Manuscript/QUEST_WIREs.tex

@@ -37,6 +37,8 @@
 \newcommand{\tabc}[1]{\multicolumn{1}{c}{#1}}
 \newcommand{\QP}{\textsc{quantum package}}
 \newcommand{\SupInf}{supporting information}
+%Vector
+\renewcommand{\vec}[1]{\bm{#1}}
 
 % Update article type if known
 \papertype{Review Article}
@@ -189,7 +191,7 @@ These basis sets have been downloaded from the \href{https://www.basissetexchang
 %==================================
 \subsection{Computational methods}
 %==================================
-
+\label{sec:methods}
 %------------------------------------------------
 \subsubsection{Reference computational methods}
 %------------------------------------------------
@@ -656,10 +658,95 @@ MAE			&				& 0.22	& 0.16	& 0.22	& 0.11	& 0.12	& 0.05	& 0.04	& 0.02	& 0.20	& 0.22
 \label{sec:website}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-\alert{Here comes the description of Mika's website.}
+{
-Here we describe the feature of the website that we have specifically designed to gather the entire data generated during these last few years.
+\newcommand{\meth}{\text{meth}}
-Thanks to this website, one can easily test and compare the accuracy of a given method with respect to various variables such as the molecule size or its family, the nature of the excited states, the size of the basis set, etc.
+\newcommand{\err}{\mathcal{E}}
+\newcommand{\nEx}{X}
+\newcommand{\nExnn}{\mathcal{X}}
+%=======================
+\subsection{Introduction}
+\label{sec:websiteIntro}
+%=======================
+The previous QUEST publications \cite{Loos_2018a,Loos_2019,Loos_2020b,Loos_2020c,Loos_2020d} expose vertical excitation data, some statistics were provided considering the most relevant parameters.
+But depending to the specific interest of quantum chemist this parameter selection can be irrelevant for his study.
+Furthermore to determine the accuracy of a new method, it must be compared with reference data, such as those of the QUEST project.
+For this we have to calculate the same type of statistics for the new method. The QUESTDB website was created exactly to solve these issues.
+%=======================
+\subsection{Specification}
+%=======================
+The website specification are the following
+\begin{itemize}
+	\item Display the QUEST excitations energy value as table
+	\item Allow to import local files from user's computer
+	\item Allow to filter data with various parameters
+	\item Calculate statistics from these parameters
+	\item Display a box plot graph to easily show the methods accuracy
+\end{itemize}
+This solve the issues described at \ref{sec:websiteIntro}
+%=======================
+\subsection{Project}
+%=======================
+The project containing two parts
 
+%------------------------------------------------
+\subsubsection{Website}
+%------------------------------------------------
+This is the main part of the project. All the calculation are made locally on the dataset page.
+Firstly the website proposes to the user to import new data \ref{sec:tools}.
+these data are added to the current session (and removed after lost the page).
+There are four multi selection list. Each list depends on the previous ones.
+These lists allow to select information about the selected sets \ref{fig:scheme}.
+Molecules \ref{fig:molecules} methods and basis \ref{sec:methods}.
+After there are many filters to choose the properties of included excitations.
+We provide also the ability to filter by molecule size or the active character percentage.
+After that we need to define a reference method to compare with (TBE by default).
+We also provide a flag to take off all the value declared not safe. We declared value as unsafe when the value have too big
+uncertainty.
+\paragraph{Statistics calculations}
+We want to calculate the accuracy of each couple method/basis compared to the reference (usually TBEs).
+For each method we define a vector containing all the energies of the user selected vertical transitions.
+With $\meth$ a couple method/basis and $E^x_\meth$ the energy of the vertical excitation $\nEx$ for the method $\meth$
+and $\err_\meth$ the error vector of the method $\meth$ compared to the reference $\text{ref}$
+\begin{equation}
+	\vec{E_\meth} = \qty{E^1_\meth, \ldots , E^\nEx_\meth}
+\end{equation}
+\begin{equation}
+	\err^x_\meth = E^x_\text{ref} - E^x_\meth
+\end{equation}
+When the vertical excitation $x$ is defined for the method $\meth$ and the method $\text{ref}$.
+So with $\nExnn$ the size of the vector $\vec{\err^x_\meth}$
+\begin{gather}
+	MSE_\meth =  \overline{{\vec{\err_\meth}}} = \frac{1}{\nExnn}\sum_{x=1}^\nExnn\err_\meth^x \\
+	MAE_\meth =  \overline{\abs{\vec{\err_\meth}}}  \\
+	RMSE_\meth = \sqrt{\overline{\vec{\err_\meth}^2}} \\
+	SDE_\meth = \sqrt{\frac{1}{\nExnn}\sum_{x=1}^\nExnn\err_x^2-MAE^2}
+\end{gather}
+These statistics allow user to determine the accuracy of each couple methods/basis.
+On the website the statistics are forwarded in a table and in a box plot graph.
+
+%------------------------------------------------
+\subsubsection{Data generation tools}
+\label{sec:tools}
+%------------------------------------------------
+There are currently two main tools to generate data \texttt{datafileBuilder} and \texttt{ADC25generator}
+\paragraph{datafileBuilder}
+The \texttt{datafileBuilder} tool is used to build datafile from {\LaTeX} \texttt{tabular}.
+The \texttt{tabular} is associated to some options and {\LaTeX} \texttt{\textbackslash newcommand} parsed by the main script and the \texttt{tabular} environment is converted to a \texttt{NumPy} 2d array.
+So the options, the {\LaTeX} \texttt{\textbackslash newcommand} to apply and the 2d array that represents the tabular environment are passed to the appropriate table parser module chosen using the \texttt{\textbackslash formatName} option in the input file.
+Each module is responsible to parse the \texttt{tabular} and return all the corresponding dataFiles as object.
+After, the main script output these objects to the corresponding files. Theses files can be used in the website
+By importing it temporarily or to make a pull request for the new data.
+The modular aspect of this tool gives us enough flexibility to easily convert many types of {\LaTeX} \texttt{tabular} to a standardized file format.
+\paragraph*{ADC25generator}
+The \texttt{ADC25generator} tool merge ADC(2) and ADC(3) metadata and calculate the ADC(2.5) energy from ADC(2) and ADC(3) datafile as
+\begin{equation}
+	E_\text{ADC(2.5)} = \frac{E_\text{ADC(2)}+E_\text{ADC(3)}}{2}
+\end{equation}
+and the value is considered as not safe when one or more value as not safe
+\begin{equation}
+	\mathrm{unsafe}_\text{ADC(2.5)} = \mathrm{unsafe}_\text{ADC(2)} \lor \mathrm{unsafe}_\text{ADC(3)}
+\end{equation}
+}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \section{Concluding remarks}
 \label{sec:ccl}