8.7 KiB
DatafileBuilder
DatafileBuilder.py is a script to read a \mathrm{\LaTeX} tabular
environment to data file for the website.
Requirement
To run the script you must have this two elements.
Command line usage
usage: datafileBuilder.py [-h] [--file FILE] [--defaultType {ABS,FLUO}]
[--format {LINE,COLUMN,TBE}] [--debug]
optional arguments:
-h, --help show this help message and exit
--file FILE
--defaultType {ABS,FLUO}
--format {LINE,COLUMN,TBE}
--debug Debug modeThe default type is ABS (for absorbtion).
The default format is LINE described below
Disclaimer
There is absolutly no guarantee of success.
If the program crach of if the result is not correct please:
- Check if the input file respect the selected format
- Simplify the \mathrm{\LaTeX} code of the input file as much as possible
Input
Input skeleton
% \newcommand area
\newcommand{}{}{}
% ther cusom commands definition with or without arguments
\newcommand{}{}
\begin{tabular}
% Tabular in one of the format supported by the script
\end{tabular}Example of input
\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}{FCI}
\newcommand{\FCI}{FCI}
\newcommand{\AVDZ}{aug-cc-pVDZ}
\newcommand{\AVTZ}{aug-cc-pVTZ}
\newcommand{\DAVTZ}{d-aug-cc-pVTZ}
\newcommand{\AVQZ}{aug-cc-pVQZ}
\newcommand{\DAVQZ}{d-aug-cc-pVQZ}
\newcommand{\TAVQZ}{t-aug-cc-pVQZ}
\newcommand{\AVPZ}{aug-cc-pV5Z}
\newcommand{\DAVPZ}{d-aug-cc-pV5Z}
\newcommand{\PopleDZ}{6-31+G(d)}
\newcommand{\pis}{\pi^\star}
\newcommand{\Ryd}{\mathrm{R}}
\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}}
\multicolumn{16}{c}{Water}\\
& \multicolumn{5}{c}{\AVDZ} & \multicolumn{4}{c}{\AVTZ}& \multicolumn{3}{c}{\AVQZ} & \multicolumn{3}{c}{Litt.}\\
State & {\CC{3}} & {\CCSDT} & {\CCSDTQ} & {\CCSDTQP} & {\exCI} & {\CC{3}} & {\CCSDT} & {\CCSDTQ} & {\exCI}& {\CC{3}} & {\CCSDT} & {\exCI} & Exp.$^a$ & Th.$^b$ & Th.$^c$\\
$^1B_1 (n \rightarrow 3s)$ &7.51&7.50&7.53&7.53&7.53 &7.60&7.59&7.62&7.62 &7.65 &7.64 &7.68 &7.41 &7.81&7.57\\
$^1A_2 (n \rightarrow 3p)$ &9.29&9.28&9.31&9.32&9.32 &9.38&9.37&9.40&9.41 &9.43 &9.41 &9.46 &9.20 &9.30&9.33\\
$^1A_1 (n \rightarrow 3s)$ &9.92&9.90&9.94&9.94&9.94 &9.97&9.95&9.98&9.99 &10.00 &9.98 &10.02 &9.67 &9.91&9.91\\
$^3B_1 (n \rightarrow 3s)$ &7.13&7.11&7.14&7.14&7.14 &7.23&7.22&7.24&7.25 &7.28 &7.26 &7.30 &7.20 &7.42&7.21\\
$^3A_2 (n \rightarrow 3p)$ &9.12&9.11&9.14&9.14&9.14 &9.22&9.20&9.23&9.24 &9.26 &9.25 &9.28 &8.90 &9.42&9.19\\
$^3A_1 (n \rightarrow 3s)$ &9.47&9.45&9.48&9.49&9.49 &9.52&9.50&9.53&9.54 &9.56 &9.54 &9.58 &9.46 &9.78&9.50\\
\end{tabular}All ‘\newcommand’ are applied to the cell of the tabular and the tabular is parsed to extract data.
General rules
The general rules to extract data correctly are:
A
$must not follow another$put space between them.The column number must be the same on each row of the
tabularPlease respect the format of each tabular.
Use standard \mathrm{\LaTeX} for the
\multicolumncommand and not a wrapper.In general use standard \mathrm{\LaTeX} instead of dirty form for example.
$A''$ % Bad $A^"$ % Bad $A^{\prime\prime}$ %GoodD’ont put comment at the end of
tabularrow (this cause a TexSoup bug).Only
tabularenvironment is supported please convertlongtableand other table format to `tabular .Only
\newcommandare supported please convert\defand\NewDocumentCommand.After executing all commands the basis and methods name must be \mathrm{\LaTeX} free (only plan text).
Unsafe values
Unsafe value (value that must not included in the statistics table and graph) must be in emphasis or with \sim symbol like
42 \sim 42
\emph{42} % unsafe=true
$\sim$ 42 % unsafe=true
42 % unsafe=falsethat set the unsafe boolean value to true in the output
data file
Formats
Generality
Transition format
$^m s[\mathrm{F}](T)$Where m is the multiplicity s is the
symetry and \mathrm{F} if it is present specifies that the
vertical transition is fluorescence
T is transition type and must be in the format
initial \rightarrow finalAll the \mathrm{\LaTeX} code in this
format must be standard latex except of the command define on the
\newcommand section
The line format
\begin{tabular}
& \multicolumn{n}{c}{Molecule} \\
& basis#1 & basis#2 & basis#n \\ % You can also use the LaTeX standard \multiculumn command
State & method#1 & method#2 method#n \\ % You can also use the LaTeX standard \multiculumn command
$Transition#1$ & value11&value#12 & ... value#1n\\
$Transition#2$ & value21&value#22 & ... value#2n\\
% All the other transition
$Transition#m$ & value#m1&value#m2 & ... value#mn\\
\end{tabular}The column format
\begin{tabular}
& & basis#1 & basis#2 & basis#n \\ % You can also use the LaTeX standard \multiculumn command
Molecule &State & method#1 & method#2 method#n \\ % You can also use the LaTeX standard \multiculumn command
molecule#1 &$Transition#11$ &value#111&value#112 ... &value#11n \\
&$Transition#12$ &value#121&value#122 &value#12n \\
% Other transition on the molecule#1
&$Transition#1m$ &value#1m1&value#1m1 &value#1nm \\
% Other molecules
molecule#k &$Transition#k1$ &value#k11&value#k12 ... &value#k1n \\
% Other transition on the molecule#k
&$Transition#km$ &value#km1&value#km2 &value#kmn \\
\end{tabular}This format is very powerfull because it can be used with multiple molecules.
The TBE format
The TBE format is a variant of the COLUMN
format but made for theoretical best estimate tabular.
Warning:
The basis is not extract from the TBE format
\begin{tabular}
& & & & TBE(FC)& \multicolumn{3}{c}{Corrected TBE} \\
& State & $f$ & \%$T_1$ & basis & Method & Corr. & Value \\
molecule#1 &$transition#11$ & fvalue#11 &\%T_1value#11& fceval#11 & not used value & not used value & eval#11 \\
&$transition#12$ & fvalue#12 &\%T_1value#12& fceval#12 & not used value & not used value & eval#12 \\
% Other transition on the same molecule
&$transition#1n$ & fvalue#12 &\%T_1value#12& fceval#1n & not used value & not used value & eval#12 \\
molecule#m &$transition#m1$ & fvalue#m1 &\%T_1value#m1& fceval#m1 & not used value & not used value & eval#k1 \\
&$transition#m2$ & fvalue#m2 &\%T_1value#m2& fceval#m2 & not used value & not used value & eval#m2 \\
% Other transition on the same molecule
&$transition#mn$ & fvalue#mn &\%T_1value#mn& fceval#mn & not used value & not used value & eval#mn \\
\end{tabular}Output
Directory strucure
data
├── abs
│ ├── molecule#1_method#1_basis#1.dat
│ ├── ...
│ ├── molecule#n_basis#m_method#k.dat
│ └── molecule#n_basis#m_method#k.dat
└── fluo
├── molecule#1_method#1_basis#1.dat
├── ...
├── molecule#n_basis#m_method#k.dat
└── molecule#n_basis#m_method#k.datWhen the debug flag is used instead of data/ the root of
output directory is data/test/
Output file
# Molecule : moleculename
# Comment :
# code : codename,[version]
# method : method,[basis]
# geom : method,[basis]
# DOI : DOI
# Initial state Final state Transition Energies (eV) %T1 Oscilator strenght unsafe
####################### ####################### ######################################## ############# ####### ################### ##############
# Number Spin Symm Number Spin Symm type E_abs %T1 f is unsafe
n s symm n s symm (excitationType) value %T1val forceval isUnsafeWhen each value are number spin value are integer symmetry and excitation type are standard LaTeX
isUnsafe is boolean corrresponded to JavaScript boolean
values true or false