from cmmde_hubbard import hubbard, azimuth def xyz2gen(geom,a1,a2,a3,b1,b2,b3,c1,c2,c3): sym = [] x = [] y = [] z = [] elements = [] with open(geom,'r') as f: Natom = int(next(f)) next(f) for line in f: arr = line.split() sym.append(arr[0]) x.append(float(arr[1])) y.append(float(arr[2])) z.append(float(arr[3])) for index,element in enumerate(sym): if sym[index] != sym[index-1]: elements.append(element) with open("in.gen", 'w') as f: types = "" if a1 != 0: types += "S" else: types += "C" print("{} {}".format(Natom,types),file=f) for i in elements: print(i, end=' ',file=f) print("",file=f) indx = 1 sindx = 0 sym_indx = [] for i,symbol in enumerate(sym): if sym[i] != sym[i-1]: sindx+=1 sym_indx.append(sindx) else: sindx+=0 sym_indx.append(sindx) for sym_indx,i,j,k in zip(sym_indx,x,y,z): print(indx,sym_indx,i,j,k,file=f) indx+=1 if 'S' in types: print("0 0 0",file=f) print("{} {} {}".format(a1,a2,a3),file=f) print("{} {} {}".format(b1,b2,b3),file=f) print("{} {} {}".format(c1,c2,c3),file=f) def poscar2gen(geom): sym = [] a = [] b = [] c = [] x = [] y = [] z = [] coord_type = [] with open(geom, 'r') as f: next(f) next(f) acell = next(f).split() bcell = next(f).split() ccell = next(f).split() a.append(acell) b.append(bcell) c.append(ccell) next(f) next(f) if 'direct' in next(f): coord_type.append("F") else: coord_type.append("S") for line in f: arr = line.split() x.append(arr[0]) y.append(arr[1]) z.append(arr[2]) sym.append(arr[3]) with open('in.gen','w') as f: elements = [] print("{} {}".format(len(sym),coord_type[-1]),file=f) for index,element in enumerate(sym): if sym[index] != sym[index-1]: elements.append(element) for i in elements: print(i, end=' ',file=f) print("",file=f) indx = 1 sindx = 0 sym_indx = [] for i,symbol in enumerate(sym): if sym[i] != sym[i-1]: sindx+=1 sym_indx.append(sindx) else: sindx+=0 sym_indx.append(sindx) for sym_indx,i,j,k in zip(sym_indx,x,y,z): print(indx,sym_indx,i,j,k,file=f) indx+=1 if 'S' or 'F' in coord_type: print("0 0 0",file=f) print("{} {} {}".format(a[0][0],a[0][1],a[0][2]),file=f) print("{} {} {}".format(b[0][0],b[0][1],b[0][2]),file=f) print("{} {} {}".format(c[0][0],c[0][1],c[0][2]),file=f) def vasp2gen(geom): sym = [] a = [] b = [] c = [] x = [] y = [] z = [] coord_type = [] with open(geom, 'r') as f: next(f) next(f) acell = next(f).split() bcell = next(f).split() ccell = next(f).split() a.append(acell) b.append(bcell) c.append(ccell) next(f) next(f) # next(f) if 'direct' in next(f): coord_type.append("F") else: coord_type.append("S") for line in f: arr = line.split() x.append(arr[0]) y.append(arr[1]) z.append(arr[2]) sym.append(arr[3]) with open('in.gen','w') as f: elements = [] print("{} {}".format(len(sym),coord_type[-1]),file=f) if len(list(set(sym))) == 1: for i in list(set(sym)): elements.append(i) else: for index,element in enumerate(sym): sym[index] != sym[index-1] elements.append(element) for i in elements: print(i, end=' ',file=f) print("",file=f) indx = 1 sindx = 0 sym_indx = [] for i,symbol in enumerate(sym): if len(set(sym)) == 1: sindx=1 sym_indx.append(sindx) else: if sym[i] != sym[i-1]: sindx+=1 sym_indx.append(sindx) else: sindx+=0 sym_indx.append(sindx) for sym_indx,i,j,k in zip(sym_indx,x,y,z): print(indx,sym_indx,i,j,k,file=f) indx+=1 if 'S' or 'F' in coord_type: print("0 0 0",file=f) print("{} {} {}".format(a[0][0],a[0][1],a[0][2]),file=f) print("{} {} {}".format(b[0][0],b[0][1],b[0][2]),file=f) print("{} {} {}".format(c[0][0],c[0][1],c[0][2]),file=f) def dftb(geom,job,activeatoms,method,parapath,dispersion,kpts,hcorr): elements = "" coord_type = "" if '.gen' in geom: with open(geom,'r') as f: arr = next(f).split() coord_type+=arr[1] elements+=next(f) elements = elements.split() if '.xyz' in geom: sym = [] elements = [] with open(geom,'r') as f: next(f) next(f) for line in f: arr = line.split() sym.append(arr[0]) for i in set(sym): elements.append(i) with open ("cmmd.in",'w') as f: if '.gen' in geom: print("""Geometry = GenFormat {{ <<< {} }}""".format(geom),file=f) if '.xyz' in geom: print("""Geometry = xyzFormat {{ <<< {} }}""".format(geom),file=f) if job == 'opt': print("""Driver = ConjugateGradient {{ MovedAtoms = {} MaxForceComponent = 1e-4 MaxSteps = 1000 OutputPrefix = "cmmd" """.format(activeatoms),file=f) print('}',file=f) if job == 'optcell': print("""Driver = ConjugateGradient {{ MovedAtoms = {} MaxForceComponent = 1e-4 MaxSteps = 1000 LatticeOpt = Yes OutputPrefix = "cmmd" """.format(activeatoms),file=f) print('}',file=f) if method == 'XTB1': kpts = kpts.split('x') shift = 0 if int(kpts[0])%2 == 0: shift+=0.5 else: shift +=0 print("""Hamiltonian = xTB {{ Method = "GFN1-xTB" kPointsAndWeights = SuperCellFolding{{ {} 0 0 0 {} 0 0 0 {} {} {} {} }} }}""".format(kpts[0],kpts[1],kpts[2],shift,shift,shift),file=f) else: print("Hamiltonian = DFTB {",file=f) if method == 'DFTB2': print("scc = Yes",file=f) print("MaxSCCIterations = 1000",file=f) if method == 'DFTB3diag': print("""scc = Yes ThirdOrder = Yes MaxSCCIterations = 1000 """,file=f) if method == 'DFTB3': print("""scc = Yes ThirdOrderFull = Yes """,file=f) ## Koreksi ikatan hidrogen hdamp = { 'DFTB3': '4.0', 'DFTB3diag': '4.95', 'DFTB2': '4.5' } if hcorr == 'hdamp': print("""HCorrection = Damping {{ Exponent = {} }}""".format(hdamp[method]),file=f) if hcorr == 'H5': print("""HCorrection = H5{ }""",file=f) if dispersion == 'D3': print("""Dispersion = DftD3 { Damping = ZeroDamping { sr6 = 0.7461 alpha6 = 14.0 } s6 = 1.0 s8 = 3.209 }""",file=f) if dispersion == 'D3BJ': print("""Dispersion = DftD3 { Damping = BeckeJohnson { a1 = 0.5719 a2 = 3.6017 } s6 = 1.0 s8 = 0.5883 }""",file=f) if dispersion == 'D3H5': print("""Dispersion = DftD3{ Damping = ZeroDamping{ sr6 = 1.25 alpha6 = 29.61 } s6 = 1.0 s8 = 0.49 HHRepulsion = Yes }""",file=f) print("""SlaterKosterFiles = Type2FileNames {{ Prefix = {}/ Separator = "-" Suffix = ".skf" """.format(parapath),file=f) print('}',file=f) # Mapping bilangan kuantum azimuth ke penamaan orbital azi2orb = {'1':'s','2':'p','3':'d','4':'f'} print("MaxAngularMomentum {",file=f) for element in elements: print("""{} = "{}" """.format(element,azi2orb[azimuth(element)]),file=f) print("}",file=f) if method == 'DFTB3': print("HubbardDerivs {",file=f) for element in elements: print("""{} = {}""".format(element,hubbard(element)),file=f) print("}",file=f) # Informasi K-points kpts = kpts.split('x') shift = 0 if int(kpts[0])%2 == 0: shift+=0.5 else: shift +=0 # if 'F' or 'S' in coord_type: if '.gen' in geom: print("""KPointsAndWeights = SuperCellFolding {{ {} 0 0 0 {} 0 0 0 {} {} {} {} }}""".format(kpts[0],kpts[1],kpts[2],shift,shift,shift),file=f) print("}", file=f) if job == 'dos': print("Analysis {",file=f) print(" ProjectStates {",file=f) for element in elements: print("""Region {{ Atoms = {} ShellResolved = Yes Label = "dos_{}" }}""".format(element,element),file=f) print(" }",file=f) print("}",file=f) print("""ParserOptions { ParserVersion = 7 }""",file=f)