source: CONFIG/UNIFORM/v5/LMDZOR_v5/GENERAL/DRIVER/lmdz.driver @ 2322

Last change on this file since 2322 was 2322, checked in by jgipsl, 8 years ago

Add error check if the year is not in forcing file for solar activity and GHG parameters.

File size: 28.4 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}_${NUM_PROC_ATM}prc.dat
257    fi
258
259    ##-- GHG forcing :
260    ##   If forcing file exist in run directory, read values for the current year
261    ##   and set in config.def. If not use the default value set in config.def
262    if [ -f SOLARANDVOLCANOES.txt ] ; then
263        IPCC_SOLAR=`grep Annee_${year} SOLARANDVOLCANOES.txt | awk -F= '{print $2}'`
264        if [ X"${IPCC_SOLAR}" = X ] ; then
265            # The grep returned empty variable, stop execution
266            IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
267            IGCM_debug_Verif_Exit
268        else
269            # Set new variable in config.def file
270            LMDZ_sed config.def solaire     ${IPCC_SOLAR}
271        fi
272    else
273        LMDZ_sed_default config.def solaire
274    fi
275
276    if [ -f CO2.txt ] ; then
277        IPCC_CO2=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
278        if [ X"${IPCC_CO2}" = X ] ; then
279            # The grep returned empty variable, stop execution
280            IGCM_debug_Exit "The file CO2.txt do not contain the current year."
281            IGCM_debug_Verif_Exit
282        else
283            # Set new variable in config.def file
284            LMDZ_sed config.def co2_ppm     ${IPCC_CO2}
285        fi
286    else
287        LMDZ_sed_default config.def co2_ppm
288    fi
289
290    if [ -f CH4.txt ] ; then
291        IPCC_CH4=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
292        if [ X"${IPCC_CH4}" = X ] ; then
293            # The grep returned empty variable, stop execution
294            IGCM_debug_Exit "The file CH4.txt do not contain the current year."
295            IGCM_debug_Verif_Exit
296        else
297            # Set new variable in config.def file
298            LMDZ_sed config.def CH4_ppb     ${IPCC_CH4}
299        fi
300     else
301        LMDZ_sed_default config.def CH4_ppb
302    fi
303
304    if [ -f N2O.txt ] ; then
305        IPCC_N2O=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
306        if [ X"${IPCC_N2O}" = X ] ; then
307            # The grep returned empty variable, stop execution
308            IGCM_debug_Exit "The file N2O.txt do not contain the current year."
309            IGCM_debug_Verif_Exit
310        else
311            # Set new variable in config.def file
312            LMDZ_sed config.def N2O_ppb     ${IPCC_N2O}
313        fi
314    else
315        LMDZ_sed_default config.def N2O_ppb
316    fi
317
318    if [ -f CFC11.txt ] ; then
319        IPCC_CFC11=`grep Annee_${year} CFC11.txt | awk -F= '{print $2}'`
320        if [ X"${IPCC_CFC11}" = X ] ; then
321            # The grep returned empty variable, stop execution
322            IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
323            IGCM_debug_Verif_Exit
324        else
325            # Set new variable in config.def file
326            LMDZ_sed config.def CFC11_ppt   ${IPCC_CFC11}
327        fi
328    else
329        LMDZ_sed_default config.def CFC11_ppt
330    fi
331
332    if [ -f CFC12.txt ] ; then
333        IPCC_CFC12=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
334        if [ X"${IPCC_CFC12}" = X ] ; then
335            # The grep returned empty variable, stop execution
336            IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
337            IGCM_debug_Verif_Exit
338        else
339            # Set new variable in config.def file
340            LMDZ_sed config.def CFC12_ppt   ${IPCC_CFC12}
341        fi
342    else
343        LMDZ_sed_default config.def CFC12_ppt
344    fi
345
346
347    ##-- Add special treatement for CARBON CYCLE
348    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
349        ATM_Carbon_Update
350    fi
351
352
353    ##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
354    ##   COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
355    if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] &&  [ ${year} -ge 1979 ]) ; then
356        LMDZ_COSP_daily=y
357    fi
358
359
360    ## output.def parameters
361    #  columns in phys_output_filekeys refer to the filenames given in phys_out_filenames in output.def : 
362    #                                            histmth       histday        histhf    histfh3h   histhf3hm   histstn
363    LMDZ_sed output.def phys_out_filekeys       "${ok_mensuel} ${ok_journe}   ${ok_hf}  ${ok_hf3h} ${ok_hf3hm} ${ok_stn}"
364    LMDZ_sed output.def ecrit_ISCCP ${LMDZ_ecrit_ISCCP}
365    LMDZ_sed output.def ok_cosp     ${LMDZ_COSP_OK}
366    LMDZ_sed output.def ok_mensuelCOSP  ${LMDZ_COSP_monthly}
367    LMDZ_sed output.def ok_journeCOSP   ${LMDZ_COSP_daily}
368    LMDZ_sed output.def ok_hfCOSP   ${LMDZ_COSP_hf}
369    LMDZ_sed output.def ok_histNMC  "${LMDZ_NMC_monthly} ${LMDZ_NMC_daily} ${LMDZ_NMC_hf}"
370
371    ## gcm.def parameters :
372    # Modification for timestep in physics due to differnt type of physics
373    # To know the time step in minutes the physics part of LMDZ use: 1440/day_step*ipysiq/nsplit_phys
374    if [ X${LMDZ_Physics} = X"NPv3.1" ] && [ ${RESOL_ATM_3D} = 96x95x39 ] ; then
375        # Time step in physics: 7.5min
376        LMDZ_sed gcm.def iphysiq     5
377    elif [ X${LMDZ_Physics} = X"NPv3.1" ] && [ ${RESOL_ATM_3D} = 144x142x39 ] ; then
378        # Time step in physics: 10min
379        LMDZ_sed gcm.def iphysiq     5
380    elif [ X${LMDZ_Physics} = X"NPv3.2" ] && [ ${RESOL_ATM_3D} = 96x95x39 ] ; then
381        # Time step in physics: 15min
382        LMDZ_sed gcm.def iphysiq     5
383    elif [ X${LMDZ_Physics} = X"NPv3.2" ] && [ ${RESOL_ATM_3D} = 144x142x39 ] ; then
384        # Time step in physics: 10min
385        LMDZ_sed gcm.def iphysiq     5
386    elif [ X${LMDZ_Physics} = X"NPv3.2" ] && [ ${RESOL_ATM_3D} = 128x118x39 ] ; then
387        # Time step in physics: 7.5min
388        LMDZ_sed gcm.def iphysiq     15
389    elif [ X${LMDZ_Physics} = X"AP" ] ; then
390        # Time step in physics: 30min
391        # Use default value for old physics
392        LMDZ_sed_default gcm.def iphysiq
393    else
394        # Warning this combination has not been prepared
395        echo ""
396        echo "WARNING!! LMDZ_Physics=${LMDZ_Physics} has not been tested with resolution ${RESOL_ATM_3D}."
397        echo " => The default timestep for iphysiq will be used. "
398        echo " => You can change the default time step in gcm.def_${RESOL_ATM_3D} but be carefull to keep the syntax: iphysiq=_AUTO_ : DEFAULT = new_value"
399        echo " => Calculate new time step in minutes in the physics of LMDZ as : 1440/day_step*ipysiq/nsplit_phys"
400        LMDZ_sed_default gcm.def iphysiq
401        echo ""
402    fi
403   
404
405
406    ## run.def parameters
407    LMDZ_sed run.def dayref   ${InitDay}
408    LMDZ_sed run.def nday     ${PeriodLengthInDays}
409    LMDZ_sed run.def raz_date ${RAZ_DATE}
410    LMDZ_sed run.def periodav ${LMDZ_periodav}
411    LMDZ_sed run.def adjust   ${LMDZ_adjust}
412
413    # Set anneeref different for gcm and ce0l
414    # Variable calend is different for a run with create_etat0_limit and the gcm
415    # Test if executable create_etat0_limit is present and lmdz.x is not present
416    if [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
417        # for case ce0l : always take current year
418        LMDZ_sed run.def anneeref ${year}
419        LMDZ_sed run.def calend   ${CalendarTypeForCreate}
420    else
421        # for case gcm : take first year of simulation
422        LMDZ_sed run.def anneeref ${InitYear}
423        LMDZ_sed run.def calend   ${CalendarTypeForLmdz}
424    fi
425
426    # Activate creation of file grilles_gcm.nc only at first period
427    if [ ${CumulPeriod} -eq 1 ] ; then
428        LMDZ_sed run.def grilles_gcm_netcdf y
429    else
430        LMDZ_sed run.def grilles_gcm_netcdf n
431    fi
432
433    ## Determine from the variable ListOfComponents in config.card coupling to external models
434    ## and set corresponding parameters in run.def
435    echo ListOfComponents now running : ${config_ListOfComponents[*]}
436
437    if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
438        echo "Activate ORCHIDEE: set VEGET=y and add INCLUDEDEF=orchidee.def in run.def"
439        LMDZ_sed run.def VEGET y
440        # Add "INCLUDEDEF=orchidee.def" before the 5th line in run.def
441        sed -i '5iINCLUDEDEF=orchidee.def' run.def
442    else
443        echo "No ORCHIDEE, set VEGET=n in run.def"
444        LMDZ_sed run.def VEGET n
445    fi
446
447    if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
448        echo "Activate coupling to ocean, set type_ocean=couple in run.def"
449        LMDZ_sed run.def type_ocean couple
450    else
451        echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
452        LMDZ_sed run.def type_ocean force
453    fi
454
455    if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
456        echo "Activate coupling to INCA: set type_trac=inca and add INCLUDEDEF=inca.def in run.def"
457        LMDZ_sed run.def type_trac inca
458        # Add "INCLUDEDEF=inca.def" before the 5th line in run.def
459        sed -i '5iINCLUDEDEF=inca.def' run.def
460    elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
461        echo "Activate coupling to REPROBUS: set type_trac=repr and add INCLUDEDEF=reprobus.def in run.def"
462        LMDZ_sed run.def type_trac repr
463        LMDZ_sed run.def config_inca none
464        # Add "INCLUDEDEF=reprobus.def" before the 5th line in run.def
465        sed -i '5iINCLUDEDEF=reprobus.def' run.def
466    else
467        echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
468        LMDZ_sed run.def type_trac lmdz
469        LMDZ_sed run.def config_inca none
470    fi
471
472
473    # config.def : Activate direct radiative effect if ok_ade=y
474    if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
475        LMDZ_sed config.def ok_ade ${lmdz_UserChoices_ok_ade}
476    else
477        LMDZ_sed config.def ok_ade n
478    fi 
479
480    # config.def : Activate indirect radiative effect if ok_aie=y
481    if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
482        LMDZ_sed config.def ok_aie ${lmdz_UserChoices_ok_aie}
483    else
484        LMDZ_sed config.def ok_aie n
485    fi 
486
487    # config.def : Activate online aerosol coupled model if aerosol_couple=y
488    if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
489        LMDZ_sed config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
490    else
491        LMDZ_sed config.def aerosol_couple n
492    fi 
493
494    # config.def : Activate reading of ozone in climatology if read_climoz=2
495    if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
496        LMDZ_sed config.def read_climoz ${lmdz_UserChoices_read_climoz}
497    else
498        LMDZ_sed config.def read_climoz 0       
499    fi 
500
501    # config.def : Choose aerosol use in radiative effect
502    #  type of coupled aerosol =1 (default) =2 => bc  only =3 => pom only =4 => seasalt only
503    # =5 => dust only =6 => all aerosol   
504    if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
505        LMDZ_sed config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
506    else
507        LMDZ_sed config.def flag_aerosol 0
508    fi 
509
510    # config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
511    if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
512        LMDZ_sed config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
513    else
514        LMDZ_sed config.def ok_cdnc n   
515    fi 
516
517    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
518    if [ X${lmdz_UserChoices_ok_guide} = Xy ] ; then
519        # Set ok_guide=y in guide.def
520        LMDZ_sed guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
521        # Add "INCLUDEDEF=guide.def" before the 5th line in run.def
522        sed -i '5iINCLUDEDEF=guide.def' run.def
523    else
524        LMDZ_sed guide.def ok_guide n
525    fi
526
527    ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
528    ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
529    if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
530        awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
531        IGCM_sys_Mv gcm.def.tmp gcm.def
532        echo
533        IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
534        echo
535        cat gcm.def
536        ByPass_hgardfou_teta=n
537        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
538    fi
539
540    ## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
541    ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
542    if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
543        sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
544        IGCM_sys_Mv gcm.def.tmp gcm.def
545        echo
546        IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
547        echo
548        cat gcm.def
549        ByPass_hgardfou_mats=n
550        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
551    fi
552
553    if ( ${FirstInitialize} ) ; then
554        if [ -f start.nc ] && [ -f startphy.nc ] ; then
555            # The restart files already exist. They have been copied from a previous run or from a CREATE job
556            echo "Restart files for LMDZ have been copied from a previous run"
557        elif [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
558            # Do nothing because it is the program for creating restart files that is running and not LMDZ
559            echo "create_etat0_limit.e will create initial start files"
560        else
561            # Restart files have to be created
562            # Old option. Now removed.
563            echo "REMOVED OPTION: Run create_etat0_limit.e to create restart files start.nc and startphy.nc for LMDZ"
564            echo "You must now create start.nc and startphy.nc before launching the model or use restart files"
565            IGCM_debug_Exit "ATM_Update: start.nc and startphy.nc files are missing!"
566            IGCM_debug_Verif_Exit
567        fi
568    fi
569
570    IGCM_debug_PopStack "ATM_Update"
571}
572
573#-----------------------------------
574function ATM_Finalize
575{
576    IGCM_debug_PushStack "ATM_Finalize"
577
578    # If the file exist, copy Bands_ file to PARAM/ in submit directory. This file will be used for the simulation.
579    # Copy also the same file into ATM/Restart at ARCHIVE directory for backup.
580    if [ -f Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ] ; then
581      if [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] ; then
582        IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
583        IGCM_sys_Put_Out Bands_${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}
584      elif [ ${CumulPeriod} -eq 1 ] && [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
585        # Special case : first period and no adjust => Save bands file with suffix _0
586        IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
587        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
588      fi
589    fi
590
591    # Add special treatement for CARBON CYCLE
592    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
593        ATM_Carbon_Finalize
594    fi
595
596    echo FINALIZE ATM !
597
598    IGCM_debug_PopStack "ATM_Finalize"
599}
600
601
602
603function ATM_Carbon_Update
604{
605    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
606
607    IGCM_debug_PushStack "ATM_Carbon_Update"
608
609    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
610    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
611    typeset PathCO2log
612    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
613   
614    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
615        ##--Initialization of fluxes to an undefined value at the first run
616        UndefinedValueCo2=-9999
617        InitPeriodCo2=0
618        InitDateBeginCo2=${UndefinedValueCo2}
619        InitYearCo2=$(( ${year} - 1 )) 
620        InitDateEndCo2=${InitYearCo2}1231
621        fCO2_ff=${UndefinedValueCo2} 
622        CO2SBG=${UndefinedValueCo2}
623        CO2LU=${UndefinedValueCo2}
624        CO2MBG=${UndefinedValueCo2}
625        CO2_ppm_prec=${UndefinedValueCo2}
626        # Get the initial value of atmosp. pco2
627        CO2_ppm=${lmdz_UserChoices_co2_init}
628       
629        IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
630        IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
631       
632        # Save CO2 values in ExeCpuLog variable contents 5 fields
633        echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
634            gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
635                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
636       
637        # Get the path where the log file co2.log is
638        PathCO2log=${SUBMIT_DIR} 
639        # Get Previous line in co2.log
640        PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
641       
642    else
643       
644        # NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
645        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
646        #SubmitRestartPath=
647        if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
648            IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
649            PathCO2log=${config_ATM_SubmitRestartPath}
650            Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
651            PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
652           
653            IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
654            IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
655           
656            # Save Last Line of control in new co2.log file
657            InitPeriodCo2=0   
658            InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
659            InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
660            fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
661            CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
662            CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
663            CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
664            CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
665            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
666           
667            echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
668                gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
669                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
670        else
671           # Get restart line in co2.log
672            PathCO2log=${SUBMIT_DIR}
673            PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
674           # Get the value of atmosp. pco2 in co2.log
675            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
676        fi
677       
678    fi
679   
680    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
681            # Modify co2_ppm in config.def only for historical run
682            # If not historical run, keep co2_ppm value set earlier by LMDZ_sed
683        LMDZ_sed config.def co2_ppm     ${CO2_ppm}
684    fi
685    IGCM_debug_PopStack "ATM_Carbon_Update"
686}
687
688
689function ATM_Carbon_Finalize
690{
691    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
692
693    IGCM_debug_PushStack "ATM_Carbon_Finalize"
694
695    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
696   
697        # Fossil fuel emission
698    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
699            # For Control, no fossil fuel emission :
700        fCO2_ff=0
701        echo "Fossil Fuel for control run  :" ${fCO2_ff}
702    else
703            # For historical, get the fossile fuel file :
704        fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
705        echo "Fossil Fuel for historical run  :" ${fCO2_ff}
706    fi
707   
708        # Get the value of ocean carbon flux
709    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
710    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
711    echo "Ocean carbon flux  :" ${CO2MBG}
712   
713        # Get the value of land fluxes
714    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
715    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
716    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
717    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
718    echo "Land carbon flux (NEP)         :" ${CO2SRF}
719    echo "LU flux          (FLUC)        :" ${CO2LU}
720    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
721   
722        # Previous CO2
723    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
724    echo "Previous CO2  :" ${CO2_ppm_prec}
725   
726        # Formula
727    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
728    echo "New CO2  :" ${CO2_ppm}
729   
730        # Save CO2 values in ExeCpuLog variable contents 5 fields
731    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
732        gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
733                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
734   
735    IGCM_debug_PopStack "ATM_Carbon_Finalize"
736}
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