ucl-ccs / fabmd

FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.

FabMD

FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.

This plugin provides functionality to extend FabSim3's workflow and remote submission capabilities to LAMMPS specific tasks.

For the full FabMD documentation, please visit https://fabmd.readthedocs.io

EasyVVUQ+FabMD

After updating the following files with your credentials

  -FabSim3/deploy/machines_user.yml
  -FabSim3/deploy/machines.yml
  -FabSim3/plugins/FabMD/machines_FabMD_user.yml
  

run the following:

  -  fabsim   <remote machine name>   lammps_init_run_analyse_campaign:fabmd_easyvvuq_InRuAn

and copy the results back to your local machine with

  -  fabsim  <remote machine name>   fetch_results

fabmd's Issues

Add a README to describe its purpose, and mention that it is a plugin for FabSim3

It'd be good to provide a link to the FabSim3 repo there as well :).

Interfacial potential based on density profile using IBI

Hello! I have learned that FabMD can perform IBI, now I want to calculate out the interfacial nonbonded potential of nanocomposites, the density profile of polymer along the surface of filler was considerd as target distribution. If possible, can you tell me the general flow of the user-defined script？I am looking forward to your reply.Thanks very much

More bugs when trying to do examples

I'm trying to work through the examples on the EasyVVUQ + FabMD

I tried to run the example using localhost.

I found that, no matter what I specified on the command line, the settings in FabMD/default_settings/lammps.yaml took precedence. I wanted to run on only one core, but fab localhost easymd_example:fabmd_easyvvuq,cores=1,wall_time=1:00:0 still ran on 24 cores (the value in default_settings/lammps.yaml)

Also, it is not clear that config_dir is a place holder for a general directory name. A user might type in in "config_dir" thinking this is required.

lammps_dummy task not exists

I got an error when I ran

fab localhost lammps_dummy:lammps_dummy,cores=1

when I checked the FabMD.py , I could not find the lammps_dummy task, and also in config_files, there is no lammps_dummy folder

Production run babysitting

We want to automate the restarting of production runs on ARCHER.

"As of 5th June, this example only works with the EasyVVUQ dev branch"

@dww100
Is this still the case, or is it safe to remove this from the start of the main tutorial?

Few minor bugs when trying to do examples

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 .