source: CONFIG/UNIFORM/v7/ICOLMDZOR_v7/GENERAL/DRIVER/lmdz.driver @ 4336

Last change on this file since 4336 was 4336, checked in by jgipsl, 5 years ago
  • Added AUTO in lmdz xml files.
  • Now activate output files for LMDZ and set there output_leveles from lmdz.card instead of using WriteFrequency? in config.card.
File size: 29.6 KB
Line 
1#!/bin/ksh
2#-----------------------------------------------------------------
3function ATM_Initialize
4{
5    IGCM_debug_PushStack "ATM_Initialize"
6
7
8    # Define the resolution only if the composant ICO for DYNAMICO is not set in config.card
9    if [ X${config_ListOfComponents_ICO} = X ] ; then
10
11        [ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) || RESOL_ATM_3D=96x95x39
12
13        RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $3}' )
14        RESOL_ATM_X=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $1}' )
15        RESOL_ATM_Y=$( echo ${RESOL_ATM_3D} | awk "-Fx" '{print $2}' )
16        RESOL_ATM_XY="${RESOL_ATM_X}x${RESOL_ATM_Y}"
17       
18    else
19        RESOL_ATM_Z=${dynamico_UserChoices_RESOL_ATM_Z}
20        RESOL_NBP=${dynamico_UserChoices_RESOL_NBP}
21    fi
22
23    ##- LMDZ physics version
24    ##  Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
25    if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
26        LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
27    else
28        LMDZ_Physics=AP
29    fi
30    echo LMDZ physics version : ${LMDZ_Physics}
31
32    ##- Create_etat0_limit version
33    ##  Define variable CREATE only if it is set in lmdz.card section UserChoices.
34    ##  This variable is only used in lmdz.card to choose input files.
35    if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
36        IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
37        CREATE=${lmdz_UserChoices_CREATE}
38        echo create_etat0_limit version : ${CREATE}
39    fi
40
41
42    ## - LMDZ choice of config.def file
43    ##   ConfType must be set in lmdz.card
44    ConfType=${lmdz_UserChoices_ConfType}
45
46
47    IGCM_debug_PopStack "ATM_Initialize"
48}
49
50#-----------------------------------------------------------------
51function ATM_Update
52{
53    IGCM_debug_PushStack "ATM_Update"
54
55    ##-- GHG forcing :
56    ##   If forcing file exist in run directory, read values for the current year
57    ##   and set in config.def. If not use the default value set in config.def
58
59    # Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
60    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)"
61    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"
62    if [ -f SOLARANDVOLCANOES.txt ] ; then
63        value=`grep Annee_${year} SOLARANDVOLCANOES.txt | awk -F= '{print $2}'`
64        if [ X"${value}" = X ] ; then
65            # The grep returned empty variable, stop execution
66            IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
67            IGCM_debug_Verif_Exit
68        fi
69    else
70        value=DEFAULT
71    fi
72    IGCM_comp_modifyDefFile nonblocker config.def solaire $value
73
74    # Read value for eccentricity from file Eccentricity.txt. If file not existing, take DEFAULT value from file.
75    if [ -f Eccentricity.txt ] ; then
76        value=`grep Annee_${year} Eccentricity.txt | awk -F= '{print $2}'`
77        if [ X"${value}" = X ] ; then
78            # The grep returned empty variable, stop execution
79            IGCM_debug_Exit "The file Eccentricity.txt do not contain the current year."
80            IGCM_debug_Verif_Exit
81        fi
82    else
83        value=DEFAULT
84    fi
85    IGCM_comp_modifyDefFile nonblocker config.def R_ecc $value
86
87    # Read value for obliquity from file Obliquity.txt. If file not existing, take DEFAULT value from file.
88    if [ -f Obliquity.txt ] ; then
89        value=`grep Annee_${year} Obliquity.txt | awk -F= '{print $2}'`
90        if [ X"${value}" = X ] ; then
91            # The grep returned empty variable, stop execution
92            IGCM_debug_Exit "The file Obliquity.txt do not contain the current year."
93            IGCM_debug_Verif_Exit
94        fi
95    else
96        value=DEFAULT
97    fi
98    IGCM_comp_modifyDefFile nonblocker config.def R_incl $value
99
100    # Read value for perihelie from file Perihelie.txt. If file not existing, take DEFAULT value from file.
101    if [ -f Perihelie.txt ] ; then
102        value=`grep Annee_${year} Perihelie.txt | awk -F= '{print $2}'`
103        if [ X"${value}" = X ] ; then
104            # The grep returned empty variable, stop execution
105            IGCM_debug_Exit "The file Perihelie.txt do not contain the current year."
106            IGCM_debug_Verif_Exit
107        fi
108    else
109        value=DEFAULT
110    fi
111    IGCM_comp_modifyDefFile nonblocker config.def R_peri $value
112
113    # Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
114    # Calculate co2_ppm_per as co2_ppm*4.
115    if [ -f CO2.txt ] ; then
116        value=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
117        if [ X"${value}" = X ] ; then
118            # The grep returned empty variable, stop execution
119            IGCM_debug_Exit "The file CO2.txt do not contain the current year."
120            IGCM_debug_Verif_Exit
121        fi
122        value4=`grep Annee_${year} CO2.txt | awk -F= '{print $2 * 4}'`
123    else
124        value=DEFAULT
125        value4=DEFAULT
126    fi
127    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
128    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm_per $value4
129
130
131    # Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
132    if [ -f CH4.txt ] ; then
133        value=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
134        if [ X"${value}" = X ] ; then
135            # The grep returned empty variable, stop execution
136            IGCM_debug_Exit "The file CH4.txt do not contain the current year."
137            IGCM_debug_Verif_Exit
138        fi
139    else
140        value=DEFAULT
141    fi
142    IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
143
144
145    # Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
146    if [ -f N2O.txt ] ; then
147        value=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
148        if [ X"${value}" = X ] ; then
149            # The grep returned empty variable, stop execution
150            IGCM_debug_Exit "The file N2O.txt do not contain the current year."
151            IGCM_debug_Verif_Exit
152        fi
153    else
154        value=DEFAULT
155    fi
156    IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
157
158    # Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
159    if [ -f CFC11.txt ] ; then
160        value=`grep Annee_${year} CFC11.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 CFC11.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 CFC11_ppt $value
170
171
172    # Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
173    if [ -f CFC12.txt ] ; then
174        value=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
175        if [ X"${value}" = X ] ; then
176            # The grep returned empty variable, stop execution
177            IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
178            IGCM_debug_Verif_Exit
179        fi
180    else
181        value=DEFAULT
182    fi
183    IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
184
185
186    ## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
187    LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
188    IGCM_debug_Print 3 "LMDZ_t_coupl "   ${LMDZ_t_coupl}
189    IGCM_comp_modifyDefFile nonblocker config.def t_coupl   ${LMDZ_t_coupl} 
190
191    ##-- Add special treatement for CARBON CYCLE
192    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
193        ATM_Carbon_Update
194    fi
195
196
197    ##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
198    ##   COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
199    if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] &&  [ ${year} -ge 1979 ]) ; then
200        LMDZ_COSP_daily=.TRUE.
201    fi
202
203    ## Modifiy
204
205    # histmth
206    if [ X${lmdz_UserChoices_output_level_histmth} = X ] || [ X${lmdz_UserChoices_output_level_histmth} = XNONE ] ; then
207        IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled FALSE
208        IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth output_level 0
209    else
210        IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled TRUE
211        IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth output_level ${lmdz_UserChoices_output_level_histmth} 
212    fi
213
214    # histday
215    if [ X${lmdz_UserChoices_output_level_histday} = X ] || [ X${lmdz_UserChoices_output_level_histday} = XNONE ] ; then
216        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled FALSE
217        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 0
218    else
219        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled TRUE
220        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level ${lmdz_UserChoices_output_level_histday} 
221    fi
222
223    # histhf
224    if [ X${lmdz_UserChoices_output_level_histhf} = X ] || [ X${lmdz_UserChoices_output_level_histhf} = XNONE ] ; then
225        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled FALSE
226        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 0
227    else
228        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled TRUE
229        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level ${lmdz_UserChoices_output_level_histhf} 
230    fi
231
232    # histmthNMC
233    if [ X${lmdz_UserChoices_output_level_histmthNMC} = X ] || [ X${lmdz_UserChoices_output_level_histmthNMC} = XNONE ] ; then
234        IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled FALSE
235        IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC output_level 0
236    else
237        IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled TRUE
238        IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC output_level ${lmdz_UserChoices_output_level_histmthNMC} 
239    fi
240
241    # histdayNMC
242    if [ X${lmdz_UserChoices_output_level_histdayNMC} = X ] || [ X${lmdz_UserChoices_output_level_histdayNMC} = XNONE ] ; then
243        IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled FALSE
244        IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC output_level 0
245    else
246        IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled TRUE
247        IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC output_level ${lmdz_UserChoices_output_level_histdayNMC} 
248    fi
249
250    # histhfNMC
251    if [ X${lmdz_UserChoices_output_level_histhfNMC} = X ] || [ X${lmdz_UserChoices_output_level_histhfNMC} = XNONE ] ; then
252        IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled FALSE
253        IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC output_level 0
254    else
255        IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled TRUE
256        IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC output_level ${lmdz_UserChoices_output_level_histhfNMC} 
257    fi
258
259    # histstrataer
260    if [ X${lmdz_UserChoices_output_level_histstrataer} = X ] || [ X${lmdz_UserChoices_output_level_histstrataer} = XNONE ] ; then
261        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled FALSE
262        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer output_level 0
263    else
264        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled TRUE
265        IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer output_level ${lmdz_UserChoices_output_level_histstrataer} 
266    fi
267
268    # histstn
269    if [ X${lmdz_UserChoices_output_level_histstn} = X ] || [ X${lmdz_UserChoices_output_level_histstn} = XNONE ] ; then
270        IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled FALSE
271        IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn output_level 0
272    else
273        IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled TRUE
274        IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn output_level ${lmdz_UserChoices_output_level_histstn} 
275    fi
276
277
278    # histmthCOSP
279    if [ X${lmdz_UserChoices_output_level_histmthCOSP} = X ] || [ X${lmdz_UserChoices_output_level_histmthCOSP} = XNONE ] ; then
280        IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled FALSE
281        IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP output_level 0
282    else
283        IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled TRUE
284        IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP output_level ${lmdz_UserChoices_output_level_histmthCOSP} 
285    fi
286
287
288    # histdayCOSP
289    if [ X${lmdz_UserChoices_output_level_histdayCOSP} = X ] || [ X${lmdz_UserChoices_output_level_histdayCOSP} = XNONE ] ; then
290        IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled FALSE
291        IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP output_level 0
292    else
293        IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled TRUE
294        IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP output_level ${lmdz_UserChoices_output_level_histdayCOSP} 
295    fi
296
297
298    # histhfCOSP
299    if [ X${lmdz_UserChoices_output_level_histhfCOSP} = X ] || [ X${lmdz_UserChoices_output_level_histhfCOSP} = XNONE ] ; then
300        IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled FALSE
301        IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP output_level 0
302    else
303        IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled TRUE
304        IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP output_level ${lmdz_UserChoices_output_level_histhfCOSP} 
305    fi
306
307
308    ## run.def parameters
309
310
311    ##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
312
313    if [ ${CumulPeriod} -eq 1 ] ; then
314        IGCM_comp_modifyDefFile blocker run.def raz_date  1
315    else
316        IGCM_comp_modifyDefFile blocker run.def raz_date  0
317    fi
318
319    ##-- Calendar type for LMDZ and create_etat0_limit
320    #    calend is read from both LMDZ dynamics and physics parts of the model
321    case ${config_UserChoices_CalendarType} in
322        leap|gregorian)
323            IGCM_comp_modifyDefFile blocker run.def calend  gregorian ;;
324        noleap)
325            IGCM_comp_modifyDefFile blocker run.def calend  earth_365d ;;
326        360d)
327            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
328        *)
329            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
330    esac
331
332
333    ## -- Modify more calendar related variables.
334    IGCM_comp_modifyDefFile blocker run.def dayref    ${InitDay}
335    # Following variables are read by LMDZ dynamics
336    IGCM_comp_modifyDefFile blocker run.def nday      ${PeriodLengthInDays}
337
338    # Set anneeref different for gcm and ce0l
339    # Test if executable create_etat0_limit is present and lmdz.x is not present
340    if [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
341        # for case ce0l : always take current year
342        IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
343       
344        # Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
345        # In more recent versions of LMDZ, this will not be needed.
346        IGCM_comp_modifyDefFile force   run.def use_filtre_fft n
347    else
348        # for case gcm : take first year of simulation
349        IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
350    fi
351   
352
353    ## Determine from the variable ListOfComponents in config.card coupling to external models
354    ## and set corresponding parameters in run.def
355    echo ListOfComponents now running : ${config_ListOfComponents[*]}
356
357    if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
358        echo "Activate ORCHIDEE, set VEGET=y in run.def"
359        IGCM_comp_modifyDefFile blocker run.def VEGET y
360    else
361        echo "No ORCHIDEE, set VEGET=n in run.def"
362        IGCM_comp_modifyDefFile blocker run.def VEGET n
363    fi
364
365    if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
366        echo "Activate coupling to ocean, set type_ocean=couple in run.def"
367        IGCM_comp_modifyDefFile blocker run.def type_ocean couple
368    else
369        echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
370        IGCM_comp_modifyDefFile nonblocker run.def type_ocean force
371    fi
372
373    if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
374        echo "Activate coupling to INCA, set type_trac=inca in run.def"
375        IGCM_comp_modifyDefFile blocker run.def type_trac inca
376    elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
377        echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
378        IGCM_comp_modifyDefFile blocker run.def type_trac repr
379        IGCM_comp_modifyDefFile blocker run.def config_inca none
380    else
381        echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
382        IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
383        IGCM_comp_modifyDefFile blocker run.def config_inca none
384    fi
385
386
387    # run.def : Activate the call to phytrac
388    if [ ! X${lmdz_UserChoices_iflag_phytrac} = X ]; then
389        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac ${lmdz_UserChoices_iflag_phytrac}
390    else
391        IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac 0
392    fi 
393
394    # physiq.def : Activate the call to phytrac
395    if [ ! X${lmdz_UserChoices_ok_bug_cv_trac} = X ]; then
396        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  ${lmdz_UserChoices_ok_bug_cv_trac}
397    else
398        IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac  n
399    fi 
400
401    # config.def : Activate direct radiative effect if ok_ade=y
402    if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
403        IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
404    else
405        IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
406    fi 
407
408    # config.def : Activate indirect radiative effect if ok_aie=y
409    if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
410        IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
411    else
412        IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
413    fi 
414
415    # config.def : Activate online aerosol coupled model if aerosol_couple=y
416    if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
417        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
418    else
419        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
420    fi 
421
422    # config.def : Activate online Ozone chemistry coupled model if chemistry_couple=y
423    if [ ! X${lmdz_UserChoices_chemistry_couple} = X ]; then
424        IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple ${lmdz_UserChoices_chemistry_couple}
425    else
426        IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple n
427    fi 
428
429    # config.def : Activate reading of ozone in climatology if read_climoz=2
430    if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
431        IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
432    else
433        IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0     
434    fi 
435
436    # config.def : Choose aerosol use in radiative effect
437    #  type of coupled aerosol =1 (default) =2 => bc  only =3 => pom only =4 => seasalt only
438    # =5 => dust only =6 => all aerosol   
439    if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
440        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
441    else
442        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
443    fi 
444
445    # config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
446    if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
447        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
448    else
449        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
450    fi 
451
452    # config.def : Activate COSP
453    if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
454        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
455    else
456        IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
457    fi 
458
459    # config.def : Modify parameter pmagic if it is set in lmdz.card
460    if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
461        IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
462    else
463        # Take default value set in config.def
464        IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
465    fi 
466
467    # physiq.def : Modify parameter tau_gl if it is set in lmdz.card
468    if [ ! X${lmdz_UserChoices_tau_gl} = X ]; then
469        IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl ${lmdz_UserChoices_tau_gl}
470    else
471        # Take default value set in physiq.def
472        IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl DEFAULT
473    fi
474   
475
476    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
477    if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
478        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
479    else
480        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
481    fi
482
483
484    # Specific ByPass option only used with LMDZ dynamcis (without DYNMAICO)
485    if [ X${config_ListOfComponents_ICO} = X ] ; then
486
487        ## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
488        ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
489        if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
490            awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
491            IGCM_sys_Mv gcm.def.tmp gcm.def
492            echo
493            IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
494            echo
495            cat gcm.def
496            ByPass_hgardfou_teta=n
497            IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
498        fi
499       
500        ## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
501        ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
502        if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
503            sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
504            IGCM_sys_Mv gcm.def.tmp gcm.def
505            echo
506            IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
507            echo
508            cat gcm.def
509            ByPass_hgardfou_mats=n
510            IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
511        fi
512    fi
513
514
515    # Add include of LMDZ context in iodef.xml
516    # In iodef.xml add on the next line after "COMPONENT CONTEXT"
517    echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
518    # Add inclusion of file context_input_lmdz.xml if this file exists
519    if [ -f context_input_lmdz.xml ] ; then
520        echo '<context id="LMDZ" src="./context_input_lmdz.xml"/>' >> add.tmp
521    fi
522    # Include xml files for output configuration if running with workflow CMIP6
523    if [ X"$( echo ${config_UserChoices_ExpType} | grep CMIP6 )" != "X" ] ; then
524        echo '<context id="LMDZ" src="./ping_lmdz.xml"/>' >> add.tmp
525        echo '<context id="LMDZ" src="./dr2xml_lmdz.xml"/>' >> add.tmp
526    fi
527    cp iodef.xml iodef.xml.tmp
528    sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
529    rm iodef.xml.tmp add.tmp
530
531    #Long Name as global attribute (if LongName is not empty)
532    if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
533        listfile=$(ls file_def*lmdz.xml)
534        echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
535        for file in ${listfile}
536        do
537            cp ${file} ${file}.tmp
538            sed -e "/<file id/r add.tmp" \
539                ${file}.tmp > ${file}
540            rm ${file}.tmp
541        done
542        rm add.tmp
543    fi
544           
545    IGCM_debug_PopStack "ATM_Update"
546}
547
548#-----------------------------------
549function ATM_Finalize
550{
551    IGCM_debug_PushStack "ATM_Finalize"
552
553    # Add special treatement for CARBON CYCLE
554    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
555        ATM_Carbon_Finalize
556    fi
557
558    echo FINALIZE ATM !
559
560    IGCM_debug_PopStack "ATM_Finalize"
561}
562
563
564
565function ATM_Carbon_Update
566{
567    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
568
569    IGCM_debug_PushStack "ATM_Carbon_Update"
570
571    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
572    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
573    typeset PathCO2log
574    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
575   
576    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
577        ##--Initialization of fluxes to an undefined value at the first run
578        UndefinedValueCo2=-9999
579        InitPeriodCo2=0
580        InitDateBeginCo2=${UndefinedValueCo2}
581        InitYearCo2=$(( ${year} - 1 )) 
582        InitDateEndCo2=${InitYearCo2}1231
583        fCO2_ff=${UndefinedValueCo2} 
584        CO2SBG=${UndefinedValueCo2}
585        CO2LU=${UndefinedValueCo2}
586        CO2MBG=${UndefinedValueCo2}
587        CO2_ppm_prec=${UndefinedValueCo2}
588        # Get the initial value of atmosp. pco2
589        CO2_ppm=${lmdz_UserChoices_co2_init}
590       
591        IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
592        IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
593       
594        # Save CO2 values in ExeCpuLog variable contents 5 fields
595        echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
596            gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
597                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
598       
599        # Get the path where the log file co2.log is
600        PathCO2log=${SUBMIT_DIR} 
601        # Get Previous line in co2.log
602        PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
603       
604    else
605       
606        # NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
607        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
608        #SubmitRestartPath=
609        if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
610            IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
611            PathCO2log=${config_ATM_SubmitRestartPath}
612            Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
613            PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
614           
615            IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
616            IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
617           
618            # Save Last Line of control in new co2.log file
619            InitPeriodCo2=0   
620            InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
621            InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
622            fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
623            CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
624            CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
625            CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
626            CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
627            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
628           
629            echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
630                gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
631                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
632        else
633           # Get restart line in co2.log
634            PathCO2log=${SUBMIT_DIR}
635            PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
636           # Get the value of atmosp. pco2 in co2.log
637            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
638        fi
639       
640    fi
641   
642    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
643        # Modify co2_ppm in config.def only for historical run
644        # If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
645        IGCM_comp_modifyDefFile force config.def co2_ppm     ${CO2_ppm}
646    fi
647    IGCM_debug_PopStack "ATM_Carbon_Update"
648}
649
650
651function ATM_Carbon_Finalize
652{
653    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
654
655    IGCM_debug_PushStack "ATM_Carbon_Finalize"
656
657    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
658   
659        # Fossil fuel emission
660    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
661            # For Control, no fossil fuel emission :
662        fCO2_ff=0
663        echo "Fossil Fuel for control run  :" ${fCO2_ff}
664    else
665            # For historical, get the fossile fuel file :
666        fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
667        echo "Fossil Fuel for historical run  :" ${fCO2_ff}
668    fi
669   
670        # Get the value of ocean carbon flux
671    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
672    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
673    echo "Ocean carbon flux  :" ${CO2MBG}
674   
675        # Get the value of land fluxes
676    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
677    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
678    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
679    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
680    echo "Land carbon flux (NEP)         :" ${CO2SRF}
681    echo "LU flux          (FLUC)        :" ${CO2LU}
682    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
683   
684        # Previous CO2
685    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
686    echo "Previous CO2  :" ${CO2_ppm_prec}
687   
688        # Formula
689    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
690    echo "New CO2  :" ${CO2_ppm}
691   
692        # Save CO2 values in ExeCpuLog variable contents 5 fields
693    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
694        gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
695                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
696   
697    IGCM_debug_PopStack "ATM_Carbon_Finalize"
698}
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