source: CONFIG/UNIFORM/v6/IPSLESM6/GENERAL/DRIVER/lmdz.driver @ 3758

Last change on this file since 3758 was 3758, checked in by acosce, 3 years ago

update IPSLESM6 to be consistent with CM6.1 (rev 3744)
+ add two flag in lmdz.card to drive iflag_phytrac and ok_bug_cv_trac (mandatory for AER configuration)

File size: 25.3 KB
Line 
1#!/bin/ksh
2#-----------------------------------------------------------------
3function ATM_Initialize
4{
5    IGCM_debug_PushStack "ATM_Initialize"
6
7    RESOL_ATM=$( echo $RESOL | awk "-Fx" '{print $2}' | awk "-F-" '{print $1}')
8
9    [ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) || RESOL_ATM_3D=96x95x39
10
11    RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $3}' )
12    RESOL_ATM_X=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $1}' )
13    RESOL_ATM_Y=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $2}' )
14    RESOL_ATM_XY="${RESOL_ATM_X}x${RESOL_ATM_Y}"
15
16    ##- LMDZ physics version
17    ##  Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
18    if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
19        LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
20    else
21        LMDZ_Physics=AP
22    fi
23    echo LMDZ physics version : ${LMDZ_Physics}
24
25    ##- Create_etat0_limit version
26    ##  Define variable CREATE only if it is set in lmdz.card section UserChoices.
27    ##  This variable is only used in lmdz.card to choose input files.
28    if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
29        IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
30        CREATE=${lmdz_UserChoices_CREATE}
31        echo create_etat0_limit version : ${CREATE}
32    fi
33
34
35    ## - LMDZ choice of config.def file
36    ##   ConfType must be set in lmdz.card
37    ConfType=${lmdz_UserChoices_ConfType}
38
39    ##- LMDZ output level, to be set in lmdz.card
40    if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
41        # OutLevel is not set. Take default value low.
42        OutLevel=low
43    else
44        OutLevel=${lmdz_UserChoices_OutLevel}
45    fi
46
47    ##-- Output frequency purpose ....
48    ##--  Initialisation  ....
49    ok_mensuel=.FALSE.
50    ok_journe=.FALSE.
51    ok_hf=.FALSE.
52    ok_hf3h=.FALSE.
53    ok_hf3hm=.FALSE.
54    ok_stn=.FALSE.
55
56
57    case ${config_UserChoices_PeriodLength} in
58        1Y|1y|1M|1m) ok_mensuel=.TRUE. ;;
59        5D|5d|1D|1d) ok_journe=.TRUE. ;;
60    esac
61
62    for frequency in ${config_ATM_WriteFrequency} ; do
63        case ${frequency} in
64            1M|1m) ok_mensuel=.TRUE. ;;
65        esac
66        case ${frequency} in
67            5D|5d|1D|1d) ok_journe=.TRUE. ;;
68        esac
69        case ${frequency} in
70            HF|hf) ok_hf=.TRUE. ;;
71        esac
72        case ${frequency} in
73            HF3h|hf3h) ok_hf3h=.TRUE. ;;
74        esac
75        case ${frequency} in
76            HF3hm|hf3hm) ok_hf3hm=.TRUE. ;;
77        esac
78        case ${frequency} in
79            STN|stn) ok_stn=.TRUE. ;;
80        esac
81    done
82
83
84##  Read LMDZ_COSP_OK in lmdz.card
85    if [ X${lmdz_UserChoices_LMDZ_COSP_OK} = Xy ] ; then
86        ##  LMDZ_COSP_OK=y, now read all other COSP variables
87        ##  Read LMDZ_COSP_monthly in lmdz.card
88        if [ X${lmdz_UserChoices_LMDZ_COSP_monthly} = Xy ] ; then
89            LMDZ_COSP_monthly=.TRUE.
90        else
91            LMDZ_COSP_monthly=.FALSE.
92        fi
93        ##  Read LMDZ_COSP_daily in lmdz.card
94        if [ X${lmdz_UserChoices_LMDZ_COSP_daily} = Xy ] ; then
95            LMDZ_COSP_daily=.TRUE.
96        else
97            LMDZ_COSP_daily=.FALSE.
98        fi
99        ##  Read LMDZ_COSP_hf in lmdz.card
100        if [ X${lmdz_UserChoices_LMDZ_COSP_hf} = Xy ] ; then
101            LMDZ_COSP_hf=.TRUE.
102        else
103            LMDZ_COSP_hf=.FALSE.
104        fi
105    else
106        # LMDZ_COSP_OK=n : All cosp output are deactivated
107        LMDZ_COSP_monthly=.FALSE.
108        LMDZ_COSP_daily=.FALSE.
109        LMDZ_COSP_hf=.FALSE.
110    fi 
111
112    ##  Read LMDZ_NMC_monthly in lmdz.card
113    if [ X${lmdz_UserChoices_LMDZ_NMC_monthly} = Xy ] ; then
114        LMDZ_NMC_monthly=.TRUE.
115    else
116        LMDZ_NMC_monthly=.FALSE.
117    fi
118   
119    ## Read LMDZ_NMC_daily in lmdz.card
120    if [ X${lmdz_UserChoices_LMDZ_NMC_daily} = Xy ] ; then
121        LMDZ_NMC_daily=.TRUE.
122    else
123        LMDZ_NMC_daily=.FALSE.
124    fi
125   
126    ## Read LMDZ_NMC_hf in lmdz.card
127    if [ X${lmdz_UserChoices_LMDZ_NMC_hf} = Xy ] ; then
128        LMDZ_NMC_hf=.TRUE.
129    else
130        LMDZ_NMC_hf=.FALSE.
131    fi
132   
133
134    IGCM_debug_PopStack "ATM_Initialize"
135}
136
137#-----------------------------------------------------------------
138function ATM_Update
139{
140    IGCM_debug_PushStack "ATM_Update"
141
142    ##-- GHG forcing :
143    ##   If forcing file exist in run directory, read values for the current year
144    ##   and set in config.def. If not use the default value set in config.def
145
146    # Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
147    IGCM_debug_Print 1 "Note that the solaire parameter is here below changed but it is only used by LMDZ for old physics(AP and NPv3.2)"
148    IGCM_debug_Print 1 "For newer physics with iflag_rrtm=1 and ok_suntime_rrtm=y, the solar constant is instead taken from solarforcing.nc file"
149    if [ -f SOLARANDVOLCANOES.txt ] ; then
150        value=`grep Annee_${year} SOLARANDVOLCANOES.txt | awk -F= '{print $2}'`
151        if [ X"${value}" = X ] ; then
152            # The grep returned empty variable, stop execution
153            IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
154            IGCM_debug_Verif_Exit
155        fi
156    else
157        value=DEFAULT
158    fi
159    IGCM_comp_modifyDefFile nonblocker config.def solaire $value
160
161
162    # Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
163    # Calculate co2_ppm_per as co2_ppm*4.
164    if [ -f CO2.txt ] ; then
165        value=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
166        if [ X"${value}" = X ] ; then
167            # The grep returned empty variable, stop execution
168            IGCM_debug_Exit "The file CO2.txt do not contain the current year."
169            IGCM_debug_Verif_Exit
170        fi
171        value4=`grep Annee_${year} CO2.txt | awk -F= '{print $2 * 4}'`
172    else
173        value=DEFAULT
174        value4=DEFAULT
175    fi
176    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
177    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm_per $value4
178
179
180    # Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
181    if [ -f CH4.txt ] ; then
182        value=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
183        if [ X"${value}" = X ] ; then
184            # The grep returned empty variable, stop execution
185            IGCM_debug_Exit "The file CH4.txt do not contain the current year."
186            IGCM_debug_Verif_Exit
187        fi
188    else
189        value=DEFAULT
190    fi
191    IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
192
193
194    # Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
195    if [ -f N2O.txt ] ; then
196        value=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
197        if [ X"${value}" = X ] ; then
198            # The grep returned empty variable, stop execution
199            IGCM_debug_Exit "The file N2O.txt do not contain the current year."
200            IGCM_debug_Verif_Exit
201        fi
202    else
203        value=DEFAULT
204    fi
205    IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
206
207    # Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
208    if [ -f CFC11.txt ] ; then
209        value=`grep Annee_${year} CFC11.txt | awk -F= '{print $2}'`
210        if [ X"${value}" = X ] ; then
211            # The grep returned empty variable, stop execution
212            IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
213            IGCM_debug_Verif_Exit
214        fi
215    else
216        value=DEFAULT
217    fi
218    IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
219
220
221    # Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
222    if [ -f CFC12.txt ] ; then
223        value=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
224        if [ X"${value}" = X ] ; then
225            # The grep returned empty variable, stop execution
226            IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
227            IGCM_debug_Verif_Exit
228        fi
229    else
230        value=DEFAULT
231    fi
232    IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
233
234
235    ## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
236    LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
237    IGCM_debug_Print 3 "LMDZ_t_coupl "   ${LMDZ_t_coupl}
238    IGCM_comp_modifyDefFile nonblocker config.def t_coupl   ${LMDZ_t_coupl} 
239
240    ##-- Add special treatement for CARBON CYCLE
241    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
242        ATM_Carbon_Update
243    fi
244
245
246    ##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
247    ##   COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
248    if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] &&  [ ${year} -ge 1979 ]) ; then
249        LMDZ_COSP_daily=.TRUE.
250    fi
251
252    ## Modifiy
253    IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
254   
255    IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
256   
257    if [ X${OutLevel} = Xlow ] || [ X${OutLevel} = Xmedium ] ; then
258        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
259    else
260        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
261    fi
262   
263    IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
264   
265    if [ X${OutLevel} = Xlow ] ; then
266        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
267    elif [ X${OutLevel} = Xmedium ] ; then
268        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
269    elif [ X${OutLevel} = Xhigh ] ; then
270        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
271    fi
272       
273    IGCM_comp_modifyXmlFile nonblocker file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
274    IGCM_comp_modifyXmlFile nonblocker file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}
275
276    IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}
277
278    IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
279    IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
280    IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
281   
282    IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
283    IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
284    IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}
285
286    # Activate the histstrataer output file only for configuration with interactive stratospheric aersols
287    # done by setting the key word LMDZ_strataero=y in lmdz.card
288    if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
289        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .TRUE.
290    else
291        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .FALSE.
292    fi
293
294
295    ## run.def parameters
296
297
298    ##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
299    if [ ${CumulPeriod} -eq 1 ] ; then
300        IGCM_comp_modifyDefFile blocker run.def raz_date  1
301    else
302        IGCM_comp_modifyDefFile blocker run.def raz_date  0
303    fi
304
305    ##-- Calendar type for LMDZ and create_etat0_limit
306    case ${config_UserChoices_CalendarType} in
307        leap|gregorian)
308            IGCM_comp_modifyDefFile blocker run.def calend  gregorian ;;
309        noleap)
310            IGCM_comp_modifyDefFile blocker run.def calend  earth_365d ;;
311        360d)
312            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
313        *)
314            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
315    esac
316
317    IGCM_comp_modifyDefFile blocker run.def dayref    ${InitDay}
318    IGCM_comp_modifyDefFile blocker run.def nday      ${PeriodLengthInDays}
319
320    # Set anneeref different for gcm and ce0l
321    # Test if executable create_etat0_limit is present and lmdz.x is not present
322    if [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
323        # for case ce0l : always take current year
324        IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
325
326        # Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
327        # In more recent versions of LMDZ, this will not be needed.
328        IGCM_comp_modifyDefFile force   run.def use_filtre_fft n
329    else
330        # for case gcm : take first year of simulation
331        IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
332    fi
333
334    ## Determine from the variable ListOfComponents in config.card coupling to external models
335    ## and set corresponding parameters in run.def
336    echo ListOfComponents now running : ${config_ListOfComponents[*]}
337
338    if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
339        echo "Activate ORCHIDEE, set VEGET=y in run.def"
340        IGCM_comp_modifyDefFile blocker run.def VEGET y
341    else
342        echo "No ORCHIDEE, set VEGET=n in run.def"
343        IGCM_comp_modifyDefFile blocker run.def VEGET n
344    fi
345
346    if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
347        echo "Activate coupling to ocean, set type_ocean=couple in run.def"
348        IGCM_comp_modifyDefFile blocker run.def type_ocean couple
349    else
350        echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
351        IGCM_comp_modifyDefFile blocker run.def type_ocean force
352    fi
353
354    if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
355        echo "Activate coupling to INCA, set type_trac=inca in run.def"
356        IGCM_comp_modifyDefFile blocker run.def type_trac inca
357    elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
358        echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
359        IGCM_comp_modifyDefFile blocker run.def type_trac repr
360        IGCM_comp_modifyDefFile blocker run.def config_inca none
361    else
362        echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
363        IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
364        IGCM_comp_modifyDefFile blocker run.def config_inca none
365    fi
366
367
368    # run.def : Activate the call to phytrac
369    if [ ! X${lmdz_UserChoices_iflag_phytrac} = X ]; then
370        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac ${lmdz_UserChoices_iflag_phytrac}
371    else
372        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac 0
373    fi 
374
375    # physiq.def : Activate the call to phytrac
376    if [ ! X${lmdz_UserChoices_ok_bug_cv_trac} = X ]; then
377        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  ${lmdz_UserChoices_ok_bug_cv_trac}
378    else
379        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  n
380    fi 
381
382    # config.def : Activate direct radiative effect if ok_ade=y
383    if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
384        IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
385    else
386        IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
387    fi 
388
389    # config.def : Activate indirect radiative effect if ok_aie=y
390    if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
391        IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
392    else
393        IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
394    fi 
395
396    # config.def : Activate online aerosol coupled model if aerosol_couple=y
397    if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
398        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
399    else
400        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
401    fi 
402
403    # config.def : Activate reading of ozone in climatology if read_climoz=2
404    if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
405        IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
406    else
407        IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0     
408    fi 
409
410    # config.def : Choose aerosol use in radiative effect
411    #  type of coupled aerosol =1 (default) =2 => bc  only =3 => pom only =4 => seasalt only
412    # =5 => dust only =6 => all aerosol   
413    if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
414        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
415    else
416        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
417    fi 
418
419    # config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
420    if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
421        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
422    else
423        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
424    fi 
425
426    # config.def : Activate COSP
427    if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
428        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
429    else
430        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
431    fi 
432
433    # config.def : Modify parameter pmagic if it is set in lmdz.card
434    if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
435        IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
436    else
437        # Take default value set in config.def
438        IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
439    fi 
440
441    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
442    if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
443        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
444    else
445        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
446    fi
447
448    ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
449    ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
450    if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
451        awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
452        IGCM_sys_Mv gcm.def.tmp gcm.def
453        echo
454        IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
455        echo
456        cat gcm.def
457        ByPass_hgardfou_teta=n
458        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
459    fi
460
461    ## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
462    ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
463    if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
464        sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
465        IGCM_sys_Mv gcm.def.tmp gcm.def
466        echo
467        IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
468        echo
469        cat gcm.def
470        ByPass_hgardfou_mats=n
471        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
472    fi
473
474    # Add include of LMDZ context in iodef.xml
475    # In iodef.xml add on next line after "COMPONENT CONTEXT"
476    #  <context id="LMDZ" src="./context_lmdz.xml"/>
477    echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
478    if [ X"$( echo ${config_UserChoices_ExpType} | grep CMIP6 )" != "X" ] ; then
479        echo '<context id="LMDZ" src="./ping_lmdz.xml"/>' >> add.tmp
480        echo '<context id="LMDZ" src="./dr2xml_lmdz.xml"/>' >> add.tmp
481    fi
482    cp iodef.xml iodef.xml.tmp
483    sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
484    rm iodef.xml.tmp add.tmp
485
486    #Long Name as global attribute (if LongName is not empty)
487    if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
488        listfile=$(ls file_def*lmdz.xml)
489        echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
490        for file in ${listfile}
491        do
492            cp ${file} ${file}.tmp
493            sed -e "/<file id/r add.tmp" \
494                ${file}.tmp > ${file}
495            rm ${file}.tmp
496        done
497        rm add.tmp
498    fi
499           
500    IGCM_debug_PopStack "ATM_Update"
501}
502
503#-----------------------------------
504function ATM_Finalize
505{
506    IGCM_debug_PushStack "ATM_Finalize"
507
508    # Add special treatement for CARBON CYCLE
509    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
510        ATM_Carbon_Finalize
511    fi
512
513    echo FINALIZE ATM !
514
515    IGCM_debug_PopStack "ATM_Finalize"
516}
517
518
519
520function ATM_Carbon_Update
521{
522    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
523
524    IGCM_debug_PushStack "ATM_Carbon_Update"
525
526    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
527    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
528    typeset PathCO2log
529    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
530   
531    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
532        ##--Initialization of fluxes to an undefined value at the first run
533        UndefinedValueCo2=-9999
534        InitPeriodCo2=0
535        InitDateBeginCo2=${UndefinedValueCo2}
536        InitYearCo2=$(( ${year} - 1 )) 
537        InitDateEndCo2=${InitYearCo2}1231
538        fCO2_ff=${UndefinedValueCo2} 
539        CO2SBG=${UndefinedValueCo2}
540        CO2LU=${UndefinedValueCo2}
541        CO2MBG=${UndefinedValueCo2}
542        CO2_ppm_prec=${UndefinedValueCo2}
543        # Get the initial value of atmosp. pco2
544        CO2_ppm=${lmdz_UserChoices_co2_init}
545       
546        IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
547        IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
548       
549        # Save CO2 values in ExeCpuLog variable contents 5 fields
550        echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
551            gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
552                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
553       
554        # Get the path where the log file co2.log is
555        PathCO2log=${SUBMIT_DIR} 
556        # Get Previous line in co2.log
557        PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
558       
559    else
560       
561        # NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
562        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
563        #SubmitRestartPath=
564        if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
565            IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
566            PathCO2log=${config_ATM_SubmitRestartPath}
567            Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
568            PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
569           
570            IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
571            IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
572           
573            # Save Last Line of control in new co2.log file
574            InitPeriodCo2=0   
575            InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
576            InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
577            fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
578            CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
579            CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
580            CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
581            CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
582            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
583           
584            echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
585                gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
586                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
587        else
588           # Get restart line in co2.log
589            PathCO2log=${SUBMIT_DIR}
590            PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
591           # Get the value of atmosp. pco2 in co2.log
592            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
593        fi
594       
595    fi
596   
597    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
598        # Modify co2_ppm in config.def only for historical run
599        # If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
600        IGCM_comp_modifyDefFile force config.def co2_ppm     ${CO2_ppm}
601    fi
602    IGCM_debug_PopStack "ATM_Carbon_Update"
603}
604
605
606function ATM_Carbon_Finalize
607{
608    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
609
610    IGCM_debug_PushStack "ATM_Carbon_Finalize"
611
612    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
613   
614        # Fossil fuel emission
615    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
616            # For Control, no fossil fuel emission :
617        fCO2_ff=0
618        echo "Fossil Fuel for control run  :" ${fCO2_ff}
619    else
620            # For historical, get the fossile fuel file :
621        fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
622        echo "Fossil Fuel for historical run  :" ${fCO2_ff}
623    fi
624   
625        # Get the value of ocean carbon flux
626    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
627    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
628    echo "Ocean carbon flux  :" ${CO2MBG}
629   
630        # Get the value of land fluxes
631    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
632    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
633    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
634    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
635    echo "Land carbon flux (NEP)         :" ${CO2SRF}
636    echo "LU flux          (FLUC)        :" ${CO2LU}
637    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
638   
639        # Previous CO2
640    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
641    echo "Previous CO2  :" ${CO2_ppm_prec}
642   
643        # Formula
644    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
645    echo "New CO2  :" ${CO2_ppm}
646   
647        # Save CO2 values in ExeCpuLog variable contents 5 fields
648    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
649        gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
650                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
651   
652    IGCM_debug_PopStack "ATM_Carbon_Finalize"
653}
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