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source: CONFIG/UNIFORM/v6/LMDZOR_v6/GENERAL/DRIVER/lmdz.driver @ 2336

Last change on this file since 2336 was 2336, checked in by jgipsl, 10 years ago
More homogenization between IPSLCM6 and LMDZOR_v6.
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
36	##-- Calendar type for LMDZ and create_etat0_limit
37	case ${config_UserChoices_CalendarType} in
38	leap\|gregorian)
39	CalendarTypeForLmdz=earth_366d
40	CalendarTypeForCreate=gregorian;;
41	noleap)
42	CalendarTypeForLmdz=earth_365d
43	CalendarTypeForCreate=${CalendarTypeForLmdz};;
44	360d)
45	CalendarTypeForLmdz=earth_360d
46	CalendarTypeForCreate=${CalendarTypeForLmdz};;
47	*)
48	CalendarTypeForLmdz=earth_360d
49	CalendarTypeForCreate=${CalendarTypeForLmdz}
50	esac
51
52	##- LMDZ physics version
53	## Read LMDZ_Physics option in lmdz.card, if not present take default value AP (old physics)
54	if [ ! X${lmdz_UserChoices_LMDZ_Physics} = X ] ; then
55	LMDZ_Physics=${lmdz_UserChoices_LMDZ_Physics}
56	else
57	LMDZ_Physics=AP
58	fi
59	echo LMDZ physics version : ${LMDZ_Physics}
60
61	##- Create_etat0_limit version
62	## Define variable CREATE only if it is set in lmdz.card section UserChoices.
63	## This variable is only used in lmdz.card to choose input files.
64	if [ ! X${lmdz_UserChoices_CREATE} = X ] ; then
65	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices CREATE
66	CREATE=${lmdz_UserChoices_CREATE}
67	echo create_etat0_limit version : ${CREATE}
68	fi
69
70
71	## - LMDZ choice of config.def file
72	## ConfType must be set in lmdz.card
73	ConfType=${lmdz_UserChoices_ConfType}
74
75	##- LMDZ output level, to be set in lmdz.card
76	if [ X${lmdz_UserChoices_OutLevel} = X ] ; then
77	# OutLevel is not set. Take default value low.
78	OutLevel=low
79	else
80	OutLevel=${lmdz_UserChoices_OutLevel}
81	fi
82
83	##-- Output frequency purpose ....
84	##-- Initialisation ....
85	ok_mensuel=n
86	ok_journe=n
87	ok_hf=n
88	ok_hf3h=n
89	ok_hf3hm=n
90	ok_stn=n
91
92	case ${config_UserChoices_PeriodLength} in
93	1Y\|1y\|1M\|1m) ok_mensuel=y ;;
94	5D\|5d\|1D\|1d) ok_journe=y ;;
95	esac
96
97	for frequency in ${config_ATM_WriteFrequency} ; do
98	case ${frequency} in
99	1M\|1m) ok_mensuel=y ;;
100	esac
101	case ${frequency} in
102	5D\|5d\|1D\|1d) ok_journe=y ;;
103	esac
104	case ${frequency} in
105	HF\|hf) ok_hf=y ;;
106	esac
107	case ${frequency} in
108	HF3h\|hf3h) ok_hf3h=y ;;
109	esac
110	case ${frequency} in
111	HF3hm\|hf3hm) ok_hf3hm=y ;;
112	esac
113	case ${frequency} in
114	STN\|stn) ok_stn=y ;;
115	esac
116	done
117
118	## Read LMDZ_NbPeriod_adjust option in lmdz.card
119	if [ X"${lmdz_UserChoices_LMDZ_NbPeriod_adjust}" = X"" ] ; then
120	# The variable is not in lmdz.card, set default value
121	LMDZ_NbPeriod_adjust=0
122	else
123	LMDZ_NbPeriod_adjust=${lmdz_UserChoices_LMDZ_NbPeriod_adjust}
124	fi
125
126	if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
127	LMDZ_Bands_file_name=${lmdz_UserChoices_LMDZ_Bands_file_name}
128	fi
129
130
131	## Read LMDZ_COSP_OK in lmdz.card
132	if [ ! X${lmdz_UserChoices_LMDZ_COSP_OK} = X ] ; then
133	LMDZ_COSP_OK=${lmdz_UserChoices_LMDZ_COSP_OK}
134	else
135	LMDZ_COSP_OK=n
136	fi
137	## Read LMDZ_COSP_monthly in lmdz.card
138	if [ ! X${lmdz_UserChoices_LMDZ_COSP_monthly} = X ] ; then
139	LMDZ_COSP_monthly=${lmdz_UserChoices_LMDZ_COSP_monthly}
140	else
141	LMDZ_COSP_monthly=n
142	fi
143	## Read LMDZ_COSP_daily in lmdz.card
144	if [ ! X${lmdz_UserChoices_LMDZ_COSP_daily} = X ] ; then
145	LMDZ_COSP_daily=${lmdz_UserChoices_LMDZ_COSP_daily}
146	else
147	LMDZ_COSP_daily=n
148	fi
149	## Read LMDZ_COSP_hf in lmdz.card
150	if [ ! X${lmdz_UserChoices_LMDZ_COSP_hf} = X ] ; then
151	LMDZ_COSP_hf=${lmdz_UserChoices_LMDZ_COSP_hf}
152	else
153	LMDZ_COSP_hf=n
154	fi
155
156	## Read LMDZ_NMC_monthly in lmdz.card
157	if [ ! X${lmdz_UserChoices_LMDZ_NMC_monthly} = X ] ; then
158	LMDZ_NMC_monthly=${lmdz_UserChoices_LMDZ_NMC_monthly}
159	else
160	LMDZ_NMC_monthly=n
161	fi
162
163	## Read LMDZ_NMC_daily in lmdz.card
164	if [ ! X${lmdz_UserChoices_LMDZ_NMC_daily} = X ] ; then
165	LMDZ_NMC_daily=${lmdz_UserChoices_LMDZ_NMC_daily}
166	else
167	LMDZ_NMC_daily=n
168	fi
169
170	## Read LMDZ_NMC_hf in lmdz.card
171	if [ ! X${lmdz_UserChoices_LMDZ_NMC_hf} = X ] ; then
172	LMDZ_NMC_hf=${lmdz_UserChoices_LMDZ_NMC_hf}
173	else
174	LMDZ_NMC_hf=n
175	fi
176
177
178	IGCM_debug_PopStack "ATM_Initialize"
179	}
180
181	#-----------------------------------------------------------------
182	function ATM_Update
183	{
184	IGCM_debug_PushStack "ATM_Update"
185
186
187	case ${config_UserChoices_PeriodLength} in
188	Y\|y)
189	LMDZ_ecrit_ISCCP=30.
190	LMDZ_periodav=30.
191	if [ "${config_UserChoices_CalendarType}" != "360d" ] ; then
192	echo Do not consider following warning if your running create_etat0_limit :
193	echo WARNING !!! For lmdz : calendartype in config.card. PeriodLength=1Y allowed only for CalendarType=360d
194	fi
195	;;
196	*)
197	LMDZ_ecrit_ISCCP=${PeriodLengthInDays}.
198	LMDZ_periodav=${PeriodLengthInDays}.
199	;;
200	esac
201
202	##-- Remise ou non a zero de la date initiale de LMDZ pour le fichier run.def
203	if [ ${CumulPeriod} -eq 1 ] ; then
204	RAZ_DATE=1
205	else
206	RAZ_DATE=0
207	fi
208
209	## Algorithme for special treatment for Bands_xxx file
210	## For CumulPeriod=1 ;
211	## IF NbPeriod_Adjust = 0 ; set LMDZ_adjust=n
212	## IF LMDZ_Bands_file_name was given in lmdz.card THEN Get Bands file directly from server. Store it later with _0 suffix.
213	## IF no LMDZ_Bands_file_name was given, start without Bands file. Store it later with _0 suffix.
214	## ELSE set LMDZ_adjust=y ; start without Bands file ; Store it later in PARAM/ directory in submit directory with suffix _1 ;
215	##
216	## For CumulPeriod=2 to LMDZ_NbPeriod_adjust ;
217	## Get Bands file from PARAM/ in submit directory (CumulPeriod-1) ; set LMDZ_adjust=y ; Store Bands file in PARAM/ ;
218	##
219	## For CumulPeriod > LMDZ_NbPeriod_adjust ; LMDZ_adjust=n ; Get Bands file from PARAM/ ; Do not store ;
220
221	if [ ${CumulPeriod} -eq 1 ] ; then
222	if [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
223	if [ ! X${LMDZ_Bands_file_name} = X ] ; then
224	IGCM_sys_Get ${LMDZ_Bands_file_name} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
225	IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
226	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"
227	fi
228	fi
229	fi
230
231	LMDZ_adjust=n
232	[ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && LMDZ_adjust=y
233
234	RefPeriod=${LMDZ_NbPeriod_adjust} #0 to use a Bands file from Restart
235	[ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] && (( RefPeriod = ${CumulPeriod} - 1 ))
236
237	# Get Bands file from PARAM directory if file exist
238	if ( [ ${CumulPeriod} -gt 1 ] && [ -f ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} ] ) ; then
239	IGCM_sys_Cp ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${RefPeriod} Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
240	IGCM_sys_Chmod u+w Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat
241	fi
242
243	##-- GHG forcing :
244	## If forcing file exist in run directory, read values for the current year
245	## and set in config.def. If not use the default value set in config.def
246
247	# Read value for solaire from file SOLARANDVOLCANOES.txt. If file not existing, take DEFAULT value from file.
248	if [ -f SOLARANDVOLCANOES.txt ] ; then
249	value=`grep Annee_${year} SOLARANDVOLCANOES.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 SOLARANDVOLCANOES.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 solaire $value
259
260
261	# Read value for co2_ppm from file CO2.txt. If file not existing, take DEFAULT value from file.
262	if [ -f CO2.txt ] ; then
263	value=`grep Annee_${year} CO2.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 CO2.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 co2_ppm $value
273
274
275	# Read value for CH4_ppb from file CH4.txt. If file not existing, take DEFAULT value from file.
276	if [ -f CH4.txt ] ; then
277	value=`grep Annee_${year} CH4.txt \| awk -F= '{print $2}'`
278	if [ X"${value}" = X ] ; then
279	# The grep returned empty variable, stop execution
280	IGCM_debug_Exit "The file CH4.txt do not contain the current year."
281	IGCM_debug_Verif_Exit
282	fi
283	else
284	value=DEFAULT
285	fi
286	IGCM_comp_modifyDefFile nonblocker config.def CH4_ppb $value
287
288
289	# Read value for N2O_ppb from file N2O.txt. If file not existing, take DEFAULT value from file.
290	if [ -f N2O.txt ] ; then
291	value=`grep Annee_${year} N2O.txt \| awk -F= '{print $2}'`
292	if [ X"${value}" = X ] ; then
293	# The grep returned empty variable, stop execution
294	IGCM_debug_Exit "The file N2O.txt do not contain the current year."
295	IGCM_debug_Verif_Exit
296	fi
297	else
298	value=DEFAULT
299	fi
300	IGCM_comp_modifyDefFile nonblocker config.def N2O_ppb $value
301
302	# Read value for CFC11_ppt from file CFC11.txt. If file not existing, take DEFAULT value from file.
303	if [ -f CFC11.txt ] ; then
304	value=`grep Annee_${year} CFC11.txt \| awk -F= '{print $2}'`
305	if [ X"${value}" = X ] ; then
306	# The grep returned empty variable, stop execution
307	IGCM_debug_Exit "The file CFC11.txt do not contain the current year."
308	IGCM_debug_Verif_Exit
309	fi
310	else
311	value=DEFAULT
312	fi
313	IGCM_comp_modifyDefFile nonblocker config.def CFC11_ppt $value
314
315
316	# Read value for CFC12_ppt from file CFC12.txt. If file not existing, take DEFAULT value from file.
317	if [ -f CFC12.txt ] ; then
318	value=`grep Annee_${year} CFC12.txt \| awk -F= '{print $2}'`
319	if [ X"${value}" = X ] ; then
320	# The grep returned empty variable, stop execution
321	IGCM_debug_Exit "The file CFC12.txt do not contain the current year."
322	IGCM_debug_Verif_Exit
323	fi
324	else
325	value=DEFAULT
326	fi
327	IGCM_comp_modifyDefFile nonblocker config.def CFC12_ppt $value
328
329
330	## Coupling Time Step : Take value of FreqCoupling set in oasis.card or if it is not set, take default value 86400
331	LMDZ_t_coupl=${oasis_UserChoices_FreqCoupling:-86400}
332	IGCM_debug_Print 3 "LMDZ_t_coupl " ${LMDZ_t_coupl}
333	IGCM_comp_modifyDefFile nonblocker config.def t_coupl ${LMDZ_t_coupl}
334
335	##-- Add special treatement for CARBON CYCLE
336	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
337	ATM_Carbon_Update
338	fi
339
340
341	##-- Set LMDZ_COSP_daily1979=y in section UserChoices in lmdz.card to activate
342	## COSP daily output for years 1979 and later (mandatory for historical CMIP5 run).
343	if ([ X"${lmdz_UserChoices_LMDZ_COSP_daily1979}" = X"y" ] && [ ${year} -ge 1979 ]) ; then
344	LMDZ_COSP_daily=y
345	fi
346
347
348	## output.def parameters
349	# columns in phys_output_filekeys refer to the filenames given in phys_out_filenames in output.def :
350	# histmth histday histhf histfh3h histhf3hm histstn
351	IGCM_comp_modifyDefFile nonblocker output.def phys_out_filekeys "${ok_mensuel} ${ok_journe} ${ok_hf} ${ok_hf3h} ${ok_hf3hm} ${ok_stn}"
352	IGCM_comp_modifyDefFile nonblocker output.def ecrit_ISCCP ${LMDZ_ecrit_ISCCP}
353	IGCM_comp_modifyDefFile nonblocker output.def ok_cosp ${LMDZ_COSP_OK}
354	IGCM_comp_modifyDefFile nonblocker output.def ok_mensuelCOSP ${LMDZ_COSP_monthly}
355	IGCM_comp_modifyDefFile nonblocker output.def ok_journeCOSP ${LMDZ_COSP_daily}
356	IGCM_comp_modifyDefFile nonblocker output.def ok_hfCOSP ${LMDZ_COSP_hf}
357	IGCM_comp_modifyDefFile nonblocker output.def ok_histNMC "${LMDZ_NMC_monthly} ${LMDZ_NMC_daily} ${LMDZ_NMC_hf}"
358
359	# XIOS XML definition
360	# Default init : files are desactivated
361	LMDZ_sed_xml file_def_histmth_lmdz.xml histmth enabled .FALSE.
362	LMDZ_sed_xml file_def_histday_lmdz.xml histday enabled .FALSE.
363	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf enabled .FALSE.
364	LMDZ_sed_xml file_def_histfh3h_lmdz.xml histfh3h enabled .FALSE.
365	LMDZ_sed_xml file_def_histhf3hm_lmdz.xml histfh3hm enabled .FALSE.
366	LMDZ_sed_xml file_def_histstn_lmdz.xml histstn enabled .FALSE.
367	LMDZ_sed_xml file_def_histmthNMC_lmdz.xml histmthNMC enabled .FALSE.
368	LMDZ_sed_xml file_def_histdayNMC_lmdz.xml histdayNMC enabled .FALSE.
369	LMDZ_sed_xml file_def_histhfNMC_lmdz.xml histhfNMC enabled .FALSE.
370	if [ X${lmdz_UserChoices_XIOS} = Xy ] ; then
371	# Default output level : 5
372	LMDZ_sed_xml file_def_histmth_lmdz.xml histmth output_level 5
373	LMDZ_sed_xml file_def_histday_lmdz.xml histday output_level 5
374	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf output_level 5
375	LMDZ_sed_xml file_def_histfh3h_lmdz.xml histfh3h output_level 5
376	LMDZ_sed_xml file_def_histhf3hm_lmdz.xml histfh3hm output_level 5
377	LMDZ_sed_xml file_def_histstn_lmdz.xml histstn output_level 5
378	LMDZ_sed_xml file_def_histmthNMC_lmdz.xml histmthNMC output_level 5
379	LMDZ_sed_xml file_def_histdayNMC_lmdz.xml histdayNMC output_level 5
380	LMDZ_sed_xml file_def_histhfNMC_lmdz.xml histhfNMC output_level 5
381	# Filling of XML files
382	if [ X${ok_mensuel} = Xy ] ; then
383	LMDZ_sed_xml file_def_histmth_lmdz.xml histmth enabled .TRUE.
384	LMDZ_sed_xml file_def_histmth_lmdz.xml histmth output_freq 1mo
385	LMDZ_sed_xml file_def_histmth_lmdz.xml histmth name histmth
386	fi
387	if [ X${ok_journe} = Xy ] ; then
388	LMDZ_sed_xml file_def_histday_lmdz.xml histday enabled .TRUE.
389	LMDZ_sed_xml file_def_histday_lmdz.xml histday output_freq 1d
390	LMDZ_sed_xml file_def_histday_lmdz.xml histday name histday
391	if [ X${OutLevel} = Xlow ] \|\| [ X${OutLevel} = Xmedium ] ; then
392	LMDZ_sed_xml file_def_histday_lmdz.xml histday output_level 2
393	fi
394	fi
395	if [ X${ok_hf} = Xy ] ; then
396	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf enabled .TRUE.
397	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf output_freq 6h
398	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf name histhf
399	if [ X${OutLevel} = Xlow ] ; then
400	LMDZ_sed_xml file_def_histhf_lmdz.xml histhf output_level 2
401	fi
402	fi
403	if [ X${ok_hf3h} = Xy ] ; then
404	LMDZ_sed_xml file_def_histhf3h_lmdz.xml histhf3h enabled .TRUE.
405	LMDZ_sed_xml file_def_histhf3h_lmdz.xml histhf3h output_freq 3h
406	LMDZ_sed_xml file_def_histhf3h_lmdz.xml histhf3h name histhf3h
407	fi
408	if [ X${ok_hf3hm} = Xy ] ; then
409	LMDZ_sed_xml file_def_histhf3hm_lmdz.xml histhf3hm enabled .TRUE.
410	LMDZ_sed_xml file_def_histhf3hm_lmdz.xml histhf3hm output_freq 3h
411	LMDZ_sed_xml file_def_histhf3hm_lmdz.xml histhf3hm name histhf3hm
412	fi
413	if [ X${ok_stn} = Xy ] ; then
414	LMDZ_sed_xml file_def_histstn_lmdz.xml histstn enabled .TRUE.
415	LMDZ_sed_xml file_def_histstn_lmdz.xml histstn output_freq 1800s
416	LMDZ_sed_xml file_def_histstn_lmdz.xml histstn name histstn
417	fi
418	if [ X${LMDZ_NMC_monthly} = Xy ] ; then
419	LMDZ_sed_xml file_def_histmthNMC_lmdz.xml histmthNMC enabled .TRUE.
420	LMDZ_sed_xml file_def_histmthNMC_lmdz.xml histmthNMC output_freq 1mo
421	LMDZ_sed_xml file_def_histmthNMC_lmdz.xml histmthNMC name histmthNMC
422	fi
423	if [ X${LMDZ_NMC_daily} = Xy ] ; then
424	LMDZ_sed_xml file_def_histdayNMC_lmdz.xml histdayNMC enabled .TRUE.
425	LMDZ_sed_xml file_def_histdayNMC_lmdz.xml histdayNMC output_freq 1d
426	LMDZ_sed_xml file_def_histdayNMC_lmdz.xml histdayNMC name histdayNMC
427	fi
428	if [ X${LMDZ_NMC_hf} = Xy ] ; then
429	LMDZ_sed_xml file_def_histhfNMC_lmdz.xml histhfNMC enabled .TRUE.
430	LMDZ_sed_xml file_def_histhfNMC_lmdz.xml histhfNMC output_freq 6h
431	LMDZ_sed_xml file_def_histhfNMC_lmdz.xml histhfNMC name histhfNMC
432	fi
433	fi
434
435	## gcm.def parameters :
436	# Modification of variable iphysiq depending on the physics
437	if [ X${LMDZ_Physics} = X"AP" ] ; then
438	value=10
439	else
440	value=DEFAULT
441	fi
442	IGCM_comp_modifyDefFile nonblocker gcm.def iphysiq $value
443
444
445	## run.def parameters
446	IGCM_comp_modifyDefFile blocker run.def dayref ${InitDay}
447	IGCM_comp_modifyDefFile blocker run.def nday ${PeriodLengthInDays}
448	IGCM_comp_modifyDefFile blocker run.def raz_date ${RAZ_DATE}
449	IGCM_comp_modifyDefFile blocker run.def periodav ${LMDZ_periodav}
450	IGCM_comp_modifyDefFile nonblocker run.def adjust ${LMDZ_adjust}
451
452	# Set anneeref different for gcm and ce0l
453	# Variable calend is different for a run with create_etat0_limit and the gcm
454	# Test if executable create_etat0_limit is present and lmdz.x is not present
455	if [ -f create_etat0_limit* ] \|\| [ -f ce0l* ] && [ ! -f lmdz.x ] ; then
456	# for case ce0l : always take current year
457	IGCM_comp_modifyDefFile blocker run.def anneeref ${year}
458	IGCM_comp_modifyDefFile blocker run.def calend ${CalendarTypeForCreate}
459	else
460	# for case gcm : take first year of simulation
461	IGCM_comp_modifyDefFile blocker run.def anneeref ${InitYear}
462	IGCM_comp_modifyDefFile blocker run.def calend ${CalendarTypeForLmdz}
463	fi
464
465	# Activate creation of file grilles_gcm.nc only at first period
466	if [ ${CumulPeriod} -eq 1 ] ; then
467	IGCM_comp_modifyDefFile nonblocker run.def grilles_gcm_netcdf y
468	else
469	IGCM_comp_modifyDefFile nonblocker run.def grilles_gcm_netcdf n
470	fi
471
472	## Determine from the variable ListOfComponents in config.card coupling to external models
473	## and set corresponding parameters in run.def
474	echo ListOfComponents now running : ${config_ListOfComponents[*]}
475
476	if [ X${config_ListOfComponents_SRF} = Xorchidee ] ; then
477	echo "Activate ORCHIDEE, set VEGET=y in run.def"
478	IGCM_comp_modifyDefFile blocker run.def VEGET y
479	else
480	echo "No ORCHIDEE, set VEGET=n in run.def"
481	IGCM_comp_modifyDefFile blocker run.def VEGET n
482	fi
483
484	if [ X${config_ListOfComponents_CPL} = Xoasis ] ; then
485	echo "Activate coupling to ocean, set type_ocean=couple in run.def"
486	IGCM_comp_modifyDefFile blocker run.def type_ocean couple
487	else
488	echo "LMDZ is running in forced mode without ocean model, set type_ocean=force in run.def"
489	IGCM_comp_modifyDefFile blocker run.def type_ocean force
490	fi
491
492	if [ X${config_ListOfComponents_CHM} = Xinca ] ; then
493	echo "Activate coupling to INCA, set type_trac=inca in run.def"
494	IGCM_comp_modifyDefFile blocker run.def type_trac inca
495	elif [ X${config_ListOfComponents_CHM} = Xreprobus ] ; then
496	echo "Activate coupling to REPROBUS, set type_trac=repr in run.def"
497	IGCM_comp_modifyDefFile blocker run.def type_trac repr
498	IGCM_comp_modifyDefFile blocker run.def config_inca none
499	else
500	echo "No coupling to chemistry model, set type_trac=lmdz in run.def"
501	IGCM_comp_modifyDefFile blocker run.def type_trac lmdz
502	IGCM_comp_modifyDefFile blocker run.def config_inca none
503	fi
504
505
506	# config.def : Activate direct radiative effect if ok_ade=y
507	if [ ! X${lmdz_UserChoices_ok_ade} = X ]; then
508	IGCM_comp_modifyDefFile nonblocker config.def ok_ade ${lmdz_UserChoices_ok_ade}
509	else
510	IGCM_comp_modifyDefFile nonblocker config.def ok_ade n
511	fi
512
513	# config.def : Activate indirect radiative effect if ok_aie=y
514	if [ ! X${lmdz_UserChoices_ok_aie} = X ]; then
515	IGCM_comp_modifyDefFile nonblocker config.def ok_aie ${lmdz_UserChoices_ok_aie}
516	else
517	IGCM_comp_modifyDefFile nonblocker config.def ok_aie n
518	fi
519
520	# config.def : Activate online aerosol coupled model if aerosol_couple=y
521	if [ ! X${lmdz_UserChoices_aerosol_couple} = X ]; then
522	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple ${lmdz_UserChoices_aerosol_couple}
523	else
524	IGCM_comp_modifyDefFile nonblocker config.def aerosol_couple n
525	fi
526
527	# config.def : Activate reading of ozone in climatology if read_climoz=2
528	if [ ! X${lmdz_UserChoices_read_climoz} = X ]; then
529	IGCM_comp_modifyDefFile nonblocker config.def read_climoz ${lmdz_UserChoices_read_climoz}
530	else
531	IGCM_comp_modifyDefFile nonblocker config.def read_climoz 0
532	fi
533
534	# config.def : Choose aerosol use in radiative effect
535	# type of coupled aerosol =1 (default) =2 => bc only =3 => pom only =4 => seasalt only
536	# =5 => dust only =6 => all aerosol
537	if [ ! X${lmdz_UserChoices_flag_aerosol} = X ]; then
538	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol ${lmdz_UserChoices_flag_aerosol}
539	else
540	IGCM_comp_modifyDefFile nonblocker config.def flag_aerosol 0
541	fi
542
543	# config.def : Activate calcul of Cloud droplet number concentration if ok_cdnc=y
544	if [ ! X${lmdz_UserChoices_ok_cdnc} = X ]; then
545	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc ${lmdz_UserChoices_ok_cdnc}
546	else
547	IGCM_comp_modifyDefFile nonblocker config.def ok_cdnc n
548	fi
549
550	# guide.def : Activate nudging if ok_guide=y set in lmdz.card
551	if [ ! X${lmdz_UserChoices_ok_guide} = X ] ; then
552	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide ${lmdz_UserChoices_ok_guide}
553	else
554	IGCM_comp_modifyDefFile nonblocker guide.def ok_guide n
555	fi
556
557	## Read ByPass_hgardfou_teta option in lmdz.card --> divide teta* by 2 if [ $ByPass_hgardfou_teta = 1 ]
558	ByPass_hgardfou_teta=${lmdz_UserChoices_ByPass_hgardfou_teta}
559	if [ X"${ByPass_hgardfou_teta}" = X"y" ] ; then
560	awk '{ if ($0 ~ /^teta.*=/) {split($0,a,"=") ; print a[1]"="a[2]/2"."} else print $0}' gcm.def > gcm.def.tmp
561	IGCM_sys_Mv gcm.def.tmp gcm.def
562	echo
563	IGCM_debug_Print 1 "ByPass_hgardfou_teta : ^teta*/2 in gcm.def"
564	echo
565	cat gcm.def
566	ByPass_hgardfou_teta=n
567	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_teta "${ByPass_hgardfou_teta}"
568	fi
569
570	## Read ByPass_hgardfou_mats option in lmdz.card --> purmats=y 2 if [ $ByPass_hgardfou_mats = 1 ]
571	ByPass_hgardfou_mats=${lmdz_UserChoices_ByPass_hgardfou_mats}
572	if [ X"${ByPass_hgardfou_mats}" = X"y" ] ; then
573	sed -e "s/^purmats=.*/purmats=y/" gcm.def > gcm.def.tmp
574	IGCM_sys_Mv gcm.def.tmp gcm.def
575	echo
576	IGCM_debug_Print 1 "ByPass_hgardfou_mats : purmats=y in gcm.def"
577	echo
578	cat gcm.def
579	ByPass_hgardfou_mats=n
580	IGCM_card_WriteOption ${SUBMIT_DIR}/COMP/lmdz.card UserChoices ByPass_hgardfou_mats "${ByPass_hgardfou_mats}"
581	fi
582
583	if [ X${lmdz_UserChoices_XIOS} = Xy ] ; then
584	# Add include of LMDZ context in iodef.xml
585	# In iodef.xml add on next line after "COMPONENT CONTEXT"
586	# <context id="LMDZ" src="./context_lmdz.xml"/>
587	echo '<context id="LMDZ" src="./context_lmdz.xml"/>' > add.tmp
588	cp iodef.xml iodef.xml.tmp
589	sed -e "/COMPONENT CONTEXT/r add.tmp" \
590	iodef.xml.tmp > iodef.xml
591	rm iodef.xml.tmp add.tmp
592	fi
593
594	IGCM_debug_PopStack "ATM_Update"
595	}
596
597	#-----------------------------------
598	function ATM_Finalize
599	{
600	IGCM_debug_PushStack "ATM_Finalize"
601
602	# If the file exist, copy Bands_ file to PARAM/ in submit directory. This file will be used for the simulation.
603	# Copy also the same file into ATM/Restart at ARCHIVE directory for backup.
604	if [ -f Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ] ; then
605	if [ ${CumulPeriod} -le ${LMDZ_NbPeriod_adjust} ] ; then
606	IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_${CumulPeriod}
607	IGCM_sys_Put_Out Bands_${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}
608	elif [ ${CumulPeriod} -eq 1 ] && [ ${LMDZ_NbPeriod_adjust} -eq 0 ] ; then
609	# Special case : first period and no adjust => Save bands file with suffix _0
610	IGCM_sys_Cp Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat ${SUBMIT_DIR}/PARAM/${config_UserChoices_JobName}_Bands_${RESOL_ATM_3D}_${NUM_PROC_ATM}prc.dat_0
611	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
612	fi
613	fi
614
615	# Add special treatement for CARBON CYCLE
616	if [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"control" ] \|\| [ X"${lmdz_UserChoices_CARBON_CYCLE}" = X"historical" ] ; then
617	ATM_Carbon_Finalize
618	fi
619
620	echo FINALIZE ATM !
621
622	IGCM_debug_PopStack "ATM_Finalize"
623	}
624
625
626
627	function ATM_Carbon_Update
628	{
629	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
630
631	IGCM_debug_PushStack "ATM_Carbon_Update"
632
633	typeset InitPeriodCo2 InitDateBeginCo2 InitDateEndCo2
634	typeset CO2SBG CO2MBG CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
635	typeset PathCO2log
636	typeset PreviousLinelog LastPeriodDateBegin LastPeriodDateEnd LastDatesPeriod LastPREFIX
637
638	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"n" ] ) ; then
639	##--Initialization of fluxes to an undefined value at the first run
640	UndefinedValueCo2=-9999
641	InitPeriodCo2=0
642	InitDateBeginCo2=${UndefinedValueCo2}
643	InitYearCo2=$(( ${year} - 1 ))
644	InitDateEndCo2=${InitYearCo2}1231
645	fCO2_ff=${UndefinedValueCo2}
646	CO2SBG=${UndefinedValueCo2}
647	CO2LU=${UndefinedValueCo2}
648	CO2MBG=${UndefinedValueCo2}
649	CO2_ppm_prec=${UndefinedValueCo2}
650	# Get the initial value of atmosp. pco2
651	CO2_ppm=${lmdz_UserChoices_co2_init}
652
653	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
654	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
655
656	# Save CO2 values in ExeCpuLog variable contents 5 fields
657	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
658	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
659	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
660
661	# Get the path where the log file co2.log is
662	PathCO2log=${SUBMIT_DIR}
663	# Get Previous line in co2.log
664	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
665
666	else
667
668	# NEW parameter in config.card (even for Overule all restarts, you must modify the line after this comment ):
669	# !! NEW for Carbone cycle !! Path where to find old co2.log file for restart CO2.
670	#SubmitRestartPath=
671	if ( ${FirstInitialize} && [ X"${config_ATM_Restart}" = X"y" ] ) ; then
672	IGCM_card_DefineVariableFromOption ${SUBMIT_DIR}/config.card ATM SubmitRestartPath
673	PathCO2log=${config_ATM_SubmitRestartPath}
674	Date_r=$( IGCM_date_ConvertFormatToGregorian ${config_ATM_RestartDate} )
675	PreviousLinelog=$( grep ${Date_r} ${PathCO2log}/co2.log )
676
677	IGCM_sys_Cp ${SUBMIT_DIR}/co2.log.init ${SUBMIT_DIR}/co2.log
678	IGCM_sys_Chmod u+w ${SUBMIT_DIR}/co2.log
679
680	# Save Last Line of control in new co2.log file
681	InitPeriodCo2=0
682	InitDateBeginCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $2}' )
683	InitDateEndCo2=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $3}' )
684	fCO2_ff=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $6}' )
685	CO2SBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $8}' )
686	CO2LU=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $9}' )
687	CO2MBG=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $7}' )
688	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $5}' )
689	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
690
691	echo "${InitPeriodCo2} ${InitDateBeginCo2} ${InitDateEndCo2} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
692	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
693	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
694	else
695	# Get restart line in co2.log
696	PathCO2log=${SUBMIT_DIR}
697	PreviousLinelog=$( tail -1 ${PathCO2log}/co2.log )
698	# Get the value of atmosp. pco2 in co2.log
699	CO2_ppm=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
700	fi
701
702	fi
703
704	if [ ${lmdz_UserChoices_CARBON_CYCLE} = historical ] ; then
705	# Modify co2_ppm in config.def only for historical run
706	# If not historical run, keep co2_ppm value set earlier by IGCM_comp_modifyDefFile
707	IGCM_comp_modifyDefFile nonblocker config.def co2_ppm ${CO2_ppm}
708	fi
709	IGCM_debug_PopStack "ATM_Carbon_Update"
710	}
711
712
713	function ATM_Carbon_Finalize
714	{
715	# This fuction will be called only if CARBON_CYCLE is set to control or historical in lmdz.card
716
717	IGCM_debug_PushStack "ATM_Carbon_Finalize"
718
719	typeset CO2SBG_3V CO2SBG CO2MBG CO2SRF CO2LU CO2_ppm CO2_ppm_prec fCO2_ff
720
721	# Fossil fuel emission
722	if [ ${lmdz_UserChoices_CARBON_CYCLE} = control ] ; then
723	# For Control, no fossil fuel emission :
724	fCO2_ff=0
725	echo "Fossil Fuel for control run :" ${fCO2_ff}
726	else
727	# For historical, get the fossile fuel file :
728	fCO2_ff=$( gawk "{if (match(\$0,\"${year}\ *${month}\")) {print \$3}}" ${SUBMIT_DIR}/PARAM/CMIP5_gridcar_CO2_emissions_fossil_fuel_Andres_1751-2007_monthly_SC.txt )
729	echo "Fossil Fuel for historical run :" ${fCO2_ff}
730	fi
731
732	# Get the value of ocean carbon flux
733	CO2MBG=$( ${SUBMIT_DIR}/COMP/lmdz_analyse_pisces_out.awk ocean.output )
734	CO2MBG=$( echo ${CO2MBG} \| sed -e "s/ *//" )
735	echo "Ocean carbon flux :" ${CO2MBG}
736
737	# Get the value of land fluxes
738	set +A CO2SBG_3V -- $( ${SUBMIT_DIR}/COMP/lmdz_analyse_stomate_out.awk out_orchidee_0000 )
739	CO2SRF=$( echo ${CO2SBG_3V[0]} \| sed -e "s/ *//" )
740	CO2LU=$( echo ${CO2SBG_3V[1]} \| sed -e "s/ *//" )
741	CO2SBG=$( echo ${CO2SBG_3V[2]} \| sed -e "s/ *//" )
742	echo "Land carbon flux (NEP) :" ${CO2SRF}
743	echo "LU flux (FLUC) :" ${CO2LU}
744	echo "Total Land carbon flux (NBP) :" ${CO2SBG}
745
746	# Previous CO2
747	CO2_ppm_prec=$( echo "${PreviousLinelog[*]}" \| gawk -F '\|' '{gsub(" ",""); print $4}' )
748	echo "Previous CO2 :" ${CO2_ppm_prec}
749
750	# Formula
751	CO2_ppm=$( echo "${CO2_ppm_prec} + (${fCO2_ff} + ${CO2MBG} + ${CO2SBG}) / 2.12" \| bc -l )
752	echo "New CO2 :" ${CO2_ppm}
753
754	# Save CO2 values in ExeCpuLog variable contents 5 fields
755	echo "${CumulPeriod} ${PeriodDateBegin} ${PeriodDateEnd} ${CO2_ppm} ${CO2_ppm_prec} ${fCO2_ff} ${CO2MBG} ${CO2SBG} ${CO2LU}" \| \
756	gawk '{printf(" %11d \| %15s \| %15s \| %22.15g \| %20.15g \| %11.8g \| %11.8g \| %12.8g \| %12.8g \n", \
757	$1,$2,$3,$4,$5,$6,$7,$8,$9)}' >> ${SUBMIT_DIR}/co2.log
758
759	IGCM_debug_PopStack "ATM_Carbon_Finalize"
760	}

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