source: Readme @ 122

                - content -

Codes under src directory:
= = = = = = = =  = = = = =
compute_metrics_csv.sh             htune_EOF.R
expe_setup.R                       htune_metric.R
extract_onemetric_csv.sh           htune_netcdf2csvMetrics.R
htune_case_setup.R                 htune_plot.R
htune_convertDesign.R              htune_test_plot.R
htune_convert.R                    kLHC.R
htune_csv2Rdata.R                  param2R.sh
htune_EmulatingMultiMetric.R       param2Rwave.sh

               - Description -

BEFORE STARTING: The LMDz model will be installed two levels higher in the tree.
Make sure to be in a "subsubdirectory" before running the model setup.
If you are in DIR1/DIR2/Hightune right now, the models will be installed in
DIR1.
This allows you to avoid reinstalling the model by staying in the DIR1
directory.
For running other models, need to have installed MUSC on your machine: http://confluence/pages/viewpage.action?pageId=248758682

Main programs :
===============

bench.sh => This bench can be used with any models just run bench.sh MODEL[LMDZ AROME ARPCLIMAT] or you can specify some option [bench.sh -help]

This bench runs the following steps:
= = =  = = = = =  = = = =  = = = = =

Step 1 : Parameter definition and generation of parametric ensemble
-------------------------------------------------------------------
   param2R.sh : define list of parameters and their range
             create the R script  ModelParam.R
   
   Usage : ./param2R.sh LHCSIZE NLHC PARAM_FILE
   Ex : ./param2R.sh 30 3 LMDZ/param_cld
   (when using this step for a second wave needs to use param2Rwave.sh)
   NLHC: if NLHC=1, then generate the maximinLHS of size LHCSIZE.

   htune_convertDesign.R, Automatically run by param2R.sh from version 9
   creates design for the emulator using ModelParam.R
   outputs : Par1D_Wave1.asc containing the parameter values
                for SCM simulations
             Wave1.RData containing normalized parameter values for
                the SCM
   Calls kLHC.R and htune_convert.R
   kLHC.R to produce the k-extended latin hyper cubes sampling
   htune_convert.R contains the different functions to transform from normalized to non normalized and vice/versa the different values of the parameters

Step 2 : serie_[MODEL].sh 
-------------------------
   the different scripts are available in the MODEL directory
   This is the only model-dependent script
   Use : ./serie_LMDZ.sh $cas $NWAVE
   TBD homogeneise in the serie_AROME.sh to be called identically
   Run a series of the model SCM reading the parameters from Par1D_Wave1.asc
   netcdf ouptut files should be put in
   ./WAVE1/[cas] 
   with names SCM_1-101.nc given in Par1D_Wave1.asc
   Also put the available LES 1D output files in WAVE1

Step 3 : Compute Metrics and convert to Rdata
---------------------------------------------
  use compute_metrics_csv.sh (call extract_onemetric_csv.sh for both LES and SCM and compute metrics through htune_netcdf2csvMetrics.R)
  Syntaxis: compute_metrics_csv.sh ARMCU_REF_Ay-theta_8_9 ARMCU_REF_zav-400-600-theta_9_9 ...
  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!! Need to change manually the number of the wave in this script file!!!!!
  !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  -> call extract_onemetric_csv.sh for both LES and the dir contains simulations
       -either use cdo to compute metrics when averaging is asked
       -either call htune_netcdf2csvMetrics.R (that call htune_metric.R) to compute other metrics ex lwp, neb metrics, Ayotte metrics)
  -> call htune_csv2Rdata.R=> to convert to Rdata
           Wave1_LES.Rdata : metrics computed on LES
           Wave1_SCM.Rdata : metrics computed on SCM
           Assume that all the files are at an hourly time frequency

   Metrics already available :
     targetvar=averaging of any variables between two different vertical levels [zav]
     targetvar=lwp, zhneb, Ay-theta (or any integral of positive/negative (theta) differences to the 1st time 
     TBD: averaging in time  relevant for stationary cases
     TBD: change 1st hour by initial time

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Available tools to draw the simulations in vertical profiles and compare them to LES:
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
=> Preliminary steps (if you want to draw the envelope of the SCM runs you need to compute the avg, min and max through cdo):
So under the WAVE/CASE/SUBCASE directory you need to run:
    cdo ensmin SCM_1-*.nc ensmin_SCM.nc
    cdo ensmax SCM_1-*.nc ensmax_SCM.nc
    cdo ensavg SCM_1-*.nc ensavg_SCM.nc     
For CNRM SCM need to before suppress the NaN values using script_modif_fillvalue.sh (then you should run the previous cdo command with new_SCM_1*nc instead of SCM_1*nc)
For LMDZ, need to run script_LMDZ.sh that do the cdo command and change the name of the variable for it to work (time_counter should be time and presnivs should at least ends with a 'f')

Then need to modify the param_CASE_SUBCASE.py:
    -need to change the list of the files you want to draw under "listfic"
    normaly you just need to change the directory for the default runs of your model
    -you can also change the type/color of lines by changing the dictionnary 'dicostyl' or 'dicocoul'
    - you can change the time at which you want to draw the vertical profile in 'dateprof'
    this file also contains the range xmin/xmax of the variable you want to draw as a dictionnary function of the name of the variable ('vmintab' and 'vmaxtab')
then run the python command:
python trace_sens_LES.py nom_variable[nom_variable=theta,u,v,rneb,qv,ql,...] param_ARM.py
=> create a figure called 'profil_'case'_'subcase'_'nom_variable'_'time'.png

TBD : could be included in the script compute_metrics_csv.sh with an automatic drawing of the profile for the variables used to compute the metrics at the given time


Step 4 : htune_EmulatingMultiMetric.R
-------------------------------------
    Emulator building reading Wave1_LES.Rdata and Wave1_SCM.Rdata
    Definition and plots of ROY spaces


Step 6: Run a second Wave: 
------------------------
param2Rwave.sh :use the RData file generated in htune_EmulatingMultiMetric.R 
        after history matching for previous waves.
        Usage : ./param2Rwave.sh WAVEN RDATA_FILE
        Ex :  ./param2Rwave.sh 2 Wave2.RData
        WAVEN should be >= 2
or use bench.sh -wave 2 -model MODEL

Functions :
===========
htune_case_setup.R : some cases caracteristics for plots
htune_metric.R : metrics computation
htune_plot.R :  plots


Imput from Exeter :
===================
StanEmulateCodeR.R which requires :
AutoLMcode.R
CustomPredict.R
impLayoutplot.R
JamesDevelopment.R
DannyDevelopment.R
MultiWaveHM.R
MySpeed1const.stan
PredictSpeed1const.stan
PredictSpeed2DWconst.stan
MySpeed1.stan
PredictSpeed1.stan
PredictSpeed2DW.stan
kLHC.R : LHS clever sampling


Discussion / conventions :
==========================
I propose to use hourly averaged outputs.
Should work for all the available cases.



Installation rstudio :
======================

Here is how to install RStudio on Ubuntu 16.04

sudo apt-get install r-base
wget https://download1.rstudio.org/rstudio-xenial-1.0.153-amd64.deb
sudo apt-get install gdebi
sudo gdebi rstudio-xenial-1.0.153-amd64.deb

then, you should be able to open RStudio by simply using the command:
rstudio

when you install the supplementary libraries for RStudio on Ubuntu, you will need to install netcdf-bin et libnetcdf-dev, otherwise
the ncdf4 library won't install correctly

You will also need to install these packages in RStudio:

install.packages(c("ncdf4","rstan","tensor","Hmisc","lhs","fields","rgl","shape","mco","far","dicekriging","GenSA","mvtnorm","loo"))

You might also need:
r-cran-rgl
libx11-dev
libglu1-mesa-dev

Nettoyage de l'outil:
= = = = = = = = = = = 
- expe_setup.sh
bench2waves.sh
bench2wavesmMetric.sh

=> modif de bench et htune_EmulatingMultiMetric.R pour avoir le n° de la vague en argument
=> modif dans extract_onemetric.sh de maximiser l'erreur sur la ref? en fait ca devrait plutot etre modifié au niveau de Disc