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source: CONFIG/UNIFORM/v6/LMDZOR_v6/GENERAL/DRIVER/lmdz.driver @ 2333

Last change on this file since 2333 was 2333, checked in by jgipsl, 10 years ago

Update to use IGCM_comp_modifyDefFile instead of local functions LMDZ_sed/LMDZ_sed_default/ORCHIDEE_sed.

Now this configuration must be used with libIGCM trunk rev 1073 or more recent.

File size: 31.0 KB

Line
1	#!/bin/ksh
2	#-----------------------------------------------------------------
3	function LMDZ_sed_xml
4	{
5	# Usage : LMDZ_sed_xml xml_file output_file attribute value
6	# In file xml_file modify at the line containing id="output_file" the attribute "attribute=xxx" into "attribute=value"
7
8	IGCM_debug_PushStack "LMDZ_sed_xml"
9	# Test if the fichier exist
10	if [ ! -f ${1} ] ; then
11	echo "WARNING : ${1} file does not exist. Following will not be done : LMDZ_sed_xml : ${1} ${2} ${3} ${4}"
12	IGCM_debug_PopStack "LMDZ_sed_xml"
13	return
14	fi
15	sed -e "/id=\"${2}\"/s/\(${3}=\"\)[^\"]*\(\"\)/\1${4}\2/" ${1} > ${1}.tmp
16	RET=$?
17	echo "LMDZ_sed_xml : ${1} ${2} ${3} ${4}"
18	\mv ${1}.tmp ${1}
19	IGCM_debug_PopStack "LMDZ_sed_xml"
20	return $RET
21	}
22
23	function ATM_Initialize
24	{
25	IGCM_debug_PushStack "ATM_Initialize"
26
27	RESOL_ATM=$( echo $RESOL \| awk "-Fx" '{print $2}' \| awk "-F-" '{print $1}')
28
29	[ -f ${SUBMIT_DIR}/../.resol ] && eval $(grep RESOL_ATM_3D ${SUBMIT_DIR}/../.resol) \|\| RESOL_ATM_3D=96x95x39
30
31	RESOL_ATM_Z=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $3}' )
32	RESOL_ATM_X=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $1}' )
33	RESOL_ATM_Y=$( echo ${RESOL_ATM_3D} \| awk "-Fx" '{print $2}' )
34	RESOL_ATM_XY="${RESOL_ATM_X}x${RESOL_ATM_Y}"
35	FreqCoupling=${oasis_UserChoices_FreqCoupling:-86400}
36
37	##-- Calendar type for LMDZ and create_etat0_limit
38	case ${config_UserChoices_CalendarType} in
39	leap\|gregorian)
40	CalendarTypeForLmdz=earth_366d
41	CalendarTypeForCreate=gregorian;;
42	noleap)
43	CalendarTypeForLmdz=earth_365d
44	CalendarTypeForCreate=${CalendarTypeForLmdz};;
45	360d)
46	CalendarTypeForLmdz=earth_360d
47	CalendarTypeForCreate=${CalendarTypeForLmdz};;
48	*)
49	CalendarTypeForLmdz=earth_360d
50	CalendarTypeForCreate=${CalendarTypeForLmdz}
51	esac
52
53	##- LMDZ physics version
54	## Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
55	if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
56	LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
57	else
58	LMDZ_Physics=AP
59	fi
60	echo LMDZ physics version : ${LMDZ_Physics}
61
62	##- Create_etat0_limit version
63	## Define variable CREATE only if it is set in lmdz.card section UserChoices.
64	## This variable is only used in lmdz.card to choose input files.
65	if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
66	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
67	CREATE=${lmdz_UserChoices_CREATE}
68	echo create_etat0_limit version : ${CREATE}
69	fi
70
71
72	## - LMDZ choice of config.def file
73	## ConfType must be set in lmdz.card
74	ConfType=${lmdz_UserChoices_ConfType}
75
76	##- LMDZ output level, to be set in lmdz.card
77	if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
78	# OutLevel is not set. Take default value low.
79	OutLevel=low
80	else
81	OutLevel=${lmdz_UserChoices_OutLevel}
82	fi
83
84	##-- Output frequency purpose ....
85	##-- Initialisation ....
86	ok_mensuel=n
87	ok_journe=n
88	ok_hf=n
89	ok_hf3h=n
90	ok_hf3hm=n
91	ok_stn=n
92
93	case ${config_UserChoices_PeriodLength} in
94	1Y\|1y\|1M\|1m) ok_mensuel=y ;;
95	5D\|5d\|1D\|1d) ok_journe=y ;;
96	esac
97
98	for frequency in ${config_ATM_WriteFrequency} ; do
99	case ${frequency} in
100	1M\|1m) ok_mensuel=y ;;
101	esac
102	case ${frequency} in
103	5D\|5d\|1D\|1d) ok_journe=y ;;
104	esac
105	case ${frequency} in
106	HF\|hf) ok_hf=y ;;
107	esac
108	case ${frequency} in
109	HF3h\|hf3h) ok_hf3h=y ;;
110	esac
111	case ${frequency} in
112	HF3hm\|hf3hm) ok_hf3hm=y ;;
113	esac
114	case ${frequency} in
115	STN\|stn) ok_stn=y ;;
116	esac
117	done
118
119	## Read LMDZ_NbPeriod_adjust option in lmdz.card
120	if [ X"${lmdz_UserChoices_LMDZ_NbPeriod_adjust}" = X"" ] ; then
121	# The variable is not in lmdz.card, set default value
122	LMDZ_NbPeriod_adjust=0
123	else
124	LMDZ_NbPeriod_adjust=${lmdz_UserChoices_LMDZ_NbPeriod_adjust}
125	fi
126
127	if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
128	LMDZ_Bands_file_name=${lmdz_UserChoices_LMDZ_Bands_file_name}
129	fi
130
131
132	## Read LMDZ_COSP_OK in lmdz.card
133	if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ] ; then
134	LMDZ_COSP_OK=${lmdz_UserChoices_LMDZ_COSP_OK}
135	else
136	LMDZ_COSP_OK=n
137	fi
138	## Read LMDZ_COSP_monthly in lmdz.card
139	if [ ! X${lmdz_UserChoices_LMDZ_COSP_monthly} = X ] ; then
140	LMDZ_COSP_monthly=${lmdz_UserChoices_LMDZ_COSP_monthly}
141	else
142	LMDZ_COSP_monthly=n
143	fi
144	## Read LMDZ_COSP_daily in lmdz.card
145	if [ ! X${lmdz_UserChoices_LMDZ_COSP_daily} = X ] ; then
146	LMDZ_COSP_daily=${lmdz_UserChoices_LMDZ_COSP_daily}
147	else
148	LMDZ_COSP_daily=n
149	fi
150	## Read LMDZ_COSP_hf in lmdz.card
151	if [ ! X${lmdz_UserChoices_LMDZ_COSP_hf} = X ] ; then
152	LMDZ_COSP_hf=${lmdz_UserChoices_LMDZ_COSP_hf}
153	else
154	LMDZ_COSP_hf=n
155	fi
156
157	## Read LMDZ_NMC_monthly in lmdz.card
158	if [ ! X${lmdz_UserChoices_LMDZ_NMC_monthly} = X ] ; then
159	LMDZ_NMC_monthly=${lmdz_UserChoices_LMDZ_NMC_monthly}
160	else
161	LMDZ_NMC_monthly=n
162	fi
163
164	## Read LMDZ_NMC_daily in lmdz.card
165	if [ ! X${lmdz_UserChoices_LMDZ_NMC_daily} = X ] ; then
166	LMDZ_NMC_daily=${lmdz_UserChoices_LMDZ_NMC_daily}
167	else
168	LMDZ_NMC_daily=n
169	fi
170
171	## Read LMDZ_NMC_hf in lmdz.card
172	if [ ! X${lmdz_UserChoices_LMDZ_NMC_hf} = X ] ; then
173	LMDZ_NMC_hf=${lmdz_UserChoices_LMDZ_NMC_hf}
174	else
175	LMDZ_NMC_hf=n
176	fi
177
178
179	IGCM_debug_PopStack "ATM_Initialize"
180	}
181
182	#-----------------------------------------------------------------
183	function ATM_Update
184	{
185	IGCM_debug_PushStack "ATM_Update"
186
187
188	case ${config_UserChoices_PeriodLength} in
189	Y\|y)
190	LMDZ_ecrit_ISCCP=30.
191	LMDZ_periodav=30.
192	if [ "${config_UserChoices_CalendarType}" != "360d" ] ; then
193	echo Do not consider following warning if your running create_etat0_limit :
194	echo WARNING !!! For lmdz : calendartype in config.card. PeriodLength=1Y allowed only for CalendarType=360d
195	fi
196	;;
197	*)
198	LMDZ_ecrit_ISCCP=${PeriodLengthInDays}.
199	LMDZ_periodav=${PeriodLengthInDays}.
200	;;
201	esac
202
203	##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
204	if [ ${CumulPeriod} -eq 1 ] ; then
205	RAZ_DATE=1
206	else
207	RAZ_DATE=0
208	fi
209
210	## Algorithme for special treatment for Bands_xxx file
211	## For CumulPeriod=1 ;
212	## IF NbPeriod_Adjust = 0 ; set LMDZ_adjust=n
213	## IF LMDZ_Bands_file_name was given in lmdz.card THEN Get Bands file directly from server. Store it later with _0 suffix.
214	## IF no LMDZ_Bands_file_name was given, start without Bands file. Store it later with _0 suffix.
215	## ELSE set LMDZ_adjust=y ; start without Bands file ; Store it later in PARAM/ directory in submit directory with suffix _1 ;
216	##
217	## For CumulPeriod=2 to LMDZ_NbPeriod_adjust ;
218	## Get Bands file from PARAM/ in submit directory (CumulPeriod-1) ; set LMDZ_adjust=y ; Store Bands file in PARAM/ ;
219	##
220	## For CumulPeriod > LMDZ_NbPeriod_adjust ; LMDZ_adjust=n ; Get Bands file from PARAM/ ; Do not store ;
221
222	if [ ${CumulPeriod} -eq 1 ] ; then
223	if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
224	if [ ! X${LMDZ_Bands_file_name} = X ] ; then
225	IGCM_sys_Get ${LMDZ_Bands_file_name} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
226	IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
227	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"
228	fi
229	fi
230	fi
231
232	LMDZ_adjust=n
233	[ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && LMDZ_adjust=y
234
235	RefPeriod=${LMDZ_NbPeriod_adjust} #0 to use a Bands file from Restart
236	[ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && (( RefPeriod = ${CumulPeriod} - 1 ))
237
238	# Get Bands file from PARAM directory if file exist
239	if ( [ ${CumulPeriod} -gt 1 ] && [ -f ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} ] ) ; then
240	IGCM_sys_Cp ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
241	IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
242	fi
243
244	##-- GHG forcing :
245	## If forcing file exist in run directory, read values for the current year
246	## and set in config.def. If not use the default value set in config.def
247
248	# Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
249	if [ -f SOLARANDVOLCANOES.txt ] ; then
250	value=`grep Annee_${year} SOLARANDVOLCANOES.txt \| awk -F= '{print $2}'`
251	if [ X"${value}" = X ] ; then
252	# The grep returned empty variable, stop execution
253	IGCM_debug_Exit "The file SOLARANDVOLCANOES.txt do not contain the current year."
254	IGCM_debug_Verif_Exit
255	fi
256	else
257	value=DEFAULT
258	fi
259	IGCM_comp_modifyDefFile nonblocker config.def solaire $value
260
261
262	# Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
263	if [ -f CO2.txt ] ; then
264	value=`grep Annee_${year} CO2.txt \| awk -F= '{print $2}'`
265	if [ X"${value}" = X ] ; then
266	# The grep returned empty variable, stop execution
267	IGCM_debug_Exit "The file CO2.txt do not contain the current year."
268	IGCM_debug_Verif_Exit
269	fi
270	else
271	value=DEFAULT
272	fi
273	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm $value
274
275
276	# Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
277	if [ -f CH4.txt ] ; then
278	value=`grep Annee_${year} CH4.txt \| awk -F= '{print $2}'`
279	if [ X"${value}" = X ] ; then
280	# The grep returned empty variable, stop execution
281	IGCM_debug_Exit "The file CH4.txt do not contain the current year."
282	IGCM_debug_Verif_Exit
283	fi
284	else
285	value=DEFAULT
286	fi
287	IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
288
289
290	# Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
291	if [ -f N2O.txt ] ; then
292	value=`grep Annee_${year} N2O.txt \| awk -F= '{print $2}'`
293	if [ X"${value}" = X ] ; then
294	# The grep returned empty variable, stop execution
295	IGCM_debug_Exit "The file N2O.txt do not contain the current year."
296	IGCM_debug_Verif_Exit
297	fi
298	else
299	value=DEFAULT
300	fi
301	IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
302
303	# Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
304	if [ -f CFC11.txt ] ; then
305	value=`grep Annee_${year} CFC11.txt \| awk -F= '{print $2}'`
306	if [ X"${value}" = X ] ; then
307	# The grep returned empty variable, stop execution
308	IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
309	IGCM_debug_Verif_Exit
310	fi
311	else
312	value=DEFAULT
313	fi
314	IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
315
316
317	# Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
318	if [ -f CFC12.txt ] ; then
319	value=`grep Annee_${year} CFC12.txt \| awk -F= '{print $2}'`
320	if [ X"${value}" = X ] ; then
321	# The grep returned empty variable, stop execution
322	IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
323	IGCM_debug_Verif_Exit
324	fi
325	else
326	value=DEFAULT
327	fi
328	IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
329
330
331	## Coupling Time Step
332	LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-${lmdz_UserChoices_t_coupl}}
333	IGCM_debug_Print 3 "LMDZ_t_coupl " ${LMDZ_t_coupl}
334	IGCM_comp_modifyDefFile nonblocker config.def t_coupl ${LMDZ_t_coupl}
335
336	##-- Add special treatement for CARBON CYCLE
337	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
338	ATM_Carbon_Update
339	fi
340
341
342	##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
343	## COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
344	if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] && [ ${year} -ge 1979 ]) ; then
345	LMDZ_COSP_daily=y
346	fi
347
348
349	## output.def parameters
350	# columns in phys_output_filekeys refer to the filenames given in phys_out_filenames in output.def :
351	# histmth histday histhf histfh3h histhf3hm histstn
352	IGCM_comp_modifyDefFile nonblocker output.def phys_out_filekeys "${ok_mensuel} ${ok_journe} ${ok_hf} ${ok_hf3h} ${ok_hf3hm} ${ok_stn}"
353	IGCM_comp_modifyDefFile nonblocker output.def ecrit_ISCCP ${LMDZ_ecrit_ISCCP}
354	IGCM_comp_modifyDefFile nonblocker output.def ok_cosp ${LMDZ_COSP_OK}
355	IGCM_comp_modifyDefFile nonblocker output.def ok_mensuelCOSP ${LMDZ_COSP_monthly}
356	IGCM_comp_modifyDefFile nonblocker output.def ok_journeCOSP ${LMDZ_COSP_daily}
357	IGCM_comp_modifyDefFile nonblocker output.def ok_hfCOSP ${LMDZ_COSP_hf}
358	IGCM_comp_modifyDefFile nonblocker output.def ok_histNMC "${LMDZ_NMC_monthly} ${LMDZ_NMC_daily} ${LMDZ_NMC_hf}"
359
360	# XIOS XML definition
361	# Default init : files are desactivated
362	LMDZ_sed_xml file_def_histmth_lmdz.xml histmth enabled .FALSE.
363	LMDZ_sed_xml file_def_histday_lmdz.xml histday enabled .FALSE.
364	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf enabled .FALSE.
365	LMDZ_sed_xml file_def_histfh3h_lmdz.xml histfh3h enabled .FALSE.
366	LMDZ_sed_xml file_def_histhf3hm_lmdz.xml histfh3hm enabled .FALSE.
367	LMDZ_sed_xml file_def_histstn_lmdz.xml histstn enabled .FALSE.
368	LMDZ_sed_xml file_def_histmthNMC_lmdz.xml histmthNMC enabled .FALSE.
369	LMDZ_sed_xml file_def_histdayNMC_lmdz.xml histdayNMC enabled .FALSE.
370	LMDZ_sed_xml file_def_histhfNMC_lmdz.xml histhfNMC enabled .FALSE.
371	if [ X${lmdz_UserChoices_XIOS} = Xy ] ; then
372	# Default output level : 5
373	LMDZ_sed_xml file_def_histmth_lmdz.xml histmth output_level 5
374	LMDZ_sed_xml file_def_histday_lmdz.xml histday output_level 5
375	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf output_level 5
376	LMDZ_sed_xml file_def_histfh3h_lmdz.xml histfh3h output_level 5
377	LMDZ_sed_xml file_def_histhf3hm_lmdz.xml histfh3hm output_level 5
378	LMDZ_sed_xml file_def_histstn_lmdz.xml histstn output_level 5
379	LMDZ_sed_xml file_def_histmthNMC_lmdz.xml histmthNMC output_level 5
380	LMDZ_sed_xml file_def_histdayNMC_lmdz.xml histdayNMC output_level 5
381	LMDZ_sed_xml file_def_histhfNMC_lmdz.xml histhfNMC output_level 5
382	# Filling of XML files
383	if [ X${ok_mensuel} = Xy ] ; then
384	LMDZ_sed_xml file_def_histmth_lmdz.xml histmth enabled .TRUE.
385	LMDZ_sed_xml file_def_histmth_lmdz.xml histmth output_freq 1mo
386	LMDZ_sed_xml file_def_histmth_lmdz.xml histmth name histmth
387	fi
388	if [ X${ok_journe} = Xy ] ; then
389	LMDZ_sed_xml file_def_histday_lmdz.xml histday enabled .TRUE.
390	LMDZ_sed_xml file_def_histday_lmdz.xml histday output_freq 1d
391	LMDZ_sed_xml file_def_histday_lmdz.xml histday name histday
392	if [ X${OutLevel} = Xlow ] \|\| [ X${OutLevel} = Xmedium ] ; then
393	LMDZ_sed_xml file_def_histday_lmdz.xml histday output_level 2
394	fi
395	fi
396	if [ X${ok_hf} = Xy ] ; then
397	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf enabled .TRUE.
398	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf output_freq 6h
399	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf name histhf
400	if [ X${OutLevel} = Xlow ] ; then
401	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf output_level 2
402	fi
403	fi
404	if [ X${ok_hf3h} = Xy ] ; then
405	LMDZ_sed_xml file_def_histhf3h_lmdz.xml histhf3h enabled .TRUE.
406	LMDZ_sed_xml file_def_histhf3h_lmdz.xml histhf3h output_freq 3h
407	LMDZ_sed_xml file_def_histhf3h_lmdz.xml histhf3h name histhf3h
408	fi
409	if [ X${ok_hf3hm} = Xy ] ; then
410	LMDZ_sed_xml file_def_histhf3hm_lmdz.xml histhf3hm enabled .TRUE.
411	LMDZ_sed_xml file_def_histhf3hm_lmdz.xml histhf3hm output_freq 3h
412	LMDZ_sed_xml file_def_histhf3hm_lmdz.xml histhf3hm name histhf3hm
413	fi
414	if [ X${ok_stn} = Xy ] ; then
415	LMDZ_sed_xml file_def_histstn_lmdz.xml histstn enabled .TRUE.
416	LMDZ_sed_xml file_def_histstn_lmdz.xml histstn output_freq 1800s
417	LMDZ_sed_xml file_def_histstn_lmdz.xml histstn name histstn
418	fi
419	if [ X${LMDZ_NMC_monthly} = Xy ] ; then
420	LMDZ_sed_xml file_def_histmthNMC_lmdz.xml histmthNMC enabled .TRUE.
421	LMDZ_sed_xml file_def_histmthNMC_lmdz.xml histmthNMC output_freq 1mo
422	LMDZ_sed_xml file_def_histmthNMC_lmdz.xml histmthNMC name histmthNMC
423	fi
424	if [ X${LMDZ_NMC_daily} = Xy ] ; then
425	LMDZ_sed_xml file_def_histdayNMC_lmdz.xml histdayNMC enabled .TRUE.
426	LMDZ_sed_xml file_def_histdayNMC_lmdz.xml histdayNMC output_freq 1d
427	LMDZ_sed_xml file_def_histdayNMC_lmdz.xml histdayNMC name histdayNMC
428	fi
429	if [ X${LMDZ_NMC_hf} = Xy ] ; then
430	LMDZ_sed_xml file_def_histhfNMC_lmdz.xml histhfNMC enabled .TRUE.
431	LMDZ_sed_xml file_def_histhfNMC_lmdz.xml histhfNMC output_freq 6h
432	LMDZ_sed_xml file_def_histhfNMC_lmdz.xml histhfNMC name histhfNMC
433	fi
434	fi
435
436	## gcm.def parameters :
437	# Modification of variable iphysiq depending on the physics
438	if [ X${LMDZ_Physics} = X"AP" ] ; then
439	value=10
440	else
441	value=DEFAULT
442	fi
443	IGCM_comp_modifyDefFile nonblocker gcm.def iphysiq $value
444
445
446	## run.def parameters
447	IGCM_comp_modifyDefFile blocker run.def dayref ${InitDay}
448	IGCM_comp_modifyDefFile blocker run.def nday ${PeriodLengthInDays}
449	IGCM_comp_modifyDefFile blocker run.def raz_date ${RAZ_DATE}
450	IGCM_comp_modifyDefFile blocker run.def periodav ${LMDZ_periodav}
451	IGCM_comp_modifyDefFile nonblocker run.def adjust ${LMDZ_adjust}
452
453	# Set anneeref different for gcm and ce0l
454	# Variable calend is different for a run with create_etat0_limit and the gcm
455	# Test if executable create_etat0_limit is present and lmdz.x is not present
456	if [ -f create_etat0_limit* ] \|\| [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
457	# for case ce0l : always take current year
458	IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
459	IGCM_comp_modifyDefFile blocker run.def calend ${CalendarTypeForCreate}
460	else
461	# for case gcm : take first year of simulation
462	IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
463	IGCM_comp_modifyDefFile blocker run.def calend ${CalendarTypeForLmdz}
464	fi
465
466	# Activate creation of file grilles_gcm.nc only at first period
467	if [ ${CumulPeriod} -eq 1 ] ; then
468	IGCM_comp_modifyDefFile nonblocker run.def grilles_gcm_netcdf y
469	else
470	IGCM_comp_modifyDefFile nonblocker run.def grilles_gcm_netcdf n
471	fi
472
473	## Determine from the variable ListOfComponents in config.card coupling to external models
474	## and set corresponding parameters in run.def
475	echo ListOfComponents now running : ${config_ListOfComponents[*]}
476
477	if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
478	echo "Activate ORCHIDEE, set VEGET=y in run.def"
479	IGCM_comp_modifyDefFile blocker run.def VEGET y
480	else
481	echo "No ORCHIDEE, set VEGET=n in run.def"
482	IGCM_comp_modifyDefFile blocker run.def VEGET n
483	fi
484
485	if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
486	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
487	IGCM_comp_modifyDefFile blocker run.def type_ocean couple
488	else
489	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
490	IGCM_comp_modifyDefFile blocker run.def type_ocean force
491	fi
492
493	if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
494	echo "Activate coupling to INCA, set type_trac=inca in run.def"
495	IGCM_comp_modifyDefFile blocker run.def type_trac inca
496	elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
497	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
498	IGCM_comp_modifyDefFile blocker run.def type_trac repr
499	IGCM_comp_modifyDefFile blocker run.def config_inca none
500	else
501	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
502	IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
503	IGCM_comp_modifyDefFile blocker run.def config_inca none
504	fi
505
506
507	# config.def : Activate direct radiative effect if ok_ade=y
508	if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
509	IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
510	else
511	IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
512	fi
513
514	# config.def : Activate indirect radiative effect if ok_aie=y
515	if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
516	IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
517	else
518	IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
519	fi
520
521	# config.def : Activate online aerosol coupled model if aerosol_couple=y
522	if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
523	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
524	else
525	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
526	fi
527
528	# config.def : Activate reading of ozone in climatology if read_climoz=2
529	if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
530	IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
531	else
532	IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0
533	fi
534
535	# config.def : Choose aerosol use in radiative effect
536	# type of coupled aerosol =1 (default) =2 => bc only =3 => pom only =4 => seasalt only
537	# =5 => dust only =6 => all aerosol
538	if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
539	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
540	else
541	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
542	fi
543
544	# config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
545	if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
546	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
547	else
548	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
549	fi
550
551	# guide.def : Activate nudging if ok_guide=y set in lmdz.card
552	if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
553	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide ${lmdz_UserChoices_ok_guide}
554	else
555	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
556	fi
557
558	## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
559	ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
560	if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
561	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
562	IGCM_sys_Mv gcm.def.tmp gcm.def
563	echo
564	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
565	echo
566	cat gcm.def
567	ByPass_hgardfou_teta=n
568	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
569	fi
570
571	## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
572	ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
573	if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
574	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
575	IGCM_sys_Mv gcm.def.tmp gcm.def
576	echo
577	IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
578	echo
579	cat gcm.def
580	ByPass_hgardfou_mats=n
581	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
582	fi
583
584	if [ X${lmdz_UserChoices_XIOS} = Xy ] ; then
585	# Add include of LMDZ context in iodef.xml
586	# In iodef.xml add on next line after "COMPONENT CONTEXT"
587	# <context id="LMDZ" src="./context_lmdz.xml"/>
588	echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
589	cp iodef.xml iodef.xml.tmp
590	sed -e "/COMPONENT CONTEXT/r add.tmp" \
591	iodef.xml.tmp > iodef.xml
592	rm iodef.xml.tmp add.tmp
593	fi
594
595	IGCM_debug_PopStack "ATM_Update"
596	}
597
598	#-----------------------------------
599	function ATM_Finalize
600	{
601	IGCM_debug_PushStack "ATM_Finalize"
602
603	# If the file exist, copy Bands_ file to PARAM/ in submit directory. This file will be used for the simulation.
604	# Copy also the same file into ATM/Restart at ARCHIVE directory for backup.
605	if [ -f Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ] ; then
606	if [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] ; then
607	IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
608	IGCM_sys_Put_Out Bands_${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}
609	elif [ ${CumulPeriod} -eq 1 ] && [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
610	# Special case : first period and no adjust => Save bands file with suffix _0
611	IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
612	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
613	fi
614	fi
615
616	# Add special treatement for CARBON CYCLE
617	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
618	ATM_Carbon_Finalize
619	fi
620
621	echo FINALIZE ATM !
622
623	IGCM_debug_PopStack "ATM_Finalize"
624	}
625
626
627
628	function ATM_Carbon_Update
629	{
630	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
631
632	IGCM_debug_PushStack "ATM_Carbon_Update"
633
634	typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
635	typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
636	typeset PathCO2log
637	typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
638
639	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
640	##--Initialization of fluxes to an undefined value at the first run
641	UndefinedValueCo2=-9999
642	InitPeriodCo2=0
643	InitDateBeginCo2=${UndefinedValueCo2}
644	InitYearCo2=$(( ${year} - 1 ))
645	InitDateEndCo2=${InitYearCo2}1231
646	fCO2_ff=${UndefinedValueCo2}
647	CO2SBG=${UndefinedValueCo2}
648	CO2LU=${UndefinedValueCo2}
649	CO2MBG=${UndefinedValueCo2}
650	CO2_ppm_prec=${UndefinedValueCo2}
651	# Get the initial value of atmosp. pco2
652	CO2_ppm=${lmdz_UserChoices_co2_init}
653
654	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
655	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
656
657	# Save CO2 values in ExeCpuLog variable contents 5 fields
658	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
659	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
660	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
661
662	# Get the path where the log file co2.log is
663	PathCO2log=${SUBMIT_DIR}
664	# Get Previous line in co2.log
665	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
666
667	else
668
669	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
670	# !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
671	#SubmitRestartPath=
672	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
673	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
674	PathCO2log=${config_ATM_SubmitRestartPath}
675	Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
676	PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
677
678	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
679	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
680
681	# Save Last Line of control in new co2.log file
682	InitPeriodCo2=0
683	InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $2}' )
684	InitDateEndCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $3}' )
685	fCO2_ff=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $6}' )
686	CO2SBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $8}' )
687	CO2LU=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $9}' )
688	CO2MBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $7}' )
689	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $5}' )
690	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
691
692	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
693	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
694	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
695	else
696	# Get restart line in co2.log
697	PathCO2log=${SUBMIT_DIR}
698	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
699	# Get the value of atmosp. pco2 in co2.log
700	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
701	fi
702
703	fi
704
705	if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
706	# Modify co2_ppm in config.def only for historical run
707	# If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
708	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm ${CO2_ppm}
709	fi
710	IGCM_debug_PopStack "ATM_Carbon_Update"
711	}
712
713
714	function ATM_Carbon_Finalize
715	{
716	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
717
718	IGCM_debug_PushStack "ATM_Carbon_Finalize"
719
720	typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
721
722	# Fossil fuel emission
723	if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
724	# For Control, no fossil fuel emission :
725	fCO2_ff=0
726	echo "Fossil Fuel for control run :" ${fCO2_ff}
727	else
728	# For historical, get the fossile fuel file :
729	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
730	echo "Fossil Fuel for historical run :" ${fCO2_ff}
731	fi
732
733	# Get the value of ocean carbon flux
734	CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
735	CO2MBG=$( echo ${CO2MBG} \| sed -e "s/ *//" )
736	echo "Ocean carbon flux :" ${CO2MBG}
737
738	# Get the value of land fluxes
739	set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
740	CO2SRF=$( echo ${CO2SBG_3V[0]} \| sed -e "s/ *//" )
741	CO2LU=$( echo ${CO2SBG_3V[1]} \| sed -e "s/ *//" )
742	CO2SBG=$( echo ${CO2SBG_3V[2]} \| sed -e "s/ *//" )
743	echo "Land carbon flux (NEP) :" ${CO2SRF}
744	echo "LU flux (FLUC) :" ${CO2LU}
745	echo "Total Land carbon flux (NBP) :" ${CO2SBG}
746
747	# Previous CO2
748	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
749	echo "Previous CO2 :" ${CO2_ppm_prec}
750
751	# Formula
752	CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" \| bc -l )
753	echo "New CO2 :" ${CO2_ppm}
754
755	# Save CO2 values in ExeCpuLog variable contents 5 fields
756	echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
757	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
758	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
759
760	IGCM_debug_PopStack "ATM_Carbon_Finalize"
761	}

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