Generating Spin Density Cube Files

orto can generate a cube file for the spin density of your system using orto gen spden.

This wraps orca_plot and generates a spin density cube file without the time consuming interactive part, or the need to write bizarre input files. The cube file is computed in parallel as part of a batch job, allowing relatively dense grids to be specified.

Setup

To use this feature, you need to first set the orto_orca_load environment variable - this specifies the command used to load the ORCA module on your system.

Typically a module system like Lmod or Environment Modules is used to manage software on HPC systems, and you will need to set this variable accordingly.

For example, when using Environment Modules, this may be set as

    export orto_orca_load="orca/6.0.1"

We advise that you set this to the version of ORCA you use most frequently.

Alternatively, you can provide the --orca_load optional argument in orto gen spden and specify the command to load ORCA - this overrides the environment variable and so can be used to submit jobs with different versions of ORCA.

Usage

To generate a spin density cube file, run

    orto gen spden <gbw_file> <nprocs>

where <gbw_file> is the path to your ORCA .gbw file, and <nprocs> is the number of cores to use in the cube file generation job.

Note

You will need .densities and .densitiesinfo files with the same basename and parent directory as the .gbw file.

This will then submit a batch job to generate the cube file.

Number of points

The number of points in the cube file is determined by the --n_pts keyword argument - if this is not specified, a default of 100 points per dimension is used.

Memory

The amount of memory to use in the cube file generation job can be specified using the --memory keyword argument, by default, 500 MB of memory is used per core.

Other Arguments

Additional command line arguments for orto gen spden can be listed by running

    orto gen spden -h

Example - Triplet Oxygen

From these files, you can use orto to generate a cube file for the spin-density of triplet molecular oxygen using four cores.

orto gen spden oxygen.gbw 4

This creates a jobscript (oxygen_spin_density_job.sh) which is then submitted to the scheduler.

After this job finishes, the file oxygen.spindens.cube will be present in the same directory as oxygen.gbw.