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source: CONFIG/UNIFORM/v6/LMDZOR_v6/GENERAL/DRIVER/lmdz.driver @ 2640

Last change on this file since 2640 was 2630, checked in by jgipsl, 9 years ago

Removed parameter grilles_gcm_netcdf not longer existing in LMDZ. Preivously
grilles_gcm_netcdf=y is now always the case.

Changed file path in comment.

File size: 28.7 KB

Line
1	#!/bin/ksh
2	#-----------------------------------------------------------------
3	function 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	#-----------------------------------------------------------------
149	function 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	## Determine from the variable ListOfComponents in config.card coupling to external models
414	## and set corresponding parameters in run.def
415	echo ListOfComponents now running : ${config_ListOfComponents[*]}
416
417	if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
418	echo "Activate ORCHIDEE, set VEGET=y in run.def"
419	IGCM_comp_modifyDefFile blocker run.def VEGET y
420	else
421	echo "No ORCHIDEE, set VEGET=n in run.def"
422	IGCM_comp_modifyDefFile blocker run.def VEGET n
423	fi
424
425	if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
426	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
427	IGCM_comp_modifyDefFile blocker run.def type_ocean couple
428	else
429	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
430	IGCM_comp_modifyDefFile blocker run.def type_ocean force
431	fi
432
433	if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
434	echo "Activate coupling to INCA, set type_trac=inca in run.def"
435	IGCM_comp_modifyDefFile blocker run.def type_trac inca
436	elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
437	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
438	IGCM_comp_modifyDefFile blocker run.def type_trac repr
439	IGCM_comp_modifyDefFile blocker run.def config_inca none
440	else
441	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
442	IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
443	IGCM_comp_modifyDefFile blocker run.def config_inca none
444	fi
445
446
447	# config.def : Activate direct radiative effect if ok_ade=y
448	if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
449	IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
450	else
451	IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
452	fi
453
454	# config.def : Activate indirect radiative effect if ok_aie=y
455	if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
456	IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
457	else
458	IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
459	fi
460
461	# config.def : Activate online aerosol coupled model if aerosol_couple=y
462	if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
463	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
464	else
465	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
466	fi
467
468	# config.def : Activate reading of ozone in climatology if read_climoz=2
469	if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
470	IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
471	else
472	IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0
473	fi
474
475	# config.def : Choose aerosol use in radiative effect
476	# type of coupled aerosol =1 (default) =2 => bc only =3 => pom only =4 => seasalt only
477	# =5 => dust only =6 => all aerosol
478	if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
479	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
480	else
481	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
482	fi
483
484	# config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
485	if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
486	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
487	else
488	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
489	fi
490
491	# guide.def : Activate nudging if ok_guide=y set in lmdz.card
492	if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
493	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide ${lmdz_UserChoices_ok_guide}
494	else
495	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
496	fi
497
498	## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
499	ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
500	if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
501	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
502	IGCM_sys_Mv gcm.def.tmp gcm.def
503	echo
504	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
505	echo
506	cat gcm.def
507	ByPass_hgardfou_teta=n
508	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
509	fi
510
511	## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
512	ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
513	if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
514	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
515	IGCM_sys_Mv gcm.def.tmp gcm.def
516	echo
517	IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
518	echo
519	cat gcm.def
520	ByPass_hgardfou_mats=n
521	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
522	fi
523
524	if [ X${lmdz_UserChoices_XIOS} = Xy ] ; then
525	# Add include of LMDZ context in iodef.xml
526	# In iodef.xml add on next line after "COMPONENT CONTEXT"
527	# <context id="LMDZ" src="./context_lmdz.xml"/>
528	echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
529	cp iodef.xml iodef.xml.tmp
530	sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
531	rm iodef.xml.tmp add.tmp
532
533	# Set ok_all_xml=y in run.def
534	IGCM_comp_modifyDefFile nonblocker run.def ok_all_xml y
535	else
536	# Deactivate ok_all_xml in run.def
537	IGCM_comp_modifyDefFile nonblocker run.def ok_all_xml n
538	fi
539
540	IGCM_debug_PopStack "ATM_Update"
541	}
542
543	#-----------------------------------
544	function ATM_Finalize
545	{
546	IGCM_debug_PushStack "ATM_Finalize"
547
548	# If the file exist, copy Bands_ file to PARAM/ in submit directory. This file will be used for the simulation.
549	# Copy also the same file into ATM/Restart at ARCHIVE directory for backup.
550	if [ -f Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ] ; then
551	if [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] ; then
552	IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
553	IGCM_sys_Put_Out Bands_${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}
554	elif [ ${CumulPeriod} -eq 1 ] && [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
555	# Special case : first period and no adjust => Save bands file with suffix _0
556	IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
557	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
558	fi
559	fi
560
561	# Add special treatement for CARBON CYCLE
562	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
563	ATM_Carbon_Finalize
564	fi
565
566	echo FINALIZE ATM !
567
568	IGCM_debug_PopStack "ATM_Finalize"
569	}
570
571
572
573	function ATM_Carbon_Update
574	{
575	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
576
577	IGCM_debug_PushStack "ATM_Carbon_Update"
578
579	typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
580	typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
581	typeset PathCO2log
582	typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
583
584	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
585	##--Initialization of fluxes to an undefined value at the first run
586	UndefinedValueCo2=-9999
587	InitPeriodCo2=0
588	InitDateBeginCo2=${UndefinedValueCo2}
589	InitYearCo2=$(( ${year} - 1 ))
590	InitDateEndCo2=${InitYearCo2}1231
591	fCO2_ff=${UndefinedValueCo2}
592	CO2SBG=${UndefinedValueCo2}
593	CO2LU=${UndefinedValueCo2}
594	CO2MBG=${UndefinedValueCo2}
595	CO2_ppm_prec=${UndefinedValueCo2}
596	# Get the initial value of atmosp. pco2
597	CO2_ppm=${lmdz_UserChoices_co2_init}
598
599	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
600	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
601
602	# Save CO2 values in ExeCpuLog variable contents 5 fields
603	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
604	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
605	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
606
607	# Get the path where the log file co2.log is
608	PathCO2log=${SUBMIT_DIR}
609	# Get Previous line in co2.log
610	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
611
612	else
613
614	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
615	# !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
616	#SubmitRestartPath=
617	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
618	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
619	PathCO2log=${config_ATM_SubmitRestartPath}
620	Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
621	PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
622
623	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
624	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
625
626	# Save Last Line of control in new co2.log file
627	InitPeriodCo2=0
628	InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $2}' )
629	InitDateEndCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $3}' )
630	fCO2_ff=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $6}' )
631	CO2SBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $8}' )
632	CO2LU=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $9}' )
633	CO2MBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $7}' )
634	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $5}' )
635	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
636
637	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
638	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
639	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
640	else
641	# Get restart line in co2.log
642	PathCO2log=${SUBMIT_DIR}
643	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
644	# Get the value of atmosp. pco2 in co2.log
645	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
646	fi
647
648	fi
649
650	if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
651	# Modify co2_ppm in config.def only for historical run
652	# If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
653	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm ${CO2_ppm}
654	fi
655	IGCM_debug_PopStack "ATM_Carbon_Update"
656	}
657
658
659	function ATM_Carbon_Finalize
660	{
661	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
662
663	IGCM_debug_PushStack "ATM_Carbon_Finalize"
664
665	typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
666
667	# Fossil fuel emission
668	if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
669	# For Control, no fossil fuel emission :
670	fCO2_ff=0
671	echo "Fossil Fuel for control run :" ${fCO2_ff}
672	else
673	# For historical, get the fossile fuel file :
674	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
675	echo "Fossil Fuel for historical run :" ${fCO2_ff}
676	fi
677
678	# Get the value of ocean carbon flux
679	CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
680	CO2MBG=$( echo ${CO2MBG} \| sed -e "s/ *//" )
681	echo "Ocean carbon flux :" ${CO2MBG}
682
683	# Get the value of land fluxes
684	set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
685	CO2SRF=$( echo ${CO2SBG_3V[0]} \| sed -e "s/ *//" )
686	CO2LU=$( echo ${CO2SBG_3V[1]} \| sed -e "s/ *//" )
687	CO2SBG=$( echo ${CO2SBG_3V[2]} \| sed -e "s/ *//" )
688	echo "Land carbon flux (NEP) :" ${CO2SRF}
689	echo "LU flux (FLUC) :" ${CO2LU}
690	echo "Total Land carbon flux (NBP) :" ${CO2SBG}
691
692	# Previous CO2
693	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
694	echo "Previous CO2 :" ${CO2_ppm_prec}
695
696	# Formula
697	CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" \| bc -l )
698	echo "New CO2 :" ${CO2_ppm}
699
700	# Save CO2 values in ExeCpuLog variable contents 5 fields
701	echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
702	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
703	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
704
705	IGCM_debug_PopStack "ATM_Carbon_Finalize"
706	}

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