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 getIonicRadii(filename):
with zopen(filename, "rt") as f:
input_string = f.read()
parser = CifParser_new.from_string(input_string)
stru = parser.get_structures(primitive=False)[0]
coordination_list, radii = get_local_envir_fromstru(stru)
print(radii)
return radii
def LocalEnvirCom(stru, migrant):
# stru = Structure.from_file(filename)
# val_eval = ValenceIonicRadiusEvaluator(stru)
# radii = val_eval.radii
coordination_list, radii = get_local_envir_fromstru(stru)
# 为了防止保存的半径信息无法匹配此处对半径信息做特殊处理，如Ag+的半径会保存为Ag、Ag+、Ag1+
# radii_keys = list(radii.keys())
# for key in radii_keys:
# radii[re.sub('[^a-zA-Z]','',key)] = radii[key]
# if re.search('[A-Z][a-z]*\+|[A-Z][a-z]*\-', key) != None:
# s1 = re.sub('\+','1+',key)
# radii[re.sub('\-','1-',s1)] = radii[key]
# minRad = 0
# for label in radii:
# if migrant in label:
# # 取最小值作为迁移离子半径
# if minRad == 0:
# minRad = radii[label]
# elif radii[label] < minRad:
# minRad = radii[label]
coord_tmp = []
nei_dis_tmp = []
min_nei_dis_tmp = []
migrant_paras = []
migrant_radii = []
for i in coordination_list:
if migrant in i["label"]:
#获取最邻近配位
nearest_atom = i["coord_nei"][0]
#最邻近配位原子的label
nei_label = nearest_atom[0]._atom_site_label
#到最邻近配位原子中心的距离
nei_dis = nearest_atom[1]
#最邻近配位原子的半径
nei_radius = radii[nei_label]
alpha_tmp = (nei_dis - nei_radius)/radii[i["label"]]
#获取所有label迁移离子配位数
coord_tmp.append(i["coord_num"])
#获取不同label迁移离子到最邻近配位原子中心的距离与表面距离
nei_dis_tmp.append(nei_dis)
#获取所有label迁移离子到最邻近配位原子表面的距离
min_nei_dis_tmp.append(nei_dis - nei_radius)
migrant_paras.append(alpha_tmp)
migrant_radii.append(radii[i["label"]])
nei_dises = list(zip(coord_tmp, zip(nei_dis_tmp, min_nei_dis_tmp)))
migrant_alpha = float(sum(migrant_paras))/len(migrant_paras)
if migrant_alpha > 1.0:
migrant_alpha = 1.0
migrant_radius = float(sum(migrant_radii))/len(migrant_radii)
return radii,migrant_radius,migrant_alpha,nei_dises,coordination_list
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