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Merge branch 'swash'

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This commit is contained in:
Edgar P. Burkhart 2022-03-07 13:41:26 +01:00
commit e59f30e876
Signed by: edpibu
GPG key ID: 9833D3C5A25BD227
6 changed files with 248 additions and 13 deletions
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4
swash/config.ini
View file

@ -9,8 +9,10 @@ hstru=Hstru.dat
poro=Poro.dat
psize=Psize.dat
out=out_data
out_nb=out_data_nb
[swash]
nb=True
input=sws/INPUT.sws
path=/opt/swash
out=out_sws
@ -18,7 +20,9 @@ mpi=4
[post]
inp=inp_post
case=sws_spec_buoy.npz
out=out_post
#nperseg=1024
dt=0.25
x0=-1000
t0=180

94
swash/processing/bathy_nb.py Normal file
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@ -0,0 +1,94 @@
import argparse
import configparser
import logging
import pathlib
import sys
import numpy as np
import pandas as pd
try:
import matplotlib.pyplot as plt
except ImportError:
plt = None
parser = argparse.ArgumentParser(description="Pre-process bathymetry")
parser.add_argument("-v", "--verbose", action="count", default=0)
args = parser.parse_args()
logging.basicConfig(level=max((10, 20 - 10 * args.verbose)))
log = logging.getLogger("bathy")
log.info("Starting bathymetry pre-processing")
config = configparser.ConfigParser()
config.read("config.ini")
root = pathlib.Path(config.get("data", "root"))
log.info(f"Reading input data from '{root}'")
bathy_hires = np.loadtxt(root.joinpath(config.get("data", "hires")))
bathy_lores = np.loadtxt(root.joinpath(config.get("data", "bathy")))
hstru = np.loadtxt(root.joinpath(config.get("data", "hstru")))
poro = np.loadtxt(root.joinpath(config.get("data", "poro")))
psize = np.loadtxt(root.joinpath(config.get("data", "psize")))
log.info("Generating grid")
x_hires = -np.arange(0, 0.5 * bathy_hires.size, 0.5)[::-1]
x_lores = -np.arange(0, 1 * bathy_lores.size, 1)[::-1]
x_hstru = -np.arange(0, 0.5 * hstru.size, 0.5)[::-1]
log.info("Generating output data")
bathy_hires_pd = pd.Series(bathy_hires.copy(), index=x_hires)
bathy_lores_pd = pd.Series(bathy_lores.copy(), index=x_lores)
bathy = pd.DataFrame(
index=bathy_lores_pd.index.union(bathy_hires_pd.index),
columns=("z", "hstru", "poro", "psize"),
data=0,
)
bathy.z[bathy_lores_pd.index] = bathy_lores_pd
bathy.z[bathy_hires_pd.index] = bathy_hires_pd
bathy.z = np.minimum(bathy.z, -15)
#bathy.loc[x_hstru, ("hstru", "poro", "psize")] = np.array(
# (hstru, poro, psize)
#).T
bathy = bathy.reindex(bathy_lores_pd.index)
log.debug(f"Bathymetry:\n{bathy}")
log.info(
f"xmin: {bathy.index.min()}, "
f"xmax: {bathy.index.max()}, "
f"n: {bathy.index.size}"
)
if config.has_option("data", "out_nb"):
out = pathlib.Path(config.get("data", "out_nb"))
log.info(f"Writing output data to '{out}'")
out.mkdir(exist_ok=True)
np.savetxt(out.joinpath("bathy.dat"), bathy.z, newline=" ")
np.savetxt(out.joinpath("hstru.dat"), bathy.hstru, newline=" ")
np.savetxt(out.joinpath("poro.dat"), bathy.poro, newline=" ")
np.savetxt(out.joinpath("psize.dat"), bathy.psize, newline=" ")
bathy.to_hdf(out.joinpath("bathy.h5"), "bathy", mode="w")
if config.getboolean("proc", "plot", fallback=False):
if plt is None:
log.error("Could not import PyPlot")
sys.exit(1)
log.info("Plotting data")
fig, ax = plt.subplots()
ax.plot(x_hires, bathy_hires, label="High-res")
ax.plot(x_lores, bathy_lores, label="Low-res")
ax.plot(bathy.index, bathy.z, ls="-.", c="k", label="Combined")
ax.plot(bathy.index, bathy.z + bathy.hstru, label="Hstru")
ax.grid()
ax.legend()
plt.show(block=True)
log.info("Processing finished")

40
swash/processing/post.py
View file

@ -7,6 +7,7 @@ import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.signal as sgl
import scipy.fft as fft
from .read_swash import *
@ -25,7 +26,7 @@ inp = pathlib.Path(config.get("post", "inp"))
root = pathlib.Path(config.get("swash", "out"))
log.info(f"Reading bathymetry from '{inp}'")
data = np.load(inp.joinpath("sws.npz"))
data = np.load(inp.joinpath(config.get("post", "case")))
x, t = data["x"], data["t"]
# Cospectral calculations
@ -35,14 +36,15 @@ t0 = config.getfloat("post", "t0")
arg_t0 = np.abs(t - t0).argmin()
dt = config.getfloat("post", "dt")
f = 1 / dt
nperseg = config.getint("post", "nperseg", fallback=None)
log.info(f"Computing reflection coefficient at x={x0}")
eta = data["watl"][t > t0, arg_x0]
u = data["vel"][t > t0, 0, arg_x0]
phi_eta = np.abs(sgl.csd(eta, eta, f))
phi_u = np.abs(sgl.csd(u, u, f))
phi_eta_u = np.abs(sgl.csd(eta, u, f))
phi_eta = np.abs(sgl.welch(eta, f, nperseg=nperseg))
phi_u = np.abs(sgl.welch(u, f, nperseg=nperseg))
phi_eta_u = np.abs(sgl.csd(eta, u, f, nperseg=nperseg))
R = np.sqrt(
(phi_eta[1] + phi_u[1] - 2 * phi_eta_u[1])
@ -53,13 +55,13 @@ R = np.sqrt(
log.info("Plotting results")
fig, (ax_watl, ax_vel) = plt.subplots(2)
ax_watl.plot(t, data["watl"][:, arg_x0], label="watl")
ax_watl.plot(t, data["watl"][:, arg_x0], lw=1, label="watl")
ax_watl.set(xlabel="t (s)", ylabel="z (m)")
ax_watl.autoscale(axis="x", tight=True)
ax_watl.grid()
ax_watl.axvline(t0, c="k", alpha=0.2)
ax_vel.plot(t, data["vel"][:, 0, arg_x0], label="vel")
ax_vel.plot(t, data["vel"][:, 0, arg_x0], lw=1, label="vel")
ax_vel.set(xlabel="t (s)", ylabel="U (m/s)")
ax_vel.autoscale(axis="x", tight=True)
ax_vel.grid()
@ -68,12 +70,24 @@ ax_vel.axvline(t0, c="k", alpha=0.2)
fig.tight_layout()
fig_r, ax_r = plt.subplots()
ax_fft = ax_r.twinx()
ax_r.plot(1 / phi_eta[0, 1:], R[1:], marker="+", lw=1)
ax_r.set(xlim=(1, 30), ylim=(0, 1), xlabel="t (s)", ylabel="R")
ax_fft.plot(
*sgl.welch(eta, 1/dt, nperseg=nperseg),
lw=1,
c="k",
alpha=0.2,
label="PSD ($\\eta$)",
)
ax_r.plot(phi_eta[0], R, marker="+", label="R")
ax_r.set(xlim=(0, 0.3), ylim=(0, 1), xlabel="f (Hz)", ylabel="R")
ax_fft.set(ylim=0, ylabel="PSD (m²/Hz)")
ax_r.grid()
ax_r.legend(loc="upper left")
ax_fft.legend(loc="upper right")
fig_r.tight_layout()
fig_x, ax_x = plt.subplots()
fig_x, ax_x = plt.subplots(figsize=(10, 1))
ax_x.plot(data["x"], -data["botl"], color="k")
ax_x.fill_between(
data["x"],
@ -83,13 +97,15 @@ ax_x.fill_between(
ax_x.axvline(x0, c="k", alpha=0.2)
ax_x.set(xlabel="x (m)", ylabel="z (m)")
ax_x.autoscale(axis="x", tight=True)
ax_x.set(aspect="equal")
fig_x.tight_layout()
out = pathlib.Path(config.get("post", "out")).joinpath(f"t{t0}x{x0}")
log.info(f"Saving plots in '{out}'")
out.mkdir(parents=True, exist_ok=True)
fig.savefig(out.joinpath(f"t.png"))
fig_r.savefig(out.joinpath(f"R.png"))
fig_x.savefig(out.joinpath(f"x.png"))
fig.savefig(out.joinpath("t.png"))
fig_r.savefig(out.joinpath("R.png"))
fig_x.savefig(out.joinpath("x.png"))
log.info("Finished post-processing")

6
swash/processing/swash.py
View file

@ -30,8 +30,12 @@ with tempfile.TemporaryDirectory(prefix="swash_", dir=".") as tmp_raw:
log.info(f"Copying files to '{tmpdir}'")
shutil.copy2(inp, tmpdir)
if config.getboolean("swash", "nb", fallback=False):
path = pathlib.Path(config.get("data", "out_nb"))
else:
path = pathlib.Path(config.get("data", "out"))
shutil.copytree(
pathlib.Path(config.get("data", "out")), tmpdir, dirs_exist_ok=True
path, tmpdir, dirs_exist_ok=True
)
if config.has_option("swash", "mpi"):

58
swash/sws/SPEC_buoy.sws Normal file
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@ -0,0 +1,58 @@
$************************* GENERAL ***************************************
PROJ 'GW' 'T1'
SET NAUT
SET LEVEL 0.94
SET MAXERR 1
SET DEPMIN 0.001
MODE DYN ONED
$************************ GRIDS ***************************************
CGRID REG -1251 0 0 1251 0 1250 0
INPGRID BOT REG -1251 0 0 1250 0 1 0 $x0 y0 theta nx-1 ny-1 dx dy
VERT 10 $nb couches
READ BOTTOM -1 'bathy.dat' 3 0 FREE
INPGRID PORO REG -1251 0 0 1250 0 1 0
INPGRID PSIZ REG -1251 0 0 1250 0 1 0
INPGRID HSTRUC REG -1251 0 0 1250 0 1 0
READINP PORO 1 'poro.dat' 3 0 FREE
READINP PSIZ 1 'psize.dat' 3 0 FREE
READINP HSTRUC 1 'hstru.dat' 3 0 FREE
$*********************** BOUNDARIES ****************************************
INIT ZERO
BOUN SHAP JON SIG PEAK DSPR DEGR
BOUN SIDE W BTYPE WEAK SMOOT 10 SEC ADDBOUNDWAVE CON SPECT 7.31 16.9 0 0 CYCLE 20 MIN
BOUN SIDE E BTYPE SOMMERFELD
$*********************** PHYSICS *******************************************
BRE 0.6 0.2
FRICTION MANN 0.08
POROsity 4 200 1.1 13
VISC V KEPS
$*********************** NUMERICS ******************************************
NONHYD BOX 1.0 PREC ILU
DISCRET UPW MOM
TIMEI 0.2 0.6
$*********************** OUTPUTS *******************************************
SET OUTLEV 1
$BLOCK 'COMPGRID' HEAD 'test.txt' LAY 4 TSEC XP DEP BOTL WATL PRESS DISCH USTAR VEL VZ VELK ZK BRKP OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'tsec.dat' TSEC OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'xp.dat' XP OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'dep.dat' DEP OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'botl.dat' BOTL OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'watl.dat' WATL OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'press.dat' PRESS OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'disch.dat' DISCH OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'ustar.dat' USTAR OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'vel.dat' VEL OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'vz.dat' VZ OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'velk.dat' VELK OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'zk.dat' ZK OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'brkp.dat' BRKP OUTPUT 000000.00 0.25 SEC
COMPUTE 000000.000 0.015 SEC 003000.000 $timeini dtini unit timefin
STOP

59
swash/sws/SPEC_buoy_nb.sws Normal file
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@ -0,0 +1,59 @@
$************************* GENERAL ***************************************
PROJ 'GW' 'T1'
SET NAUT
SET LEVEL 0.94
SET MAXERR 1
SET DEPMIN 0.001
MODE DYN ONED
$************************ GRIDS ***************************************
CGRID REG -1251 0 0 1251 0 1250 0
INPGRID BOT REG -1251 0 0 1250 0 1 0 $x0 y0 theta nx-1 ny-1 dx dy
VERT 10 $nb couches
READ BOTTOM -1 'bathy.dat' 3 0 FREE
INPGRID PORO REG -1251 0 0 1250 0 1 0
INPGRID PSIZ REG -1251 0 0 1250 0 1 0
INPGRID HSTRUC REG -1251 0 0 1250 0 1 0
READINP PORO 1 'poro.dat' 3 0 FREE
READINP PSIZ 1 'psize.dat' 3 0 FREE
READINP HSTRUC 1 'hstru.dat' 3 0 FREE
$*********************** BOUNDARIES ****************************************
INIT ZERO
BOUN SHAP JON SIG PEAK DSPR DEGR
BOUN SIDE W BTYPE WEAK SMOOT 10 SEC ADDBOUNDWAVE CON SPECT 7.31 16.9 0 0 CYCLE 20 MIN
$BOUN SIDE E BTYPE SOMMERFELD
SPON E 50
$*********************** PHYSICS *******************************************
BRE 0.6 0.2
FRICTION MANN 0.08
POROsity 4 200 1.1 13
VISC V KEPS
$*********************** NUMERICS ******************************************
NONHYD BOX 1.0 PREC ILU
DISCRET UPW MOM
TIMEI 0.2 0.6
$*********************** OUTPUTS *******************************************
SET OUTLEV 1
$BLOCK 'COMPGRID' HEAD 'test.txt' LAY 4 TSEC XP DEP BOTL WATL PRESS DISCH USTAR VEL VZ VELK ZK BRKP OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'tsec.dat' TSEC OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'xp.dat' XP OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'dep.dat' DEP OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'botl.dat' BOTL OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'watl.dat' WATL OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'press.dat' PRESS OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'disch.dat' DISCH OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'ustar.dat' USTAR OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'vel.dat' VEL OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'vz.dat' VZ OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'velk.dat' VELK OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'zk.dat' ZK OUTPUT 000000.00 0.25 SEC
BLOCK 'COMPGRID' NOHEAD 'brkp.dat' BRKP OUTPUT 000000.00 0.25 SEC
COMPUTE 000000.000 0.015 SEC 003000.000 $timeini dtini unit timefin
STOP