pmb.center_molecule_in_simulation_box fails for non-cubic boxes

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

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pmb.center_molecule_in_simulation_box fails for non-cubic boxes #43

Closed kosovan closed 2 months ago

kosovan commented 2 months ago

Current implementation

box_center = [espresso_system.box_l[0]/2.0]*3

should be replace with

box_center = [ espresso_system.box_l[0]/2.0, espresso_system.box_l[1]/2.0, espresso_system.box_l[2]/2.0 ]

pm-blanco commented 2 months ago

@paobtorres could you please take care of this?