The folder structure

For reference, this is the file structure of adaptiveMD.

{shared_folder}/             # referenced by `shared://` and set in the `Resource`
  adaptivemd/                #                               set in the `Resource`
    projects/
      {project-name-1}/      # referenced by `project://`
        trajs/
          00000000/
          00000001/
          ...
        models/
    workers/                 # referenced by `sandbox://`
      staging_area/          # referenced by `staging://`
      worker.{task_UUID}/    # referenced by `worker://` (only the current one)
      ...

1. {shared_folder}: is specific to your HPC or locally is usually chosen to be $HOME. The 2. adaptivemd: is the main folder where we will place all files. You can access the shared folder, there are no restrictions, but this should be restricted to loading input files like previous existing projects, etc. A stored files are place within this directory.
2. projects: will contain a single folder per Project, make sure that your project names are short but descriptive to later find files. All files you want to keep for later should be placed here.
3. workers: this folder is specific to the worker scheduler (there is also the possibility to use radical.pilot which uses radical.pilot.sandbox). It contains all temporary folders used by the workers to execute your tasks. Each task get a unique folder that also contains the UUID of the task to be handle. It is set up with all files and then in it your task is executed.
4. staging_area: This is also a temporary folder that contains files that are used by the workers for multiple tasks. Normally a task generating factory knows which files it will need multiple times
5. trajs: is a folder used by engines to place trajectories in.