gmsh2nek¶

Nek5000 provides a conversion tool to convert Gmsh <https://gmsh.info> meshes (.msh files) into Nek meshes (.re2 files) called gmsh2nek. The source code is located in nek5000/tools, and it can be compiled from that directory with ./maketools gmsh2nek. In addition to the compilers necessary to use Nek5000, gmsh2nek requires cmake. See Before You Begin for more information on dependencies. Once it is compiled, the executable will be available in nek5000/bin.

Before converting a Gmsh mesh, make sure to save it with the appropriate format. Both ASCII and binary version 2 formats are supported. The Binary format is recommend for large meshes. The appropriate options from Gmsh are shown in Fig. 10.

Fig. 10 Recommended options when saving a Gmsh mesh for compatibility with Nek5000

Note

Leave both boxes unchecked when exporting the mesh from Gmsh.

The procedure for running gmsh2nek is simpler compared to exo2nek. The expected input steps are as follows:

It will first ask you for the dimension of the mesh (either 2 or 3).
Next, it will ask for the input Gmsh file. The .msh extension is implied and should not be included.
The tool will then begin converting the mesh and will print a summary of the boundary IDs.
Finally, it will ask for the number of periodic boundary pairs (see Periodic Boundaries below). If your mesh has none, simply enter 0.
gmsh2nek will then output a new .re2 file with the same file name as the input Gmsh file.

An example is shown below with the expected user input highlighted.

Enter mesh dimension: 3
Input .msh file name: pipe
 total node number is         8569
 total quad element number is          416
 total hex element number is          960
 ******************************************************
 Boundary info summary
 BoundaryName     BoundaryID
 Inlet           1
 Outlet           2
 Wall           3
 ******************************************************
 Enter number of periodic boundary surface pairs:
0

writing pipe.re2

When using a converted Gmsh mesh, the user must set up boundary condition in the .usr file in either the usrdat or usrdat2 subroutines, e.g.

do iel=1,nelv
do ifc=1,2*ndim
  id_face = BoundaryID(ifc,iel)
  if (id_face.eq.1) then        ! surface 1 for inlet
     cbc(ifc,iel,1) = 'v  '
  elseif (id_face.eq.2) then    ! surface 2 for outlet
     cbc(ifc,iel,1) = 'O  '
  elseif (id_face.eq.3) then    ! surface 3 for wall
     cbc(ifc,iel,1) = 'W  '
  endif
enddo
enddo

or

call setbc(1,1,'v  ') ! set bcID 1 to inlet for field 1 (velocity)
call setbc(2,1,'O  ') ! set bcID 2 to outlet for field 1 (velocity)
call setbc(3,1,'W  ') ! set bcID 3 to wall for field 1 (velocity)

Periodic Boundaries¶

Periodic boundaries in Nek5000 are implemented on a mesh connectivity level. They must have a conformal element face distribution with a consistent offset vector. Only translational periodicity is supported in gmsh2nek.

Example:	The example below describes the expected inputs for a mesh with a single pair of periodic boundaries.

First, the user must provide the number of periodic surface pairs. In this case, we have 1.

Enter number of periodic boundary surface pairs
1

Next the user specifies which surface IDs are periodic. Here, we set the inlet (sideset 1) to be periodic with the outlet (sideset 2).

input surface 1 and  surface 2  sideSet ID
1 2

The sideset 1 element faces will be mapped to sideset 2 element faces accordingly. However, this requires that you have conformal meshes on sidesets 1 and 2. The P boundary tag will be assigned to the cbc array, while the sideset ID number is still avaialble in the BoundaryID array.

Note

Mulitple pairs of periodic boundaries are supported

Conjugate Heat Transfer Meshes¶

Coming soon!