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# # Time-dependent mesh checkpoints
# As we have seen in the previous examples, we store information about the connectivity,
# the coordinates of the mesh nodes,
# as well as a reference element. Note that the only thing that can change for a mesh
# during a simulation are the coordinate of the mesh nodes.
# In the following example, we will demonstrate how to write a time-dependent mesh
# checkpoint to disk.
# First, we create a simple function to compute the volume of a mesh
# +
import logging
from pathlib import Path
from mpi4py import MPI
import ipyparallel as ipp
import adios4dolfinx
def compute_volume(mesh, time_stamp):
from mpi4py import MPI
import dolfinx
import ufl
# Compute the volume of the mesh
vol_form = dolfinx.fem.form(1 * ufl.dx(domain=mesh))
vol_local = dolfinx.fem.assemble_scalar(vol_form)
vol_glob = mesh.comm.allreduce(vol_local, op=MPI.SUM)
if mesh.comm.rank == 0:
print(f"{mesh.comm.rank + 1}/{mesh.comm.size} Time: {time_stamp} Mesh Volume: {vol_glob}")
def write_meshes(filename: Path):
from mpi4py import MPI
import dolfinx
import numpy as np
import adios4dolfinx
# Create a unit cube
mesh = dolfinx.mesh.create_unit_cube(
MPI.COMM_WORLD,
3,
6,
5,
cell_type=dolfinx.mesh.CellType.hexahedron,
ghost_mode=dolfinx.mesh.GhostMode.shared_facet,
)
# Write mesh to file, associated with time stamp 1.5
adios4dolfinx.write_mesh(filename, mesh, engine="BP4", time=1.5)
compute_volume(mesh, 1.5)
mesh.geometry.x[:, 0] += 0.1 * mesh.geometry.x[:, 0]
mesh.geometry.x[:, 1] += 0.3 * mesh.geometry.x[:, 1] * np.sin(mesh.geometry.x[:, 2])
compute_volume(mesh, 3.3)
# Write mesh to file, associated with time stamp 3.3
# Note that we set the mode to append, as we have already created the file
# and we do not want to overwrite the existing data
adios4dolfinx.write_mesh(
filename, mesh, engine="BP4", time=3.3, mode=adios4dolfinx.adios2_helpers.adios2.Mode.Append
)
# -
# We write the sequence of meshes to file
# +
mesh_file = Path("timedep_mesh.bp")
n = 3
with ipp.Cluster(engines="mpi", n=n, log_level=logging.ERROR) as cluster:
# Write mesh to file
cluster[:].push({"compute_volume": compute_volume})
query = cluster[:].apply_async(write_meshes, mesh_file)
query.wait()
assert query.successful(), query.error
print("".join(query.stdout))
# -
# # Reading a time dependent mesh
# The only thing we need to do to read the mesh is to send in the associated time stamp,
# which we do by adding `time=time_stamp` when calling {py:func}`adios4dolfinx.read_mesh`.
second_mesh = adios4dolfinx.read_mesh(mesh_file, comm=MPI.COMM_WORLD, engine="BP4", time=3.3)
compute_volume(second_mesh, 3.3)
first_mesh = adios4dolfinx.read_mesh(mesh_file, comm=MPI.COMM_WORLD, engine="BP4", time=1.5)
compute_volume(first_mesh, 1.5)
# We observe that the volume of the mesh has changed, as we have perturbed the mesh
# between the two time stamps.
# We also note that we can read the meshes in on a different number of processes than
# we wrote them with and in a different order (as long as the time stamps are correct).
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