Reg. the creation of a mesh file for the reactive domain

Dear Sir,

For the reactive transport coupled with PHREEQC, I want to create a mesh file (.vtu) with bulk_node_ids and bulk_element_ids.

But, I couldn’t produce such a .vtu file with both bulk_node_ids and bulk_element_ids from the .msh file generated from Gmsh. I used msh2vtu to do so.

Please let me know how to create a .vtu file with both bulk_node_ids and bulk_element_ids for the reactive domain through the command lines.

I am attaching the files for your reference.

Pavan. (712.1 KB)

Check the answer given here

Dear lurpi,

I know how to convert .vtu from .msh files using msh2vtu command. But, my question is specifically about generating a .vtu file that has bulk_node_ids and bulk_element_ids.

Anyhow I even tried the command that you suggested GMSH2OGS, but couldn’t fulfil my requirement.

Let me know how to create such a file.


use the OGS tool identifySubdomains

identifySubdomains -m mesh.vtu -o numbered_ mesh.vtu

then you obtain a numbered_mesh.vtu with what you need .

See Identify subdomains in bulk mesh. for further informations.

Dear lurpi,

I could notice that the identifySubdomains command creates a boundary mesh with bulk_node_ids and bulk_element_ids. But, in my case, I need those ids for the entire domain not just for the boundaries.

Please go to Tests/Data/Parabolic/ComponentTransport/ReactiveTransport, and you can see that all the examples in that folder needed a reactive domain mesh file. I need to generate a similar mesh file that has all the ids (bulk_node_ids and bulk_element_ids).


In the command

identifySubdomains -m mesh.vtu -o numbered_ mesh.vtu

replace ‘mesh.vtu’ with whatever vtu you need to process. A domain is a subdomain of itself, it will work.

Thanks, Lurpi. It worked.

I have another question, how to assign a random distribution of material parameters to the mesh (e.g., porosity and permeability)?

I have no direct experience. Check

as well as the publication Hydro-mechanical continuum modelling of fluid percolation through rock salt - ScienceDirect

I suggest you to open a different question, related to the definition of random fields: OGS: [case] RandomFieldMeshElementParameter