source: CONFIG/UNIFORM/v6/IPSLCM6/GENERAL/DRIVER/lmdz.driver @ 4672

Last change on this file since 4672 was 4672, checked in by tlurton, 2 years ago

Added new STRATAER historical experiment.

File size: 29.4 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 $value
199
200    # Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
201    # Calculate co2_ppm_per as co2_ppm*4.
202    if [ -f CO2.txt ] ; then
203        value=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
204        if [ X"${value}" = X ] ; then
205            # The grep returned empty variable, stop execution
206            IGCM_debug_Exit "The file CO2.txt do not contain the current year."
207            IGCM_debug_Verif_Exit
208        fi
209        value4=`grep Annee_${year} CO2.txt | awk -F= '{print $2 * 4}'`
210    else
211        value=DEFAULT
212        value4=DEFAULT
213    fi
214    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
215    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm_per $value4
216
217
218    # Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
219    if [ -f CH4.txt ] ; then
220        value=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
221        if [ X"${value}" = X ] ; then
222            # The grep returned empty variable, stop execution
223            IGCM_debug_Exit "The file CH4.txt do not contain the current year."
224            IGCM_debug_Verif_Exit
225        fi
226    else
227        value=DEFAULT
228    fi
229    IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
230
231
232    # Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
233    if [ -f N2O.txt ] ; then
234        value=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
235        if [ X"${value}" = X ] ; then
236            # The grep returned empty variable, stop execution
237            IGCM_debug_Exit "The file N2O.txt do not contain the current year."
238            IGCM_debug_Verif_Exit
239        fi
240    else
241        value=DEFAULT
242    fi
243    IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
244
245    # Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
246    if [ -f CFC11.txt ] ; then
247        value=`grep Annee_${year} CFC11.txt | awk -F= '{print $2}'`
248        if [ X"${value}" = X ] ; then
249            # The grep returned empty variable, stop execution
250            IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
251            IGCM_debug_Verif_Exit
252        fi
253    else
254        value=DEFAULT
255    fi
256    IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
257
258
259    # Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
260    if [ -f CFC12.txt ] ; then
261        value=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
262        if [ X"${value}" = X ] ; then
263            # The grep returned empty variable, stop execution
264            IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
265            IGCM_debug_Verif_Exit
266        fi
267    else
268        value=DEFAULT
269    fi
270    IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
271
272
273    ## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
274    LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
275    IGCM_debug_Print 3 "LMDZ_t_coupl "   ${LMDZ_t_coupl}
276    IGCM_comp_modifyDefFile nonblocker config.def t_coupl   ${LMDZ_t_coupl} 
277
278    ##-- Add special treatement for CARBON CYCLE
279    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
280        ATM_Carbon_Update
281    fi
282
283
284    ##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
285    ##   COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
286    if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] &&  [ ${year} -ge 1979 ]) ; then
287        LMDZ_COSP_daily=.TRUE.
288    fi
289
290    ## Modifiy
291    IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
292   
293    IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
294   
295    if [ X${OutLevel} = Xlow ] || [ X${OutLevel} = Xmedium ] ; then
296        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
297    else
298        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
299    fi
300   
301    IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
302   
303    if [ X${OutLevel} = Xlow ] ; then
304        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
305    elif [ X${OutLevel} = Xmedium ] ; then
306        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
307    elif [ X${OutLevel} = Xhigh ] ; then
308        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
309    fi
310       
311    IGCM_comp_modifyXmlFile nonblocker file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
312    IGCM_comp_modifyXmlFile nonblocker file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}
313
314    IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}
315
316    IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
317    IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
318    IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
319   
320    IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
321    IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
322    IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}
323
324    # Activate the histstrataer output files only for configuration with interactive stratospheric aerosols
325    # done by setting the key word LMDZ_strataero=y in lmdz.card
326    if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
327        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .TRUE.
328    IGCM_comp_modifyXmlFile nonblocker file_def_histdaystrataer_lmdz.xml histdaystrataer enabled .TRUE.
329    else
330        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .FALSE.
331    IGCM_comp_modifyXmlFile nonblocker file_def_histdaystrataer_lmdz.xml histdaystrataer enabled .FALSE.
332    fi
333
334
335    ## run.def parameters
336
337
338    ##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
339    if [ ${CumulPeriod} -eq 1 ] ; then
340        IGCM_comp_modifyDefFile blocker run.def raz_date  1
341    else
342        IGCM_comp_modifyDefFile blocker run.def raz_date  0
343    fi
344
345    ##-- Calendar type for LMDZ and create_etat0_limit
346    case ${config_UserChoices_CalendarType} in
347        leap|gregorian)
348            IGCM_comp_modifyDefFile blocker run.def calend  gregorian ;;
349        noleap)
350            IGCM_comp_modifyDefFile blocker run.def calend  earth_365d ;;
351        360d)
352            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
353        *)
354            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
355    esac
356
357    IGCM_comp_modifyDefFile blocker run.def dayref    ${InitDay}
358    IGCM_comp_modifyDefFile blocker run.def nday      ${PeriodLengthInDays}
359
360    # Set anneeref different for gcm and ce0l
361    # Test if executable create_etat0_limit is present and lmdz.x is not present
362    if [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
363        # for case ce0l : always take current year
364        IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
365
366        # Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
367        # In more recent versions of LMDZ, this will not be needed.
368        IGCM_comp_modifyDefFile force   run.def use_filtre_fft n
369    else
370        # for case gcm : take first year of simulation
371        IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
372    fi
373
374    ## Determine from the variable ListOfComponents in config.card coupling to external models
375    ## and set corresponding parameters in run.def
376    echo ListOfComponents now running : ${config_ListOfComponents[*]}
377
378    if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
379        echo "Activate ORCHIDEE, set VEGET=y in run.def"
380        IGCM_comp_modifyDefFile blocker run.def VEGET y
381    else
382        echo "No ORCHIDEE, set VEGET=n in run.def"
383        IGCM_comp_modifyDefFile blocker run.def VEGET n
384    fi
385
386    if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
387        echo "Activate coupling to ocean, set type_ocean=couple in run.def"
388        IGCM_comp_modifyDefFile blocker run.def type_ocean couple
389    else
390        echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
391        IGCM_comp_modifyDefFile nonblocker run.def type_ocean force
392    fi
393
394    if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
395    echo "Activate coupling to INCA, set type_trac=inca in run.def"
396    IGCM_comp_modifyDefFile blocker run.def type_trac inca
397    elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
398    echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
399    IGCM_comp_modifyDefFile blocker run.def type_trac repr
400        IGCM_comp_modifyDefFile blocker run.def config_inca none
401    elif [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
402        echo "No coupling to chemistry model but it is a LMDZ STRATAER configuration, set type_trac=coag in run.def"
403        IGCM_comp_modifyDefFile blocker run.def type_trac coag
404        IGCM_comp_modifyDefFile blocker run.def config_inca none
405    else
406    echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
407    IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
408        IGCM_comp_modifyDefFile blocker run.def config_inca none
409    fi
410
411    # run.def : Activate the call to phytrac
412    if [ ! X${lmdz_UserChoices_iflag_phytrac} = X ]; then
413        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac ${lmdz_UserChoices_iflag_phytrac}
414    elif [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
415    IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac 1
416    else
417        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac 0
418    fi 
419
420    # physiq.def : Activate the call to phytrac
421    if [ ! X${lmdz_UserChoices_ok_bug_cv_trac} = X ]; then
422        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  ${lmdz_UserChoices_ok_bug_cv_trac}
423    else
424        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  n
425    fi 
426
427    # config.def : Activate direct radiative effect if ok_ade=y
428    if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
429        IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
430    else
431        IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
432    fi 
433
434    # config.def : Activate indirect radiative effect if ok_aie=y
435    if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
436        IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
437    else
438        IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
439    fi 
440
441    # config.def : Activate online aerosol coupled model if aerosol_couple=y
442    if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
443        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
444    else
445        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
446    fi 
447
448    # config.def : Activate online Ozone chemistry coupled model if chemistry_couple=y
449    if [ ! X${lmdz_UserChoices_chemistry_couple} = X ]; then
450        IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple ${lmdz_UserChoices_chemistry_couple}
451    else
452        IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple n
453    fi 
454
455    # config.def : Activate reading of ozone in climatology if read_climoz=2
456    if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
457        IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
458    else
459        IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0     
460    fi 
461
462    # config.def : Choose aerosol use in radiative effect
463    #  type of coupled aerosol =1 (default) =2 => bc  only =3 => pom only =4 => seasalt only
464    # =5 => dust only =6 => all aerosol   
465    if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
466        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
467    else
468        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
469    fi 
470
471    # config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
472    if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
473        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
474    else
475        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
476    fi 
477
478    # config.def : Activate COSP
479    if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
480        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
481    else
482        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
483    fi 
484
485    # config.def : Modify parameter pmagic if it is set in lmdz.card
486    if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
487        IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
488    else
489        # Take default value set in config.def
490        IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
491    fi 
492
493    # config.def : Modify parameter ok_volcan if it is set in lmdz.card
494    if [ ! X${lmdz_UserChoices_ok_volcan} = X ]; then
495    IGCM_comp_modifyDefFile nonblocker config.def ok_volcan ${lmdz_UserChoices_ok_volcan}
496    else
497    # Take default value set in config.def
498    IGCM_comp_modifyDefFile nonblocker config.def ok_volcan DEFAULT
499    fi
500
501    # config.def : set ok_volcan to y if we are in the strataero config
502    if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
503    IGCM_comp_modifyDefFile nonblocker config.def ok_volcan y
504    else
505    IGCM_comp_modifyDefFile nonblocker config.def ok_volcan DEFAULT
506    fi
507
508    # Note: ok_volcan is a flag allowing a double-call with/without natural forcing (instead of with/without anthro forcing).
509
510    # physiq.def : Modify parameter tau_gl if it is set in lmdz.card
511    if [ ! X${lmdz_UserChoices_tau_gl} = X ]; then
512        IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl ${lmdz_UserChoices_tau_gl}
513    else
514        # Take default value set in physiq.def
515        IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl DEFAULT
516    fi
517   
518
519    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
520    if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
521        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
522    else
523        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
524    fi
525
526
527    ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
528    ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
529    if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
530        awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
531        IGCM_sys_Mv gcm.def.tmp gcm.def
532        echo
533        IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
534        echo
535        cat gcm.def
536        ByPass_hgardfou_teta=n
537        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
538    fi
539
540    ## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
541    ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
542    if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
543        sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
544        IGCM_sys_Mv gcm.def.tmp gcm.def
545        echo
546        IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
547        echo
548        cat gcm.def
549        ByPass_hgardfou_mats=n
550        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
551    fi
552
553    # Add include of LMDZ context in iodef.xml
554    # In iodef.xml add on the next line after "COMPONENT CONTEXT"
555    echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
556    # Add inclusion of file context_input_lmdz.xml if this file exists
557    if [ -f context_input_lmdz.xml ] ; then
558        echo '<context id="LMDZ" src="./context_input_lmdz.xml"/>' >> add.tmp
559    fi
560    # Include xml files for output configuration if running with workflow CMIP6
561    if [ X"$( echo ${config_UserChoices_ExpType} | grep CMIP6 )" != "X" ] ; then
562        echo '<context id="LMDZ" src="./ping_lmdz.xml"/>' >> add.tmp
563        echo '<context id="LMDZ" src="./dr2xml_lmdz.xml"/>' >> add.tmp
564    fi
565    cp iodef.xml iodef.xml.tmp
566    sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
567    rm iodef.xml.tmp add.tmp
568
569    #Long Name as global attribute (if LongName is not empty)
570    if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
571        listfile=$(ls file_def*lmdz.xml)
572        echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
573        for file in ${listfile}
574        do
575            cp ${file} ${file}.tmp
576            sed -e "/<file id/r add.tmp" \
577                ${file}.tmp > ${file}
578            rm ${file}.tmp
579        done
580        rm add.tmp
581    fi
582
583    #Compression level (if CompressionLevel is not empty)
584    if [ ! "X${config_UserChoices_CompressionLevel}" = "X" ] ; then
585    echo "NetCDF output files compression level is " ${config_UserChoices_CompressionLevel}
586    listfile=$(ls file_def*lmdz.xml)
587    for file in ${listfile}
588    do
589        sed -i -e "s/\(compression_level=\"\)[^\"]*\(\"\)/\1${config_UserChoices_CompressionLevel}\2/" ${file}
590    done
591    fi
592
593           
594    IGCM_debug_PopStack "ATM_Update"
595}
596
597#-----------------------------------
598function ATM_Finalize
599{
600    IGCM_debug_PushStack "ATM_Finalize"
601
602    # Add special treatement for CARBON CYCLE
603    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
604        ATM_Carbon_Finalize
605    fi
606
607    echo FINALIZE ATM !
608
609    IGCM_debug_PopStack "ATM_Finalize"
610}
611
612
613
614function ATM_Carbon_Update
615{
616    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
617
618    IGCM_debug_PushStack "ATM_Carbon_Update"
619
620    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
621    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
622    typeset PathCO2log
623    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
624   
625    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
626        ##--Initialization of fluxes to an undefined value at the first run
627        UndefinedValueCo2=-9999
628        InitPeriodCo2=0
629        InitDateBeginCo2=${UndefinedValueCo2}
630        InitYearCo2=$(( ${year} - 1 )) 
631        InitDateEndCo2=${InitYearCo2}1231
632        fCO2_ff=${UndefinedValueCo2} 
633        CO2SBG=${UndefinedValueCo2}
634        CO2LU=${UndefinedValueCo2}
635        CO2MBG=${UndefinedValueCo2}
636        CO2_ppm_prec=${UndefinedValueCo2}
637        # Get the initial value of atmosp. pco2
638        CO2_ppm=${lmdz_UserChoices_co2_init}
639       
640        IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
641        IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
642       
643        # Save CO2 values in ExeCpuLog variable contents 5 fields
644        echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
645            gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
646                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
647       
648        # Get the path where the log file co2.log is
649        PathCO2log=${SUBMIT_DIR} 
650        # Get Previous line in co2.log
651        PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
652       
653    else
654       
655        # NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
656        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
657        #SubmitRestartPath=
658        if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
659            IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
660            PathCO2log=${config_ATM_SubmitRestartPath}
661            Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
662            PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
663           
664            IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
665            IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
666           
667            # Save Last Line of control in new co2.log file
668            InitPeriodCo2=0   
669            InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
670            InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
671            fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
672            CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
673            CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
674            CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
675            CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
676            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
677           
678            echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
679                gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
680                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
681        else
682           # Get restart line in co2.log
683            PathCO2log=${SUBMIT_DIR}
684            PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
685           # Get the value of atmosp. pco2 in co2.log
686            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
687        fi
688       
689    fi
690   
691    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
692        # Modify co2_ppm in config.def only for historical run
693        # If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
694        IGCM_comp_modifyDefFile force config.def co2_ppm     ${CO2_ppm}
695    fi
696    IGCM_debug_PopStack "ATM_Carbon_Update"
697}
698
699
700function ATM_Carbon_Finalize
701{
702    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
703
704    IGCM_debug_PushStack "ATM_Carbon_Finalize"
705
706    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
707   
708        # Fossil fuel emission
709    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
710            # For Control, no fossil fuel emission :
711        fCO2_ff=0
712        echo "Fossil Fuel for control run  :" ${fCO2_ff}
713    else
714            # For historical, get the fossile fuel file :
715        fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
716        echo "Fossil Fuel for historical run  :" ${fCO2_ff}
717    fi
718   
719        # Get the value of ocean carbon flux
720    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
721    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
722    echo "Ocean carbon flux  :" ${CO2MBG}
723   
724        # Get the value of land fluxes
725    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
726    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
727    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
728    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
729    echo "Land carbon flux (NEP)         :" ${CO2SRF}
730    echo "LU flux          (FLUC)        :" ${CO2LU}
731    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
732   
733        # Previous CO2
734    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
735    echo "Previous CO2  :" ${CO2_ppm_prec}
736   
737        # Formula
738    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
739    echo "New CO2  :" ${CO2_ppm}
740   
741        # Save CO2 values in ExeCpuLog variable contents 5 fields
742    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
743        gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
744                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
745   
746    IGCM_debug_PopStack "ATM_Carbon_Finalize"
747}
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