source: CONFIG/UNIFORM/v6/LMDZOR_v6/GENERAL/DRIVER/lmdz.driver @ 2605

Last change on this file since 2605 was 2605, checked in by jgipsl, 8 years ago
  • Put back NMC monthly output as default for LMDZOR experiments
  • More simplifications
File size: 29.0 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    case ${config_UserChoices_PeriodLength} in
57        1Y|1y|1M|1m) ok_mensuel=.TRUE. ;;
58        5D|5d|1D|1d) ok_journe=.TRUE. ;;
59    esac
60
61    for frequency in ${config_ATM_WriteFrequency} ; do
62        case ${frequency} in
63            1M|1m) ok_mensuel=.TRUE. ;;
64        esac
65        case ${frequency} in
66            5D|5d|1D|1d) ok_journe=.TRUE. ;;
67        esac
68        case ${frequency} in
69            HF|hf) ok_hf=.TRUE. ;;
70        esac
71        case ${frequency} in
72            HF3h|hf3h) ok_hf3h=.TRUE. ;;
73        esac
74        case ${frequency} in
75            HF3hm|hf3hm) ok_hf3hm=.TRUE. ;;
76        esac
77        case ${frequency} in
78            STN|stn) ok_stn=.TRUE. ;;
79        esac
80    done
81
82    ## Read LMDZ_NbPeriod_adjust option in lmdz.card
83    if [ X"${lmdz_UserChoices_LMDZ_NbPeriod_adjust}" = X"" ] ; then
84        # The variable is not in lmdz.card, set default value
85        LMDZ_NbPeriod_adjust=0
86    else       
87        LMDZ_NbPeriod_adjust=${lmdz_UserChoices_LMDZ_NbPeriod_adjust}
88    fi
89
90    if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
91        LMDZ_Bands_file_name=${lmdz_UserChoices_LMDZ_Bands_file_name}
92    fi
93
94
95    ##  Read LMDZ_COSP_OK in lmdz.card
96    if [ X${lmdz_UserChoices_LMDZ_COSP_OK} = Xy ] ; then
97        ##  LMDZ_COSP_OK=y, now read all other COSP variables
98        ##  Read LMDZ_COSP_monthly in lmdz.card
99        if [ X${lmdz_UserChoices_LMDZ_COSP_monthly} = Xy ] ; then
100            LMDZ_COSP_monthly=.TRUE.
101        else
102            LMDZ_COSP_monthly=.FALSE.
103        fi
104        ##  Read LMDZ_COSP_daily in lmdz.card
105        if [ X${lmdz_UserChoices_LMDZ_COSP_daily} = Xy ] ; then
106            LMDZ_COSP_daily=.TRUE.
107        else
108            LMDZ_COSP_daily=.FALSE.
109        fi
110        ##  Read LMDZ_COSP_hf in lmdz.card
111        if [ X${lmdz_UserChoices_LMDZ_COSP_hf} = Xy ] ; then
112            LMDZ_COSP_hf=.TRUE.
113        else
114            LMDZ_COSP_hf=.FALSE.
115        fi
116    else
117        # LMDZ_COSP_OK=n : All cosp output are deactivated
118        LMDZ_COSP_monthly=.FALSE.
119        LMDZ_COSP_daily=.FALSE.
120        LMDZ_COSP_hf=.FALSE.
121    fi 
122
123    ##  Read LMDZ_NMC_monthly in lmdz.card
124    if [ X${lmdz_UserChoices_LMDZ_NMC_monthly} = Xy ] ; then
125        LMDZ_NMC_monthly=.TRUE.
126    else
127        LMDZ_NMC_monthly=.FALSE.
128    fi
129   
130    ## Read LMDZ_NMC_daily in lmdz.card
131    if [ X${lmdz_UserChoices_LMDZ_NMC_daily} = Xy ] ; then
132        LMDZ_NMC_daily=.TRUE.
133    else
134        LMDZ_NMC_daily=.FALSE.
135    fi
136   
137    ## Read LMDZ_NMC_hf in lmdz.card
138    if [ X${lmdz_UserChoices_LMDZ_NMC_hf} = Xy ] ; then
139        LMDZ_NMC_hf=.TRUE.
140    else
141        LMDZ_NMC_hf=.FALSE.
142    fi
143   
144
145    IGCM_debug_PopStack "ATM_Initialize"
146}
147
148#-----------------------------------------------------------------
149function ATM_Update
150{
151    IGCM_debug_PushStack "ATM_Update"
152
153
154    ## Algorithme for special treatment for Bands_xxx file
155    ## For CumulPeriod=1 ;
156    ##        IF NbPeriod_Adjust = 0 ; set LMDZ_adjust=n
157    ##                                IF LMDZ_Bands_file_name was given in lmdz.card THEN Get Bands file directly from server. Store it later with _0 suffix.
158    ##                                IF no LMDZ_Bands_file_name was given, start without Bands file. Store it later with _0 suffix.
159    ##        ELSE set LMDZ_adjust=y ; start without Bands file ; Store it later in PARAM/ directory in submit directory with suffix _1 ;
160    ##
161    ## For CumulPeriod=2 to LMDZ_NbPeriod_adjust ;
162    ##       Get Bands file from PARAM/ in submit directory (CumulPeriod-1) ; set LMDZ_adjust=y ; Store Bands file in PARAM/ ;
163    ##
164    ## For CumulPeriod > LMDZ_NbPeriod_adjust ; LMDZ_adjust=n ; Get Bands file from PARAM/ ; Do not store ;
165
166    if [ ${CumulPeriod} -eq 1 ] ; then
167        if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
168            if [ ! X${LMDZ_Bands_file_name} = X ] ; then
169                IGCM_sys_Get ${LMDZ_Bands_file_name} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
170                IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
171                IGCM_debug_Print 1 "Bands file forced to ${LMDZ_Bands_file_name} and stored in ${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0"
172            fi
173        fi
174    fi
175
176    LMDZ_adjust=n
177    [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && LMDZ_adjust=y
178
179    RefPeriod=${LMDZ_NbPeriod_adjust} #0 to use a Bands file from Restart
180    [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && (( RefPeriod = ${CumulPeriod} - 1 )) 
181
182    # Get Bands file from PARAM directory if file exist
183    if ( [ ${CumulPeriod} -gt 1 ] && [ -f ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} ] ) ; then
184        IGCM_sys_Cp ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
185        IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
186    fi
187
188    ##-- GHG forcing :
189    ##   If forcing file exist in run directory, read values for the current year
190    ##   and set in config.def. If not use the default value set in config.def
191
192    # Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
193    if [ -f SOLARANDVOLCANOES.txt ] ; then
194        value=`grep Annee_${year} SOLARANDVOLCANOES.txt | awk -F= '{print $2}'`
195        if [ X"${value}" = X ] ; then
196            # The grep returned empty variable, stop execution
197            IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
198            IGCM_debug_Verif_Exit
199        fi
200    else
201        value=DEFAULT
202    fi
203    IGCM_comp_modifyDefFile nonblocker config.def solaire $value
204
205
206    # Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
207    if [ -f CO2.txt ] ; then
208        value=`grep Annee_${year} CO2.txt | awk -F= '{print $2}'`
209        if [ X"${value}" = X ] ; then
210            # The grep returned empty variable, stop execution
211            IGCM_debug_Exit "The file CO2.txt do not contain the current year."
212            IGCM_debug_Verif_Exit
213        fi
214    else
215        value=DEFAULT
216    fi
217    IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
218
219
220    # Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
221    if [ -f CH4.txt ] ; then
222        value=`grep Annee_${year} CH4.txt | awk -F= '{print $2}'`
223        if [ X"${value}" = X ] ; then
224            # The grep returned empty variable, stop execution
225            IGCM_debug_Exit "The file CH4.txt do not contain the current year."
226            IGCM_debug_Verif_Exit
227        fi
228    else
229        value=DEFAULT
230    fi
231    IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
232
233
234    # Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
235    if [ -f N2O.txt ] ; then
236        value=`grep Annee_${year} N2O.txt | awk -F= '{print $2}'`
237        if [ X"${value}" = X ] ; then
238            # The grep returned empty variable, stop execution
239            IGCM_debug_Exit "The file N2O.txt do not contain the current year."
240            IGCM_debug_Verif_Exit
241        fi
242    else
243        value=DEFAULT
244    fi
245    IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
246
247    # Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
248    if [ -f CFC11.txt ] ; then
249        value=`grep Annee_${year} CFC11.txt | awk -F= '{print $2}'`
250        if [ X"${value}" = X ] ; then
251            # The grep returned empty variable, stop execution
252            IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
253            IGCM_debug_Verif_Exit
254        fi
255    else
256        value=DEFAULT
257    fi
258    IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
259
260
261    # Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
262    if [ -f CFC12.txt ] ; then
263        value=`grep Annee_${year} CFC12.txt | awk -F= '{print $2}'`
264        if [ X"${value}" = X ] ; then
265            # The grep returned empty variable, stop execution
266            IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
267            IGCM_debug_Verif_Exit
268        fi
269    else
270        value=DEFAULT
271    fi
272    IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
273
274
275    ## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
276    LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
277    IGCM_debug_Print 3 "LMDZ_t_coupl "   ${LMDZ_t_coupl}
278    IGCM_comp_modifyDefFile nonblocker config.def t_coupl   ${LMDZ_t_coupl} 
279
280    ##-- Add special treatement for CARBON CYCLE
281    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
282        ATM_Carbon_Update
283    fi
284
285
286    ##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
287    ##   COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
288    if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] &&  [ ${year} -ge 1979 ]) ; then
289        LMDZ_COSP_daily=.TRUE.
290    fi
291
292    ## Modifiy
293    IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
294   
295    IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
296   
297    if [ X${OutLevel} = Xlow ] || [ X${OutLevel} = Xmedium ] ; then
298        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
299    else
300        IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
301    fi
302   
303    IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
304   
305    if [ X${OutLevel} = Xlow ] ; then
306        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
307    elif [ X${OutLevel} = Xmedium ] ; then
308        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
309    elif [ X${OutLevel} = Xhigh ] ; then
310        IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
311    fi
312       
313#       IGCM_comp_modifyXmlFile force file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
314#       IGCM_comp_modifyXmlFile force file_def_histhf3h_lmdz.xml histhf3h output_freq 3h
315#       IGCM_comp_modifyXmlFile force file_def_histhf3h_lmdz.xml histhf3h name histhf3h
316
317#       IGCM_comp_modifyXmlFile force file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}
318#       IGCM_comp_modifyXmlFile force file_def_histhf3hm_lmdz.xml histhf3hm output_freq 3h
319#       IGCM_comp_modifyXmlFile force file_def_histhf3hm_lmdz.xml histhf3hm name histhf3hm
320
321    IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}
322
323    IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
324    IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
325    IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
326   
327    IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
328    IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
329    IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}
330       
331
332    ## gcm.def parameters :
333    # Modification of variable iphysiq depending on the physics
334    if [ X${LMDZ_Physics} = X"AP" ] ; then
335        if [ ${RESOL_ATM_3D} = 96x95x39 ]; then
336            value=10
337        elif [ ${RESOL_ATM_3D} = 144x142x39 ]; then
338            value=15
339        else
340            IGCM_debug_Print 1 "LMDZ_Physics=${LMDZ_Physics} has not been tested for the current resolution RESOL_ATM_3D=${RESOL_ATM_3D}. "
341            IGCM_debug_Print 1 "iphysiq must be defined for the current combination of resolution and phyiscs package"
342            IGCM_debug_Exit "You need to add a special case in lmdz.driver to handle the above combination."
343        fi
344    elif [ X${LMDZ_Physics} = X"NPv3.1" ] ; then
345        if  [ ${RESOL_ATM_3D} = 96x95x39 ] ; then
346            value=5
347        elif [ ${RESOL_ATM_3D} = 144x142x39 ] ; then
348            value=5
349        else
350            IGCM_debug_Print 1 "LMDZ_Physics=${LMDZ_Physics} has not been tested for the current resolution RESOL_ATM_3D=${RESOL_ATM_3D}. "
351            IGCM_debug_Print 1 "iphysiq must be defined for the current combination of resolution and phyiscs package"
352            IGCM_debug_Exit "You need to add a special case in lmdz.driver to handle the above combination."
353        fi
354    elif [ X${LMDZ_Physics} = X"NPv3.2" ] ; then
355        if [ ${RESOL_ATM_3D} = 96x95x39 ] ; then
356            value=5
357        elif [ ${RESOL_ATM_3D} = 144x142x39 ] ; then
358            value=5
359        elif [ ${RESOL_ATM_3D} = 128x118x39 ] ; then
360            value=15
361        else
362            IGCM_debug_Print 1 "LMDZ_Physics=${LMDZ_Physics} has not been tested for the current resolution RESOL_ATM_3D=${RESOL_ATM_3D}. "
363            IGCM_debug_Print 1 "iphysiq must be defined for the current combination of resolution and phyiscs package"
364            IGCM_debug_Exit "You need to add a special case in lmdz.driver to handle the above combination."
365        fi
366    else
367        # Take default value set in gcm.def
368        value=DEFAULT
369    fi
370    IGCM_comp_modifyDefFile nonblocker gcm.def iphysiq $value
371   
372
373    ## run.def parameters
374
375
376    ##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
377    if [ ${CumulPeriod} -eq 1 ] ; then
378        IGCM_comp_modifyDefFile blocker run.def raz_date  1
379    else
380        IGCM_comp_modifyDefFile blocker run.def raz_date  0
381    fi
382
383    ##-- Calendar type for LMDZ and create_etat0_limit
384    case ${config_UserChoices_CalendarType} in
385        leap|gregorian)
386            IGCM_comp_modifyDefFile blocker run.def calend  gregorian ;;
387        noleap)
388            IGCM_comp_modifyDefFile blocker run.def calend  earth_365d ;;
389        360d)
390            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
391        *)
392            IGCM_comp_modifyDefFile blocker run.def calend  earth_360d ;;
393    esac
394
395    IGCM_comp_modifyDefFile blocker run.def dayref    ${InitDay}
396    IGCM_comp_modifyDefFile blocker run.def nday      ${PeriodLengthInDays}
397    IGCM_comp_modifyDefFile nonblocker run.def adjust ${LMDZ_adjust}
398
399    # Set anneeref different for gcm and ce0l
400    # Test if executable create_etat0_limit is present and lmdz.x is not present
401    if [ -f create_etat0_limit* ] || [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
402        # for case ce0l : always take current year
403        IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
404
405        # Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
406        # In more recent versions of LMDZ, this will not be needed.
407        IGCM_comp_modifyDefFile force   run.def use_filtre_fft n
408    else
409        # for case gcm : take first year of simulation
410        IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
411    fi
412
413    # Activate creation of file grilles_gcm.nc only at first period
414    if [ ${CumulPeriod} -eq 1 ] ; then
415        IGCM_comp_modifyDefFile nonblocker run.def grilles_gcm_netcdf y
416    else
417        IGCM_comp_modifyDefFile nonblocker run.def grilles_gcm_netcdf n
418    fi
419
420    ## Determine from the variable ListOfComponents in config.card coupling to external models
421    ## and set corresponding parameters in run.def
422    echo ListOfComponents now running : ${config_ListOfComponents[*]}
423
424    if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
425        echo "Activate ORCHIDEE, set VEGET=y in run.def"
426        IGCM_comp_modifyDefFile blocker run.def VEGET y
427    else
428        echo "No ORCHIDEE, set VEGET=n in run.def"
429        IGCM_comp_modifyDefFile blocker run.def VEGET n
430    fi
431
432    if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
433        echo "Activate coupling to ocean, set type_ocean=couple in run.def"
434        IGCM_comp_modifyDefFile blocker run.def type_ocean couple
435    else
436        echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
437        IGCM_comp_modifyDefFile blocker run.def type_ocean force
438    fi
439
440    if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
441        echo "Activate coupling to INCA, set type_trac=inca in run.def"
442        IGCM_comp_modifyDefFile blocker run.def type_trac inca
443    elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
444        echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
445        IGCM_comp_modifyDefFile blocker run.def type_trac repr
446        IGCM_comp_modifyDefFile blocker run.def config_inca none
447    else
448        echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
449        IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
450        IGCM_comp_modifyDefFile blocker run.def config_inca none
451    fi
452
453
454    # config.def : Activate direct radiative effect if ok_ade=y
455    if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
456        IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
457    else
458        IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
459    fi 
460
461    # config.def : Activate indirect radiative effect if ok_aie=y
462    if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
463        IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
464    else
465        IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
466    fi 
467
468    # config.def : Activate online aerosol coupled model if aerosol_couple=y
469    if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
470        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
471    else
472        IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
473    fi 
474
475    # config.def : Activate reading of ozone in climatology if read_climoz=2
476    if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
477        IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
478    else
479        IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0     
480    fi 
481
482    # config.def : Choose aerosol use in radiative effect
483    #  type of coupled aerosol =1 (default) =2 => bc  only =3 => pom only =4 => seasalt only
484    # =5 => dust only =6 => all aerosol   
485    if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
486        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
487    else
488        IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
489    fi 
490
491    # config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
492    if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
493        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
494    else
495        IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
496    fi 
497
498    # guide.def : Activate nudging if ok_guide=y set in lmdz.card
499    if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
500        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide  ${lmdz_UserChoices_ok_guide}
501    else
502        IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
503    fi
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    if [ X${lmdz_UserChoices_XIOS}  = Xy ] ; then
532        # Add include of LMDZ context in iodef.xml
533        # In iodef.xml add on next line after "COMPONENT CONTEXT"
534        #  <context id="LMDZ" src="./context_lmdz.xml"/>
535        echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
536        cp iodef.xml iodef.xml.tmp
537        sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
538        rm iodef.xml.tmp add.tmp
539
540        # Set ok_all_xml=y in run.def
541        IGCM_comp_modifyDefFile nonblocker run.def ok_all_xml y
542    else
543        # Deactivate ok_all_xml in run.def
544        IGCM_comp_modifyDefFile nonblocker run.def ok_all_xml n
545    fi
546   
547    IGCM_debug_PopStack "ATM_Update"
548}
549
550#-----------------------------------
551function ATM_Finalize
552{
553    IGCM_debug_PushStack "ATM_Finalize"
554
555    # If the file exist, copy Bands_ file to PARAM/ in submit directory. This file will be used for the simulation.
556    # Copy also the same file into ATM/Restart at ARCHIVE directory for backup.
557    if [ -f Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ] ; then
558      if [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] ; then
559        IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
560        IGCM_sys_Put_Out Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${R_OUT_ATM_R}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
561      elif [ ${CumulPeriod} -eq 1 ] && [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
562        # Special case : first period and no adjust => Save bands file with suffix _0
563        IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
564        IGCM_sys_Put_Out Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${R_OUT_ATM_R}/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
565      fi
566    fi
567
568    # Add special treatement for CARBON CYCLE
569    if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] || [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
570        ATM_Carbon_Finalize
571    fi
572
573    echo FINALIZE ATM !
574
575    IGCM_debug_PopStack "ATM_Finalize"
576}
577
578
579
580function ATM_Carbon_Update
581{
582    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
583
584    IGCM_debug_PushStack "ATM_Carbon_Update"
585
586    typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
587    typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
588    typeset PathCO2log
589    typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
590   
591    if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
592        ##--Initialization of fluxes to an undefined value at the first run
593        UndefinedValueCo2=-9999
594        InitPeriodCo2=0
595        InitDateBeginCo2=${UndefinedValueCo2}
596        InitYearCo2=$(( ${year} - 1 )) 
597        InitDateEndCo2=${InitYearCo2}1231
598        fCO2_ff=${UndefinedValueCo2} 
599        CO2SBG=${UndefinedValueCo2}
600        CO2LU=${UndefinedValueCo2}
601        CO2MBG=${UndefinedValueCo2}
602        CO2_ppm_prec=${UndefinedValueCo2}
603        # Get the initial value of atmosp. pco2
604        CO2_ppm=${lmdz_UserChoices_co2_init}
605       
606        IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
607        IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
608       
609        # Save CO2 values in ExeCpuLog variable contents 5 fields
610        echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
611            gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
612                              $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
613       
614        # Get the path where the log file co2.log is
615        PathCO2log=${SUBMIT_DIR} 
616        # Get Previous line in co2.log
617        PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
618       
619    else
620       
621        # NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
622        # !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
623        #SubmitRestartPath=
624        if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
625            IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
626            PathCO2log=${config_ATM_SubmitRestartPath}
627            Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
628            PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
629           
630            IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
631            IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
632           
633            # Save Last Line of control in new co2.log file
634            InitPeriodCo2=0   
635            InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $2}' )
636            InitDateEndCo2=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $3}' )
637            fCO2_ff=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $6}' )
638            CO2SBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $8}' )
639            CO2LU=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $9}' )
640            CO2MBG=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $7}' )
641            CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $5}' )
642            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
643           
644            echo "${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)}' >> ${SUBMIT_DIR}/co2.log
647        else
648           # Get restart line in co2.log
649            PathCO2log=${SUBMIT_DIR}
650            PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
651           # Get the value of atmosp. pco2 in co2.log
652            CO2_ppm=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
653        fi
654       
655    fi
656   
657    if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
658            # Modify co2_ppm in config.def only for historical run
659            # If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
660        IGCM_comp_modifyDefFile nonblocker config.def co2_ppm     ${CO2_ppm}
661    fi
662    IGCM_debug_PopStack "ATM_Carbon_Update"
663}
664
665
666function ATM_Carbon_Finalize
667{
668    # This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
669
670    IGCM_debug_PushStack "ATM_Carbon_Finalize"
671
672    typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
673   
674        # Fossil fuel emission
675    if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
676            # For Control, no fossil fuel emission :
677        fCO2_ff=0
678        echo "Fossil Fuel for control run  :" ${fCO2_ff}
679    else
680            # For historical, get the fossile fuel file :
681        fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
682        echo "Fossil Fuel for historical run  :" ${fCO2_ff}
683    fi
684   
685        # Get the value of ocean carbon flux
686    CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
687    CO2MBG=$( echo ${CO2MBG} | sed -e "s/ *//" )
688    echo "Ocean carbon flux  :" ${CO2MBG}
689   
690        # Get the value of land fluxes
691    set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
692    CO2SRF=$( echo ${CO2SBG_3V[0]} | sed -e "s/ *//" )
693    CO2LU=$( echo ${CO2SBG_3V[1]} | sed -e "s/ *//" )
694    CO2SBG=$( echo ${CO2SBG_3V[2]} | sed -e "s/ *//" )
695    echo "Land carbon flux (NEP)         :" ${CO2SRF}
696    echo "LU flux          (FLUC)        :" ${CO2LU}
697    echo "Total Land carbon flux (NBP)   :" ${CO2SBG}
698   
699        # Previous CO2
700    CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" | gawk -F '|' '{gsub(" ",""); print $4}' )
701    echo "Previous CO2  :" ${CO2_ppm_prec}
702   
703        # Formula
704    CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" | bc -l )
705    echo "New CO2  :" ${CO2_ppm}
706   
707        # Save CO2 values in ExeCpuLog variable contents 5 fields
708    echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" |   \
709        gawk '{printf("  %11d | %15s | %15s | %22.15g | %20.15g | %11.8g | %11.8g | %12.8g | %12.8g \n", \
710                           $1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
711   
712    IGCM_debug_PopStack "ATM_Carbon_Finalize"
713}
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