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Corner-sharing板块

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koko
2025-09-11 00:02:20 +08:00
parent 29557a7757
commit 71f6ae8928
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38
corner-sharing/data/31468.cif Normal file
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# generated using pymatgen
data_LiCaN
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 3.64796900
_cell_length_b 5.52501055
_cell_length_c 8.47816147
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural LiCaN
_chemical_formula_sum 'Li4 Ca4 N4'
_cell_volume 170.87791425
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Li Li0 1 0.25000000 0.57470608 0.04709782 1
Li Li1 1 0.75000000 0.42529392 0.95290218 1
Li Li2 1 0.75000000 0.07470608 0.45290218 1
Li Li3 1 0.25000000 0.92529392 0.54709782 1
Ca Ca4 1 0.25000000 0.47404325 0.65602265 1
Ca Ca5 1 0.75000000 0.97404325 0.84397735 1
Ca Ca6 1 0.25000000 0.02595675 0.15602265 1
Ca Ca7 1 0.75000000 0.52595675 0.34397735 1
N N8 1 0.75000000 0.73867475 0.09223915 1
N N9 1 0.75000000 0.76132525 0.59223915 1
N N10 1 0.25000000 0.26132525 0.90776085 1
N N11 1 0.25000000 0.23867475 0.40776085 1

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corner-sharing/data/31960.cif Normal file
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# generated using pymatgen
data_LiMnP2O7
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 5.25142097
_cell_length_b 7.02679723
_cell_length_c 8.10844188
_cell_angle_alpha 67.45244204
_cell_angle_beta 91.00449580
_cell_angle_gamma 94.92721598
_symmetry_Int_Tables_number 1
_chemical_formula_structural LiMnP2O7
_chemical_formula_sum 'Li2 Mn2 P4 O14'
_cell_volume 275.27628245
_cell_formula_units_Z 2
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Li Li0 1 0.29423100 0.84940800 0.98967300 1
Li Li1 1 0.72912400 0.05829500 0.44408000 1
Mn Mn2 1 0.21163500 0.24645200 0.73057400 1
Mn Mn3 1 0.77433900 0.77679000 0.26788900 1
P P4 1 0.76538900 0.88233400 0.82926500 1
P P5 1 0.71702000 0.54643400 0.69361300 1
P P6 1 0.25244500 0.12414800 0.17347900 1
P P7 1 0.27754500 0.46668700 0.30356000 1
O O8 1 0.26490100 0.36116500 0.15736200 1
O O9 1 0.87078800 0.36209700 0.75555500 1
O O10 1 0.05215500 0.95840100 0.79506700 1
O O11 1 0.13267600 0.65874000 0.21631800 1
O O12 1 0.15482500 0.30259200 0.47566800 1
O O13 1 0.97235900 0.04141700 0.23366200 1
O O14 1 0.30350700 0.13962100 0.98191200 1
O O15 1 0.45463100 0.00906700 0.29681400 1
O O16 1 0.42714800 0.49615000 0.68292000 1
O O17 1 0.81361200 0.72810700 0.51905700 1
O O18 1 0.59076200 0.00704300 0.68713100 1
O O19 1 0.67292400 0.85485100 0.01791400 1
O O20 1 0.75280800 0.64575700 0.84373300 1
O O21 1 0.56472700 0.51694900 0.32641200 1

198
corner-sharing/utils/analyze_env_st.py Normal file
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#!/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")