From a00e811d5cf694ad5e0eec2bc47675dd89e8d820 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Fri, 16 Oct 2020 17:43:16 +0200 Subject: [PATCH 01/15] Start working on website section --- Manuscript/QUEST_WIREs.tex | 46 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index c85336e..ac411b7 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -589,6 +589,52 @@ Additionally, we also provide a specific analysis for each type of excited state \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. 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. +%======================= +\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 irrelevent 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 for that. +%======================= +\subsection{Specification} +%======================= +Consider +The website specification are the following +\begin{itemize} + \item Display the QUEST excitation varues as table + \item Allow to import local file from the local coputer + \item Allow to filter data with various parameters + \item Calculate statistics from this parameters + \item Display a box plot graph to easly show the methods accuracy +\end{itemize} + +this solve the issues described at \ref{sec:websiteIntro} +\subsection{Project} +The project containing two parts + +%------------------------------------------------ +\subsubsection{Website} +%------------------------------------------------ +The website is the main part of the project. +With the website we can find all the data from the QUEST project and make various statistics calculation. + + +%------------------------------------------------ +\subsubsection{Data generation tools} +%------------------------------------------------ +There are currently two main tool to generate data \texttt{datafileBuilder} and \texttt{ADC25generator} +\paragraph{datafileBuilder} +\paragraph*{ADC25generator} +The \texttt{ADC25generator} tool merge ADC(2) and ADC(3) metadata and calculate the ADC(2.3) energy as +\begin{equation} + E_\text{ADC(23)} = \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(23)} = \mathrm{unsafe}_\text{ADC(2)} \lor \mathrm{unsafe}_\text{ADC(3)} +\end{equation} %%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Concluding remarks} From 308be26c449409c198ed54ace88eb6e680a4020c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Wed, 21 Oct 2020 14:40:49 +0200 Subject: [PATCH 02/15] Fix typo --- Manuscript/QUEST_WIREs.tex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index ac411b7..685e8ae 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -603,7 +603,7 @@ For this we have to calculate the same type of statistics for the new method. Th Consider The website specification are the following \begin{itemize} - \item Display the QUEST excitation varues as table + \item Display the QUEST excitations energie value as table \item Allow to import local file from the local coputer \item Allow to filter data with various parameters \item Calculate statistics from this parameters From a76ace515b9c198f52310a426655e43d24e17af4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Thu, 22 Oct 2020 13:24:20 +0200 Subject: [PATCH 03/15] Complete the information on website with details on the statisticals calculations --- Manuscript/QUEST_WIREs.tex | 48 +++++++++++++++++++++++++++++++------- 1 file changed, 40 insertions(+), 8 deletions(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 685e8ae..4aa9a7b 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -30,6 +30,8 @@ \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} @@ -181,7 +183,7 @@ Doubly- and triply-augmented basis sets are usually employed for Rydberg states %================================== \subsection{Computational methods} %================================== - +\label{sec:methods} %------------------------------------------------ \subsubsection{Reference computational methods} %------------------------------------------------ @@ -594,7 +596,7 @@ Thanks to this website, one can easily test and compare the accuracy of a given \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 irrelevent for his study. +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 for that. %======================= @@ -603,11 +605,11 @@ For this we have to calculate the same type of statistics for the new method. Th Consider The website specification are the following \begin{itemize} - \item Display the QUEST excitations energie value as table - \item Allow to import local file from the local coputer + \item Display the QUEST excitations energy value as table + \item Allow to import local file from the local computer \item Allow to filter data with various parameters \item Calculate statistics from this parameters - \item Display a box plot graph to easly show the methods accuracy + \item Display a box plot graph to easely show the methods accuracy \end{itemize} this solve the issues described at \ref{sec:websiteIntro} @@ -617,12 +619,42 @@ The project containing two parts %------------------------------------------------ \subsubsection{Website} %------------------------------------------------ -The website is the main part of the project. -With the website we can find all the data from the QUEST project and make various statistics calculation. - +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 for multi selection dropdown list. Each dropdown depend to the previous. +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. +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 $\text{meth}$ a couple method/basis and $E^x_\text{meth}$ the energy of the vertical excitation $x$ for the method $\text{meth}$. +And $\mathcal{E}_\text{meth}$ the error vector of the method $\text{meth}$ compared to the reference $\text{ref}$ +\begin{equation} + \vec{E_\text{meth}} = \qty{E^1_\text{meth}, \ldots , E^X_\text{meth}} +\end{equation} +\begin{equation} + \mathcal{E}^x_\text{meth} = E^x_\text{ref} - E^x_\text{meth} +\end{equation} +When the vertical excitation $x$ is defined for the method $\text{meth}$ and the method $\text{ref}$. +So with $X$ the size of the vector $\vec{\mathcal{E}^x_\text{meth}}$ +\begin{gather} + MSE_\text{meth} = \overline{{\vec{\mathcal{E}_\text{meth}}}} \\ + MAE_\text{meth} = \overline{\abs{\vec{\mathcal{E}_\text{meth}}}} \\ + RMSE_\text{meth} = \sqrt{\overline{\vec{\mathcal{E}_\text{meth}}^2}} \\ + SDE_\text{meth} = \sqrt{\frac{1}{X}\sum_{x=1}^X\mathcal{E}_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 tabular and in a box plot graph. %------------------------------------------------ \subsubsection{Data generation tools} +\label{sec:tools} %------------------------------------------------ There are currently two main tool to generate data \texttt{datafileBuilder} and \texttt{ADC25generator} \paragraph{datafileBuilder} From ad27f6a1d3c1a4f2f29a53e6b7431421e7b326b5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Fri, 23 Oct 2020 10:59:18 +0200 Subject: [PATCH 04/15] Fix space before point --- Manuscript/QUEST_WIREs.tex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 4aa9a7b..bf47689 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -619,7 +619,7 @@ The project containing two parts %------------------------------------------------ \subsubsection{Website} %------------------------------------------------ -All the calculation are made locally on the dataset page . +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 for multi selection dropdown list. Each dropdown depend to the previous. From 55b002931a268962bfa6461f5dc42bd17f4f7e89 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Mon, 26 Oct 2020 15:24:02 +0100 Subject: [PATCH 05/15] Fix typ --- Manuscript/QUEST_WIREs.tex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index bf47689..75ef4c9 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -609,7 +609,7 @@ The website specification are the following \item Allow to import local file from the local computer \item Allow to filter data with various parameters \item Calculate statistics from this parameters - \item Display a box plot graph to easely show the methods accuracy + \item Display a box plot graph to easily show the methods accuracy \end{itemize} this solve the issues described at \ref{sec:websiteIntro} From f1021c4ac0e7dcac68e75e288bf0250e4fd92188 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Mon, 26 Oct 2020 15:24:53 +0100 Subject: [PATCH 06/15] Add text about datafileBuilder --- Manuscript/QUEST_WIREs.tex | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 75ef4c9..5463398 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -658,6 +658,12 @@ On the website the statistics are forwarded in a tabular and in a box plot graph %------------------------------------------------ There are currently two main tool 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{\\newcommand} parsed by the main script and the \texttt{tabular} environment is converted to a \texttt{NumPy} 2d array. +So the options, \texttt{\\newcommand} and 2d array are passed to the appropriate table parser module chosen using the the \texttt{\\formatName} option in the input file. +Each module is responsible to parse the \texttt{tabular} and return all the corresponding dataFiles as object. +After theses object are outputted to files by the main script. Theses file can be used in the website. +The modular aspect of this tool give us enough flexibility to easily convert0 many type of {\LaTeX} \texttt{tabular} to an uniformized file format. \paragraph*{ADC25generator} The \texttt{ADC25generator} tool merge ADC(2) and ADC(3) metadata and calculate the ADC(2.3) energy as \begin{equation} From 7add11dae55c2c3cfe8bcb49e5a674c00ea16843 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Tue, 27 Oct 2020 11:48:58 +0100 Subject: [PATCH 07/15] Add local commands for website chapter and fix error vector size --- Manuscript/QUEST_WIREs.tex | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index be71649..6bf223c 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -662,6 +662,11 @@ MAE & & 0.22 & 0.16 & 0.22 & 0.11 & 0.12 & 0.05 & 0.04 & 0.02 & 0.20 & 0.22 Here we describe the feature of the website that we have specifically designed to gather the entire data generated during these last few years. 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{\meth}{\text{meth}} +\newcommand{\err}{\mathcal{E}} +\newcommand{\nEx}{X} +\newcommand{\nExnn}{\mathcal{X}} \subsection{Introduction} \label{sec:websiteIntro} %======================= @@ -703,21 +708,21 @@ 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 $\text{meth}$ a couple method/basis and $E^x_\text{meth}$ the energy of the vertical excitation $x$ for the method $\text{meth}$. -And $\mathcal{E}_\text{meth}$ the error vector of the method $\text{meth}$ compared to the reference $\text{ref}$ +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_\text{meth}} = \qty{E^1_\text{meth}, \ldots , E^X_\text{meth}} + \vec{E_\meth} = \qty{E^1_\meth, \ldots , E^\nEx_\meth} \end{equation} \begin{equation} - \mathcal{E}^x_\text{meth} = E^x_\text{ref} - E^x_\text{meth} + \err^x_\meth = E^x_\text{ref} - E^x_\meth \end{equation} -When the vertical excitation $x$ is defined for the method $\text{meth}$ and the method $\text{ref}$. -So with $X$ the size of the vector $\vec{\mathcal{E}^x_\text{meth}}$ +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_\text{meth} = \overline{{\vec{\mathcal{E}_\text{meth}}}} \\ - MAE_\text{meth} = \overline{\abs{\vec{\mathcal{E}_\text{meth}}}} \\ - RMSE_\text{meth} = \sqrt{\overline{\vec{\mathcal{E}_\text{meth}}^2}} \\ - SDE_\text{meth} = \sqrt{\frac{1}{X}\sum_{x=1}^X\mathcal{E}_x^2-MAE^2} + MSE_\meth = \overline{{\vec{\err_\meth}}} \\ + 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 tabular and in a box plot graph. @@ -743,7 +748,7 @@ And the value is considered as not safe when one or more value as not safe \begin{equation} \mathrm{unsafe}_\text{ADC(23)} = \mathrm{unsafe}_\text{ADC(2)} \lor \mathrm{unsafe}_\text{ADC(3)} \end{equation} - +} %%%%%%%%%%%%%%%%%%%%%%%%%%%%% \section{Concluding remarks} \label{sec:ccl} From dff5f2bc7a85994694ed4be44337b8c2ac713a94 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Tue, 27 Oct 2020 11:53:39 +0100 Subject: [PATCH 08/15] MSE explicit --- Manuscript/QUEST_WIREs.tex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 6bf223c..8de3660 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -719,7 +719,7 @@ And $\err_\meth$ the error vector of the method $\meth$ compared to the referenc 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}}} \\ + 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} From 77f2ed4faae84644c7d01a90feefc176b6c655e4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Tue, 27 Oct 2020 11:59:40 +0100 Subject: [PATCH 09/15] Fix \newcommand in text --- Manuscript/QUEST_WIREs.tex | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 8de3660..895cc9c 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -734,8 +734,8 @@ On the website the statistics are forwarded in a tabular and in a box plot graph There are currently two main tool 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{\\newcommand} parsed by the main script and the \texttt{tabular} environment is converted to a \texttt{NumPy} 2d array. -So the options, \texttt{\\newcommand} and 2d array are passed to the appropriate table parser module chosen using the the \texttt{\\formatName} option in the input file. +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, \texttt{\textbackslash newcommand} and 2d array are passed to the appropriate table parser module chosen using the the \texttt{\\formatName} option in the input file. Each module is responsible to parse the \texttt{tabular} and return all the corresponding dataFiles as object. After theses object are outputted to files by the main script. Theses file can be used in the website. The modular aspect of this tool give us enough flexibility to easily convert0 many type of {\LaTeX} \texttt{tabular} to an uniformized file format. From 2680710ad196b5413cba49ba29ffc6bce0101bcf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Wed, 28 Oct 2020 15:32:39 +0100 Subject: [PATCH 10/15] Replace tabular by table --- Manuscript/QUEST_WIREs.tex | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 895cc9c..5451c42 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -725,7 +725,7 @@ So with $\nExnn$ the size of the vector $\vec{\err^x_\meth}$ 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 tabular and in a box plot graph. +On the website the statistics are forwarded in a table and in a box plot graph. %------------------------------------------------ \subsubsection{Data generation tools} From 21ebf55635a937e7c322b98e8e2bcbf3730efb89 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Wed, 28 Oct 2020 16:59:17 +0100 Subject: [PATCH 11/15] Many fixes and addition for the website section --- Manuscript/QUEST_WIREs.tex | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 5451c42..f296ae2 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -661,18 +661,18 @@ MAE & & 0.22 & 0.16 & 0.22 & 0.11 & 0.12 & 0.05 & 0.04 & 0.02 & 0.20 & 0.22 \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. 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{\meth}{\text{meth}} \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. +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 for that. %======================= \subsection{Specification} @@ -681,14 +681,16 @@ Consider The website specification are the following \begin{itemize} \item Display the QUEST excitations energy value as table - \item Allow to import local file from the local computer + \item Allow to import local files from the local computer \item Allow to filter data with various parameters - \item Calculate statistics from this 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 %------------------------------------------------ @@ -731,22 +733,23 @@ 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 tool to generate data \texttt{datafileBuilder} and \texttt{ADC25generator} +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, \texttt{\textbackslash newcommand} and 2d array are passed to the appropriate table parser module chosen using the the \texttt{\\formatName} option in the input file. +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 theses object are outputted to files by the main script. Theses file can be used in the website. -The modular aspect of this tool give us enough flexibility to easily convert0 many type of {\LaTeX} \texttt{tabular} to an uniformized file format. +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 uniformed file format. \paragraph*{ADC25generator} -The \texttt{ADC25generator} tool merge ADC(2) and ADC(3) metadata and calculate the ADC(2.3) energy as +The \texttt{ADC25generator} tool merge ADC(2) and ADC(3) metadata and calculate the ADC(2.5) energy from ADC(2) ADC(3) as \begin{equation} - E_\text{ADC(23)} = \frac{E_\text{ADC(2)}+E_\text{ADC(3)}}{2} + 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(23)} = \mathrm{unsafe}_\text{ADC(2)} \lor \mathrm{unsafe}_\text{ADC(3)} + \mathrm{unsafe}_\text{ADC(2.5)} = \mathrm{unsafe}_\text{ADC(2)} \lor \mathrm{unsafe}_\text{ADC(3)} \end{equation} } %%%%%%%%%%%%%%%%%%%%%%%%%%%%% From 4842e4a1d32b4b076ea276c8bc6a10676c151030 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Thu, 29 Oct 2020 16:54:24 +0100 Subject: [PATCH 12/15] Remove alone word --- Manuscript/QUEST_WIREs.tex | 1 - 1 file changed, 1 deletion(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index f296ae2..07b0f95 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -677,7 +677,6 @@ For this we have to calculate the same type of statistics for the new method. Th %======================= \subsection{Specification} %======================= -Consider The website specification are the following \begin{itemize} \item Display the QUEST excitations energy value as table From 87de29b62da874243a8f7e1f4653b465e03f89a5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Thu, 29 Oct 2020 17:34:11 +0100 Subject: [PATCH 13/15] Improve website part --- Manuscript/QUEST_WIREs.tex | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 07b0f95..0bed6b8 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -698,7 +698,7 @@ The project containing two parts 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 for multi selection dropdown list. Each dropdown depend to the previous. +There are for multi selection dropdown 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. @@ -708,9 +708,9 @@ We also provide a flag to take off all the value declared not safe. We declared 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 $\text{ref}$ +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} @@ -740,9 +740,9 @@ So the options, the {\LaTeX} \texttt{\textbackslash newcommand} to apply and the 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 uniformed file format. +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) ADC(3) as +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} From 58dc670491d3d9477c24ddd5eb2dccd131cf724b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Mon, 2 Nov 2020 17:02:10 +0100 Subject: [PATCH 14/15] Remove Titou website \alert --- Manuscript/QUEST_WIREs.tex | 3 --- 1 file changed, 3 deletions(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 0bed6b8..0525738 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -658,9 +658,6 @@ 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. -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{\meth}{\text{meth}} \newcommand{\err}{\mathcal{E}} From b19a8cf5852c851c022575377a811233b331b59e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Micka=C3=ABl=20V=C3=A9ril?= Date: Mon, 2 Nov 2020 17:27:40 +0100 Subject: [PATCH 15/15] Last fix before titou looks --- Manuscript/QUEST_WIREs.tex | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/Manuscript/QUEST_WIREs.tex b/Manuscript/QUEST_WIREs.tex index 0525738..6e74470 100644 --- a/Manuscript/QUEST_WIREs.tex +++ b/Manuscript/QUEST_WIREs.tex @@ -670,20 +670,19 @@ MAE & & 0.22 & 0.16 & 0.22 & 0.11 & 0.12 & 0.05 & 0.04 & 0.02 & 0.20 & 0.22 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 for that. +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 the local computer + \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} +This solve the issues described at \ref{sec:websiteIntro} %======================= \subsection{Project} %======================= @@ -692,14 +691,14 @@ The project containing two parts %------------------------------------------------ \subsubsection{Website} %------------------------------------------------ -All the calculation are made locally on the dataset page. +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 for multi selection dropdown list. each list depends on the previous ones +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. +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. @@ -717,7 +716,7 @@ and $\err_\meth$ the error vector of the method $\meth$ compared to the referenc 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 \\ + 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} @@ -743,7 +742,7 @@ The \texttt{ADC25generator} tool merge ADC(2) and ADC(3) metadata and calculate \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 +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}