def AllCom3(filename, standard, migrant=None, rad_flag=True, effective_rad=True, rad_file=None, rad_store_in_vasp=True):
radii = {}
if rad_flag and effective_rad:
#考虑如何利用migrant_radius与migrant_alpha
radii, migrant_radius, migrant_alpha, nei_dises = LocalEnvirCom(filename,migrant)
if migrant:
remove_filename = getRemoveMigrantFilename(filename,migrant)
else:
remove_filename = filename
rad_flag = False
atmnet = AtomNetwork.read_from_CIF(remove_filename, radii, rad_flag, rad_file)
if migrant:
os.remove(remove_filename)
prefixname = filename.replace(".cif","")
vornet,edge_centers,fcs = atmnet.perform_voronoi_decomposition(False)
sym_vornet,voids = get_Symmetry(atmnet, vornet)
writeBIFile(prefixname+"_origin.bi",atmnet,sym_vornet)
writeVaspFile(prefixname+"_origin.vasp",atmnet,sym_vornet,rad_store_in_vasp)
minRad = standard*migrant_alpha*0.85
channels = Channel.findChannels(sym_vornet,atmnet,minRad,prefixname+".net")
dims = []
if len(channels)==0:
dims.append(0)
else:
for i in channels:
dims.append(i["dim"])
return migrant_alpha,radii,minRad,nei_dises,dims,voids
def AllCom2(filename, probe_rad, num_sample, migrant=None, rad_flag=True, effective_rad=True, rad_file=None, rad_store_in_vasp=True, minRad=0.0, maxRad=0.0):
radii = {}
if rad_flag and effective_rad:
radii = getIonicRadii(filename)
if migrant:
remove_filename = getRemoveMigrantFilename(filename,migrant)
else:
remove_filename = filename
atmnet = AtomNetwork.read_from_CIF(remove_filename, radii, rad_flag, rad_file)
# high_accur_atmnet = atmnet.copy()
# high_accuracy_atmnet(high_accur_atmnet, "S50")
if migrant:
os.remove(remove_filename)
prefixname = filename.replace(".cif","")
# vornet,edge_centers,fcs = high_accur_atmnet.perform_voronoi_decomposition(False)
vornet,edge_centers,fcs = atmnet.perform_voronoi_decomposition(False)
sym_vornet,voids = get_Symmetry(atmnet, vornet)
writeBIFile(prefixname+"_origin.bi",atmnet,sym_vornet)
writeVaspFile(prefixname+"_origin.vasp",atmnet,sym_vornet,rad_store_in_vasp)
writeVaspFile(prefixname+"_selected.vasp",atmnet,sym_vornet,rad_store_in_vasp,minRad,maxRad)
channels = Channel.findChannels(sym_vornet,atmnet,minRad,prefixname+"_channel.net")
dims = []
for i in channels:
dims.append(i["dim"])
return dims,voids
def ASACom(filename, probe_rad, num_sample, migrant=None, rad_flag=True, effective_rad=True, rad_file=None):
radii = {}
if rad_flag and effective_rad:
radii = LocalEnvirCom(filename)
if migrant:
remove_filename = getRemoveMigrantFilename(filename,migrant)
else:
remove_filename = filename
atmnet = AtomNetwork.read_from_CIF(remove_filename, radii, rad_flag, rad_file)
if migrant:
os.remove(remove_filename)
prefixname = filename.replace(".cif","")
asa_new(prefixname+".zsa",False,atmnet,probe_rad,probe_rad,num_sample)
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 VoidNetCom(filename, migrant=None, rad_flag=True, effective_rad=True, rad_file=None):
radii = {}
if rad_flag and effective_rad:
radii = LocalEnvirCom(filename)
if migrant:
remove_filename = getRemoveMigrantFilename(filename,migrant)
else:
remove_filename = filename
atmnet = AtomNetwork.read_from_CIF(remove_filename, radii, rad_flag, rad_file)
vornet,edge_centers,fcs = atmnet.perform_voronoi_decomposition(False)
if migrant:
os.remove(remove_filename)
prefixname = filename.replace(".cif","")
writeZVisFile(prefixname+".zvis", False, atmnet, vornet)
def ConnValCom(filename, migrant=None, rad_flag=True, effective_rad=True, rad_file=None):
radii = {}
if rad_flag and effective_rad:
radii = LocalEnvirCom(filename)
if migrant:
remove_filename = getRemoveMigrantFilename(filename,migrant)
else:
remove_filename = filename
atmnet = AtomNetwork.read_from_CIF(remove_filename, radii, rad_flag, rad_file)
if migrant:
os.remove(remove_filename)
prefixname = filename.replace(".cif","")
Ri,Rf,Rif = atmnet.through_VorNet(prefixname+".res")
return Ri,Rf,Rif
def ChannelCom(filename, probe_rad, migrant=None, rad_flag=True, effective_rad=True, rad_file=None):
radii = {}
if rad_flag and effective_rad:
radii = LocalEnvirCom(filename)
if migrant:
remove_filename = getRemoveMigrantFilename(filename,migrant)
else:
remove_filename = filename
atmnet = AtomNetwork.read_from_CIF(remove_filename, radii, rad_flag, rad_file)
vornet,edge_centers,fcs = atmnet.perform_voronoi_decomposition(False)
if migrant:
os.remove(remove_filename)
prefixname = filename.replace(".cif","")
Channel.findChannels(vornet,atmnet,probe_rad,prefixname+".net")
def main():
path = "./cifs/"
filetype = ".cif"
filenames = batch_read_filename(path, filetype)
for file in filenames:
whole_filename = file + ".cif"
whole_radfilename = file + ".rad"
out_whole_file = file + ".res"
infile = path + whole_filename
inradfile = path + whole_radfilename
outfile = path + out_whole_file
remove_filename = getRemoveMigrantFilename(infile, "Li")
atmnet = AtomNetwork.read_from_CIF(remove_filename, rad_file=inradfile)
atmnet.calculate_free_sphere_parameters(outfile)
def ConnValListCom(filename, migrant=None, rad_flag=True, effective_rad=True, rad_file=None):
radii = {}
if rad_flag and effective_rad:
radii = LocalEnvirCom(filename)
if migrant:
remove_filename = getRemoveMigrantFilename(filename,migrant)
else:
remove_filename = filename
atmnet = AtomNetwork.read_from_CIF(remove_filename, radii, rad_flag, rad_file)
vornet,edge_centers,fcs = atmnet.perform_voronoi_decomposition(False)
if migrant:
os.remove(remove_filename)
prefixname = filename.replace(".cif","")
conn = connection_values_list(prefixname+".resex",vornet)
return conn
def BIComputation(filename, migrant=None, rad_flag=True, effective_rad=True, rad_file=None, rad_store_in_vasp=True, minRad=0.0, maxRad=0.0):
radii = {}
if rad_flag and effective_rad:
radii,migrant_radius,migrant_alpha, nei_dises = LocalEnvirCom(filename,migrant)
if migrant:
remove_filename = getRemoveMigrantFilename(filename,migrant)
else:
remove_filename = filename
atmnet = AtomNetwork.read_from_CIF(remove_filename, radii, rad_flag, rad_file)
vornet,edge_centers,fcs = atmnet.perform_voronoi_decomposition(False)
#delete temp file
if migrant:
os.remove(remove_filename)
prefixname = filename.replace(".cif","")
writeBIFile(prefixname+"_origin.bi",atmnet,vornet)
writeBIFile(prefixname+"_selected.bi",atmnet,vornet)
writeVaspFile(prefixname+"_origin.vasp",atmnet,vornet,rad_store_in_vasp)
writeVaspFile(prefixname+"_selected.vasp",atmnet,vornet,rad_store_in_vasp,minRad,maxRad)
def AllCom(filename, probe_rad, num_sample, migrant=None, rad_flag=True, effective_rad=True, rad_file=None, minRad=0.0, maxRad=0.0):
radii = {}
if rad_flag and effective_rad:
#考虑如何利用migrant_radius与migrant_alpha
symm_number, radii,migrant_radius,migrant_alpha, nei_dises,coordination_list = LocalEnvirCom(filename,migrant)
if migrant:
remove_filename = getRemoveMigrantFilename(filename,migrant)
else:
remove_filename = filename
atmnet = AtomNetwork.read_from_CIF(remove_filename, radii, rad_flag, rad_file)
# high_accur_atmnet = atmnet.copy()
# high_accuracy_atmnet(high_accur_atmnet, "S50")
if migrant:
os.remove(remove_filename)
prefixname = filename.replace(".cif","")
# vornet,edge_centers,fcs = high_accur_atmnet.perform_voronoi_decomposition(False)
vornet,edge_centers,fcs = atmnet.perform_voronoi_decomposition(False)
sym_vornet,voids = get_Symmetry(atmnet, vornet)
writeNETFile(prefixname+"_origin.net",atmnet,sym_vornet)
writeVaspFile(prefixname+"_origin.vasp",atmnet,sym_vornet)
probe_rad = migrant_radius*migrant_alpha
minRad = migrant_radius*migrant_alpha*0.85
maxRad = migrant_radius*migrant_alpha*1.15
print(minRad)
print(maxRad)
writeNETFile(prefixname+"_origin.net",atmnet,sym_vornet,minRad,maxRad)
writeVaspFile(prefixname+"_selected.vasp",atmnet,sym_vornet,minRad,maxRad)
channels = Channel.findChannels(sym_vornet,atmnet,0.60,prefixname+".net")
conn = connection_values_list(prefixname+".resex", sym_vornet)
oneD,twoD,threeD = ConnStatus(minRad, conn)
dims = []
for i in channels:
dims.append(i["dim"])
return conn,oneD,twoD,threeD,nei_dises,dims,voids,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
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
renderer.SetBackground(0.0,0.3,0.1)
renderer.ResetCamera()
renderer.GetActiveCamera().Azimuth(30)
renderer.GetActiveCamera().Elevation(-30)
renderer.GetActiveCamera().Zoom(1)
renderer.ResetCameraClippingRange()
renWin.AddRenderer(renderer)
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin)
iRen.Initialize()
renWin.Render()
return iRen
if __name__ == '__main__':
radii = {}
atmnet = AtomNetwork.read_from_CIF("icsd_16713.cif", radii, False, None)
vornet,edge_centers,fcs = atmnet.perform_voronoi_decomposition(False)
channels = Channel.findChannels(vornet,1.1,"icsd_16713.net")
print(channels[0].nodes)
print(channels[0].connections)
#test code
#atmnet = [['Li1+', [0.2029999941587448, 0.550000011920929, 0.3399999141693115]], ['Li1+', [0.7970000058412552, 0.550000011920929, 0.1600000262260437]], ['Li1+', [0.7970000058412552, 0.44999998807907104, 0.6600000262260437]], ['Li1+', [0.2029999941587448, 0.44999998807907104, 0.8399999737739563]], ['Li1+', [0.703000009059906, 0.050000011920928955, 0.3399999141693115]], ['Li1+', [0.296999990940094, 0.050000011920928955, 0.1600000262260437]], ['Li1+', [0.296999990940094, 0.949999988079071, 0.6600000262260437]], ['Li1+', [0.703000009059906, 0.949999988079071, 0.8399999737739563]], ['C4+', [0.0, 0.9429999999701977, 0.75]], ['C4+', [0.0, 0.05700000002980232, 0.25]], ['C4+', [0.5, 0.4429999887943268, 0.75]], ['C4+', [0.5, 0.5569999814033508, 0.25]], ['O2-', [0.0, 0.6870000064373016, 0.75]], ['O2-', [0.0, 0.31299999356269836, 0.25]], ['O2-', [0.5, 0.18700000643730164, 0.75]], ['O2-', [0.5, 0.812999963760376, 0.25]], ['O2-', [0.14499999582767487, 0.06699997186660767, 0.8199999928474426]], ['O2-', [0.8550000041723251, 0.06699997186660767, 0.6800000071525574]], ['O2-', [0.8550000041723251, 0.9330000281333923, 0.18000000715255737]], ['O2-', [0.14499999582767487, 0.9330000281333923, 0.3199999928474426]], ['O2-', [0.6449999809265137, 0.5669999718666077, 0.8199999928474426]], ['O2-', [0.35500001907348633, 0.5669999718666077, 0.6800000071525574]], ['O2-', [0.35500001907348633, 0.4330000877380371, 0.18000000715255737]], ['O2-', [0.6449999809265137, 0.4330000877380371, 0.3199999928474426]]]
#channels=[1,2]
iRen = renderer = Display(atmnet, channels[0])
iRen.Start()
from cavd.netstorage import AtomNetwork
from cavd.netio import *
remove_filename = getRemoveMigrantFilename("Li2CO3-LDA.cif", "Li")
atmnet = AtomNetwork.read_from_CIF(remove_filename, False)
vornet, edge_centers, fcs = atmnet.perform_voronoi_decomposition()
writeBIfile("Li2CO3-LDA.bi", vornet, 0.2)
writeVaspFile("Li2CO3-LDA.vasp", atmnet, vornet, True, 0.2)
if atmnet.through_VorNet("Li2CO3-LDA.res", 0.5):
print("a sphere with radius id 0.5A can free through in this structure!")
else:
print(
"a sphere with radius id 0.5A can not free through in this structure!")