def along1(ENGINE, rang=5, recur=100, refine=False, explore=True):
ENGINE.set_groups_as_molecules()
[
g.set_move_generator(
TranslationAlongSymmetryAxisGenerator(axis=1, amplitude=0.1))
for g in ENGINE.groups
]
# set selector
centers = [
np.sum(ENGINE.realCoordinates[g.indexes], axis=0) / len(g)
for g in ENGINE.groups
]
distances = [np.sqrt(np.add.reduce(c**2)) for c in centers]
order = np.argsort(distances)
recur = 200
gs = RecursiveGroupSelector(DefinedOrderSelector(ENGINE, order=order),
recur=recur,
refine=refine,
explore=explore)
ENGINE.set_group_selector(gs)
# number of steps
nsteps = recur * len(ENGINE.groups)
for stepIdx in range(rang):
LOGGER.info("Running 'along1' mode step %i" % (stepIdx))
ENGINE.run(numberOfSteps=nsteps, saveFrequency=nsteps)
def along_axis_2():
# run engine translation along axis 2
xyzPath="along2.xyz"
if os.path.isfile(xyzPath): os.remove(xyzPath)
_,_,_,_,X,Y,Z =get_principal_axis(ENGINE.realCoordinates)
print("Translation along symmetry axis 2: ", Z)
[g.set_move_generator(TranslationAlongSymmetryAxisGenerator(amplitude=0.5, axis=2)) for g in ENGINE.groups]
ENGINE.run(numberOfSteps=nsteps, saveFrequency=2*nsteps, xyzFrequency=xyzFrequency, xyzPath=xyzPath, restartPdb=None)