source: CONFIG/UNIFORM/v6/LMDZOR_v6.2/GENERAL/DRIVER/lmdz.driver @ 4463

Last change on this file since 4463 was 4463, checked in by jgipsl, 5 years ago

Set ResolAtm? and OptMode? in config.card. Read resolution from ResolAtm? instead of from .resol.
File size: 28.7 KB
Line 
1#!/bin/ksh
2#-----------------------------------------------------------------
3function ATM_Initialize
4{
5    IGCM_debug_PushStack "ATM_Initialize"
6
7    # Read the resolution from the variables ResolAtm set in config.card UserChoices section or from .resol file
8    if [ X$ResolAtm != X ] ; then
9        # ResolAtm is set in config.card
10        RESOL_ATM_3D=${ResolAtm}
11    elif [ -f ${SUBMIT_DIR}/../.resol ] ; then
12        # ResolAtm was not set in config.card, try to read .resol file
13        eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) || RESOL_ATM_3D=96x95x39
14    else
15        IGCM_debug_Exit "ResolAtm is not set in config.card and the .resol file does not exist."
16        IGCM_debug_Verif_Exit
17    fi
18   
19    IGCM_debug_Print 1 "The atomsopheric resolution is ${RESOL_ATM_3D} " 
20
21    RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $3}' )
22    RESOL_ATM_X=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $1}' )
23    RESOL_ATM_Y=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $2}' )
24    RESOL_ATM_XY="${RESOL_ATM_X}x${RESOL_ATM_Y}"
25
26    ##- LMDZ physics version
27    ##  Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
28    if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
29        LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
30    else
31        LMDZ_Physics=AP
32    fi
33    echo LMDZ physics version : ${LMDZ_Physics}
34
35    ##- Create_etat0_limit version
36    ##  Define variable CREATE only if it is set in lmdz.card section UserChoices.
37    ##  This variable is only used in lmdz.card to choose input files.
38    if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
39        IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
40        CREATE=${lmdz_UserChoices_CREATE}
41        echo create_etat0_limit version : ${CREATE}
42    fi
43
44
45    ## - LMDZ choice of config.def file
46    ##   ConfType must be set in lmdz.card
47    ConfType=${lmdz_UserChoices_ConfType}
48
49    ##- LMDZ output level, to be set in lmdz.card
50    if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
51        # OutLevel is not set. Take default value low.
52        OutLevel=low
53    else
54        OutLevel=${lmdz_UserChoices_OutLevel}
55    fi
56
57    ##-- Output frequency purpose ....
58    ##--  Initialisation  ....
59    ok_mensuel=.FALSE.
60    ok_journe=.FALSE.
61    ok_hf=.FALSE.
62    ok_hf3h=.FALSE.
63    ok_hf3hm=.FALSE.
64    ok_stn=.FALSE.
65
66
67    case ${config_UserChoices_PeriodLength} in
68        1Y|1y|1M|1m) ok_mensuel=.TRUE. ;;
69        5D|5d|1D|1d) ok_journe=.TRUE. ;;
70    esac
71
72    for frequency in ${config_ATM_WriteFrequency} ; do
73        case ${frequency} in
74            1M|1m) ok_mensuel=.TRUE. ;;
75        esac
76        case ${frequency} in
77            5D|5d|1D|1d) ok_journe=.TRUE. ;;
78        esac
79        case ${frequency} in
80            HF|hf) ok_hf=.TRUE. ;;
81        esac
82        case ${frequency} in
83            HF3h|hf3h) ok_hf3h=.TRUE. ;;
84        esac
85        case ${frequency} in
86            HF3hm|hf3hm) ok_hf3hm=.TRUE. ;;
87        esac
88        case ${frequency} in
89            STN|stn) ok_stn=.TRUE. ;;
90        esac
91    done
92
93
94##  Read LMDZ_COSP_OK in lmdz.card
95    if [ X${lmdz_UserChoices_LMDZ_COSP_OK} = Xy ] ; then
96        ##  LMDZ_COSP_OK=y, now read all other COSP variables
97        ##  Read LMDZ_COSP_monthly in lmdz.card
98        if [ X${lmdz_UserChoices_LMDZ_COSP_monthly} = Xy ] ; then
99            LMDZ_COSP_monthly=.TRUE.
100        else
101            LMDZ_COSP_monthly=.FALSE.
102        fi
103        ##  Read LMDZ_COSP_daily in lmdz.card
104        if [ X${lmdz_UserChoices_LMDZ_COSP_daily} = Xy ] ; then
105            LMDZ_COSP_daily=.TRUE.
106        else
107            LMDZ_COSP_daily=.FALSE.
108        fi
109        ##  Read LMDZ_COSP_hf in lmdz.card
110        if [ X${lmdz_UserChoices_LMDZ_COSP_hf} = Xy ] ; then
111            LMDZ_COSP_hf=.TRUE.
112        else
113            LMDZ_COSP_hf=.FALSE.
114        fi
115    else
116        # LMDZ_COSP_OK=n : All cosp output are deactivated
117        LMDZ_COSP_monthly=.FALSE.
118        LMDZ_COSP_daily=.FALSE.
119        LMDZ_COSP_hf=.FALSE.
120    fi 
121
122    ##  Read LMDZ_NMC_monthly in lmdz.card
123    if [ X${lmdz_UserChoices_LMDZ_NMC_monthly} = Xy ] ; then
124        LMDZ_NMC_monthly=.TRUE.
125    else
126        LMDZ_NMC_monthly=.FALSE.
127    fi
128   
129    ## Read LMDZ_NMC_daily in lmdz.card
130    if [ X${lmdz_UserChoices_LMDZ_NMC_daily} = Xy ] ; then
131        LMDZ_NMC_daily=.TRUE.
132    else
133        LMDZ_NMC_daily=.FALSE.
134    fi
135   
136    ## Read LMDZ_NMC_hf in lmdz.card
137    if [ X${lmdz_UserChoices_LMDZ_NMC_hf} = Xy ] ; then
138        LMDZ_NMC_hf=.TRUE.
139    else
140        LMDZ_NMC_hf=.FALSE.
141    fi
142   
143
144    IGCM_debug_PopStack "ATM_Initialize"
145}
146
147#-----------------------------------------------------------------
148function ATM_Update
149{
150    IGCM_debug_PushStack "ATM_Update"
151
152    ##-- GHG forcing :
153    ##   If forcing file exist in run directory, read values for the current year
154    ##   and set in config.def. If not use the default value set in config.def
155
156    # Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
157    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)"
158    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"
159    if [ -f SOLARANDVOLCANOES.txt ] ; then
160        value=`grep Annee_${year} SOLARANDVOLCANOES.txt | awk -F= '{print $2}'`
161        if [ X"${value}" = X ] ; then
162            # The grep returned empty variable, stop execution
163            IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
164            IGCM_debug_Verif_Exit
165        fi
166    else
167        value=DEFAULT
168    fi
169    IGCM_comp_modifyDefFile nonblocker config.def solaire $value
170
171    # Read value for eccentricity from file Eccentricity.txt. If file not existing, take DEFAULT value from file.
172    if [ -f Eccentricity.txt ] ; then
173        value=`grep Annee_${year} Eccentricity.txt | awk -F= '{print $2}'`
174        if [ X"${value}" = X ] ; then
175            # The grep returned empty variable, stop execution
176            IGCM_debug_Exit "The file Eccentricity.txt do not contain the current year."
177            IGCM_debug_Verif_Exit
178        fi
179    else
180        value=DEFAULT
181    fi
182    IGCM_comp_modifyDefFile nonblocker config.def R_ecc $value
183
184    # Read value for obliquity from file Obliquity.txt. If file not existing, take DEFAULT value from file.
185    if [ -f Obliquity.txt ] ; then
186        value=`grep Annee_${year} Obliquity.txt | awk -F= '{print $2}'`
187        if [ X"${value}" = X ] ; then
188            # The grep returned empty variable, stop execution
189            IGCM_debug_Exit "The file Obliquity.txt do not contain the current year."
190            IGCM_debug_Verif_Exit
191        fi
192    else
193        value=DEFAULT
194    fi
195    IGCM_comp_modifyDefFile nonblocker config.def R_incl $value
196
197    # Read value for perihelie from file Perihelie.txt. If file not existing, take DEFAULT value from file.
198    if [ -f Perihelie.txt ] ; then
199        value=`grep Annee_${year} Perihelie.txt | awk -F= '{print $2}'`
200        if [ X"${value}" = X ] ; then
201            # The grep returned empty variable, stop execution
202            IGCM_debug_Exit "The file Perihelie.txt do not contain the current year."
203            IGCM_debug_Verif_Exit
204        fi
205    else
206        value=DEFAULT
207    fi
208    IGCM_comp_modifyDefFile nonblocker config.def R_peri $value
209
210    # Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
211    # Calculate co2_ppm_per as co2_ppm*4.
212    if [ -f CO2.txt ] ; then
213        value=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
214        if [ X"${value}" = X ] ; then
215            # The grep returned empty variable, stop execution
216            IGCM_debug_Exit "The file CO2.txt do not contain the current year."
217            IGCM_debug_Verif_Exit
218        fi
219        value4=`grep Annee_${year} CO2.txt | awk -F= '{print $2 * 4}'`
220    else
221        value=DEFAULT
222        value4=DEFAULT
223    fi
224    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
225    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm_per $value4
226
227
228    # Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
229    if [ -f CH4.txt ] ; then
230        value=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
231        if [ X"${value}" = X ] ; then
232            # The grep returned empty variable, stop execution
233            IGCM_debug_Exit "The file CH4.txt do not contain the current year."
234            IGCM_debug_Verif_Exit
235        fi
236    else
237        value=DEFAULT
238    fi
239    IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
240
241
242    # Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
243    if [ -f N2O.txt ] ; then
244        value=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
245        if [ X"${value}" = X ] ; then
246            # The grep returned empty variable, stop execution
247            IGCM_debug_Exit "The file N2O.txt do not contain the current year."
248            IGCM_debug_Verif_Exit
249        fi
250    else
251        value=DEFAULT
252    fi
253    IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
254
255    # Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
256    if [ -f CFC11.txt ] ; then
257        value=`grep Annee_${year} CFC11.txt | awk -F= '{print $2}'`
258        if [ X"${value}" = X ] ; then
259            # The grep returned empty variable, stop execution
260            IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
261            IGCM_debug_Verif_Exit
262        fi
263    else
264        value=DEFAULT
265    fi
266    IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
267
268
269    # Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
270    if [ -f CFC12.txt ] ; then
271        value=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
272        if [ X"${value}" = X ] ; then
273            # The grep returned empty variable, stop execution
274            IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
275            IGCM_debug_Verif_Exit
276        fi
277    else
278        value=DEFAULT
279    fi
280    IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
281
282
283    ## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
284    LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
285    IGCM_debug_Print 3 "LMDZ_t_coupl "   ${LMDZ_t_coupl}
286    IGCM_comp_modifyDefFile nonblocker config.def t_coupl   ${LMDZ_t_coupl} 
287
288    ##-- Add special treatement for CARBON CYCLE
289    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
290        ATM_Carbon_Update
291    fi
292
293
294    ##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
295    ##   COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
296    if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] &&  [ ${year} -ge 1979 ]) ; then
297        LMDZ_COSP_daily=.TRUE.
298    fi
299
300    ## Modifiy
301    IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
302   
303    IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
304   
305    if [ X${OutLevel} = Xlow ] || [ X${OutLevel} = Xmedium ] ; then
306        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
307    else
308        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
309    fi
310   
311    IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
312   
313    if [ X${OutLevel} = Xlow ] ; then
314        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
315    elif [ X${OutLevel} = Xmedium ] ; then
316        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
317    elif [ X${OutLevel} = Xhigh ] ; then
318        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
319    fi
320       
321    IGCM_comp_modifyXmlFile nonblocker file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
322    IGCM_comp_modifyXmlFile nonblocker file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}
323
324    IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}
325
326    IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
327    IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
328    IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
329   
330    IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
331    IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
332    IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}
333
334    # Activate the histstrataer output file only for configuration with interactive stratospheric aersols
335    # done by setting the key word LMDZ_strataero=y in lmdz.card
336    if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
337        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .TRUE.
338    else
339        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .FALSE.
340    fi
341
342
343    ## run.def parameters
344
345
346    ##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
347    if [ ${CumulPeriod} -eq 1 ] ; then
348        IGCM_comp_modifyDefFile blocker run.def raz_date  1
349    else
350        IGCM_comp_modifyDefFile blocker run.def raz_date  0
351    fi
352
353    ##-- Calendar type for LMDZ and create_etat0_limit
354    case ${config_UserChoices_CalendarType} in
355        leap|gregorian)
356            IGCM_comp_modifyDefFile blocker run.def calend  gregorian ;;
357        noleap)
358            IGCM_comp_modifyDefFile blocker run.def calend  earth_365d ;;
359        360d)
360            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
361        *)
362            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
363    esac
364
365    IGCM_comp_modifyDefFile blocker run.def dayref    ${InitDay}
366    IGCM_comp_modifyDefFile blocker run.def nday      ${PeriodLengthInDays}
367
368    # Set anneeref different for gcm and ce0l
369    # Test if executable create_etat0_limit is present and lmdz.x is not present
370    if [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
371        # for case ce0l : always take current year
372        IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
373
374        # Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
375        # In more recent versions of LMDZ, this will not be needed.
376        IGCM_comp_modifyDefFile force   run.def use_filtre_fft n
377    else
378        # for case gcm : take first year of simulation
379        IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
380    fi
381
382    ## Determine from the variable ListOfComponents in config.card coupling to external models
383    ## and set corresponding parameters in run.def
384    echo ListOfComponents now running : ${config_ListOfComponents[*]}
385
386    if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
387        echo "Activate ORCHIDEE, set VEGET=y in run.def"
388        IGCM_comp_modifyDefFile blocker run.def VEGET y
389    else
390        echo "No ORCHIDEE, set VEGET=n in run.def"
391        IGCM_comp_modifyDefFile blocker run.def VEGET n
392    fi
393
394    if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
395        echo "Activate coupling to ocean, set type_ocean=couple in run.def"
396        IGCM_comp_modifyDefFile blocker run.def type_ocean couple
397    else
398        echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
399        IGCM_comp_modifyDefFile nonblocker run.def type_ocean force
400    fi
401
402    if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
403        echo "Activate coupling to INCA, set type_trac=inca in run.def"
404        IGCM_comp_modifyDefFile blocker run.def type_trac inca
405    elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
406        echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
407        IGCM_comp_modifyDefFile blocker run.def type_trac repr
408        IGCM_comp_modifyDefFile blocker run.def config_inca none
409    else
410        echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
411        IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
412        IGCM_comp_modifyDefFile blocker run.def config_inca none
413    fi
414
415
416    # run.def : Activate the call to phytrac
417    if [ ! X${lmdz_UserChoices_iflag_phytrac} = X ]; then
418        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac ${lmdz_UserChoices_iflag_phytrac}
419    else
420        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac 0
421    fi 
422
423    # run.def : Activate the new calving
424    if [ ! X${lmdz_UserChoices_cpl_old_calving} = X ]; then
425        IGCM_comp_modifyDefFile nonblocker run.def cpl_old_calving ${lmdz_UserChoices_cpl_old_calving}
426    else
427        IGCM_comp_modifyDefFile nonblocker run.def cpl_old_calving y
428    fi 
429
430    # physiq.def : Activate the call to phytrac
431    if [ ! X${lmdz_UserChoices_ok_bug_cv_trac} = X ]; then
432        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  ${lmdz_UserChoices_ok_bug_cv_trac}
433    else
434        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  n
435    fi 
436
437    # config.def : Activate direct radiative effect if ok_ade=y
438    if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
439        IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
440    else
441        IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
442    fi 
443
444    # config.def : Activate indirect radiative effect if ok_aie=y
445    if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
446        IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
447    else
448        IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
449    fi 
450
451    # config.def : Activate online aerosol coupled model if aerosol_couple=y
452    if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
453        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
454    else
455        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
456    fi 
457
458    # config.def : Activate online Ozone chemistry coupled model if chemistry_couple=y
459    if [ ! X${lmdz_UserChoices_chemistry_couple} = X ]; then
460        IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple ${lmdz_UserChoices_chemistry_couple}
461    else
462        IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple n
463    fi 
464
465    # config.def : Activate reading of ozone in climatology if read_climoz=2
466    if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
467        IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
468    else
469        IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0     
470    fi 
471
472    # config.def : Choose aerosol use in radiative effect
473    #  type of coupled aerosol =1 (default) =2 => bc  only =3 => pom only =4 => seasalt only
474    # =5 => dust only =6 => all aerosol   
475    if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
476        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
477    else
478        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
479    fi 
480
481    # config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
482    if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
483        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
484    else
485        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
486    fi 
487
488    # config.def : Activate COSP
489    if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
490        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
491    else
492        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
493    fi 
494
495    # config.def : Modify parameter pmagic if it is set in lmdz.card
496    if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
497        IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
498    else
499        # Take default value set in config.def
500        IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
501    fi 
502
503    # physiq.def : Modify parameter tau_gl if it is set in lmdz.card
504    if [ ! X${lmdz_UserChoices_tau_gl} = X ]; then
505        IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl ${lmdz_UserChoices_tau_gl}
506    else
507        # Take default value set in physiq.def
508        IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl DEFAULT
509    fi
510   
511
512    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
513    if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
514        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
515    else
516        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
517    fi
518
519
520    ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
521    ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
522    if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
523        awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
524        IGCM_sys_Mv gcm.def.tmp gcm.def
525        echo
526        IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
527        echo
528        cat gcm.def
529        ByPass_hgardfou_teta=n
530        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
531    fi
532
533    ## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
534    ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
535    if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
536        sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
537        IGCM_sys_Mv gcm.def.tmp gcm.def
538        echo
539        IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
540        echo
541        cat gcm.def
542        ByPass_hgardfou_mats=n
543        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
544    fi
545
546    # Add include of LMDZ context in iodef.xml
547    # In iodef.xml add on the next line after "COMPONENT CONTEXT"
548    echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
549    # Add inclusion of file context_input_lmdz.xml if this file exists
550    if [ -f context_input_lmdz.xml ] ; then
551        echo '<context id="LMDZ" src="./context_input_lmdz.xml"/>' >> add.tmp
552    fi
553    # Include xml files for output configuration if running with workflow CMIP6
554    if [ X"$( echo ${config_UserChoices_ExpType} | grep CMIP6 )" != "X" ] ; then
555        echo '<context id="LMDZ" src="./ping_lmdz.xml"/>' >> add.tmp
556        echo '<context id="LMDZ" src="./dr2xml_lmdz.xml"/>' >> add.tmp
557    fi
558    cp iodef.xml iodef.xml.tmp
559    sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
560    rm iodef.xml.tmp add.tmp
561
562    #Long Name as global attribute (if LongName is not empty)
563    if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
564        listfile=$(ls file_def*lmdz.xml)
565        echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
566        for file in ${listfile}
567        do
568            cp ${file} ${file}.tmp
569            sed -e "/<file id/r add.tmp" \
570                ${file}.tmp > ${file}
571            rm ${file}.tmp
572        done
573        rm add.tmp
574    fi
575
576    #Compression level (if CompressionLevel is not empty)
577    if [ ! "X${config_UserChoices_CompressionLevel}" = "X" ] ; then
578    echo "NetCDF output files compression level is " ${config_UserChoices_CompressionLevel}
579    listfile=$(ls file_def*lmdz.xml)
580    for file in ${listfile}
581    do
582        sed -i -e "s/\(compression_level=\"\)[^\"]*\(\"\)/\1${config_UserChoices_CompressionLevel}\2/" ${file}
583    done
584    fi
585
586           
587    IGCM_debug_PopStack "ATM_Update"
588}
589
590#-----------------------------------
591function ATM_Finalize
592{
593    IGCM_debug_PushStack "ATM_Finalize"
594
595    # Add special treatement for CARBON CYCLE
596    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
597        ATM_Carbon_Finalize
598    fi
599
600    echo FINALIZE ATM !
601
602    IGCM_debug_PopStack "ATM_Finalize"
603}
604
605
606
607function ATM_Carbon_Update
608{
609    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
610
611    IGCM_debug_PushStack "ATM_Carbon_Update"
612
613    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
614    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
615    typeset PathCO2log
616    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
617   
618    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
619        ##--Initialization of fluxes to an undefined value at the first run
620        UndefinedValueCo2=-9999
621        InitPeriodCo2=0
622        InitDateBeginCo2=${UndefinedValueCo2}
623        InitYearCo2=$(( ${year} - 1 )) 
624        InitDateEndCo2=${InitYearCo2}1231
625        fCO2_ff=${UndefinedValueCo2} 
626        CO2SBG=${UndefinedValueCo2}
627        CO2LU=${UndefinedValueCo2}
628        CO2MBG=${UndefinedValueCo2}
629        CO2_ppm_prec=${UndefinedValueCo2}
630        # Get the initial value of atmosp. pco2
631        CO2_ppm=${lmdz_UserChoices_co2_init}
632       
633        IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
634        IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
635       
636        # Save CO2 values in ExeCpuLog variable contents 5 fields
637        echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
638            gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
639                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
640       
641        # Get the path where the log file co2.log is
642        PathCO2log=${SUBMIT_DIR} 
643        # Get Previous line in co2.log
644        PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
645       
646    else
647       
648        # NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
649        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
650        #SubmitRestartPath=
651        if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
652            IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
653            PathCO2log=${config_ATM_SubmitRestartPath}
654            Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
655            PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
656           
657            IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
658            IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
659           
660            # Save Last Line of control in new co2.log file
661            InitPeriodCo2=0   
662            InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
663            InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
664            fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
665            CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
666            CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
667            CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
668            CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
669            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
670           
671            echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
672                gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
673                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
674        else
675           # Get restart line in co2.log
676            PathCO2log=${SUBMIT_DIR}
677            PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
678           # Get the value of atmosp. pco2 in co2.log
679            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
680        fi
681       
682    fi
683   
684    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
685        # Modify co2_ppm in config.def only for historical run
686        # If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
687        IGCM_comp_modifyDefFile force config.def co2_ppm     ${CO2_ppm}
688    fi
689    IGCM_debug_PopStack "ATM_Carbon_Update"
690}
691
692
693function ATM_Carbon_Finalize
694{
695    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
696
697    IGCM_debug_PushStack "ATM_Carbon_Finalize"
698
699    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
700   
701        # Fossil fuel emission
702    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
703            # For Control, no fossil fuel emission :
704        fCO2_ff=0
705        echo "Fossil Fuel for control run  :" ${fCO2_ff}
706    else
707            # For historical, get the fossile fuel file :
708        fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
709        echo "Fossil Fuel for historical run  :" ${fCO2_ff}
710    fi
711   
712        # Get the value of ocean carbon flux
713    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
714    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
715    echo "Ocean carbon flux  :" ${CO2MBG}
716   
717        # Get the value of land fluxes
718    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
719    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
720    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
721    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
722    echo "Land carbon flux (NEP)         :" ${CO2SRF}
723    echo "LU flux          (FLUC)        :" ${CO2LU}
724    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
725   
726        # Previous CO2
727    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
728    echo "Previous CO2  :" ${CO2_ppm_prec}
729   
730        # Formula
731    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
732    echo "New CO2  :" ${CO2_ppm}
733   
734        # Save CO2 values in ExeCpuLog variable contents 5 fields
735    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
736        gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
737                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
738   
739    IGCM_debug_PopStack "ATM_Carbon_Finalize"
740}
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