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Update website (without merge conflict) #4

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loos merged 8 commits from mveril/QUESTDB:website into master 2020-11-19 16:26:16 +01:00
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.gitignore vendored
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@ -22,6 +22,7 @@
*latexmk
*.run.xml
*-blx.bib
*.thm
# pdf output
QUEST_WIREs.pdf

44
Manuscript/QUEST_WIREs.tex
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@ -15,7 +15,7 @@
% \documentclass[blind,alpha-refs]{wiley-article}
% Add additional packages here if required
\usepackage{graphicx,dcolumn,bm,xcolor,microtype,multirow,amscd,amsmath,amssymb,amsfonts,physics,longtable,mhchem,siunitx,rotating,threeparttable,threeparttablex}
\usepackage{graphicx,dcolumn,bm,xcolor,microtype,multirow,amscd,amsmath,amssymb,amsfonts,physics,longtable,mhchem,siunitx,rotating,threeparttable,threeparttablex,ntheorem}
\usepackage[
colorlinks=true,
@ -324,7 +324,7 @@ A Python code associated with this procedure is provided in the {\SupInf}.
The singlet and triplet FCI/6-31+G(d) excitation energies and their corresponding error bars estimated with the method presented above based on Gaussian random variables are reported in Table \ref{tab:cycles}.
For the sake of comparison, we also report the CC3 and CCSDT vertical energies from Ref.~\cite{Loos_2020b} computed in the same basis.
%DJ: discuter en 1 ligne de la diff CC3/CCSDT ? Ce ne sont pas des Žtats "durs" ˆ avoir ?
%DJ: discuter en 1 ligne de la diff CC3/CCSDT ? Ce ne sont pas des <EFBFBD>tats "durs" <20> avoir ?
The estimated values of the excitation energies obtained via a three-point linear extrapolation considering the three largest CIPSI wave functions are also gathered in Table \ref{tab:cycles}.
In this case, the error bar is estimated via the extrapolation distance, \ie, the difference in excitation energies obtained with the three-point linear extrapolation and the largest CIPSI wave function.
This strategy has been considered in some of our previous works \cite{Loos_2020b,Loos_2020c,Loos_2020e}.
@ -516,7 +516,7 @@ We refer the interested reader to the {\SupInf} for a detailed discussion of eac
% The outliers are shown as dots.
% \label{fig:QUEST5_stat}}
%\end{figure}
%DJ: Bcp de choses pour cette Fig: 1) la caption dans la Fig est illisible + enelver AVTZ + mettre les mŽthoides dans un ordre logique
%DJ: Bcp de choses pour cette Fig: 1) la caption dans la Fig est illisible + enelver AVTZ + mettre les m<EFBFBD>thoides dans un ordre logique
%DJ: Ce n'est que pour Quest 5 ou c'est l'ensemble ??? Pas sur de savoir de vos valeurs en fait
%DJ: que les safes states ?
@ -1121,7 +1121,7 @@ MAE & & 0.22 & 0.16 & 0.22 & 0.11 & 0.12 & 0.05 & 0.04 & 0.02 & 0.20 & 0.22
{
\newcommand{\meth}{\text{meth}}
\newcommand{\err}{\mathcal{E}}
\newcommand{\err}{e}
\newcommand{\nEx}{X}
\newcommand{\nExnn}{\mathcal{X}}
%=======================
@ -1144,6 +1144,29 @@ The website specification are the following
\item Display a box plot graph to easily show the methods accuracy
\end{itemize}
This solve the issues described at \ref{sec:websiteIntro}
%=======================
\subsection{Usage}
%=======================
We built the website to meet mainly two useage.
\theoremstyle{break}
\theorembodyfont{\normalfont}
\newtheorem{scenar}{Scenario}{}
\begin{scenar}
\label{scenar:choose}
The user wants to choose a method for his calculation or a series of calculations.
Of course he search a compromise between the accuracy and the cost of the method.
In this case he wants to compare the accuracy of each method with a subset of excitations data corresponding to his target.
He can optimise the filter to correspond to his target (Molecular size, molecule or excitation type).
If it is possible he can only select the target molecule when this molecule is available in the QUEST data.
\end{scenar}
\begin{scenar}
\label{scenar:new}
The user has created a new method and wants to compare its accuracy with the methods of the QUEST project.
Fistly he has to create an input file for the Python tools (see Sec.~\ref{sec:gentools}) by formating the calculated results as a {\LaTeX} \texttt{tabular}.
After the data generation using the same python tools we are used to import the QUEST data, he must to import the new absorption and the fluorescence data files using the button on the website.
So the new data are used in the same way than the references data to generate statistics and he can use the website to compute the statistics in order to compare the methods.
\end{scenar}
%=======================
\subsection{Project}
%=======================
@ -1153,11 +1176,11 @@ 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:gentools}.
Firstly the website proposes to the user to import new data (see Sec.~\ref{sec:gentools}).
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}.
Molecules \ref{fig:molecules} methods and basis (see Sec.~\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).
@ -1180,15 +1203,20 @@ So with $\nExnn$ the size of the vector $\vec{\err^x_\meth}$
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.
These statistics data inform about the accuracy of the methods compared to the reference.
\begin{gather}
SDE_\meth = \sqrt{\frac{1}{\nExnn}\sum_{x=1}^\nExnn(\err_x-MAE)^2}
\end{gather}
This statistics data inform about the precision of the methods compared to the reference.
On the website the statistics are forwarded in a table and in a box plot graph.
%------------------------------------------------
\subsubsection{Data generation tools}
\label{sec:gentools}
%------------------------------------------------
There are multiple that we used to generate the data.
These tools can also be used by the user (see scenario \ref{scenar:new})
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}.