mirror of
https://github.com/LCPQ/QUESTDB_website.git
synced 2024-11-04 21:24:00 +01:00
309 lines
10 KiB
Python
309 lines
10 KiB
Python
from collections import OrderedDict
|
|
from TexSoup import TexSoup
|
|
from .LaTeX import newCommand
|
|
from .utils import getValFromCell,checkFloat
|
|
from TexSoup import TexNode
|
|
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)
|
|
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")
|
|
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=[]):
|
|
def getSubtableIndex(table):
|
|
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
|
|
subtablesindex.append((firstindex,np.size(table,0)))
|
|
return subtablesindex
|
|
|
|
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],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.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,forces=oscilatorForces,isUnsafe=uns[i]))
|
|
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
|