mirror of
https://github.com/LCPQ/QUESTDB_website.git
synced 2024-08-27 14:41:50 +02:00
440 lines
16 KiB
Python
440 lines
16 KiB
Python
from collections import OrderedDict
|
|
from TexSoup import TexSoup
|
|
from .LaTeX import newCommand
|
|
from .utils import getValFromCell,checkFloat
|
|
from TexSoup import TexNode,TexEnv
|
|
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()
|
|
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)
|
|
mystr=str(lst[0])
|
|
mathsoup=None
|
|
try:
|
|
mathsoup=TexSoup(mystr)
|
|
except:
|
|
print(f"Error when parsing latex state: {mystr}")
|
|
exit(-1)
|
|
newCommand.runAll(mathsoup,commands)
|
|
st=str(mathsoup)
|
|
m=re.match(r"^\^(?P<multiplicity>\d)(?P<symm>[^\s\[(]*)\s*(?:\[(?:\\mathrm{)?(?P<special>\w)(?:})\])?\s*(:?\((?P<type>[^\)]*)\))?",st)
|
|
seq=m.group("multiplicity","symm")
|
|
mul=int(m.group("multiplicity"))
|
|
symm=m.group("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((mul,symm,trsp,tygrp))
|
|
lst=[]
|
|
for index,item in enumerate(tmplst):
|
|
unformfirststate=(firstState.multiplicity,firstState.symetry)
|
|
countlst=[unformfirststate]+[(it[0],it[1]) for it in tmplst[:index+1]]
|
|
countitem=(item[0],item[1])
|
|
count=countlst.count(countitem)
|
|
lst.append((state(count,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=[]):
|
|
def getSubtableIndex(table,firstindex=2,column=0,count=1):
|
|
subtablesindex=list()
|
|
i=firstindex+count
|
|
while i<np.size(table,0):
|
|
if str(table[i,column])!="":
|
|
subtablesindex.append((firstindex,i-1))
|
|
firstindex=i
|
|
i+=count
|
|
else:
|
|
i+=1
|
|
subtablesindex.append((firstindex,np.size(table,0)))
|
|
return subtablesindex
|
|
|
|
datalist=list()
|
|
switcher={
|
|
dataType.ABS:AbsDataFile,
|
|
dataType.FLUO:FluoDataFile,
|
|
}
|
|
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],default=default,firstState=firstState,commands=commands)
|
|
datacls=dict()
|
|
for index,cell in enumerate(col[3:]):
|
|
if str(cell)!="":
|
|
val,unsafe=getValFromCell(cell)
|
|
finst=finsts[index]
|
|
dt=finst[1]
|
|
if dt in datacls:
|
|
data=datacls[dt]
|
|
else:
|
|
cl=switcher[dt]
|
|
data=cl()
|
|
datacls[dt]=data
|
|
data.molecule=mymolecule
|
|
data.method=mymethod
|
|
data.excitations.append(excitationValue(firstState,finst[0],val,type=finst[2],isUnsafe=unsafe))
|
|
for value in datacls.values():
|
|
datalist.append(value)
|
|
return datalist
|
|
elif format==Format.COLUMN:
|
|
subtablesindex=getSubtableIndex(table)
|
|
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,unsafe=getValFromCell(cell)
|
|
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.DOUBLECOLUMN:
|
|
datacls=dict()
|
|
subtablesMol=getSubtableIndex(table)
|
|
for firstMol, lastMol in subtablesMol:
|
|
mymolecule=str(table[firstMol,0])
|
|
moltable=table[firstMol:lastMol+1,:]
|
|
subtablestrans=getSubtableIndex(moltable,firstindex=0,column=1,count=2)
|
|
for firstTrans,lastTrans in subtablestrans:
|
|
mytrans=moltable[firstTrans:lastTrans+1,:]
|
|
mytransdesc=mytrans[0:2,1]
|
|
for i in range(2):
|
|
try:
|
|
mathsoup=TexSoup(mytransdesc[i])
|
|
except:
|
|
print(f"Error when parsing latex state: {str(mytransdesc[i])}")
|
|
exit(-1)
|
|
newCommand.runAll(mathsoup,commands)
|
|
mytransdesc[i]=str(mathsoup)
|
|
for colindex in range(3,np.size(table,1)):
|
|
col=mytrans[:,colindex]
|
|
mybasis=str(table[1,colindex])
|
|
for index,cell in enumerate(col):
|
|
methodnameAT1=str(mytrans[index,2])
|
|
PTString=r"($\%T_1$)"
|
|
HasT1=methodnameAT1.endswith(PTString)
|
|
if HasT1:
|
|
methodname=methodnameAT1[:-len(PTString)]
|
|
else:
|
|
methodname=str(methodnameAT1)
|
|
mymethod=method(methodname,mybasis)
|
|
strcell=str(cell)
|
|
if strcell!="":
|
|
if HasT1:
|
|
m=re.match(r"^(?P<value>[-+]?\d+\.?\d*)\s*(?:\((?P<T1>\d+\.?\d*)\\\%\))?",strcell)
|
|
val,unsafe=getValFromCell(TexSoup(m.group("value")))
|
|
T1=m.group("T1")
|
|
else:
|
|
m=re.match(r"^[-+]?\d+\.?\d*",strcell)
|
|
val,unsafe=getValFromCell(TexSoup(m.group(0)))
|
|
T1=None
|
|
if (mymolecule,mymethod.name,mymethod.basis) in datacls:
|
|
data=datacls[(mymolecule,mymethod.name,mymethod.basis)]
|
|
else:
|
|
data=AbsDataFile()
|
|
data.molecule=mymolecule
|
|
data.method=mymethod
|
|
datacls[(mymolecule,mymethod.name,mymethod.basis)]=data
|
|
infin=mytransdesc[0].split(r"\rightarrow")
|
|
for i,item in enumerate(infin):
|
|
m=re.match(r"^(?P<number>\d)\\[,:;\s]\s*\^(?P<multiplicity>\d)(?P<sym>\S*)",item.strip())
|
|
infin[i]=state(m.group("number"),m.group("multiplicity"),m.group("sym"))
|
|
data.excitations.append(excitationValue(infin[0],infin[1],val,type=mytransdesc[1],isUnsafe=unsafe,T1=T1))
|
|
for value in datacls.values():
|
|
datalist.append(value)
|
|
return datalist
|
|
elif format==Format.EXOTICCOLUMN:
|
|
import json
|
|
subtablesindex=getSubtableIndex(table)
|
|
for first, last in subtablesindex:
|
|
valDic=dict()
|
|
mymolecule=str(table[first,0])
|
|
for col in range(2,np.size(table,1)):
|
|
col=table[:,col]
|
|
basis=str(col[0])
|
|
mymethcell=list(col[1])
|
|
if isinstance(mymethcell[0],TexNode) and mymethcell[0].name=="$":
|
|
kindSoup=TexSoup("".join(list(mymethcell[0].expr.all)))
|
|
newCommand.runAll(kindSoup,commands)
|
|
kind=str(kindSoup)
|
|
methodnameSoup=TexSoup(mymethcell[1].value)
|
|
newCommand.runAll(methodnameSoup,commands)
|
|
methodname=str(methodnameSoup)
|
|
else:
|
|
kind=""
|
|
methtex=col[1]
|
|
newCommand.runAll(methtex,commands)
|
|
methodname=str(methtex)
|
|
mymethod=method(methodname,basis)
|
|
methkey=json.dumps(mymethod.__dict__)
|
|
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,unsafe=getValFromCell(cell)
|
|
finst=finsts[index]
|
|
dt=finst[1]
|
|
if dt in valDic:
|
|
dtDic=valDic[dt]
|
|
else:
|
|
dtDic=dict()
|
|
valDic[dt]=dtDic
|
|
if not methkey in dtDic:
|
|
dtDic[methkey]=dict()
|
|
dataDic=dtDic[methkey]
|
|
exkey=(json.dumps(finst[0].__dict__,),finst[2])
|
|
if not exkey in dataDic:
|
|
dataDic[exkey]=dict()
|
|
if kind=='':
|
|
dataDic[exkey][kind]=(val,unsafe)
|
|
else:
|
|
dataDic[exkey][kind]=val
|
|
#data.excitations.append(excitationValue(firstState,finst[0],val,type=finst[2]))
|
|
for dt,methdic in valDic.items():
|
|
for methstring,exdic in methdic.items():
|
|
data=switcher[dt]()
|
|
data.molecule=mymolecule
|
|
methdic=json.loads(methstring)
|
|
data.method=method(methdic["name"],methdic["basis"])
|
|
for exstr,values in exdic.items():
|
|
stDict=json.loads(exstr[0])
|
|
ty=exstr[1]
|
|
st=state(stDict["number"],stDict["multiplicity"],stDict["symetry"])
|
|
T1=values["\\%T_1"] if "\\%T_1" in values else None
|
|
oF= values["f"] if "f" in values else None
|
|
unsafe,val=values[""]
|
|
data.excitations.append(excitationValue(firstState,st,val,type=ty,T1=T1,isUnsafe=unsafe,oscilatorForces=oF))
|
|
datalist.append(data)
|
|
return datalist
|
|
elif format==Format.TBE:
|
|
subtablesindex=getSubtableIndex(table)
|
|
for first, last in subtablesindex:
|
|
datacls=dict()
|
|
mymolecule=str(table[first,0])
|
|
mymethod=(method("TBE(FC)"),method("TBE"))
|
|
finsts=dataFileBase.convertState(table[first:last+1,1],default=default,firstState=firstState,commands=commands)
|
|
for index,row in enumerate(table[first:last+1,]):
|
|
oscilatorForces=checkFloat(str(row[2]))
|
|
T1 = checkFloat(str(row[3]))
|
|
val,unsafe = getValFromCell(row[4])
|
|
corr,unsafecorr = getValFromCell(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]
|
|
uns=[unsafe,unsafecorr]
|
|
for i in range(2):
|
|
datamtbe[i].excitations.append(excitationValue(firstState,finst[0],vs[i],type=finst[2],T1=T1,oscilatorForces=oscilatorForces,isUnsafe=uns[i]))
|
|
for value in datacls.values():
|
|
for dat in value:
|
|
datalist.append(dat)
|
|
return datalist
|
|
elif format==Format.DOUBLETBE:
|
|
datacls=dict()
|
|
subtablesMol=getSubtableIndex(table)
|
|
for firstMol, lastMol in subtablesMol:
|
|
data=AbsDataFile()
|
|
data.molecule=str(table[firstMol,0])
|
|
data.method=method("TBE","CBS")
|
|
for mytrans in table[firstMol:lastMol+1]:
|
|
try:
|
|
mathsoup=TexSoup(mytrans[1])
|
|
except:
|
|
print(f"Error when parsing latex state: {str(mytransdesc[i])}")
|
|
exit(-1)
|
|
newCommand.runAll(mathsoup,commands)
|
|
mytransdesc=str(mathsoup)
|
|
infin=mytransdesc.split(r"\rightarrow")
|
|
for i,item in enumerate(infin):
|
|
m=re.match(r"^(?P<number>\d)\\[,:;\s]\s*\^(?P<multiplicity>\d)(?P<sym>\S*)",item.strip())
|
|
infin[i]=state(m.group("number"),m.group("multiplicity"),m.group("sym"))
|
|
cell=mytrans[6]
|
|
val,unsafe=getValFromCell(cell)
|
|
data.excitations.append(excitationValue(infin[0],infin[1],val,isUnsafe=unsafe))
|
|
datalist.append(data)
|
|
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,prefix=None):
|
|
subpath=datadir/self.GetFileType().name.lower()
|
|
if not subpath.exists():
|
|
subpath.mkdir()
|
|
molsoup=TexSoup(self.molecule)
|
|
molcomp=list(molsoup.contents)[0]
|
|
molfilename=self.molecule if isinstance(molcomp,str) else molcomp.args[0].value
|
|
molfilename=molfilename.lower().replace(" ","_")
|
|
fileNameComp=[molfilename,self.method.name]
|
|
if self.method.basis:
|
|
fileNameComp.append(self.method.basis)
|
|
if prefix:
|
|
fileNameComp.append(prefix)
|
|
fileName="_".join(fileNameComp)+".dat"
|
|
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=" {:7s} {:5s} {:10s} {:7s} {:5s} {:12s} {:39s} {:13s} {:14s} {: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 excitationBase:
|
|
def __init__(self,initial, final,type=None, T1=None,isUnsafe=False):
|
|
self.initial = initial
|
|
self.final = final
|
|
self.type = type
|
|
self.T1 = T1
|
|
self.isUnsafe = isUnsafe
|
|
|
|
class excitationValue(excitationBase):
|
|
def __init__(self,initial, final, value, type=None, T1=None,isUnsafe=False,oscilatorForces=None):
|
|
super(excitationValue,self).__init__(initial, final,type=type,T1=T1,isUnsafe=False)
|
|
self.value = value
|
|
self.oscilatorForces = oscilatorForces
|