['Sediment3File']='sedi3.dat'
model.config['LayerFile']='sedilayer.dat'
model.config['tbFile']='Seditb.dat'
model.config['tbmaxFile']='Seditbmax.dat'
return model
