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source: CONFIG/UNIFORM/v7/ICOLMDZOR_v7/GENERAL/DRIVER/lmdz.driver @ 4311

Last change on this file since 4311 was 4281, checked in by jgipsl, 5 years ago

Update config:

Before the component ATM was used for DYNAMCIO-LMDZphysics together. Now they have been seperated in 2 components: ICO for the icosahedral part which is here DYNAMCIO. ATM is kept for LMDZ phyiscs. Note that when running without DYNMACIO, the component ICO is not present and the component ATM represents both LMDZ dynamics and physics.

lmdz.driver and lmdz.card are copied from LMDZOR_v6.2. Small changes are done to work with or without DYNAMCIO.

.def files for LMDZ are copied from LMDZOR_v6.2

File size: 28.7 KB

Line
1	#!/bin/ksh
2	#-----------------------------------------------------------------
3	function 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	fi
21
22	##- LMDZ physics version
23	## Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
24	if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
25	LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
26	else
27	LMDZ_Physics=AP
28	fi
29	echo LMDZ physics version : ${LMDZ_Physics}
30
31	##- Create_etat0_limit version
32	## Define variable CREATE only if it is set in lmdz.card section UserChoices.
33	## This variable is only used in lmdz.card to choose input files.
34	if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
35	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
36	CREATE=${lmdz_UserChoices_CREATE}
37	echo create_etat0_limit version : ${CREATE}
38	fi
39
40
41	## - LMDZ choice of config.def file
42	## ConfType must be set in lmdz.card
43	ConfType=${lmdz_UserChoices_ConfType}
44
45	##- LMDZ output level, to be set in lmdz.card
46	if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
47	# OutLevel is not set. Take default value low.
48	OutLevel=low
49	else
50	OutLevel=${lmdz_UserChoices_OutLevel}
51	fi
52
53	##-- Output frequency purpose ....
54	##-- Initialisation ....
55	ok_mensuel=.FALSE.
56	ok_journe=.FALSE.
57	ok_hf=.FALSE.
58	ok_hf3h=.FALSE.
59	ok_hf3hm=.FALSE.
60	ok_stn=.FALSE.
61
62
63	case ${config_UserChoices_PeriodLength} in
64	1Y\|1y\|1M\|1m) ok_mensuel=.TRUE. ;;
65	5D\|5d\|1D\|1d) ok_journe=.TRUE. ;;
66	esac
67
68	for frequency in ${config_ATM_WriteFrequency} ; do
69	case ${frequency} in
70	1M\|1m) ok_mensuel=.TRUE. ;;
71	esac
72	case ${frequency} in
73	5D\|5d\|1D\|1d) ok_journe=.TRUE. ;;
74	esac
75	case ${frequency} in
76	HF\|hf) ok_hf=.TRUE. ;;
77	esac
78	case ${frequency} in
79	HF3h\|hf3h) ok_hf3h=.TRUE. ;;
80	esac
81	case ${frequency} in
82	HF3hm\|hf3hm) ok_hf3hm=.TRUE. ;;
83	esac
84	case ${frequency} in
85	STN\|stn) ok_stn=.TRUE. ;;
86	esac
87	done
88
89
90	## Read LMDZ_COSP_OK in lmdz.card
91	if [ X${lmdz_UserChoices_LMDZ_COSP_OK} = Xy ] ; then
92	## LMDZ_COSP_OK=y, now read all other COSP variables
93	## Read LMDZ_COSP_monthly in lmdz.card
94	if [ X${lmdz_UserChoices_LMDZ_COSP_monthly} = Xy ] ; then
95	LMDZ_COSP_monthly=.TRUE.
96	else
97	LMDZ_COSP_monthly=.FALSE.
98	fi
99	## Read LMDZ_COSP_daily in lmdz.card
100	if [ X${lmdz_UserChoices_LMDZ_COSP_daily} = Xy ] ; then
101	LMDZ_COSP_daily=.TRUE.
102	else
103	LMDZ_COSP_daily=.FALSE.
104	fi
105	## Read LMDZ_COSP_hf in lmdz.card
106	if [ X${lmdz_UserChoices_LMDZ_COSP_hf} = Xy ] ; then
107	LMDZ_COSP_hf=.TRUE.
108	else
109	LMDZ_COSP_hf=.FALSE.
110	fi
111	else
112	# LMDZ_COSP_OK=n : All cosp output are deactivated
113	LMDZ_COSP_monthly=.FALSE.
114	LMDZ_COSP_daily=.FALSE.
115	LMDZ_COSP_hf=.FALSE.
116	fi
117
118	## Read LMDZ_NMC_monthly in lmdz.card
119	if [ X${lmdz_UserChoices_LMDZ_NMC_monthly} = Xy ] ; then
120	LMDZ_NMC_monthly=.TRUE.
121	else
122	LMDZ_NMC_monthly=.FALSE.
123	fi
124
125	## Read LMDZ_NMC_daily in lmdz.card
126	if [ X${lmdz_UserChoices_LMDZ_NMC_daily} = Xy ] ; then
127	LMDZ_NMC_daily=.TRUE.
128	else
129	LMDZ_NMC_daily=.FALSE.
130	fi
131
132	## Read LMDZ_NMC_hf in lmdz.card
133	if [ X${lmdz_UserChoices_LMDZ_NMC_hf} = Xy ] ; then
134	LMDZ_NMC_hf=.TRUE.
135	else
136	LMDZ_NMC_hf=.FALSE.
137	fi
138
139
140	IGCM_debug_PopStack "ATM_Initialize"
141	}
142
143	#-----------------------------------------------------------------
144	function ATM_Update
145	{
146	IGCM_debug_PushStack "ATM_Update"
147
148	##-- GHG forcing :
149	## If forcing file exist in run directory, read values for the current year
150	## and set in config.def. If not use the default value set in config.def
151
152	# Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
153	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)"
154	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"
155	if [ -f SOLARANDVOLCANOES.txt ] ; then
156	value=`grep Annee_${year} SOLARANDVOLCANOES.txt \| awk -F= '{print $2}'`
157	if [ X"${value}" = X ] ; then
158	# The grep returned empty variable, stop execution
159	IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
160	IGCM_debug_Verif_Exit
161	fi
162	else
163	value=DEFAULT
164	fi
165	IGCM_comp_modifyDefFile nonblocker config.def solaire $value
166
167	# Read value for eccentricity from file Eccentricity.txt. If file not existing, take DEFAULT value from file.
168	if [ -f Eccentricity.txt ] ; then
169	value=`grep Annee_${year} Eccentricity.txt \| awk -F= '{print $2}'`
170	if [ X"${value}" = X ] ; then
171	# The grep returned empty variable, stop execution
172	IGCM_debug_Exit "The file Eccentricity.txt do not contain the current year."
173	IGCM_debug_Verif_Exit
174	fi
175	else
176	value=DEFAULT
177	fi
178	IGCM_comp_modifyDefFile nonblocker config.def R_ecc $value
179
180	# Read value for obliquity from file Obliquity.txt. If file not existing, take DEFAULT value from file.
181	if [ -f Obliquity.txt ] ; then
182	value=`grep Annee_${year} Obliquity.txt \| awk -F= '{print $2}'`
183	if [ X"${value}" = X ] ; then
184	# The grep returned empty variable, stop execution
185	IGCM_debug_Exit "The file Obliquity.txt do not contain the current year."
186	IGCM_debug_Verif_Exit
187	fi
188	else
189	value=DEFAULT
190	fi
191	IGCM_comp_modifyDefFile nonblocker config.def R_incl $value
192
193	# Read value for perihelie from file Perihelie.txt. If file not existing, take DEFAULT value from file.
194	if [ -f Perihelie.txt ] ; then
195	value=`grep Annee_${year} Perihelie.txt \| awk -F= '{print $2}'`
196	if [ X"${value}" = X ] ; then
197	# The grep returned empty variable, stop execution
198	IGCM_debug_Exit "The file Perihelie.txt do not contain the current year."
199	IGCM_debug_Verif_Exit
200	fi
201	else
202	value=DEFAULT
203	fi
204	IGCM_comp_modifyDefFile nonblocker config.def R_peri $value
205
206	# Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
207	# Calculate co2_ppm_per as co2_ppm*4.
208	if [ -f CO2.txt ] ; then
209	value=`grep Annee_${year} CO2.txt \| awk -F= '{print $2}'`
210	if [ X"${value}" = X ] ; then
211	# The grep returned empty variable, stop execution
212	IGCM_debug_Exit "The file CO2.txt do not contain the current year."
213	IGCM_debug_Verif_Exit
214	fi
215	value4=`grep Annee_${year} CO2.txt \| awk -F= '{print $2 * 4}'`
216	else
217	value=DEFAULT
218	value4=DEFAULT
219	fi
220	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
221	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm_per $value4
222
223
224	# Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
225	if [ -f CH4.txt ] ; then
226	value=`grep Annee_${year} CH4.txt \| awk -F= '{print $2}'`
227	if [ X"${value}" = X ] ; then
228	# The grep returned empty variable, stop execution
229	IGCM_debug_Exit "The file CH4.txt do not contain the current year."
230	IGCM_debug_Verif_Exit
231	fi
232	else
233	value=DEFAULT
234	fi
235	IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
236
237
238	# Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
239	if [ -f N2O.txt ] ; then
240	value=`grep Annee_${year} N2O.txt \| awk -F= '{print $2}'`
241	if [ X"${value}" = X ] ; then
242	# The grep returned empty variable, stop execution
243	IGCM_debug_Exit "The file N2O.txt do not contain the current year."
244	IGCM_debug_Verif_Exit
245	fi
246	else
247	value=DEFAULT
248	fi
249	IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
250
251	# Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
252	if [ -f CFC11.txt ] ; then
253	value=`grep Annee_${year} CFC11.txt \| awk -F= '{print $2}'`
254	if [ X"${value}" = X ] ; then
255	# The grep returned empty variable, stop execution
256	IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
257	IGCM_debug_Verif_Exit
258	fi
259	else
260	value=DEFAULT
261	fi
262	IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
263
264
265	# Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
266	if [ -f CFC12.txt ] ; then
267	value=`grep Annee_${year} CFC12.txt \| awk -F= '{print $2}'`
268	if [ X"${value}" = X ] ; then
269	# The grep returned empty variable, stop execution
270	IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
271	IGCM_debug_Verif_Exit
272	fi
273	else
274	value=DEFAULT
275	fi
276	IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
277
278
279	## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
280	LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
281	IGCM_debug_Print 3 "LMDZ_t_coupl " ${LMDZ_t_coupl}
282	IGCM_comp_modifyDefFile nonblocker config.def t_coupl ${LMDZ_t_coupl}
283
284	##-- Add special treatement for CARBON CYCLE
285	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
286	ATM_Carbon_Update
287	fi
288
289
290	##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
291	## COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
292	if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] && [ ${year} -ge 1979 ]) ; then
293	LMDZ_COSP_daily=.TRUE.
294	fi
295
296	## Modifiy
297	IGCM_comp_modifyXmlFile nonblocker file_def_histmth_lmdz.xml histmth enabled ${ok_mensuel}
298
299	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday enabled ${ok_journe}
300
301	if [ X${OutLevel} = Xlow ] \|\| [ X${OutLevel} = Xmedium ] ; then
302	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 2
303	else
304	IGCM_comp_modifyXmlFile nonblocker file_def_histday_lmdz.xml histday output_level 5
305	fi
306
307	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf enabled ${ok_hf}
308
309	if [ X${OutLevel} = Xlow ] ; then
310	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 5
311	elif [ X${OutLevel} = Xmedium ] ; then
312	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 6
313	elif [ X${OutLevel} = Xhigh ] ; then
314	IGCM_comp_modifyXmlFile nonblocker file_def_histhf_lmdz.xml histhf output_level 7
315	fi
316
317	IGCM_comp_modifyXmlFile nonblocker file_def_histhf3h_lmdz.xml histhf3h enabled ${ok_hf3h}
318	IGCM_comp_modifyXmlFile nonblocker file_def_histhf3hm_lmdz.xml histhf3hm enabled ${ok_hf3hm}
319
320	IGCM_comp_modifyXmlFile nonblocker file_def_histstn_lmdz.xml histstn enabled ${ok_stn}
321
322	IGCM_comp_modifyXmlFile nonblocker file_def_histmthNMC_lmdz.xml histmthNMC enabled ${LMDZ_NMC_monthly}
323	IGCM_comp_modifyXmlFile nonblocker file_def_histdayNMC_lmdz.xml histdayNMC enabled ${LMDZ_NMC_daily}
324	IGCM_comp_modifyXmlFile nonblocker file_def_histhfNMC_lmdz.xml histhfNMC enabled ${LMDZ_NMC_hf}
325
326	IGCM_comp_modifyXmlFile nonblocker file_def_histmthCOSP_lmdz.xml histmthCOSP enabled ${LMDZ_COSP_monthly}
327	IGCM_comp_modifyXmlFile nonblocker file_def_histdayCOSP_lmdz.xml histdayCOSP enabled ${LMDZ_COSP_daily}
328	IGCM_comp_modifyXmlFile nonblocker file_def_histhfCOSP_lmdz.xml histhfCOSP enabled ${LMDZ_COSP_hf}
329
330	# Activate the histstrataer output file only for configuration with interactive stratospheric aersols
331	# done by setting the key word LMDZ_strataero=y in lmdz.card
332	if [ X${lmdz_UserChoices_LMDZ_strataero} = Xy ] ; then
333	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .TRUE.
334	else
335	IGCM_comp_modifyXmlFile nonblocker file_def_histstrataer_lmdz.xml histstrataer enabled .FALSE.
336	fi
337
338
339	## run.def parameters
340
341
342	##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
343
344	if [ ${CumulPeriod} -eq 1 ] ; then
345	IGCM_comp_modifyDefFile blocker run.def raz_date 1
346	else
347	IGCM_comp_modifyDefFile blocker run.def raz_date 0
348	fi
349
350	##-- Calendar type for LMDZ and create_etat0_limit
351	# calend is read from both LMDZ dynamics and physics parts of the model
352	case ${config_UserChoices_CalendarType} in
353	leap\|gregorian)
354	IGCM_comp_modifyDefFile blocker run.def calend gregorian ;;
355	noleap)
356	IGCM_comp_modifyDefFile blocker run.def calend earth_365d ;;
357	360d)
358	IGCM_comp_modifyDefFile blocker run.def calend earth_360d ;;
359	*)
360	IGCM_comp_modifyDefFile blocker run.def calend earth_360d ;;
361	esac
362
363
364	## -- Modify more calendar related variables. These variables are only read by LMDZ dynamics part.
365	# Set them to dummy if component ICO (DYNAMICO) is set in config.card.
366	if [ X${config_ListOfComponents_ICO} = X ] ; then
367	# Following variables are read by LMDZ dynamics
368	IGCM_comp_modifyDefFile blocker run.def dayref ${InitDay}
369	IGCM_comp_modifyDefFile blocker run.def nday ${PeriodLengthInDays}
370
371	# Set anneeref different for gcm and ce0l
372	# Test if executable create_etat0_limit is present and lmdz.x is not present
373	if [ -f create_etat0_limit* ] \|\| [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
374	# for case ce0l : always take current year
375	IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
376
377	# Temporary, set use_filtre_fft=n because we now use dyn3d for ce0l version where fft is not implemented.
378	# In more recent versions of LMDZ, this will not be needed.
379	IGCM_comp_modifyDefFile force run.def use_filtre_fft n
380	else
381	# for case gcm : take first year of simulation
382	IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
383	fi
384
385	else
386	# ICO is found in config.card which means that DYNMAICO is activated.
387	# Set these variables to DUMMY. They will not be read.
388	IGCM_comp_modifyDefFile blocker run.def dayref DUMMY
389	IGCM_comp_modifyDefFile blocker run.def nday DUMMY
390	IGCM_comp_modifyDefFile blocker run.def anneeref DUMMY
391	IGCM_comp_modifyDefFile force run.def use_filtre_fft DUMMY
392	fi
393
394	## Determine from the variable ListOfComponents in config.card coupling to external models
395	## and set corresponding parameters in run.def
396	echo ListOfComponents now running : ${config_ListOfComponents[*]}
397
398	if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
399	echo "Activate ORCHIDEE, set VEGET=y in run.def"
400	IGCM_comp_modifyDefFile blocker run.def VEGET y
401	else
402	echo "No ORCHIDEE, set VEGET=n in run.def"
403	IGCM_comp_modifyDefFile blocker run.def VEGET n
404	fi
405
406	if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
407	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
408	IGCM_comp_modifyDefFile blocker run.def type_ocean couple
409	else
410	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
411	IGCM_comp_modifyDefFile nonblocker run.def type_ocean force
412	fi
413
414	if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
415	echo "Activate coupling to INCA, set type_trac=inca in run.def"
416	IGCM_comp_modifyDefFile blocker run.def type_trac inca
417	elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
418	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
419	IGCM_comp_modifyDefFile blocker run.def type_trac repr
420	IGCM_comp_modifyDefFile blocker run.def config_inca none
421	else
422	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
423	IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
424	IGCM_comp_modifyDefFile blocker run.def config_inca none
425	fi
426
427
428	# run.def : Activate the call to phytrac
429	if [ ! X${lmdz_UserChoices_iflag_phytrac} = X ]; then
430	IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac ${lmdz_UserChoices_iflag_phytrac}
431	else
432	IGCM_comp_modifyDefFile nonblocker run.def iflag_phytrac 0
433	fi
434
435	# physiq.def : Activate the call to phytrac
436	if [ ! X${lmdz_UserChoices_ok_bug_cv_trac} = X ]; then
437	IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac ${lmdz_UserChoices_ok_bug_cv_trac}
438	else
439	IGCM_comp_modifyDefFile nonblocker physiq.def ok_bug_cv_trac n
440	fi
441
442	# config.def : Activate direct radiative effect if ok_ade=y
443	if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
444	IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
445	else
446	IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
447	fi
448
449	# config.def : Activate indirect radiative effect if ok_aie=y
450	if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
451	IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
452	else
453	IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
454	fi
455
456	# config.def : Activate online aerosol coupled model if aerosol_couple=y
457	if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
458	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
459	else
460	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
461	fi
462
463	# config.def : Activate online Ozone chemistry coupled model if chemistry_couple=y
464	if [ ! X${lmdz_UserChoices_chemistry_couple} = X ]; then
465	IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple ${lmdz_UserChoices_chemistry_couple}
466	else
467	IGCM_comp_modifyDefFile nonblocker config.def chemistry_couple n
468	fi
469
470	# config.def : Activate reading of ozone in climatology if read_climoz=2
471	if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
472	IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
473	else
474	IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0
475	fi
476
477	# config.def : Choose aerosol use in radiative effect
478	# type of coupled aerosol =1 (default) =2 => bc only =3 => pom only =4 => seasalt only
479	# =5 => dust only =6 => all aerosol
480	if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
481	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
482	else
483	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
484	fi
485
486	# config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
487	if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
488	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
489	else
490	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
491	fi
492
493	# config.def : Activate COSP
494	if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ]; then
495	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp ${lmdz_UserChoices_LMDZ_COSP_OK}
496	else
497	IGCM_comp_modifyDefFile nonblocker config.def ok_cosp n
498	fi
499
500	# config.def : Modify parameter pmagic if it is set in lmdz.card
501	if [ ! X${lmdz_UserChoices_pmagic} = X ]; then
502	IGCM_comp_modifyDefFile nonblocker config.def pmagic ${lmdz_UserChoices_pmagic}
503	else
504	# Take default value set in config.def
505	IGCM_comp_modifyDefFile nonblocker config.def pmagic DEFAULT
506	fi
507
508	# physiq.def : Modify parameter tau_gl if it is set in lmdz.card
509	if [ ! X${lmdz_UserChoices_tau_gl} = X ]; then
510	IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl ${lmdz_UserChoices_tau_gl}
511	else
512	# Take default value set in physiq.def
513	IGCM_comp_modifyDefFile nonblocker physiq.def tau_gl DEFAULT
514	fi
515
516
517	# guide.def : Activate nudging if ok_guide=y set in lmdz.card
518	if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
519	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide ${lmdz_UserChoices_ok_guide}
520	else
521	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
522	fi
523
524
525	# Specific ByPass option only used with LMDZ dynamcis (without DYNMAICO)
526	if [ X${config_ListOfComponents_ICO} = X ] ; then
527
528	## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
529	ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
530	if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
531	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
532	IGCM_sys_Mv gcm.def.tmp gcm.def
533	echo
534	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
535	echo
536	cat gcm.def
537	ByPass_hgardfou_teta=n
538	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
539	fi
540
541	## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
542	ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
543	if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
544	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
545	IGCM_sys_Mv gcm.def.tmp gcm.def
546	echo
547	IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
548	echo
549	cat gcm.def
550	ByPass_hgardfou_mats=n
551	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
552	fi
553	fi
554
555
556	# Add include of LMDZ context in iodef.xml
557	# In iodef.xml add on the next line after "COMPONENT CONTEXT"
558	echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
559	# Add inclusion of file context_input_lmdz.xml if this file exists
560	if [ -f context_input_lmdz.xml ] ; then
561	echo '<context id="LMDZ" src="./context_input_lmdz.xml"/>' >> add.tmp
562	fi
563	# Include xml files for output configuration if running with workflow CMIP6
564	if [ X"$( echo ${config_UserChoices_ExpType} \| grep CMIP6 )" != "X" ] ; then
565	echo '<context id="LMDZ" src="./ping_lmdz.xml"/>' >> add.tmp
566	echo '<context id="LMDZ" src="./dr2xml_lmdz.xml"/>' >> add.tmp
567	fi
568	cp iodef.xml iodef.xml.tmp
569	sed -e "/COMPONENT CONTEXT/r add.tmp" iodef.xml.tmp > iodef.xml
570	rm iodef.xml.tmp add.tmp
571
572	#Long Name as global attribute (if LongName is not empty)
573	if [ ! "X${config_UserChoices_LongName}" = "X" ] ; then
574	listfile=$(ls file_def*lmdz.xml)
575	echo "<variable id=\"LongName\" type=\"string\">${config_UserChoices_LongName}</variable>" > add.tmp
576	for file in ${listfile}
577	do
578	cp ${file} ${file}.tmp
579	sed -e "/<file id/r add.tmp" \
580	${file}.tmp > ${file}
581	rm ${file}.tmp
582	done
583	rm add.tmp
584	fi
585
586	IGCM_debug_PopStack "ATM_Update"
587	}
588
589	#-----------------------------------
590	function ATM_Finalize
591	{
592	IGCM_debug_PushStack "ATM_Finalize"
593
594	# Add special treatement for CARBON CYCLE
595	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
596	ATM_Carbon_Finalize
597	fi
598
599	echo FINALIZE ATM !
600
601	IGCM_debug_PopStack "ATM_Finalize"
602	}
603
604
605
606	function ATM_Carbon_Update
607	{
608	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
609
610	IGCM_debug_PushStack "ATM_Carbon_Update"
611
612	typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
613	typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
614	typeset PathCO2log
615	typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
616
617	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
618	##--Initialization of fluxes to an undefined value at the first run
619	UndefinedValueCo2=-9999
620	InitPeriodCo2=0
621	InitDateBeginCo2=${UndefinedValueCo2}
622	InitYearCo2=$(( ${year} - 1 ))
623	InitDateEndCo2=${InitYearCo2}1231
624	fCO2_ff=${UndefinedValueCo2}
625	CO2SBG=${UndefinedValueCo2}
626	CO2LU=${UndefinedValueCo2}
627	CO2MBG=${UndefinedValueCo2}
628	CO2_ppm_prec=${UndefinedValueCo2}
629	# Get the initial value of atmosp. pco2
630	CO2_ppm=${lmdz_UserChoices_co2_init}
631
632	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
633	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
634
635	# Save CO2 values in ExeCpuLog variable contents 5 fields
636	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
637	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
638	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
639
640	# Get the path where the log file co2.log is
641	PathCO2log=${SUBMIT_DIR}
642	# Get Previous line in co2.log
643	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
644
645	else
646
647	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
648	# !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
649	#SubmitRestartPath=
650	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
651	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
652	PathCO2log=${config_ATM_SubmitRestartPath}
653	Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
654	PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
655
656	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
657	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
658
659	# Save Last Line of control in new co2.log file
660	InitPeriodCo2=0
661	InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $2}' )
662	InitDateEndCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $3}' )
663	fCO2_ff=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $6}' )
664	CO2SBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $8}' )
665	CO2LU=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $9}' )
666	CO2MBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $7}' )
667	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $5}' )
668	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
669
670	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
671	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
672	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
673	else
674	# Get restart line in co2.log
675	PathCO2log=${SUBMIT_DIR}
676	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
677	# Get the value of atmosp. pco2 in co2.log
678	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
679	fi
680
681	fi
682
683	if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
684	# Modify co2_ppm in config.def only for historical run
685	# If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
686	IGCM_comp_modifyDefFile force config.def co2_ppm ${CO2_ppm}
687	fi
688	IGCM_debug_PopStack "ATM_Carbon_Update"
689	}
690
691
692	function ATM_Carbon_Finalize
693	{
694	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
695
696	IGCM_debug_PushStack "ATM_Carbon_Finalize"
697
698	typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
699
700	# Fossil fuel emission
701	if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
702	# For Control, no fossil fuel emission :
703	fCO2_ff=0
704	echo "Fossil Fuel for control run :" ${fCO2_ff}
705	else
706	# For historical, get the fossile fuel file :
707	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
708	echo "Fossil Fuel for historical run :" ${fCO2_ff}
709	fi
710
711	# Get the value of ocean carbon flux
712	CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
713	CO2MBG=$( echo ${CO2MBG} \| sed -e "s/ *//" )
714	echo "Ocean carbon flux :" ${CO2MBG}
715
716	# Get the value of land fluxes
717	set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
718	CO2SRF=$( echo ${CO2SBG_3V[0]} \| sed -e "s/ *//" )
719	CO2LU=$( echo ${CO2SBG_3V[1]} \| sed -e "s/ *//" )
720	CO2SBG=$( echo ${CO2SBG_3V[2]} \| sed -e "s/ *//" )
721	echo "Land carbon flux (NEP) :" ${CO2SRF}
722	echo "LU flux (FLUC) :" ${CO2LU}
723	echo "Total Land carbon flux (NBP) :" ${CO2SBG}
724
725	# Previous CO2
726	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
727	echo "Previous CO2 :" ${CO2_ppm_prec}
728
729	# Formula
730	CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" \| bc -l )
731	echo "New CO2 :" ${CO2_ppm}
732
733	# Save CO2 values in ExeCpuLog variable contents 5 fields
734	echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
735	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
736	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
737
738	IGCM_debug_PopStack "ATM_Carbon_Finalize"
739	}

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