[ase-users] writing trajectories of a subsystem

[Efrem Braun]

Hi,

I'm using ASE to calculate diffusion coefficients of molecules within a
framework, and for this I only need the trajectory file to report the
positions of the adsorbate molecules themselves. The trajectory files are
pretty large, and so cutting out the unnecessary information of the
framework atoms would be helpful. Is there a way to do this?

I tried the following, but it didn't work. Using the example of running an
MD simulation of a box of water molecules (
https://wiki.fysik.dtu.dk/ase/tutorials/tipnp_equil/tipnp_equil.html), I
made the highlighted change:

####################################################################
from ase import Atoms
from ase.constraints import FixBondLengths
from ase.calculators.tip3p import TIP3P, rOH, angleHOH
from ase.md import Langevin
import ase.units as units
from ase.io.trajectory import Trajectory
import numpy as np

# Set up water box at 20 deg C density
x = angleHOH * np.pi / 180 / 2
pos = [[0, 0, 0],
       [0, rOH * np.cos(x), rOH * np.sin(x)],
       [0, rOH * np.cos(x), -rOH * np.sin(x)]]
atoms = Atoms('OH2', positions=pos)

vol = ((18.01528 / 6.022140857e23) / (0.9982 / 1e24))**(1 / 3.)
atoms.set_cell((vol, vol, vol))
atoms.center()

atoms = atoms.repeat((3, 3, 3))
atoms.set_pbc(True)

# RATTLE-type constraints on O-H1, O-H2, H1-H2.
atoms.constraints = FixBondLengths([(3 * i + j, 3 * i + (j + 1) % 3)
                                   for i in range(3**3)
                                   for j in [0, 1, 2]])

tag = 'tip3p_27mol_equil'
atoms.calc = TIP3P(rc=4.5)
md = Langevin(atoms, 1 * units.fs, temperature=300 * units.kB,
              friction=0.01, logfile=tag + '.log')

traj = Trajectory(tag + '.traj', 'w', atoms[0:10])
# I also tried the following, with the same result:
# atoms_subsystem = atoms[0:10]
# traj = Trajectory(tag + '.traj', 'w', atoms_subsystem)
md.attach(traj.write, interval=1)
md.run(4000)
####################################################################

The trajectory that was printed did not show any of the atoms moving from
their initial system. It seems like the "atoms" object was copied instead
of having atoms_subsystem pointing to a reference of the original object,
even though https://wiki.fysik.dtu.dk/ase/ase/atom.html indicates that this
shouldn't be.

Any ideas?

Efrem Braun
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