mirror of
https://github.com/LCPQ/QUESTDB_website.git
synced 2024-12-26 14:23:42 +01:00
261 lines
8.7 KiB
Markdown
261 lines
8.7 KiB
Markdown
# DatafileBuilder
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DatafileBuilder.py is a script to read a $\mathrm{\LaTeX}$ `tabular` environment to data file for the website.
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## Requirement
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To run the script you must have this two elements.
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- [Python](https://www.python.org/)≥3
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- [TexSoup](https://github.com/alvinwan/TexSoup)
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## Command line usage
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```
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usage: datafileBuilder.py [-h] [--file FILE] [--defaultType {ABS,FLUO}]
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[--format {LINE,COLUMN,TBE}] [--debug]
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optional arguments:
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-h, --help show this help message and exit
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--file FILE
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--defaultType {ABS,FLUO}
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--format {LINE,COLUMN,TBE}
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--debug Debug mode
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```
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The default type is `ABS` (for absorbtion).
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The default format is `LINE ` described [below](#the-line-format)
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## Disclaimer
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There is **absolutly no guarantee** of success.
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If the program crach of if the result is not correct please:
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- Check if the input file respect the selected [format](#formats)
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- **Simplify** the $\mathrm{\LaTeX}$ code of the input file as much as possible
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## Input
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### Input skeleton
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```latex
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% \newcommand area
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\newcommand{}{}{}
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% ther cusom commands definition with or without arguments
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\newcommand{}{}
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\begin{tabular}
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% Tabular in one of the format supported by the script
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\end{tabular}
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```
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### Example of input
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```latex
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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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\newcommand{\AVDZ}{aug-cc-pVDZ}
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\newcommand{\AVTZ}{aug-cc-pVTZ}
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\newcommand{\DAVTZ}{d-aug-cc-pVTZ}
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\newcommand{\AVQZ}{aug-cc-pVQZ}
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\newcommand{\DAVQZ}{d-aug-cc-pVQZ}
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\newcommand{\TAVQZ}{t-aug-cc-pVQZ}
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\newcommand{\AVPZ}{aug-cc-pV5Z}
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\newcommand{\DAVPZ}{d-aug-cc-pV5Z}
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\newcommand{\PopleDZ}{6-31+G(d)}
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\newcommand{\pis}{\pi^\star}
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\newcommand{\Ryd}{\mathrm{R}}
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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}{Water}\\
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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.$^a$ & Th.$^b$ & Th.$^c$\\
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$^1B_1 (n \rightarrow 3s)$ &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\\
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$^1A_2 (n \rightarrow 3p)$ &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\\
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$^1A_1 (n \rightarrow 3s)$ &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\\
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$^3B_1 (n \rightarrow 3s)$ &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\\
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$^3A_2 (n \rightarrow 3p)$ &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\\
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$^3A_1 (n \rightarrow 3s)$ &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\\
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\end{tabular}
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```
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All '\newcommand' are applied to the cell of the tabular and the tabular is parsed to extract data.
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### General rules
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The general rules to extract data correctly are:
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- A `$` must not follow another `$` put space between them.
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- The column number must be the same on each row of the `tabular`
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- Please respect the format of each tabular.
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- Use standard $\mathrm{\LaTeX}$ for the `\multicolumn` command and not a wrapper.
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- In general use standard $\mathrm{\LaTeX}$ instead of dirty form for example.
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```latex
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$A''$ % Bad
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$A^"$ % Bad
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$A^{\prime\prime}$ %Good
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```
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- D'ont put comment at the end of `tabular ` row (this cause a TexSoup bug).
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- Only `tabular` environment is supported please convert `longtable` and other table format to `tabular .
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- Only `\newcommand` are supported please convert `\def` and `\NewDocumentCommand`.
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- After executing all commands the basis and methods name must be $\mathrm{\LaTeX}$ free (only plan text).
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### Unsafe values
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Unsafe value (value that must not included in the statistics table and graph) must be in emphasis or with $\sim$ symbol like
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> *42*
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> $\sim 42$
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```latex
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\emph{42} % unsafe=true
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$\sim$ 42 % unsafe=true
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42 % unsafe=false
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```
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that set the unsafe boolean value to `true ` in the output data file
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#### Formats
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##### Generality
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###### Transition format
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```latex
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$^m s[\mathrm{F}](T)$
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```
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Where `m` is the multiplicity `s` is the symetry and `\mathrm{F}` if it is present specifies that the vertical transition is fluorescence
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T is transition type and must be in the format
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```latex
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initial \rightarrow final
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```
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All the $\mathrm{\LaTeX}$ code in this format must be standard latex except of the command define on the `\newcommand` section
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##### The line format
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```latex
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\begin{tabular}
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& \multicolumn{n}{c}{Molecule} \\
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& basis#1 & basis#2 & basis#n \\ % You can also use the LaTeX standard \multiculumn command
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State & method#1 & method#2 method#n \\ % You can also use the LaTeX standard \multiculumn command
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$Transition#1$ & value11&value#12 & ... value#1n\\
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$Transition#2$ & value21&value#22 & ... value#2n\\
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% All the other transition
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$Transition#m$ & value#m1&value#m2 & ... value#mn\\
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\end{tabular}
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```
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##### The column format
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```latex
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\begin{tabular}
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& & basis#1 & basis#2 & basis#n \\ % You can also use the LaTeX standard \multiculumn command
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Molecule &State & method#1 & method#2 method#n \\ % You can also use the LaTeX standard \multiculumn command
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molecule#1 &$Transition#11$ &value#111&value#112 ... &value#11n \\
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&$Transition#12$ &value#121&value#122 &value#12n \\
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% Other transition on the molecule#1
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&$Transition#1m$ &value#1m1&value#1m1 &value#1nm \\
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% Other molecules
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molecule#k &$Transition#k1$ &value#k11&value#k12 ... &value#k1n \\
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% Other transition on the molecule#k
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&$Transition#km$ &value#km1&value#km2 &value#kmn \\
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\end{tabular}
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```
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This format is very powerfull because it can be used with multiple molecules.
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##### The TBE format
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The `TBE` format is a variant of the `COLUMN` format but made for theoretical best estimate tabular.
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> Warning:
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>
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> The basis is not extract from the TBE format
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```latex
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\begin{tabular}
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& & & & TBE(FC)& \multicolumn{3}{c}{Corrected TBE} \\
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& State & $f$ & \%$T_1$ & basis & Method & Corr. & Value \\
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molecule#1 &$transition#11$ & fvalue#11 &\%T_1value#11& fceval#11 & not used value & not used value & eval#11 \\
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&$transition#12$ & fvalue#12 &\%T_1value#12& fceval#12 & not used value & not used value & eval#12 \\
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% Other transition on the same molecule
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&$transition#1n$ & fvalue#12 &\%T_1value#12& fceval#1n & not used value & not used value & eval#12 \\
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molecule#m &$transition#m1$ & fvalue#m1 &\%T_1value#m1& fceval#m1 & not used value & not used value & eval#k1 \\
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&$transition#m2$ & fvalue#m2 &\%T_1value#m2& fceval#m2 & not used value & not used value & eval#m2 \\
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% Other transition on the same molecule
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&$transition#mn$ & fvalue#mn &\%T_1value#mn& fceval#mn & not used value & not used value & eval#mn \\
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\end{tabular}
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```
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## Output
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### Directory strucure
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```
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data
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├── abs
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│ ├── molecule#1_method#1_basis#1.dat
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│ ├── ...
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│ ├── molecule#n_basis#m_method#k.dat
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│ └── molecule#n_basis#m_method#k.dat
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└── fluo
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├── molecule#1_method#1_basis#1.dat
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├── ...
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├── molecule#n_basis#m_method#k.dat
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└── molecule#n_basis#m_method#k.dat
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```
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When the debug flag is used instead of `data/` the root of output directory is `data/test/`
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### Output file
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```
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# Molecule : moleculename
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# Comment :
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# code : codename,[version]
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# method : method,[basis]
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# geom : method,[basis]
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# DOI : DOI,[isSupporting]
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# Initial state Final state Transition Energies (eV) %T1 Oscilator forces unsafe
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####################### ####################### ######################################## ############# ####### ################### ##############
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# Number Spin Symm Number Spin Symm type E_abs %T1 f is unsafe
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n s symm n s symm (excitationType) value %T1val forceval isUnsafe
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```
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When each value are number spin value are integer symmetry and excitation type are standard LaTeX
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isSupporting and isUnsafe are boolean corrresponded to `JavaScript` boolean values `true` or `false`
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