[ase-users] Split POSCAR/CONTCAR files

[fabian]

Dear Oscar,
Thank you very much for your fast reply! This is exactly what i want to do!


If my slab consist of different species , for example Cu and O atoms, is 
it correct to change this line


slab_i = [a.index for a in atoms if a.symbol == 'Cu']


to



slab_i = [a.index for a in atoms if a.symbol == 'Cu','O'] ?


All the best


fabian


Am 18.04.2017 um 23:25 schrieb Oscar Xavier Guerrero:
> Sorry, in the previous example I forgot to convert from list to an 
> atoms object.
>
> This should work:
>
> from ase.io <http://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 <mailto: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 <http://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
>     <https://github.com/izxle/VaspTools>
>
>
>
>
>
>
>
>
>     2017-04-18 2:52 GMT-05:00 fabian via ase-users
>     <ase-users at listserv.fysik.dtu.dk
>     <mailto: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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