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icsd_compare_parallel.py
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#!/usr/bin/env python3
import numpy as np
import xlsxwriter
from multiprocessing import Pool
import bibtexparser
import argparse
import string
# from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
# from pymatgen.core.structure import Structure
import pychemia
import spglib
from pymatgen.core import Element
import wyckoff_list
import string
import networkx as nx
import time
periodic = pychemia.utils.periodic
x_list = []
for x in string.ascii_uppercase:
x_list.append(x)
for x in string.ascii_uppercase:
for y in string.ascii_uppercase:
x_list.append(x+y)
# def get_structure(args):
# st_calc = args[0]['structure']
# st_icsd = args[1]['structure']
# symprec = args[2]
# icsd_id = str(args[0]['_id'])
# print(f'{st_calc.formula:10} | {icsd_id:30}')
# # print(st, st_icsd, symprec)
# sigfigs = int(-np.log10(symprec))
# try:
# for i in range(st_icsd.natom):
# st_icsd = shift(st_icsd, symprec, np.random.randint(st_icsd.natom), True)
# st_icsd = sort_sites(st_icsd, symprec)
# st_icsd = shift(st_icsd, symprec, np.random.randint(st_icsd.natom), True)
# st_icsd = get_primitive(st_icsd, symprec)
# st_icsd = shift(st_icsd, symprec, np.random.randint(st_icsd.natom), True)
# st_icsd = get_conventional(st_icsd, symprec)
# # time.sleep(0.2 + 1 * np.random.random())
# st_icsd = shift(st_icsd, symprec)
# st_icsd = get_standardized(st_icsd, symprec)
# st_icsd = sort_sites(st_icsd, symprec)
# st_calc = shift(st_calc, symprec)
# st_calc = get_conventional(st_calc, symprec)
# for i in range(st_calc.natom):
# st_calc = shift(st_calc, symprec, np.random.randint(st_calc.natom), True)
# st_calc = sort_sites(st_calc, symprec)
# st_calc = shift(st_calc, symprec, np.random.randint(st_calc.natom), True)
# st_calc = get_primitive(st_calc, symprec)
# st_calc = shift(st_calc, symprec, np.random.randint(st_calc.natom), True)
# st_calc = get_conventional(st_calc, symprec)
# st_calc = shift(st_calc, symprec)
# st_calc = get_standardized(st_calc, symprec)
# st_calc = sort_sites(st_calc, symprec)
# except:
# st_calc = args[0]['structure']
# st_icsd = args[1]['structure']
# st_calc.symbols = ["Error" for x in st_calc.symbols]
# return [{'structure':st_calc, '_id':args[0]['_id']}, {'structure':st_icsd, '_id':args[1]['_id']}]
def get_structure(args):
st_calc = args[0]['structure']
st_icsd = args[1]['structure']
symprec = args[2]
icsd_id = str(args[0]['_id'])
print(f'{st_calc.formula:10} | {icsd_id:30}')
# print(st, st_icsd, symprec)
sigfigs = int(-np.log10(symprec))
try:
if (st_calc.natom != st_icsd.natom):
st_calc = rattle(st_calc)
st_icsd = rattle(st_icsd)
st_calc, st_icsd = match_structures(st_calc, st_icsd, count=0)
except:
st_calc = args[0]['structure']
st_icsd = args[1]['structure']
st_calc.symbols = ["Error" for x in st_calc.symbols]
return [{'structure':st_calc, '_id':args[0]['_id']}, {'structure':st_icsd, '_id':args[1]['_id']}]
def parallel_query(db_calc, db_icsd,
symprec=1e-5, nproc=2,
query={'status.relaxed': True}):
to_standardize = []
print("preparing data for parallel")
sigfigs = int(-np.log10(symprec))
for i, entry_calc in enumerate(db_calc.entries.find(query)):
mp_id = entry_calc['properties']['mp_id']
entry_icsd = db_icsd.entries.find_one({'$and': [{"properties.mp_id":mp_id},
{"properties.standardized":True},
{"properties.theoretical":False}
]})
if entry_icsd:
_id_icsd = entry_icsd['_id']
_id = entry_calc['_id']
st_icsd = db_icsd.get_structure(entry_icsd['_id'])
st = db_calc.get_structure(entry_calc['_id'])
to_standardize.append([{'structure':st, '_id':_id}, {'structure':st_icsd, '_id':_id_icsd}, symprec])
with Pool(nproc) as p:
results = p.map(get_structure, to_standardize)
return results
def to_excel(db_calc, db_icsd,
filename="xc_db_analysis.xlsx",
symprec=1e-5,
nproc=1,
query={'status.relaxed': True}):
sigfigs = int(-np.log10(symprec))
# only lattice parameters
head_l = ['XC',
'Chemical formula',
'SPG symbol',
'SPG number',
'Family',
'Lattice DOF',
'Bandgap', 'Direct gap',
'nspecies', 'natoms',
'a DOF', "b DOF", "c DOF",
'a', 'b', 'c',
'a ICSD', 'b ICSD', 'c ICSD',
'a error', 'b error','c error',
'Ea', 'Eb', 'Ec',
'Isodirectional error',
'(RSME abc).(DOF)', '(MAE abc).(DOF)','(ME abc).(DOF)',
'alpha', 'beta', 'gamma',
'alpha ICSD', 'beta ICSD', 'gamma ICSD',
'Same SPG',
'MP ID',"ICSD code"]
# lattice + species
head_ls = ['XC',
'Chemical formula',
'SPG symbol',
'SPG number',
'Family',
'Lattice DOF',
'Bandgap', 'Direct gap',
'Species symbols',
"Element class",
'Element block',
"Element group",
'Element period',
'Element electronegativity',
'nspecies', 'natoms',
'a DOF', "b DOF", "c DOF",
'a', 'b', 'c',
'a ICSD', 'b ICSD', 'c ICSD',
'a error', 'b error','c error',
'Isodirectional error',
'Ea', 'Eb', 'Ec',
'(RSME abc).(DOF)', '(MAE abc).(DOF)','(ME abc).(DOF)',
'alpha', 'beta', 'gamma',
'alpha ICSD', 'beta ICSD', 'gamma ICSD',
'Same SPG',
'MP ID',"ICSD code",]
# only Wyckoff
head_w = ['XC',
'Atom symbol',
'SPG symbol',
'SPG number',
'Family',
'Bandgap', 'Direct gap',
"Element class",
'Element block',
"Element group",
'Element electronegativity',
'Element period',
'Wyckoff DOF',
'nspecies', 'natoms',
'x DOF', "y DOF", "z DOF",
'Multiplicity',
'Wyckoff letter',
"Representation",
'x', 'y', 'z',
'x ICSD', 'y ICSD', 'z ICSD',
'a ICSD', 'b ICSD', 'c ICSD',
'Ex', 'Ey', 'Ez',
'x error','y error', 'z error',
'(RSME xyz).(DOF)', '(MAE xyz).(DOF)',
'skip',
'Same SPG',
"Chemical formula",
'MP ID',"ICSD code",
'Threshold',
]
# references
head_r = ['MP ID',"ICSD code", "Chemical formula", "Chemical name"]
# metadata about the studied structures
head_m = ['SPG symbol',
'SPG number',
'Family',
'Species symbols',
"Element class",
'Element block',
"Element group",
'Element electronegativity',
'Element period',
'nspecies', 'natoms',
'Chemical formula',
'MP ID',"ICSD code"]
workbook = xlsxwriter.Workbook(filename)
worksheet_l = workbook.add_worksheet("lattice")
worksheet_ls = workbook.add_worksheet("lattice+species")
worksheet_w = workbook.add_worksheet("wyckoff")
worksheet_m = workbook.add_worksheet("metadata")
worksheet_r = workbook.add_worksheet("references")
worksheet_l.freeze_panes(1, 2) # Freeze the first row.worksheet.
worksheet_ls.freeze_panes(1, 2) # Freeze the first row.worksheet.
worksheet_w.freeze_panes(1, 2) # Freeze the first row.worksheet.
worksheet_r.freeze_panes(1, 0) # Freeze the first row.worksheet.
worksheet_m.freeze_panes(1, 0) # Freeze the first row.worksheet.
# create formatings
header_format = workbook.add_format({'bold': True,
'align': 'center',
'valign': 'vcenter',
})
header_format.set_text_wrap()
header_format.set_border()
center_format_nf = workbook.add_format({'align': 'center'})
center_format_nf.set_border()
float_format_nf = workbook.add_format({'num_format': '#,##0.00', 'align': 'center'})
float_format_nf.set_border()
int_format_nf = workbook.add_format({'num_format': '#,##0', 'align': 'center'})
int_format_nf.set_border()
percent_format_nf = workbook.add_format({'num_format': '0.00%', 'align': 'center'})
percent_format_nf.set_border()
center_format_c = workbook.add_format({'align': 'center'})
center_format_c.set_bg_color('#C7E4EE')
center_format_c.set_border()
float_format_c = workbook.add_format({'num_format': '#,##0.00', 'align': 'center'})
float_format_c.set_bg_color('#C7E4EE')
float_format_c.set_border()
int_format_c = workbook.add_format({'num_format': '#,##0', 'align': 'center'})
int_format_c.set_bg_color('#C7E4EE')
int_format_c.set_border()
percent_format_c = workbook.add_format({'num_format': '0.00%', 'align': 'center'})
percent_format_c.set_bg_color('#C7E4EE')
percent_format_c.set_border()
float_format_red = workbook.add_format({'num_format': '#,##0.0', 'align': 'center'})
float_format_red.set_bg_color('#D9ECDB')
float_format_red.set_border()
col_number_l = {}
for i, title in enumerate(head_l):
worksheet_l.write_string(0, i, title, header_format)
col_number_l[title] = i
# worksheet.write_rich_string(0,
# col_number_l[],
# 'j = k',
# superscript, '(n-1)',
# center)
col_number_ls = {}
for i, title in enumerate(head_ls):
worksheet_ls.write_string(0, i, title, header_format)
col_number_ls[title] = i
col_number_w = {}
for i, title in enumerate(head_w):
worksheet_w.write_string(0, i, title, header_format)
col_number_w[title] = i
threshold = 0.3
worksheet_w.write_number(1, i, threshold, float_format_nf)
cn_thr = "$"+x_list[i]+"$"+str(2)
col_number_r = {}
for i, title in enumerate(head_r):
worksheet_r.write_string(0, i, title, header_format)
col_number_r[title] = i
col_number_m = {}
for i, title in enumerate(head_m):
worksheet_m.write_string(0, i, title, header_format)
col_number_m[title] = i
added_materials = []
row_l = 1
row_w = 1
row_ls = 1
row_r = 1
row_m = 1
entries = parallel_query(db_calc, db_icsd,
symprec=symprec, nproc=nproc,
query=query)
wf = open("errors.txt", 'w')
for ientry in entries:
_id_calc = ientry[0]["_id"]
_id_icsd = ientry[1]["_id"]
st = ientry[0]['structure']
st_icsd = ientry[1]['structure']
entry_calc = db_calc.entries.find_one({'_id':_id_calc})
entry_icsd = db_icsd.entries.find_one({'_id':_id_icsd})
if "Error" in st.symbols:
print("++++++++++++++++++++++++++")
print("++++++++++++++++++++++++++")
print("++++++++++++++++++++++++++")
print(st.formula, _id_calc)
print("++++++++++++++++++++++++++")
print("++++++++++++++++++++++++++")
print("++++++++++++++++++++++++++")
wf.write(st.formula+str(_id_calc)+"\n")
continue
mp_id = entry_calc['properties']['mp_id']
xc = entry_calc['properties']['xc']
gap_spin_channel = min([x for x in entry_calc['properties']['band_gap']])
bandgap = entry_calc['properties']['band_gap'][gap_spin_channel]['gap']
direct_gap = entry_calc['properties']['band_gap'][gap_spin_channel]['direct']
code_icsd = entry_icsd['properties']['code_ICSD']
formula = entry_icsd['properties']['cif'][f'{code_icsd}-ICSD']["_chemical_formula_structural"]
name = entry_icsd['properties']['cif'][f'{code_icsd}-ICSD']["_chemical_name_common"]
reduced_icsd = st_icsd.reduced
cs_icsd = pychemia.crystal.CrystalSymmetry(st_icsd)
spg_no = cs_icsd.number(symprec)
spg_symbol = cs_icsd.symbol(symprec)
family = cs_icsd.crystal_system().lower()
a_icsd = st_icsd.lattice.a
b_icsd = st_icsd.lattice.b
c_icsd = st_icsd.lattice.c
alpha_icsd = st_icsd.lattice.alpha
beta_icsd = st_icsd.lattice.beta
gamma_icsd = st_icsd.lattice.gamma
spg_no_icsd = spg_no # entry_icsd['properties']['crystal_symmetry']['number']
cs = pychemia.crystal.CrystalSymmetry(st)
if st.natom != st_icsd.natom:
print("---------------------------------------------------------")
print(st.composition,"|", st_icsd.composition)
print(mp_id, spg_no, "|", code_icsd, spg_no_icsd)
print("---------------------------------------------------------")
continue
a = st.lattice.a
b = st.lattice.b
c = st.lattice.c
reduced = st.reduced
alpha = st.lattice.alpha
beta = st.lattice.beta
gamma = st.lattice.gamma
# print(st_icsd)
# print(st)
# print(st.composition,"|", st_icsd.composition)
print(f'{mp_id:10} | {code_icsd:10}')
natom = st.natom
nspecies = st.nspecies
symbols = st.symbols
wyckoff_analysis = get_wyckoffs(st, symprec, True)
crystal = pychemia.crystal.CrystalSymmetry(st)
crystal_family = crystal.crystal_system(symprec)
inner = wyckoff_analysis['inner_degrees_of_freedom']
lattice_degrees_of_freedom = get_lattice_degrees_of_freedom(crystal_family.lower(), st.lattice, sigfigs)
outer = lattice_degrees_of_freedom
multiplicity = wyckoff_analysis['multiplicity']
wyckoff_letter = wyckoff_analysis['wyckoff_letter']
wyckoff_rep = wyckoff_analysis['representation']
dof_format = [int_format_nf, float_format_red]
worksheet_l.write_number(row_l, col_number_l['Lattice DOF'], sum(outer), int_format_nf)
worksheet_l.write_number(row_l, col_number_l['a DOF'], outer[0], dof_format[int(outer[0])])
worksheet_l.write_number(row_l, col_number_l['b DOF'], outer[1], dof_format[int(outer[1])])
worksheet_l.write_number(row_l, col_number_l['c DOF'], outer[2], dof_format[int(outer[2])])
worksheet_l.write_number(row_l, col_number_l['a'], a, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['b'], b, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['c'], c, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['alpha'], alpha, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['beta'], beta, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['gamma'], gamma, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['a ICSD'], a_icsd, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['b ICSD'], b_icsd, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['c ICSD'], c_icsd, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['alpha ICSD'], alpha_icsd, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['beta ICSD'], beta_icsd, float_format_nf)
worksheet_l.write_number(row_l, col_number_l['gamma ICSD'], gamma_icsd, float_format_nf)
worksheet_l.write_string(row_l, col_number_l["MP ID"], mp_id, center_format_nf)
worksheet_l.write(row_l, col_number_l["ICSD code"], code_icsd, center_format_nf)
worksheet_l.write_string(row_l, col_number_l["Chemical formula"], formula, center_format_nf)
worksheet_l.write_string(row_l, col_number_l['XC'], xc, center_format_nf)
worksheet_l.write_number(row_l, col_number_l['SPG number'], spg_no, int_format_nf)
worksheet_l.write_string(row_l, col_number_l["SPG symbol"], spg_symbol, center_format_nf)
worksheet_l.write_string(row_l, col_number_l["Family"], family, center_format_nf)
worksheet_l.write_number(row_l, col_number_l['Bandgap'], bandgap, float_format_nf)
worksheet_l.write_boolean(row_l, col_number_l['Direct gap'], direct_gap, center_format_nf)
worksheet_l.write_number(row_l, col_number_l['nspecies'], nspecies, int_format_nf)
worksheet_l.write_number(row_l, col_number_l['natoms'], natom, int_format_nf)
worksheet_l.write_boolean(row_l, col_number_l['Same SPG'], spg_no == spg_no_icsd, center_format_nf)
cn_a_err = x_list[col_number_l['a error']]+str(row_l+1)
cn_a = x_list[col_number_l['a']]+str(row_l+1)
cn_a_icsd = x_list[col_number_l['a ICSD']]+str(row_l+1)
worksheet_l.write_formula(cn_a_err, f'={cn_a}-{cn_a_icsd}', float_format_nf)
cn_b_err = x_list[col_number_l['b error']]+str(row_l+1)
cn_b = x_list[col_number_l['b']]+str(row_l+1)
cn_b_icsd = x_list[col_number_l['b ICSD']]+str(row_l+1)
worksheet_l.write_formula(cn_b_err, f'={cn_b}-{cn_b_icsd}', float_format_nf)
cn_c_err = x_list[col_number_l['c error']]+str(row_l+1)
cn_c = x_list[col_number_l['c']]+str(row_l+1)
cn_c_icsd = x_list[col_number_l['c ICSD']]+str(row_l+1)
worksheet_l.write_formula(cn_c_err, f'={cn_c}-{cn_c_icsd}', float_format_nf)
cn_isodir = x_list[col_number_l['Isodirectional error']]+str(row_l+1)
worksheet_l.write_formula(cn_isodir, f'=IF(ABS(SUM(SIGN({cn_a_err})+SIGN({cn_b_err})+SIGN({cn_c_err})))=3, TRUE, FALSE)', float_format_nf)
# relative errors
cn_Ea = x_list[col_number_l['Ea']]+str(row_l+1)
worksheet_l.write_formula(cn_Ea, f'=({cn_a}-{cn_a_icsd})/{cn_a_icsd}', float_format_nf)
cn_Eb = x_list[col_number_l['Eb']]+str(row_l+1)
worksheet_l.write_formula(cn_Eb, f'=({cn_b}-{cn_b_icsd})/{cn_b_icsd}', float_format_nf)
cn_Ec = x_list[col_number_l['Ec']]+str(row_l+1)
worksheet_l.write_formula(cn_Ec, f'=({cn_c}-{cn_c_icsd})/{cn_c_icsd}', float_format_nf)
if sum(outer) != 0:
cn_out_a = x_list[col_number_l['a DOF']]+str(row_l+1)
cn_out_b = x_list[col_number_l['b DOF']]+str(row_l+1)
cn_out_c = x_list[col_number_l['c DOF']]+str(row_l+1)
cn_rsme_abc = x_list[col_number_l['(RSME abc).(DOF)']]+str(row_l+1)
worksheet_l.write(cn_rsme_abc, f'=(({cn_a_err}*{cn_out_a})^2+({cn_b_err}*{cn_out_b})^2+({cn_c_err}*{cn_out_c})^2)/SUM({cn_out_a}, {cn_out_b}, {cn_out_c})', float_format_nf)
cn_mae_abc = x_list[col_number_l['(MAE abc).(DOF)']]+str(row_l+1)
worksheet_l.write(cn_mae_abc, f'=(ABS({cn_a_err}*{cn_out_a})+ABS({cn_b_err}*{cn_out_b})+ABS({cn_c_err}*{cn_out_c}))/SUM({cn_out_a}, {cn_out_b}, {cn_out_c})', float_format_nf)
cn_me_abc = x_list[col_number_l['(ME abc).(DOF)']]+str(row_l+1)
worksheet_l.write(cn_me_abc, f'=({cn_a_err}*{cn_out_a}+{cn_b_err}*{cn_out_b}+{cn_c_err}*{cn_out_c})/SUM({cn_out_a}, {cn_out_b}, {cn_out_c})', float_format_nf)
row_l += 1
for ispc in range(nspecies):
if ispc == 0:
int_format = int_format_c
dof_format = [int_format_c, float_format_red]
float_format = float_format_c
center_format = center_format_c
percent_format = percent_format_c
else:
int_format = int_format_nf
dof_format = [int_format_nf, float_format_red]
float_format = float_format_nf
center_format = center_format_nf
percent_format = percent_format_nf
sym = st.species[ispc]
worksheet_ls.write_string(row_ls, col_number_ls["Species symbols"], sym, center_format)
worksheet_ls.write_string(row_ls, col_number_ls['Element class'], get_element_class(sym), center_format)
worksheet_ls.write_string(row_ls, col_number_ls["Element block"], periodic.block(sym), center_format)
worksheet_ls.write_number(row_ls, col_number_ls['Element group'], periodic.group(sym), int_format)
worksheet_ls.write_number(row_ls, col_number_ls['Element period'], periodic.period(sym), int_format)
worksheet_ls.write_number(row_ls, col_number_ls['Element electronegativity'], periodic.electronegativity(sym), float_format)
worksheet_ls.write_number(row_ls, col_number_ls['Lattice DOF'], sum(outer), int_format)
worksheet_ls.write_number(row_ls, col_number_ls['a DOF'], outer[0], dof_format[int(outer[0])])
worksheet_ls.write_number(row_ls, col_number_ls['b DOF'], outer[1], dof_format[int(outer[1])])
worksheet_ls.write_number(row_ls, col_number_ls['c DOF'], outer[2], dof_format[int(outer[2])])
worksheet_ls.write_number(row_ls, col_number_ls['a'], a, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['b'], b, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['c'], c, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['alpha'], alpha, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['beta'], beta, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['gamma'], gamma, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['a ICSD'], a_icsd, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['b ICSD'], b_icsd, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['c ICSD'], c_icsd, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['alpha ICSD'], alpha_icsd, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['beta ICSD'], beta_icsd, float_format)
worksheet_ls.write_number(row_ls, col_number_ls['gamma ICSD'], gamma_icsd, float_format)
worksheet_ls.write_string(row_ls, col_number_ls["MP ID"], mp_id, center_format)
worksheet_ls.write(row_ls, col_number_ls["ICSD code"], code_icsd, center_format)
worksheet_ls.write_string(row_ls, col_number_ls["Chemical formula"], formula, center_format_nf)
worksheet_ls.write_string(row_ls, col_number_ls['XC'], xc, center_format)
worksheet_ls.write_number(row_ls, col_number_ls['SPG number'], spg_no, int_format)
worksheet_ls.write_string(row_ls, col_number_ls["SPG symbol"], spg_symbol, center_format)
worksheet_ls.write_string(row_ls, col_number_ls["Family"], family, center_format)
worksheet_ls.write_number(row_ls, col_number_ls['Bandgap'], bandgap, float_format)
worksheet_ls.write_boolean(row_ls, col_number_ls['Direct gap'], direct_gap, center_format)
worksheet_ls.write_number(row_ls, col_number_ls['nspecies'], nspecies, int_format)
worksheet_ls.write_number(row_ls, col_number_ls['natoms'], natom, int_format)
worksheet_ls.write_boolean(row_ls, col_number_ls['Same SPG'], spg_no == spg_no_icsd, center_format)
cn_a_err = x_list[col_number_ls['a error']]+str(row_ls+1)
cn_a = x_list[col_number_ls['a']]+str(row_ls+1)
cn_a_icsd = x_list[col_number_ls['a ICSD']]+str(row_ls+1)
worksheet_ls.write_formula(cn_a_err, f'={cn_a}-{cn_a_icsd}', float_format_nf)
cn_b_err = x_list[col_number_ls['b error']]+str(row_ls+1)
cn_b = x_list[col_number_ls['b']]+str(row_ls+1)
cn_b_icsd = x_list[col_number_ls['b ICSD']]+str(row_ls+1)
worksheet_ls.write_formula(cn_b_err, f'={cn_b}-{cn_b_icsd}', float_format_nf)
cn_c_err = x_list[col_number_ls['c error']]+str(row_ls+1)
cn_c = x_list[col_number_ls['c']]+str(row_ls+1)
cn_c_icsd = x_list[col_number_ls['c ICSD']]+str(row_ls+1)
worksheet_ls.write_formula(cn_c_err, f'={cn_c}-{cn_c_icsd}', float_format_nf)
cn_isodir = x_list[col_number_ls['Isodirectional error']]+str(row_ls+1)
worksheet_ls.write_formula(cn_isodir, f'=IF(ABS(SUM(SIGN({cn_a_err})+SIGN({cn_b_err})+SIGN({cn_c_err})))=3, TRUE, FALSE)', float_format_nf)
# relative errors
cn_Ea = x_list[col_number_ls['Ea']]+str(row_ls+1)
worksheet_ls.write_formula(cn_Ea, f'=({cn_a}-{cn_a_icsd})/{cn_a_icsd}', float_format_nf)
cn_Eb = x_list[col_number_ls['Eb']]+str(row_ls+1)
worksheet_ls.write_formula(cn_Eb, f'=({cn_b}-{cn_b_icsd})/{cn_b_icsd}', float_format_nf)
cn_Ec = x_list[col_number_ls['Ec']]+str(row_ls+1)
worksheet_ls.write_formula(cn_Ec, f'=({cn_c}-{cn_c_icsd})/{cn_c_icsd}', float_format_nf)
if sum(outer) != 0:
cn_out_a = x_list[col_number_ls['a DOF']]+str(row_ls+1)
cn_out_b = x_list[col_number_ls['b DOF']]+str(row_ls+1)
cn_out_c = x_list[col_number_ls['c DOF']]+str(row_ls+1)
cn_rsme_abc = x_list[col_number_ls['(RSME abc).(DOF)']]+str(row_ls+1)
worksheet_ls.write(cn_rsme_abc, f'=SQRT((({cn_a_err}*{cn_out_a})^2+({cn_b_err}*{cn_out_b})^2+({cn_c_err}*{cn_out_c})^2)/SUM({cn_out_a}, {cn_out_b}, {cn_out_c}))', float_format_nf)
cn_mae_abc = x_list[col_number_ls['(MAE abc).(DOF)']]+str(row_ls+1)
worksheet_ls.write(cn_mae_abc, f'=(ABS({cn_a_err}*{cn_out_a})+ABS({cn_b_err}*{cn_out_b})+ABS({cn_c_err}*{cn_out_c}))/SUM({cn_out_a}, {cn_out_b}, {cn_out_c})', float_format_nf)
cn_me_abc = x_list[col_number_ls['(ME abc).(DOF)']]+str(row_ls+1)
worksheet_ls.write(cn_me_abc, f'=({cn_a_err}*{cn_out_a}+{cn_b_err}*{cn_out_b}+{cn_c_err}*{cn_out_c})/SUM({cn_out_a}, {cn_out_b}, {cn_out_c})', float_format_nf)
row_ls += 1
for iatom in range(natom):
if iatom == 0:
dof_format = [int_format_c, float_format_red]
int_format = int_format_c
float_format = float_format_c
center_format = center_format_c
percent_format = percent_format_c
else:
int_format = int_format_nf
dof_format = [int_format_nf, float_format_red]
float_format = float_format_nf
center_format = center_format_nf
percent_format = percent_format_nf
sym = symbols[iatom]
worksheet_w.write_string(row_w, col_number_w['Element class'], get_element_class(sym), center_format)
worksheet_w.write_string(row_w, col_number_w["Element block"], periodic.block(sym), center_format)
worksheet_w.write_number(row_w, col_number_w['Element group'], periodic.group(sym), int_format)
worksheet_w.write_number(row_w, col_number_w['Element period'], periodic.period(sym), int_format)
worksheet_w.write_number(row_w, col_number_w['Element electronegativity'], periodic.electronegativity(sym), float_format)
worksheet_w.write_string(row_w, col_number_w['XC'], xc, center_format)
worksheet_w.write_number(row_w, col_number_w['SPG number'], spg_no, int_format)
worksheet_w.write_string(row_w, col_number_w["SPG symbol"], spg_symbol, center_format)
worksheet_w.write_string(row_w, col_number_w["Family"], family, center_format)
worksheet_w.write_number(row_w, col_number_w['Bandgap'], bandgap, float_format)
worksheet_w.write_boolean(row_w, col_number_w['Direct gap'], direct_gap, center_format)
worksheet_w.write_string(row_w, col_number_w["Atom symbol"], symbols[iatom], center_format)
worksheet_w.write_number(row_w, col_number_w['Wyckoff DOF'], sum(inner[iatom]), int_format)
worksheet_w.write_number(row_w, col_number_w['nspecies'], nspecies, int_format)
worksheet_w.write_number(row_w, col_number_w['natoms'], natom, int_format)
worksheet_w.write_string(row_w, col_number_w["MP ID"], mp_id, center_format)
worksheet_w.write(row_w, col_number_w["ICSD code"], code_icsd, center_format)
worksheet_w.write_string(row_w, col_number_w["Chemical formula"], formula, center_format)
worksheet_w.write_number(row_w, col_number_w['x DOF'], inner[iatom][0], dof_format[int(inner[iatom][0])])
worksheet_w.write_number(row_w, col_number_w['y DOF'], inner[iatom][1], dof_format[int(inner[iatom][1])])
worksheet_w.write_number(row_w, col_number_w['z DOF'], inner[iatom][2], dof_format[int(inner[iatom][2])])
worksheet_w.write_number(row_w, col_number_w['Multiplicity'], multiplicity[iatom], int_format)
worksheet_w.write_string(row_w, col_number_w['Wyckoff letter'], wyckoff_letter[iatom], center_format)
worksheet_w.write_string(row_w, col_number_w['Representation'], str(wyckoff_rep[iatom]), center_format)
worksheet_w.write_number(row_w, col_number_w['x'], reduced[iatom][0], float_format)
worksheet_w.write_number(row_w, col_number_w['y'], reduced[iatom][1], float_format)
worksheet_w.write_number(row_w, col_number_w['z'], reduced[iatom][2], float_format)
worksheet_w.write_number(row_w, col_number_w['x ICSD'], reduced_icsd[iatom][0], float_format)
worksheet_w.write_number(row_w, col_number_w['y ICSD'], reduced_icsd[iatom][1], float_format)
worksheet_w.write_number(row_w, col_number_w['z ICSD'], reduced_icsd[iatom][2], float_format)
worksheet_w.write_number(row_w, col_number_w['a ICSD'], a_icsd, float_format)
worksheet_w.write_number(row_w, col_number_w['b ICSD'], b_icsd, float_format)
worksheet_w.write_number(row_w, col_number_w['c ICSD'], c_icsd, float_format)
worksheet_w.write_boolean(row_w, col_number_w['Same SPG'], spg_no == spg_no_icsd, center_format)
cn_Ex = x_list[col_number_w['Ex']]+str(row_w+1)
cn_x = x_list[col_number_w['x']]+str(row_w+1)
cn_x_icsd = x_list[col_number_w['x ICSD']]+str(row_w+1)
worksheet_w.write_formula(cn_Ex, f'=MIN(ABS({cn_x}-{cn_x_icsd}), ABS({cn_x}-1-{cn_x_icsd}), ABS({cn_x}+1-{cn_x_icsd}))', float_format)
cn_Ey = x_list[col_number_w['Ey']]+str(row_w+1)
cn_y = x_list[col_number_w['y']]+str(row_w+1)
cn_y_icsd = x_list[col_number_w['y ICSD']]+str(row_w+1)
worksheet_w.write_formula(cn_Ey, f'=MIN(ABS({cn_y}-{cn_y_icsd}), ABS({cn_y}-1-{cn_y_icsd}), ABS({cn_y}+1-{cn_y_icsd}))', float_format)
cn_Ez = x_list[col_number_w['Ez']]+str(row_w+1)
cn_z = x_list[col_number_w['z']]+str(row_w+1)
cn_z_icsd = x_list[col_number_w['z ICSD']]+str(row_w+1)
worksheet_w.write_formula(cn_Ez, f'=MIN(ABS({cn_z}-{cn_z_icsd}), ABS({cn_z}-1-{cn_z_icsd}), ABS({cn_z}+1-{cn_z_icsd}))', float_format)
cn_x_err = x_list[col_number_w['x error']]+str(row_w+1)
cn_a_icsd = x_list[col_number_w['a ICSD']]+str(row_w+1)
worksheet_w.write_formula(cn_x_err, f'=MIN(ABS({cn_x}-{cn_x_icsd}), ABS({cn_x}-1-{cn_x_icsd}), ABS({cn_x}+1-{cn_x_icsd}))*{cn_a_icsd}', float_format)
cn_y_err = x_list[col_number_w['y error']]+str(row_w+1)
cn_b_icsd = x_list[col_number_w['b ICSD']]+str(row_w+1)
worksheet_w.write_formula(cn_y_err, f'=MIN(ABS({cn_y}-{cn_y_icsd}), ABS({cn_y}-1-{cn_y_icsd}), ABS({cn_y}+1-{cn_y_icsd}))*{cn_b_icsd}', float_format)
cn_z_err = x_list[col_number_w['z error']]+str(row_w+1)
cn_c_icsd = x_list[col_number_w['c ICSD']]+str(row_w+1)
worksheet_w.write_formula(cn_z_err, f'=MIN(ABS({cn_z}-{cn_z_icsd}), ABS({cn_z}-1-{cn_z_icsd}), ABS({cn_z}+1-{cn_z_icsd}))*{cn_c_icsd}', float_format)
if sum(inner[iatom]) != 0:
cn_in_x = x_list[col_number_w['x DOF']]+str(row_w+1)
cn_in_y = x_list[col_number_w['y DOF']]+str(row_w+1)
cn_in_z = x_list[col_number_w['z DOF']]+str(row_w+1)
cn_rsme_xyz = x_list[col_number_w['(RSME xyz).(DOF)']]+str(row_w+1)
worksheet_w.write(cn_rsme_xyz, f'=SQRT((({cn_x_err}*{cn_in_x})^2+({cn_y_err}*{cn_in_y})^2+({cn_z_err}*{cn_in_z})^2)/SUM({cn_in_x}, {cn_in_y}, {cn_in_z}))', float_format)
cn_mae_xyz = x_list[col_number_w['(MAE xyz).(DOF)']]+str(row_w+1)
worksheet_w.write(cn_mae_xyz, f'=(ABS({cn_x_err}*{cn_in_x})+ABS({cn_y_err}*{cn_in_y})+ABS({cn_z_err}*{cn_in_z}))/SUM({cn_in_x}, {cn_in_y}, {cn_in_z})', float_format)
cn_skip = x_list[col_number_w['skip']]+str(row_w+1)
worksheet_w.write_formula(cn_skip, f'=OR(IF({cn_x_err}*{cn_in_x}>{cn_thr}, TRUE, FALSE), IF({cn_y_err}*{cn_in_y}>{cn_thr}, TRUE, FALSE), IF({cn_z_err}*{cn_in_z}>{cn_thr}, TRUE, FALSE))', center_format)
row_w += 1
if mp_id not in added_materials:
bib = bibtexparser.loads(entry_icsd['properties']['bib'])
worksheet_r.write_string(row_r, col_number_r["MP ID"], mp_id, center_format_nf)
worksheet_r.write_string(row_r, col_number_r["ICSD code"], code_icsd, center_format_nf)
worksheet_r.write_string(row_r, col_number_r["Chemical formula"], formula, center_format_nf)
worksheet_r.write_string(row_r, col_number_r["Chemical name"], name, center_format_nf)
for x in bib.entries[0]:
if x in col_number_r:
worksheet_r.write(row_r, col_number_r[x], bib.entries[0][x], center_format_nf)
else:
i = len(col_number_r)
worksheet_r.write_string(0, i, x, header_format)
col_number_r[x] = i
worksheet_r.write(row_r, col_number_r[x], bib.entries[0][x], center_format_nf)
row_r+=1
for ispc in range(nspecies):
if ispc == 0:
int_format = int_format_c
float_format = float_format_c
center_format = center_format_c
percent_format = percent_format_c
else:
int_format = int_format_nf
float_format = float_format_nf
center_format = center_format_nf
percent_format = percent_format_nf
sym = st.species[ispc]
worksheet_m.write_string(row_m, col_number_m['Element class'], get_element_class(sym), center_format)
worksheet_m.write_string(row_m, col_number_m["Element block"], periodic.block(sym), center_format)
worksheet_m.write_number(row_m, col_number_m['Element group'], periodic.group(sym), int_format)
worksheet_m.write_number(row_m, col_number_m['Element period'], periodic.period(sym), int_format)
worksheet_m.write_number(row_m, col_number_m['Element electronegativity'], periodic.electronegativity(sym), float_format)
worksheet_m.write_string(row_m, col_number_m["Species symbols"], sym, center_format)
worksheet_m.write_string(row_m, col_number_m["MP ID"], mp_id, center_format)
worksheet_m.write(row_m, col_number_m["ICSD code"], code_icsd, center_format)
worksheet_m.write_number(row_m, col_number_m['SPG number'], spg_no, int_format)
worksheet_m.write_string(row_m, col_number_m["SPG symbol"], spg_symbol, center_format)
worksheet_m.write_string(row_m, col_number_m["Family"], family, center_format)
worksheet_m.write_number(row_m, col_number_m['nspecies'], nspecies, int_format)
worksheet_m.write_number(row_m, col_number_m['natoms'], natom, int_format)
worksheet_m.write_string(row_m, col_number_m['Chemical formula'], formula, center_format)
row_m += 1
added_materials.append(mp_id)
cn_x_err_start = x_list[col_number_w['x error']]+str(2)
cn_z_err_end = x_list[col_number_w['z error']]+str(row_w)
float_format_red = workbook.add_format({'num_format': '#,##0.0', 'align': 'center', 'bg_color': '#FFC7CE', 'font_color': '#9C0006'})
float_format_red.set_border()
worksheet_w.conditional_format(f'{cn_x_err_start}:{cn_z_err_end}', {'type': 'cell',
'criteria': '>=',
'value': cn_thr,
'format': float_format_red})
workbook.close()
wf.close()
return
def get_wyckoffs(structure, symprec=1e-2, order=False):
sigfigs = int(-np.log10(symprec))
structure.reduced[structure.reduced.round(sigfigs) >= 1] -= 1
structure.reduced[structure.reduced.round(sigfigs) < 0] += 1
crystal_symmetry = pychemia.crystal.CrystalSymmetry(structure)
spg = crystal_symmetry.number(symprec=symprec)
wyckoffs = np.array(
crystal_symmetry.get_symmetry_dataset(
symprec=symprec)['wyckoffs'],
dtype='<U3')
equi_atoms= crystal_symmetry.get_symmetry_dataset(
symprec=symprec)['equivalent_atoms']
representation = wyckoff_list.get_wyckoff(spg)
dof = np.zeros((structure.natom, 3), dtype=int)
take_wyckoff = np.zeros((structure.natom))
take_lattice = np.zeros((structure.natom))
take_lattice[0] = 1
wyck_idx = {}
i = 1
for letter in string.ascii_lowercase:
wyck_idx[letter] = -1 * i
i += 1
for ieq in set(equi_atoms):
idx = equi_atoms == ieq
take_wyckoff[np.where(idx)[0][0]] = 1
wyckoff_lookup = {}
for i, rep in enumerate(representation[::-1]):
m = len(rep)
l = string.ascii_lowercase[i]
wyckoff_lookup[f"{m}{l}"] = rep
current_representation = []
if order:
identifiers = []
for iatom, sym in enumerate(structure.symbols):
l = wyckoffs[iatom]
m = len(representation[wyck_idx[l]])
# wyckoffs[iatom] = str(m) + l
e = equi_atoms[iatom]
identifiers.append(f"{m}{l}-{sym}-{e}")
identifiers = np.array(identifiers)
current_representation = np.empty_like(structure.reduced,
dtype=(np.str_,10))
for _id in np.unique(identifiers):
idx = identifiers == _id
frac_coords = structure.reduced[idx].round(sigfigs)
ml = _id.split('-')[0]
# maps coordinates to the wyckoff_list
mapper = match(frac_coords, wyckoff_lookup[ml], symprec)
# print(mapper)
for ix, iy in enumerate(np.where(idx)[0]):
current_representation[iy] = [x.strip() for x in wyckoff_lookup[ml][mapper[ix]]]
mmm = []
www = []
for iatom in range(structure.natom):
wyckoff_letter = wyckoffs[iatom]
www.append(wyckoff_letter)
rep = representation[wyck_idx[wyckoff_letter]]
multplicity = len(rep)
mmm.append(multplicity)
wyckoffs[iatom] = str(multplicity) + wyckoff_letter
if len(current_representation)!=0:
if take_wyckoff[iatom] == 1:
for ix in range(3):
rep = current_representation[iatom][ix]
if 'x' in rep or 'y' in rep or 'z' in rep:
dof[iatom, ix] = 1
return {'wyckoffs': wyckoffs[take_wyckoff.astype(np.bool_)].tolist(),
'symmetry_species': np.array(structure.symbols)[take_wyckoff.astype(np.bool_)].tolist(),
'inner_degrees_of_freedom': dof.tolist(),
'representation': current_representation,
'multiplicity': mmm,
'wyckoff_letter': www,
"equivalent_atoms": equi_atoms}
def get_primitive(st, symprec=1e-2):
cs = pychemia.crystal.CrystalSymmetry(st)
return cs.find_primitive(symprec)
def get_conventional(st, symprec=1e-2):
cs = pychemia.crystal.CrystalSymmetry(st)
return cs.refine_cell(symprec)
def get_standardized(st, symprec=1e-2, primitive=False):
cs = pychemia.crystal.CrystalSymmetry(st)
return cs.get_new_structure(spglib.standardize_cell(cs.spglib_cell,symprec=symprec))
def get_lattice_degrees_of_freedom(family, lattice, sigfigs):
a, b, c = [round(x, sigfigs) for x in [lattice.a, lattice.b, lattice.c]]
if family in ['cubic', 'trigonal']:
if a==b and b==c:
return [1, 0, 0]
else:
return [1/3, 1/3, 1/3]
elif family in ['hexagonal', 'tetragonal']:
if a == b or b == c:
return [1, 0, 1]
elif a == c :
return [1, 1, 0]
else:
return [1/3, 1/3, 1/3]
elif family in ['triclinic', 'monoclinic', 'orthorhombic']:
return [1, 1, 1]
def sort_sites(st, symprec=1e-2, ascending=True):
# First: Sort sites using the distance to the origin
sigfigs = int(-np.log10(symprec))
# st.reduced = st.reduced.round(sigfigs)
st.reduced[st.reduced >= 1] -= 1
st.reduced[st.reduced < 0] += 1
reduced = st.reduced.copy()
reduced = reduced.round(1)
norms = [np.linalg.norm(x).round(sigfigs) for x in st.reduced]
x = reduced[:, 0]
y = reduced[:, 1]
z = reduced[:, 2]
wyckoff_analysis = get_wyckoffs(st, symprec, False)
equi_atoms= wyckoff_analysis['equivalent_atoms']
symbols = []
multiplicity = wyckoff_analysis['multiplicity']
wyckoff_letter = wyckoff_analysis['wyckoff_letter']
for iatom in range(st.natom):
symbols.append(f"{multiplicity[iatom]}{wyckoff_letter[iatom]}{st.symbols[iatom]}{equi_atoms[iatom]}")
# print sorted_indices
to_sort = np.array(list(zip(symbols, x, y, z, norms)),
dtype=[('symbols', np.unicode_, 16),
('x', np.float64),
('y', np.float64),
('z', np.float64),
('norm', np.float64),])
idx = np.argsort(to_sort, order=('symbols', 'x', 'y', 'z', 'norm'), )
if ascending:
idx = np.flip(idx)
# Second: Sort again using the atomic number
st.sort_sites_using_list(idx)
return st.copy()
def shift(st, symprec=1e-2, which=0, random=False):
st = sort_sites(st, symprec, False)
shift_selections = [-3/4, -2/3, -1/2, -1/3, -1/4, 1/4, 1/3, 1/2, 2/3, 3/4]
if random:
a1 = np.random.choice(shift_selections)
a2 = np.random.choice(shift_selections)
a3 = np.random.choice(shift_selections)
else:
a1 = 0.0
a2 = 0.0
a3 = 0.0
reduced = np.zeros_like(st.reduced)
reduced[:, 0] = st.reduced[:, 0] - st.reduced[which,0] + a1
reduced[:, 1] = st.reduced[:, 1] - st.reduced[which,1] + a2
reduced[:, 2] = st.reduced[:, 2] - st.reduced[which,2] + a3
st = pychemia.core.Structure(symbols=st.symbols, cell=st.cell, reduced=reduced)
return st
def match(frac_coords, wyckoffs, symprec=1e-2):
sigfigs = int(-np.log10(symprec))
G = nx.Graph()
def conv(xyz):
if ('x' not in xyz) and ('y' not in xyz) and ('z' not in xyz):
fraction = xyz.strip().split('/')
if len(fraction) ==2:
ret=float(fraction[0])/float(fraction[1])
else:
ret= float(fraction[0])
if ret>=1:
ret-=1
elif ret<0:
ret+=1
return round(ret , sigfigs)
else:
return xyz
def is_number(x):
return type(x) is float
mapper = {x:[] for x,_ in enumerate(wyckoffs)}
for ipos, rep in enumerate(wyckoffs):
x = conv(rep[0])
y = conv(rep[1])
z = conv(rep[2])
G.add_node(f"{ipos}-w", coords=[x,y,z])
for jpos, fc in enumerate(frac_coords):
G.add_node(f"{jpos}-c", coords=fc)
for ipos, rep in enumerate(wyckoffs):
x = conv(rep[0])
y = conv(rep[1])
z = conv(rep[2])
for jpos, fc in enumerate(frac_coords):
xp = fc[0]
yp = fc[1]
zp = fc[2]
if not is_number(x):
if not is_number(y):
if not is_number(z):
continue
else :
if z==zp:
G.add_edge(f"{ipos}-w", f"{jpos}-c", weight=1)
else:
if not is_number(z):
if y==yp:
G.add_edge(f"{ipos}-w", f"{jpos}-c", weight=1)
else :
if y==yp and z==zp:
G.add_edge(f"{ipos}-w", f"{jpos}-c", weight=2)
else:
if not is_number(y):
if not is_number(z):
if x==xp:
G.add_edge(f"{ipos}-w", f"{jpos}-c", weight=1)
else :
if x==xp and z==zp:
G.add_edge(f"{ipos}-w", f"{jpos}-c", weight=2)
else:
if not is_number(z):
if x==xp and y==yp:
G.add_edge(f"{ipos}-w", f"{jpos}-c", weight=2)
else:
if x==xp and y==yp and z==zp:
G.add_edge(f"{ipos}-w", f"{jpos}-c", weight=3)
for ipos, rep in enumerate(wyckoffs):
x = conv(rep[0])
y = conv(rep[1])
z = conv(rep[2])
if not is_number(x):
if not is_number(y):
if not is_number(z):
for jpos, fc in enumerate(frac_coords):
xp = fc[0]
yp = fc[1]
zp = fc[2]
if len(G.edges(f"{jpos}-c")) == 0:
G.add_edge(f"{ipos}-w", f"{jpos}-c", weight=1)
break
for inode in G.nodes():
edges = np.array([e for e in G.edges(inode, data='weight')])
if len(edges) in [0,1]:
continue
weights = edges[:, 2].astype(int)
idx = np.flip(np.argsort(weights))
for i in range(1, len(idx)):
u = edges[idx][i][0]
v = edges[idx][i][1]
G.remove_edge(u, v)
jnode = edges[idx][0][1]
edges = np.array([e for e in G.edges(jnode, data='weight')])
for e in edges:
u = e[0]
v = e[1]
if u==jnode and v==inode:
continue
else:
G.remove_edge(u, v)
for ipos, rep in enumerate(wyckoffs):
if len(G.edges(f"{ipos}-w")) == 0:
for jpos, fc in enumerate(frac_coords):
if len(G.edges(f"{jpos}-c")) == 0:
G.add_edge(f"{ipos}-w", f"{jpos}-c", weight=1)
break
mapper = {}
for e in G.edges():
u = int(e[0].split("-")[0])
v = int(e[1].split("-")[0])
mapper[v]=u
return mapper
def match_structures(st1, st2, symprec=1e-2, count=0):
sigfigs = int(-np.log10(symprec))
st1.reduced[st1.reduced.round(sigfigs) >= 1] -= 1
st2.reduced[st2.reduced.round(sigfigs) < 0] += 1
if count>100:
print("++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++")
print(f"reached max recurssion {count}")