Gaussian tutorial

A simple, beginner-friendly guide to the Flying Nimbus programs.

The big picture

These tools work together as a pipeline:

Bulma → Vegeta → Flying Nimbus

Bulma prepares files from quantum-chemistry data.
Vegeta uses the optimized structure and Hessian to build velocity and mode-related outputs.
Flying Nimbus reads trajectory-based data and turns it into spectra that you can compare, export, and analyze.

Quick overview

Program	Main job	Typical inputs	Typical outputs
Bulma	Build inputs and extract useful files	XYZ geometry, Gaussian/ORCA/Q-Chem outputs	optimized XYZ, Hessian files, BOMD/OPT/FREQ input
Vegeta	Build velocity and mode-related outputs	equilibrium XYZ, flat Hessian	`velocity.xyz`, optional bohr/s velocities, frequencies, optional `cnorm`
Flying Nimbus	Compute, compare, and analyze spectra	equilibrium XYZ, trajectory, Hessian, `cnorm`, spectra files	plotted spectra, CSV export, peak metrics

Bulma GUI Tutorial

Bulma is the preparation tool. This is where you usually:

create an optimization or frequency input
extract the final optimized geometry
extract the Hessian
prepare BOMD inputs
and, if needed, convert BOMD data into files that are easier to use later in Flying Nimbus

Bulma splash screen

Bulma splash screen.

How about the GUI

The most important ideas are simple:

Choose the working directory first
Use the left sidebar to switch between Opt, Hessian, BOMD, and About
Use the Help panel on the right whenever a field name is unclear
Always check the Log panel at the bottom after you run something

If you are unsure about a field, keep the default and only change the options you understand.

Step 1 — Create an optimization or frequency input

On the Opt page, start by selecting the workdir. Then choose the software row that matches your code, such as Gaussian, ORCA, or Q-Chem.

Bulma Opt page

Bulma Opt page. The working directory is at the top, the software-specific settings are in the middle, the help panel is on the right, and the log is at the bottom.

As a beginner, focus on these fields first:

geometry input file
job type
theory
basis set
charge
multiplicity
number of processors
memory
optional dispersion

A completed example looks like this:

Bulma completed Opt example

Completed Bulma example. The log confirms the command and the file that was written.

What to check after clicking Run

The log should finish cleanly
The output file name should appear in the log
If nothing is written, the first things to check are the workdir and the input path

Step 2 — Extract the optimized geometry

Inside Opt, Bulma also lets you extract the last optimized geometry from a finished output file. This is useful when you want a clean .xyz file to pass to Vegeta or Flying Nimbus.

Bulma geometry extraction

Bulma can extract the optimized geometry into a new XYZ file.

Step 3 — Extract the Hessian

Use the Hessian page when you need the Hessian matrix and its flat-vector version. The flat version is the one Vegeta typically uses later.

Bulma Hessian extraction

Bulma Hessian extraction page.

A good beginner rule is:

keep both outputs if possible
label them clearly
and store them in the same working directory as the optimized geometry

Step 4 — Generate a BOMD input

The BOMD → Generate tab is where you build a dynamics input from an equilibrium geometry and a velocity file.

Bulma BOMD generate page

Bulma BOMD generate page.

The fields you will usually care about most are:

XYZ: the equilibrium geometry
Velocity file: usually the file produced by Vegeta,
stepsize
npoints
dyn-out
optional dispersion
and the shared ab initio settings

A safe beginner order is:

prepare the geometry
prepare the velocity file
then generate the BOMD input

Step 5 — BOMD → Parse → Nimbus

The Parse → Nimbus tab converts BOMD-style outputs into files that are easier to use in Flying Nimbus.

This tab is especially useful when you already have a finished dynamics run and want to move from raw trajectory-style output to spectral analysis.

Pay attention to:

the selected parser type
the input log or output file
the equilibrium geometry template if requested
the frame range
the base name for the generated outputs
and any optional energy export

A good beginner habit is to keep the output base name simple and descriptive, because you will see that name again later in Flying Nimbus.

Step 6 — BOMD → Custom args

The Custom args tab is the advanced escape hatch.

Use it when:

the GUI does not expose the exact option you need
you already know the command-line syntax
or you want to reproduce a command exactly

As a beginner, only use this page when the normal tabs are not enough. If you do use it, copy the command carefully and test with short runs first.

Common beginner mistakes in Bulma

Forgetting to set the workdir
Using the wrong output file when extracting the optimized geometry
Sending the wrong Hessian file to Vegeta
Mixing files from different molecules or different calculations in the same folder
Changing too many advanced settings at once

Vegeta GUI Tutorial

Vegeta sits between Bulma and Flying Nimbus. It uses the optimized structure and Hessian to generate velocities and other mode-related outputs.

Vegeta splash screen

Vegeta splash screen.

Step 1 — Files page

The Files page is where you load the key inputs.

Vegeta Files page

Vegeta Files page.

The most important fields are:

working directory
equilibrium XYZ
flat Hessian
optional geometry-only output

For a first run, keep it simple: load the optimized geometry from Bulma, load the flat Hessian from Bulma, and leave the optional output fields alone unless you know you need them.

Step 2 — Modes page

The Modes page is where the main configuration happens.

Vegeta Modes page

Vegeta Modes page.

Here is how to read it:

nrotrasl controls how translational and rotational modes are handled
on and off let you excite specific modes or switch them off
freq threshold can be left alone at first, it is used to remove low frequency modes below the threshold
zero-velocity atoms is useful only when you deliberately want some atoms to have zero velocity
normal modes movies is optional and mainly for inspection and visualization

Step 3 — Export page

The Export page controls the output names.

Vegeta Export page

Vegeta Export page after a successful run.

The main outputs are usually:

velocity.xyz
optional bohr/s velocity output
optional cnorm file
frequency information written to the working directory

What you usually keep from Vegeta

a velocity file for later dynamics work
frequency information (freq.dat)
an optional cnorm file when Flying Nimbus needs it

Common mistakes in Vegeta

Using the wrong geometry for the Hessian
Mixing Hessians and structures from different jobs
Excluding or exciting modes without keeping track of what was removed or excited

Flying Nimbus GUI Tutorial

Flying Nimbus splash screen

Flying Nimbus splash screen.

Flying Nimbus is the analysis and visualization tool. It reads structural and dynamics information and turns it into spectra that you can compare and analyze inside the GUI.

Presets

At the top of the GUI, Flying Nimbus includes Load preset and Save preset buttons.

These are useful when:

you repeat the same analysis often
you want to save a known-good setup
or you want to compare different analyses without retyping everything

Step 1 — Files page

The Files page collects the core inputs.

Flying Nimbus Files page

Flying Nimbus Files page.

The key inputs are:

working directory
equilibrium XYZ
trajectory
Hessian
optional cnorm file
output prefix for plots

Step 2 — Dynamics page

The Dynamics page controls how the trajectory file is interpreted.

Flying Nimbus Dynamics page, upper part

Flying Nimbus Dynamics page: upper part.

Flying Nimbus Dynamics page, lower part

Flying Nimbus Dynamics page: lower part.

Treat this page in two layers:

The basic layer

Start with the main run settings shown in the screenshots, such as:

nrotrasl
nstart
ncorr
nbeads
nbeadstep
dt

For Gaussian trajectory files and non-linear molecules, the default values are usually fine.

The selective-analysis layer

The lower part lets you narrow the analysis.

Common examples:

select only specific modes
select only specific atoms (atomwise spectra)
choose whether the calculation is done in normal-mode or Cartesian form
choose whether you want time averaged spectra or not (TA). We recommend using TA as default
reuse or overwrite the cnorm file