running MeshMaker file that includes atmosphere and soil
I use MeshMaker to create the MESH file.
My model includes atmosphere and soil and therefore I put the reference on the ground. I copy the input file that I run with MeshMaker.
I think MeshMaker cannot create the MESH file with both positive and negative values for Z direction, because the results of the following input file includes only negative values in Z direction.
I wonder if someone can help me in that issue, because the TOUGH support group is not responsive.
First of all you do not need to have positive Z direction to assign atm BC. The coordinates are for plotting, but are not used in the code. Second, if you want to have the coordinates you want, you can go to: https://tough.lbl.gov/software/tough-pre-and-post-processors/ and download TOUGH ancillary code MoveMesh.
I do not understand your question. The meshmaker assigns the first rock type to all the elements in your mesh. Most likely you will need to modify them. If you do not understand why each element is associated with the rock type (either rock name, or the sequence number in your rocks block, which are the same) in your model, I suggest you read TOUGH2 manu. That is probably how I would explain to you as well.
Please be precise when you describe your question. Are you running embedded MESHMAKER in TOUGH2? Please make it clear which version of TOUGH you are using. I get lost of what you are trying to do (previously you were asking how to make the coordinates positive for assigning atmospheric boundary condition and that is what I was answering). I do not have the special meshmaker you have. Sorry I cannot help.