mirror of
https://github.com/LCPQ/QUESTDB_website.git
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332 lines
10 KiB
Python
332 lines
10 KiB
Python
from collections import OrderedDict
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from TexSoup import TexSoup
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from .LaTeX import newCommand,extractMath
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from .utils import getValFromCell,checkFloat
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from TexSoup import TexNode,TexEnv
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from enum import IntEnum,auto,unique,IntFlag
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from .formats import getFormatHandlers
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import re
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import os
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import numpy as np
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import json
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class state:
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def __init__(self,number, multiplicity, symmetry):
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self.number = number
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self.multiplicity = multiplicity
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self.symmetry = symmetry
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@staticmethod
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def fromString(string):
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m=re.match(r"^(?P<number>\d)\s*\^(?P<multiplicity>\d)(?P<sym>\S*)",string)
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num=m.group('number')
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mul=m.group('multiplicity')
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sym=m.group('sym')
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return state(num,mul,sym)
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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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def datafileSelector(dataType):
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switcher={
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DataType.ABS:AbsDataFile,
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DataType.FLUO:FluoDataFile,
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}
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return switcher[dataType]
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def getSubtablesRange(table,firstindex=2,column=0,count=1):
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subtablesRange=list()
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i=firstindex+count
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while i<np.size(table,0):
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if str(table[i,column])!="":
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subtablesRange.append(range(firstindex,i))
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firstindex=i
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i+=count
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else:
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i+=1
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subtablesRange.append(range(firstindex,np.size(table,0)))
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return subtablesRange
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class exSet(object):
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def __init__(self,name,index=0):
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self.name=name
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self.index=index
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def __str__(self):
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return f"{self.name},{self.index}"
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@staticmethod
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def fromString(string):
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vals = string.split(",")
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if len(vals)>1:
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return exSet(vals[0],int(vals[1]))
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else:
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return exSet(vals[0])
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def getDOI(self):
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import yaml
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from pathlib import Path
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yamlpath=Path(__file__)/"../../statics/data/index.yaml"
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with yamlpath.open("r") as f:
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db = yaml.load(f,yaml.loader.FullLoader)
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sets=db["sets"]
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if self.name in db["sets"]:
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return sets[self.name][self.index]
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def isSameSet(self,otherSet):
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return self.name == otherSet.name
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def isSameArticle(self,otherSet):
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if (self.name==otherSet.name and self.index==otherSet.index):
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return True
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else:
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return self.getDOI() == otherSet.getDOI()
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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.set = ''
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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,initialState,default=DataType.ABS,commands=[]):
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tmplst=[]
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for TexState in StateTablelist:
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st=str(extractMath(TexState,Soup=True,commands=commands))
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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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mul=int(m.group("multiplicity"))
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symm=m.group("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((mul,symm,trsp,tygrp))
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lst=[]
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for index,item in enumerate(tmplst):
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unforminitialstate=(int(initialState.multiplicity),initialState.symmetry)
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countlst=[unforminitialstate]+[(it[0],it[1]) for it in tmplst[:index+1]]
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countitem=(item[0],item[1])
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count=countlst.count(countitem)
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lst.append((state(count,item[0],item[1]),item[2],item[3]))
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return lst
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def _OnReadMetaPair(self, key, value):
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if key == "molecule":
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self.molecule = value
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elif key == "comment":
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self.comment = value
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elif key == "code":
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self.code = code.fromString(value)
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elif key == "method":
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self.method = method.fromString(value)
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elif key == "set":
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self.set = exSet.fromString(value)
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@staticmethod
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def readFromTable(table,TexOps, commands=[]):
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for formatName,Cls in getFormatHandlers():
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if formatName.lower()==TexOps.format.lower():
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handler=Cls(TexOps,commands)
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break
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else:
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raise ValueError()
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return handler.readFromTable(table)
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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["set"]="" if self.set is None else self.set
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return dic
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def _OnReadMeta(self,line,dataType):
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#get key value
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match = dataFileBase._GetMetaRexEx().match(line)
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# normalize key to lower
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key = match.group(1).lower()
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# if data has value
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if match.group(2):
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val = match.group(2)
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self._OnReadMetaPair(key, val)
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@staticmethod
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def _OnReadRow(line):
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vals = re.findall(r"\([^\)]+\)|\S+",line)
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start = state(int(vals[0]), int(vals[1]), vals[2])
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end = state(int(vals[3]), int(vals[4]), vals[5])
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Type = vals[6] if (len(vals) >= 7) else None
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if Type == "_":
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Type = None
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if Type:
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m = re.match(r"^\(([^\)]*)\)$",Type)
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if m:
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Type = m[1]
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val = vals[7] if len(vals) >= 8 else str(np.NaN)
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T1 = vals[8] if len(vals) >= 9 else str(np.NaN)
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oscilatorForces = vals[9] if len(vals) >= 10 else str(np.NaN)
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isUnsafe = vals[10] == json.dumps(True) if len(vals) >= 11 else False
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ex = excitationValue(start, end, val, Type,T1,isUnsafe,oscilatorForces)
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return ex
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@staticmethod
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def _GetMetaRexEx():
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#metadata RegExp (start with #; maybe somme spaces; : ; maybe somme space; datas)
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return re.compile(r"^#\s*([A-Za-z_]+)\s*:\s*(.*)$")
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@staticmethod
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def readFile(stream,dataType):
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lines = stream.readlines()
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# for each line with metadata
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ismetaArea = True
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dat = datafileSelector(dataType)()
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for line in lines:
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#if it's not empty line
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line = line.strip()
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if line:
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# if # may be metadata or comment
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if line[0] == "#":
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# if it's metadata
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if ismetaArea and dataFileBase._GetMetaRexEx().match(line):
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dat._OnReadMeta(line,dataType)
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else: # else its row
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ismetaArea = False
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dat.excitations.append(dat._OnReadRow(line))
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return dat
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def toFile(self,datadir,suffix=None):
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subpath=datadir/self.GetFileType().name.lower()
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if not subpath.exists():
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os.makedirs(str(subpath))
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molsoup=TexSoup(self.molecule)
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molfilename="".join(molsoup.text).replace("\\","")
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molfilename=molfilename.lower()
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fileNameComp=[molfilename,self.method.name]
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if self.method.basis:
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fileNameComp.append(self.method.basis)
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if suffix:
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fileNameComp.append(suffix)
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fileName="_".join(fileNameComp).replace(" ","_")+".dat"
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if os.sep in fileName:
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raise ValueError(f"fileName must be a pure file name not a path: {fileName}")
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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 Oscillator strength 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=" {:7s} {:5s} {:10s} {:7s} {:5s} {:12s} {:39s} {:13s} {:14s} {: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.symmetry,
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str(ex.final.number),
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str(ex.final.multiplicity),
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ex.final.symmetry,"("+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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json.dumps(ex.isUnsafe))
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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=None):
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self.name = name
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self.version = version
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@staticmethod
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def fromString(string):
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vals = string.split(",")
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return code(*vals)
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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 _OnReadMetaPair(self, key, value):
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if key == "geom":
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self.geometry = method.fromString(value)
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else:
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super(oneStateDataFileBase,self)._OnReadMetaPair(key, value)
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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("set")
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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 excitationBase:
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def __init__(self,initial, final,type=None, T1=None,isUnsafe=False):
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self.initial = initial
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self.final = final
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self.type = type
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self.T1 = T1
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self.isUnsafe = isUnsafe
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class excitationValue(excitationBase):
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def __init__(self,initial, final, value, type=None, T1=None,isUnsafe=False,oscilatorForces=None):
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super(excitationValue,self).__init__(initial, final,type=type,T1=T1,isUnsafe=isUnsafe)
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self.value = value
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self.oscilatorForces = oscilatorForces
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