Difference between "basis components" and "original basis"

[ats5482]

Hi,

I'm writing a Python script to parse React_output.txt files to speed up the process of plotting the results of multiple experiments at once on the same figure. To start, I'm trying to recreate a figure you can already make in Gtplot: components in fluid (mol/L) vs Rxn progress.

To calculate the concentration of the components in the fluid, does Gtplot use the "Basis components" or "Original basis" table from the React output file? The reported moles differ slightly and I'm not sure why. Also, to go from mol to mol/L, is it dividing by the bulk volume in the corresponding Step #?

 

Thanks!

-- Adam

[Jia Wang]

Hello Adam,

The Original Basis section and the Components in Fluid (in Gtplot) represent the same concentrations. Gtplot uses the values from the simulation output file that ends with the file extension .gtp. The values in React_text output are rounded to fewer significant digits than .gtp files. Perhaps this is where the discrepancies are coming from? If you would like to see the exact values from Gtplot, you can go to Config -> Output... -> select the radio button for "character" on the line that says "XML". If you run the input file again, React will print the Gtplot file in a human readable format, which you can open and view in a text editor.

The mol/L unit is the moles divided by the fluid volume reported in that step. The bulk volume is made up of the fluid volume, mineral volume, and inert volume. If there are no mineral present and no inert volume set, then your bulk volume is equal to your fluid volume.

Hope this helps,
Jia Wang
Aqueous Solutions LLC

[Jia Wang]

Hello Adam,

I think I misunderstood your initial question. Were you referring to the "Basis composition" section that prints out to React_output.txt by setting the “print basis long” command?

If so, the "Basis components" section in the React_output.txt file will show the minerals and species that express the bulk composition that is swapped in the initial system and is updated as the reaction path proceeds. The "Original basis" is the composition expressed in terms of the basis species in the thermo dataset loaded. For example, if you had set up the initial fluid by swapping in Calcite for HCO3-, then the "basis components" will list Calcite but HCO3- will still appear in the "Original basis" section. You can still check that they represent the same bulk composition by calculating the mole numbers of the elemental composition for both sections and see that they are the same.

The "Components in fluid" plotted in Gtplot are the concentrations in "Original basis".

Hope this helps,
Jia

 

[ats5482]

Hi Jia,

Re your second message: Yes, I was confused by the option in output settings that lets you print "basis composition" in addition to "original basis composition" (the one turned on by default). I wasn't sure which of those two tables I should use if I want to re-create a "components in fluid" plot in Python. Based on your explanation, I will use the original basis composition table.

Also, yes, I think the discrepancy in what I calculated by hand vs what Gtplot showed me was due to the different significant figures between the XML and React_output files.

Thank you for your help!

-- Adam

[Jia Wang]

Hello Adam,

You're welcome. I am glad that was helpful. Hope the rest of your project goes well.

Best,
Jia