Various small changes - Githubissues

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

6 stars 8 forks source link

Various small changes #72

Closed davidbbeyer closed 3 months ago

davidbbeyer commented 3 months ago

@pm-blanco I have addressed the points raised by the reviewer:

In all samples and tests, instances of reaction ensemble objects have been renamed to cpH and grxmc to be more descriptive
The SEED has been renamed to seed
The activity coefficient is now a mandatory argument of GCMC and G-RxMC, i.e. it even needs to be provided for an ideal system. Sample script and tests have been updated accordingly.
The charge q of a particle was changed to the charge number z

Furthermore, I fixed some typos I found.

davidbbeyer commented 3 months ago

@pm-blanco I have implemented the suggested changes and added a test.

davidbbeyer commented 3 months ago

I have removed the print statement
pmb.calculate_net_charge now has an additional boolean argument dimensionless that allows one to set if it should return the charge with a dimension or dimensionless. In my opinion, this is a clean option, since removing the units from the nested dictionaries is cumbersome.
Unrelated, but I also added unit tests for pymbe_library.generate_coordinates_outside_sphere() and pymbe_library.generate_random_points_in_a_sphere() to increase the code coverage

davidbbeyer commented 3 months ago

I have implemented your suggestions.