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https://github.com/LCPQ/QUESTDB_website.git
synced 2024-07-22 18:57:38 +02:00
Fix missing
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4448d8d9db
@ -24,7 +24,7 @@
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\newcommand{\DAVPZ}{d-\emph{aug}-cc-pV5Z}
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\newcommand{\PopleDZ}{6-31+G(d)}
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\begin{table}{llcccccc}
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\begin{tabular}{llcccccc}
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& & & & TBE(FC)& \multicolumn{3}{c}{Corrected TBE} \\
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& State & $f$ & \%$T_1$ & AVTZ & Method & Corr. & Value \\
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Acetaldehyde &$^1A''(\mathrm{V};n \rightarrow \pis)$ & 0.000 &91.3& 4.31 & {\exCI}/AVTZ & AVQZ &4.31 \\
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@ -99,7 +99,7 @@
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&$^1A' (\Ryd;n \rightarrow 3s)$ &0.001 &88.6 &6.77$^a$ & & &6.81 \\
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&$^1A' (\mathrm{V};\pi \rightarrow \pis)$ &0.251 &89.3 &7.63 &{\exCI}/AVTZ & AVQZ &7.64 \\
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&$^1A' (\Ryd;n \rightarrow 3p)$ &0.111 &89.6 &7.38$^b$ &{\CCSDT}/AVTZ& AVQZ &7.41 \\
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&$^3A'' (\mathrm{V};n \rightarrow \pis)$ & &97.7 &5.38$^c$ &{\exCI}/AVDZ& AVQZ &5.37 \\%X-EX
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&$^3A'' (\mathrm{V};n \rightarrow \pis)$ & &97.7 &5.38$^c$ &{\exCI}/AVDZ& AVQZ &5.37 \\
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&$^3A' (\mathrm{V};\pi \rightarrow \pis)$ & &98.2 &5.81$^c$ & & &5.81 \\
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Hydrogen chloride & $^1\Pi (\mathrm{CT})$ &0.056 &94.3 &7.84 & {\exCI}/AVQZ &dAV5Z &7.86 \\
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Hydrogen sulfide &$^1A_2 (\Ryd;n \rightarrow 4p)$ & &94.6 &6.18 & {\exCI}/AVQZ &dAV5Z &6.10 \\
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@ -120,7 +120,7 @@
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&$^1A' (\mathrm{V};n,n \rightarrow \pis,\pis)$ &0.000 &2.5 &4.72 & {\exCI}/AVTZ & AVQZ & 4.69 \\
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&$^1A' (\Ryd;n \rightarrow 3s/3p)$ &0.006 &90.8 &6.40$^a$ &{\exCI}/AVDZ & AVQZ &6.42 \\
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&$^3A'' (\mathrm{V};n \rightarrow \pis)$ & &98.4 &1.16 & & &1.16 \\
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&$^3A' (\mathrm{V};\pi \rightarrow \pis)$ & &98.9 &5.60 & & &5.61 <EFBFBD>\\
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&$^3A' (\mathrm{V};\pi \rightarrow \pis)$ & &98.9 &5.60 & & &5.61 \\
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&$^1A'' [\mathrm{F}] (\mathrm{V};n \rightarrow \pis)$ & &92.7&1.67$^a$ &{\exCI}/AVDZ & AVQZ &1.66 \\
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Streptocyanine-C1&$^1B_2 (\mathrm{V};\pi \rightarrow \pis)$ & 0.347 &88.7&7.13$^a$ & {\exCI}/AVDZ & AVQZ &7.12 \\
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& $^3B_2 (\mathrm{V};\pi \rightarrow \pis)$ & &98.3 &5.52 & {\exCI}/AVTZ & AVQZ &5.52 \\
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@ -137,4 +137,4 @@
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& $^3B_1 (\Ryd; n \rightarrow 3s)$ & &98.1 &7.25 & & &7.33 \\
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& $^3A_2 (\Ryd; n \rightarrow 3p)$ & &98.0 &9.24 & & &9.30 \\
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& $^3A_1 (\Ryd; n \rightarrow 3s)$ & &98.2 &9.54 & & &9.59 \\
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\end{tabular}
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\end{tabular}
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@ -78,7 +78,7 @@ class DOI {
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}
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class excitationBase {
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constructor(initial, final, type, T1=null) {
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constructor(initial, final, type=null, T1=null) {
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this.initial = initial;
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this.final = final
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if (type !== null) {
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@ -5,15 +5,15 @@ from enum import IntEnum,auto,unique
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import numpy as np
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from pathlib import Path
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from lib import LaTeX
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from lib.Orientation import Orientation
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from lib.Format import Format
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from TexSoup import TexSoup
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from lib.data import dataFileBase,dataType
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import argparse
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DEBUG=False
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DEBUG=True
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parser = argparse.ArgumentParser()
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parser.add_argument('--file', type=argparse.FileType('r'))
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parser.add_argument('--defaultType', type=str, choices=[t.name for t in list(dataType)])
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parser.add_argument('--MoleculeOrentation',type=str, choices=[t.name for t in list(Orientation)],default=Orientation.LINE.name)
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parser.add_argument('--format',type=str, choices=[t.name for t in list(Format)],default=Format.LINE.name)
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args = parser.parse_args()
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print(args)
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lines=args.file.readlines()
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@ -26,6 +26,6 @@ if DEBUG:
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datapath=datapath/"test"
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if not datapath.exists():
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datapath.mkdir()
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datalst=dataFileBase.readFromTable(dat,orientation=Orientation[args.MoleculeOrentation],default=dataType[args.defaultType])
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datalst=dataFileBase.readFromTable(dat,format=Format[args.format],default=dataType[args.defaultType])
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for data in datalst:
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data.toFile(datapath)
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@ -1,5 +1,6 @@
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from enum import IntEnum,auto,unique
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@unique
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class Orientation(IntEnum):
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class Format(IntEnum):
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LINE=auto()
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COLUMN=auto()
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COLUMN=auto()
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TBE=auto()
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@ -1,6 +1,6 @@
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from collections import OrderedDict
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from enum import IntEnum,auto,unique,IntFlag
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from .Orientation import Orientation
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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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@ -53,18 +53,18 @@ class dataFileBase(object):
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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]))
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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,orientation=Orientation.LINE,default=dataType.ABS ,firstState=state(1,1,"A_1")):
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def readFromTable(table,format=Format.LINE,default=dataType.ABS ,firstState=state(1,1,"A_1")):
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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 orientation==Orientation.LINE:
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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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@ -84,11 +84,11 @@ class dataFileBase(object):
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data=cl()
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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))
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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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else:
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elif format==Format.COLUMN:
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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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@ -96,11 +96,6 @@ class dataFileBase(object):
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subtablesindex.append((firstindex,i-1))
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firstindex=i
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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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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)
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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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@ -121,10 +116,41 @@ class dataFileBase(object):
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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))
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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=list()
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firstindex=2
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for i in range(2,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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for first, last in subtablesindex:
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mymolecule=str(table[first,0])
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mymethod="TBE"
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finsts=dataFileBase.convertState(table[first:last+1,1],default=default,firstState=firstState)
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for row in table[first,last+1]:
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OscilatorForces=float(str(cell.contents)[2])
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T1 = float(str(list(cell.contents)[3]))
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val = float(str(list(cell.contents)[4]))
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corr = float(str(list(cell.contents[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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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],T1=T1,corrected=corr))
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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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def getMetadata(self):
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dic=OrderedDict()
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dic["Molecule"]=self.molecule
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@ -145,11 +171,11 @@ class dataFileBase(object):
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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 Energies (eV) Oscilator forces
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####################### ####################### ################# ###################
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# Number Spin Symm Number Spin Symm E_{:5s} Corr \n""".format(self.GetFileType().name.lower()))
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# Initial state Final state Transition Energies (eV) %T1 Oscilator forces
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####################### ####################### ################ ################# ####### ###################
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# Number Spin Symm Number Spin Symm type E_{:5s} Corr %T1 f \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}{:8s}{:8s}{}\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.value) if ex.value is not None else "_",str(ex.corrected) if ex.corrected is not None else "_",str(ex.OscilatorForces) if ex.OscilatorForces is not None else "_")
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mystr=" {:8s}{:7s}{:10s}{:8s}{:6s}{:13s}{:16s}{:8s}{:10s}{:15s}{}\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.corrected) if ex.corrected is not None else "_",str(ex.T1) if ex.T1 is not None else "_", str(ex.oscilatorForces) if ex.oscilatorForces is not None else "_")
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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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@ -233,13 +259,19 @@ class ZPEDataFile(twoStateDataFileBase):
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return dataType.ZPE
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class excitationBase:
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def __init__(self,initial, final):
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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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class excitationValue(excitationBase):
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def __init__(self,initial, final, value,*args):
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super(excitationValue,self).__init__(initial, final)
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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.Corrcorrectedection=args[0] if len(args)>0 else None
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self.OscilatorForces=args[1] if len(args)>1 else None
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self.corrected=kwarg["corrected"] if "corrected" in kwarg else None
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self.oscilatorForces=kwarg["forces"] if "forces" in kwarg else None
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