QUESTDB_website/docs/datafileBuilder.md

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.

• Python≥3
• TexSoup

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 mode

The 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}{exFCI}
\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 tabular

• Please respect the format of each tabular.

• Use standard \mathrm{\LaTeX} for the \multicolumn command and not a wrapper.

• In general use standard \mathrm{\LaTeX} instead of dirty form for example.

  $A''$ % Bad
  $A^"$ % Bad
  $A^{\prime\prime}$ %Good

• D’ont put comment at the end of tabular row (this cause a TexSoup bug).

• Only tabular environment is supported please convert longtable and other table format to `tabular .

• Only \newcommand are supported please convert \def and \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=false

that 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 final

All 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.dat

When 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,[isSupporting]

# Initial state            Final state                        Transition                    Energies (eV)   %T1    Oscilator forces     unsafe
#######################  #######################  ########################################  ############# ####### ################### ##############
# Number  Spin  Symm       Number  Spin  Symm         type                                    E_abs         %T1            f            is unsafe
  n       s      symm      n       s     symm         (excitationType)                        value         %T1val         forceval     isUnsafe

When each value are number spin value are integer symmetry and excitation type are standard LaTeX

isSupporting and isUnsafe are boolean corrresponded to JavaScript boolean values true or false