feat: parallelize viscosity calculation

[ltalirz]

Run 3 different temperatures in parallel.

[codecov]

Codecov Report

❌ Patch coverage is 66.66667% with 56 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
amorphouspy/src/amorphouspy/pipelines/viscosity.py	9.09%	30 Missing ⚠️
...morphouspy_api/src/amorphouspy_api/routers/jobs.py	23.52%	13 Missing ⚠️
...py_api/src/amorphouspy_api/routers/jobs_helpers.py	65.00%	7 Missing ⚠️
amorphouspy_api/src/amorphouspy_api/pipeline.py	87.23%	6 Missing ⚠️

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[ltalirz]

@Atilaac one question: in the current "master" workflow, we run the viscosity after the melt quench.
I guess that doesn't really make sense and we should start them in parallel to the melt quench that goes to room temperature (from the same random input structure), right?

[Atilaac]

Since we do liquid viscosity, you can run them in parallel. Just start from the same random structure and cool it using the same cooling rate to the temperature of interest, so you can claim that this viscosity is from the same trajectory as the glass.
You only need to wait for the glass to be made for the properties that require a glass structure, such as CTE and Elastic moduli

[ltalirz]

@Atilaac / @Gitdowski I think I'm making a mistake in the LAMMPS settings in the viscosity run here - can you spot it?

"Command 'mpiexec -n 3 --oversubscribe lmp_mpi -in lmp.in' returned non-zero exit status 1.
LAMMPS stdout:
t with -dE/dr.
WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:466)
WARNING: New thermo_style command, previous thermo_modify settings will be lost (src/output.cpp:904)\n\nCITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE\n\nYour simulation uses code contributions which should be cited:\n- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419\nThe log file lists these citations in BibTeX format.\n\nCITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE\n
Generated 0 of 10 mixed pair_coeff terms from geometric mixing rule
WARNING: One or more atoms are time integrated more than once (src/modify.cpp:296)
...

ERROR: Lost atoms: original 6000 current 5142 (src/thermo.cpp:494)
Last command: run 10000

[ltalirz]

The relevant code should be in amorphouspy/src/amorphouspy/pipelines/viscosity.py

[Atilaac]

I will have a look

[Atilaac]

I think I managed to find the problem and a fix. Now, should I push it here or in a separate PR?

[ltalirz]

Thanks a lot - feel free to push directly here

[ltalirz]

Just checking whether you forgot to push or whether you found something else to check

[Atilaac]

I did not forget to push, I'm still working on it.

[Atilaac]

Can you check now if it is working on your sample? I tried many glasses with Li2O, mainly Li2O:20, SiO2:80 (the one you suggested), and Li2O:15, Na2O:18, SiO2:67. Both the viscosity and elastic moduli workflows are working locally for me.

[ltalirz]

Thanks a lot @Atilaac , will do!
I'll also have a close look at your commit to understand what was the problem here

[Atilaac]

Check the commit message; I have a description there. Some other changes are more about reducing code duplication and have nothing to do with the problem directly.

[ltalirz]

btw, I notice you included a pixi.lock update in your commit. I will revert this since it led to problems on my side. Feel free to open a separate PR for this.