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:
define_particle now takes sigma, cutoff and offset as optional arguments.
sigma defaults to None. No LJ interactions are set up for particles with sigma or epsilon of None, maintaining the same behavior as before. The user gets a warning message informing that no LJ have been set up for those type of particles.
If the user sets sigma=0, no LJ interactions are set for those particles corresponding to ideally behaving particles, maintaining the same behavior as before.
cutoff defaults to 2**(1./6) reduced_length, maintaining the same behavior as before.
offset defaults to 0. This introduces a new behavior as the user now needs to set-up on its own the offset instead of hard-coding that sigma = 1 reduced_length
A new CI test has been introduced testsuite/lj_tests.py with several unit tests for define_particle and setup_lj_interactions
Fixes #19
List of changes:
define_particle
now takessigma
,cutoff
andoffset
as optional arguments.sigma
defaults to None. No LJ interactions are set up for particles withsigma
orepsilon
of None, maintaining the same behavior as before. The user gets a warning message informing that no LJ have been set up for those type of particles.sigma=0
, no LJ interactions are set for those particles corresponding to ideally behaving particles, maintaining the same behavior as before.cutoff
defaults to2**(1./6) reduced_length
, maintaining the same behavior as before.offset
defaults to 0. This introduces a new behavior as the user now needs to set-up on its own the offset instead of hard-coding thatsigma = 1 reduced_length
testsuite/lj_tests.py
with several unit tests fordefine_particle
andsetup_lj_interactions