pymech.neksuite#

This module contains the functions used to interact with Nek5000 files. The Contents of neksuite are reported at the bottom of this page.

readnek#

This function reads the binary .f%05d files that Nek5000 uses to store output flow fields.

The only input needed by this function is:

  • fname: a string containing the name of the file;

readnek() is clever enough to figure out the rest. The output is a single pymech.core.HexaData data structure containing all the information that was stored in the file.

Note

If you are only interested in the metadata (for example, the simulation time) of a solution file a quicker solution would be to execute pymech.neksuite.field.read_header()

writenek#

This function writes a binary .f%05d file in the same format that Nek5000 uses to store output flow fields. It is therefore possible to open this file with VisIt or Paraview.

The inputs needed by this function are:

  • fname: a string containing the name of the file;

  • data: a single pymech.core.HexaData data structure containing the data to be written to file.

writenek() produces no output.

readrea#

This function reads an ASCII .rea file that Nek5000 uses to store simulation parameters and mesh (when a .re2 file is absent). ONLY the mesh is actually read, all parameters are disregarded.

The only input needed by this function is:

  • fname: a string containing the name of the file;

readrea() is clever enough to figure out the rest. The output is a single pymech.core.HexaData data structure containing the mesh that was stored in the file.

writerea#

This function writes an ASCII .rea file in the same format that Nek5000 uses to store simulation parameters and mesh. ONLY the mesh is actually written, all simulation parameters are initialised to sensible defaults.

The inputs needed by this function are:

  • fname: a string containing the name of the file;

  • data: a single pymech.core.HexaData data structure containing the mesh to be written to file.

writerea() produces no output.

readre2 and writere2#

These functions are analagous to readrea and writerea but works with the newer, binary .re2 mesh files. New in pymech 1.4.0.

Contents of neksuite#

class pymech.neksuite.field.Header(wdsz, orders, nb_elems, nb_elems_file, time, istep, fid, nb_files, variables: str | bytes = _Nothing.NOTHING, realtype: str = _Nothing.NOTHING, nb_pts_elem: int = _Nothing.NOTHING, nb_dims: int = _Nothing.NOTHING, nb_vars: Tuple[int, ...] = _Nothing.NOTHING)[source]#

Dataclass for Nek5000 field file header. This relies on the package attrs and its ability to do type-validation and type-conversion of the header metadata.

pymech.neksuite.field.read_header(path_or_file_obj: str | PathLike | BinaryIO) → Header[source]#

Make a pymech.neksuite.Header instance from a file buffer opened in binary mode.

pymech.neksuite.field.readnek(fname, dtype='float64', skip_vars=())[source]#

A function for reading binary data from the nek5000 binary format

Parameters:

  • fname (str) – File name

  • dtype (str or type) – Floating point data type. See also pymech.core.Elem.

  • skip_vars (tuple[str]) – Variables to skip. Valid values to skip are ("x", "y", "z", "ux", "uy", "uz", "pressure", "temperature", "s01", "s02", ...). It also accept some extra values ("vx", "vy", "vz", "p", "t"). If empty (default), it reads all variables available in the file.

pymech.neksuite.field.writenek(fname, data)[source]#

A function for writing binary data in the nek5000 binary format

Parameters:
pymech.neksuite.mesh.readre2(fname)[source]#

A function for reading .re2 files for nek5000

Parameters:

fname (str) – file name

pymech.neksuite.mesh.readrea(fname)[source]#

A function for reading .rea files for nek5000

Parameters:

fname (str) – file name

pymech.neksuite.mesh.writere2(fname, data)[source]#

A function for writing binary .re2 files for nek5000

Parameters:
pymech.neksuite.mesh.writerea(fname, data)[source]#

A function for writing ascii .rea files for nek5000

Parameters:
pymech.neksuite.map.readma2(fname)[source]#

A function for reading binary map files (*.ma2) for nek5000.

The map file comtains, for each element in the mesh, the id of the MPI rank that owns it followed by the ids of the vertices of the element in the global address space.

The partitioning is determined by generating the undirected graph formed by the mesh, then repeatedly computing and deviding the graph using the Fiedler vector of the graph Laplacian.

Parameters:

fname (str) – file name

Returns:

  • cell (2d int ndarray) – list of the vertices for each element of the mesh (in global address space)

  • procmap (1d int ndarray) – processor map (0-based) indicating ownership for each element of the mesh

Note

See usage for more details.