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JingChen-Thu · 2025-11-25T13:16:11Z

Add an example to build initial model for teleseismic tomography based on the crust 1.0 model and ak135 model.

…smic tomography

Copilot

Pull request overview

This PR adds a new example demonstrating how to build an initial velocity model for teleseismic tomography by combining the CRUST1.0 crustal model with the ak135 mantle model. The example includes a Python script that loads these community models, interpolates them onto a computational grid, and smoothly blends them at intermediate depths.

Key Changes

Python script to generate combined CRUST1.0 + ak135 velocity models with configurable depth transitions
YAML configuration file defining the computational domain and inversion parameters for a real-world teleseismic tomography case
Shell script to execute the model generation workflow with proper references to source publications

Reviewed changes

Copilot reviewed 3 out of 4 changed files in this pull request and generated 9 comments.

File	Description
`examples/scripts_of_generate_community_model/1_crust1.0_ak135_model.py`	Core Python script that loads CRUST1.0 and ak135 models, performs depth-dependent linear interpolation between them, and applies optional smoothing and monotonicity constraints
`examples/scripts_of_generate_community_model/3_input_params/input_params_real.yaml`	Configuration file defining the computational domain (Thailand region, -50 to 550 km depth), inversion grid parameters, and model update settings
`examples/scripts_of_generate_community_model/run_this_example.sh`	Bash script that executes the model generation with citations to the CRUST1.0 and ak135 publications
`.gitignore`	Updated to exclude generated Jupyter notebooks and figure directories for the new example

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examples/scripts_of_generate_community_model/1_crust1.0_ak135_model.py

Copilot · 2025-11-25T23:49:42Z

examples/scripts_of_generate_community_model/1_crust1.0_ak135_model.py

+# %%
+# Step 2. Generate the ATT model based on ak135 model.
+
+# Load the 1D ak135 model from the .h5 file.


Missing documentation: The script references 'ak135.h5' but there's no comment explaining where this file should be obtained or what format it should have (e.g., expected keys in the HDF5 file: 'model' containing a 2D array with columns [depth, velocity]). Consider adding a comment explaining how to obtain or prepare this file.

Suggested change

# Load the 1D ak135 model from the .h5 file.

# Load the 1D ak135 model from the .h5 file.

# The file 'ak135.h5' should be an HDF5 file containing a dataset named 'model',

# which is a 2D array with columns [depth, velocity] (depth in km, velocity in km/s).

# You can obtain ak135 model data from published sources (e.g., https://www.seismology.ethz.ch/en/research-and-teaching/products-software/ak135-model/)

# and convert it to HDF5 format using Python and h5py. Example:

# import h5py, numpy as np

# data = np.array([[depth1, vel1], [depth2, vel2], ...])

# with h5py.File('ak135.h5', 'w') as f: f.create_dataset('model', data=data)

@JingChen-Thu How do you think to add information about ak135.h5 like this?

Sure, this will be more informative.

examples/scripts_of_generate_community_model/run_this_example.sh

examples/scripts_of_generate_community_model/3_input_params/input_params_real.yaml

Copilot · 2025-11-25T23:49:43Z

examples/scripts_of_generate_community_model/3_input_params/input_params_real.yaml

+#################################################
+parallel: # parameters for parallel computation
+  n_sims: 8 # number of simultanoues runs (parallel the sources)
+  ndiv_rtp: [1, 1, 1] # number of subdivision on each direction (parallel the computional domain)


Typo in comment: "computional domain" should be "computational domain".

examples/scripts_of_generate_community_model/1_crust1.0_ak135_model.py

Copilot · 2025-11-25T23:49:43Z

examples/scripts_of_generate_community_model/3_input_params/input_params_real.yaml

+  #                                               lat = mid_lat_inv+(lat_inv[i]-mid_lat_inv)*(dep_inv[k]-trapezoid[1])/(trapezoid[2]-trapezoid[1])*trapezoid[0]; 
+  #                                               dep = dep_inv[k];
+  # if trapezoid[2] <= dep_inv[k],                lon = mid_lon_inv+(lon_inv[i]-mid_lon_inv)*trapezoid[0]; 
+  #                                               lat = mid_lat_inv+(lat_inv[i]-mid_lat_inv)*trapezoid[0]; 


Documentation bug: The formula uses "lat_inv[i]" but should use "lat_inv[j]" to be consistent with the comment on line 141 which correctly uses index "j" for latitude. The same issue appears on line 147 where "lat_inv[i]" should also be "lat_inv[j]".

Suggested change

# lat = mid_lat_inv+(lat_inv[i]-mid_lat_inv)*(dep_inv[k]-trapezoid[1])/(trapezoid[2]-trapezoid[1])*trapezoid[0];

# dep = dep_inv[k];

# if trapezoid[2] <= dep_inv[k], lon = mid_lon_inv+(lon_inv[i]-mid_lon_inv)*trapezoid[0];

# lat = mid_lat_inv+(lat_inv[i]-mid_lat_inv)*trapezoid[0];

# lat = mid_lat_inv+(lat_inv[j]-mid_lat_inv)*(dep_inv[k]-trapezoid[1])/(trapezoid[2]-trapezoid[1])*trapezoid[0];

# dep = dep_inv[k];

# if trapezoid[2] <= dep_inv[k], lon = mid_lon_inv+(lon_inv[i]-mid_lon_inv)*trapezoid[0];

# lat = mid_lat_inv+(lat_inv[j]-mid_lat_inv)*trapezoid[0];

examples/scripts_of_generate_community_model/3_input_params/input_params_real.yaml

…model.py typo Co-authored-by: Copilot <[email protected]>

…model.py Co-authored-by: Copilot <[email protected]>

…put_params_real.yaml typo Co-authored-by: Copilot <[email protected]>

typo Co-authored-by: Copilot <[email protected]>

mnagaso

Thank you for adding this example!

JingChen-Thu added 2 commits November 25, 2025 20:59

add an example to build model based on crust1.0 and ak135 for telesei…

abb5f1f

…smic tomography

add citations

fd92b53

xumi1993 requested a review from Copilot November 25, 2025 23:46

Copilot started reviewing on behalf of xumi1993 November 25, 2025 23:46 View session

Copilot finished reviewing on behalf of xumi1993 November 25, 2025 23:48

Copilot AI reviewed Nov 25, 2025

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mnagaso self-requested a review November 26, 2025 02:30

mnagaso and others added 6 commits November 26, 2025 11:31

Update examples/scripts_of_generate_community_model/1_crust1.0_ak135_…

8b26db9

…model.py typo Co-authored-by: Copilot <[email protected]>

Update examples/scripts_of_generate_community_model/1_crust1.0_ak135_…

f925bff

…model.py Co-authored-by: Copilot <[email protected]>

Update examples/scripts_of_generate_community_model/3_input_params/in…

dc9f1b8

…put_params_real.yaml typo Co-authored-by: Copilot <[email protected]>

Update examples/scripts_of_generate_community_model/3_input_params/in…

3974cec

…put_params_real.yaml typo Co-authored-by: Copilot <[email protected]>

Update examples/scripts_of_generate_community_model/3_input_params/in…

b1cb0fa

…put_params_real.yaml typo Co-authored-by: Copilot <[email protected]>

Update examples/scripts_of_generate_community_model/run_this_example.sh

bfb4306

typo Co-authored-by: Copilot <[email protected]>

mnagaso approved these changes Nov 26, 2025

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mnagaso merged commit 4849c05 into devel Nov 26, 2025
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add an example to build model based on crust1.0 and ak135 for telesei…#52

add an example to build model based on crust1.0 and ak135 for telesei…#52
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-# Load the 1D ak135 model from the .h5 file.
+# Load the 1D ak135 model from the .h5 file.
+# The file 'ak135.h5' should be an HDF5 file containing a dataset named 'model',
+# which is a 2D array with columns [depth, velocity] (depth in km, velocity in km/s).
+# You can obtain ak135 model data from published sources (e.g., https://www.seismology.ethz.ch/en/research-and-teaching/products-software/ak135-model/)
+# and convert it to HDF5 format using Python and h5py. Example:
+# import h5py, numpy as np
+# data = np.array([[depth1, vel1], [depth2, vel2], ...])
+# with h5py.File('ak135.h5', 'w') as f: f.create_dataset('model', data=data)

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Pull request overview

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