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Complete datafileBuilder.md docmentation file

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# DatafileBuilder # DatafileBuilder
DatafileBuilder.py is a script to read a $\LaTeX$ `tabular` environment to data file for the website DatafileBuilder.py is a script to read a $\mathrm{\LaTeX}$ `tabular` environment to data file for the website.
## Requirement ## Requirement
To run the script you must have this two elements To run the script you must have this two elements.
- Python≥3 - [Python](https://www.python.org/)≥3
- [TexSoup](https://github.com/alvinwan/TexSoup) - [TexSoup](https://github.com/alvinwan/TexSoup)
## Warning ## Command line usage
There is absolutly no guarantee of success ```
usage: datafileBuilder.py [-h] [--file FILE] [--defaultType {ABS,FLUO}]
[--format {LINE,COLUMN,TBE}] [--debug]
## Example input 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](#the-line-format)
## 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](#formats)
- **Simplify** the $\mathrm{\LaTeX}$ code of the input file as much as possible
## Input
### Input skeleton
```latex
% \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
```latex ```latex
\newcommand{\TDDFT}{TD-DFT} \newcommand{\TDDFT}{TD-DFT}
@ -31,7 +69,7 @@ There is absolutly no guarantee of success
\newcommand{\exCI}{exFCI} \newcommand{\exCI}{exFCI}
\newcommand{\FCI}{FCI} \newcommand{\FCI}{FCI}
% basis
\newcommand{\AVDZ}{aug-cc-pVDZ} \newcommand{\AVDZ}{aug-cc-pVDZ}
\newcommand{\AVTZ}{aug-cc-pVTZ} \newcommand{\AVTZ}{aug-cc-pVTZ}
\newcommand{\DAVTZ}{d-aug-cc-pVTZ} \newcommand{\DAVTZ}{d-aug-cc-pVTZ}
@ -42,7 +80,7 @@ There is absolutly no guarantee of success
\newcommand{\DAVPZ}{d-aug-cc-pV5Z} \newcommand{\DAVPZ}{d-aug-cc-pV5Z}
\newcommand{\PopleDZ}{6-31+G(d)} \newcommand{\PopleDZ}{6-31+G(d)}
% greek shortcut
\newcommand{\pis}{\pi^\star} \newcommand{\pis}{\pi^\star}
\newcommand{\Ryd}{\mathrm{R}} \newcommand{\Ryd}{\mathrm{R}}
@ -59,21 +97,21 @@ There is absolutly no guarantee of success
\end{tabular} \end{tabular}
``` ```
all '\newcommand' are applied to the cell of the tabular and the tabular is parsed to extract data All '\newcommand' are applied to the cell of the tabular and the tabular is parsed to extract data.
## General rules ### General rules
The general rules to extract data correctly are: The general rules to extract data correctly are:
- A `$` must not follow another `$` put space between them. - A `$` must not follow another `$` put space between them.
- The column number must be the same on each line in `tabular` - The column number must be the same on each row of the `tabular`
- Please respect the format of each tabular - Please respect the format of each tabular.
- Use standard $\LaTeX$ for the `multicolumn ` command and not a wrapper - Use standard $\mathrm{\LaTeX}$ for the `\multicolumn` command and not a wrapper.
- In general use standard $\LaTeX$ instead of dirty form for example - In general use standard $\mathrm{\LaTeX}$ instead of dirty form for example.
```latex ```latex
$A''$ % Bad $A''$ % Bad
@ -81,19 +119,140 @@ The general rules to extract data correctly are:
$A^{\prime\prime}$ %Good $A^{\prime\prime}$ %Good
``` ```
- D'ont put comment at the end of `tabular ` row (this cause a TexSoup bug) - 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 ` - Only `tabular` environment is supported please convert `longtable` and other table format to `tabular .
- After executing all commands the basis and methods name must be $\LaTeX$ free (only plan text)
- 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 values
Unsafe value (value that must not included in the statistics table and graph) must be in emphasis like Unsafe value (value that must not included in the statistics table and graph) must be in emphasis or with $\sim$ symbol like
$\emph{6.2}$ > *42*
> $\sim 42$
```latex ```latex
\emph{6.2} \emph{42} % unsafe=true
$\sim$ 42 % unsafe=true
42 % unsafe=false
``` ```
that set the unsafe that set the unsafe boolean value to true in the output data file
#### Formats
##### Generality
###### Transition format
```latex
$^m s[\mathrm{F}](T)$
```
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
```latex
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
```latex
\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
```latex
\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` but made for theoretical best estimate tabular
> Warning:
>
> The basis is not extract from the TBE format
```latex
\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`