source: CONFIG/UNIFORM/v5/LMDZ_v5/GENERAL/DRIVER/lmdz.driver @ 1934

Last change on this file since 1934 was 1934, checked in by jgipsl, 12 years ago

Added configuration avec only LMDZ. This is the same as LMDZOR but without "the orchidee parts". Compilation is slightly different.
File size: 24.7 KB
Line 
1#!/bin/ksh
2#-----------------------------------------------------------------
3function LMDZ_sed
4{
5# Usage : LMDZ_sed filedef var_name myvalue
6#         In file filedef modify the line containing var_name=xxx into var_name=myvalue
7    IGCM_debug_PushStack "LMDZ_sed"
8   
9    # Test if the fichier exist
10    if [ ! -f ${1} ] ; then
11        echo "WARNING : ${1} file does not exist. Following will not be done : LMDZ_sed : ${1} ${2} ${3}"
12        return
13    fi
14
15    sed -e "s/^${2}\ *=.*/${2}= ${3}/" ${1} > ${1}.tmp
16    RET=$?
17    echo "LMDZ_sed : ${1} ${2} ${3}"
18    \mv ${1}.tmp ${1}
19
20    IGCM_debug_PopStack "LMDZ_sed"
21    return $RET
22}
23function LMDZ_sed_default
24{
25# Usage : LMDZ_sed_default filedef var_name
26#         In file filedef modify the line  "var_name=xxx DEFAULT= myvalue"
27#         into "var_name=myvalue"
28    IGCM_debug_PushStack "LMDZ_sed_default"
29
30    DefValue=$( grep ${2} ${1}  | awk -F"DEFAULT.=*" '{print $2}')
31
32    LMDZ_sed  ${1} ${2} $DefValue
33    IGCM_debug_PopStack "LMDZ_sed_default"
34    return $RET
35}
36
37
38function ATM_Initialize
39{
40    IGCM_debug_PushStack "ATM_Initialize"
41
42    RESOL_ATM=$( echo $RESOL | awk "-Fx" '{print $2}' | awk "-F-" '{print $1}')
43
44    [ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) || RESOL_ATM_3D=96x95x19
45
46    RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $3}' )
47    RESOL_ATM_X=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $1}' )
48    RESOL_ATM_Y=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $2}' )
49    RESOL_ATM_XY="${RESOL_ATM_X}x${RESOL_ATM_Y}"
50
51    ##-- Calendar type for LMDZ and create_etat0_limit
52    case ${config_UserChoices_CalendarType} in
53        leap|gregorian)
54            CalendarTypeForLmdz=earth_366d
55            CalendarTypeForCreate=gregorian;;
56        noleap)
57            CalendarTypeForLmdz=earth_365d
58            CalendarTypeForCreate=${CalendarTypeForLmdz};;
59        360d)
60            CalendarTypeForLmdz=earth_360d
61            CalendarTypeForCreate=${CalendarTypeForLmdz};;
62        *)
63            CalendarTypeForLmdz=earth_360d
64            CalendarTypeForCreate=${CalendarTypeForLmdz}
65    esac
66
67    ##- LMDZ physics version
68    ##  Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
69    if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
70        LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
71    else
72        LMDZ_Physics=AP
73    fi
74    echo LMDZ physics version : ${LMDZ_Physics}
75
76    ##- Create_etat0_limit version
77    ##  Define variable CREATE only if it is set in lmdz.card section UserChoices.
78    ##  This variable is only used in lmdz.card to choose input files.
79    if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
80        IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
81        CREATE=${lmdz_UserChoices_CREATE}
82        echo create_etat0_limit version : ${CREATE}
83    fi
84
85
86    ## - LMDZ choice of config.def file
87    ##   ConfType must be set in lmdz.card
88    ConfType=${lmdz_UserChoices_ConfType}
89
90    ##- LMDZ output level, to be set in lmdz.card
91    if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
92        # OutLevel is not set. Take default value low.
93        OutLevel=low
94    else
95        OutLevel=${lmdz_UserChoices_OutLevel}
96    fi
97
98    ##-- Output frequency purpose ....
99    ##--  Initialisation  ....
100    ok_mensuel=n
101    ok_journe=n
102    ok_hf=n
103    ok_hf3h=n
104    ok_hf3hm=n
105    ok_stn=n
106
107    case ${config_UserChoices_PeriodLength} in
108        1Y|1y|1M|1m) ok_mensuel=y ;;
109        5D|5d|1D|1d) ok_journe=y ;;
110    esac
111
112    for frequency in ${config_ATM_WriteFrequency} ; do
113        case ${frequency} in
114            1M|1m) ok_mensuel=y ;;
115        esac
116        case ${frequency} in
117            5D|5d|1D|1d) ok_journe=y ;;
118        esac
119        case ${frequency} in
120            HF|hf) ok_hf=y ;;
121        esac
122        case ${frequency} in
123            HF3h|hf3h) ok_hf3h=y ;;
124        esac
125        case ${frequency} in
126            HF3hm|hf3hm) ok_hf3hm=y ;;
127        esac
128        case ${frequency} in
129            STN|stn) ok_stn=y ;;
130        esac
131    done
132
133    ## Read LMDZ_NbPeriod_adjust option in lmdz.card
134    if [ X"${lmdz_UserChoices_LMDZ_NbPeriod_adjust}" = X"" ] ; then
135        # The variable is not in lmdz.card, set default value
136        LMDZ_NbPeriod_adjust=0
137    else       
138        LMDZ_NbPeriod_adjust=${lmdz_UserChoices_LMDZ_NbPeriod_adjust}
139    fi
140
141    if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
142        LMDZ_Bands_file_name=${lmdz_UserChoices_LMDZ_Bands_file_name}
143    fi
144
145
146    ##  Read LMDZ_COSP_OK in lmdz.card
147    if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ] ; then
148        LMDZ_COSP_OK=${lmdz_UserChoices_LMDZ_COSP_OK}
149    else
150        LMDZ_COSP_OK=n
151    fi
152    ##  Read LMDZ_COSP_monthly in lmdz.card
153    if [ ! X${lmdz_UserChoices_LMDZ_COSP_monthly} = X ] ; then
154        LMDZ_COSP_monthly=${lmdz_UserChoices_LMDZ_COSP_monthly}
155    else
156        LMDZ_COSP_monthly=n
157    fi
158    ##  Read LMDZ_COSP_daily in lmdz.card
159    if [ ! X${lmdz_UserChoices_LMDZ_COSP_daily} = X ] ; then
160        LMDZ_COSP_daily=${lmdz_UserChoices_LMDZ_COSP_daily}
161    else
162        LMDZ_COSP_daily=n
163    fi
164    ##  Read LMDZ_COSP_hf in lmdz.card
165    if [ ! X${lmdz_UserChoices_LMDZ_COSP_hf} = X ] ; then
166        LMDZ_COSP_hf=${lmdz_UserChoices_LMDZ_COSP_hf}
167    else
168        LMDZ_COSP_hf=n
169    fi
170
171    ##  Read LMDZ_NMC_monthly in lmdz.card
172    if [ ! X${lmdz_UserChoices_LMDZ_NMC_monthly} = X ] ; then
173        LMDZ_NMC_monthly=${lmdz_UserChoices_LMDZ_NMC_monthly}
174    else
175        LMDZ_NMC_monthly=n
176    fi
177
178    ## Read LMDZ_NMC_daily in lmdz.card
179    if [ ! X${lmdz_UserChoices_LMDZ_NMC_daily} = X ] ; then
180        LMDZ_NMC_daily=${lmdz_UserChoices_LMDZ_NMC_daily}
181    else
182        LMDZ_NMC_daily=n
183    fi
184   
185    ## Read LMDZ_NMC_hf in lmdz.card
186    if [ ! X${lmdz_UserChoices_LMDZ_NMC_hf} = X ] ; then
187        LMDZ_NMC_hf=${lmdz_UserChoices_LMDZ_NMC_hf}
188    else
189        LMDZ_NMC_hf=n
190    fi
191
192
193    IGCM_debug_PopStack "ATM_Initialize"
194}
195
196#-----------------------------------------------------------------
197function ATM_Update
198{
199    IGCM_debug_PushStack "ATM_Update"
200
201
202    case ${config_UserChoices_PeriodLength} in
203        *Y|*y) 
204               LMDZ_ecrit_ISCCP=30.
205               LMDZ_periodav=30.
206               if [ "${config_UserChoices_CalendarType}" != "360d" ] ; then
207                  echo Do not consider following warning if your running create_etat0_limit :
208                  echo WARNING !!! For lmdz : calendartype in config.card. PeriodLength=1Y allowed only for CalendarType=360d
209               fi
210               ;;
211        *)
212               LMDZ_ecrit_ISCCP=${PeriodLengthInDays}.
213               LMDZ_periodav=${PeriodLengthInDays}.
214               ;;
215    esac
216 
217    ##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
218    if [ ${CumulPeriod} -eq 1 ] ; then
219        RAZ_DATE=1
220    else
221        RAZ_DATE=0
222    fi
223
224    ## Algorithme for special treatment for Bands_xxx file
225    ## For CumulPeriod=1 ;
226    ##        IF NbPeriod_Adjust = 0 ; set LMDZ_adjust=n
227    ##                                IF LMDZ_Bands_file_name was given in lmdz.card THEN Get Bands file directly from server. Store it later with _0 suffix.
228    ##                                IF no LMDZ_Bands_file_name was given, start without Bands file. Store it later with _0 suffix.
229    ##        ELSE set LMDZ_adjust=y ; start without Bands file ; Store it later in PARAM/ directory in submit directory with suffix _1 ;
230    ##
231    ## For CumulPeriod=2 to LMDZ_NbPeriod_adjust ;
232    ##       Get Bands file from PARAM/ in submit directory (CumulPeriod-1) ; set LMDZ_adjust=y ; Store Bands file in PARAM/ ;
233    ##
234    ## For CumulPeriod > LMDZ_NbPeriod_adjust ; LMDZ_adjust=n ; Get Bands file from PARAM/ ; Do not store ;
235
236    if [ ${CumulPeriod} -eq 1 ] ; then
237        if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
238            if [ ! X${LMDZ_Bands_file_name} = X ] ; then
239                IGCM_sys_Get ${LMDZ_Bands_file_name} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
240                IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
241                IGCM_debug_Print 1 "Bands file forced to ${LMDZ_Bands_file_name} and stored in ${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0"
242            fi
243        fi
244    fi
245
246    LMDZ_adjust=n
247    [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && LMDZ_adjust=y
248
249    RefPeriod=${LMDZ_NbPeriod_adjust} #0 to use a Bands file from Restart
250    [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && (( RefPeriod = ${CumulPeriod} - 1 )) 
251
252    # Get Bands file from PARAM directory if file exist
253    if [ ${CumulPeriod} -gt 1 && -f ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} ] ; then
254        IGCM_sys_Cp ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
255        IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
256    fi
257
258    ##-- GHG forcing :
259    ##   If forcing file exist in run directory, read values for the current year and modify config.def
260    if [ -f SOLARANDVOLCANOES.txt ] ; then
261        IPCC_SOLAR=`grep Annee_${year} SOLARANDVOLCANOES.txt | awk -F= '{print $2}'`
262        LMDZ_sed config.def solaire     ${IPCC_SOLAR}
263    else
264        LMDZ_sed_default config.def solaire
265    fi
266    if [ -f CO2.txt ] ; then
267        IPCC_CO2=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
268        LMDZ_sed config.def co2_ppm     ${IPCC_CO2}
269    else
270        LMDZ_sed_default config.def co2_ppm
271    fi
272
273
274    if [ -f CH4.txt ] ; then
275        IPCC_CH4=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
276        LMDZ_sed config.def CH4_ppb     ${IPCC_CH4}
277    else
278        LMDZ_sed_default config.def CH4_ppb
279    fi
280    if [ -f N2O.txt ] ; then
281        IPCC_N2O=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
282        LMDZ_sed config.def N2O_ppb     ${IPCC_N2O}
283    else
284        LMDZ_sed_default config.def N2O_ppb
285    fi
286    if [ -f CFC11.txt ] ; then
287        IPCC_CFC11=`grep Annee_${year} CFC11.txt | awk -F= '{print $2}'`
288        LMDZ_sed config.def CFC11_ppt   ${IPCC_CFC11}
289    else
290        LMDZ_sed_default config.def CFC11_ppt
291    fi
292    if [ -f CFC12.txt ] ; then
293        IPCC_CFC12=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
294        LMDZ_sed config.def CFC12_ppt   ${IPCC_CFC12}
295    else
296        LMDZ_sed_default config.def CFC12_ppt
297    fi
298
299
300    ##-- Add special treatement for CARBON CYCLE
301    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
302        ATM_Carbon_Update
303    fi
304
305
306    ##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
307    ##   COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
308    if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] &&  [ ${year} -ge 1979 ]) ; then
309        LMDZ_COSP_daily=y
310    fi
311
312
313    ## output.def parameters
314    #  columns in phys_output_filekeys refer to the filenames given in phys_out_filenames in output.def : 
315    #                                            histmth       histday        histhf    histfh3h   histhf3hm   histstn
316    LMDZ_sed output.def phys_out_filekeys       "${ok_mensuel} ${ok_journe}   ${ok_hf}  ${ok_hf3h} ${ok_hf3hm} ${ok_stn}"
317    LMDZ_sed output.def ecrit_ISCCP ${LMDZ_ecrit_ISCCP}
318    LMDZ_sed output.def ok_cosp     ${LMDZ_COSP_OK}
319    LMDZ_sed output.def ok_mensuelCOSP  ${LMDZ_COSP_monthly}
320    LMDZ_sed output.def ok_journeCOSP   ${LMDZ_COSP_daily}
321    LMDZ_sed output.def ok_hfCOSP   ${LMDZ_COSP_hf}
322    LMDZ_sed output.def ok_histNMC  "${LMDZ_NMC_monthly} ${LMDZ_NMC_daily} ${LMDZ_NMC_hf}"
323
324    ## gcm.def parameters :
325    # Modification only for new physics
326    if [ X${LMDZ_Physics} = X"NPv3.1" ] ; then
327        LMDZ_sed gcm.def iphysiq     5
328    else
329        LMDZ_sed_default gcm.def iphysiq
330    fi
331
332
333    ## run.def parameters
334    LMDZ_sed run.def dayref   ${InitDay}
335    LMDZ_sed run.def nday     ${PeriodLengthInDays}
336    LMDZ_sed run.def raz_date ${RAZ_DATE}
337    LMDZ_sed run.def periodav ${LMDZ_periodav}
338    LMDZ_sed run.def adjust   ${LMDZ_adjust}
339
340    # Set anneeref different for gcm and ce0l
341    # Variable calend is different for a run with create_etat0_limit and the gcm
342    # Test if executable create_etat0_limit is present and lmdz.x is not present
343    if [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
344        # for case ce0l : always take current year
345        LMDZ_sed run.def anneeref ${year}
346        LMDZ_sed run.def calend   ${CalendarTypeForCreate}
347    else
348        # for case gcm : take first year of simulation
349        LMDZ_sed run.def anneeref ${InitYear}
350        LMDZ_sed run.def calend   ${CalendarTypeForLmdz}
351    fi
352
353    # Activate creation of file grilles_gcm.nc only at first period
354    if [ ${CumulPeriod} -eq 1 ] ; then
355        LMDZ_sed run.def grilles_gcm_netcdf y
356    else
357        LMDZ_sed run.def grilles_gcm_netcdf n
358    fi
359
360    ## Determine from the variable ListOfComponents in config.card coupling to external models
361    ## and set corresponding parameters in run.def
362    echo ListOfComponents now running : ${config_ListOfComponents[*]}
363
364    if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
365        echo "Activate ORCHIDEE, set VEGET=y in run.def"
366        LMDZ_sed run.def VEGET y
367    else
368        echo "No ORCHIDEE, set VEGET=n in run.def"
369        LMDZ_sed run.def VEGET n
370    fi
371
372    if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
373        echo "Activate coupling to ocean, set type_ocean=couple in run.def"
374        LMDZ_sed run.def type_ocean couple
375    else
376        echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
377        LMDZ_sed run.def type_ocean force
378    fi
379
380    if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
381        echo "Activate coupling to INCA, set type_trac=inca in run.def"
382        LMDZ_sed run.def type_trac inca
383    elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
384        echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
385        LMDZ_sed run.def type_trac repr
386        LMDZ_sed run.def config_inca none
387    else
388        echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
389        LMDZ_sed run.def type_trac lmdz
390        LMDZ_sed run.def config_inca none
391    fi
392
393
394    # config.def : If running with Reprobus, desactivate ok_ade, ok_aie and read_climoz
395    if [ X${config_ListOfComponents_CHM} = Xreprobus ]  ; then
396        LMDZ_sed config.def ok_ade n
397        LMDZ_sed config.def ok_aie n
398        LMDZ_sed config.def aerosol_couple n
399        LMDZ_sed config.def read_climoz 0
400    elif [ X${config_ListOfComponents_CHM} = Xinca ]; then
401        case ${CHEM} in
402            AER)
403                LMDZ_sed config.def ok_ade y
404                LMDZ_sed config.def ok_aie n
405                LMDZ_sed config.def aerosol_couple y
406                LMDZ_sed config.def read_climoz 0
407                ;;
408            NMHC_AER)
409                LMDZ_sed config.def ok_ade y
410                LMDZ_sed config.def ok_aie n
411                LMDZ_sed config.def aerosol_couple y
412                LMDZ_sed config.def read_climoz 0
413                ;;
414            GES)
415                LMDZ_sed config.def ok_ade n
416                LMDZ_sed config.def ok_aie n
417                LMDZ_sed config.def aerosol_couple n
418                LMDZ_sed config.def read_climoz 0
419        esac
420
421    else
422        LMDZ_sed config.def ok_ade y
423        LMDZ_sed config.def ok_aie y
424        LMDZ_sed config.def aerosol_couple n
425        LMDZ_sed config.def read_climoz 2
426    fi
427
428    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
429    if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
430        LMDZ_sed guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
431    else
432        LMDZ_sed guide.def ok_guide n
433    fi
434
435    ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
436    ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
437    if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
438        awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
439        IGCM_sys_Mv gcm.def.tmp gcm.def
440        echo
441        IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
442        echo
443        cat gcm.def
444        ByPass_hgardfou_teta=n
445        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
446    fi
447
448    ## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
449    ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
450    if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
451        sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
452        IGCM_sys_Mv gcm.def.tmp gcm.def
453        echo
454        IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
455        echo
456        cat gcm.def
457        ByPass_hgardfou_mats=n
458        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
459    fi
460
461    if ( ${FirstInitialize} ) ; then
462        if [ -f start.nc ] && [ -f startphy.nc ] ; then
463            # The restart files already exist. They have been copied from a previous run or from a CREATE job
464            echo "Restart files for LMDZ have been copied from a previous run"
465        elif [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
466            # Do nothing because it is the program for creating restart files that is running and not LMDZ
467            echo "create_etat0_limit.e will create initial start files"
468        else
469            # Restart files have to be created
470            echo "Run create_etat0_limit.e to create restart files start.nc and startphy.nc for LMDZ"
471            if [ ${DRYRUN} -le 2 ] ; then
472                ##-- suppression of ozone file construction --
473                cp config.def config.def.save
474                LMDZ_sed config.def read_climoz 0
475                IGCM_sys_Cp ${R_EXE}/create_etat0_limit.e ${RUN_DIR}/.
476                if [ ${DRYRUN} -le 1 ] ; then
477                    ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e
478                    IGCM_sys_Put_Out start.nc    ${R_OUT_ATM_R}/${config_UserChoices_JobName}_${PeriodDateBegin}_start.nc
479                    IGCM_sys_Put_Out startphy.nc ${R_OUT_ATM_R}/${config_UserChoices_JobName}_${PeriodDateBegin}_startphy.nc
480                fi
481                IGCM_sys_Mv config.def.save config.def
482            else
483                echo "EXECUTION of ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e simulated"
484                echo "EXECUTION of ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e simulated for DRYRUN = " $DRYRUN >> stack
485            fi
486        fi
487    fi
488
489    IGCM_debug_PopStack "ATM_Update"
490}
491
492#-----------------------------------
493function ATM_Finalize
494{
495    IGCM_debug_PushStack "ATM_Finalize"
496
497    # If the file exist, copy Bands_ file to PARAM/ in submit directory. This file will be used for the simulation.
498    # Copy also the same file into ATM/Restart at ARCHIVE directory for backup.
499    if [ -f Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ] ; then
500      if [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] ; then
501        IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
502        IGCM_sys_Put_Out Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${R_OUT_ATM_R}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
503      elif [ ${CumulPeriod} -eq 1 ] && [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
504        # Special case : first period and no adjust => Save bands file with suffix _0
505        IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
506        IGCM_sys_Put_Out Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${R_OUT_ATM_R}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
507      fi
508    fi
509
510    # Add special treatement for CARBON CYCLE
511    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
512        ATM_Carbon_Finalize
513    fi
514
515    echo FINALIZE ATM !
516
517    IGCM_debug_PopStack "ATM_Finalize"
518}
519
520
521
522function ATM_Carbon_Update
523{
524    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
525
526    IGCM_debug_PushStack "ATM_Carbon_Update"
527
528    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
529    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
530    typeset PathCO2log
531    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
532   
533    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
534        ##--Initialization of fluxes to an undefined value at the first run
535        UndefinedValueCo2=-9999
536        InitPeriodCo2=0
537        InitDateBeginCo2=${UndefinedValueCo2}
538        InitYearCo2=$(( ${year} - 1 )) 
539        InitDateEndCo2=${InitYearCo2}1231
540        fCO2_ff=${UndefinedValueCo2} 
541        CO2SBG=${UndefinedValueCo2}
542        CO2LU=${UndefinedValueCo2}
543        CO2MBG=${UndefinedValueCo2}
544        CO2_ppm_prec=${UndefinedValueCo2}
545        # Get the initial value of atmosp. pco2
546        CO2_ppm=${lmdz_UserChoices_co2_init}
547       
548        IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
549        IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
550       
551        # Save CO2 values in ExeCpuLog variable contents 5 fields
552        echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
553            gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
554                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
555       
556        # Get the path where the log file co2.log is
557        PathCO2log=${SUBMIT_DIR} 
558        # Get Previous line in co2.log
559        PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
560       
561    else
562       
563        # NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
564        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
565        #SubmitRestartPath=
566        if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
567            IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
568            PathCO2log=${config_ATM_SubmitRestartPath}
569            Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
570            PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
571           
572            IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
573            IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
574           
575            # Save Last Line of control in new co2.log file
576            InitPeriodCo2=0   
577            InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
578            InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
579            fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
580            CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
581            CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
582            CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
583            CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
584            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
585           
586            echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
587                gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
588                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
589        else
590           # Get restart line in co2.log
591            PathCO2log=${SUBMIT_DIR}
592            PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
593           # Get the value of atmosp. pco2 in co2.log
594            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
595        fi
596       
597    fi
598   
599    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
600            # Modify co2_ppm in config.def only for historical run
601            # If not historical run, keep co2_ppm value set earlier by LMDZ_sed
602        LMDZ_sed config.def co2_ppm     ${CO2_ppm}
603    fi
604    IGCM_debug_PopStack "ATM_Carbon_Update"
605}
606
607
608function ATM_Carbon_Finalize
609{
610    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
611
612    IGCM_debug_PushStack "ATM_Carbon_Finalize"
613
614    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
615   
616        # Fossil fuel emission
617    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
618            # For Control, no fossil fuel emission :
619        fCO2_ff=0
620        echo "Fossil Fuel for control run  :" ${fCO2_ff}
621    else
622            # For historical, get the fossile fuel file :
623        fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
624        echo "Fossil Fuel for historical run  :" ${fCO2_ff}
625    fi
626   
627        # Get the value of ocean carbon flux
628    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
629    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
630    echo "Ocean carbon flux  :" ${CO2MBG}
631   
632        # Get the value of land fluxes
633    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
634    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
635    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
636    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
637    echo "Land carbon flux (NEP)         :" ${CO2SRF}
638    echo "LU flux          (FLUC)        :" ${CO2LU}
639    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
640   
641        # Previous CO2
642    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
643    echo "Previous CO2  :" ${CO2_ppm_prec}
644   
645        # Formula
646    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
647    echo "New CO2  :" ${CO2_ppm}
648   
649        # Save CO2 values in ExeCpuLog variable contents 5 fields
650    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
651        gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
652                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
653   
654    IGCM_debug_PopStack "ATM_Carbon_Finalize"
655}
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