Version:

This documentation is not for the latest stable Salvus version.

This tutorial is presented as Python code running inside a Jupyter Notebook, the recommended way to use Salvus. To run it yourself you can copy/type each individual cell or directly download the full notebook, including all required files.

# Semi-analytic Test - Acoustic

• Reference solution: Gar6more2D
• Physics: Acoustic wave equation

In this notebook we will use Gar6more2D to generate a set of of semi-analytic solutions to the 2-D acoustic wave equation, and then compare these solutions to those computed within Salvus.

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%config Completer.use_jedi = False
%matplotlib inline

# Stdlib packages
import os
import pathlib
import shutil
import subprocess

# Third party packages
import matplotlib.pyplot as plt
import numpy as np
import pyasdf

# Import things from SalvusFlow
from salvus.flow import api

# Configuration helpers from SalvusFlow.
from salvus.flow import simple_config as sc

# And some helper functions to run the integration tests.
from integration_test_mesh_helper import (
get_mesh,
Physics,
AnalyticCode,
)

# Number of processes SalvusCompute will run with.
# Get it from the environment or default to 4.
MPI_RANKS = int(os.environ.get("NUM_MPI_RANKS", 4))
# Choose on which site to run this.
SALVUS_FLOW_SITE_NAME = os.environ.get("SITE_NAME", "local")

## Gar6more2D

First we must compile and run Gar6more2D. The Gar6more2D git repository is included here as a submodule, as long as the module has been pulled the following paths should work on your machine. The next cell should compile Gar6more2D in the default location (if it has not been compiled yet).

# Set up the paths for the Gar6more2D data and binaries.
gar6more2d_base_path = pathlib.Path("gar6more2d")
gar6more2d_build_path = gar6more2d_base_path / "build"
gar6more2d_bin = gar6more2d_build_path / "Gar6more2D.out"
gar6more2d_par_file_path = gar6more2d_build_path / "Gar6more2D.dat"

# Compile Gar6more2D if it has not been compiled yet.
os.makedirs(gar6more2d_build_path, exist_ok=True)
if not os.path.exists(gar6more2d_bin):
assert (
subprocess.run(["cmake", ".."], cwd=gar6more2d_build_path).returncode
== 0
)
assert (
subprocess.run(["make", "-j4"], cwd=gar6more2d_build_path).returncode
== 0
)

Now we generate the parameter file to pass to Gar6more2D. We choose a medium which is infinite on 3 sides, and which has a pressure-free boundary at the bottom. We use a ricker source-time function to generate the acoustic wavefield, with a center frequency of $100$ $Hz$. We place this source $250$ $m$ above the free surface boundary $(0, 250)$, and place 5 receivers $50$ $m$ above the same boundary, spaced equidistantly from $x = -200 m$ to $x = +200 m$. We compute the solution between $0$ and $0.1$ seconds, with a sampling interval of $1 \times 10^{-4}$ seconds, for a total of $1000$ time samples. We also choose an acoustic wave velocity of $5800$ $m/s$ and a density of $2600$ $kg/m^3$, which corresponds to a bulk modulus $\mu$ of $8.7464 \times 10^{10}$.

# Generate and write the parameter file. Set the time step so we can use the same sampling rate in Salvus.
amplitude = 1e2
time_step = 1e-4
center_frequency = 100.0
gar6more2d_par_file = """2 infinite medium (1), free surface (2), wall boundary (3) or bilayered medium(4)
0 first layer : acoustic (0) elastodynamic (1), poroelastic (2)
{center_frequency:.2e} Central frequency of the source
{amplitude:.2e} Amplitude of the source
2d-2 0d0 Delay of the source
250d0 Height of the source
50d0 Height of the line of receivers
-200d0 Abscissa of the first receiver
200d0  Abscissa of the last receiver
0 Start time
1d-1 Stop time
{time_step:.2e} Time step
1000 Number of intervals for the numerical computation of the convolution
87464000000 2600 mu and rho
""".format(
time_step=time_step, amplitude=amplitude, center_frequency=center_frequency
)
with open(gar6more2d_par_file_path, "w") as fh:
fh.write(gar6more2d_par_file)

Now, we generate the semi-analytic pressure solution, and read the results into an obspy stream object.

# Run code.
gar6more2d_data_file = gar6more2d_build_path / "P.dat"
if not os.path.exists(gar6more2d_data_file):
subprocess.run(["./Gar6more2D.out"], cwd=gar6more2d_build_path, check=True)

gar6more2d_data = read_gar6more(gar6more2d_data_file)

## Salvus

Now, we will run a fully numerical simulations in Salvus, and attempt to replicate the semi-analytic seismograms. For the sake of brevity, we've left the specifics of the mesh and parameter file generation to the integration_test_mesh_helper.py module, which is shared between all integration test instances. Feel free to peak inside to see how the meshes are made -- or alternatively check out the meshing tutorials for a more in-depth explanation.

# Adjust the scaling of the source term to be equivalent to what is
# used in GAR6MORE.
bulk_modulus = 8.7464e10
gar6more_scale = bulk_modulus / (2 * np.pi ** 2 * center_frequency ** 2)
source_amplitude = amplitude / gar6more_scale

Use the helper objects in SalvusFlow to generate sources, receivers, and boundary conditions.

source = sc.source.cartesian.ScalarPoint2D(
x=500.0,
y=250.0,
f=source_amplitude,
source_time_function=sc.source.stf.Ricker(
center_frequency=center_frequency
),
)
# Generate 5 cartesian receivers, spaced between X=300 and X=700 meters.
station_code=str(i), x=x, y=50, fields=["phi"]
)
for i, x in enumerate(range(300, 701, 100))
]
boundary = sc.boundary.HomogeneousDirichlet(side_sets=["y0"])

Finally run the simulations for a number of different shape mapping orders.

output_dirs = []

# Run for a number of different orders.
for order in [1, 2, 4, 7]:

# Setup the mesh for this simulation.
mesh = get_mesh(
dimension=2,
analytic_code=AnalyticCode.Gar6more2D,
physics=Physics.ACOUSTIC,
n_elem_per_wavelength=2,
polynomial_order=max(4, order),
shape_order=min(4, order),
)

# Unique job name.
job_name = f"GAR6MORE2D_ACOUSTIC_ORDER_{order}"
output_dirs.append(pathlib.Path(job_name) / "output")

# Configure Salvus
w = sc.simulation.Waveform()
w.set_mesh(mesh)

w.physics.wave_equation.start_time_in_seconds = -2e-2
w.physics.wave_equation.end_time_in_seconds = 8e-2
w.physics.wave_equation.time_step_in_seconds = time_step

# The input files can optionally be already validated.
w.validate()

api.run(
site_name=SALVUS_FLOW_SITE_NAME,
output_folder=output_dirs[-1],
input_file=w,
ranks=MPI_RANKS,
get_all=True,
overwrite=True,
)
Job job_2104062122504396_5cb75c9440 running on local_f64 with 4 rank(s).
Site information:
* Salvus version: 0.11.29
* Floating point size: 64

There should be something here! The notebook has been saved without widget output.
* Downloaded 65.0 KB of results to GAR6MORE2D_ACOUSTIC_ORDER_1/output.
* Total run time: 1.13 seconds.
* Pure simulation time: 0.72 seconds.
Job job_2104062122603928_8a48fb85c9 running on local_f64 with 4 rank(s).
Site information:
* Salvus version: 0.11.29
* Floating point size: 64
-> Current Task: Time loop complete* Downloaded 65.0 KB of results to GAR6MORE2D_ACOUSTIC_ORDER_2/output.
* Total run time: 1.97 seconds.
* Pure simulation time: 1.79 seconds.
Job job_2104062122598784_2474843e8f running on local_f64 with 4 rank(s).
Site information:
* Salvus version: 0.11.29
* Floating point size: 64

There should be something here! The notebook has been saved without widget output.
* Downloaded 65.0 KB of results to GAR6MORE2D_ACOUSTIC_ORDER_4/output.
* Total run time: 1.44 seconds.
* Pure simulation time: 1.09 seconds.
Job job_2104062122056940_26311e2b8b running on local_f64 with 4 rank(s).
Site information:
* Salvus version: 0.11.29
* Floating point size: 64

There should be something here! The notebook has been saved without widget output.
* Downloaded 65.0 KB of results to GAR6MORE2D_ACOUSTIC_ORDER_7/output.
* Total run time: 2.26 seconds.
* Pure simulation time: 2.00 seconds.


## Compare Both

Finally, we'll now read in the seismograms from Salvus, and plot them overtop the semi-analytic solutions we generated in Gar6more2D. If you've used all the default settings, things should match up exactly. However, feel free to play with some parameters to see how the accuracy can be increased or decreased. Note that, since these are our actual analytic tests, a reduction in accuracy may cause the np.testing.assert_allclose line to fail. If you encounter this, and would still like to see the effect of your changes on the seismograms, feel free to comment out that line.

# Setup the figure.
f, ax = plt.subplots(5, 1, figsize=(15, 30), sharex=True)
ax[0].set_title("Integration Test (Gar6more2D // Acoustic)")

# Plot analytic data.
for a, g in zip(ax, gar6more2d_data):
a.plot(g, label="Gar6more2D")

# Read in the data produced by Salvus.
for output_dir in output_dirs:
with pyasdf.ASDFDataSet(output_dir / "receivers.h5", mode="r") as dataset:

# Loop over the receivers in both Gar6more2D and Salvus,
# and plot them overtop of one another.
for a, s, g in zip(ax, dataset.waveforms, gar6more2d_data):

# Get both solutions.
analytic = g
salvus = s.phi[0].data
np.testing.assert_allclose(analytic, salvus, atol=1e-3)

# Plot.
order = output_dir.parent.name.split("_")[-1][0]
a.plot(salvus, label=f"Salvus (Shape order {order})", ls="dashed")
a.set_xlabel("Time sample")
a.set_ylabel("Pressure")
a.legend()

# plt.show()
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