source: CONFIG/UNIFORM/v5/LMDZOR_v5.2/GENERAL/DRIVER/lmdz.driver @ 2208

Last change on this file since 2208 was 2208, checked in by sdipsl, 8 years ago

Fix call stack tree

File size: 25.9 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} ${3}"
12        IGCM_debug_PopStack "LMDZ_sed"
13        return
14    fi
15
16    sed -e "s/^${2}\ *=.*/${2}= ${3}/" ${1} > ${1}.tmp
17    RET=$?
18    echo "LMDZ_sed : ${1} ${2} ${3}"
19    \mv ${1}.tmp ${1}
20
21    IGCM_debug_PopStack "LMDZ_sed"
22    return $RET
23}
24function LMDZ_sed_default
25{
26# Usage : LMDZ_sed_default filedef var_name
27#         In file filedef modify the line  "var_name=xxx DEFAULT= myvalue"
28#         into "var_name=myvalue"
29    IGCM_debug_PushStack "LMDZ_sed_default"
30
31    DefValue=$( grep ${2} ${1}  | awk -F"DEFAULT.=*" '{print $2}')
32
33    LMDZ_sed  ${1} ${2} $DefValue
34    IGCM_debug_PopStack "LMDZ_sed_default"
35    return $RET
36}
37
38
39function ATM_Initialize
40{
41    IGCM_debug_PushStack "ATM_Initialize"
42
43    RESOL_ATM=$( echo $RESOL | awk "-Fx" '{print $2}' | awk "-F-" '{print $1}')
44
45    [ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) || RESOL_ATM_3D=96x95x19
46
47    RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $3}' )
48    RESOL_ATM_X=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $1}' )
49    RESOL_ATM_Y=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $2}' )
50    RESOL_ATM_XY="${RESOL_ATM_X}x${RESOL_ATM_Y}"
51
52    ##-- Calendar type for LMDZ and create_etat0_limit
53    case ${config_UserChoices_CalendarType} in
54        leap|gregorian)
55            CalendarTypeForLmdz=earth_366d
56            CalendarTypeForCreate=gregorian;;
57        noleap)
58            CalendarTypeForLmdz=earth_365d
59            CalendarTypeForCreate=${CalendarTypeForLmdz};;
60        360d)
61            CalendarTypeForLmdz=earth_360d
62            CalendarTypeForCreate=${CalendarTypeForLmdz};;
63        *)
64            CalendarTypeForLmdz=earth_360d
65            CalendarTypeForCreate=${CalendarTypeForLmdz}
66    esac
67
68    ##- LMDZ physics version
69    ##  Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
70    if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
71        LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
72    else
73        LMDZ_Physics=AP
74    fi
75    echo LMDZ physics version : ${LMDZ_Physics}
76
77    ##- Create_etat0_limit version
78    ##  Define variable CREATE only if it is set in lmdz.card section UserChoices.
79    ##  This variable is only used in lmdz.card to choose input files.
80    if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
81        IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
82        CREATE=${lmdz_UserChoices_CREATE}
83        echo create_etat0_limit version : ${CREATE}
84    fi
85
86
87    ## - LMDZ choice of config.def file
88    ##   ConfType must be set in lmdz.card
89    ConfType=${lmdz_UserChoices_ConfType}
90
91    ##- LMDZ output level, to be set in lmdz.card
92    if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
93        # OutLevel is not set. Take default value low.
94        OutLevel=low
95    else
96        OutLevel=${lmdz_UserChoices_OutLevel}
97    fi
98
99    ##-- Output frequency purpose ....
100    ##--  Initialisation  ....
101    ok_mensuel=n
102    ok_journe=n
103    ok_hf=n
104    ok_hf3h=n
105    ok_hf3hm=n
106    ok_stn=n
107
108    case ${config_UserChoices_PeriodLength} in
109        1Y|1y|1M|1m) ok_mensuel=y ;;
110        5D|5d|1D|1d) ok_journe=y ;;
111    esac
112
113    for frequency in ${config_ATM_WriteFrequency} ; do
114        case ${frequency} in
115            1M|1m) ok_mensuel=y ;;
116        esac
117        case ${frequency} in
118            5D|5d|1D|1d) ok_journe=y ;;
119        esac
120        case ${frequency} in
121            HF|hf) ok_hf=y ;;
122        esac
123        case ${frequency} in
124            HF3h|hf3h) ok_hf3h=y ;;
125        esac
126        case ${frequency} in
127            HF3hm|hf3hm) ok_hf3hm=y ;;
128        esac
129        case ${frequency} in
130            STN|stn) ok_stn=y ;;
131        esac
132    done
133
134    ## Read LMDZ_NbPeriod_adjust option in lmdz.card
135    if [ X"${lmdz_UserChoices_LMDZ_NbPeriod_adjust}" = X"" ] ; then
136        # The variable is not in lmdz.card, set default value
137        LMDZ_NbPeriod_adjust=0
138    else       
139        LMDZ_NbPeriod_adjust=${lmdz_UserChoices_LMDZ_NbPeriod_adjust}
140    fi
141
142    if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
143        LMDZ_Bands_file_name=${lmdz_UserChoices_LMDZ_Bands_file_name}
144    fi
145
146
147    ##  Read LMDZ_COSP_OK in lmdz.card
148    if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ] ; then
149        LMDZ_COSP_OK=${lmdz_UserChoices_LMDZ_COSP_OK}
150    else
151        LMDZ_COSP_OK=n
152    fi
153    ##  Read LMDZ_COSP_monthly in lmdz.card
154    if [ ! X${lmdz_UserChoices_LMDZ_COSP_monthly} = X ] ; then
155        LMDZ_COSP_monthly=${lmdz_UserChoices_LMDZ_COSP_monthly}
156    else
157        LMDZ_COSP_monthly=n
158    fi
159    ##  Read LMDZ_COSP_daily in lmdz.card
160    if [ ! X${lmdz_UserChoices_LMDZ_COSP_daily} = X ] ; then
161        LMDZ_COSP_daily=${lmdz_UserChoices_LMDZ_COSP_daily}
162    else
163        LMDZ_COSP_daily=n
164    fi
165    ##  Read LMDZ_COSP_hf in lmdz.card
166    if [ ! X${lmdz_UserChoices_LMDZ_COSP_hf} = X ] ; then
167        LMDZ_COSP_hf=${lmdz_UserChoices_LMDZ_COSP_hf}
168    else
169        LMDZ_COSP_hf=n
170    fi
171
172    ##  Read LMDZ_NMC_monthly in lmdz.card
173    if [ ! X${lmdz_UserChoices_LMDZ_NMC_monthly} = X ] ; then
174        LMDZ_NMC_monthly=${lmdz_UserChoices_LMDZ_NMC_monthly}
175    else
176        LMDZ_NMC_monthly=n
177    fi
178
179    ## Read LMDZ_NMC_daily in lmdz.card
180    if [ ! X${lmdz_UserChoices_LMDZ_NMC_daily} = X ] ; then
181        LMDZ_NMC_daily=${lmdz_UserChoices_LMDZ_NMC_daily}
182    else
183        LMDZ_NMC_daily=n
184    fi
185   
186    ## Read LMDZ_NMC_hf in lmdz.card
187    if [ ! X${lmdz_UserChoices_LMDZ_NMC_hf} = X ] ; then
188        LMDZ_NMC_hf=${lmdz_UserChoices_LMDZ_NMC_hf}
189    else
190        LMDZ_NMC_hf=n
191    fi
192
193
194    IGCM_debug_PopStack "ATM_Initialize"
195}
196
197#-----------------------------------------------------------------
198function ATM_Update
199{
200    IGCM_debug_PushStack "ATM_Update"
201
202
203    case ${config_UserChoices_PeriodLength} in
204        *Y|*y) 
205               LMDZ_ecrit_ISCCP=30.
206               LMDZ_periodav=30.
207               if [ "${config_UserChoices_CalendarType}" != "360d" ] ; then
208                  echo Do not consider following warning if your running create_etat0_limit :
209                  echo WARNING !!! For lmdz : calendartype in config.card. PeriodLength=1Y allowed only for CalendarType=360d
210               fi
211               ;;
212        *)
213               LMDZ_ecrit_ISCCP=${PeriodLengthInDays}.
214               LMDZ_periodav=${PeriodLengthInDays}.
215               ;;
216    esac
217 
218    ##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
219    if [ ${CumulPeriod} -eq 1 ] ; then
220        RAZ_DATE=1
221    else
222        RAZ_DATE=0
223    fi
224
225    ## Algorithme for special treatment for Bands_xxx file
226    ## For CumulPeriod=1 ;
227    ##        IF NbPeriod_Adjust = 0 ; set LMDZ_adjust=n
228    ##                                IF LMDZ_Bands_file_name was given in lmdz.card THEN Get Bands file directly from server. Store it later with _0 suffix.
229    ##                                IF no LMDZ_Bands_file_name was given, start without Bands file. Store it later with _0 suffix.
230    ##        ELSE set LMDZ_adjust=y ; start without Bands file ; Store it later in PARAM/ directory in submit directory with suffix _1 ;
231    ##
232    ## For CumulPeriod=2 to LMDZ_NbPeriod_adjust ;
233    ##       Get Bands file from PARAM/ in submit directory (CumulPeriod-1) ; set LMDZ_adjust=y ; Store Bands file in PARAM/ ;
234    ##
235    ## For CumulPeriod > LMDZ_NbPeriod_adjust ; LMDZ_adjust=n ; Get Bands file from PARAM/ ; Do not store ;
236
237    if [ ${CumulPeriod} -eq 1 ] ; then
238        if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
239            if [ ! X${LMDZ_Bands_file_name} = X ] ; then
240                IGCM_sys_Get ${LMDZ_Bands_file_name} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
241                IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
242                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"
243            fi
244        fi
245    fi
246
247    LMDZ_adjust=n
248    [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && LMDZ_adjust=y
249
250    RefPeriod=${LMDZ_NbPeriod_adjust} #0 to use a Bands file from Restart
251    [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && (( RefPeriod = ${CumulPeriod} - 1 )) 
252
253    # Get Bands file from PARAM directory if file exist
254    if ( [ ${CumulPeriod} -gt 1 ] && [ -f ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} ] ) ; then
255        IGCM_sys_Cp ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
256        IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
257    fi
258
259    ##-- GHG forcing :
260    ##   If forcing file exist in run directory, read values for the current year and modify config.def
261    if [ -f SOLARANDVOLCANOES.txt ] ; then
262        IPCC_SOLAR=`grep Annee_${year} SOLARANDVOLCANOES.txt | awk -F= '{print $2}'`
263        LMDZ_sed config.def solaire     ${IPCC_SOLAR}
264    else
265        LMDZ_sed_default config.def solaire
266    fi
267    if [ -f CO2.txt ] ; then
268        IPCC_CO2=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
269        LMDZ_sed config.def co2_ppm     ${IPCC_CO2}
270    else
271        LMDZ_sed_default config.def co2_ppm
272    fi
273
274
275    if [ -f CH4.txt ] ; then
276        IPCC_CH4=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
277        LMDZ_sed config.def CH4_ppb     ${IPCC_CH4}
278    else
279        LMDZ_sed_default config.def CH4_ppb
280    fi
281    if [ -f N2O.txt ] ; then
282        IPCC_N2O=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
283        LMDZ_sed config.def N2O_ppb     ${IPCC_N2O}
284    else
285        LMDZ_sed_default config.def N2O_ppb
286    fi
287    if [ -f CFC11.txt ] ; then
288        IPCC_CFC11=`grep Annee_${year} CFC11.txt | awk -F= '{print $2}'`
289        LMDZ_sed config.def CFC11_ppt   ${IPCC_CFC11}
290    else
291        LMDZ_sed_default config.def CFC11_ppt
292    fi
293    if [ -f CFC12.txt ] ; then
294        IPCC_CFC12=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
295        LMDZ_sed config.def CFC12_ppt   ${IPCC_CFC12}
296    else
297        LMDZ_sed_default config.def CFC12_ppt
298    fi
299
300
301    ##-- Add special treatement for CARBON CYCLE
302    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
303        ATM_Carbon_Update
304    fi
305
306
307    ##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
308    ##   COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
309    if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] &&  [ ${year} -ge 1979 ]) ; then
310        LMDZ_COSP_daily=y
311    fi
312
313
314    ## output.def parameters
315    #  columns in phys_output_filekeys refer to the filenames given in phys_out_filenames in output.def : 
316    #                                            histmth       histday        histhf    histfh3h   histhf3hm   histstn
317    LMDZ_sed output.def phys_out_filekeys       "${ok_mensuel} ${ok_journe}   ${ok_hf}  ${ok_hf3h} ${ok_hf3hm} ${ok_stn}"
318    LMDZ_sed output.def ecrit_ISCCP ${LMDZ_ecrit_ISCCP}
319    LMDZ_sed output.def ok_cosp     ${LMDZ_COSP_OK}
320    LMDZ_sed output.def ok_mensuelCOSP  ${LMDZ_COSP_monthly}
321    LMDZ_sed output.def ok_journeCOSP   ${LMDZ_COSP_daily}
322    LMDZ_sed output.def ok_hfCOSP   ${LMDZ_COSP_hf}
323    LMDZ_sed output.def ok_histNMC  "${LMDZ_NMC_monthly} ${LMDZ_NMC_daily} ${LMDZ_NMC_hf}"
324
325    ## gcm.def parameters :
326    # Modification only for new physics
327    if [ X${LMDZ_Physics} = X"NPv3.1" ] ; then
328        LMDZ_sed gcm.def iphysiq     5
329    else
330        LMDZ_sed_default gcm.def iphysiq
331    fi
332
333
334    ## run.def parameters
335    LMDZ_sed run.def dayref   ${InitDay}
336    LMDZ_sed run.def nday     ${PeriodLengthInDays}
337    LMDZ_sed run.def raz_date ${RAZ_DATE}
338    LMDZ_sed run.def periodav ${LMDZ_periodav}
339    LMDZ_sed run.def adjust   ${LMDZ_adjust}
340
341    # Set anneeref different for gcm and ce0l
342    # Variable calend is different for a run with create_etat0_limit and the gcm
343    # Test if executable create_etat0_limit is present and lmdz.x is not present
344    if [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
345        # for case ce0l : always take current year
346        LMDZ_sed run.def anneeref ${year}
347        LMDZ_sed run.def calend   ${CalendarTypeForCreate}
348    else
349        # for case gcm : take first year of simulation
350        LMDZ_sed run.def anneeref ${InitYear}
351        LMDZ_sed run.def calend   ${CalendarTypeForLmdz}
352    fi
353
354    # Activate creation of file grilles_gcm.nc only at first period
355    if [ ${CumulPeriod} -eq 1 ] ; then
356        LMDZ_sed run.def grilles_gcm_netcdf y
357    else
358        LMDZ_sed run.def grilles_gcm_netcdf n
359    fi
360
361    ## Determine from the variable ListOfComponents in config.card coupling to external models
362    ## and set corresponding parameters in run.def
363    echo ListOfComponents now running : ${config_ListOfComponents[*]}
364
365    if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
366        echo "Activate ORCHIDEE: set VEGET=y and add INCLUDEDEF=orchidee.def in run.def"
367        LMDZ_sed run.def VEGET y
368        # Add "INCLUDEDEF=orchidee.def" before the 5th line in run.def
369        sed -i '5iINCLUDEDEF=orchidee.def' run.def
370    else
371        echo "No ORCHIDEE, set VEGET=n in run.def"
372        LMDZ_sed run.def VEGET n
373    fi
374
375    if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
376        echo "Activate coupling to ocean, set type_ocean=couple in run.def"
377        LMDZ_sed run.def type_ocean couple
378    else
379        echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
380        LMDZ_sed run.def type_ocean force
381    fi
382
383    if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
384        echo "Activate coupling to INCA: set type_trac=inca and add INCLUDEDEF=inca.def in run.def"
385        LMDZ_sed run.def type_trac inca
386        # Add "INCLUDEDEF=inca.def" before the 5th line in run.def
387        sed -i '5iINCLUDEDEF=inca.def' run.def
388    elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
389        echo "Activate coupling to REPROBUS: set type_trac=repr and add INCLUDEDEF=reprobus.def in run.def"
390        LMDZ_sed run.def type_trac repr
391        LMDZ_sed run.def config_inca none
392        # Add "INCLUDEDEF=reprobus.def" before the 5th line in run.def
393        sed -i '5iINCLUDEDEF=reprobus.def' run.def
394    else
395        echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
396        LMDZ_sed run.def type_trac lmdz
397        LMDZ_sed run.def config_inca none
398    fi
399
400
401    # config.def : Activate direct radiative effect if ok_ade=y
402    if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
403        LMDZ_sed config.def ok_ade ${lmdz_UserChoices_ok_ade}
404    else
405        LMDZ_sed config.def ok_ade n
406    fi 
407
408    # config.def : Activate indirect radiative effect if ok_aie=y
409    if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
410        LMDZ_sed config.def ok_aie ${lmdz_UserChoices_ok_aie}
411    else
412        LMDZ_sed config.def ok_aie n
413    fi 
414
415    # config.def : Activate online aerosol coupled model if aerosol_couple=y
416    if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
417        LMDZ_sed config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
418    else
419        LMDZ_sed config.def aerosol_couple n
420    fi 
421
422    # config.def : Activate reading of ozone in climatology if read_climoz=2
423    if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
424        LMDZ_sed config.def read_climoz ${lmdz_UserChoices_read_climoz}
425    else
426        LMDZ_sed config.def read_climoz 0       
427    fi 
428
429    # config.def : Choose aerosol use in radiative effect
430    #  type of coupled aerosol =1 (default) =2 => bc  only =3 => pom only =4 => seasalt only
431    # =5 => dust only =6 => all aerosol   
432    if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
433        LMDZ_sed config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
434    else
435        LMDZ_sed config.def flag_aerosol 0
436    fi 
437
438    # config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
439    if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
440        LMDZ_sed config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
441    else
442        LMDZ_sed config.def ok_cdnc n   
443    fi 
444
445    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
446    if [ X${lmdz_UserChoices_ok_guide} = Xy ] ; then
447        # Set ok_guide=y in guide.def
448        LMDZ_sed guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
449        # Add "INCLUDEDEF=guide.def" before the 5th line in run.def
450        sed -i '5iINCLUDEDEF=guide.def' run.def
451    else
452        LMDZ_sed guide.def ok_guide n
453    fi
454
455    ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
456    ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
457    if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
458        awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
459        IGCM_sys_Mv gcm.def.tmp gcm.def
460        echo
461        IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
462        echo
463        cat gcm.def
464        ByPass_hgardfou_teta=n
465        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
466    fi
467
468    ## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
469    ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
470    if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
471        sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
472        IGCM_sys_Mv gcm.def.tmp gcm.def
473        echo
474        IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
475        echo
476        cat gcm.def
477        ByPass_hgardfou_mats=n
478        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
479    fi
480
481    if ( ${FirstInitialize} ) ; then
482        if [ -f start.nc ] && [ -f startphy.nc ] ; then
483            # The restart files already exist. They have been copied from a previous run or from a CREATE job
484            echo "Restart files for LMDZ have been copied from a previous run"
485        elif [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
486            # Do nothing because it is the program for creating restart files that is running and not LMDZ
487            echo "create_etat0_limit.e will create initial start files"
488        else
489            # Restart files have to be created
490            echo "Run create_etat0_limit.e to create restart files start.nc and startphy.nc for LMDZ"
491            if [ ${DRYRUN} -le 2 ] ; then
492                ##-- suppression of ozone file construction --
493                cp config.def config.def.save
494                LMDZ_sed config.def read_climoz 0
495                IGCM_sys_Cp ${R_EXE}/create_etat0_limit.e ${RUN_DIR}/.
496                if [ ${DRYRUN} -le 1 ] ; then
497                    ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e
498                    IGCM_sys_Put_Out start.nc    ${R_OUT_ATM_R}/${config_UserChoices_JobName}_${PeriodDateBegin}_start.nc
499                    IGCM_sys_Put_Out startphy.nc ${R_OUT_ATM_R}/${config_UserChoices_JobName}_${PeriodDateBegin}_startphy.nc
500                fi
501                IGCM_sys_Mv config.def.save config.def
502            else
503                echo "EXECUTION of ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e simulated"
504                echo "EXECUTION of ${HOST_MPIRUN_COMMAND} -np 1 ./create_etat0_limit.e simulated for DRYRUN = " $DRYRUN >> stack
505            fi
506        fi
507    fi
508
509    IGCM_debug_PopStack "ATM_Update"
510}
511
512#-----------------------------------
513function ATM_Finalize
514{
515    IGCM_debug_PushStack "ATM_Finalize"
516
517    # If the file exist, copy Bands_ file to PARAM/ in submit directory. This file will be used for the simulation.
518    # Copy also the same file into ATM/Restart at ARCHIVE directory for backup.
519    if [ -f Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ] ; then
520      if [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] ; then
521        IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
522        IGCM_sys_Put_Out Bands_${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}
523      elif [ ${CumulPeriod} -eq 1 ] && [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
524        # Special case : first period and no adjust => Save bands file with suffix _0
525        IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
526        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
527      fi
528    fi
529
530    # Add special treatement for CARBON CYCLE
531    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
532        ATM_Carbon_Finalize
533    fi
534
535    echo FINALIZE ATM !
536
537    IGCM_debug_PopStack "ATM_Finalize"
538}
539
540
541
542function ATM_Carbon_Update
543{
544    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
545
546    IGCM_debug_PushStack "ATM_Carbon_Update"
547
548    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
549    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
550    typeset PathCO2log
551    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
552   
553    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
554        ##--Initialization of fluxes to an undefined value at the first run
555        UndefinedValueCo2=-9999
556        InitPeriodCo2=0
557        InitDateBeginCo2=${UndefinedValueCo2}
558        InitYearCo2=$(( ${year} - 1 )) 
559        InitDateEndCo2=${InitYearCo2}1231
560        fCO2_ff=${UndefinedValueCo2} 
561        CO2SBG=${UndefinedValueCo2}
562        CO2LU=${UndefinedValueCo2}
563        CO2MBG=${UndefinedValueCo2}
564        CO2_ppm_prec=${UndefinedValueCo2}
565        # Get the initial value of atmosp. pco2
566        CO2_ppm=${lmdz_UserChoices_co2_init}
567       
568        IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
569        IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
570       
571        # Save CO2 values in ExeCpuLog variable contents 5 fields
572        echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
573            gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
574                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
575       
576        # Get the path where the log file co2.log is
577        PathCO2log=${SUBMIT_DIR} 
578        # Get Previous line in co2.log
579        PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
580       
581    else
582       
583        # NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
584        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
585        #SubmitRestartPath=
586        if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
587            IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
588            PathCO2log=${config_ATM_SubmitRestartPath}
589            Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
590            PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
591           
592            IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
593            IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
594           
595            # Save Last Line of control in new co2.log file
596            InitPeriodCo2=0   
597            InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
598            InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
599            fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
600            CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
601            CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
602            CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
603            CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
604            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
605           
606            echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
607                gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
608                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
609        else
610           # Get restart line in co2.log
611            PathCO2log=${SUBMIT_DIR}
612            PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
613           # Get the value of atmosp. pco2 in co2.log
614            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
615        fi
616       
617    fi
618   
619    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
620            # Modify co2_ppm in config.def only for historical run
621            # If not historical run, keep co2_ppm value set earlier by LMDZ_sed
622        LMDZ_sed config.def co2_ppm     ${CO2_ppm}
623    fi
624    IGCM_debug_PopStack "ATM_Carbon_Update"
625}
626
627
628function ATM_Carbon_Finalize
629{
630    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
631
632    IGCM_debug_PushStack "ATM_Carbon_Finalize"
633
634    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
635   
636        # Fossil fuel emission
637    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
638            # For Control, no fossil fuel emission :
639        fCO2_ff=0
640        echo "Fossil Fuel for control run  :" ${fCO2_ff}
641    else
642            # For historical, get the fossile fuel file :
643        fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
644        echo "Fossil Fuel for historical run  :" ${fCO2_ff}
645    fi
646   
647        # Get the value of ocean carbon flux
648    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
649    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
650    echo "Ocean carbon flux  :" ${CO2MBG}
651   
652        # Get the value of land fluxes
653    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
654    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
655    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
656    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
657    echo "Land carbon flux (NEP)         :" ${CO2SRF}
658    echo "LU flux          (FLUC)        :" ${CO2LU}
659    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
660   
661        # Previous CO2
662    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
663    echo "Previous CO2  :" ${CO2_ppm_prec}
664   
665        # Formula
666    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
667    echo "New CO2  :" ${CO2_ppm}
668   
669        # Save CO2 values in ExeCpuLog variable contents 5 fields
670    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
671        gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
672                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
673   
674    IGCM_debug_PopStack "ATM_Carbon_Finalize"
675}
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