[ase-users] Split POSCAR/CONTCAR files
fabian
Fabian.T89 at web.de
Tue May 2 12:21:57 CEST 2017
Dear Oscar,
I have an additional requtest.
Is it possible to read the constraints from the CONTCAR file and write
them to the split files for the slab and the adsorbate?
At the moment i am using this code based on your supplied solution, but
there are no selective dynamics constraints written to the new Files.
Ideally i would like to write them
directly just as they are written in the CONTCAR file without the need
to rewrite them.
/*from ase.io import read, write*//*
*//*from ase.atoms import Atoms*//*
*//*from ase.constraints import FixAtoms*//*
*//*atoms = read('CONTCAR')*//*
*//*# assuming the adsorbate has no Cu and O*//*
*//*
*//*slab_elms = ['Cu', 'O']*//*
*//*slab_i = [a.index for a in atoms if a.symbol in slab_elms]*//*
*//*
*//*ads_i = [a.index for a in atoms if a.symbol not in slab_elms]*//*
*//*
*//*# 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)*//*
*//*#Slab*//*
*//*c = FixAtoms(indices=[atom.index for atom in slab if atom.tag > 2])*//*
*//*slab.set_constraint(c)*//*
*//*print slab.get_cell()*//*
*//*ns = [x.index for x in sorted(slab, key=lambda x: [ 'Cu',
'O'].index(x.symbol))]*//*
*//*slab = slab[ns]*//*
*//*print slab.get_cell()*//*
*//*#Ads*//*
*//*#print ads.get_cell()*//*
*//*#na = [y.index for y in sorted(ads, key=lambda y: [ 'C',
'H'].index(y.symbol))]*//*
*//*#ads = ads[na]*//*
*//*#print ads.get_cell()*//*
*//**//*
*//*write('POSCAR', slab, vasp5=True, sort=True,
direct=False,long_format=True, format='vasp')*//*
*//*write('POSCAR_2', ads, vasp5=True, sort=True, direct=False,
format='vasp')*//*
*/
Is this possible?In the code above the line /*if atom.tag > 2 */the
seems to be ignored? Is it possible to write each new POSCAR file into a
new Folder which is also created by the script directly?
Thanks in advance
Fabian
Am 19.04.2017 um 18:11 schrieb Oscar Xavier Guerrero:
> No, you would have to use in:
>
> slab_elms = ['Cu', 'O']
> slab_i = [a.index for a in atoms if a.symbol *in slab_elms*]
>
> This is correct only if you have no O in your adsorbate. Otherwise, it
> would be better to use height to separate.
>
>
> 2017-04-19 2:56 GMT-05:00 fabian <Fabian.T89 at web.de
> <mailto:Fabian.T89 at web.de>>:
>
> 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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>>
>
>
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