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https://github.com/LCPQ/QUESTDB_website.git
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309 lines
10 KiB
Python
309 lines
10 KiB
Python
from collections import OrderedDict
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from TexSoup import TexSoup
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from .LaTeX import newCommand
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from .utils import getValFromCell,checkFloat
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from TexSoup import TexNode
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from enum import IntEnum,auto,unique,IntFlag
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from .Format import Format
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import re
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import numpy as np
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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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@property
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def IsTBE(self):
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return self.method.name=="TBE"
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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,default=dataType.ABS,firstState=state(1,1,"A_1"),commands=[]):
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tmplst=[]
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for TexState in StateTablelist:
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math=TexState.find("$")
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lst=list(math.contents)
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mystr=str(lst[0])
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mathsoup=None
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try:
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mathsoup=TexSoup(mystr)
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except:
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print(f"Error when parsing latex state: {mystr}")
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exit(-1)
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newCommand.runAll(mathsoup,commands)
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st=str(mathsoup)
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m=re.match(r"^\^(?P<multiplicity>\d)(?P<symm>[^\s\[(]*)\s*(?:\[(?:\\mathrm{)?(?P<special>\w)(?:})\])?\s*(:?\((?P<type>[^\)]*)\))?",st)
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seq=m.group("multiplicity","symm")
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spgrp=m.group("special")
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if spgrp is not None and spgrp=="F":
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trsp=dataType.FLUO
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else:
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trsp=default
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tygrp=m.group("type")
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tmplst.append((*seq,trsp,tygrp))
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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]),item[2],item[3]))
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return lst
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@staticmethod
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def readFromTable(table,format=Format.LINE,default=dataType.ABS ,firstState=state(1,1,"A_1"),commands=[]):
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def getSubtableIndex(table):
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subtablesindex=list()
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firstindex=2
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for i in range(3,np.size(table,0)):
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if str(table[i,0])!="":
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subtablesindex.append((firstindex,i-1))
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firstindex=i
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subtablesindex.append((firstindex,np.size(table,0)))
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return subtablesindex
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datalist=list()
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switcher={
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dataType.ABS:AbsDataFile,
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dataType.FLUO:FluoDataFile,
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dataType.ZPE:ZPEDataFile
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}
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if format==Format.LINE:
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for col in range(1,np.size(table,1)):
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col=table[:,col]
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mymolecule=str(col[0])
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mymethod=method(str(col[2]),str(col[1]))
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finsts=dataFileBase.convertState(table[3:,0],default=default,firstState=firstState,commands=commands)
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datacls=dict()
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for index,cell in enumerate(col[3:]):
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if str(cell)!="":
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val,unsafe=getValFromCell(cell)
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finst=finsts[index]
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dt=finst[1]
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if dt in datacls:
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data=datacls[dt]
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else:
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cl=switcher[dt]
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data=cl()
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datacls[dt]=data
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data.molecule=mymolecule
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data.method=mymethod
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data.excitations.append(excitationValue(firstState,finst[0],val,type=finst[2],isUnsafe=unsafe))
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for value in datacls.values():
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datalist.append(value)
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return datalist
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elif format==Format.COLUMN:
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subtablesindex=getSubtableIndex(table)
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for first, last in subtablesindex:
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for col in range(2,np.size(table,1)):
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datacls=dict()
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col=table[:,col]
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mymolecule=str(table[first,0])
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mymethod=method(str(col[1]),str(col[0]))
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finsts=dataFileBase.convertState(table[first:last+1,1],default=default,firstState=firstState,commands=commands)
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for index,cell in enumerate(col[first:last+1]):
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if str(cell)!="":
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val,unsafe=getValFromCell(cell)
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finst=finsts[index]
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dt=finst[1]
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if dt in datacls:
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data=datacls[dt]
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else:
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cl=switcher[dt]
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data=cl()
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data.molecule=mymolecule
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data.method=mymethod
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datacls[dt]=data
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data.excitations.append(excitationValue(firstState,finst[0],val,type=finst[2]))
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for value in datacls.values():
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datalist.append(value)
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return datalist
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elif format==Format.TBE:
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subtablesindex=getSubtableIndex(table)
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for first, last in subtablesindex:
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datacls=dict()
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mymolecule=str(table[first,0])
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mymethod=(method("TBE(FC)"),method("TBE"))
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finsts=dataFileBase.convertState(table[first:last+1,1],default=default,firstState=firstState,commands=commands)
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for index,row in enumerate(table[first:last+1,]):
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oscilatorForces=checkFloat(str(row[2]))
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T1 = checkFloat(str(row[3]))
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val,unsafe = getValFromCell(row[4])
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corr,unsafecorr = getValFromCell(row[7])
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finst=finsts[index]
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dt=finst[1]
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if dt in datacls:
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datamtbe = datacls[dt]
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else:
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cl=switcher[dt]
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datamtbe=[]
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for met in mymethod:
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data=cl()
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data.molecule=mymolecule
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data.method=met
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datamtbe.append(data)
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datacls[dt]=datamtbe
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vs=[val,corr]
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uns=[unsafe,unsafecorr]
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for i in range(2):
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datamtbe[i].excitations.append(excitationValue(firstState,finst[0],vs[i],type=finst[2],T1=T1,forces=oscilatorForces,isUnsafe=uns[i]))
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for value in datacls.values():
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for dat in value:
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datalist.append(dat)
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return datalist
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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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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)
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file=subpath/fileName
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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 Transition Energies (eV) %T1 Oscilator forces unsafe
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####################### ####################### ######################################## ############# ####### ################### ##############
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# Number Spin Symm Number Spin Symm type E_{:5s} %T1 f is unsafe\n""".format(self.GetFileType().name.lower()))
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for ex in self.excitations:
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mystr=" {:8s}{:7s}{:10s}{:8s}{:6s}{:13s}{:40s}{:14s}{:15s}{:13s}{}\n".format(
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str(ex.initial.number),
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str(ex.initial.multiplicity),
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ex.initial.symetry,
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str(ex.final.number),
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str(ex.final.multiplicity),
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ex.final.symetry,"("+str(ex.type)+")" if ex.type is not None else "_",
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str(ex.value) if ex.value is not None else "_",
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str(ex.T1) if ex.T1 is not None else "_",
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str(ex.oscilatorForces) if ex.oscilatorForces is not None else "_",
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str(ex.isUnsafe).lower())
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f.write(mystr)
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class method:
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def __init__(self,name, *args):
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self.name = name
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self.basis=args[0] if len(args)>0 else None
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@staticmethod
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def fromString(string):
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vals = string.split(",")
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return method(*vals)
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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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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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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, **kwargs):
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self.initial = initial
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self.final = final
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self.type = kwargs["type"] if "type" in kwargs else None
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self.T1 = kwargs["T1"] if "T1" in kwargs else None
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self.isUnsafe = kwargs["isUnsafe"] if "isUnsafe" in kwargs else False
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class excitationValue(excitationBase):
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def __init__(self,initial, final, value,**kwarg):
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supkwarg=kwarg.copy()
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for item in ["forces","corrected"]:
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if item in supkwarg:
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supkwarg.pop(item)
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super(excitationValue,self).__init__(initial, final,**supkwarg)
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self.value = value
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self.oscilatorForces=kwarg["forces"] if "forces" in kwarg else None
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