Corner-sharing板块
This commit is contained in:
198
corner-sharing/utils/analyze_env_st.py
Normal file
198
corner-sharing/utils/analyze_env_st.py
Normal file
@@ -0,0 +1,198 @@
|
||||
#!/usr/bin/env python
|
||||
# This code extracts the lithium environment of all of lithium sites provided in a structure file.
|
||||
import os, sys
|
||||
import numpy as np
|
||||
import scipy
|
||||
import argparse
|
||||
from scipy.spatial import ConvexHull
|
||||
from itertools import permutations
|
||||
from pymatgen.core.structure import Structure
|
||||
from pymatgen.core.periodic_table import *
|
||||
from pymatgen.core.composition import *
|
||||
from pymatgen.ext.matproj import MPRester
|
||||
from pymatgen.io.vasp.outputs import *
|
||||
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
|
||||
from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments
|
||||
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SimplestChemenvStrategy
|
||||
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import *
|
||||
|
||||
__author__ = "KyuJung Jun"
|
||||
__version__ = "0.1"
|
||||
__maintainer__ = "KyuJung Jun"
|
||||
__email__ = "kjun@berkeley.edu"
|
||||
__status__ = "Development"
|
||||
|
||||
'''
|
||||
Input for the script : path to the structure file supported by Pymatgen
|
||||
Structures with partial occupancy should be ordered or modified to full occupancy by Pymatgen.
|
||||
'''
|
||||
parser = argparse.ArgumentParser()
|
||||
parser.add_argument('structure', help='path to the structure file supported by Pymatgen', nargs='?')
|
||||
parser.add_argument('envtype', help='both, tet, oct, choosing which perfect environment to reference to', nargs='?')
|
||||
args = parser.parse_args()
|
||||
|
||||
|
||||
class HiddenPrints:
|
||||
'''
|
||||
class to reduce the output lines
|
||||
'''
|
||||
|
||||
def __enter__(self):
|
||||
self._original_stdout = sys.stdout
|
||||
sys.stdout = open(os.devnull, 'w')
|
||||
|
||||
def __exit__(self, exc_type, exc_val, exc_tb):
|
||||
sys.stdout.close()
|
||||
sys.stdout = self._original_stdout
|
||||
|
||||
|
||||
def non_elements(struct, sp='Li'):
|
||||
'''
|
||||
struct : structure object from Pymatgen
|
||||
sp : the mobile specie
|
||||
returns the structure with all of the mobile specie (Li) removed
|
||||
'''
|
||||
num_li = struct.species.count(Element(sp))
|
||||
species = list(set(struct.species))
|
||||
try:
|
||||
species.remove(Element("O"))
|
||||
except ValueError:
|
||||
print("没有O")
|
||||
try:
|
||||
species.remove(Element("S"))
|
||||
except ValueError:
|
||||
print("没有S")
|
||||
try:
|
||||
species.remove(Element("N"))
|
||||
except ValueError:
|
||||
print("没有N")
|
||||
stripped = struct.copy()
|
||||
stripped.remove_species(species)
|
||||
stripped = stripped.get_sorted_structure(reverse=True)
|
||||
return stripped
|
||||
|
||||
|
||||
def site_env(coord, struct, sp="Li", envtype='both'):
|
||||
'''
|
||||
coord : Fractional coordinate of the target atom
|
||||
struct : structure object from Pymatgen
|
||||
sp : the mobile specie
|
||||
envtype : This sets the reference perfect structure. 'both' compares CSM_tet and CSM_oct and assigns to the lower one.
|
||||
'tet' refers to the perfect tetrahedron and 'oct' refers to the perfect octahedron
|
||||
result : a dictionary of environment information
|
||||
'''
|
||||
stripped = non_elements(struct)
|
||||
with_li = stripped.copy()
|
||||
with_li.append(sp, coord, coords_are_cartesian=False, validate_proximity=False)
|
||||
with_li = with_li.get_sorted_structure()
|
||||
tet_oct_competition = []
|
||||
if envtype == 'both' or envtype == 'tet':
|
||||
for dist in np.linspace(1, 4, 601):
|
||||
neigh = with_li.get_neighbors(with_li.sites[0], dist)
|
||||
if len(neigh) < 4:
|
||||
continue
|
||||
elif len(neigh) > 4:
|
||||
break
|
||||
neigh_coords = [i.coords for i in neigh]
|
||||
with HiddenPrints():
|
||||
lgf = LocalGeometryFinder(only_symbols=["T:4"])
|
||||
lgf.setup_structure(structure=with_li)
|
||||
lgf.setup_local_geometry(isite=0, coords=neigh_coords)
|
||||
try:
|
||||
site_volume = ConvexHull(neigh_coords).volume
|
||||
tet_env_list = []
|
||||
for i in range(20):
|
||||
tet_env = {'csm': lgf.get_coordination_symmetry_measures()['T:4']['csm'], 'vol': site_volume,
|
||||
'type': 'tet'}
|
||||
tet_env_list.append(tet_env)
|
||||
tet_env = min(tet_env_list, key=lambda x: x['csm'])
|
||||
tet_oct_competition.append(tet_env)
|
||||
|
||||
except Exception as e:
|
||||
print(e)
|
||||
print("This site cannot be recognized as tetrahedral site")
|
||||
if len(neigh) == 4:
|
||||
break
|
||||
if envtype == 'both' or envtype == 'oct':
|
||||
for dist in np.linspace(1, 4, 601):
|
||||
neigh = with_li.get_neighbors(with_li.sites[0], dist)
|
||||
if len(neigh) < 6:
|
||||
continue
|
||||
elif len(neigh) > 6:
|
||||
break
|
||||
neigh_coords = [i.coords for i in neigh]
|
||||
with HiddenPrints():
|
||||
lgf = LocalGeometryFinder(only_symbols=["O:6"], permutations_safe_override=False)
|
||||
lgf.setup_structure(structure=with_li)
|
||||
lgf.setup_local_geometry(isite=0, coords=neigh_coords)
|
||||
try:
|
||||
site_volume = ConvexHull(neigh_coords).volume
|
||||
oct_env_list = []
|
||||
for i in range(20):
|
||||
'''
|
||||
20 times sampled in case of the algorithm "APPROXIMATE_FALLBACK" is used. Large number of permutations
|
||||
are performed, but the default value in the function "coordination_geometry_symmetry_measures_fallback_random"
|
||||
(NRANDOM=10) is often too small. This is not a problem if algorithm of "SEPARATION_PLANE" is used.
|
||||
'''
|
||||
oct_env = {'csm': lgf.get_coordination_symmetry_measures()['O:6']['csm'], 'vol': site_volume,
|
||||
'type': 'oct'}
|
||||
oct_env_list.append(oct_env)
|
||||
oct_env = min(oct_env_list, key=lambda x: x['csm'])
|
||||
tet_oct_competition.append(oct_env)
|
||||
|
||||
except Exception as e:
|
||||
print(e)
|
||||
print("This site cannot be recognized as octahedral site")
|
||||
if len(neigh) == 6:
|
||||
break
|
||||
|
||||
if len(tet_oct_competition) == 0:
|
||||
return {'csm': np.nan, 'vol': np.nan, 'type': 'Non_' + envtype}
|
||||
elif len(tet_oct_competition) == 1:
|
||||
return tet_oct_competition[0]
|
||||
elif len(tet_oct_competition) == 2:
|
||||
csm1 = tet_oct_competition[0]
|
||||
csm2 = tet_oct_competition[1]
|
||||
if csm1['csm'] > csm2['csm']:
|
||||
return csm2
|
||||
else:
|
||||
return csm1
|
||||
|
||||
|
||||
def extract_sites(struct, sp="Li", envtype='both'):
|
||||
'''
|
||||
struct : structure object from Pymatgen
|
||||
envtype : 'tet', 'oct', or 'both'
|
||||
sp : target element to analyze environment
|
||||
|
||||
'''
|
||||
envlist = []
|
||||
for i in range(len(struct.sites)):
|
||||
if struct.sites[i].specie != Element(sp):
|
||||
continue
|
||||
site = struct.sites[i]
|
||||
singleenv = site_env(site.frac_coords, struct, sp, envtype)
|
||||
envlist.append({'frac_coords': site.frac_coords, 'type': singleenv['type'], 'csm': singleenv['csm'],
|
||||
'volume': singleenv['vol']})
|
||||
return envlist
|
||||
|
||||
|
||||
def export_envs(envlist, sp='Li', envtype='both', fname=None):
|
||||
'''
|
||||
envlist : list of dictionaries of environment information
|
||||
fname : Output file name
|
||||
'''
|
||||
if not fname:
|
||||
fname = "extracted_environment_info" + "_" + sp + "_" + envtype + ".dat"
|
||||
with open(fname, 'w') as f:
|
||||
|
||||
f.write('List of environment information\n')
|
||||
f.write('Species : ' + sp + "\n")
|
||||
f.write('Envtype : ' + envtype + "\n")
|
||||
for index, i in enumerate(envlist):
|
||||
f.write("Site index " + str(index) + ": " + str(i) + '\n')
|
||||
|
||||
|
||||
struct = Structure.from_file("../data/31960.cif")
|
||||
site_info = extract_sites(struct, envtype="both")
|
||||
export_envs(site_info, sp="Li", envtype="both")
|
||||
Reference in New Issue
Block a user