from collections import OrderedDict from TexSoup import TexSoup from .LaTeX import newCommand from enum import IntEnum,auto,unique,IntFlag from .Format import Format import re import numpy as np class state: def __init__(self,number, multiplicity, symetry): self.number = number self.multiplicity = multiplicity self.symetry = symetry @unique class dataType(IntEnum): ABS=auto() FLUO=auto() ZPE=auto() class dataFileBase(object): def __init__(self): self.molecule = '' self.comment = '' self.code = None self.method = None self.excitations = [] self.DOI = '' @property def IsTBE(self): return self.method.name=="TBE" @staticmethod def GetFileType(): pass @staticmethod def convertState(StateTablelist,default=dataType.ABS,firstState=state(1,1,"A_1"),commands=[]): tmplst=[] for TexState in StateTablelist: math=TexState.find("$") lst=list(math.contents) mathsoup=TexSoup(str(lst[0])) newCommand.runAll(mathsoup,commands) st=str(mathsoup) m=re.match(r"^\^(?P\d)(?P[^\s\[(]*)\s*(?:\[(?:\\mathrm{)?(?P\w)(?:})\])?\s*\((?P[^\)]*)\)",st) seq=m.group("multiplicity","symm") spgrp=m.group("special") if spgrp is not None and spgrp=="F": trsp=dataType.FLUO else: trsp=default tygrp=m.group("type") tmplst.append((*seq,trsp,tygrp)) lst=[] for index,item in enumerate(tmplst): unformfirststate=(str(firstState.multiplicity),firstState.symetry) count=([unformfirststate]+tmplst[:index+1]).count(item) lst.append((state(count,int(item[0]),item[1]),item[2],item[3])) return lst @staticmethod def readFromTable(table,format=Format.LINE,default=dataType.ABS ,firstState=state(1,1,"A_1"),commands=[]): datalist=list() switcher={ dataType.ABS:AbsDataFile, dataType.FLUO:FluoDataFile, dataType.ZPE:ZPEDataFile } if format==Format.LINE: for col in range(1,np.size(table,1)): col=table[:,col] mymolecule=str(col[0]) mymethod=method(str(col[2]),str(col[1])) finsts=dataFileBase.convertState(table[3:,0],firstState,commands=commands) datacls=dict() for index,cell in enumerate(col[3:]): if str(cell)!="": val= list(cell.contents)[0] val=float(str(val)) finst=finsts[index] dt=finst[1] if dt in datacls: data=datacls[dt] else: cl=switcher[dt] data=cl() data.molecule=mymolecule data.method=mymethod data.excitations.append(excitationValue(firstState,finst[0],val,type=finst[2],isUnsafe=False)) for datamtbe in datacls.values(): datalist.append(datamtbe) return datalist elif format==Format.COLUMN: subtablesindex=list() firstindex=2 for i in range(3,np.size(table,0)): if str(table[i,0])!="": subtablesindex.append((firstindex,i-1)) firstindex=i for first, last in subtablesindex: for col in range(2,np.size(table,1)): datacls=dict() col=table[:,col] mymolecule=str(table[first,0]) mymethod=method(str(col[1]),str(col[0])) finsts=dataFileBase.convertState(table[first:last+1,1],default=default,firstState=firstState,commands=commands) for index,cell in enumerate(col[first:last+1]): if str(cell)!="": val= list(cell.contents)[0] val=float(str(val)) finst=finsts[index] dt=finst[1] if dt in datacls: data=datacls[dt] else: cl=switcher[dt] data=cl() data.molecule=mymolecule data.method=mymethod datacls[dt]=data data.excitations.append(excitationValue(firstState,finst[0],val,type=finst[2])) for value in datacls.values(): datalist.append(value) return datalist elif format==Format.TBE: subtablesindex=list() firstindex=2 for i in range(3,np.size(table,0)): if str(table[i,0])!="": subtablesindex.append((firstindex,i-1)) firstindex=i for first, last in subtablesindex: datacls=dict() mymolecule=str(table[first,0]) mymethod=(method("TBE"),method("TBE-corr")) finsts=dataFileBase.convertState(table[first:last+1,1],default=default,firstState=firstState,commands=commands) for index,row in enumerate(table[first:last+1,]): def toFloat(x): try: return float(x) except ValueError: return None oscilatorForces=toFloat(str(row[2])) T1 = toFloat(str(row[3])) val = toFloat(str(row[4])) corr = toFloat(str(row[7])) finst=finsts[index] dt=finst[1] if dt in datacls: datamtbe = datacls[dt] else: cl=switcher[dt] datamtbe=[] for met in mymethod: data=cl() data.molecule=mymolecule data.method=met datamtbe.append(data) datacls[dt]=datamtbe vs=[val,corr] for i in range(2): datamtbe[i].excitations.append(excitationValue(firstState,finst[0],vs[i],type=finst[2],T1=T1,forces=oscilatorForces)) for value in datacls.values(): for dat in value: datalist.append(dat) return datalist def getMetadata(self): dic=OrderedDict() dic["Molecule"]=self.molecule dic["Comment"]=self.comment dic["code"]="" if self.code is None else self.code.toDataString() dic["method"]="" if self.method is None else self.method.toDataString() dic["DOI"]="" if self.DOI is None else self.DOI return dic def toFile(self,datadir): subpath=datadir/self.GetFileType().name.lower() if not subpath.exists(): subpath.mkdir() fileName="{}_{}.dat".format(self.molecule.lower().replace(" ","_"),self.method.name) if self.method.basis==None else "{}_{}_{}.dat".format(self.molecule.lower().replace(" ","_"),self.method.name,self.method.basis) file=subpath/fileName if not file.exists(): with file.open("w") as f: for key,value in self.getMetadata().items(): if value is not None: f.write("# {:9s}: {}\n".format(key,value)) f.write(""" # Initial state Final state Transition Energies (eV) %T1 Oscilator forces unsafe ####################### ####################### ######################################## ############# ####### ################### ############## # Number Spin Symm Number Spin Symm type E_{:5s} %T1 f is unsafe\n""".format(self.GetFileType().name.lower())) for ex in self.excitations: mystr=" {:8s}{:7s}{:10s}{:8s}{:6s}{:13s}{:40s}{:14s}{:15s}{:13s}{}\n".format( str(ex.initial.number), str(ex.initial.multiplicity), ex.initial.symetry, str(ex.final.number), str(ex.final.multiplicity), ex.final.symetry,"("+str(ex.type)+")" if ex.type is not None else "_", str(ex.value) if ex.value is not None else "_", str(ex.T1) if ex.T1 is not None else "_", str(ex.oscilatorForces) if ex.oscilatorForces is not None else "_", str(ex.isUnsafe).lower()) f.write(mystr) class method: def __init__(self,name, *args): self.name = name self.basis=args[0] if len(args)>0 else None @staticmethod def fromString(string): vals = string.split(",") return method(*vals) def __str__(self): string = self.name if (self.basis): string+= '/' + self.basis return string def toDataString(self): string=self.name if (self.basis): string+=","+self.basis return string class code: def __init__(self,name, version): self.name = name self.version = version def toDataString(self): string=self.name if (self.version): string+=","+self.version return string class oneStateDataFileBase(dataFileBase): def __init__(self): super(oneStateDataFileBase,self).__init__() self.geometry = None def getMetadata(self): dic=super(oneStateDataFileBase,self).getMetadata() dic["geom"]= "" if self.geometry is None else self.geometry.toDataString() dic.move_to_end("DOI") return dic class AbsDataFile(oneStateDataFileBase): def __init__(self): super(AbsDataFile,self).__init__() @staticmethod def GetFileType(): return dataType.ABS class FluoDataFile(oneStateDataFileBase): def __init__(self): super(FluoDataFile,self).__init__() @staticmethod def GetFileType(): return dataType.FLUO class twoStateDataFileBase(dataFileBase): def __init__(self): super(twoStateDataFileBase,self).__init__() self.GS=None self.ES=None def getMetadata(self): dic=super(twoStateDataFileBase,self).getMetadata() dic["GS"]= "" if self.GS is None else self.GS.toDataString() dic["ES"]="" if self.ES is None else self.ES.toDataString() dic.move_to_end("DOI") return dic class ZPEDataFile(twoStateDataFileBase): def __init__(self): super(ZPEDataFile,self).__init__() @staticmethod def GetFileType(): return dataType.ZPE class excitationBase: def __init__(self,initial, final, **kwargs): self.initial = initial self.final = final self.type = kwargs["type"] if "type" in kwargs else None self.T1 = kwargs["T1"] if "T1" in kwargs else None self.isUnsafe = kwargs["isUnsafe"] if "isUnsafe" in kwargs else False class excitationValue(excitationBase): def __init__(self,initial, final, value,**kwarg): supkwarg=kwarg.copy() for item in ["forces","corrected"]: if item in supkwarg: supkwarg.pop(item) super(excitationValue,self).__init__(initial, final,**supkwarg) self.value = value self.oscilatorForces=kwarg["forces"] if "forces" in kwarg else None