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Support molecule on first column instead of on first line on tex (see example2.tex)

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Mickaël Véril 2019-11-19 13:52:53 +01:00
parent 0af6b2d551
commit 92da17ea23
4 changed files with 121 additions and 20 deletions
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66
docs/example2.tex Normal file
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@ -0,0 +1,66 @@
\newcommand{\TDDFT}{TD-DFT}
\newcommand{\CASSCF}{CASSCF}
\newcommand{\CASPT}{CASPT2}
\newcommand{\ADC}[1]{ADC(#1)}
\newcommand{\CC}[1]{CC#1}
\newcommand{\CCSD}{CCSD}
\newcommand{\EOMCCSD}{EOM-CCSD}
\newcommand{\CCSDT}{CCSDT}
\newcommand{\CCSDTQ}{CCSDTQ}
\newcommand{\CCSDTQP}{CCSDTQP}
\newcommand{\CI}{CI}
\newcommand{\sCI}{sCI}
\newcommand{\exCI}{exFCI}
\newcommand{\FCI}{FCI}
% basis
\newcommand{\AVDZ}{\emph{aug}-cc-pVDZ}
\newcommand{\AVTZ}{\emph{aug}-cc-pVTZ}
\newcommand{\DAVTZ}{d-\emph{aug}-cc-pVTZ}
\newcommand{\AVQZ}{\emph{aug}-cc-pVQZ}
\newcommand{\DAVQZ}{d-\emph{aug}-cc-pVQZ}
\newcommand{\TAVQZ}{t-\emph{aug}-cc-pVQZ}
\newcommand{\AVPZ}{\emph{aug}-cc-pV5Z}
\newcommand{\DAVPZ}{d-\emph{aug}-cc-pV5Z}
\newcommand{\PopleDZ}{6-31+G(d)}
\begin{tabular}{ll|ccc|ccc|cc}
& & \multicolumn{3}{c}{\AVDZ} & \multicolumn{3}{c}{\AVTZ} & \multicolumn{2}{c}{Litt.}\\
Molecule &State & {\CC{3}} & {\CCSDT} & {\exCI} & {\CC{3}} & {\CCSDT} & {\exCI}& Exp. & Theo. \\
Acetaldehyde &$^1A'' (n \rightarrow \pis)$ &4.34&4.32&4.34& 4.31&4.29&4.31 & 4.27$^a$ &4.29$^b$ \\
&$^3A'' (n \rightarrow \pis)$ &3.96&3.95&3.98& 3.95&3.94&4.0$^c$ & 3.97$^a$ &3.97$^b$ \\
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$^e$ \\
&$^1B_2 (\pi \rightarrow \pis)$ &6.77&6.78&6.82& 6.73&6.75&6.7$^c$ & 7.00$^f$ & 7.11$^e$ \\
&$^3B_2 (\pi \rightarrow \pis)$ &4.34&4.35&4.35& 4.34& &4.38 & 4.16$^f$ & 4.28$^g$ \\
&$^3B_1 (\sigma \rightarrow \pis)$ &6.43&6.43&6.43& 6.40& &6.45 & & 6.40$^g$ \\
Diazomethane &$^1A_2 (\pi \rightarrow \pis)$ &3.10&3.10&3.09& 3.07&3.07&3.14 & 3.14$^h$ &3.21$^i$ \\
&$^1B_1 (\pi \rightarrow 3s)$ &5.32&5.35&5.35& 5.45&5.48&5.54 & &5.33$^i$ \\
&$^1A_1 (\pi \rightarrow \pis)$ &5.80&5.82&5.79& 5.84&5.86&5.90 & 5.9$^h$ &5.85$^i$ \\
&$^3A_2 (\pi \rightarrow \pis)$ &2.84&2.84&2.81& 2.83&2.82&2.8$^c$ & &2.92$^j$ \\
&$^3A_1 (\pi \rightarrow \pis)$ &4.05&4.04&4.03& 4.03&4.02&4.05 & &3.97$^j$ \\
&$^3B_1 (\pi \rightarrow 3s)$ &5.17&5.20&5.18& 5.31&5.34&5.35 & & \\
&$^3A_1 (\pi \rightarrow 3p)$ &6.83&6.83&6.81& 6.80& &6.82 & &7.02$^j$ \\
&$^1A'' [\mathrm{F}] (\pi \rightarrow \pis)$ &0.68&0.67&0.65& 0.68&0.67&0.71 & & \\
Formamide &$^1A'' (n \rightarrow \pis)$ &5.71&5.68&5.70 &5.66&5.63&5.7$^c$&5.8$^k$ &5.63$^l$ \\
&$^1A' (n \rightarrow 3s)$ &6.65&6.64&6.67 &6.74&6.74& &6.35$^k$ &6.62$^l$ \\
&$^1A' (\pi \rightarrow \pis)$$^m$ &7.63&7.62&7.64 &7.62& &7.63 &7.37$^k$ &7.22$^l$ \\
&$^1A' (n \rightarrow 3p)$$^m$ &7.31&7.29& &7.40&7.38& &7.73$^k$ &7.66$^l$ \\
&$^3A'' (n \rightarrow \pis)$ &5.42&5.39&5.42 &5.38& &5.4$^c$ &5.2$^k$ &5.34$^l$ \\
&$^3A' (\pi \rightarrow \pis)$ &5.83&5.81&5.82 &5.82& &5.7$^c$ & &5.74$^l$ \\
Ketene &$^1A_2 (\pi \rightarrow \pis)$ &3.89&3.88&3.84& 3.88&3.87&3.86 &3.7$^n$ &3.74$^o$ \\
&$^1B_1 (n \rightarrow 3s)$ &5.83&5.86&5.88& 5.96&5.99&6.01 &5.86$^n$&5.82$^o$ \\
&$^1A_2 (\pi \rightarrow 3p)$ &7.05&7.09&7.08& 7.16&7.20&7.18 & &7.00$^o$ \\
&$^3A_2 (n \rightarrow \pis)$ &3.79&3.78&3.79& 3.78&3.78&3.77 &3.8$^p$ &3.62$^q$\\
&$^3A_1 (\pi \rightarrow \pis)$ &5.62&5.61&5.64& 5.61&5.60&5.61 &5$^p$ &5.42$^q$\\
&$^3B_1 (n \rightarrow 3s)$ &5.63&5.66&5.68& 5.76&5.80&5.79 &5.8$^p$ &5.69$^q$\\
&$^3A_2 (\pi \rightarrow 3p)$ &7.01&7.05&7.07& 7.12&7.17&7.12 & & \\
&$^1A''[\mathrm{F}] (\pi \rightarrow \pis)$ &1.00&0.99&0.96& 1.00&1.00&1.00 & & \\
Nitrosomethane&$^1A'' (n \rightarrow \pis)$ &2.00&1.98&1.99& 1.96&1.95&2.0$^c$ &1.83$^r$&1.76$^s$\\
&$^1A' (n,n \rightarrow \pis,\pis)$ &5.75&5.26&4.81& 5.76&5.29 &4.72 & &4.96$^s$\\
&$^1A' (n \rightarrow 3s/3p)$ &6.20&6.19&6.29& 6.31&6.30&6.4$^c$ & &6.54$^s$\\
&$^3A'' (n \rightarrow \pis)$ &1.13&1.12&1.15& 1.14&1.13&1.16 & &1.42$^t$\\
&$^3A' (\pi \rightarrow \pis)$ &5.54&5.54&5.56& 5.51& &5.60 & &5.55$^t$\\
&$^1A'' [\mathrm{F}] (n \rightarrow \pis)$ &1.70&1.69&1.70& 1.69&1.66 &1.7$^c$ & & \\
Streptocyanine-C1&$^1B_2 (\pi \rightarrow \pis)$ &7.14&7.12&7.14& 7.13&7.11&7.1$^c$ & &7.16$^u$\\
& $^3B_2 (\pi \rightarrow \pis)$ &5.48&5.47&5.47& 5.48&5.47&5.52 & & \\
\end{tabular}

10
tools/datafileBuilder.py
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@ -1,16 +1,19 @@
#!/usr/bin/env python3 #!/usr/bin/env python3
import sys import sys
import re import re
from enum import IntEnum,auto,unique
import numpy as np import numpy as np
from pathlib import Path from pathlib import Path
from lib import LaTeX from lib import LaTeX
from lib.Orientation import Orientation
from TexSoup import TexSoup from TexSoup import TexSoup
from lib.data import AbsDataFile,ZPEDataFile,FluoDataFile,dataType from lib.data import AbsDataFile,ZPEDataFile,FluoDataFile,dataType
import argparse import argparse
DEBUG=False DEBUG=True
parser = argparse.ArgumentParser() parser = argparse.ArgumentParser()
parser.add_argument('--file', type=argparse.FileType('r')) parser.add_argument('--file', type=argparse.FileType('r'))
parser.add_argument('--type', type=str, choices=[t.name for t in list(dataType)]) parser.add_argument('--type', type=str, choices=[t.name for t in list(dataType)])
parser.add_argument('--MoleculeOrentation',type=str, choices=[t.name for t in list(Orientation)],default=Orientation.LINE.name)
args = parser.parse_args() args = parser.parse_args()
print(args) print(args)
lines=args.file.readlines() lines=args.file.readlines()
@ -29,5 +32,6 @@ switcher={
dataType.ZPE: ZPEDataFile dataType.ZPE: ZPEDataFile
} }
filecls=switcher.get(dataType[args.type]) filecls=switcher.get(dataType[args.type])
for col in range(1,np.size(dat,1)): datalst=filecls.readFromTable(dat,Orientation[args.MoleculeOrentation])
filecls.readFromTable(dat,col).toFile(datapath) for data in datalst:
data.toFile(datapath)

5
tools/lib/Orientation.py Normal file
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from enum import IntEnum,auto,unique
@unique
class Orientation(IntEnum):
LINE=auto()
COLUMN=auto()

60
tools/lib/data.py
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@ -1,6 +1,8 @@
from collections import OrderedDict from collections import OrderedDict
from enum import IntEnum,auto,unique from enum import IntEnum,auto,unique
from .Orientation import Orientation
import re import re
import numpy as np
class state: class state:
def __init__(self,number, multiplicity, symetry): def __init__(self,number, multiplicity, symetry):
@ -43,19 +45,43 @@ class dataFileBase(object):
return lst return lst
@classmethod @classmethod
def readFromTable(cls, table,column,firstState=state(1,1,"A_1")): def readFromTable(cls, table,orientation=Orientation.LINE ,firstState=state(1,1,"A_1")):
data=cls() datalist=list()
col=table[:,column] if orientation==Orientation.LINE:
data.molecule=str(col[0]) for col in range(1,np.size(table,1)):
data.method=method(str(col[2]),str(col[1])) data=cls()
finsts=cls.convertState(table[3:,0],firstState) col=table[:,col]
for index,cell in enumerate(col[3:]): data.molecule=str(col[0])
if str(cell)!="": data.method=method(str(col[2]),str(col[1]))
val= list(cell.contents)[0] finsts=cls.convertState(table[3:,0],firstState)
val=float(str(val)) for index,cell in enumerate(col[3:]):
data.excitations.append(excitationValue(firstState,finsts[index],val)) if str(cell)!="":
return data val= list(cell.contents)[0]
val=float(str(val))
data.excitations.append(excitationValue(firstState,finsts[index],val))
datalist.append(data)
return datalist
else:
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
for first, last in subtablesindex:
for col in range(2,np.size(table,1)):
data=cls()
col=table[:,col]
data.molecule=str(table[first,0])
data.method=method(str(col[1]),str(col[0]))
finsts=cls.convertState(table[first:last+1,1],firstState)
for index,cell in enumerate(col[first:last+1]):
if str(cell)!="":
val= list(cell.contents)[0]
val=float(str(val))
data.excitations.append(excitationValue(firstState,finsts[index],val))
datalist.append(data)
return datalist
def getMetadata(self): def getMetadata(self):
dic=OrderedDict() dic=OrderedDict()
dic["Molecule"]=self.molecule dic["Molecule"]=self.molecule
@ -130,8 +156,8 @@ class oneStateDataFileBase(dataFileBase):
return dic return dic
@classmethod @classmethod
def readFromTable(cls, table,column,firstState=state(1,1,"A_1")): def readFromTable(cls, table,orientation=Orientation.LINE,firstState=state(1,1,"A_1")):
data=super().readFromTable(table,column,firstState=firstState) data=super().readFromTable(table,orientation,firstState=firstState)
return data return data
class AbsDataFile(oneStateDataFileBase): class AbsDataFile(oneStateDataFileBase):
def __init__(self): def __init__(self):
@ -156,8 +182,8 @@ class twoStateDataFileBase(dataFileBase):
self.ES=None self.ES=None
@classmethod @classmethod
def readFromTable(cls, table,column,firstState=state(1,1,"A_1")): def readFromTable(cls, table,orientation=Orientation.LINE,firstState=state(1,1,"A_1")):
data=super().readFromTable(table,column,firstState=firstState) data=super().readFromTable(table,Orientation,firstState=firstState)
return data return data
def getMetadata(self): def getMetadata(self):
dic=super(twoStateDataFileBase,self).getMetadata() dic=super(twoStateDataFileBase,self).getMetadata()