Input-output

Table of Contents

• Mesh
• Three-dimensional field output
• Checkpoint files

Mesh

Neko has its own mesh format, .nmsh. All meshes should be 3D and consist of hexahedral elements. A 2D or 1D case can be mimicked by having a single element across selected axes and applying periodic boundary conditions.

A native mesh generator for simple box meshes, called genmeshbox, is part of Neko, and is used in some of the examples, for example advecting_cone. The usage is straightforward, and is well described by the help string provided when running the utility.

The main way of obtaining a .nmsh is converting a Nek5000 .re2 mesh file using the rea2nbin utility. Nek5000, in turn, has several converters among its tools, such as gmsh2nek. The latter is also available under the contrib directory in Neko. The workflow is thus to export your mesh into a format, which can be converted to .re2, and then convert the .re2 to .nmsh. Of course one can also use native Nek5000 tools to produce the .re2, such as genbox. In the future, native support for other formats than .nmsh will be added for convenience.

It should be noted, that the .re2 format allows to store boundary conditions. This is relevant for users that have old Nek5000 cases, who wish to convert them to Neko. Boundary conditions are converted and used by Neko, and for these boundaries one does not need to provide information in the boundary_types keyword in the case file. This is why in some of the examples, boundary_types is only filled for some of the boundaries. However, since this feature complicates the code and leads to somewhat confusing case setups, it is planned to deprecate it at some point. Note that periodic boundaries are also directly encoded into the mesh file, and this will remain so in the future.

Three-dimensional field output

Neko stores the 3D fields with results in the .fld format, which is the same as in Nek5000. The advantage of adopting this format, is that there is a reader in Paraview and VisIt, which can be used to visualize them. Note that the latest version of Paraview actually has two reader for .fld. For now, Neko has only been tested with the older reader, which uses VisIt under the hood. A file with the .nek5000 extension is used as the entry point for the readers and stores some metadata. Users may also find the Python package pymech useful for working with .flds. Note that only the first output .fld file stores the mesh.

Checkpoint files

Simulations cannot be restarted from .fld files. Instead, separate checkpoint files can be output for the purpose of restarts. These contain additional information allowing a clean restart, with, e.g., the correct time integration order. A separate file format, .chkp is adopted for the checkpoint files.