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Support molecule on first column instead of on first line on tex (see example2.tex)
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docs/example2.tex
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66
docs/example2.tex
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\newcommand{\TDDFT}{TD-DFT}
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\newcommand{\CASSCF}{CASSCF}
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\newcommand{\CASPT}{CASPT2}
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\newcommand{\ADC}[1]{ADC(#1)}
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\newcommand{\CC}[1]{CC#1}
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\newcommand{\CCSD}{CCSD}
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\newcommand{\EOMCCSD}{EOM-CCSD}
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\newcommand{\CCSDT}{CCSDT}
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\newcommand{\CCSDTQ}{CCSDTQ}
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\newcommand{\CCSDTQP}{CCSDTQP}
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\newcommand{\CI}{CI}
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\newcommand{\sCI}{sCI}
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\newcommand{\exCI}{exFCI}
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\newcommand{\FCI}{FCI}
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% basis
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\newcommand{\AVDZ}{\emph{aug}-cc-pVDZ}
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\newcommand{\AVTZ}{\emph{aug}-cc-pVTZ}
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\newcommand{\DAVTZ}{d-\emph{aug}-cc-pVTZ}
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\newcommand{\AVQZ}{\emph{aug}-cc-pVQZ}
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\newcommand{\DAVQZ}{d-\emph{aug}-cc-pVQZ}
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\newcommand{\TAVQZ}{t-\emph{aug}-cc-pVQZ}
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\newcommand{\AVPZ}{\emph{aug}-cc-pV5Z}
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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{tabular}{ll|ccc|ccc|cc}
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& & \multicolumn{3}{c}{\AVDZ} & \multicolumn{3}{c}{\AVTZ} & \multicolumn{2}{c}{Litt.}\\
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Molecule &State & {\CC{3}} & {\CCSDT} & {\exCI} & {\CC{3}} & {\CCSDT} & {\exCI}& Exp. & Theo. \\
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Acetaldehyde &$^1A'' (n \rightarrow \pis)$ &4.34&4.32&4.34& 4.31&4.29&4.31 & 4.27$^a$ &4.29$^b$ \\
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&$^3A'' (n \rightarrow \pis)$ &3.96&3.95&3.98& 3.95&3.94&4.0$^c$ & 3.97$^a$ &3.97$^b$ \\
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Cyclopropene &$^1B_1 (\sigma \rightarrow \pis)$ &6.72&6.71&6.7$^c$&6.68&6.68&6.6$^c$& 6.45$^d$ & 6.89$^e$ \\
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&$^1B_2 (\pi \rightarrow \pis)$ &6.77&6.78&6.82& 6.73&6.75&6.7$^c$ & 7.00$^f$ & 7.11$^e$ \\
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&$^3B_2 (\pi \rightarrow \pis)$ &4.34&4.35&4.35& 4.34& &4.38 & 4.16$^f$ & 4.28$^g$ \\
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&$^3B_1 (\sigma \rightarrow \pis)$ &6.43&6.43&6.43& 6.40& &6.45 & & 6.40$^g$ \\
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Diazomethane &$^1A_2 (\pi \rightarrow \pis)$ &3.10&3.10&3.09& 3.07&3.07&3.14 & 3.14$^h$ &3.21$^i$ \\
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&$^1B_1 (\pi \rightarrow 3s)$ &5.32&5.35&5.35& 5.45&5.48&5.54 & &5.33$^i$ \\
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&$^1A_1 (\pi \rightarrow \pis)$ &5.80&5.82&5.79& 5.84&5.86&5.90 & 5.9$^h$ &5.85$^i$ \\
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&$^3A_2 (\pi \rightarrow \pis)$ &2.84&2.84&2.81& 2.83&2.82&2.8$^c$ & &2.92$^j$ \\
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&$^3A_1 (\pi \rightarrow \pis)$ &4.05&4.04&4.03& 4.03&4.02&4.05 & &3.97$^j$ \\
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&$^3B_1 (\pi \rightarrow 3s)$ &5.17&5.20&5.18& 5.31&5.34&5.35 & & \\
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&$^3A_1 (\pi \rightarrow 3p)$ &6.83&6.83&6.81& 6.80& &6.82 & &7.02$^j$ \\
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&$^1A'' [\mathrm{F}] (\pi \rightarrow \pis)$ &0.68&0.67&0.65& 0.68&0.67&0.71 & & \\
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Formamide &$^1A'' (n \rightarrow \pis)$ &5.71&5.68&5.70 &5.66&5.63&5.7$^c$&5.8$^k$ &5.63$^l$ \\
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&$^1A' (n \rightarrow 3s)$ &6.65&6.64&6.67 &6.74&6.74& &6.35$^k$ &6.62$^l$ \\
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&$^1A' (\pi \rightarrow \pis)$$^m$ &7.63&7.62&7.64 &7.62& &7.63 &7.37$^k$ &7.22$^l$ \\
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&$^1A' (n \rightarrow 3p)$$^m$ &7.31&7.29& &7.40&7.38& &7.73$^k$ &7.66$^l$ \\
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&$^3A'' (n \rightarrow \pis)$ &5.42&5.39&5.42 &5.38& &5.4$^c$ &5.2$^k$ &5.34$^l$ \\
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&$^3A' (\pi \rightarrow \pis)$ &5.83&5.81&5.82 &5.82& &5.7$^c$ & &5.74$^l$ \\
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Ketene &$^1A_2 (\pi \rightarrow \pis)$ &3.89&3.88&3.84& 3.88&3.87&3.86 &3.7$^n$ &3.74$^o$ \\
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&$^1B_1 (n \rightarrow 3s)$ &5.83&5.86&5.88& 5.96&5.99&6.01 &5.86$^n$&5.82$^o$ \\
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&$^1A_2 (\pi \rightarrow 3p)$ &7.05&7.09&7.08& 7.16&7.20&7.18 & &7.00$^o$ \\
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&$^3A_2 (n \rightarrow \pis)$ &3.79&3.78&3.79& 3.78&3.78&3.77 &3.8$^p$ &3.62$^q$\\
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&$^3A_1 (\pi \rightarrow \pis)$ &5.62&5.61&5.64& 5.61&5.60&5.61 &5$^p$ &5.42$^q$\\
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&$^3B_1 (n \rightarrow 3s)$ &5.63&5.66&5.68& 5.76&5.80&5.79 &5.8$^p$ &5.69$^q$\\
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&$^3A_2 (\pi \rightarrow 3p)$ &7.01&7.05&7.07& 7.12&7.17&7.12 & & \\
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&$^1A''[\mathrm{F}] (\pi \rightarrow \pis)$ &1.00&0.99&0.96& 1.00&1.00&1.00 & & \\
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Nitrosomethane&$^1A'' (n \rightarrow \pis)$ &2.00&1.98&1.99& 1.96&1.95&2.0$^c$ &1.83$^r$&1.76$^s$\\
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&$^1A' (n,n \rightarrow \pis,\pis)$ &5.75&5.26&4.81& 5.76&5.29 &4.72 & &4.96$^s$\\
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&$^1A' (n \rightarrow 3s/3p)$ &6.20&6.19&6.29& 6.31&6.30&6.4$^c$ & &6.54$^s$\\
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&$^3A'' (n \rightarrow \pis)$ &1.13&1.12&1.15& 1.14&1.13&1.16 & &1.42$^t$\\
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&$^3A' (\pi \rightarrow \pis)$ &5.54&5.54&5.56& 5.51& &5.60 & &5.55$^t$\\
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&$^1A'' [\mathrm{F}] (n \rightarrow \pis)$ &1.70&1.69&1.70& 1.69&1.66 &1.7$^c$ & & \\
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Streptocyanine-C1&$^1B_2 (\pi \rightarrow \pis)$ &7.14&7.12&7.14& 7.13&7.11&7.1$^c$ & &7.16$^u$\\
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& $^3B_2 (\pi \rightarrow \pis)$ &5.48&5.47&5.47& 5.48&5.47&5.52 & & \\
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\end{tabular}
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@ -1,16 +1,19 @@
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#!/usr/bin/env python3
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import sys
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import re
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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 TexSoup import TexSoup
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from lib.data import AbsDataFile,ZPEDataFile,FluoDataFile,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('--type', 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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args = parser.parse_args()
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print(args)
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lines=args.file.readlines()
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@ -29,5 +32,6 @@ switcher={
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dataType.ZPE: ZPEDataFile
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}
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filecls=switcher.get(dataType[args.type])
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for col in range(1,np.size(dat,1)):
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filecls.readFromTable(dat,col).toFile(datapath)
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datalst=filecls.readFromTable(dat,Orientation[args.MoleculeOrentation])
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for data in datalst:
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data.toFile(datapath)
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5
tools/lib/Orientation.py
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5
tools/lib/Orientation.py
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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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LINE=auto()
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COLUMN=auto()
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@ -1,6 +1,8 @@
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from collections import OrderedDict
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from enum import IntEnum,auto,unique
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from .Orientation import Orientation
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import re
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import numpy as np
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class state:
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def __init__(self,number, multiplicity, symetry):
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@ -43,9 +45,12 @@ class dataFileBase(object):
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return lst
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@classmethod
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def readFromTable(cls, table,column,firstState=state(1,1,"A_1")):
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def readFromTable(cls, table,orientation=Orientation.LINE ,firstState=state(1,1,"A_1")):
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datalist=list()
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if orientation==Orientation.LINE:
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for col in range(1,np.size(table,1)):
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data=cls()
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col=table[:,column]
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col=table[:,col]
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data.molecule=str(col[0])
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data.method=method(str(col[2]),str(col[1]))
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finsts=cls.convertState(table[3:,0],firstState)
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@ -54,8 +59,29 @@ class dataFileBase(object):
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val= list(cell.contents)[0]
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val=float(str(val))
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data.excitations.append(excitationValue(firstState,finsts[index],val))
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return data
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datalist.append(data)
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return datalist
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else:
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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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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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for col in range(2,np.size(table,1)):
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data=cls()
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col=table[:,col]
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data.molecule=str(table[first,0])
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data.method=method(str(col[1]),str(col[0]))
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finsts=cls.convertState(table[first:last+1,1],firstState)
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for index,cell in enumerate(col[first:last+1]):
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if str(cell)!="":
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val= list(cell.contents)[0]
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val=float(str(val))
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data.excitations.append(excitationValue(firstState,finsts[index],val))
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datalist.append(data)
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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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@ -130,8 +156,8 @@ class oneStateDataFileBase(dataFileBase):
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return dic
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@classmethod
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def readFromTable(cls, table,column,firstState=state(1,1,"A_1")):
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data=super().readFromTable(table,column,firstState=firstState)
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def readFromTable(cls, table,orientation=Orientation.LINE,firstState=state(1,1,"A_1")):
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data=super().readFromTable(table,orientation,firstState=firstState)
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return data
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class AbsDataFile(oneStateDataFileBase):
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def __init__(self):
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@ -156,8 +182,8 @@ class twoStateDataFileBase(dataFileBase):
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self.ES=None
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@classmethod
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def readFromTable(cls, table,column,firstState=state(1,1,"A_1")):
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data=super().readFromTable(table,column,firstState=firstState)
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def readFromTable(cls, table,orientation=Orientation.LINE,firstState=state(1,1,"A_1")):
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data=super().readFromTable(table,Orientation,firstState=firstState)
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return data
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def getMetadata(self):
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dic=super(twoStateDataFileBase,self).getMetadata()
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