Look at the aggregated and lowpass data - is it actually lowpassing?
"""
import numpy as np
import matplotlib.pyplot as plt
import xarray as xr
from stompy import utils
import stompy.model.delft.waq_scenario as waq
import dwaq_transport
from stompy.plot import plot_utils
##
# This does not integrate over the timesteps, but dwaq_transport will handle that.
hydro=waq.HydroFiles('hydro-wy2013c_adj-agg_lp_2d/com-wy2013c_adj_agg_lp_2d.hyd')
##
scalar_name="stormwater"
scalar3_data_fn="scalar_data/%s-with_bc3.nc"%scalar_name
scalar4_data_fn="scalar_data_agg_lp_2d/%s-with_bc4.nc"%scalar_name
scalar3_nc=xr.open_dataset(scalar3_data_fn)
scalar4_nc=xr.open_dataset(scalar4_data_fn)
##
g=unstructured_grid.UnstructuredGrid.from_ugrid(scalar_nc)
##
return cleaned
else:
return shp_in
# Processing:
# remove multipolygons from inputs
shp = clean_shapefile(agg_grid_shp)
##
six.moves.reload_module(waq)
# open the original dwaq hydrodynamics
hydro_orig = waq.HydroFiles(hyd_fn)
# create object representing aggregated hydrodynamics
# sparse_layers: for z-layer inputs this can be True, in which cases cells are only output for the
# layers in which they are above the bed. Usually a bad idea. Parts of DWAQ assume
# each 2D cell exists across all layers
# agg_boundaries: if True, multiple boundary inputs entering a single aggregated cell will be
# merged into a single boundary input. Generally best to keep this as False.
hydro_agg = waq.HydroAggregator(hydro_in=hydro_orig,
agg_shp=shp,
sparse_layers=False,
agg_boundaries=False)
##
bdefs = hydro_agg.boundary_defs()
# Some preprocessing (this is necessary even if it's not an MPI run)
model.partition()
# Do it
model.run_model()
return model
# Run/load small hydro run:
model=base_model(force=False)
##
# 'model' represents the whole DFM model.
# dwaq.Hydro, and subclasses like dwaq.HydroFiles, represent
# the hydro information used by DWAQ.
base_hydro=dwaq.HydroFiles(model.hyd_output())
##
# Design a tracer release
# this is a simple gaussian blob.
def release_conc_fn(X):
X=X[...,:2] # drop z coordinate if it's there
X0=np.array([250,250]) # center of gaussian
L=50
c=np.exp( -((X-X0)**2).sum(axis=-1)/L**2 )
c=c/c.max() # make max value 1
return c
# Get the grid that DWAQ will use:
grid=base_hydro.grid()
"""
from __future__ import print_function
import argparse
import sys, os
import numpy as np
import stompy.model.delft.waq_scenario as waq
parser = argparse.ArgumentParser(
description='Adjust DFM D-WAQ output to add missing BC fluxes.')
parser.add_argument('hyd_fn',
metavar='dfm_out.hyd',
type=str,
help='path to hyd file')
args = parser.parse_args()
hyd_fn = args.hyd_fn
print("Opening hydro from %s" % hyd_fn)
hydro = waq.HydroFiles(hyd_fn)
print("Adjusting flows, updating %s in place" % hydro.get_path('flows-file'))
hydro.adjust_boundaries_for_conservation()
print("Done")
extra_fields=('salinity',
'temp',
'TotalDepth',
'VertDisper',
'volume',
'depth')
self.map_format=['binary']
self.map_output+=extra_fields
self.hist_output+=extra_fields
self.map_time_step=10000 # hourly
self.mon_time_step=3000 # half-hourly (had been daily)
self.hist_time_step=3000 # half-hourly (had been daily)
##
hydro=waq.HydroFiles(hyd_path="../../delft/sfb_ocean/sfb_ocean/runs/short_test_13/global/com-merged.hyd",
enable_write_symlink=True)
sec=datetime.timedelta(seconds=1)
start_time=hydro.time0+hydro.t_secs[ 0]*sec
stop_time=hydro.time0+hydro.t_secs[-4]*sec
scen=Scen(hydro=hydro,
start_time=start_time,
stop_time=stop_time,
base_path='dwaqA01')
##
scen.cmd_default()
import os
import stompy.model.delft.waq_scenario as dwaq
from stompy.model.delft import dfm_grid
six.moves.reload_module(dfm_grid)
six.moves.reload_module(dwaq)
##
# 'Feb15_Feb20_2017_09172018'
# 'Feb11_Jun06_2017_08082018-rusty'
hyd_path = ('/home/rusty/mirrors/ucd-X/mwtract/TASK2_Modeling/'
'Hydrodynamic_Model_Files/DELFT3D/Model Run Files/'
'Feb15_Feb20_2017_09172018'
'/DFM_DELWAQ_FlowFM/FlowFM.hyd')
hydro = dwaq.HydroFiles(hyd_path)
##
class AgeTracers(dwaq.Scenario):
# not required, but dwaq allows 3 lines of descriptive
# text for the run.
desc = ('Age tracers', 'testing multiple tracer approaches', 'v00')
# time steps are in HHMMSS, so 1000 is 10 minutes
# 1 hour unstable, 10 minutes okay.
time_step = 1000
# map output hourly - and 10000 is 1 hour
map_time_step = 10000
def init_substances(self):
params['ACTIVE_VertDisp'] = 1.0
return params
def init_substances(self):
subs = super(Scen, self).init_substances()
subs['NO3'] = Sub(0)
return subs
#def init_bcs(self):
#def init_loads(self):
hydro = waq.HydroFiles(
"../../dflowfm/runs/20180807_grid98_16_single/DFM_DELWAQ_flowfm/flowfm.hyd"
)
# if it runs all the way to the end of the hydro, the bad fluxes on the last step
# appear to cause a gmres error.
scen = Scen(hydro) # this is still setup
scen.delft_bin = "/home/rusty/src/dfm/1.4.6/bin"
os.environ['LD_LIBRARY_PATH'] = "/home/rusty/src/dfm/1.4.6/lib"
scen.share_path = "/home/rusty/src/dfm/1.4.6/share/delft3d"
scen.map_output += ('TotalDepth', 'Depth', 'LocalDepth')
os.path.exists(scen.base_path) and shutil.rmtree(scen.base_path) # for dev
scen.cmd_default() # actually write delwaq's input files
scen.cmd_delwaq1(
"""
import six
import os
import shutil
import datetime
import logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger()
import stompy.model.delft.waq_scenario as waq
##
hydro_in = waq.HydroFiles(
"hydro-wy2013c_adj-agg_lp_2d/com-wy2013c_adj_agg_lp_2d.hyd")
class TimeIntegrator(waq.TimeIntegrator):
enable_write_symlink = False
sparse_layers = False
agg_boundaries = False
stride_secs = 86400 * 1
def get_hydro():
# Trying a 3 day cutoff
return TimeIntegrator(hydro_in, stride_secs=stride_secs)
# Specify locations of outside data sources:
# POTW data, checked out in subdirectory:
potw_fn='/hpcvol1/zhenlin/sfbay/common/sfbay_potw/outputs/sfbay_potw.nc'
# Selection of hydrodynamics data:
# this has spatially variable shear stresses output from the hydrorun
rel_hyd_path="/hpcvol1/Mugunthan/Inputs/hydro/WY2013/agg141_tau-lp-pass_params/com-agg141_tau-lp.hyd"
# Load those external datasets:
sfbay_potw=xr.open_dataset(potw_fn)
# External reference to radiance data defined in radsurf() in Scen() class
hydro=waq_scenario.HydroFiles(hyd_path=rel_hyd_path,enable_write_symlink=True)
##
PC=waq_scenario.ParameterConstant
Sub=waq_scenario.Substance
IC=waq_scenario.Initial
class Scen(BayDynamo.BayDynamo):
name="sfbay_dynamo000"
desc=('sfbay_dynamo000',
'wy2013',
'full run')
base_x_dispersion = 0. # m**2/s - constant horizontal dispersion coefficient
integration_option="""16.62 ;
LOWER-ORDER-AT-BOUND NODISP-AT-BOUND
import six
import os
import shutil
from stompy.model.delft import waq_scenario as waq
from stompy.model.delft import dfm_grid
##
six.moves.reload_module(waq)
##
hydro = waq.HydroFiles("../../dflowfm/csc_95/DFM_DELWAQ_FlowFM/FlowFM.hyd")
Sub = waq.Substance
class Scen(waq.Scenario):
# csc_sed_9500: map output interval too small
# csc_sed_9501: output every 30 minutes
base_path = "csc_sed_9501"
map_formats = ['binary']
# With integration_option="15.60"
# 3000 was unstable.
# 1000 was unstable.
# 500 stable at least to 5%, running ~ 600x realtime
# Also tried 1000 with integration_option="21.70" and "16.70", no better.
# 21.70 appears to be about 15% faster than 15.60, a little over 700x.
# that was outputting a lot.
##
g=dfm_grid.DFMGrid(map_ds)
##
plt.figure(1).clf()
g.plot_edges(lw=0.5,color='k')
ncoll=g.plot_nodes(values=map_ds.NetNode_z.values )
cbar=plot_utils.cbar(ncoll)
##
hydro=waq.HydroFiles('runs/short_28/DFM_DELWAQ_short_28/short_28.hyd')
hyd_g=hydro.grid()
# This file is truncated, and currently waq won't infer n_seg:
kmx=20
hydro._n_seg=hyd_g.Ncells() * kmx
vols=hydro.volumes(hydro.t_secs[1])
A=hydro.planform_areas()
seg_depth = vols/A.data
##
aggregator=agg.get_hydro()
##
g_agg=aggregator.grid()
Nagg=1+aggregator.elt_global_to_agg_2d.max()
# Get a consistent unaggregated grid -- the one from scalar_map is bad.
# g_waq=dfm_grid.DFMGrid(scalar_map) # BAD
# This grid matches both the scalar fields coming out of WAQ, and
# the aggregation mapping
waq_hyd_dir='/opt/data/delft/sfb_dfm_v2/runs/wy2013c/DFM_DELWAQ_wy2013c_adj'
g_waq=dfm_grid.DFMGrid(os.path.join(waq_hyd_dir,'wy2013c_waqgeom.nc'))
#
hyd=waq.HydroFiles(os.path.join(waq_hyd_dir,"wy2013c.hyd"))
# Not needed, right?
agg_lp_2d_dir='hydro-wy2013c_adj-agg_lp_2d'
hydro_2d=waq.HydroFiles('hydro-wy2013c_adj-agg_lp_2d/com-wy2013c_adj_agg_lp_2d.hyd')
import lowpass_wy2013c
lp_secs=lowpass_wy2013c.lp_secs
lp_hyd=lowpass_wy2013c.get_hydro()
##
npad=int(5*lp_secs / 86400.)
daily_pad=np.zeros(npad)
import xarray as xr
import matplotlib.pyplot as plt
from stompy.spatial import proj_utils
from stompy.grid import unstructured_grid
import stompy.model.delft.waq_scenario as waq
from stompy.model.delft import hydro_utils
from stompy import utils
srv_xy=[615117,4224383]
pc_ll=[-(122+2.4/60.),(38+3.3/60.)]
pc_xy=proj_utils.mapper('WGS84','EPSG:26910')(pc_ll)
ges_xy=[629223,4233353]
fpx_xy=[630728,4257433]
hydro=waq.HydroFiles('/hpcvol1/cascade/WY2011/DFM_DELWAQ_sal+temp/sal+temp.hyd')
g=hydro.grid()
plt.figure()
g.plot_edges(lw=0.3,color='k')
plt.axis('equal')
t0=utils.to_dt64(hydro.time0)
t1=t0+np.timedelta64(170,'D')
tn=t1+np.timedelta64(10,'D')
srv=hydro_utils.extract_water_level(hydro,srv_xy,t1,tn).isel(station=0)
pc=hydro_utils.extract_water_level(hydro,pc_xy,t1,tn).isel(station=0)
ges=hydro_utils.extract_water_level(hydro,ges_xy,t1,tn).isel(station=0)
"""
import six
import os
import shutil
import datetime
import logging
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger()
import stompy.model.delft.waq_scenario as waq
##
hydro_lp = waq.HydroFiles(
hyd_path='hydro-wy2013c_adj-agg_lp/com-wy2013c_adj_agg_lp.hyd')
# Depth-integrate
class DepthAggregator(waq.HydroAggregator):
def __init__(self, **kwargs):
super(DepthAggregator, self).__init__(merge_only=True, **kwargs)
def find_maxima(self):
super(DepthAggregator, self).find_maxima()
self.n_agg_layers = 1
def get_agg_k(self, proc, k, seg):
return 0 # all layers to 1