#!/bin/ksh

########################################################################

#D- Flag to determine if this job in a standalone mode
#D- Default : value from AA_job if any
StandAlone=${StandAlone:=true}

#D- Increased verbosity (1, 2, 3)
#D- Default : value from AA_job if any
Verbosity=${Verbosity:=3}

#D- Low level debug : to bypass lib test checks and stack construction
#D- Default : value from AA_job if any
DEBUG_debug=${DEBUG_debug:=false}


########################################################################

MODIPSL=$1
libIGCM=${libIGCM:=${MODIPSL}/libIGCM}

. ${libIGCM}/libIGCM_debug/libIGCM_debug.ksh
. ${libIGCM}/libIGCM_card/libIGCM_card.ksh
. ${libIGCM}/libIGCM_date/libIGCM_date.ksh
#-------
. ${libIGCM}/libIGCM_sys/libIGCM_sys.ksh
. ${libIGCM}/libIGCM_config/libIGCM_config.ksh
. ${libIGCM}/libIGCM_comp/libIGCM_comp.ksh
. ${libIGCM}/libIGCM_post/libIGCM_post.ksh
#-------
( ${DEBUG_debug} ) && IGCM_debug_Check
( ${DEBUG_debug} ) && IGCM_card_Check
( ${DEBUG_debug} ) && IGCM_date_Check

#D--------------------------------------------------------------------==
#D- 0.1 COMMON ENVIRONMENT
#D-     - Read libIGCM compatibility version in config.card
#D-     - Read UserChoices section
#D-     - Read Ensemble section
#D-     - Read Post section
#D-     - Define all netcdf output directories
#D--------------------------------------------------------------------==
IGCM_config_CommonConfiguration ${SUBMIT_DIR}/config.card


#D--------------------------------------------------------------------==
#D- 1. INITIALIZE CONFIGURATION
#D-    - Simulation configuration
#D-    - Simulation parameters
#D-    - Execution parameter
#D-    - Define input files directory
#D-    - Read or initialize CumulPeriod
#D-    - run.card
#D---------------------------------------------------------------------==
IGCM_config_Initialize



########################################################################
#set -vx
########################################################################
# Script input parameters

Group=$2
# Site name
SiteArg=$3
Site=${SiteArg:=Gu}
export Site
## Time in years in file for this site :
#DureeArg=$4
#DUREE=${DureeArg:=1}
#export DUREE
#
## First year in file for this site :
#FirstArg=$5
#FYEAR=${FirstArg:=1}
#export FYEAR
#
#(( LYEAR=FYEAR+DUREE-1 ))
#export LYEAR


# Atlas Name : 
AtlasCfgArg=$4
AtlasCfg=${AtlasCfgArg:=atlas_FLUXNET.cfg}

# observation_file
eval observation_file_pathArg=$5
observation_file=${observation_file_pathArg}
echo observation_file=${observation_file}

# Modulo for SpinUp years 
ModuloArg=${8}
echo "ModuloArg:" $ModuloArg

IGCM_sys_MkdirWork ${RUN_DIR_PATH}
echo "RUN_DIR_PATH ${RUN_DIR_PATH} ok."
IGCM_sys_Cd ${RUN_DIR_PATH}

if [ ${StandAlone} = true ] ; then
    CARD_DIR=${SUBMIT_DIR}
else
    CARD_DIR=${RUN_DIR_PATH}/$( basename ${SUBMIT_DIR} )
    IGCM_sys_Get_Master ${SUBMIT_DIR} ${RUN_DIR_PATH}
fi

#
# First of all
#
IGCM_card_DefineArrayFromSection ${CARD_DIR}/config.card UserChoices
typeset option
for option in ${config_UserChoices[*]} ; do
    IGCM_card_DefineVariableFromOption ${CARD_DIR}/config.card UserChoices ${option}
done
#
echo
IGCM_debug_Print 1 "DefineArrayFromOption  : config_UserChoices"
IGCM_debug_PrintVariables 3 config_UserChoices_JobName
if [ 3 -le ${Verbosity} ] ; then
    echo "--------------Debug3-->" "config_UserChoices_LongName="
    echo "--------------Debug3-->" \"${config_UserChoices_LongName}\"
fi
IGCM_debug_PrintVariables 3 config_UserChoices_TagName
IGCM_debug_PrintVariables 3 config_UserChoices_CalendarType
IGCM_debug_PrintVariables 3 config_UserChoices_DateBegin
IGCM_debug_PrintVariables 3 config_UserChoices_DateEnd
IGCM_debug_PrintVariables 3 config_UserChoices_PeriodLength
echo


# FLAG = SECHIBA, OK_STOMATE
IGCM_card_DefineVariableFromOption ${CARD_DIR}/ensemble.card UserChoices ok_stomate
if [ X${ensemble_UserChoices_ok_stomate} = Xn ] ; then
    export FLAG=SECHIBA
else
    export FLAG=OK_STOMATE
fi


#==================================

SpinUpJob=${Site}${config_UserChoices_JobName}
set -A liste_fichiers_with_path -- $( \ls -rt ${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${config_UserChoices_JobName}/${SpinUpJob}HIST/SRF/Output/MO/*_sechiba_history.nc )
echo liste_fichiers_with_path=${liste_fichiers_with_path}
ii=0
for filetmp in ${liste_fichiers_with_path[@]} ; do
    (( ii = ii + 1 ))
    file=$( echo ${filetmp} | xargs basename )
done
if [ $ii -ne 1 ] ; then
  echo "Error. More than one file found. ii=$ii"
  exit
fi
echo file=$file

# Get and sed atlas
IGCM_sys_Cp ${CARD_DIR}/${AtlasCfg} ./atlas.cfg
IGCM_sys_Cp ${CARD_DIR}/ORCHIDEE_3dif.jnl ./ORCHIDEE_3dif.jnl
    
IGCM_sys_Cp -Rp ${liste_fichiers_with_path[0]} .

# old history file
reference_file_pathArg=$6
if [ X${reference_file_pathArg} == XNONE ] ; then
    reference_file_path=${liste_fichiers_with_path}
else
    reference_file_path=${reference_file_pathArg}
fi

eval reference_file=${reference_file_path}
sed -e "s,RRRRRRR,${reference_file},g" -e "s,VVVVVVV,${observation_file},g" atlas.cfg > atlas_.cfg

echo "REFERENCE ATLAS for file : " ${file} ${reference_file} ${observation_file}
reference_config=$7
atlas -o ${SpinUpJob}_${reference_config} atlas_.cfg ${file}

# Remove small files before saving
if [ X$CleanSmallFiles = Xyes ] ; then
  tmpdir=${SpinUpJob}_${reference_config}
  # Remove .info .tex .jnl .stdout .jpg .pdf (deuxieme niveau )
  echo "Remove small files before saving : "
  sumfilestoremove=$(( $( find ${tmpdir} -name "*.info" | wc -l ) +  $( find ${tmpdir} -name "*.tex" | wc -l ) +  $( find ${tmpdir} -name "*.jnl" | wc -l ) + $( find ${tmpdir} -name "*.stdout" | wc -l ) + $( find ${tmpdir} -name "*.pdf" | wc -l ) ))
  echo "Following $sumfilestoremove files listed below will be removed: "

  find ${tmpdir} -name "*.info"
  find ${tmpdir} -name "*.tex" 
  find ${tmpdir} -name "*.jnl" 
  find ${tmpdir} -name "*.stdout"
  find ${tmpdir} -name "*.pdf" 

  # Now remove them
  find ${tmpdir} -name "*.info" -print -exec rm -f '{}' \;
  find ${tmpdir} -name "*.tex" -print -exec rm -f '{}' \;
  find ${tmpdir} -name "*.jnl" -print -exec rm -f '{}' \;
  find ${tmpdir} -name "*.stdout" -print -exec rm -f '{}' \;
  find ${tmpdir} -name "*.pdf" -print -exec rm -f '{}' \;

else
  echo "No clean of small files will be done."
fi


# Save files
R_SAVE=${R_OUT}/${config_UserChoices_TagName}/${config_UserChoices_SpaceName}/${config_UserChoices_ExperimentName}/${config_UserChoices_JobName}/fluxnet_taylor_diff_${config_UserChoices_JobName}_${reference_config}_${Group}

echo "Before IGCM_sys_Put_Dir : destination= ${R_SAVE}"
IGCM_sys_Put_Dir ${SpinUpJob}_${reference_config} ${R_SAVE}

IGCM_sys_Rm -Rf ${SpinUpJob}_${reference_config}



# # Get and Apply Patch
# . ${MODIPSL}/libIGCM/libIGCM_post/IGCM_Patch_20070220_histcom_time_axis.ksh
# for file in ${liste_fichiers[*]} ; do 
#     IGCM_Patch_20070220_histcom_time_axis ${file}
# done

# # look at files
# echo "after Patch" IGCM_Patch_20070220_histcom_time_axis
# \ls -lrt  *_sechiba_history.nc

# Concat files
#IGCM_sys_ncrcat -o ${SpinUpJob}_1M_sechiba_history.nc ${liste_fichiers[*]}

IGCM_sys_Rm -Rf  ${liste_fichiers[*]}

IGCM_sys_RmRunDir -Rf ${RUN_DIR_PATH}