Fix atoms in StructureData

General Usage
1

Hello everyone,

I’m creating several surface structures to be calculated with AiiDA-VASP. First, I create all structures with ASE and use the FixAtoms class to fix the bottom layers of my slab. Then I transform these ASE Atoms structures into a list of StructureData as input for my WorkChain. However, when I look at the generated POSCAR in the remote computer I noticed that it did not fix the atoms. What is the proper way to do this?

Thanks in advance!
Thiago

2

Hi Thiago!

Currently the StructureData doesn’t store such calculation settings, so the ASE constraints aren’t transferred initializing them from the ASE Atoms.

I’ve never run any calculations with aiida-vasp, but it seems there is an input for setting selective dynamics on the VaspCalculation:

This is subsequently passed to the PoscarParser class:

I played around with the PoscarParser a bit, and you can indeed pass selective dynamics to the parser via the options argument as a list of lists. See the following minimal example:

from ase import Atoms
from ase.constraints import FixAtoms

from aiida import orm, load_profile
from aiida_vasp.parsers.content_parsers.poscar import PoscarParser

load_profile()

d = 2.9
L = 10.0

atoms = Atoms(
    symbols=['Au', 'Cu'],
    positions=[[0, L / 2, L / 2], [d, L / 2, L / 2]],
    cell=[2 * d, L, L],
    pbc=[1, 0, 0]
)

poscar_parser = PoscarParser(
    data=orm.StructureData(ase=atoms),
    options={'positions_dof': [[True, True, True], [False, False, False]]}
)
poscar_parser.write('POSCAR')

Now the POSCAR will indeed contain:

Selective dynamics
Direct
  0.000000000000   0.500000000000   0.500000000000 T T T
  0.500000000000   0.500000000000   0.500000000000 F F F

So I’m assuming you can fix atom positions by specifying the dynamics input as follows:

builder = VaspCalculation.get_builder()

builder.dynamics = orm.Dict(
    {'positions_dof': [[True, True, True], [False, False, False]]}
)

Along with the other inputs of course. :slight_smile:

Hope it works!

3 Likes
3

Hi Marnik!

I see! I managed to use your example as guide for my own system and it worked perfectly.

Thanks a lot for the fast and detailed response, I really appreciate it!
Kind regards,
Thiago

1 Like
4

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