Commit 3495ee5a authored by Youngseob KIM's avatar Youngseob KIM

Correction for TP 2021.

parent b991d65d
......@@ -31,7 +31,7 @@
\newcommand*{\micro}{\ensureupmath{\upmu}}
\author[]{Youngseob Kim}
\title[TP POLU1]{Travaux Pratiques\\Environnement atmosphérique et qualité de l'air}
\title[TP POLU1]{Travaux Pratiques POLU1}
\setbeamercovered{transparent}
%\setbeamertemplate{bibliography item}{\insertbiblabel}
......@@ -39,7 +39,7 @@
%\setbeamertemplate{navigation symbols}{}
\institute[]{CEREA (ENPC -- EDF R\&D)}
\date{25 mai 2020}
\date{10 mai 2021}
%\date{\today}
\subject{Modélisation de qualité de l'air}
......@@ -174,46 +174,44 @@
\end{frame}
%%%%
\begin{frame}[fragile]{Connection via SSH to CEREA server}
\begin{block}{Linux or Mac}
- Open Terminal application if you are on a linux system or Mac.\\
- Type \code{ssh YourID@cerea.enpc.fr} and password
\end{block}
\begin{block}{Windows}
- Launch MobaXterm application\\
- Type \code{ssh YourID@cerea.enpc.fr} and password
\end{block}
If your login is successful, please follow the next step
\begin{Verbatim}[fontsize=\small]
> ssh YourMachine
> mkdir /net/libre/<YourMachine>/YourID
> cd /net/libre/<YourMachine>/YourID
\end{Verbatim}
% On-line workshop using the connection to CEREA server.
% %%%%
% \begin{frame}[fragile]{Connection via SSH to CEREA server}
% \begin{block}{Linux or Mac}
% - Open Terminal application if you are on a linux system or Mac.\\
% - Type \code{ssh YourID@cerea.enpc.fr} and password
% \end{block}
% \begin{block}{Windows}
% - Launch MobaXterm application\\
% - Type \code{ssh YourID@cerea.enpc.fr} and password
% \end{block}
% If your login is successful, please follow the next step
% \begin{Verbatim}[fontsize=\small]
% > ssh YourMachine
% > mkdir /net/libre/<YourMachine>/YourID
% > cd /net/libre/<YourMachine>/YourID
% \end{Verbatim}
\end{frame}
% \end{frame}
%%%%
\begin{frame}[fragile]{Download source files and configuration files}
\begin{block}{}
You need to download and extract the archive
\code{tp\_polu1.tar.bz2} in your working directory.
Choose Ubuntu in the booting page and login as \code{user}.\\
Open \code{Terminal} application.
\begin{Verbatim}[fontsize=\small]
> cp /net/libre/trami/kimy/tp_polu1.tar.bz2 .
Don't forget the small dot in the end
> tar -xjvf tp_polu1.tar.bz2
\begin{block}{}
Move to your working directory for this hands-on session.
\begin{Verbatim}[fontsize=\scriptsize]
> cd tp_polu1
\end{Verbatim}
\end{block}
\begin{block}{}
Please check if you have the following sub-folders in \code{tp\_polu1}:
......@@ -238,15 +236,26 @@ Please check if you have the following sub-folders in \code{tp\_polu1}:
%%%
\begin{frame}[fragile]{Input and output files}
\begin{block}{Link to input data}
\begin{block}{Input data}
% You need to download and extract the archive
% \code{data.tar.bz2} in your working directory.
% > rsync -av
% /net/libre/izapa/tp_test/tp_polu1/simulation_2016/data .
% Download from \code{\url{https://cerea.enpc.fr/tp_polu1}}
\begin{Verbatim}[fontsize=\small]
> cd simulation_2016
> ln -s
/net/libre/izapa/tp_test/tp_polu1/simulation_2016/data .
> ls data
bc: boundary condition
bio: biogenic emissions
dep: deposition velocity
emissions: anthropogenic emissions
ground: geographical data
ic: initial condition
meteo: meteorological data
photolysis: photolysis rate
\end{Verbatim}
\end{block}
......@@ -262,7 +271,6 @@ Please check if you have the following sub-folders in \code{tp\_polu1}:
\end{frame}
%%%%
\section{Processing}
......@@ -272,7 +280,7 @@ It is compiled by typing \code{scons}.
\begin{Verbatim}[fontsize=\small]
> cd ../Polyphemus-1.11.1/processing/scram-soap
> scons -j4 mpi=yes
> scons -j6 mpi=yes
\end{Verbatim}
Check if the executable \code{polair3d-scram-soap-cb05} has been generated
......@@ -298,7 +306,7 @@ Three configuration files
\item \code{polair3d.cfg}: main configuration file (informations on the options of the simulation
\item \code{polair3d-data.cfg}: configuration file to describe input data files
\item \code{polair3d-saver.cfg}: parameters to save output results
\end{itemize}
\end{itemize}
Three input data files
\begin{itemize}
\item \code{levels.dat}: list of vertical levels
......@@ -317,7 +325,7 @@ Three input data files
\begin{Verbatim}[fontsize=\scriptsize]
[domain]
Date_min = 20161130+12-00 Delta_t = 600. Nt = 6
Date_min = 20161130+00-00 Delta_t = 600. Nt = 48
x_min = 1.2 Delta_x = 0.02 Nx = 115
y_min = 47.9 Delta_y = 0.02 Ny = 110
Nz = 14
......@@ -380,16 +388,16 @@ Result_dir: ../results/
\begin{block}{}
\scriptsize
Check your current directory is \code{/net/libre/YourMachine/YourID/
tp\_polu1/simulation\_2016/config/}
Check your current directory is \code{/home/user/tp\_polu1/simulation\_2016/config/}
\begin{Verbatim}[fontsize=\scriptsize]
> pwd
\end{Verbatim}
Make a link to the compiled program to use it. Don't miss {\huge .} at the end of the line.
\begin{Verbatim}[fontsize=\scriptsize]
> ln -s ../../Polyphemus-1.11.1/processing/scram-soap/polair3d-scram-soap-cb05 .
> mpirun -n 4 polair3d-scram-soap-cb05 polair3d.cfg
> mpirun -n 12 polair3d-scram-soap-cb05 polair3d.cfg
\end{Verbatim}
\end{block}
......@@ -401,13 +409,12 @@ tp\_polu1/simulation\_2016/config/}
Module: SOA computation approach:equilibrium
Module: without sea salt in isorropia
Performing iteration #0
Current date: 2016-11-30 12:00
Current date: 2016-11-30 00:00
Performing iteration #1
Current date: 2016-11-30 12:10
Current date: 2016-11-30 00:10
Performing iteration #2
Current date: 2016-11-30 12:20
Current date: 2016-11-30 00:20
\end{Verbatim}
The simulation ends within ten minutes.
\end{frame}
......@@ -439,6 +446,8 @@ The simulation ends within ten minutes.
\begin{verbatim}
> cd ../../Polyphemus-1.11.1/utils
> scons get_info_float
> scons mult_nb_float
> scons add_float
\end{verbatim}
Move to the directory which contains simulation output.
......@@ -507,7 +516,6 @@ For dust, the total mass of \code{PMD} is \code{PMD\_0 + PMD\_1 + PMD\_2 + PMD\_
\end{itemize}
\end{block}
\end{frame}
......@@ -525,45 +533,69 @@ For dust, the total mass of \code{PMD} is \code{PMD\_0 + PMD\_1 + PMD\_2 + PMD\_
\end{itemize}
\end{block}
\end{frame}
\end{frame}
%%%%%
\begin{frame}[fragile]{Post-processing program: MakePM.py}
\begin{verbatim}
> cd ../../utils/
\end{verbatim}
Check the path in \code{MakePM.cfg}
\begin{block}
\code{InputDirectory = /home/user/tp\_polu1/simulation\_2016/results/}
\end{block}
Edit \code{MakePM.cfg} in \code{vi}\\
press the key \code{i} to begin editing.\\
press the key \code{Ctrl + c} to stop editing.\\
type \code{:wq} to save changes and exit \code{vi}
\begin{verbatim}
> python MakePM.py MakePM.cfg
> cd ../simulation_2016/results
> ls PM*
\end{verbatim}
Check if you have new files including \code{PM10.bin} and \code{PM2.5.bin}
\end{frame}
%%%%%
\begin{frame}[fragile]{Computed concentrations}
\begin{frame}[fragile]{Exercise 1: Computed concentrations}
1. Compute the concentration of the following species using \code{get\_info\_float}.
\begin{block}{Concentrations of pollutants (in $\micro$g m$^{-3}$)}
\begin{itemize}
\item \small Ozone:
\item \small NO$_x$:
\item \small OH:
\item \small PM$_{10}$:
\item \small PM$_{2.5}$:
\item \small Ozone, NO$_x$, OH
\item \small PM$_{10}$, PM$_{2.5}$
\end{itemize}
\end{block}
\begin{block}{Chemical composition of PM$_{10}$ (in $\micro$g m$^{-3}$)}
\begin{itemize}
\item \small Dust:
\item \small Black carbon:
\item \small Dust, Black carbon
\item \small Secondary inorgainc aerosols (sulfate, nitrate, ammonium):
\item \small Total anthropogenic organic aerosols:
\item \small Total biogenic organic aerosols:
\end{itemize}
\end{block}
Please send the results by e-mail to youngseob.kim@enpc.fr
2. Which chemical species are dominating in PM$_{10}$ concentration in Paris and what would you suggest to reduce PM$_{10}$ concentration in Paris ?
\end{frame}
\section{Scenario for an emission reduction}
%%%%%%%%%%%%%%%%%%%%%%%% Frame
\begin{frame}[fragile]{Description of the scenario}
\begin{frame}[fragile]{Scenario for an emission reduction}
\begin{block}{Background}
European emission standards for exhaust emissions of new vehicles changed from Euro 5 to Euro 6 in 2014. Standards for NO$_x$ emission have reduced by 45\% for diesel vehicles.
......@@ -572,14 +604,12 @@ European emission standards for exhaust emissions of new vehicles changed from E
\begin{block}{Correction on NOx emissions}
\begin{Verbatim}[fontsize=\scriptsize]
> cd ../../Polyphemus-1.11.1/utils
> scons mult_nb_float
> cd ../../simulation_2016
> mdkir data_modif
> cd data_modif
> ln -s ../../Polyphemus-1.11.1/utils/mult_nb_float .
> ./mult_nb_float ../data/emissions/surface-emissions/NO.bin 0.45 NO_modif.bin
> ./mult_nb_float ../data/emissions/surface-emissions/NO2.bin 0.45 NO2_modif.bin
> ./mult_nb_float ../data/emissions/surface-emissions/NO.bin 0.45 NO.bin
> ./mult_nb_float ../data/emissions/surface-emissions/NO2.bin 0.45 NO2.bin
\end{Verbatim}
\end{block}
......@@ -588,18 +618,22 @@ European emission standards for exhaust emissions of new vehicles changed from E
% %%%%%%%%%%%%%%%%%%%%%%%% Frame
\begin{frame}[fragile]{Configuration file}
1. Open \code{polair3d-data.cfg} using \code{vi} application
\begin{Verbatim}[fontsize=\scriptsize]
> cd ../config
> cd ..
> cp -rf config config_sim2
> cd config_sim2
> vi polair3d-data.cfg
\end{Verbatim}
2. Edit \code{polair3d-data.cfg} in \code{vi}\\
press the key \code{i} to begin editing.\\
press the key \code{Ctrl + c} to stop editing.\\
type \code{:wq} to save changes and exit \code{vi}
% {\scriptsize
% Edit \code{polair3d-data.cfg} using \code{vi}\\
% press the key \code{i} to begin editing.\\
% press the key \code{Ctrl + c} to stop editing.\\
% type \code{:wq} to save changes and exit \code{vi}
% }
\begin{block}{NO and NO2 emission files are changed in \code{polair3d-data.cfg}}
\begin{block}{NO and NO2 emission files are changed in polair3d-data.cfg}
\begin{Verbatim}[fontsize=\scriptsize]
[surface_emission]
......@@ -610,12 +644,14 @@ Fields: ALD2 CH4 ETHA IOLE MEOH SO2 XYL ALDX CO ETOH HC8 ISOP NH3 OLE TERP ETH
FORM HONO PAR TOL API LIM SULF POAhP POAlP POAmP
Filename: <Directory_data>/emissions/surface-emissions/&f.bin
NO: ../data_modif/NO_modif.bin
NO2: ../data_modif/NO2_modif.bin
NO: ../data_modif/NO.bin
NO2: ../data_modif/NO2.bin
\end{Verbatim}
\end{block}
Remove NO and NO2 from ''Fields'' to use the new ones instead of the old ones.
\end{frame}
......@@ -632,7 +668,7 @@ NO2: ../data_modif/NO2_modif.bin
press the key \code{Ctrl + c} to stop editing.\\
type \code{:wq} to save changes and exit \code{vi}
\begin{block}{Modification in \code{polair3d-saver.cfg}}
\begin{block}{Modification in polair3d-saver.cfg}
\begin{Verbatim}[fontsize=\scriptsize]
Result_dir: ../results_sim2/
\end{Verbatim}
......@@ -644,34 +680,96 @@ Result_dir: ../results_sim2/
\end{Verbatim}
\end{frame}
% %%%%%%%%%%%%%%%%%%%%%%%% Frame
\begin{frame}[fragile]{Launch a simulation}
%%%%%
\begin{frame}[fragile]{Launch a simulation and run again MakePM.py}
To launch a simulation,
\begin{Verbatim}[fontsize=\scriptsize]
> cd config
> mpirun -n 4 polair3d-scram-soap-cb05 polair3d.cfg
> cd config_sim2
> mpirun -n 12 polair3d-scram-soap-cb05 polair3d.cfg
\end{Verbatim}
\begin{block}{Comparison of concentrations}
\centering
\begin{tabular}{|c|c|c|}
\hline
Species & Simulation 1 & Simulation 2 \\
\hline
Ozone & & \\
\hline
NO & & \\
\hline
NO2 & & \\
\hline
Nitrate & & \\
\hline
\end{tabular}
Post-processing program \code{MakePM.py}
\begin{verbatim}
> cd ../../utils/
\end{verbatim}
Edit \code{MakePM.cfg} in \code{vi}\\
press the key \code{i} to begin editing.\\
\begin{block}
\code{InputDirectory = /home/user/tp\_polu1/simulation\_2016/results\_sim2/}
\end{block}
press the key \code{Ctrl + c} to stop editing.\\
type \code{:wq} to save changes and exit \code{vi}
\begin{verbatim}
> python MakePM.py MakePM.cfg
\end{verbatim}
\end{frame}
%%%%%
\begin{frame}[fragile]{Post-processing program: disp\_diff.py}
Edit \code{disp\_diff.cfg} in \code{vi}\\
press the key \code{i} to begin editing.\\
\begin{verbatim}
Species: O3
ModelName1: Reference
Directory1: /home/user/tp_polu1/simulation_2016/results/
ModelName2: Emission_reduction
Directory2: /home/user/tp_polu1/simulation_2016/results_sim2/
\end{verbatim}
press the key \code{Ctrl + c} to stop editing.\\
type \code{:wq} to save changes and exit \code{vi}
\begin{verbatim}
> python disp_diff.py disp_diff.cfg
\end{verbatim}
\end{frame}
\begin{frame}[fragile]{Exercise 2}
\begin{block}{}
1. Make the figures on the concentrations of NO$_{x}$ and ozone and nitrate using \code{disp\_diff.py}
2. Compare differences between the simulation results and explain why the ozone and nitrate concentration are changed in the second simulation.
\end{block}
Please send the results by e-mail to youngseob.kim@enpc.fr
PNG-format figures are automatically generated in \code{figures} folder.
\begin{verbatim}
> eog figures/O3_sim1.png
\end{verbatim}
Please send the results of Exercise 1 and 2 by e-mail to youngseob.kim@enpc.fr
\end{frame}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment