mirror of
https://github.com/LCPQ/QUESTDB_website.git
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185 lines
5.3 KiB
Python
185 lines
5.3 KiB
Python
from collections import OrderedDict
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from enum import IntEnum,auto,unique
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import re
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class state:
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def __init__(self,number, multiplicity, symetry):
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self.number = number
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self.multiplicity = multiplicity
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self.symetry = symetry
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@unique
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class dataType(IntEnum):
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ABS=auto()
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FLUO=auto()
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ZPE=auto()
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class dataFileBase(object):
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def __init__(self):
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self.molecule = ''
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self.comment = ''
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self.code = None
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self.method = None
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self.excitations = []
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self.DOI = ''
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@staticmethod
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def GetFileType():
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pass
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@staticmethod
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def convertState(StateTablelist,firstState=state(1,1,"A_1")):
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tmplst=[]
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for TexState in StateTablelist:
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st=list(TexState.find("$").contents)[0]
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m=re.match(r"^\^(?P<multiplicity>\d)(?P<GPS>\S+)",st)
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seq=m.groups()
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tmplst.append(seq)
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lst=[]
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for index,item in enumerate(tmplst):
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unformfirststate=(str(firstState.multiplicity),firstState.symetry)
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count=([unformfirststate]+tmplst[:index+1]).count(item)
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lst.append(state(count,int(item[0]),item[1]))
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return lst
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@classmethod
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def readFromTable(cls, table,column,firstState=state(1,1,"A_1")):
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data=cls()
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col=table[:,column]
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data.molecule=str(col[0])
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data.method=method(str(col[2]),str(col[1]))
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finsts=cls.convertState(table[3:,0],firstState)
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for index,cell in enumerate(col[3:]):
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if str(cell)!="":
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val= list(cell.contents)[0]
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val=float(str(val))
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data.excitations.append(excitationValue(firstState,finsts[index],val))
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return data
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def getMetadata(self):
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dic=OrderedDict()
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dic["Molecule"]=self.molecule
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dic["Comment"]=self.comment
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dic["code"]="" if self.code is None else self.code.toDataString()
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dic["method"]="" if self.method is None else self.method.toDataString()
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dic["DOI"]="" if self.DOI is None else self.DOI
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return dic
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def toFile(self,datadir):
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subpath=datadir/self.GetFileType().name.lower()
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if not subpath.exists():
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subpath.mkdir()
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file=subpath/"{}_{}_{}.dat".format(self.molecule.lower().replace(" ","_"),self.method.name,self.method.basis)
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if not file.exists():
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with file.open("w") as f:
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for key,value in self.getMetadata().items():
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if value is not None:
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f.write("# {:9s}: {}\n".format(key,value))
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f.write("""
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# Initial state Final state Energies (eV)
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####################### ####################### ###############
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# Spin Number Symm Spin Number Symm E_{}\n""".format(self.GetFileType().name.lower()))
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for ex in self.excitations:
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mystr=" {:6s}{:9s}{:10s}{:6s}{:8s}{: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.value))
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f.write(mystr)
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class method:
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def __init__(self,name, basis):
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self.name = name
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self.basis = basis
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@staticmethod
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def fromString(string):
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vals = string.split(",")
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if (vals.length == 2):
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return method(vals[0], vals[1])
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else:
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return method(vals[0], None)
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def __str__(self):
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string = self.name
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if (self.basis):
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string+= '/' + self.basis
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return string
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def toDataString(self):
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string=self.name
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if (self.basis):
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string+=","+self.basis
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return string
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class code:
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def __init__(self,name, version):
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self.name = name
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self.version = version
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def toDataString(self):
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string=self.name
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if (self.version):
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string+=","+self.version
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return string
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class oneStateDataFileBase(dataFileBase):
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def __init__(self):
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super(oneStateDataFileBase,self).__init__()
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self.geometry = None
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def getMetadata(self):
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dic=super(oneStateDataFileBase,self).getMetadata()
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dic["geom"]= "" if self.geometry is None else self.geometry.toDataString()
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dic.move_to_end("DOI")
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return dic
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@classmethod
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def readFromTable(cls, table,column,firstState=state(1,1,"A_1")):
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data=super().readFromTable(table,column,firstState=firstState)
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return data
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class AbsDataFile(oneStateDataFileBase):
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def __init__(self):
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super(AbsDataFile,self).__init__()
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@staticmethod
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def GetFileType():
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return dataType.ABS
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class FluoDataFile(oneStateDataFileBase):
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def __init__(self):
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super(FluoDataFile,self).__init__()
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@staticmethod
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def GetFileType():
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return dataType.FLUO
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class twoStateDataFileBase(dataFileBase):
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def __init__(self):
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super(twoStateDataFileBase,self).__init__()
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self.GS=None
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self.ES=None
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@classmethod
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def readFromTable(cls, table,column,firstState=state(1,1,"A_1")):
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data=super().readFromTable(table,column,firstState=firstState)
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return data
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def getMetadata(self):
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dic=super(twoStateDataFileBase,self).getMetadata()
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dic["GS"]= "" if self.GS is None else self.GS.toDataString()
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dic["ES"]="" if self.ES is None else self.ES.toDataString()
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dic.move_to_end("DOI")
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return dic
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class ZPEDataFile(twoStateDataFileBase):
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def __init__(self):
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super(ZPEDataFile,self).__init__()
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@staticmethod
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def GetFileType():
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return dataType.ZPE
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class excitationBase:
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def __init__(self,initial, final):
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self.initial = initial
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self.final = final
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class excitationValue(excitationBase):
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def __init__(self,initial, final, value):
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super(excitationValue,self).__init__(initial, final)
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self.value = value |