Develop

README.md

@@ -2,6 +2,11 @@
 
 ## History
 
+**Develop**
+
+- New functionality for Regional simulations.
+- Option to use ERA5 data as an initial condition.
+
 **1.4.0**
 - Compatibility with MONAN 1.4.3-rc.
 - Support for multi-environment: 'Jaci' supercomputer (intel and gnu compilers and PBS scheduler) and 'Egeon' cluster (gnu compiler and SLURM scheduler).

scripts/0.run_all.bash

@@ -41,9 +41,10 @@ EXECS=${DIRHOMED}/execs;               mkdir -p ${EXECS}
 github_link="https://github.com/monanadmin/MONAN-Model.git"
 monan_branch=1.4.3-rc
 convertmpas_branch=1.2.0
-EXP=GFS
-RES=1024002       #Options: 40962=120km;163842=60km;655362=30Km;1024002=24km;2621442=15Km;5898242=10Km
-YYYYMMDDHHi=2026012000
+EXP=GFS                    #Options - GFS or ERA
+RES=1024002                #Options - Global: 40962=120km; 163842=60km; 655362=30Km; 1024002=24km; 2621442=15Km; 5898242=10Km
+                           #Options - Regional: 655362.REG.AMS_CAR=30km; 5898242.REG.AMS_CAR=10km; 23592962.REG.AMS_CAR=5km
+YYYYMMDDHHi=2026070100     #Check dates disponible for the initial condition (CI) using ERA5
 FCST=24
 #----------------------------------------------------------------------
 

scripts/1.install_monan.bash

@@ -219,9 +219,6 @@ MAKE_OUT_FILE="make_\${DATE_TIME_NOW}_.output.atmosphere"
 
 make clean CORE=atmosphere
 make -j 8 ${MAKE_TARG} CORE=atmosphere OPENMP=true USE_PIO2=false PRECISION=single 2>&1 | tee \${MAKE_OUT_FILE}
-#make -j 8 ${MAKE_TARG} CORE=atmosphere OPENMP=true USE_PIO2=true PRECISION=single 2>&1 | tee \${MAKE_OUT_FILE}
-
-#make -j 8 intel-xd2000 CORE=atmosphere OPENMP=true USE_PIO2=false PRECISION=single OPTIMIZATION_LEVEL=O1 FFLAGS_OPT=-O1 CFLAGS_OPT=-O1 CXXFLAGS_OPT=-O1 2>&1 | tee \${MAKE_OUT_FILE}
 
 
 #CR: TODO: put verify here if executable was created ok
@@ -235,9 +232,6 @@ MAKE_OUT_FILE="make_\${DATE_TIME_NOW}_.output.init_atmosphere"
 
 make clean CORE=init_atmosphere
 make -j 8 ${MAKE_TARG2} CORE=init_atmosphere OPENMP=true USE_PIO2=false PRECISION=single 2>&1 | tee \${MAKE_OUT_FILE}
-#make -j 8 ${MAKE_TARG2} CORE=init_atmosphere OPENMP=true USE_PIO2=true PRECISION=single 2>&1 | tee \${MAKE_OUT_FILE}
-
-#make -j 8 intel-xd2000 CORE=init_atmosphere OPENMP=true USE_PIO2=false PRECISION=single OPTIMIZATION_LEVEL=O1 FFLAGS_OPT=-O1 CFLAGS_OPT=-O1 CXXFLAGS_OPT=-O1 2>&1 | tee \${MAKE_OUT_FILE}
 
 
 mv ${MONANDIR}/init_atmosphere_model ${EXECS}

scripts/2.pre_processing.bash

@@ -25,7 +25,7 @@ then
    echo ""
    echo "${0} EXP_NAME/OP RESOLUTION LABELI FCST"
    echo ""
-   echo "EXP_NAME    :: Forcing: GFS"
+   echo "EXP_NAME    :: Forcing: GFS or ERA"
    echo "            :: Others options to be added later..."
    echo "RESOLUTION  :: number of points in resolution model grid, e.g: 1024002  (24 km)"
    echo "                                                                 40962  (120 km)"
@@ -52,7 +52,7 @@ echo "---- Pre Processing ----"
 echo ""
 
 
-# Standart directories variables:---------------------------------------
+# Standard directories variables:---------------------------------------
 DIRHOMES=${DIR_SCRIPTS}/scripts_CD-CT; mkdir -p ${DIRHOMES}    
 DIRHOMED=${DIR_DADOS}/scripts_CD-CT;   mkdir -p ${DIRHOMED}  
 SCRIPTS=${DIRHOMES}/scripts;           mkdir -p ${SCRIPTS}
@@ -80,8 +80,6 @@ final_date=${yyyymmddhhf:0:4}-${yyyymmddhhf:4:2}-${yyyymmddhhf:6:2}_${yyyymmddhh
 export DIRRUN=${DIRHOMED}/run.${YYYYMMDDHHi}; rm -fr ${DIRRUN}; mkdir -p ${DIRRUN}
 #-------------------------------------------------------
 
-
-
 echo -e  "${GREEN}==>${NC} Scripts_CD-CT last commit: \n"
 git log | head -1
 
@@ -95,31 +93,63 @@ then
 	ln -sf ${DIRDADOS}/MONAN_datain/datain/WPS_GEOG ${DATAIN}
 fi
 
-
 # Creating the x1.${RES}.static.nc file once, if does not exist yet:---------------
-if [ ! -s ${DATAIN}/fixed/x1.${RES}.static.nc ]
-then
-   echo -e "${GREEN}==>${NC} Creating static.bash for submiting init_atmosphere to create x1.${RES}.static.nc...\n"
-   time ./make_static.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST}
+if [[ ${EXP} == "GFS" || ${EXP} == "ERA" ]]; then
+   if [ ! -s ${DATAIN}/fixed/x1.${RES}.static.nc ]
+   then
+      echo -e "${GREEN}==>${NC} Creating static.bash for submiting init_atmosphere to create x1.${RES}.static.nc...\n"
+      time ./make_static.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST}
+   else
+      echo -e "${GREEN}==>${NC} File x1.${RES}.static.nc already exist in ${DATAIN}/fixed.\n"
+   fi
 else
-   echo -e "${GREEN}==>${NC} File x1.${RES}.static.nc already exist in ${DATAIN}/fixed.\n"
+   echo -e  "\n${RED}==>${NC} ***** ATTENTION *****\n"
+   echo -e  "${RED}==>${NC} Static phase fails! Please select EXP=GFS or EXP=ERA5.\n"
+   echo -e  "${RED}==>${NC} Exiting script. \n"
+   exit -1
 fi
-#----------------------------------------------------------------------------------
 
+#----------------------------------------------------------------------------------
 
 # Degrib phase:---------------------------------------------------------------------
-echo -e  "${GREEN}==>${NC} Running Degrib:\n"
-time ./make_degrib.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST}
+if [[ ${EXP} == "GFS" ]]
+then
+   echo -e  "${GREEN}==>${NC} Submitting Degrib for GFS data...\n"
+   time ./make_degrib_GFS.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST}
+elif [[ ${EXP} == "ERA" ]]
+then
+   echo -e  "${GREEN}==>${NC} Submitting Degrib for ERA5 data...\n"
+   time ./make_degrib_ERA5.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST}
+else
+   echo -e  "\n${RED}==>${NC} ***** ATTENTION *****\n"
+   echo -e  "${RED}==>${NC} Degrib phase fails! Please select EXP=GFS or EXP=ERA5.\n"
+   echo -e  "${RED}==>${NC} Exiting script. \n"
+   exit -1
+fi
 #----------------------------------------------------------------------------------
 
-
-
-
 # Init Atmosphere phase:------------------------------------------------------------
-echo -e  "${GREEN}==>${NC} Running Init Atmosphere...\n"
-time ./make_initatmos.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST}
-#----------------------------------------------------------------------------------
-
-
+if [[ ${EXP} == "GFS" || ${EXP} == "ERA" ]]; then
+   echo -e  "${GREEN}==>${NC} Submitting Init Atmosphere for real case...\n"
+   time ./make_initatmos.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST}
+else
+   echo -e  "\n${RED}==>${NC} ***** ATTENTION *****\n"
+   echo -e  "${RED}==>${NC} Init Atmosphere phase fails! Please select EXP=GFS or EXP=ERA5.\n"
+   echo -e  "${RED}==>${NC} Exiting script. \n"
+   exit -1
+fi
 
+# LBCs phase:------------------------------------------------------------
+if [[ $MODERUN == "R" ]]; then
+   echo -e  "${GREEN}==>${NC} Regional simulation: submitting Init Atmosphere to generate lateral boundary conditions...\n"
+   time ./make_lbcs.bash ${EXP} ${RES} ${YYYYMMDDHHi} ${FCST}
+elif [[ $MODERUN == "G" ]]; then
+   echo -e  "${GREEN}==>${NC} Global simulation: no need for lateral boundary conditions.\n"
+else
+   echo -e  "\n${RED}==>${NC} ***** ATTENTION *****\n"
+   echo -e  "${RED}==>${NC} LBCs phase fails! Please select MODERUN=R or G.\n"
+   echo -e  "${RED}==>${NC} Exiting script. \n"
+   exit -1
+fi
+#----------------------------------------------------------------------------------
 

scripts/3.run_model.bash

@@ -8,10 +8,10 @@ umask 022
 #     
 #     Performs the following tasks:
 # 
-#        o VCheck all input files before 
-#        o Creates the submition script
+#        o Check all input files before 
+#        o Creates the submission script
 #        o Submit the model
-#        o Veriffy all files generated
+#        o Verify all files generated
 #        
 #
 #-----------------------------------------------------------------------------#
@@ -23,7 +23,7 @@ then
    echo ""
    echo "${0} [EXP_NAME/OP] RESOLUTION LABELI FCST"
    echo ""
-   echo "EXP_NAME    :: Forcing: GFS"
+   echo "EXP_NAME    :: Forcing: GFS or ERA"
    echo "RESOLUTION  :: number of points in resolution model grid, e.g: 1024002  (24 km)"
    echo "LABELI      :: Initial date YYYYMMDDHH, e.g.: 2024010100"
    echo "FCST        :: Forecast hours, e.g.: 24 or 36, etc."
@@ -89,30 +89,62 @@ printf -v t_strout "%02d:%02d:%02d" "$h" "$m" "$s"
 # From now on, CONFI_LEN_DISP becames cte = 0.0, pickin up this value from static file.
 
 # Calculating default parameters for different resolutions
-if [ $RES -eq 1024002 ]; then  #24Km
+# global mesh
+if [[ "$RES" == "40962" ]]; then      #120Km
+   CONFIG_DT=600.0
+   CONFIG_CONV_INTERVAL="00:15:00"
+elif [[ "$RES" == "163842" ]]; then   #60Km
+   CONFIG_DT=300.0
+   CONFIG_CONV_INTERVAL="00:15:00"
+elif [[ "$RES" == "655362" ]]; then   #30Km
+   CONFIG_DT=150.0
+   CONFIG_CONV_INTERVAL="00:15:00"
+elif [[ "$RES" == "1024002" ]]; then  #24Km
    CONFIG_DT=150.0
    CONFIG_CONV_INTERVAL="00:15:00"
-elif [ $RES -eq 2621442 ]; then  #15Km
+elif [[ "$RES" == "2621442" ]]; then  #15Km
    CONFIG_DT=90.0
    CONFIG_CONV_INTERVAL="00:15:00"
-elif [ $RES -eq 40962 ]; then  #120Km
-   CONFIG_DT=600.0
+elif [[ "$RES" == "5898242" ]]; then  #10Km
+   CONFIG_DT=60.0
    CONFIG_CONV_INTERVAL="00:15:00"
-elif [ $RES -eq 163842 ]; then  #60Km
-   CONFIG_DT=300.0
+elif [[ "$RES" == "23592962" ]]; then  #5km
+   CONFIG_DT=30.0
    CONFIG_CONV_INTERVAL="00:15:00"
-elif [ $RES -eq 655362 ]; then  #30Km
+elif [[ "$RES" == "65536002" ]]; then  #3Km
+   CONFIG_DT=18.0
+   CONFIG_CONV_INTERVAL="00:15:00"
+# regional mesh
+elif [[ "$RES" == "655362.REG.AMS_CAR" ]]; then #30 km (AMS + Caribe)
    CONFIG_DT=150.0
    CONFIG_CONV_INTERVAL="00:15:00"
-elif [ $RES -eq 5898242 ]; then  #10Km
+elif [[ "$RES" == "5898242.REG.AMS_CAR" ]]; then #10 km (AMS + Caribe)
    CONFIG_DT=60.0
    CONFIG_CONV_INTERVAL="00:15:00"
-elif [ $RES -eq 65536002 ]; then  #3Km
-   CONFIG_DT=18.0
+elif [[ "$RES" == "23592962.REG.AMS_CAR" ]]; then #5 km (AMS + Caribe)
+   CONFIG_DT=30.0
    CONFIG_CONV_INTERVAL="00:15:00"
+else
+    echo -e  "\n${RED}==>${NC} ***** ATTENTION *****\n"
+    echo -e  "${RED}==>${NC} [${0}] Simulation parameters for resolution $RES have not been set! Edit them in '3.run_model.bash'.\n"
+    exit -1
 fi
 #-------------------------------------------------------
 
+# Setting configuration to apply or not lateral boundary conditions and output filename
+if [[ $MODERUN == "R" ]]; then
+   APPLY_LBCS=true
+   RORG=R
+elif [[ $MODERUN == "G" ]]; then
+   APPLY_LBCS=false
+   RORG=G
+else
+   echo -e  "\n${RED}==>${NC} ***** ATTENTION *****\n"
+   echo -e  "${RED}==>${NC} Atmosphere phase fails! Please select MODERUN=R (Regional) or MODERUN=G (Global) in 'setenv.bash' so that MONAN knows whether to read or not lateral boundary conditions.\n"
+   echo -e  "${RED}==>${NC} Exiting script. \n"
+   exit -1
+fi
+#-------------------------------------------------------
 
 # Calculating final forecast dates in model namelist format: DD_HH:MM:SS 
 # using: start_date(yyyymmdd) + FCST(hh) :
@@ -128,18 +160,16 @@ then
       cd ${DATAIN}/fixed
       echo -e "${GREEN}==>${NC} downloading meshes tgz files ... \n"
       wget https://www2.mmm.ucar.edu/projects/mpas/atmosphere_meshes/x1.${RES}.tar.gz
-      wget https://www2.mmm.ucar.edu/projects/mpas/atmosphere_meshes/x1.${RES}_static.tar.gz
       tar -xzvf x1.${RES}.tar.gz
-      tar -xzvf x1.${RES}_static.tar.gz
    fi
    echo -e "${GREEN}==>${NC} Creating x1.${RES}.graph.info.part.${cores} ... \n"
    cd ${DATAIN}/fixed
    gpmetis -minconn -contig -niter=200 x1.${RES}.graph.info ${cores}
-   rm -fr x1.${RES}.tar.gz x1.${RES}_static.tar.gz
+   rm -fr x1.${RES}.tar.gz
 fi
 
 
-files_needed=("${SCRIPTS}/namelists/stream_list.atmosphere.output" ""${SCRIPTS}/namelists/stream_list.atmosphere.diagnostics${VARTABLE} "${SCRIPTS}/namelists/stream_list.atmosphere.surface" "${EXECS}/atmosphere_model" "${DATAIN}/fixed/x1.${RES}.static.nc" "${DATAIN}/fixed/x1.${RES}.graph.info.part.${cores}" "${DATAOUT}/${YYYYMMDDHHi}/Pre/x1.${RES}.init.nc" "${DATAIN}/fixed/Vtable.GFS")
+files_needed=("${SCRIPTS}/namelists/stream_list.atmosphere.output" ""${SCRIPTS}/namelists/stream_list.atmosphere.diagnostics${VARTABLE} "${SCRIPTS}/namelists/stream_list.atmosphere.surface" "${EXECS}/atmosphere_model" "${DATAIN}/fixed/x1.${RES}.static.nc" "${DATAIN}/fixed/x1.${RES}.graph.info.part.${cores}" "${DATAOUT}/${YYYYMMDDHHi}/Pre/x1.${RES}.init.nc" "${DATAIN}/fixed/Vtable.${EXP}")
 for file in "${files_needed[@]}"
 do
   if [ ! -s "${file}" ]
@@ -157,16 +187,18 @@ cp -f ${DATAIN}/fixed/*DATA ${DIRRUN}
 cp -f ${DATAIN}/fixed/x1.${RES}.static.nc ${DIRRUN}
 cp -f ${DATAIN}/fixed/x1.${RES}.graph.info.part.${cores} ${DIRRUN}
 cp -f ${DATAOUT}/${YYYYMMDDHHi}/Pre/x1.${RES}.init.nc ${DIRRUN}
-cp -f ${DATAIN}/fixed/Vtable.GFS ${DIRRUN}
+cp -f ${DATAIN}/fixed/Vtable.${EXP} ${DIRRUN}
 
-
-if [ ${EXP} = "GFS" ]
+if [[ $MODERUN == "R" ]]; then
+   cp -f ${DATAOUT}/${YYYYMMDDHHi}/Pre/lbc*.nc ${DIRRUN}
+fi
+if [[ ${EXP} == "GFS" ||  ${EXP} == "ERA" ]]
 then
    sed -e "s,#LABELI#,${start_date},g;s,#FCSTS#,${DD_HHMMSS_forecast},g;s,#RES#,${RES},g;
-s,#CONFIG_DT#,${CONFIG_DT},g;s,#CONFIG_LEN_DISP#,${CONFIG_LEN_DISP},g;s,#CONFIG_CONV_INTERVAL#,${CONFIG_CONV_INTERVAL},g" \
+s,#CONFIG_DT#,${CONFIG_DT},g;s,#CONFIG_LEN_DISP#,${CONFIG_LEN_DISP},g;s,#CONFIG_CONV_INTERVAL#,${CONFIG_CONV_INTERVAL},g;s,#APPLY_LBCS#,${APPLY_LBCS},g" \
    ${SCRIPTS}/namelists/namelist.atmosphere.TEMPLATE > ${DIRRUN}/namelist.atmosphere
 
-   sed -e "s,#RES#,${RES},g;s,#CIORIG#,${EXP},g;s,#LABELI#,${YYYYMMDDHHi},g;s,#NLEV#,${NLEV},g" \
+   sed -e "s,#RES#,${RES},g;s,#RORG#,${RORG},g;s,#LBCINT#,${LBCINT},g;s,#CIORIG#,${EXP},g;s,#LABELI#,${YYYYMMDDHHi},g;s,#NLEV#,${NLEV},g" \
    ${SCRIPTS}/namelists/streams.atmosphere.TEMPLATE > ${DIRRUN}/streams.atmosphere
 fi
 cp -f ${SCRIPTS}/namelists/stream_list.atmosphere.output ${DIRRUN}
@@ -271,7 +303,7 @@ do
    i=$(printf "%04d" ${ii})
    hh=${YYYYMMDDHHi:8:2}
    currentdate=$(date -d "${YYYYMMDDHHi:0:8} ${hh}:00:00 $(echo "(${i}-1)*${t_strout:0:2}" | bc) hours $(echo "(${i}-1)*${t_strout:3:2}" | bc) minutes $(echo "(${i}-1)*${t_strout:6:2}" | bc) seconds" +"%Y%m%d%H.%M.%S")
-   file=MONAN_DIAG_G_MOD_${EXP}_${YYYYMMDDHHi}_${currentdate}.x${RES}L${NLEV}.nc
+   file=MONAN_DIAG_${RORG}_MOD_${EXP}_${YYYYMMDDHHi}_${currentdate}.x${RES}L${NLEV}.nc
 
    if [ ! -s ${DATAOUT}/${YYYYMMDDHHi}/Model/${file} ]
    then