Few minor bugs when trying to do examples

[NicolasMonnier]

I had few issues trying to run the FabMD plugin with FabSim3 on my local laptot (I had the same errors on remote). I think most of them exists because the documentation is probably out of date with the recent FabSim3.

1. I tried to follow indication in doc/RunEnsemble-examples.md to run the example1
   As indicated I used fab localhost lammps_ensemble:lammps_ensemble_example1 and get the following error :
   RuntimeError: Must declare input_name_in_config: the generic name which sweep directory files will be changed to
   Indeed, in FabMD.py l.75 teh variable input_name_in_config must be define

2. Then I tried to run fab localhost lammps_ensemble:lammps_ensemble_example1,input_name_in_config=data.peptide and had the following error :
   ERROR: no files were found in the sweep_dir of this run_ensemble command
   After investigated, i found out that the run_ensemble() function in fab.py is looking for directories in the SWEEP dir. But in the lammps_ensemble_example1/SWEEP/ dir, there is only files. (in.indent*)

So I just created a specific directory for each of in.indent file and it worked.

3. Last one was with the same command and the directories in the SWEEP dir.
   The lammps runs failed. The log.lammps showed this :
   ERROR: unknow atom style
   Investigations reveal that I probably didn't install lammps correctly to do run with this kind of input. (My lammps worked with some examples in the lammps github project).

So It's just minor bugs but probably usefull to be highlithed .

[djgroen]

Hi Robbie. Could you look into this one when you have some free time?

[djgroen]

I am working my way through this myself now. I pinged David Wright to see if I can get the missing gromacs example still...

[djgroen]

I fixed lammps_ensemble_example1. It was missing in the config dir, and there was a legacy error trigger that became obsolete after the SWEEP dir revamp :).

[djgroen]

I believe 1 and 2 are solved now. @NicolasMonnier would you be able to give it a quick test?

[NicolasMonnier]

Yep I'll try to do it this morning