[ase-users] Split POSCAR/CONTCAR files

[Oscar Xavier Guerrero]

Sorry, in the previous example I forgot to convert from list to an atoms
object.

This should work:

from ase.io import read, write
from ase.atoms import Atoms
atoms = read('CONTCAR')
# assuming the slab is only composed of Cu and the adsorbate has no Cu
slab_i = [a.index for a in atoms if a.symbol == 'Cu']
ads_i = [a.index for a in atoms if a.symbol != 'Cu']
# you could also use height as the threshold
th = max(a.z for a in atoms if a.symbol == 'Cu')
# you can also use constraints to set the th
slb = {atoms[i].symbol for i in atoms.constraints[0].index}
th = max(a.z for a in atoms if a.symbol in alb)

slab_i = [a.index for a in atoms if a.z <= th]
ads_i = [a.index for a in atoms if a.z > th]

# this is a quick fix, maybe there's a better method
slab = atoms.copy()
for i in sorted(ads_i, reverse=True):
    del slab[i]
ads = atoms.copy()
for i in sorted(slab_i, reverse=True):
    del ads[i]

# or you could use Atoms
slab = Atoms([a for a in atoms if a.index in slab_i])
ads = Atoms([a for a in atoms if a.index in ads_i])
cell = atoms.get_cell()
slab.set_cell(cell)
ads.set_cell(cell)
constraint = atoms.constraints[0]
slab.set_constraints(constraint)
ads.set_constraints(constraint)

write('slab.vasp', slab, vasp5=True, sort=True, direct=True, format='vasp')
write('ads.vasp', ads, vasp5=True, sort=True, direct=True, format='vasp')

If you have any questions I'm happy to help.


2017-04-18 15:53 GMT-05:00 Oscar Xavier Guerrero <oscarxavier.ox at gmail.com>:

> Hello Fabian,
>
> You can read POSCAR/CONTCAR files with ase.io.read, you get an atoms
> object with all the information the file had. Then you can copy parts of
> that atoms object into other atoms object. Then use the ase.io.write
> function to write POSCAR files for each of the new atoms objects. Since you
> have a slab and an adsorbate, you can use the height as a threshold. It
> really depends on your systems.
>
> Here's an example:
>
> from ase.io import read, write
> atoms = read('CONTCAR')
> # assuming the slab is only composed of Cu and the adsorbate has no Cu
> slab = [a for a in atoms if a.symbol == 'Cu']
> ads = [a for a in atoms if a.symbol != 'Cu']
> # you could also use height as the threshold
> th = max(a.z for a in atoms if a.symbol == 'Cu')
> # you can also use constraints to set the th
> slb = {atoms[i].symbol for i in atoms.constraints[0].index}
> th = max(a.z for a in atoms if a.symbol in alb)
>
> slab = [a for a in atoms if a.z <= th]
> ads = [a for a in atoms if a.z > th]
>
> write('slab.vasp', slab, vasp5=True, sort=True, direct=True, format='vasp')
> write('ads.vasp', ads, vasp5=True, sort=True, direct=True, format='vasp')
>
> If you have any questions I'm happy to help.
>
> P.S. heres my github with some of my scripts. https://github.com/
> izxle/VaspTools
>
>
>
>
>
>
>
>
> 2017-04-18 2:52 GMT-05:00 fabian via ase-users <
> ase-users at listserv.fysik.dtu.dk>:
>
>> Dear all,
>>
>> I want to perform a series of charge density difference calculations. Therefore i want to split the geometry optimised CONTCAR file
>> containing the coordinates from the slab and the Molecule into tow files containing only slab or Molecule coordinates. At the moment i am doing this
>> manually. Can someone give me a hint how to read positions and constraints as well as atom types from the POSCAR/CONTCAR files and later write them into two new POSCAR Files?
>> I would like to be able to either fix all atomic coordinates or leave the as they are.
>> Atom types could also be extracted from OUTCAR or POTCAR files. For now it is sufficient to perform the split based on the ATOM tag.
>> Unfortunately i am completely stuck.
>>
>> All the best
>>
>> fabian
>>
>>
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>
>
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