mirror of
https://github.com/LCPQ/QUESTDB_website.git
synced 2024-12-26 06:14:38 +01:00
331 lines
10 KiB
Python
331 lines
10 KiB
Python
from collections import OrderedDict
|
|
from TexSoup import TexSoup
|
|
from .LaTeX import newCommand,extractMath
|
|
from .utils import getValFromCell,checkFloat
|
|
from TexSoup import TexNode,TexEnv
|
|
from enum import IntEnum,auto,unique,IntFlag
|
|
from .formats import getFormatHandlers
|
|
import re
|
|
import os
|
|
import numpy as np
|
|
import json
|
|
|
|
class state:
|
|
def __init__(self,number, multiplicity, symmetry):
|
|
self.number = number
|
|
self.multiplicity = multiplicity
|
|
self.symmetry = symmetry
|
|
@staticmethod
|
|
def fromString(string):
|
|
m=re.match(r"^(?P<number>\d)\s*\^(?P<multiplicity>\d)(?P<sym>\S*)",string)
|
|
num=m.group('number')
|
|
mul=m.group('multiplicity')
|
|
sym=m.group('sym')
|
|
return state(num,mul,sym)
|
|
@unique
|
|
class DataType(IntEnum):
|
|
ABS=auto()
|
|
FLUO=auto()
|
|
|
|
def datafileSelector(dataType):
|
|
switcher={
|
|
DataType.ABS:AbsDataFile,
|
|
DataType.FLUO:FluoDataFile,
|
|
}
|
|
return switcher[dataType]
|
|
|
|
def getSubtablesRange(table,firstindex=2,column=0,count=1):
|
|
subtablesRange=list()
|
|
i=firstindex+count
|
|
while i<np.size(table,0):
|
|
if str(table[i,column])!="":
|
|
subtablesRange.append(range(firstindex,i))
|
|
firstindex=i
|
|
i+=count
|
|
else:
|
|
i+=1
|
|
subtablesRange.append(range(firstindex,np.size(table,0)))
|
|
return subtablesRange
|
|
|
|
class exSet(object):
|
|
def __init__(self,name,index=0):
|
|
self.name=name
|
|
self.index=index
|
|
|
|
def __str__(self):
|
|
return f"{self.name},{self.index}"
|
|
|
|
@staticmethod
|
|
def fromString(string):
|
|
vals = string.split(",")
|
|
if len(vals)>1:
|
|
return exSet(vals[0],int(vals[1]))
|
|
else:
|
|
return exSet(vals[0])
|
|
|
|
def getDOI(self):
|
|
import yaml
|
|
from pathlib import Path
|
|
yamlpath=Path(__file__)/"../../statics/data/index.yaml"
|
|
with yamlpath.open("r") as f:
|
|
db = yaml.load(f,yaml.loader.FullLoader)
|
|
sets=db["sets"]
|
|
if self.name in db["sets"]:
|
|
return sets[self.name][self.index]
|
|
|
|
def isSameSet(self,otherSet):
|
|
return self.name == otherSet.name
|
|
|
|
def isSameArticle(self,otherSet):
|
|
if (self.name==otherSet.name and self.index==otherSet.index):
|
|
return True
|
|
else:
|
|
return self.getDOI() == self.getDOI()
|
|
|
|
class dataFileBase(object):
|
|
def __init__(self):
|
|
self.molecule = ''
|
|
self.comment = ''
|
|
self.code = None
|
|
self.method = None
|
|
self.excitations = []
|
|
self.set = ''
|
|
|
|
@property
|
|
def IsTBE(self):
|
|
return self.method.name=="TBE"
|
|
|
|
@staticmethod
|
|
def GetFileType():
|
|
pass
|
|
|
|
@staticmethod
|
|
def convertState(StateTablelist,initialState,default=DataType.ABS,commands=[]):
|
|
tmplst=[]
|
|
for TexState in StateTablelist:
|
|
st=str(extractMath(TexState,Soup=True,commands=commands))
|
|
m=re.match(r"^\^(?P<multiplicity>\d)(?P<symm>[^\s\[(]*)\s*(?:\[(?:\\mathrm{)?(?P<special>\w)(?:})\])?\s*(:?\((?P<type>[^\)]*)\))?",st)
|
|
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):
|
|
unforminitialstate=(int(initialState.multiplicity),initialState.symmetry)
|
|
countlst=[unforminitialstate]+[(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
|
|
def _OnReadMetaPair(self, key, value):
|
|
if key == "molecule":
|
|
self.molecule = value
|
|
elif key == "comment":
|
|
self.comment = value
|
|
elif key == "code":
|
|
self.code = code.fromString(value)
|
|
elif key == "method":
|
|
self.method = method.fromString(value)
|
|
elif key == "set":
|
|
self.set = exSet.fromString(value)
|
|
|
|
@staticmethod
|
|
def readFromTable(table,TexOps, commands=[]):
|
|
for formatName,Cls in getFormatHandlers():
|
|
if formatName.lower()==TexOps.format.lower():
|
|
handler=Cls(TexOps,commands)
|
|
break
|
|
else:
|
|
raise ValueError()
|
|
return handler.readFromTable(table)
|
|
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["set"]="" if self.set is None else self.set
|
|
return dic
|
|
|
|
def _OnReadMeta(self,line,dataType):
|
|
#get key value
|
|
match = dataFileBase._GetMetaRexEx().match(line)
|
|
# normalize key to lower
|
|
key = match.group(1).lower()
|
|
# if data has value
|
|
if match.group(2):
|
|
val = match.group(2)
|
|
self._OnReadMetaPair(key, val)
|
|
@staticmethod
|
|
def _OnReadRow(line):
|
|
vals = re.findall(r"\([^\)]+\)|\S+",line)
|
|
start = state(int(vals[0]), int(vals[1]), vals[2])
|
|
end = state(int(vals[3]), int(vals[4]), vals[5])
|
|
Type = vals[6] if (len(vals) >= 7) else None
|
|
if Type == "_":
|
|
Type = None
|
|
if Type:
|
|
m = re.match(r"^\(([^\)]*)\)$",Type)
|
|
if m:
|
|
Type = m[1]
|
|
val = vals[7] if len(vals) >= 8 else str(np.NaN)
|
|
T1 = vals[8] if len(vals) >= 9 else str(np.NaN)
|
|
oscilatorForces = vals[9] if len(vals) >= 10 else str(np.NaN)
|
|
isUnsafe = vals[10] == json.dumps(True) if len(vals) >= 11 else False
|
|
ex = excitationValue(start, end, val, Type,T1,isUnsafe,oscilatorForces)
|
|
return ex
|
|
|
|
@staticmethod
|
|
def _GetMetaRexEx():
|
|
#metadata RegExp (start with #; maybe somme spaces; : ; maybe somme space; datas)
|
|
return re.compile(r"^#\s*([A-Za-z_]+)\s*:\s*(.*)$")
|
|
|
|
@staticmethod
|
|
def readFile(stream,dataType):
|
|
lines = stream.readlines()
|
|
# for each line with metadata
|
|
ismetaArea = True
|
|
dat = datafileSelector(dataType)()
|
|
for line in lines:
|
|
#if it's not empty line
|
|
line = line.strip()
|
|
if line:
|
|
# if # may be metadata or comment
|
|
if line[0] == "#":
|
|
# if it's metadata
|
|
if ismetaArea and dataFileBase._GetMetaRexEx().match(line):
|
|
dat._OnReadMeta(line,dataType)
|
|
else: # else its row
|
|
ismetaArea = False
|
|
dat.excitations.append(dat._OnReadRow(line))
|
|
return dat
|
|
|
|
def toFile(self,datadir,suffix=None):
|
|
subpath=datadir/self.GetFileType().name.lower()
|
|
if not subpath.exists():
|
|
os.makedirs(str(subpath))
|
|
molsoup=TexSoup(self.molecule)
|
|
molcomp=list(molsoup.contents)[0]
|
|
molfilename=self.molecule if isinstance(molcomp,str) else molcomp.args[0].value
|
|
molfilename=molfilename.lower()
|
|
fileNameComp=[molfilename,self.method.name]
|
|
if self.method.basis:
|
|
fileNameComp.append(self.method.basis)
|
|
if suffix:
|
|
fileNameComp.append(suffix)
|
|
fileName="_".join(fileNameComp).replace(" ","_")+".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 Oscillator strength 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.symmetry,
|
|
str(ex.final.number),
|
|
str(ex.final.multiplicity),
|
|
ex.final.symmetry,"("+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 "_",
|
|
json.dumps(ex.isUnsafe))
|
|
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=None):
|
|
self.name = name
|
|
self.version = version
|
|
|
|
@staticmethod
|
|
def fromString(string):
|
|
vals = string.split(",")
|
|
return code(*vals)
|
|
|
|
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 _OnReadMetaPair(self, key, value):
|
|
if key == "geom":
|
|
self.geometry = method.fromString(value)
|
|
else:
|
|
super(oneStateDataFileBase,self)._OnReadMetaPair(key, value)
|
|
|
|
def getMetadata(self):
|
|
dic=super(oneStateDataFileBase,self).getMetadata()
|
|
dic["geom"]= "" if self.geometry is None else self.geometry.toDataString()
|
|
dic.move_to_end("set")
|
|
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=isUnsafe)
|
|
self.value = value
|
|
self.oscilatorForces = oscilatorForces
|