source: CONFIG/UNIFORM/v6/IPSLCM6/GENERAL/DRIVER/lmdz.driver @ 4462

Last change on this file since 4462 was 4462, checked in by aclsce, 2 years ago
  • Added the handling of new LMDZ histdaystrataer xml file.
File size: 28.2 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 ${LMDZ_COSP_hf}
323
324    # Activate the histstrataer output file only for configuration with interactive stratospheric aersols
325    # done by setting the key word LMDZ_strataero=y in lmdz.card
326    if [ X${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${config_ListOfComponents_CHM} = Xreprobus ] ; then
398        echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
399        IGCM_comp_modifyDefFile blocker run.def type_trac repr
400        IGCM_comp_modifyDefFile blocker run.def config_inca none
401    else
402        echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
403        IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
404        IGCM_comp_modifyDefFile blocker run.def config_inca none
405    fi
406
407
408    # run.def : Activate the call to phytrac
409    if [ ! X${lmdz_UserChoices_iflag_phytrac} = X ]; then
410        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac ${lmdz_UserChoices_iflag_phytrac}
411    else
412        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac 0
413    fi 
414
415    # physiq.def : Activate the call to phytrac
416    if [ ! X${lmdz_UserChoices_ok_bug_cv_trac} = X ]; then
417        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  ${lmdz_UserChoices_ok_bug_cv_trac}
418    else
419        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  n
420    fi 
421
422    # config.def : Activate direct radiative effect if ok_ade=y
423    if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
424        IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
425    else
426        IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
427    fi 
428
429    # config.def : Activate indirect radiative effect if ok_aie=y
430    if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
431        IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
432    else
433        IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
434    fi 
435
436    # config.def : Activate online aerosol coupled model if aerosol_couple=y
437    if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
438        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
439    else
440        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
441    fi 
442
443    # config.def : Activate online Ozone chemistry coupled model if chemistry_couple=y
444    if [ ! X${lmdz_UserChoices_chemistry_couple} = X ]; then
445        IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple ${lmdz_UserChoices_chemistry_couple}
446    else
447        IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple n
448    fi 
449
450    # config.def : Activate reading of ozone in climatology if read_climoz=2
451    if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
452        IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
453    else
454        IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0     
455    fi 
456
457    # config.def : Choose aerosol use in radiative effect
458    #  type of coupled aerosol =1 (default) =2 => bc  only =3 => pom only =4 => seasalt only
459    # =5 => dust only =6 => all aerosol   
460    if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
461        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
462    else
463        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
464    fi 
465
466    # config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
467    if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
468        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
469    else
470        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
471    fi 
472
473    # config.def : Activate COSP
474    if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
475        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
476    else
477        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
478    fi 
479
480    # config.def : Modify parameter pmagic if it is set in lmdz.card
481    if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
482        IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
483    else
484        # Take default value set in config.def
485        IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
486    fi 
487
488    # physiq.def : Modify parameter tau_gl if it is set in lmdz.card
489    if [ ! X${lmdz_UserChoices_tau_gl} = X ]; then
490        IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl ${lmdz_UserChoices_tau_gl}
491    else
492        # Take default value set in physiq.def
493        IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl DEFAULT
494    fi
495   
496
497    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
498    if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
499        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
500    else
501        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
502    fi
503
504
505    ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
506    ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
507    if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
508        awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
509        IGCM_sys_Mv gcm.def.tmp gcm.def
510        echo
511        IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
512        echo
513        cat gcm.def
514        ByPass_hgardfou_teta=n
515        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
516    fi
517
518    ## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
519    ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
520    if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
521        sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
522        IGCM_sys_Mv gcm.def.tmp gcm.def
523        echo
524        IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
525        echo
526        cat gcm.def
527        ByPass_hgardfou_mats=n
528        IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
529    fi
530
531    # Add include of LMDZ context in iodef.xml
532    # In iodef.xml add on the next line after "COMPONENT CONTEXT"
533    echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
534    # Add inclusion of file context_input_lmdz.xml if this file exists
535    if [ -f context_input_lmdz.xml ] ; then
536        echo '<context id="LMDZ" src="./context_input_lmdz.xml"/>' >> add.tmp
537    fi
538    # Include xml files for output configuration if running with workflow CMIP6
539    if [ X"$( echo ${config_UserChoices_ExpType} | grep CMIP6 )" != "X" ] ; then
540        echo '<context id="LMDZ" src="./ping_lmdz.xml"/>' >> add.tmp
541        echo '<context id="LMDZ" src="./dr2xml_lmdz.xml"/>' >> add.tmp
542    fi
543    cp iodef.xml iodef.xml.tmp
544    sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
545    rm iodef.xml.tmp add.tmp
546
547    #Long Name as global attribute (if LongName is not empty)
548    if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
549        listfile=$(ls file_def*lmdz.xml)
550        echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
551        for file in ${listfile}
552        do
553            cp ${file} ${file}.tmp
554            sed -e "/<file id/r add.tmp" \
555                ${file}.tmp > ${file}
556            rm ${file}.tmp
557        done
558        rm add.tmp
559    fi
560
561    #Compression level (if CompressionLevel is not empty)
562    if [ ! "X${config_UserChoices_CompressionLevel}" = "X" ] ; then
563    echo "NetCDF output files compression level is " ${config_UserChoices_CompressionLevel}
564    listfile=$(ls file_def*lmdz.xml)
565    for file in ${listfile}
566    do
567        sed -i -e "s/\(compression_level=\"\)[^\"]*\(\"\)/\1${config_UserChoices_CompressionLevel}\2/" ${file}
568    done
569    fi
570
571           
572    IGCM_debug_PopStack "ATM_Update"
573}
574
575#-----------------------------------
576function ATM_Finalize
577{
578    IGCM_debug_PushStack "ATM_Finalize"
579
580    # Add special treatement for CARBON CYCLE
581    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
582        ATM_Carbon_Finalize
583    fi
584
585    echo FINALIZE ATM !
586
587    IGCM_debug_PopStack "ATM_Finalize"
588}
589
590
591
592function ATM_Carbon_Update
593{
594    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
595
596    IGCM_debug_PushStack "ATM_Carbon_Update"
597
598    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
599    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
600    typeset PathCO2log
601    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
602   
603    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
604        ##--Initialization of fluxes to an undefined value at the first run
605        UndefinedValueCo2=-9999
606        InitPeriodCo2=0
607        InitDateBeginCo2=${UndefinedValueCo2}
608        InitYearCo2=$(( ${year} - 1 )) 
609        InitDateEndCo2=${InitYearCo2}1231
610        fCO2_ff=${UndefinedValueCo2} 
611        CO2SBG=${UndefinedValueCo2}
612        CO2LU=${UndefinedValueCo2}
613        CO2MBG=${UndefinedValueCo2}
614        CO2_ppm_prec=${UndefinedValueCo2}
615        # Get the initial value of atmosp. pco2
616        CO2_ppm=${lmdz_UserChoices_co2_init}
617       
618        IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
619        IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
620       
621        # Save CO2 values in ExeCpuLog variable contents 5 fields
622        echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
623            gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
624                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
625       
626        # Get the path where the log file co2.log is
627        PathCO2log=${SUBMIT_DIR} 
628        # Get Previous line in co2.log
629        PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
630       
631    else
632       
633        # NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
634        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
635        #SubmitRestartPath=
636        if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
637            IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
638            PathCO2log=${config_ATM_SubmitRestartPath}
639            Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
640            PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
641           
642            IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
643            IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
644           
645            # Save Last Line of control in new co2.log file
646            InitPeriodCo2=0   
647            InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
648            InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
649            fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
650            CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
651            CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
652            CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
653            CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
654            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
655           
656            echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
657                gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
658                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
659        else
660           # Get restart line in co2.log
661            PathCO2log=${SUBMIT_DIR}
662            PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
663           # Get the value of atmosp. pco2 in co2.log
664            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
665        fi
666       
667    fi
668   
669    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
670        # Modify co2_ppm in config.def only for historical run
671        # If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
672        IGCM_comp_modifyDefFile force config.def co2_ppm     ${CO2_ppm}
673    fi
674    IGCM_debug_PopStack "ATM_Carbon_Update"
675}
676
677
678function ATM_Carbon_Finalize
679{
680    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
681
682    IGCM_debug_PushStack "ATM_Carbon_Finalize"
683
684    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
685   
686        # Fossil fuel emission
687    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
688            # For Control, no fossil fuel emission :
689        fCO2_ff=0
690        echo "Fossil Fuel for control run  :" ${fCO2_ff}
691    else
692            # For historical, get the fossile fuel file :
693        fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
694        echo "Fossil Fuel for historical run  :" ${fCO2_ff}
695    fi
696   
697        # Get the value of ocean carbon flux
698    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
699    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
700    echo "Ocean carbon flux  :" ${CO2MBG}
701   
702        # Get the value of land fluxes
703    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
704    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
705    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
706    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
707    echo "Land carbon flux (NEP)         :" ${CO2SRF}
708    echo "LU flux          (FLUC)        :" ${CO2LU}
709    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
710   
711        # Previous CO2
712    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
713    echo "Previous CO2  :" ${CO2_ppm_prec}
714   
715        # Formula
716    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
717    echo "New CO2  :" ${CO2_ppm}
718   
719        # Save CO2 values in ExeCpuLog variable contents 5 fields
720    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
721        gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
722                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
723   
724    IGCM_debug_PopStack "ATM_Carbon_Finalize"
725}
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