Add the substitution and remove utility for structure manipulations

qzhu2017 / PyXtal

A code to generate atomic structure with symmetry

MIT License

234 stars 59 forks source link

Add the substitution and remove utility for structure manipulations #219

Closed qzhu2017 closed 1 year ago

qzhu2017 commented 1 year ago

Remove_species(), e.g., we have ZnCN2, and we want to remove all N atoms
Substitute, based on SiO2, we want to make Zn(CN)2 by substitution. Here we need to make sure that the substitution between CN and O will be reasonable.

qzhu2017 commented 1 year ago

from pyxtal import pyxtal
c = pyxtal()
c.from_seed("pyxtal/database/cifs/lt_cristobalite.cif")
print(c)
c.resort_species(['Si'])
print(c)
c.from_seed("pyxtal/database/cifs/ht_KNbBO.cif")
print(c)
c.resort_species(['K', 'O', 'Nb'])
print(c)

qzhu2017 commented 1 year ago

check if the structure can be relaxed by GULP with uff4mof.