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Creae datafileBuilder and other python lib to manipulate datafile
This commit is contained in:
parent
5c76b08c2d
commit
10ca75a0f0
3
.gitignore
vendored
3
.gitignore
vendored
@ -4,4 +4,5 @@ public
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*.DS_Store
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*.swp
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*.out
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public
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public
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__pycache__
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43
docs/example.tex
Normal file
43
docs/example.tex
Normal file
@ -0,0 +1,43 @@
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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}{l|p{.6cm}p{1.1cm}p{1.4cm}p{1.7cm}p{.9cm}|p{.6cm}p{1.1cm}p{1.4cm}p{.9cm}|p{.6cm}p{1.1cm}p{.9cm}|p{.7cm}p{.7cm}p{.7cm}}
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\multicolumn{16}{c}{Dinitrogen}\\
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& \multicolumn{5}{c}{\AVDZ} & \multicolumn{4}{c}{\AVTZ}& \multicolumn{3}{c}{\AVQZ} & \multicolumn{3}{c}{Litt.}\\
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State & {\CC{3}} & {\CCSDT} & {\CCSDTQ} & {\CCSDTQP} & {\exCI} & {\CC{3}} & {\CCSDT} & {\CCSDTQ} & {\exCI}& {\CC{3}} & {\CCSDT} & {\exCI} & Exp.$^a$ & Exp.$^b$ & Th.$^c$\\
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$^1\Pi_g (n \rightarrow \pis)$ &9.44 &9.41 & 9.41 &9.41 & 9.41 &9.34 &9.33 &9.32 &9.34 &9.33 &9.31 &9.34 &9.31 &9.31 &9.27 \\
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$^1\Sigma_u^- (\pi \rightarrow \pis)$ &10.06 &10.06& 10.06&10.05& 10.05 &9.88 &9.89 &9.88 &9.88 &9.87 &9.88 &9.92 &9.92 &9.92 &10.09 \\
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$^1\Delta_u (\pi \rightarrow \pis)$ &10.43 &10.44& 10.43&10.43& 10.43 &10.29&10.30 & &10.29 &10.27 &10.28 &10.31 &10.27 &10.27 &10.54 \\
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$^1\Sigma_g^+ (\Ryd)$ &13.23 &13.20& 13.18&13.18& 13.18 &13.01&13.00 &12.97 &12.98 &12.90 &12.89 &12.89 & &12.2 &12.20 \\
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$^1\Pi_u (\Ryd)$ &13.28 &13.17& 13.13&13.13& 13.12 &13.22&13.14 &13.09 &13.03 &13.17 & &13.1$^d$&12.78 &12.90 &12.84 \\
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$^1\Sigma_u^+ (\Ryd)$ &13.14 &13.13& 13.11&13.11& 13.11 &13.12&13.12 &13.09 &13.09 &13.09 &13.09 &13.2$^d$&12.96 &12.98 &12.82 \\
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$^1\Pi_u (\Ryd)$ &13.64 &13.59& 13.56&13.56& 13.56 &13.49&13.45 &13.42 &13.46 &13.42 &13.37 &13.7$^d$&13.10 &13.24 &13.61 \\
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$^3\Sigma_u^+ (\pi \rightarrow \pis)$ &7.67 &7.68& 7.69 &7.70 & 7.70 &7.68 &7.69 &7.70 &7.70 &7.71 &7.71 &7.74 &7.75 &7.75 &7.56 \\
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$^3\Pi_g (n \rightarrow \pis)$ &8.07 &8.06& 8.05 &8.05 & 8.05 &8.04 &8.03 &8.02 &8.01 &8.04 &8.04 &8.03 &8.04 &8.04 &8.05 \\
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$^3\Delta_u (\pi \rightarrow \pis)$ &8.97 &8.96& 8.96 &8.96 & 8.96 &8.87 &8.87 &8.87 &8.87 &8.87 &8.87 &8.88 &8.88 &8.88 &8.93 \\
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$^3\Sigma_u^- (\pi \rightarrow \pis)$ &9.78 &9.76& 9.75 &9.75& 9.75 &9.68 &9.68 &9.66 &9.66 &9.68 & &9.66 &9.67 &9.67 &9.86 \\
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\end{tabular}
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@ -1,9 +1,9 @@
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# Molecule : Water
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# Comment : Delta ZPE energies of the water molecule
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# code : Gaussian16
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# method : B3LYP,6-31+G*
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# GS : CC3,aug-cc-pVTZ
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# ES : CC2,cc-pVDZ
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# method : B3LYP,6-31+G*
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# DOI : 10.1021/acs.jctc.8b00406
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# Initial state Final state Energies (eV)
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33
tools/datafileBuilder.py
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33
tools/datafileBuilder.py
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@ -0,0 +1,33 @@
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#!/usr/bin/env python
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import sys
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import re
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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 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=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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args = parser.parse_args()
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print(args)
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lines=args.file.readlines()
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soup=TexSoup(lines)
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commands=[LaTeX.newCommand(cmd) for cmd in soup.find_all("newcommand")]
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dat=LaTeX.tabularToData(soup.tabular,commands)
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scriptpath=Path(sys.argv[0]).resolve()
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datapath=scriptpath.parents[1]/"static"/"data"
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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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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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filecls=switcher.get(dataType[args.type])
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for col in range(3,np.size(dat,1)):
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filecls.readFromTable(dat,col).toFile(datapath)
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130
tools/lib/LaTeX.py
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130
tools/lib/LaTeX.py
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@ -0,0 +1,130 @@
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import re
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from TexSoup import TexSoup,TexCmd,TexNode
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from .utils import *
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import itertools
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from enum import Enum
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from abc import ABCMeta
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class commandBase(metaclass=ABCMeta):
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def __init__(self,source,supportedTexType):
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if not (source.name==supportedTexType):
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raise ValueError(source+" is not a "+supportedTexType)
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self.source=source
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def __str__(self):
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return self.source.__str__
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def __repr__(self):
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return self.source.__repr__()
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class newCommand(commandBase):
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def __init__(self,source):
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super(newCommand, self).__init__(source,"newcommand")
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@property
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def commandName(self):
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return self.source.args[0].value[1:]
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@property
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def argNum(self):
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return 0 if self.source.args[1].type!='optional' else self.source.args[1].value
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@property
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def result(self):
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return nodify(list(self.source.args[len(self.source.args)-1].contents))
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def exist(self,tex):
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exist=tex.find(self.commandName)!=None
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return exist
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def run(self,tex):
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cmds=list(tex.find_all(self.commandName))
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if len(cmds)==0:
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raise ValueError("Command not found in tex")
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else:
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for cmd in cmds:
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if self.argNum==0:
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res=self.result
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else:
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resultstr=str(self.result)
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res=TexSoup(re.sub('\#([1-{}])'.format(self.argNum),lambda m: cmd.args[int(m.group(1))-1].value,resultstr))
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soup=TexSoup(res)
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tex.replace(cmd,soup)
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def tryrun():
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cmds=list(tex.find_all(self.commandName))
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if len(cmds)!=0:
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for cmd in cmds:
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if self.argNum==0:
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res=self.result
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else:
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res=re.sub('#[1-{}]'.format(self.argNum),lambda m: cmd.args[int(m.group(1))-1],self.result)
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soup=TexSoup(res)
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tex.replace(cmd,soup)
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@staticmethod
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def runAll(tex,collection):
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cmds=[cmd for cmd in collection if cmd.exist(tex)]
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if(len(cmds)>0):
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for cmd in cmds:
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cmd.run(tex)
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newCommand.runAll(tex,collection)
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class columnAlignment(Enum):
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Left = "l"
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Right = "r"
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Center = "c"
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class multiColumn(commandBase):
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def __init__(self,source):
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super(multiColumn,self).__init__(source,"multicolumn")
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@property
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def cols(self):
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return int(self.source.args[0].value)
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@property
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def align(self):
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return columnAlignment(self.source.args[1].value)
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@property
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def contents(self):
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return nodify(list(self.source.args[2].contents))
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def tabularToData(table,commands=None):
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if table.name=="tabular":
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ctable=str(table)
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ctable=ctable.split("\n")
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ctable=ctable[1:len(ctable)-1]
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rows=[x.strip() for x in ''.join(ctable).split(r'\\') if x.strip()!='']
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ltable=[]
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ltable=[[c.strip() for c in r.split("&")] for r in rows]
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lnewtable=[]
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for row in ltable:
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r=[]
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for item in row:
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texitem=TexSoup(item)
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child=list(texitem.children)
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if(len(child)==1 and child[0].name=="multicolumn"):
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mcolel=child[0]
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mcol=multiColumn(mcolel)
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el=mcol.contents
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if commands!=None:
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newCommand.runAll(el,commands)
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for i in range(int(mcol.cols)):
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r.append(el)
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else:
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if type(item) is str:
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el=TexSoup(item)
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else:
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el=item
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el=desarg(el)
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if commands!=None:
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newCommand.runAll(el,commands)
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r.append(el)
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lnewtable.append(r)
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lens=[len(x) for x in lnewtable]
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#Check if all rows have the same dimension
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if(len(set(lens))!=1):
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raise ValueError("This tabular is not supported")
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import numpy as np
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table=np.array(lnewtable,TexNode)
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return table
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else:
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raise ValueError("Only tabular LaTeX environment is supported")
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0
tools/lib/__init__.py
Normal file
0
tools/lib/__init__.py
Normal file
185
tools/lib/data.py
Normal file
185
tools/lib/data.py
Normal file
@ -0,0 +1,185 @@
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from collections import OrderedDict
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from enum import IntEnum,auto,unique
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import re
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class state:
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def __init__(self,number, multiplicity, symetry):
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self.number = number
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self.multiplicity = multiplicity
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self.symetry = symetry
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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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ZPE=auto()
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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.DOI = ''
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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,firstState=state(1,1,"A_1")):
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tmplst=[]
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for TexState in StateTablelist:
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st=list(TexState.find("$").contents)[0]
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m=re.match(r"^\^(?P<multiplicity>\d)(?P<GPS>\S+)",st)
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seq=m.groups()
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tmplst.append(seq)
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lst=[]
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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]))
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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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data=cls()
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col=table[:,column]
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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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for index,cell in enumerate(col[3:]):
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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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return data
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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["DOI"]="" if self.DOI is None else self.DOI
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return dic
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def toFile(self,datadir):
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subpath=datadir/self.GetFileType().name.lower()
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if not subpath.exists():
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subpath.mkdir()
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file=subpath/"{}_{}_{}.dat".format(self.molecule.lower(),self.method.name,self.method.basis)
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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("# {}: {}\n".format(key,value))
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f.write("""
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# Initial state Final state Energies (eV)
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####################### ####################### ###############
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# Spin Number Symm Spin Number Symm E_{}\n""".format(self.GetFileType().name.lower()))
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for ex in self.excitations:
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mystr=" {:6s}{:9s}{:10s}{:6s}{:8s}{:13s}{}\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))
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f.write(mystr)
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class method:
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def __init__(self,name, basis):
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self.name = name
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self.basis = basis
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@staticmethod
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def fromString(string):
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vals = string.split(",")
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if (vals.length == 2):
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return method(vals[0], vals[1])
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else:
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return method(vals[0], None)
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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):
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self.name = name
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self.version = version
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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 getMetadata(self):
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dic=super(oneStateDataFileBase,self).getMetadata()
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dic["Geometry"]= "" if self.geometry is None else self.geometry.toDataString()
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dic.move_to_end("DOI")
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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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return data
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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 twoStateDataFileBase(dataFileBase):
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def __init__(self):
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super(twoStateDataFileBase,self).__init__()
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self.GS=None
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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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return data
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def getMetadata(self):
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dic=super(twoStateDataFileBase,self).getMetadata()
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dic["GS"]= "" if self.GS is None else self.GS.toDataString()
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dic["ES"]="" if self.ES is None else self.ES.toDataString()
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dic.move_to_end("DOI")
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return dic
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class ZPEDataFile(twoStateDataFileBase):
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def __init__(self):
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super(ZPEDataFile,self).__init__()
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@staticmethod
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def GetFileType():
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return dataType.ZPE
|
||||
|
||||
class excitationBase:
|
||||
def __init__(self,initial, final):
|
||||
self.initial = initial
|
||||
self.final = final
|
||||
|
||||
class excitationValue(excitationBase):
|
||||
def __init__(self,initial, final, value):
|
||||
super(excitationValue,self).__init__(initial, final)
|
||||
self.value = value
|
||||
23
tools/lib/utils.py
Normal file
23
tools/lib/utils.py
Normal file
@ -0,0 +1,23 @@
|
||||
import itertools
|
||||
import sys
|
||||
from TexSoup import TexEnv,TexNode, RArg
|
||||
from collections.abc import Iterable
|
||||
def nodify(TexArray,envName="[tex]",parent=None):
|
||||
env=TexEnv(envName,TexArray)
|
||||
node=TexNode(env)
|
||||
node.parent=parent
|
||||
return node
|
||||
def desarg(tex):
|
||||
lst=[]
|
||||
for item in tex.contents:
|
||||
if type(item) is RArg:
|
||||
myitem=item.contents
|
||||
if type(myitem) is list:
|
||||
for myit in myitem:
|
||||
lst.append(myit)
|
||||
else:
|
||||
lst.append(myit)
|
||||
else:
|
||||
myitem=item
|
||||
lst.append(myitem)
|
||||
return nodify(lst,tex.name,tex.parent)
|
||||
Loading…
Reference in New Issue
Block a user