source: CMIP6/C4MIP/ssp534-over-bgc/DRIVER/lmdz.driver @ 6442

Last change on this file since 6442 was 5991, checked in by cpipsl, 3 years ago

biogeochemically-coupled version of the RCP3.4 overshoot scenario branching from SSP58.5
File size: 29.5 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 $value
160
161    # Read value for eccentricity from file Eccentricity.txt. If file not existing, take DEFAULT value from file.
162    if [ -f Eccentricity.txt ] ; then
163        value=`grep Annee_${year} Eccentricity.txt | awk -F= '{print $2}'`
164        if [ X"${value}" = X ] ; then
165            # The grep returned empty variable, stop execution
166            IGCM_debug_Exit "The file Eccentricity.txt do not contain the current year."
167            IGCM_debug_Verif_Exit
168        fi
169    else
170        value=DEFAULT
171    fi
172    IGCM_comp_modifyDefFile nonblocker config.def R_ecc $value
173
174    # Read value for obliquity from file Obliquity.txt. If file not existing, take DEFAULT value from file.
175    if [ -f Obliquity.txt ] ; then
176        value=`grep Annee_${year} Obliquity.txt | awk -F= '{print $2}'`
177        if [ X"${value}" = X ] ; then
178            # The grep returned empty variable, stop execution
179            IGCM_debug_Exit "The file Obliquity.txt do not contain the current year."
180            IGCM_debug_Verif_Exit
181        fi
182    else
183        value=DEFAULT
184    fi
185    IGCM_comp_modifyDefFile nonblocker config.def R_incl $value
186
187    # Read value for perihelie from file Perihelie.txt. If file not existing, take DEFAULT value from file.
188    if [ -f Perihelie.txt ] ; then
189        value=`grep Annee_${year} Perihelie.txt | awk -F= '{print $2}'`
190        if [ X"${value}" = X ] ; then
191            # The grep returned empty variable, stop execution
192            IGCM_debug_Exit "The file Perihelie.txt do not contain the current year."
193            IGCM_debug_Verif_Exit
194        fi
195    else
196        value=DEFAULT
197    fi
198    IGCM_comp_modifyDefFile nonblocker config.def R_peri $value
199
200    # Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
201    # Calculate co2_ppm_per as co2_ppm*4.
202    if [ -f CO2_hist.txt ] ; then
203        #value=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
204        value=`grep Annee_1850 CO2_hist.txt | awk -F= '{print $2}'`
205        if [ X"${value}" = X ] ; then
206            # The grep returned empty variable, stop execution
207            IGCM_debug_Exit "The file CO2_hist.txt do not contain the current year."
208            IGCM_debug_Verif_Exit
209        fi
210        #value4=`grep Annee_${year} CO2.txt | awk -F= '{print $2 * 4}'`
211        value4=`grep Annee_1850 CO2_hist.txt | awk -F= '{print $2 * 4}'`
212    else
213        value=DEFAULT
214        value4=DEFAULT
215    fi
216    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
217    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm_per $value4
218
219
220    # Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
221    if [ -f CH4.txt ] ; then
222        value=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
223        if [ X"${value}" = X ] ; then
224            # The grep returned empty variable, stop execution
225            IGCM_debug_Exit "The file CH4.txt do not contain the current year."
226            IGCM_debug_Verif_Exit
227        fi
228    else
229        value=DEFAULT
230    fi
231    IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
232
233
234    # Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
235    if [ -f N2O.txt ] ; then
236        value=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
237        if [ X"${value}" = X ] ; then
238            # The grep returned empty variable, stop execution
239            IGCM_debug_Exit "The file N2O.txt do not contain the current year."
240            IGCM_debug_Verif_Exit
241        fi
242    else
243        value=DEFAULT
244    fi
245    IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
246
247    # Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
248    if [ -f CFC11.txt ] ; then
249        value=`grep Annee_${year} CFC11.txt | awk -F= '{print $2}'`
250        if [ X"${value}" = X ] ; then
251            # The grep returned empty variable, stop execution
252            IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
253            IGCM_debug_Verif_Exit
254        fi
255    else
256        value=DEFAULT
257    fi
258    IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
259
260
261    # Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
262    if [ -f CFC12.txt ] ; then
263        value=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
264        if [ X"${value}" = X ] ; then
265            # The grep returned empty variable, stop execution
266            IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
267            IGCM_debug_Verif_Exit
268        fi
269    else
270        value=DEFAULT
271    fi
272    IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
273
274
275    ## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
276    LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
277    IGCM_debug_Print 3 "LMDZ_t_coupl "   ${LMDZ_t_coupl}
278    IGCM_comp_modifyDefFile nonblocker config.def t_coupl   ${LMDZ_t_coupl} 
279
280    ##-- Add special treatement for CARBON CYCLE
281    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
282        ATM_Carbon_Update
283    fi
284
285
286    ##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
287    ##   COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
288    if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] &&  [ ${year} -ge 1979 ]) ; then
289        LMDZ_COSP_daily=.TRUE.
290    fi
291
292    ## Modifiy
293    IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
294   
295    IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
296   
297    if [ X${OutLevel} = Xlow ] || [ X${OutLevel} = Xmedium ] ; then
298        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
299    else
300        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
301    fi
302   
303    IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
304   
305    if [ X${OutLevel} = Xlow ] ; then
306        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
307    elif [ X${OutLevel} = Xmedium ] ; then
308        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
309    elif [ X${OutLevel} = Xhigh ] ; then
310        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
311    fi
312       
313    IGCM_comp_modifyXmlFile nonblocker file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
314    IGCM_comp_modifyXmlFile nonblocker file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}
315
316    IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}
317
318    IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
319    IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
320    IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
321   
322    IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
323    IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
324    IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}
325
326    # Activate the histstrataer output files only for configuration with interactive stratospheric aerosols
327    # done by setting the key word LMDZ_strataero=y in lmdz.card
328    if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
329        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .TRUE.
330    IGCM_comp_modifyXmlFile nonblocker file_def_histdaystrataer_lmdz.xml histdaystrataer enabled .TRUE.
331    else
332        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .FALSE.
333    IGCM_comp_modifyXmlFile nonblocker file_def_histdaystrataer_lmdz.xml histdaystrataer enabled .FALSE.
334    fi
335
336
337    ## run.def parameters
338
339
340    ##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
341    if [ ${CumulPeriod} -eq 1 ] ; then
342        IGCM_comp_modifyDefFile blocker run.def raz_date  1
343    else
344        IGCM_comp_modifyDefFile blocker run.def raz_date  0
345    fi
346
347    ##-- Calendar type for LMDZ and create_etat0_limit
348    case ${config_UserChoices_CalendarType} in
349        leap|gregorian)
350            IGCM_comp_modifyDefFile blocker run.def calend  gregorian ;;
351        noleap)
352            IGCM_comp_modifyDefFile blocker run.def calend  earth_365d ;;
353        360d)
354            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
355        *)
356            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
357    esac
358
359    IGCM_comp_modifyDefFile blocker run.def dayref    ${InitDay}
360    IGCM_comp_modifyDefFile blocker run.def nday      ${PeriodLengthInDays}
361
362    # Set anneeref different for gcm and ce0l
363    # Test if executable create_etat0_limit is present and lmdz.x is not present
364    if [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
365        # for case ce0l : always take current year
366        IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
367
368        # Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
369        # In more recent versions of LMDZ, this will not be needed.
370        IGCM_comp_modifyDefFile force   run.def use_filtre_fft n
371    else
372        # for case gcm : take first year of simulation
373        IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
374    fi
375
376    ## Determine from the variable ListOfComponents in config.card coupling to external models
377    ## and set corresponding parameters in run.def
378    echo ListOfComponents now running : ${config_ListOfComponents[*]}
379
380    if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
381        echo "Activate ORCHIDEE, set VEGET=y in run.def"
382        IGCM_comp_modifyDefFile blocker run.def VEGET y
383    else
384        echo "No ORCHIDEE, set VEGET=n in run.def"
385        IGCM_comp_modifyDefFile blocker run.def VEGET n
386    fi
387
388    if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
389        echo "Activate coupling to ocean, set type_ocean=couple in run.def"
390        IGCM_comp_modifyDefFile blocker run.def type_ocean couple
391    else
392        echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
393        IGCM_comp_modifyDefFile nonblocker run.def type_ocean force
394    fi
395
396    if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
397    echo "Activate coupling to INCA, set type_trac=inca in run.def"
398    IGCM_comp_modifyDefFile blocker run.def type_trac inca
399    elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
400    echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
401    IGCM_comp_modifyDefFile blocker run.def type_trac repr
402        IGCM_comp_modifyDefFile blocker run.def config_inca none
403    elif [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
404        echo "No coupling to chemistry model but it is a LMDZ STRATAER configuration, set type_trac=coag in run.def"
405        IGCM_comp_modifyDefFile blocker run.def type_trac coag
406        IGCM_comp_modifyDefFile blocker run.def config_inca none
407    else
408    echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
409    IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
410        IGCM_comp_modifyDefFile blocker run.def config_inca none
411    fi
412
413    # run.def : Activate the call to phytrac
414    if [ ! X${lmdz_UserChoices_iflag_phytrac} = X ]; then
415        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac ${lmdz_UserChoices_iflag_phytrac}
416    elif [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
417    IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac 1
418    else
419        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac 0
420    fi 
421
422    # physiq.def : Activate the call to phytrac
423    if [ ! X${lmdz_UserChoices_ok_bug_cv_trac} = X ]; then
424        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  ${lmdz_UserChoices_ok_bug_cv_trac}
425    else
426        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  n
427    fi 
428
429    # config.def : Activate direct radiative effect if ok_ade=y
430    if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
431        IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
432    else
433        IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
434    fi 
435
436    # config.def : Activate indirect radiative effect if ok_aie=y
437    if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
438        IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
439    else
440        IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
441    fi 
442
443    # config.def : Activate online aerosol coupled model if aerosol_couple=y
444    if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
445        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
446    else
447        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
448    fi 
449
450    # config.def : Activate online Ozone chemistry coupled model if chemistry_couple=y
451    if [ ! X${lmdz_UserChoices_chemistry_couple} = X ]; then
452        IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple ${lmdz_UserChoices_chemistry_couple}
453    else
454        IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple n
455    fi 
456
457    # config.def : Activate reading of ozone in climatology if read_climoz=2
458    if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
459        IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
460    else
461        IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0     
462    fi 
463
464    # config.def : Choose aerosol use in radiative effect
465    #  type of coupled aerosol =1 (default) =2 => bc  only =3 => pom only =4 => seasalt only
466    # =5 => dust only =6 => all aerosol   
467    if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
468        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
469    else
470        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
471    fi 
472
473    # config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
474    if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
475        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
476    else
477        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
478    fi 
479
480    # config.def : Activate COSP
481    if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
482        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
483    else
484        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
485    fi 
486
487    # config.def : Modify parameter pmagic if it is set in lmdz.card
488    if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
489        IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
490    else
491        # Take default value set in config.def
492        IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
493    fi 
494
495    # config.def : Modify parameter ok_volcan if it is set in lmdz.card
496    if [ ! X${lmdz_UserChoices_ok_volcan} = X ]; then
497    IGCM_comp_modifyDefFile nonblocker config.def ok_volcan ${lmdz_UserChoices_ok_volcan}
498    else
499    # Take default value set in config.def
500    IGCM_comp_modifyDefFile nonblocker config.def ok_volcan DEFAULT
501    fi
502
503    # config.def : set ok_volcan to y if we are in the strataero config
504    if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
505    IGCM_comp_modifyDefFile nonblocker config.def ok_volcan y
506    else
507    IGCM_comp_modifyDefFile nonblocker config.def ok_volcan DEFAULT
508    fi
509
510    # Note: ok_volcan is a flag allowing a double-call with/without natural forcing (instead of with/without anthro forcing).
511
512    # physiq.def : Modify parameter tau_gl if it is set in lmdz.card
513    if [ ! X${lmdz_UserChoices_tau_gl} = X ]; then
514        IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl ${lmdz_UserChoices_tau_gl}
515    else
516        # Take default value set in physiq.def
517        IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl DEFAULT
518    fi
519   
520
521    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
522    if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
523        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
524    else
525        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
526    fi
527
528
529    ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
530    ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
531    if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
532        awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
533        IGCM_sys_Mv gcm.def.tmp gcm.def
534        echo
535        IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
536        echo
537        cat gcm.def
538        ByPass_hgardfou_teta=n
539        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
540    fi
541
542    ## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
543    ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
544    if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
545        sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
546        IGCM_sys_Mv gcm.def.tmp gcm.def
547        echo
548        IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
549        echo
550        cat gcm.def
551        ByPass_hgardfou_mats=n
552        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
553    fi
554
555    # Add include of LMDZ context in iodef.xml
556    # In iodef.xml add on the next line after "COMPONENT CONTEXT"
557    echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
558    # Add inclusion of file context_input_lmdz.xml if this file exists
559    if [ -f context_input_lmdz.xml ] ; then
560        echo '<context id="LMDZ" src="./context_input_lmdz.xml"/>' >> add.tmp
561    fi
562    # Include xml files for output configuration if running with workflow CMIP6
563    if [ X"$( echo ${config_UserChoices_ExpType} | grep CMIP6 )" != "X" ] ; then
564        echo '<context id="LMDZ" src="./ping_lmdz.xml"/>' >> add.tmp
565        echo '<context id="LMDZ" src="./dr2xml_lmdz.xml"/>' >> add.tmp
566    fi
567    cp iodef.xml iodef.xml.tmp
568    sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
569    rm iodef.xml.tmp add.tmp
570
571    #Long Name as global attribute (if LongName is not empty)
572    if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
573        listfile=$(ls file_def*lmdz.xml)
574        echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
575        for file in ${listfile}
576        do
577            cp ${file} ${file}.tmp
578            sed -e "/<file id/r add.tmp" \
579                ${file}.tmp > ${file}
580            rm ${file}.tmp
581        done
582        rm add.tmp
583    fi
584
585    #Compression level (if CompressionLevel is not empty)
586    if [ ! "X${config_UserChoices_CompressionLevel}" = "X" ] ; then
587    echo "NetCDF output files compression level is " ${config_UserChoices_CompressionLevel}
588    listfile=$(ls file_def*lmdz.xml)
589    for file in ${listfile}
590    do
591        sed -i -e "s/\(compression_level=\"\)[^\"]*\(\"\)/\1${config_UserChoices_CompressionLevel}\2/" ${file}
592    done
593    fi
594
595           
596    IGCM_debug_PopStack "ATM_Update"
597}
598
599#-----------------------------------
600function ATM_Finalize
601{
602    IGCM_debug_PushStack "ATM_Finalize"
603
604    # Add special treatement for CARBON CYCLE
605    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
606        ATM_Carbon_Finalize
607    fi
608
609    echo FINALIZE ATM !
610
611    IGCM_debug_PopStack "ATM_Finalize"
612}
613
614
615
616function ATM_Carbon_Update
617{
618    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
619
620    IGCM_debug_PushStack "ATM_Carbon_Update"
621
622    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
623    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
624    typeset PathCO2log
625    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
626   
627    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
628        ##--Initialization of fluxes to an undefined value at the first run
629        UndefinedValueCo2=-9999
630        InitPeriodCo2=0
631        InitDateBeginCo2=${UndefinedValueCo2}
632        InitYearCo2=$(( ${year} - 1 )) 
633        InitDateEndCo2=${InitYearCo2}1231
634        fCO2_ff=${UndefinedValueCo2} 
635        CO2SBG=${UndefinedValueCo2}
636        CO2LU=${UndefinedValueCo2}
637        CO2MBG=${UndefinedValueCo2}
638        CO2_ppm_prec=${UndefinedValueCo2}
639        # Get the initial value of atmosp. pco2
640        CO2_ppm=${lmdz_UserChoices_co2_init}
641       
642        IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
643        IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
644       
645        # Save CO2 values in ExeCpuLog variable contents 5 fields
646        echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
647            gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
648                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
649       
650        # Get the path where the log file co2.log is
651        PathCO2log=${SUBMIT_DIR} 
652        # Get Previous line in co2.log
653        PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
654       
655    else
656       
657        # NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
658        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
659        #SubmitRestartPath=
660        if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
661            IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
662            PathCO2log=${config_ATM_SubmitRestartPath}
663            Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
664            PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
665           
666            IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
667            IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
668           
669            # Save Last Line of control in new co2.log file
670            InitPeriodCo2=0   
671            InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
672            InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
673            fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
674            CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
675            CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
676            CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
677            CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
678            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
679           
680            echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
681                gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
682                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
683        else
684           # Get restart line in co2.log
685            PathCO2log=${SUBMIT_DIR}
686            PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
687           # Get the value of atmosp. pco2 in co2.log
688            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
689        fi
690       
691    fi
692   
693    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
694        # Modify co2_ppm in config.def only for historical run
695        # If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
696        IGCM_comp_modifyDefFile force config.def co2_ppm     ${CO2_ppm}
697    fi
698    IGCM_debug_PopStack "ATM_Carbon_Update"
699}
700
701
702function ATM_Carbon_Finalize
703{
704    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
705
706    IGCM_debug_PushStack "ATM_Carbon_Finalize"
707
708    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
709   
710        # Fossil fuel emission
711    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
712            # For Control, no fossil fuel emission :
713        fCO2_ff=0
714        echo "Fossil Fuel for control run  :" ${fCO2_ff}
715    else
716            # For historical, get the fossile fuel file :
717        fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
718        echo "Fossil Fuel for historical run  :" ${fCO2_ff}
719    fi
720   
721        # Get the value of ocean carbon flux
722    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
723    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
724    echo "Ocean carbon flux  :" ${CO2MBG}
725   
726        # Get the value of land fluxes
727    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
728    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
729    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
730    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
731    echo "Land carbon flux (NEP)         :" ${CO2SRF}
732    echo "LU flux          (FLUC)        :" ${CO2LU}
733    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
734   
735        # Previous CO2
736    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
737    echo "Previous CO2  :" ${CO2_ppm_prec}
738   
739        # Formula
740    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
741    echo "New CO2  :" ${CO2_ppm}
742   
743        # Save CO2 values in ExeCpuLog variable contents 5 fields
744    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
745        gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
746                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
747   
748    IGCM_debug_PopStack "ATM_Carbon_Finalize"
749}
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