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pyMBE-dev / pyMBE

pyMBE provides tools to facilitate building up molecules with complex architectures in the Molecular Dynamics software ESPResSo. For an up-to-date API documention please check our website:
https://pymbe-dev.github.io/pyMBE/pyMBE.html
GNU General Public License v3.0
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21 make calculate hh donnan independent of espresso #22

Closed davidbbeyer closed 4 months ago

davidbbeyer commented 5 months ago

@pm-blanco I have adapted the function calculate_HH_Donnan so that it is completely independent of ESPResSo now. The input is now simply the a dictionary containing the concentrations of all macromolecular species in the system. Furthermore, I have removed the separate sample script on the unified G-RxMC method and simply added a command-line argument to the sample script, so one can select between the standard formulation and the one with unified ion types.

pm-blanco commented 5 months ago

@davidbbeyer thank you for taking care of this issue, I will review it ASAP. Meanwhile, could you please provide a small for the CI to check this function?

davidbbeyer commented 5 months ago

@pm-blanco Sure, I can do that. Maybe we can just test the implementation of the grand-reaction method (for an ideal gas) against this function?

pm-blanco commented 5 months ago

@davidbbeyer I would do something even simpler than that. I would generate a set of reference data value for a couple of cases, save it in the data folder of the testsuite and I would do a test test runs that function and checks that it still produces the same data. In this way it can be a very fast test for the CI. Please, if you follow this approach, save the data in the format than the other files there for consistency.

pm-blanco commented 4 months ago

@davidbbeyer could you please also change the argument object_name in calculate_HH for molecule_name?