SeismicMesh 1.2.44

2D/3D serial and parallel triangular mesh generation and mesh improvement for seismology

SeismicMesh: Mesh generation for Seismology in Python

2D/3D triangular meshing for a slab of Earth based on modifications to the DistMesh algorithm. SeismicMesh is distributed under GPL3.

Installation

For installation, SeismicMesh needs CGAL and pybind11:

sudo apt install libcgal-dev python-pybind11

After that, SeismicMesh can be installed from the Python Package Index (pypi), so with:

pip install -U SeismicMesh

For more detailed information about installation and requirements see:

Install - How to install SeismicMesh.

Example

The user can quickly build quality 2D/3D meshes from seismic velocity models in serial/parallel. For example in 3D::

First, to run this code below you must download the benchmark 3D EAGE velocity model from here

The result of running the code below. Note, the seismic velocity data has been interpolated onto the vertices of the mesh.

import numpy as np
import zipfile

from mpi4py import MPI
import meshio

import SeismicMesh

comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()


if rank == 0:
    # Dimensions of model (number of grid points in z, x, and y)
    nx, ny, nz = 676, 676, 210

    path = "velocity_models/Salt_Model_3D/3-D_Salt_Model/VEL_GRIDS/"
    # Extract Saltf@@ from SALTF.ZIP
    zipfile.ZipFile(path + "SALTF.ZIP", "r").extract("Saltf@@", path=path)

    # Load data into a numpy array
    with open(path + "Saltf@@", "r") as file:
        vp = np.fromfile(file, dtype=np.dtype("float32").newbyteorder(">"))
        vp = vp.reshape(nx, ny, nz, order="F")
        vp = np.flipud(vp.transpose((2, 0, 1)))  # z, x and then y
else:
    vp = np.zeros(shape=(1, 1, 1))
    vp[:] = 1500.0

# The domain is defined (in this case) as a cube and domain extents are provided in meters

# Bounding box describing domain extents (corner coordinates)
bbox = (-4200, 0, 0, 13520, 0, 13520)

# A graded sizing function is created from the velocity model along with a signed distance function by passing
# the velocity grid that we created above. More details for the :class:`MeshSizeFunction` can be found here
# https://seismicmesh.readthedocs.io/en/par3d/api.html#seimsicmesh-meshsizefunction

ef = SeismicMesh.MeshSizeFunction(
    bbox=bbox,
    velocity_grid=vp,
    dt=0.001,
    freq=2,
    wl=5,
    grade=0.25,
    hmin=150,
    hmax=5e3,
    domain_ext=250,
    padstyle="linear_ramp",
)

ef = ef.build()

# The user then calls the mesh generator

# Construct a mesh generator object
mshgen = SeismicMesh.MeshGenerator(ef)

# Build the mesh
points, cells = mshgen.build(max_iter=75, axis=1)

# For 3D mesh generation, we provide an implementation to bound the minimum dihedral angle::

points, cells = mshgen.build(
    points=points, mesh_improvement=True, max_iter=50, min_dh_bound=5,
)

# Meshes can be written quickly to disk using meshio and visualized with Paraview::

if rank == 0:
    meshio.write_points_cells(
        "EAGE_Salt.vtk", points / 1000.0, [("tetra", cells)],
    )

More information

All other information is available at: https://seismicmesh.readthedocs.io

Getting started - Learn the basics about the program and the application domain.

Tutorials - Tutorials that will guide you through the main features.