Jupyter Notebook

Note that everything here is fully automatically tested against - and thus guaranteed to work - only for the latest versions of all the Salvus packages. So please update if anything works differently on your machine.

# Introduction¶

Sometimes it is useful to interact with third-party meshing software. This may be case, for example, when using meshes based on CAD models. Salvus supports the use of such meshes, and has automated readers for a collection of open-source mesh formats. In this tutorial we'll give an overview of the currently supported formats along with an example of their use. The first thing to do of course is to import the required Python packages.

%matplotlib inline
%autosave 0

from pathlib import Path

import h5py
import matplotlib.pyplot as plt
import numpy as np
import salvus_mesh.unstructured_mesh as um
from salvus_flow import api
from salvus_flow import simple_config as sc
from typing import List

Autosave disabled


Also, to make our lives a bit easier, we'll write a few short functions that will help us quickly generate Salvus inputs as we proceed

def get_basic_source(
*, frequency: float, physics: str, location: List
) -> sc.source:
"""Gets a simple physics- and dimension-dependent source.

Args:
frequency: Center frequency of the (Ricker) wavelet.
physics: Physics of the source.
location: Location of the source.

Returns:
SalvusFlow source object appropriate for the specified physics.
"""

l = location
src = sc.source.cartesian
s = sc.stf.Ricker(center_frequency=frequency)
if physics == "acoustic":
return src.ScalarPoint3D(
x=l[0], y=l[1], z=l[2], f=1, source_time_function=s
)

return src.VectorPoint3D(
x=l[0], y=l[1], z=l[2], fx=1.0, fy=1.0, fz=0.0, source_time_function=s
)


# Exodus¶

Exodus is one of the more common third-party mesh formats, and salvus_mesh can read Exodus files natively. In the following example we'll read some Exodus meshes into Salvus and run some simulations. We'll focus on two use cases: a purely elastic simulation, and a coupled fluid-solid simulation.

## Elastic¶

### Mesh¶

# Read mesh from Exodus file.
mesh = um.UnstructuredMesh.from_exodus("./data/exodus/glass.e")

# Find the surface of mesh.
mesh.find_surface(side_set_name="surface")

# Tensorize the element nodes.
mesh.tensorize(order=1)

# Mark simulation as elastic.
mesh.attach_field("fluid", np.zeros(mesh.nelem))

# Attach parameters.
pars = {"VP": 5800, "VS": 4000, "RHO": 2600}
template = np.ones_like(mesh.get_element_nodes()[:, :, 0])
for key, value in pars.items():
mesh.attach_field(key, template * value)

# Visualize.
mesh


<salvus_mesh.unstructured_mesh.UnstructuredMesh at 0x7f64f5a8ee10>


### Setup¶

# Set up simulation.
w = sc.simulation.Waveform(
mesh=mesh,
sources=get_basic_source(
frequency=100.0, physics="elastic", location=[0, 0, 70]
),
)

# Generate a movie.
w.output.volume_data.format = "hdf5"
w.output.volume_data.filename = "movie.h5"
w.output.volume_data.fields = ["displacement"]
w.output.volume_data.sampling_interval_in_time_steps = 100

# Validate simulation parameters.
w.validate()


### Simulate¶

api.run(
ranks=2,
get_all=True,
input_file=w,
site_name="local",
output_folder="output",
)

Job job_1908041602401991_43120eb14c running on local with 2 rank(s).
Site information:
* Salvus version: 0.9.8-32-g18bc6850
* Floating point size: 32


* Downloaded 42.1 MB of results to output.
* Total run time: 9.02 seconds.
* Pure simulation time: 8.48 seconds.

<salvus_flow.sites.salvus_job.SalvusJob at 0x7f64f5af5710>


### Analyze¶

Snapshot of the magnitude of dynamic elastic displacement, visualized using Paraview and the output .xdmf file.

## Coupled¶

### Mesh¶

# Read mesh from Exodus file.
mesh_solid = um.UnstructuredMesh.from_exodus("./data/exodus/solid.e")
mesh_fluid = um.UnstructuredMesh.from_exodus("./data/exodus/fluid.e")

# Tensorize the element nodes.
mesh_solid.tensorize(order=1)
mesh_fluid.tensorize(order=1)

# Mark fluid and solid elements.
mesh_solid.attach_field("fluid", np.zeros(mesh_solid.nelem))
mesh_fluid.attach_field("fluid", np.ones(mesh_fluid.nelem))

# Attach parameters (elastic).
pars = {"VP": 5800, "VS": 4000, "RHO": 2600}
template = np.ones_like(mesh_solid.get_element_nodes()[:, :, 0])
for key, value in pars.items():
mesh_solid.attach_field(key, template * value)

# Attach parameters (acoustic).
pars = {"VP": 1500, "VS": 0, "RHO": 1000}
template = np.ones_like(mesh_fluid.get_element_nodes()[:, :, 0])
for key, value in pars.items():
mesh_fluid.attach_field(key, template * value)

# Combine both element blocks.
mesh = mesh_solid + mesh_fluid

# Find the surface of mesh.
mesh.find_surface(side_set_name="surface")

# Visualize.
mesh


<salvus_mesh.unstructured_mesh.UnstructuredMesh at 0x7f64f113e470>


### Setup¶

# Set up simulation.
w = sc.simulation.Waveform(
mesh=mesh,
sources=get_basic_source(
frequency=100.0, physics="acoustic", location=[0, -30, 70]
),
)

# Set your simulation length here.
# w.physics.wave_equation.end_time_in_seconds = ?

# Generate a movie.
w.output.volume_data.format = "hdf5"
w.output.volume_data.filename = "movie.h5"
w.output.volume_data.fields = ["displacement", "phi_tt"]
w.output.volume_data.sampling_interval_in_time_steps = 100

# Validate simulation parameters.
w.validate()


### Simulate¶

api.run(
ranks=2,
get_all=True,
input_file=w,
site_name="local",
output_folder="output_coupled",
)

Job job_1908041602037229_4bfd3d9f0f running on local with 2 rank(s).
Site information:
* Salvus version: 0.9.8-32-g18bc6850
* Floating point size: 32


* Downloaded 31.0 MB of results to output_coupled.
* Total run time: 8.18 seconds.
* Pure simulation time: 7.74 seconds.

<salvus_flow.sites.salvus_job.SalvusJob at 0x7f64f1498e80>


### Analyze¶

Snapshot of the magnitude of dynamic elastic displacement and the acoustic pressure, visualized using Paraview and the output .xdmf file.