def ConnValListCom(filename, migrant=None, rad_flag=True, rad_dict=None):
with zopen(filename, "rt") as f:
input_string = f.read()
parser = CifParser_new.from_string(input_string)
stru = parser.get_structures(primitive=False)[0]
species = [str(sp).replace("Specie ","") for sp in stru.species]
elements = [re.sub('[^a-zA-Z]','',sp) for sp in species]
if migrant not in elements:
raise ValueError("The input migrant ion not in the input structure! Please check it.")
coord_list,effec_radii = get_local_envir_fromstru(stru)
radii = {}
if rad_flag:
if rad_dict:
radii = rad_dict
else:
radii = effec_radii
atmnet = AtomNetwork.read_from_RemoveMigrantCif(filename, migrant, radii, rad_flag)
vornet,edge_centers,fcs,faces = atmnet.perform_voronoi_decomposition(True)
add_fcs_vornet = vornet.add_facecenters(faces)
prefixname = filename.replace(".cif","")
conn = connection_values_list(prefixname+".resex",add_fcs_vornet)
return conn
def BIComputation(filename, migrant, rad_flag=True, lower=0.0, upper=0.0, rad_dict=None):
with zopen(filename, "rt") as f:
input_string = f.read()
parser = CifParser_new.from_string(input_string)
stru = parser.get_structures(primitive=False)[0]
species = [str(sp).replace("Specie ","") for sp in stru.species]
elements = [re.sub('[^a-zA-Z]','',sp) for sp in species]
if migrant not in elements:
raise ValueError("The input migrant ion not in the input structure! Please check it.")
coordination_list, radii = get_local_envir_fromstru(stru)
radii = {}
if rad_flag:
if rad_dict:
radii = rad_dict
else:
radii = effec_radii
atmnet = AtomNetwork.read_from_RemoveMigrantCif(filename, migrant, radii, rad_flag)
prefixname = filename.replace(".cif","")
vornet,edge_centers,fcs,faces = atmnet.perform_voronoi_decomposition(True)
add_fcs_vornet = vornet.add_facecenters(faces)
writeVaspFile(prefixname+"_origin.vasp",atmnet,add_fcs_vornet)
if lower and not upper:
writeVaspFile(prefixname+"_selected.vasp",atmnet, add_fcs_vornet, lower, 10.0)
if not lower and upper:
writeVaspFile(prefixname+"_selected.vasp",atmnet, add_fcs_vornet, 0.0, upper)
if lower and upper:
writeVaspFile(prefixname+"_selected.vasp",atmnet, add_fcs_vornet, lower, upper)
def AllCom9(filename, standard, migrant=None, rad_flag=True, effective_rad=True, rad_file=None):
radii = {}
with zopen(filename, "rt") as f:
input_string = f.read()
parser = CifParser_new.from_string(input_string)
stru = parser.get_structures(primitive=False)[0]
# print(stru)
#获取空间群号与符号
symm_number,symm_sybol = parser.get_symme()
#获取icsd cif文件中的对称操作
sitesym = parser.get_sym_opt()
radii,migrant_radius,migrant_alpha,nei_dises,coordination_list = LocalEnvirCom(stru,migrant)
atmnet = AtomNetwork.read_from_RemoveMigrantCif(filename, migrant, radii, False, None)
prefixname = filename.replace(".cif","")
vornet,edge_centers,fcs,faces = atmnet.perform_voronoi_decomposition(False)
symprec = 0.01
sym_opt_num = len(sitesym)
voids_num = len(vornet.nodes)
sym_vornet,voids = get_labeled_vornet(vornet, sitesym, symprec)
uni_voids_num = len(voids)
voids_abs = []
voids_rad = []
for void in sym_vornet.nodes:
voids_abs.append(void[2])
voids_rad.append(void[3])
# print("voids")
# print(voids_abs)
vorosites = [voids_abs]
vororad = [voids_rad]
recover_rate, recover_state, migrate_mindis = rediscovery_byRad_kdTree_onlyVertex(stru, migrant, vorosites, vororad)
writeNETFile(prefixname+"_origin.net",atmnet,sym_vornet)
writeVaspFile(prefixname+"_origin.vasp",atmnet,sym_vornet)
conn_val = connection_values_list(prefixname+".resex", sym_vornet)
minRad = standard*migrant_alpha*0.85
dim_network,connect = ConnStatus(conn_val,minRad)
channels = Channel.findChannels(sym_vornet,atmnet,minRad,prefixname+"_select.net")
dims_channel = []
if len(channels)==0:
dims_channel.append(0)
else:
for i in channels:
dims_channel.append(i["dim"])
writeVaspFile(prefixname+"_select.vasp",atmnet,sym_vornet,minRad,5.0)
# channels = Channel.findChannels(sym_vornet,atmnet,0,prefixname+"_0.net")
return radii,symm_sybol,symm_number,symprec,voids_num,sym_opt_num,uni_voids_num,minRad,migrant_alpha,nei_dises,migrant_radius,conn_val,connect,dim_network,dims_channel,recover_rate,recover_state,migrate_mindis,coordination_list
def bmd_com(filename, migrant, rad_flag=True, lower=None, upper=10.0, rad_dict=None, symprec=0.01):
with zopen(filename, "rt") as f:
input_string = f.read()
parser = CifParser_new.from_string(input_string)
stru = parser.get_structures(primitive=False)[0]
species = [str(sp).replace("Specie ","") for sp in stru.species]
elements = [re.sub('[^a-zA-Z]','',sp) for sp in species]
if migrant not in elements:
raise ValueError("The input migrant ion not in the input structure! Please check it.")
effec_radii,migrant_radius,migrant_alpha,nei_dises,coordination_list = LocalEnvirCom(stru,migrant)
radii = {}
if rad_flag:
if rad_dict:
radii = rad_dict
else:
radii = effec_radii
atmnet = AtomNetwork.read_from_RemoveMigrantCif(filename, migrant, radii, rad_flag)
prefixname = filename.replace(".cif","")
vornet,edge_centers,fcs,faces = atmnet.perform_voronoi_decomposition(True)
add_fcs_vornet = vornet.add_facecenters(faces)
sitesym = parser.get_sym_opt()
sym_vornet,voids = get_labeled_vornet(add_fcs_vornet, sitesym, symprec)
writeVaspFile(prefixname+"_origin.vasp",atmnet,sym_vornet)
writeNETFile(prefixname+"_origin.net",atmnet,sym_vornet)
voids_abs = []
for void in sym_vornet.nodes:
voids_abs.append(void[2])
bottlenecks = []
for bt in sym_vornet.edges:
bottlenecks.append(bt[2])
vorosites = [voids_abs, bottlenecks, fcs]
recover_rate, recover_state, migrate_mindis = rediscovery_kdTree(migrant,vorosites,stru)
minRad = 0.0
if lower:
minRad = lower
else:
standard = STD_SURF_DIS[migrant]
minRad = standard*migrant_alpha*0.85
conn_val = connection_values_list(prefixname+".resex", sym_vornet)
dim_network,connect = ConnStatus(minRad, conn_val)
writeVaspFile(prefixname+".vasp",atmnet, sym_vornet, minRad, upper)
channels = Channel.findChannels(sym_vornet, atmnet, minRad, prefixname+".net")
dims = []
for i in channels:
dims.append(i["dim"])
return radii, minRad, conn_val, connect, dim_network, dims, migrate_mindis
def AllCom6(filename, standard, migrant=None, rad_flag=True, effective_rad=True, rad_file=None):
radii = {}
with zopen(filename, "rt") as f:
input_string = f.read()
parser = CifParser_new.from_string(input_string)
stru = parser.get_structures(primitive=False)[0]
#获取空间群号与符号
symm_number,symm_sybol = parser.get_symme()
#获取icsd cif文件中的对称操作
sitesym = parser.get_sym_opt()
if rad_flag and effective_rad:
#考虑如何利用migrant_radius与migrant_alpha
radii,migrant_radius,migrant_alpha,nei_dises,coordination_list = LocalEnvirCom(stru,migrant)
if migrant:
atmnet = AtomNetwork.read_from_RemoveMigrantCif(filename, migrant, radii, rad_flag, rad_file)
else:
atmnet = AtomNetwork.read_from_CIF(filename, radii, rad_flag, rad_file)
prefixname = filename.replace(".cif","")
vornet,edge_centers,fcs = atmnet.perform_voronoi_decomposition(False)
symprec = 0.01
sym_opt_num = len(sitesym)
voids_num = len(vornet.nodes)
sym_vornet,voids = get_labeled_vornet(vornet, sitesym, symprec)
uni_voids_num = len(voids)
# 衡量计算得到的对称性独立的间隙数与 对称性独立间隙最小数 之间的差异
dif = abs(uni_voids_num - voids_num/sym_opt_num) / (voids_num/sym_opt_num)
recover_rate, recover_state, true_recover_dis = rediscovery(migrant,voids,stru)
writeNETFile(prefixname+"_origin.net",atmnet,sym_vornet)
writeVaspFile(prefixname+"_origin.vasp",atmnet,sym_vornet)
conn_val = connection_values_list(prefixname+".resex", sym_vornet)
minRad = standard*migrant_alpha*0.85
dim_network,connect = ConnStatus(conn_val,minRad)
writeVaspFile(prefixname+"_"+str(round(minRad,4))+".vasp",atmnet,sym_vornet,minRad,5.0)
channels = Channel.findChannels(sym_vornet,atmnet,minRad,prefixname+"_"+str(round(minRad,4))+".net")
dims_channel = []
if len(channels)==0:
dims_channel.append(0)
else:
for i in channels:
dims_channel.append(i["dim"])
# return symm_sybol,symm_number,symprec,uni_voids_num,conn_val,connect,dim_network,dims_channel,migrant_alpha,radii,minRad,nei_dises,recover_rate, recover_state, true_recover_dis,coordination_list
return symm_sybol, symm_number, sym_opt_num, voids_num, symprec, uni_voids_num, dis, recover_rate, recover_state, true_recover_dis
def ChannelCom(filename, probe_rad = None, migrant=None, rad_flag=True, rad_dict=None, symprec=0.01):
with zopen(filename, "rt") as f:
input_string = f.read()
parser = CifParser_new.from_string(input_string)
stru = parser.get_structures(primitive=False)[0]
radii = {}
if rad_flag:
if rad_dict:
radii = rad_dict
else:
coordination_list, effec_radii = get_local_envir_fromstru(stru)
radii = effec_radii
species = [str(sp).replace("Specie ","") for sp in stru.species]
elements = [re.sub('[^a-zA-Z]','',sp) for sp in species]
if migrant:
if migrant not in elements:
raise ValueError("The input migrant ion not in the input structure! Please check it.")
atmnet = AtomNetwork.read_from_RemoveMigrantCif(filename, migrant, radii, rad_flag)
else:
atmnet = AtomNetwork.read_from_CIF(filename, radii, rad_flag)
vornet,edge_centers,fcs,faces = atmnet.perform_voronoi_decomposition(True)
add_fcs_vornet = vornet.add_facecenters(faces)
sitesym = parser.get_sym_opt()
sym_vornet,voids = get_labeled_vornet(add_fcs_vornet, sitesym, symprec)
prefixname = filename.replace(".cif","")
writeNETFile(prefixname+"_origin.net",atmnet,sym_vornet)
channels = Channel.findChannels(sym_vornet, atmnet, probe_rad, prefixname+".net")
dims = []
for i in channels:
dims.append(i["dim"])
return dims
def AllCom(filename, minRad, maxRad, migrant=None, rad_flag=True, effective_rad=True, rad_file=None):
radii = {}
with zopen(filename, "rt") as f:
input_string = f.read()
parser = CifParser_new.from_string(input_string)
stru = parser.get_structures(primitive=False)[0]
# print(stru)
#获取空间群号与符号
symm_number,symm_sybol = parser.get_symme()
#获取icsd cif文件中的对称操作
sitesym = parser.get_sym_opt()
radii,migrant_radius,migrant_alpha,nei_dises,coordination_list = LocalEnvirCom(stru,migrant)
atmnet = AtomNetwork.read_from_RemoveMigrantCif(filename, migrant, radii, True, None)
prefixname = filename.replace(".cif","")
vornet,edge_centers,fcs,faces = atmnet.perform_voronoi_decomposition(True)
symprec = 0.01
sym_opt_num = len(sitesym)
voids_num = len(vornet.nodes)
# writeNETFile(prefixname+"_origin_nofcs.net",atmnet,vornet)
add_fcs_vornet = vornet.add_facecenters(faces)
# writeNETFile(prefixname+"_origin_addfcs.net",atmnet,add_fcs_vornet)
# writeVaspFile(prefixname+"_origin_addfcs.vasp",atmnet,add_fcs_vornet)
# spg_vornet,uq_voids = get_equivalent_vornet(add_fcs_vornet, 0.01)
sym_vornet,voids = get_labeled_vornet(add_fcs_vornet, sitesym, symprec)
uni_voids_num = len(voids)
voids_abs = []
voids_rad = []
for void in sym_vornet.nodes:
voids_abs.append(void[2])
voids_rad.append(void[3])
# print("voids")
# print(voids_abs)
bottlenecks = []
bottlenecs_rad = []
for bt in sym_vornet.edges:
frac_bt = bt[2]
# frac_bt = [round(p%1.0, 6) for p in frac_bt]
# frac_bt = [p%1.0 for p in frac_bt]
# if frac_bt not in bottlenecks:
bottlenecks.append(frac_bt)
bottlenecs_rad.append(bt[3])
# print("bottlenecks")
# print(bottlenecks)
# print("fcs",fcs)
fcens = []
fcens_rad = []
for fc in fcs:
fcens.append(fc[0])
fcens_rad.append(fc[1])
# print("facecenters")
# print(facecenters)
vorosites = [voids_abs, bottlenecks, fcens]
vororad = [voids_rad, bottlenecs_rad, fcens_rad]
# recover_rate, recover_state, migrate_mindis = rediscovery_kdTree(migrant,vorosites,stru)
recover_rate, recover_state, migrate_mindis = rediscovery_byRad_kdTree(stru, migrant, vorosites, vororad)
writeNETFile(prefixname+"_origin.net",atmnet,sym_vornet)
writeVaspFile(prefixname+"_origin.vasp",atmnet,sym_vornet)
conn_val = connection_values_list(prefixname+".resex", sym_vornet)
dim_network,connect = ConnStatus(conn_val, minRad, maxRad)
channels = Channel.findChannels2(sym_vornet,atmnet,minRad,maxRad,prefixname+"_select.net")
dims_channel = []
if len(channels)==0:
dims_channel.append(0)
else:
for i in channels:
dims_channel.append(i["dim"])
writeVaspFile(prefixname+"_select.vasp",atmnet,sym_vornet,minRad,maxRad)
# channels = Channel.findChannels(sym_vornet,atmnet,0,prefixname+"_0.net")
return radii,symm_sybol,symm_number,symprec,voids_num,sym_opt_num,uni_voids_num,minRad,migrant_alpha,nei_dises,migrant_radius,conn_val,connect,dim_network,dims_channel,recover_rate,recover_state,migrate_mindis,coordination_list
def AllCom5(filename, standard, migrant=None, rad_flag=True, effective_rad=True, rad_file=None):
radii = {}
with zopen(filename, "rt") as f:
input_string = f.read()
parser = CifParser_new.from_string(input_string)
stru = parser.get_structures(primitive=False)[0]
#获取空间群号与符号
symm_number,symm_sybol = parser.get_symme()
if rad_flag and effective_rad:
#考虑如何利用migrant_radius与migrant_alpha
radii,migrant_radius,migrant_alpha,nei_dises,coordination_list = LocalEnvirCom(stru,migrant)
if migrant:
atmnet = AtomNetwork.read_from_RemoveMigrantCif(filename, migrant, radii, rad_flag, rad_file)
else:
atmnet = AtomNetwork.read_from_CIF(filename, radii, rad_flag, rad_file)
prefixname = filename.replace(".cif","")
vornet,edge_centers,fcs = atmnet.perform_voronoi_decomposition(False)
print("\nSymmetry number from cif: ", symm_number)
max_symm = 0
positions = []
lattice = vornet.lattice
for i in vornet.nodes:
positions.append(i[2])
for j in range(10):
symprec = 0.01 + j*0.01
symm_num_vornet = get_symnum_sites(lattice, positions, symprec)
if max_symm < symm_num_vornet:
max_symm = symm_num_vornet
max_symm_info = (max_symm, symprec)
if symm_num_vornet == symm_number:
print("Distance tolerance in Cartesian coordinates to find crystal symmetry: ",symprec)
print("Symmetry number from Voronoi network: ", symm_num_vornet)
print("\n")
sym_vornet, voids = get_equivalent_vornet(vornet,symprec)
break
#在0.01-0.10范围内均无法得到与cif文件中一致的空间群号，使用在此过程中出现的最大值代替
elif j == 9:
print("The Symmetry calculated from Vornet (with symprec 0.01-0.1) is different from that obtained from cif files.")
print("Using the lagest value of symm_num_vornet instead!")
symm_num_vornet = max_symm_info[0]
symprec = max_symm_info[1]
print("Distance tolerance in Cartesian coordinates to find crystal symmetry: ",symprec)
print("Symmetry number of Voronoi network: ", symm_num_vornet)
print("\n")
sym_vornet, voids = get_equivalent_vornet(vornet,symprec)
recover_rate, recover_state, true_recover_dis = rediscovery(migrant,voids,stru)
writeNETFile(prefixname+"_origin.net",atmnet,sym_vornet)
writeVaspFile(prefixname+"_origin.vasp",atmnet,sym_vornet)
conn_val = connection_values_list(prefixname+".resex", sym_vornet)
minRad = standard*migrant_alpha*0.85
dim_network,connect = ConnStatus(conn_val,minRad)
writeVaspFile(prefixname+"_"+str(round(minRad,4))+".vasp",atmnet,sym_vornet,minRad,5.0)
channels = Channel.findChannels(sym_vornet,atmnet,minRad,prefixname+"_"+str(round(minRad,4))+".net")
dims_channel = []
if len(channels)==0:
dims_channel.append(0)
else:
for i in channels:
dims_channel.append(i["dim"])
return symm_sybol,symm_number,symm_num_vornet,symprec,conn_val,connect,dim_network,dims_channel,migrant_alpha,radii,minRad,nei_dises,recover_rate, recover_state, true_recover_dis,coordination_list
def AllCom8(filename, standard, migrant=None, rad_flag=True, effective_rad=True, rad_file=None):
radii = {}
with zopen(filename, "rt") as f:
input_string = f.read()
parser = CifParser_new.from_string(input_string)
stru = parser.get_structures(primitive=False)[0]
# print(stru)
#获取空间群号与符号
symm_number,symm_sybol = parser.get_symme()
#获取icsd cif文件中的对称操作
sitesym = parser.get_sym_opt()
radii,migrant_radius,migrant_alpha,nei_dises,coordination_list = LocalEnvirCom(stru,migrant)
atmnet = AtomNetwork.read_from_RemoveMigrantCif(filename, migrant, radii, True, None)
prefixname = filename.replace(".cif","")
vornet,edge_centers,fcs,faces = atmnet.perform_voronoi_decomposition(True)
writeVaspFile(prefixname+"_origin_nofcs.vasp",atmnet,vornet)
spg_vornet,uq_voids = get_equivalent_vornet(vornet, 0.01)
symprec = 0.01
sym_opt_num = len(sitesym)
voids_num = len(vornet.nodes)
writeNETFile(prefixname+"_origin_nofcs.net",atmnet,vornet)
add_fcs_vornet = vornet.add_facecenters(faces)
writeNETFile(prefixname+"_origin_addfcs.net",atmnet,add_fcs_vornet)
writeVaspFile(prefixname+"_origin_addfcs.vasp",atmnet,add_fcs_vornet)
spg_vornet,uq_voids = get_equivalent_vornet(add_fcs_vornet, 0.01)
sym_vornet,voids = get_labeled_vornet(add_fcs_vornet, sitesym, symprec)
uni_voids_num = len(voids)
voids_abs = []
for void in sym_vornet.nodes:
voids_abs.append(void[2])
# print("voids")
# print(voids_abs)
bottlenecks = []
for bt in sym_vornet.edges:
bottlenecks.append(bt[2])
# print("bottlenecks")
# print(bottlenecks)
# print("fcs",fcs)
# facecenters = []
# for fc in fcs:
# facecenters.append(atmnet.absolute_to_relative(fc[0], fc[1], fc[2]))
# print("facecenters")
# print(facecenters)
vorosites = [voids_abs, bottlenecks, fcs]
recover_rate, recover_state, migrate_mindis = rediscovery_kdTree(migrant,vorosites,stru)
writeNETFile(prefixname+"_origin.net",atmnet,sym_vornet)
writeVaspFile(prefixname+"_origin.vasp",atmnet,sym_vornet)
conn_val = connection_values_list(prefixname+".resex", sym_vornet)
minRad = standard*migrant_alpha*0.85
dim_network,connect = ConnStatus(minRad, conn_val)
writeVaspFile(prefixname+"_"+str(round(minRad,4))+".vasp",atmnet,sym_vornet,minRad,5.0)
channels = Channel.findChannels(sym_vornet,atmnet,0,prefixname+"_0.net")
channels = Channel.findChannels(sym_vornet,atmnet,minRad,prefixname+"_"+str(round(minRad,4))+".net")
return symm_sybol,symm_number,symprec,voids_num,sym_opt_num,uni_voids_num,recover_rate,recover_state,migrate_mindis