pbc in `TrajectoryData`

[dbidoggia]

Dear all,
I would like to propose adding a pbc array to TrajectoryData.

Recently, in (aiidateam/aiida-quantumespresso@20ac738), we introduced the possibility to use TrajectoryData as input for NEB calculations in AiiDA-quantumespresso.
In this context, having both the cell and the pbc configuration would allow for the correct generation of the k-points grid.
More generally, I believe that storing the pbc information is useful to preserve knowledge about the system’s dimensionality.

[mbercx]

Thanks @dbidoggia! Could you clarify what you want to add/change? Note that you can already set an array if you'd like:

from aiida import orm, load_profile 
load_profile()

trajectory = orm.TrajectoryData()
trajectory.set_array('pbc', np.array([True, True, True]))

And use this when generating the k-points grid. Would you like the TrajectoryData to do this automatically based on the structure inputs, e.g.:

from aiida import orm, load_profile 
from ase.build import bulk
import numpy as np

load_profile()

structure = orm.StructureData(ase=bulk('LiF', crystalstructure='rocksalt', a=4.03, cubic=True))

trajectory = orm.TrajectoryData(
    structurelist=[
        structure,
        structure,
        structure
    ]
)

Currently, trajectory.get_arraynames() will only contain ['positions', 'steps', 'cells'].

[dbidoggia]

Dear @mbercx, I'll try to clarify my thoughts.
Now while constructing a TrajectoryData from a StructureData, unless you manually set an array, you lose pbc information and when you try to get back a frame you end up with pbc=[True, True, True]:

from ase import Atoms
from aiida import load_profile, orm

load_profile()

ase_structure = Atoms('H', positions=[[0, 0, 0]], pbc=[True, False, False], cell=[10.0, 10.0, 10.0])
structure = orm.StructureData(ase=ase_structure).get_ase()

trajectory = orm.TrajectoryData([structure])

structure2 = trajectory.get_step_structure(0)

Essentially in set_structurelist:

aiida-core/src/aiida/orm/nodes/data/array/trajectory.py

Line 172 in 239cbf9

def set_structurelist(self, structurelist):

I propose to directly extract pbc if present in the input structures and set them back to StructureData in get_step_structure.

[mbercx]

Thanks @dbidoggia for the clarification! I see your point, and agree. The code snippet you write above should return exactly the same structure, so I would classify this as a bug.

[rikigigi]

see also #6376

[mbercx]

Thanks @rikigigi! We have some aiida-core coding days coming up next week. I'll see if I can't fix this issue then, if you or @dbidoggia haven't started working on it yet?

[dbidoggia]

@mbercx no, we are not working at it right now. If you are going to do that it would be great.