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examples/scripts_of_generate_community_model/1_crust1.0_ak135_model.py Normal file
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# %%
from pytomoatt.model import ATTModel
import os
import numpy as np
import h5py
# %% [markdown]
# # Step 1. Generate the ATT model based on the crust1.0 model.
# %%
# generate the .h5 model for TomoATT based on the crust1.0 model. Nearest extrapolation is used.
param_file = "./3_input_params/input_params_real.yaml"
am_crust1p0 = ATTModel(param_file)
am_crust1p0.grid_data_crust1(type="vp")
# %% [markdown]
# # Step 2. Generate the ATT model based on ak135 model.
# %%
# Step 2. Generate the ATT model based on ak135 model.
# ak135.h5 has a three-column dataset 'model'. First column: depth (in km), second column: Vp (in km/s), third column: Vs (in km/s).
# a text version of the ak135 model can be found in Kennett et al. (1995):
# Kennett, B. L., Engdahl, E. R., & Buland, R. (1995). Constraints on seismic velocities in the Earth from traveltimes. Geophysical Journal International, 122(1), 108-124.
# Load the 1D ak135 model from the .h5 file.
with h5py.File('ak135.h5', 'r') as f:
points_ak135 = f['model'][:]
am_ak135 = ATTModel(param_file)
# interpolate the 1D ak135 velocity model to the depths of the ATT model.
vel_1d = np.interp(am_ak135.depths, points_ak135[:,0], points_ak135[:,1], left=points_ak135[0,1], right=points_ak135[-1,1])
# Set the 3D velocity model by tiling the 1D velocity model along lat and lon directions.
am_ak135.vel = np.tile(vel_1d[:, None, None], (1, am_ak135.n_rtp[1], am_ak135.n_rtp[2]))
# %% [markdown]
# # Step 3. Combine ak135 model with crust1.0 model
# %%
# 1. set two depths
# if depth < depth_1, vel = crust1p0
# if depth_1 <= depth <= depth_2, vel = linear_interp between crust1p0 and ak135
# if depth > depth_2, vel = ak135
am_combined = ATTModel(param_file)
depth_1 = 35.0
depth_2 = 70.0
ratio = (am_ak135.depths - depth_1) / (depth_2 - depth_1)
ratio = np.clip(ratio, 0.0, 1.0)
ratio_3d = np.tile(ratio[:, None, None], (1, am_ak135.n_rtp[1], am_ak135.n_rtp[2]))
# linear interpolation
am_combined.vel = am_crust1p0.vel * (1 - ratio_3d) + am_ak135.vel * ratio_3d
# %% [markdown]
# # Step 4. post processing (OPTIONAL)
# %%
am_processed = am_combined.copy()
# 1. (OPTIONAL) monotonic increase check
# Ensure that the velocity model increases monotonically with depth.
am_processed.vel[::-1,:,:] = np.maximum.accumulate(am_processed.vel[::-1,:,:], axis=0)
# 2. (OPTIONAL) Gaussian smoothing to the combined model to avoid sharp discontinuities.
## Upgrade PyTomoATT to version 0.2.10 or later to use this function.
am_processed.smooth(sigma=am_processed.d_rtp, unit_deg=True, mode='nearest') # standard deviation for Gaussian kernel along each axis (ddep, dlat, dlon)
# %%
# output as .h5 file
n_rtp = am_processed.n_rtp
fname = f"constant_velocity_N{n_rtp[0]:d}_{n_rtp[1]:d}_{n_rtp[2]:d}_PyTomoATT.h5"
am_processed.write(fname)
# %%
# visualization of the central lat-lon slice
import matplotlib.pyplot as plt
dep = am_processed.depths
vel = am_processed.vel[:, am_processed.n_rtp[1]//2, am_processed.n_rtp[2]//2]
lat = am_processed.latitudes[am_processed.n_rtp[1]//2]
lon = am_processed.longitudes[am_processed.n_rtp[2]//2]
fig = plt.figure(figsize=(6,6))
ax = fig.add_subplot(1,1,1)
ax.plot(vel, dep, label='Velocity', color='blue')
ax.invert_yaxis()
ax.set_xlabel('Vp (km/s)', fontsize=16)
ax.set_ylabel('Depth (km)', fontsize=16)
ax.tick_params(axis='x', labelsize=16)
ax.tick_params(axis='y', labelsize=16)
ax.set_title(f'Velocity Profile at Lat: {lat:.2f}, Lon: {lon:.2f}', fontsize=16)
ax.grid()
ax.legend(fontsize=16)
plt.show()
os.makedirs("figs", exist_ok=True)
fig.savefig("figs/velocity_profile_lat%.2f_lon%.2f.png"%(lat, lon), facecolor='white', edgecolor='white', bbox_inches='tight')

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examples/scripts_of_generate_community_model/3_input_params/input_params_real.yaml Normal file
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version: 3
#################################################
# computational domain #
#################################################
domain:
min_max_dep: [-50, 550] # depth in km
min_max_lat: [10.5, 22.5] # latitude in degree
min_max_lon: [95.5, 107.5] # longitude in degree
n_rtp: [121, 121, 121] # number of nodes in depth,latitude,longitude direction
#################################################
# traveltime data file path #
#################################################
source:
src_rec_file: 1_src_rec_files/src_rec_file.dat # source receiver file path
swap_src_rec: false # swap source and receiver
#################################################
# initial model file path #
#################################################
model:
init_model_path: 2_models/model_init_N121_121_121.h5 # path to initial model file
#################################################
# parallel computation settings #
#################################################
parallel: # parameters for parallel computation
n_sims: 8 # number of simultaneous runs (parallel the sources)
ndiv_rtp: [1, 1, 1] # number of subdivision on each direction (parallel the computional domain)
############################################
# output file setting #
############################################
output_setting:
output_dir: OUTPUT_FILES/OUTPUT_FILES_real # path to output directory (default is ./OUTPUT_FILES/)
output_source_field: false # True: output the traveltime field and adjoint field of all sources at each iteration. Default: false. File: 'out_data_sim_group_X'.
output_kernel: false
output_final_model: true # True: output merged final model. This file can be used as the input model for TomoATT. Default: true. File: 'model_final.h5'.
output_middle_model: false # True: output merged intermediate models during inversion. This file can be used as the input model for TomoATT. Default: false. File: 'middle_model_step_XXXX.h5'
output_in_process: false # True: output at each inv iteration, otherwise, only output step 0, Niter-1, Niter. Default: true. File: 'out_data_sim_group_0'.
output_in_process_data: false # True: output src_rec_file at each inv iteration, otherwise, only output step 0, Niter-2, Niter-1. Default: true. File: 'src_rec_file_step_XXXX.dat'
single_precision_output: false # True: output results in single precision. Default: false.
verbose_output_level: 0 # output internal parameters, (to do)
output_file_format: 0 # 0: hdf5, 1: ascii
# output files:
# File: 'out_data_grid.h5'. Keys: ['Mesh']['elem_conn'], element index;
# ['Mesh']['node_coords_p'], phi coordinates of nodes;
# ['Mesh']['node_coords_t'], theta coordinates of nodes;
# ['Mesh']['node_coords_r'], r coordinates of nodes;
# ['Mesh']['node_coords_x'], phi coordinates of elements;
# ['Mesh']['node_coords_y'], theta coordinates of elements;
# ['Mesh']['node_coords_z'], r coordinates of elements;
# File: 'out_data_sim_group_0'. Keys: ['model']['vel_inv_XXXX'], velocity model at iteration XXXX;
# ['model']['xi_inv_XXXX'], xi model at iteration XXXX;
# ['model']['eta_inv_XXXX'], eta model at iteration XXXX
# ['model']['Ks_inv_XXXX'], sensitivity kernel related to slowness at iteration XXXX
# ['model']['Kxi_inv_XXXX'], sensitivity kernel related to xi at iteration XXXX
# ['model']['Keta_inv_XXXX'], sensitivity kernel related to eta at iteration XXXX
# ['model']['Ks_density_inv_XXXX'], kernel density of Ks at iteration XXXX
# ['model']['Kxi_density_inv_XXXX'], kernel density of Kxi at iteration XXXX
# ['model']['Keta_density_inv_XXXX'], kernel density of Keta at iteration XXXX
# ['model']['Ks_over_Kden_inv_XXXX'], slowness kernel over kernel density at iteration XXXX
# ['model']['Kxi_over_Kden_inv_XXXX'], xi kernel over kernel density at iteration XXXX
# ['model']['Keta_over_Kden_inv_XXXX'], eta kernel over kernel density at iteration XXXX
# ['model']['Ks_update_inv_XXXX'], slowness kernel over kernel density at iteration XXXX, smoothed by inversion grid
# ['model']['Kxi_update_inv_XXXX'], xi kernel over kernel density at iteration XXXX, smoothed by inversion grid
# ['model']['Keta_update_inv_XXXX'], eta kernel over kernel density at iteration XXXX, smoothed by inversion grid
# ['1dinv']['vel_1dinv_inv_XXXX'], 2d velocity model at iteration XXXX, in 1d inversion mode
# ['1dinv']['r_1dinv'], r coordinates (depth), in 1d inversion mode
# ['1dinv']['t_1dinv'], t coordinates (epicenter distance), in 1d inversion mode
# File: 'src_rec_file_step_XXXX.dat' or 'src_rec_file_forward.dat'. The synthetic traveltime data file.
# File: 'final_model.h5'. Keys: ['eta'], ['xi'], ['vel'], the final model.
# File: 'middle_model_step_XXXX.h5'. Keys: ['eta'], ['xi'], ['vel'], the model at step XXXX.
# File: 'inversion_grid.txt'. The location of inversion grid nodes
# File: 'objective_function.txt'. The objective function value at each iteration
# File: 'out_data_sim_group_X'. Keys: ['src_YYYY']['time_field_inv_XXXX'], traveltime field of source YYYY at iteration XXXX;
# ['src_YYYY']['adjoint_field_inv_XXXX'], adjoint field of source YYYY at iteration XXXX;
# ['1dinv']['time_field_1dinv_YYYY_inv_XXXX'], 2d traveltime field of source YYYY at iteration XXXX, in 1d inversion mode
# ['1dinv']['adjoint_field_1dinv_YYYY_inv_XXXX'], 2d adjoint field of source YYYY at iteration XXXX, in 1d inversion mode
#################################################
# inversion or forward modeling #
#################################################
# run mode
# 0 for forward simulation only,
# 1 for inversion
# 2 for earthquake relocation
# 3 for inversion + earthquake relocation
# 4 for 1d model inversion
run_mode: 1
have_tele_data: true # An error will be reported if false but source out of study region is used. Default: false.
###################################################
# model update parameters setting #
###################################################
model_update:
max_iterations: 80 # maximum number of inversion iterations
step_length: 0.01 # the initial step length of model perturbation. 0.01 means maximum 1% perturbation for each iteration.
# parameters for optim_method 0 (gradient_descent)
optim_method_0:
# if step_method:1. if the angle between the current and the previous gradients is greater than step_length_gradient_angle, step size -> step length * step_length_change[0].
# otherwise, step size -> step length * step_length_change[1].
step_length_gradient_angle: 120 # default: 120.0
step_length_change: [0.5, 1.41] # default: [0.5,1.2]
Kdensity_coe: 0.3 # default: 0.0, range: 0.0 - 1.0
# parameters for smooth method 0 (multigrid model parametrization)
# inversion grid can be viewed in OUTPUT_FILES/inversion_grid.txt
n_inversion_grid: 5 # number of inversion grid sets
uniform_inv_grid_dep: false # true if use uniform inversion grid for dep, false if use flexible inversion grid
uniform_inv_grid_lat: false # true if use uniform inversion grid for lat, false if use flexible inversion grid
uniform_inv_grid_lon: false # true if use uniform inversion grid for lon, false if use flexible inversion grid
# settings for flexible inversion grid
dep_inv: [-50, -25, 0, 50, 100, 150, 200, 275, 350, 425, 500, 600,700] # inversion grid for vel in depth (km)
lat_inv: [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] # inversion grid for vel in latitude (degree)
lon_inv: [95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108] # inversion grid for vel in longitude (degree)
trapezoid: [1, 0, 50] # usually set as [1.0, 0.0, 50.0] (default)
# if we want to use another inversion grid for inverting anisotropy, set invgrid_ani: true (default: false)
invgrid_ani: false
# ---------- flexible inversion grid setting for anisotropy ----------
# settings for flexible inversion grid for anisotropy
dep_inv_ani: [-5, -2, 0, 3, 7, 12, 17, 23, 30, 38, 47, 57] # inversion grid for ani in depth (km)
lat_inv_ani: [-2.8, -2.3, -1.8, -1.3, -0.8, -0.3, 0.2, 0.7, 1.2, 1.7, 2.2, 2.7] # inversion grid for ani in latitude (degree)
lon_inv_ani: [-1.2, -0.9, -0.6, -0.3, 0, 0.3, 0.6, 0.9, 1.2] # inversion grid for ani in longitude (degree)
trapezoid_ani: [1, 0, 50] # usually set as [1.0, 0.0, 50.0] (default)
# Carefully change trapezoid and trapezoid_ani, if you really want to use trapezoid inversion grid, increasing the inversion grid spacing with depth to account for the worse data coverage in greater depths.
# The trapezoid_ inversion grid with index (i,j,k) in longitude, latitude, and depth is defined as:
# if dep_inv[k] < trapezoid[1], lon = lon_inv[i];
# lat = lat_inv[j];
# dep = dep_inv[k];
# if trapezoid[1] <= dep_inv[k] < trapezoid[2], lon = mid_lon_inv+(lon_inv[i]-mid_lon_inv)*(dep_inv[k]-trapezoid[1])/(trapezoid[2]-trapezoid[1])*trapezoid[0];
# 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];
# dep = dep_inv[k];
# The shape of trapezoid inversion gird (x) looks like:
#
# lon_inv[0] [1] [2] [3] [4]
# |<-------- (lon_inv[end] - lon_inv[0]) ---->|
# dep_inv[0] | x x x x x |
# | |
# dep_inv[1] | x x x x x |
# | |
# dep_inv[2] = trapezoid[1] / x x x x x \
# / \
# dep_inv[3] / x x x x x \
# / \
# dep_inv[4] = trapezoid[2] / x x x x x \
# | |
# dep_inv[5] | x x x x x |
# | |
# dep_inv[6] | x x x x x |
# |<---- trapezoid[0]* (lon_inv[end] - lon_inv[0]) ------>|
# -------------- using absolute traveltime data --------------
abs_time:
use_abs_time: false # 'true' for using absolute traveltime data to update model parameters; 'false' for not using (no need to set parameters in this section)
# -------------- using common source differential traveltime data --------------
cs_dif_time:
use_cs_time: true # 'true' for using common source differential traveltime data to update model parameters; 'false' for not using (no need to set parameters in this section)
# -------------- using common receiver differential traveltime data --------------
cr_dif_time:
use_cr_time: false # 'true' for using common receiver differential traveltime data to update model parameters; 'false' for not using (no need to set parameters in this section)
# -------------- inversion parameters --------------
update_slowness : true # update slowness (velocity) or not. default: true
update_azi_ani : false # update azimuthal anisotropy (xi, eta) or not. default: false
use_sta_correction: true
# initial_sta_correction_file: 4_initial_station_correct/station_correction_file_step_0010.dat # the path of initial station correction
step_length_sta_correction: 0.01 # step length relate to the update of station correction terms

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examples/scripts_of_generate_community_model/ak135.h5 Normal file
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examples/scripts_of_generate_community_model/run_this_example.sh Normal file
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#!/bin/bash
# run the script to generate HDF5 model files based on community models
# 1. crust1.0 (Laske et al., 2013) + ak135 model (Kennett et al., 1995)
python 1_crust1.0_ak135_model.py
# References:
# Laske, G., Masters, G., Ma, Z., & Pasyanos, M. (2013, April). Update on CRUST1. 0—A 1-degree global model of Earth’s crust. In Geophysical research abstracts (Vol. 15, No. 15, p. 2658).
# Kennett, B. L., Engdahl, E. R., & Buland, R. (1995). Constraints on seismic velocities in the Earth from traveltimes. Geophysical Journal International, 122(1), 108-124.