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| from pymatgen import Structure,Element
import numpy as np
def atom_selection(struct,in_str=None):
r'''
select atoms by three different schemes:
1. by atomic index
2. by element symbol
3. by fractional coordinates range
'''
tip="""
select atoms by following ways:
1. atomic index in POSCAR
i.e. : 1 2 4-8 10 12-30
i.e. : 1 2 4 8 10
2. atomic label
i.e. : Si O
3. atomic position
i.e. : 0 0.5 | 0.2 0.4 | 0.3 0.7
this means atoms with 0<x<0.5,
0.2<y<0.4 and 0.3<z<0.7 will be seleted
or just specific the z coordinates,
i.e. : ||0.3 0.7
"""
print(tip)
def parse_index(in_str):
atom_index=[]
tmp_str=in_str.split()
for i in tmp_str:
if '-' not in i:
atom_index.append(int(i))
else:
atom_index.extend(range(int(i.split('-')[0]),int(i.split('-')[1])+1))
return [i-1 for i in atom_index]
def parse_label(in_str):
atom_label= [Element(elem) for elem in in_str.split()]
atom_index=[]
for i, site in enumerate(struct.sites):
if site.specie in atom_label:
atom_index.append(i)
return atom_index
def parse_range(in_str):
def check_frac(coord,lim):
con=[False]*3
for i in range(3):
con[i]=coord[i]>=lim[i][0] and coord[i]<=lim[i][1]
if np.all(con):
return True
else:
return False
coord_range={}
tmp_str=in_str.split();tmp1_str=' '.join(tmp_str);tmp2_str=tmp1_str.split("|")
icount=0
for i in tmp2_str:
if i=='':
coord_range[icount]=''
else:
coord_range[icount]=[float(x) for x in i.split()]
icount+=1
for key in coord_range.keys():
if coord_range[key]=='':
coord_range[key]=[0,1]
atom_index=[]
for i, site in enumerate(struct.sites):
if check_frac(site.frac_coords,coord_range):
atom_index.append(i)
return atom_index
if "|" in in_str.strip():
atom_index_list=parse_range(in_str)
else:
for str in in_str.strip():
if str.isalpha():
atom_index_list=parse_label(in_str)
return atom_index_list,in_str
atom_index_list=parse_index(in_str)
return atom_index_list,in_str
def constrain(struct,in_str=None):
natom=struct.num_sites
atom_index,in_str=atom_selection(struct,in_str)
selective_dynamics=[[True for col in range(3)] for row in range(natom)]
for i in range(natom):
if i in atom_index:
selective_dynamics[i]=[False,False,False]
tmp_struct=Structure(struct.lattice,struct.species,struct.frac_coords,site_properties={'selective_dynamics':selective_dynamics})
return tmp_struct
if __name__=='__main__':
from pymatgen.io.vasp import Poscar
st=Structure.from_file('L1-Te2.vasp')
in_str='||0.0 0.5'
cst=constrain(st,in_str=in_str)
poscar=Poscar(cst)
print(st)
print(poscar)
poscar.comment=poscar.comment+' |--> '+in_str
poscar.write_file('Fixed.vasp')
|
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