Using Output as Input in FEniCSx and Solving Potential Equation

dokken · October 14, 2024, 8:06am

There are various ways of reading this, see for instance:

Reading node based data from "Legacy" XDMFFile

opened 05:09PM - 15 Jul 23 UTC

enhancement dolfin-legacy

quick and "dirty" python version of reading data at geometry nodes. Should be p…roperly implemented with ADIOS2. ```python from pathlib import Path import adios4dolfinx import dolfinx import numpy as np from mpi4py import MPI with dolfinx.io.XDMFFile(MPI.COMM_WORLD, "idealized_LV_ref_0.xdmf", "r") as xdmf: mesh = xdmf.read_mesh(name="mesh", xpath="Xdmf/Domain/Grid") import basix import h5py def read_mesh_data(file_path:Path, mesh: dolfinx.mesh.Mesh, data_path:str): assert file_path.is_file(), f"File {file_path} does not exist" infile = h5py.File(file_path, "r", driver="mpio", comm=mesh.comm) num_nodes_global = mesh.geometry.index_map().size_global assert data_path in infile.keys(), f"Data {data_path} does not exist" dataset = infile[data_path] shape = dataset.shape assert shape[0] == num_nodes_global, f"Got data of shape {shape}, expected {num_nodes_global, shape[1]}" dtype = dataset.dtype # Read data locally on each process local_input_range = adios4dolfinx.comm_helpers.compute_local_range(mesh.comm, num_nodes_global) local_input_data = dataset[local_input_range[0]:local_input_range[1]] # Create appropriate function space (based on coordinate map) assert len(mesh.geometry.cmaps) == 1, "Mixed cell-type meshes not supported" element = basix.ufl.element( basix.ElementFamily.P, mesh.topology.cell_name(), mesh.geometry.cmaps[0].degree, mesh.geometry.cmaps[0].variant, shape=(shape[1],), gdim=mesh.geometry.dim) # Assumption: Same doflayout for geometry and function space, cannot test in python V = dolfinx.fem.FunctionSpace(mesh, element) uh = dolfinx.fem.Function(V, name=data_path) # Assume that mesh is first order for now assert mesh.geometry.cmaps[0].degree == 1, "Only linear meshes supported" x_dofmap = mesh.geometry.dofmap igi = np.array(mesh.geometry.input_global_indices, dtype=np.int64) global_geom_input = igi[x_dofmap] global_geom_owner = adios4dolfinx.utils.index_owner(mesh.comm, global_geom_input.reshape(-1), num_nodes_global) for i in range(shape[1]): arr_i = adios4dolfinx.comm_helpers.send_dofs_and_recv_values(global_geom_input.reshape(-1), global_geom_owner, mesh.comm, local_input_data[:,i], local_input_range[0]) dof_pos = x_dofmap.reshape(-1)*shape[1]+i uh.x.array[dof_pos] = arr_i infile.close() return uh infile = Path("idealized_LV_ref_0.h5") for data in ["f0", "n0", "phi", "psi", "s0"]: uh = read_mesh_data(infile, mesh, data) with dolfinx.io.XDMFFile(mesh.comm, f"{data}.xdmf", "w") as xdmf: xdmf.write_mesh(mesh) xdmf.write_function(uh) ``` ref: https://fenicsproject.discourse.group/t/i-o-from-xdmf-hdf5-files-in-dolfin-x/3122/47

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Using Output as Input in FEniCSx and Solving Potential Equation

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