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!")