# Generating MO Cube Files

`orto` can generate cube files for the molecular orbitals (MOs) of your system using `orto gen orbs`.

This wraps `orca_plot` and generates cube files without the time consuming interactive part, or the need to write bizarre input files. Cube files are computed in parallel as part of a batch job, so large numbers of orbitals with high resolution can be computed with ease.


## 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

::: {code-block} bash
    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 orbs` 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 cube files for your canonical MOs, run

::: {code-block} bash
    orto gen orbs <gbw_file> <orb_number(s)> <nprocs>
:::

where `<gbw_file>` is the path to your _ORCA_ `.gbw` file, `<orb_number(s)>` is a list of the MO indices (zero-indexed) for which you want to generate cube files, and `<nprocs>` is the number of cores to use in the cube file generation job.

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

::: {note}
You will need the `.densitiesinfo` file with the same basename and parent directory as the `.gbw` 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.

### Alpha and Beta MOs

By default, cube files will be generated for the alpha MOs of your system.

To generate cube files for the beta MOs, use the `--beta` flag in `orto gen orbs`.


### Other Arguments

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

::: {code-block} bash
    orto gen orbs -h
:::

## Example - Water

From [these](water.zip) files, you can use `orto` to generate cube files for the HOMO and LUMO of water using four cores.

:::{code-block} bash
orto gen orbs water.gbw 4 5 4
:::

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

After this job finishes, the files `water.mo4a.cube` and `water.mo5a.cube` will be present in the same directory as `water.gbw`.