Get started

Starting a Jupyter Lab environment

In order to get started with LavAtmos we first need to run the docker image that contains Thermoengine (see Installation). Open your terminal and change your working directory to wherever you cloned Thermoengine:

cd path/to/Thermoengine

Note: make sure to change path/to/ to the actual path on your system.

Next, run the following command:

./run_docker_locally.sh

If needed (check with your system admin if allowed!) run the above command using sudo. If working correctly, you should get a URL in your terminal that you can then copy and paste into a web browser. This will bring you to a Jupyter lab environment in which you will now be able to run LavAtmos.

Importing LavAtmos

In order to run the instructions given below directly from a Jupyter notebook file, check out the notebook directory on the Github page.

First of all, ensure that you are working within the LavAtmos directory:

import os
os.chdir('path/to/Thermoengine/LavAtmos')

Note: Make sure to change path/to/ to the actual path in your system.

You should then be able to import LavAtmos using:

import lavatmos

Defining a melt composition

The melt compositions can be passed to LavAtmos in the form of dictionaries (just as for MELTS). An often used composition is Bulk Silicate Earth (BSE):

comp_BSE = {'SiO2': 45.4,\
            'MgO': 36.76,\
            'Al2O3': 4.48,\
            'TiO2': 0.21,\
            'FeO': 8.1,\
            'CaO': 3.65,\
            'Na2O': 0.349,\
            'K2O': 0.031}

The LavAtmos repository also contains some preset compositions which can be imported directly using:

vf13_comps_df = pd.read_csv('/home/jovyan/ThermoEngine/LavAtmos/data/input/vf2013_comps.csv',index_col=0)
vf13_comps = {}
for name in vf13_comps_df.columns:
    vf13_comps[name] = vf13_comps_df[name].to_dict()
print(vf13_comps['BSE'])

Note: MELTS, which is used to calculate the melt thermodynamics, may not always be able to converge on a composition. It generally works well for naturally occuring compositions.

Running the equilibrium calculations

Initialize a LavAtmos object:

system = lavatmos.melt_vapor_system()

Define the temperatures for which you want to perform the calculations:

T = np.arange(1500,4050,50)

And perform the gas-melt equilibrium calculations using the vaporise function:

results = system.vaporise(T, comp_BSE)
print(results)