submit_gmx_analyses_lintf2_ether

Submit Gromacs analysis tools for systems containing LiTFSI and linear poly(ethylene oxides) of arbitrary length (including dimethyl ether) to the Slurm Workload Manager of an HPC cluster.

This script is designed to be used on the Palma2 HPC cluster of the University of Münster or on the Bagheera HPC cluster of the research group of Professor Heuer.

Options

Required Arguments

--system

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.

--settings

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.

--scripts

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 ls path/to/hpc_submit_scripts/analysis/lintf2_ether/gmx/.

0

All scripts.

1

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).

2

All scripts analyzing a slab in xy plane.

3

All trjconv scripts.

4

All RDFs (bulk and slab-z).

4.1

All bulk RDFs.

4.2

All slab-z RDFs.

5

All MSDs.

6

All z-profiles (density-z* and potential-z*).

7

All z-densmaps.

Options for Trajectory Reading

--begin

First frame (in ps) to read from trajectory. Default: 0.

--end

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.

--every

Only use frame if t MOD every == first time (in ps). Default: 0.

Options for MSD Calculation

--beginfit

Start lag time for fitting the MSD (in ps), -1 is 10%. Default: -1.

--endfit

End lag time for fitting the MSD (in ps), -1 is 90%. Default: -1.

--restart

Time (in ps) between restarting points in trajectory for MSD calculation. Default: 1000.

Options for Distance Resolved Quantities (like RDFs)

--binwidth

Bin width (in nm) for distance resolved quantities. Default: 0.005.

Options for Tools That Analyze Slabs in xy Plane

--zmin

Lower boundary (in nm) of the slab in xy plane. Default: 0.

--zmax

Upper boundary (in nm) of the slab in xy plane. Default: Maximum length of the simulation box in z direction (inferred from $settings_out_$system.gro).

--slabwidth

Slab width (in nm) to use when --discretize or --center-slab is given. Default: 0.1.

--discretize

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.

--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.

Gromacs-Specifig Options

--gmx-lmod

If running on a cluster which uses the Lmod module system, specifiy here which file to source (relative to the lmod subdirectory of this project) to load Gromacs. Default: 'palma/2019a/gmx2018-8_foss.sh'.

--gmx-exe

Name of the Gromacs executable. Default: 'gmx'.

Sbatch Options

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.

Config File

This script reads options from the following sections of a Configuration File:

  • [submit]

  • [submit.analysis]

  • [submit.analysis.lintf2_ether]

  • [submit.analysis.lintf2_ether.gmx]

  • [sbatch]

  • [sbatch.analysis]

  • [sbatch.analysis.lintf2_ether]

  • [sbatch.analysis.lintf2_ether.gmx]

Notes

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.