125 molar amount missing in solution

[ka-sarthak]

Resolves #125

Summary by Sourcery

Add 'amount_of_substance' to the SolutionComponent class and enhance mass calculation logic. Improve description formatting for concentration fields in MolarConcentration.

New Features:

• Introduce 'amount_of_substance' as a new quantity in the SolutionComponent class, allowing automatic calculation if mass and molecular mass are available.

Enhancements:

• Improve the description formatting for 'calculated_concentration' and 'measured_concentration' in the MolarConcentration class for better readability.
• Enhance the mass calculation logic in the SolutionComponent class to automatically compute mass if volume and density or amount of substance and molecular mass are available.

[sourcery-ai]

Reviewer's Guide by Sourcery

This PR adds support for tracking the molar amount (amount of substance) of solution components and improves the calculation of molar concentrations. The implementation includes automatic calculation of mass and molar amounts based on available properties, and updates the concentration calculation to use the new amount_of_substance field directly.

Updated class diagram for SolutionComponent

classDiagram
    class SolutionComponent {
        +float mass
        +float density
        +float amount_of_substance
        +calculate_molar_concentration(volume: Quantity, logger: BoundLogger)
        +normalize(archive: EntryArchive, logger: BoundLogger)
    }
    class MolarConcentration {
        +float calculated_concentration
        +float measured_concentration
    }
    SolutionComponent --> MolarConcentration
    note for SolutionComponent "Added amount_of_substance attribute and updated methods for calculation."

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File-Level Changes

Change	Details	Files
Added new amount_of_substance field to track molar quantities	Added new Quantity field with mole unit and appropriate metadata Added description explaining automatic calculation from mass and molecular mass	src/nomad_material_processing/solution/general.py
Enhanced mass field documentation and calculation logic	Updated mass field description to explain automatic calculation scenarios Added bidirectional calculation between mass and amount_of_substance	src/nomad_material_processing/solution/general.py
Improved molar concentration calculation	Simplified concentration calculation to use amount_of_substance directly Removed dependency on _calculate_moles helper method for concentration calculation	src/nomad_material_processing/solution/general.py
Code formatting and documentation improvements	Reformatted multi-line string descriptions to use triple quotes consistently Improved line wrapping for better readability	src/nomad_material_processing/solution/general.py

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#125	Add a quantity to store the molar amount (amount of substance) in a solution component	✅

Possibly linked issues

• molar amount missing in solution #125: The PR adds amount_of_substance to SolutionComponent, directly addressing the issue of missing molar amount.

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[sourcery-ai]

Hey @ka-sarthak - I've reviewed your changes and they look great!

Here's what I looked at during the review

• 🟢 General issues: all looks good
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

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[ka-sarthak]

@schumannj Can you check if it works as intended? You can pull this branch and create solution entries.

[schumannj]

Hi Sartak. I had a look at the code and it looks good so far. I will try out locally now.

[schumannj]

There is one thing I was wondering about, in how far things get overwritten, if an entry gets reprocessed and e.g. a single value, e.g. mass gets corrected. How does nomad figure out which quantities are written in person and what was calculated previously. Not entirely sure if that could be a problem. And probably not really related to this issue. I try to see if I can make an example.

[ka-sarthak]

I think NOMAD does not provide a way to keep track of what came from the user and what is written by the normalizer.

Every time the normalizer runs, self gives the current state (which usually contains data entered from the ELN). But it also might contain data from a previous normalization. Both of these data are indiscernible. You are right, this can be confusing. Ideally, quantities that are interactable should not have a lot of automation.

Currently mass and amount_of_substance can be changed by the normalizer. Do you think this can lead to confusion and we should remove some of the automation?

[schumannj]

I find this is a difficult question. and really depends on how it is used. Initially I was thinking of having nomad calculate the mass from a desired concentration/amount_of_substance and then correcting the mass accoring to the real value that was measured on the balance. But maybe this is to much overthinking. I guess the most important thing is for the community plugins to represent the final data for publishing.

[schumannj]

I just tested the branch. Looks in principle good. I noticed that when I create a solution with 1L of H2O and 1.5 mol NaCl, the mass of the total solution is only given as the mass of the solute.

[schumannj]

Ah I see, there is a warning in the logs, it is missing the mass, of course. should this rather be an error? so it flags up more visibly? But maybe not, once the density is picked up from pubchem it should be resolved anyway.

[ka-sarthak]

Yeah, thing is we are not getting density from the PubChem, so you have to supply either the mass, or both volume and density, to calculate the mass

[schumannj]

Oh why not? it is marked as a todo in the code. I thought this was planned.

Oh I guess there are too many different values to choose from.

[ka-sarthak]

Exactly, it depends on the external factors like temperature and pressure. So it's much safer to get this input from the user

[ka-sarthak]

Or they can simply add mass and volume. The final density of the solution will be computed based on these values for all the components.

[schumannj]

Makes sense. Then you can remove the line 171.
The default value of density is a bit strange. In the main solution section it is g/ml, which is more standard compared to 'gram/liter'. I wondered why my solution is so light, with a density of 1

[ka-sarthak]

I will make all the units for density to be g/ml as it seems to be the standard

[schumannj]

The options for the units of mass are very diverse, I have never seen all those crazy units, where are they suddenly coming from? has nomad.units been updated? but I cannot find mg or mikro gram. (Probably not an issue for here.)
I will approve the review. Looks good!

[ka-sarthak]

Ah yeah, there's a bunch of new empirical units. Like bag? No idea where they came from.