Simulation Mesh

When running Amanzi in the structured mode, the mesh is generated internally and the user is not required to specify it explicitly.

When running Amanzi in the unstructured mode, it is possible to ask Amanzi to internally generate the mesh or read a mesh that is generated by an external tool like LaGriT and written out in the Exodus II format.

If the mesh is internally generated and the simulation is being run on multiple cores, the mesh will automatically be distributed over the multiple processors.

If the mesh is externally generated and the simulation is on multiple cores, then the user has two options for distributing the mesh across processors. In the first option, the complete mesh exists in a single Exodus II file which is read in, partitioned and distributed to the various processors. The input file must have an extension of .exo for this option. The second option is to prepartition the mesh on disk using the splitexo script under the bin directory of the Amanzi tree into files and letting Amanzi read each one in one processor (Nemesis I files are Exodus II files with extra information allowing them to be used in a parallel setting). To specify a prepartitioned file in the Nemesis I format, users must specify the filename with a .exo or .par extension. No processor or partition number needs to be specified even though the files on disk have a processor suffix. Thus, a serial mesh might be specified as mymesh.exo while a mesh partitioned into four parts, mymesh.par.0, mymesh.par.1, mymesh.par.2, mymesh.par.2 would be specified as mymesh.exo or mymesh.par.