The name of the system to analyze, e.g.
'LiTFSI_PEO_20-1'for an LiTFSI/PEO electrolyte with an ether-oxygen-to-lithium ratio of 20:1. You can give any string here. See notes below.
The used simulation settings, e.g.
'pr_npt298_pr_nh'for a production run in an NPT ensemble at 298 K utilizing a Parrinello-Rahman barostat and an Nose-Hoover thermostat. You can give any string here. See notes below.
Select the analysis script(s) to submit. Either give the name(s) of the script(s) (without file extension) or give one of the following number options. If you give multiple script names, provide them space-separated as one enquoted string. To list all possible script names type
All scripts analyzing the bulk system (i.e. exclude scripts that analyze only a part, e.g. a slab, of the system, but still include anisotropic analyses, e.g. z-profiles).
All scripts analyzing a slab in xy plane.
All trjconv scripts.
All RDFs (bulk and slab-z).
All bulk RDFs.
All slab-z RDFs.
All z-profiles (density-z* and potential-z*).
Options for Trajectory Reading
First frame (in ps) to read from trajectory. Default:
Last frame (in ps) to read from trajectory. Default: Last frame in
$settings_out_$system.log. Reading from .log files compressed with gzip, bzip2, XZ or LZMA is supported.
Only use frame if t MOD every == first time (in ps). Default:
Options for MSD Calculation
Start lag time for fitting the MSD (in ps), -1 is 10%. Default:
End lag time for fitting the MSD (in ps), -1 is 90%. Default:
Time (in ps) between restarting points in trajectory for MSD calculation. Default:
Options for Distance Resolved Quantities (like RDFs)
Bin width (in nm) for distance resolved quantities. Default:
Options for Tools That Analyze Slabs in xy Plane
Lower boundary (in nm) of the slab in xy plane. Default:
Upper boundary (in nm) of the slab in xy plane. Default: Maximum length of the simulation box in z direction (inferred from
Slab width (in nm) to use when --discretize or --center-slab is given. Default:
Divide the simulation box from --zmin to --zmax in slabs of width --slabwidth and submit all scripts analyzing slabs in xy plane that were selected with --scripts for each created slab. Must not be used together with --center-slab.
Create a slab in xy plane of width --slabwidth exactly in the center of the simulation box (in z direction, inferred from
$settings_out_$system.gro) and submit all scripts analyzing slabs in xy plane that were selected with --scripts for that slab. Must not be used together with --discretize. If given, --zmin and --zmax are ignored.
If running on a cluster which uses the Lmod module system, specifiy here which file to source (relative to the
lmodsubdirectory of this project) to load Gromacs. Default:
Name of the Gromacs executable. Default:
You can provide arbitrary other options to this script. All these other options are parsed directly to the sbatch Slurm command without further introspection or validation. This means, you can parse any option to sbatch but you are responsible for providing correct options.
This script reads options from the following sections of a Configuration File:
The --system and --settings options allow (or enforces) you to choose systematic names for the input and output files of your simulations. Besides a better overview, this enables an easy automation of preparation and analysis tasks.
If input files required for the scripts selected with --scripts cannot be found, the submission script will terminate with an error message before submitting the job(s) to the Slurm Workload Manager.