The word Substance refers to a homogeneous chemical composition. This may be an element (e.g. Nitrogen, Oxygen), a compound (e.g. Nitrogen Dioxide, Benzene) or a complex mix of different compounds (Vodka, Blood). Substances are not directly interacted with by players during the game - they are simply a data template. A Substance is specific to its state - for example: Water and Ice are considered different substances.

This is mostly relevant the most to Chemistry, but in terms of atmos we can see part of this system as a combination of gasses flowing and mixing in the atmosphere of the station, as they might have reactions with each other.

The Atmospherics system (atmos).

Gasses must be able to be transferred through a complex network of pipes, and must regulate pressure between rooms. For example, if a low pressure room is adjacent to a high pressure room, and the door between them is open, air should flow from the high pressure room into the low pressure room, until pressure is equalized. Ideally, this should cause wind that, if strong enough, should blow anything not buckled down in the direction of the airflow.

The gas in the atmosphere may not be a singular gas, actually that will rarely be the case. Most atmosphere will be made up of a mix of gases. Gases naturally mix together and equalize over time, much in the way pressure equalizes overtime.

It is important to manage both the pressure and gas mixture of the atmosphere in your work station.