Regression: Name change to fix/division/coccus from fix/divide/coccus

[joeweaver]

A number of the included examples still use fix/divide/coccus rather than the updated name fix/division/coccus. Example in biofilm-het

I can go through and update them.

Related to this are a few other issues:

1. The naming convention of the files no longer matches how the fix is named, we should probably update that for consistency.
2. The old name is still used in some error strings and documentation.

If you agree regarding those fixes, I can create some new issues to track progress/remind me to fix them up.

Longer term, we should consider some CI testing to catch regressions like this.

[joeweaver]

While fixing these up, I noticed a couple other issues in making sure all the examples run out of the box. I'll be submitting them once I'm sure I understand each issue. To keep track of which examples work with this specific issue, I'm creating a checklist. Checkmarks denote that they have been updated locally and are probably fixed, but other issues may be preventing the example from fully running.

The fix in these cases is updating the relevant input script(s) to use the string "nufeb/division/coccus" instead of 'nufeb/divide' or 'nufeb/divide/coccus'

• [x] biofilm-het
• [x] biofilm-het-summit
• [x] closed-system
• [x] coccus
• [x] joe
• [x] kokkos
• [x] phototroph
• [x] property-nufeb

[joeweaver]

Updates pushed with this commit

[joeweaver]

Probably no need to open an issue for each variation of this fix.

Updated nufeb/monod/het nufeb/monod/aobetc to use nufeb/growth/het etc in this commit

[joeweaver]

Issue also cropped up with death becoming death/diameter and eps adhesion fixes. Also fixed some atom.in files to drop the no longer valid final column. See commits a and b.

[joeweaver]

Should be nearly there. @shelllbw , there's two classes of examples I can't quite get working because I'm not yet familiar enough with either the relevant fix or the case.

closed-system

Seems to be an error with the parameters sent to nufeb/adhesion/eps. Relevant error message:

ERROR: Can't find group in fix nufeb/adhesion/eps (../fix_adhesion_eps.cpp:48)
Last command: fix eps_ext het nufeb/adhesion/eps 2 eps 1.3 30 5678

kokkos The various jathilake2017 file are problematic, it looks like the diffusion_reaction fixes don't specific the boundary types.

ERROR: Illegal fix nufeb/diffusion_reaction command (../fix_diffusion_reaction.cpp:38)
Last command: fix diff_sub all nufeb/diffusion_reaction sub 1.6e-9 1e-4

When convenient, can you take a look at those two sub-issues? Once they're fixed up all the examples in repo should work with the latest version.

[shelllbw]

Sure, I will take a look. Where do you find the second example? It was removed from examples/

[joeweaver]

They're found under:

./examples/kokkos/jayathilake2017.lmp
./examples/kokkos/kokkos/comm_kokkos/jayathilake2017.lmp
./examples/kokkos/kokkos/jayathilake2017-kokkos.lmp
./examples/kokkos/kokkos/comm_classic/jayathilake2017.lmp