The Adsorbate class#

Overview#

In order for many of the calculations included in pyGAPS to be performed, properties of the adsorbed phase must be known. To make the process as simple and as painless as possible, the Adsorbate class is provided.

At creation, an isotherm asks for an adsorbate parameter, a string which pyGAPS looks up in an internal list (pygaps.ADSORBATE_LIST). If any known adsorbate name/alias matches, this connects the isotherm object and the existing adsorbate class. This global list is populated as import-time with the adsorbates stored in the internal database. The user can also add their own adsorbate to the list, or upload it to the database for permanent storage.

Any calculations/conversions then rely on the Adsorbate for providing parameters such as saturation pressure, molar mass and density.

Note

For a complete list of methods and individual descriptions look at the Adsorbate class reference.

Creating an Adsorbate#

The creation process of an Adsorbate is similar to that of other pyGAPS classes. Some parameters are strictly required for instantiation, while others are recognised and can then be accessed by class members. All other parameters passed are saved as well in an internal dictionary called properties.

An example of how to create an adsorbate:

my_adsorbate = pygaps.Adsorbate(
    'butane',                         # Required
    formula = 'C4H10',                # Recognised
    alias = ['n-butane', 'Butane'],   # Recognised
    backend_name = 'butane',          # Recognised, Required for CoolProp interaction
    saturation_pressure = 2.2,        # Recognised
    carbon_number = 4,                # User specific
)

To view a summary of the adsorbate properties:

my_adsorbate.print_info()

Hint

Some properties are recognised and available from the class:

my_adsorbate.formula
>> 'C4H10'

All other custom properties are found in the Adsorbate.properties dictionary.

my_adsorbate.properties["carbon_number"]
>> 4

Note

It is unlikely that you will need to manually create an adsorbate, as more than 150 compounds are already included with pyGAPS.

Retrieving an Adsorbate#

A selection of the most common gas and vapour adsorbates is already stored in the internal database. At import-time, they are automatically loaded into memory and stored in pygaps.ADSORBATE_LIST.

len(pygaps.ADSORBATE_LIST)
>> 176

To retrieve an Adsorbate from this list, the easiest way is by using the class method: find() which works with any of the compound aliases.

# all return the same Adsorbate instance
ads = pygaps.Adsorbate.find("butane")
ads = pygaps.Adsorbate.find("n-butane")
ads = pygaps.Adsorbate.find("c4h10")

Adsorbate class methods#

The Adsorbate class has methods which allow the properties of the adsorbate to be either calculated using the CoolProp or REFPROP backend or retrieved as a string from the internal dictionary. The properties which can be calculated are:

Molar mass: molar_mass().
Triple point pressure: p_triple().
Triple point temperature: t_triple().
Critical point pressure: p_critical().
Critical point temperature: t_critical().
Saturation pressure: saturation_pressure().
Surface tension: surface_tension().
Liquid density: liquid_density().
Molar liquid density: liquid_molar_density().
Gas density: gas_density().
Molar gas density: gas_molar_density().
Enthalpy of vaporisation: enthalpy_vaporisation().
Enthalpy of liquefaction: enthalpy_liquefaction().

For example, for the Adsorbate created above, to get the vapour pressure at 25 degrees in bar.

my_adsorbate.saturation_pressure(298, unit='bar')
>> 2.8

Caution

The properties calculated are only valid if the backend equation of state is usable at the required states and is accurate enough. Be aware of the limitations of CoolProp and REFPROP. More info here.

Each method also accepts a bool parameter calculate, True by default. If set to False, the property will not be calculated by the thermodynamic backend. Instead, the value from the properties dictionary will be returned. This is static and supplied by the user, but can be useful for adsorbates without a thermodynamic backend.

my_adsorbate.saturation_pressure(298, calculate=False)
>> 2.2              # Value in the `properties` dictionary

For calculations of other properties, the CoolProp backend can be accessed directly using the backend property. To calculate the reducing temperature for example.

my_adsorbate.backend.T_reducing()

Adsorbate management#

If an Adsorbate is manually created, a user can add it to the list of adsorbates by appending it.

# To store in the main list
pygaps.ADSORBATE_LIST.append(my_adsorbate)

A useful shorthand is to pass an optional parameter store at creation

# Automatically stored in ADSORBATE_LIST
ads = pygaps.Adsorbate("acetylene", store=True)

Warning

This makes the adsorbate available only in the current session. No permanent changes to the internal adsorbates are made this way.

To permanently store a custom adsorbate for later use or make modifications to exiting adsorbates, the user must upload it to the internal database. This can be done as:

import pygaps.parsing as pgp

# To permanently store in the database
pgp.adsorbate_to_db(ads_new)

# To store any modifications to an adsorbate in the database
pgp.adsorbate_to_db(ads_modified, overwrite=True)

For more info, check out the sqlite section of the manual.