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source: tags/ORCHIDEE_4_1/ORCHIDEE/src_sechiba/chemistry.f90 @ 8119

Last change on this file since 8119 was 7526, checked in by josefine.ghattas, 2 years ago
Work on interpolations: Merge revision 7509-7511, 7515 and 7516 as done on branch ORCHIDEE_2_2. Note reinf_slope, alb_vis, alb_nir and woodharvest have no valid data because these interpolations are not done. See ticket #812
Property svn:keywords set to `Date Revision HeadURL`
File size: 103.3 KB

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1	! ================================================================================================================================
2	! MODULE : chemistry
3	!
4	! CONTACT : orchidee-help _at_ listes.ipsl.fr
5	!
6	! LICENCE : IPSL (2006)
7	! This software is governed by the CeCILL licence see ORCHIDEE/ORCHIDEE_CeCILL.LIC
8	!
9	!>\BRIEF
10	!!
11	!!\n DESCRIPTION:
12	!!
13	!! RECENT CHANGE(S): The content of this module were previously part of the diffuco module.
14	!! ok_inca changed name into ok_bvoc and DIFFUCO_OK_INCA changed into CHEMISTRY_BVOC
15	!! LEAFAGE_OK_INCA changed name into CHEMISTRY_LEAFAGE
16	!!
17	!! $HeadURL$
18	!! $Date$
19	!! $Revision$
20	!! \n
21	!_ ================================================================================================================================
22
23	MODULE chemistry
24
25	USE ioipsl
26	USE constantes
27	USE qsat_moisture
28	USE sechiba_io_p
29	USE ioipsl
30	USE pft_parameters
31	USE grid
32	USE time, ONLY : one_day, dt_sechiba, julian_diff, one_hour, one_year
33	USE ioipsl_para
34	USE xios_orchidee
35	USE function_library, ONLY :lai_to_biomass
36
37	IMPLICIT NONE
38
39	PRIVATE
40	PUBLIC :: chemistry_xios_initialize, chemistry_initialize, chemistry_bvoc, chemistry_flux_interface, chemistry_clear
41
42
43	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_iso !! Isoprene emissions from vegetation (kgC.m^{-2}.s^{-1})
44	!$OMP THREADPRIVATE(flx_iso)
45	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_mono !! Monoterpene emissions from vegetation (kgC.m^{-2}.s^{-1})
46	!$OMP THREADPRIVATE(flx_mono)
47	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_ORVOC !! Other Volatile Organic Compound emissions from vegetation (kgC.m^{-2}.s^{-1})
48	!$OMP THREADPRIVATE(flx_ORVOC)
49	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_MBO !! 2-methyl-3-buten-2-ol emissions from vegetation (mainly pines in America) (kgC.m^{-2}.s^{-1})
50	!$OMP THREADPRIVATE(flx_MBO)
51	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_methanol !! Methanol emissions from vegetation (kgC.m^{-2}.s^{-1})
52	!$OMP THREADPRIVATE(flx_methanol)
53	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_acetone !! Acetone emissions from vegetation (kgC.m^{-2}.s^{-1})
54	!$OMP THREADPRIVATE(flx_acetone)
55	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_acetal !! Acetaldehyde emissions from vegetation (kgC.m^{-2}.s^{-1})
56	!$OMP THREADPRIVATE(flx_acetal)
57	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_formal !! Formaldehyde emissions from vegetation (kgC.m^{-2}.s^{-1})
58	!$OMP THREADPRIVATE(flx_formal)
59	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_acetic !! Acetic acid emissions from vegetation (kgC.m^{-2}.s^{-1})
60	!$OMP THREADPRIVATE(flx_acetic)
61	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_formic !! Formic acid emissions from vegetation (kgC.m^{-2}.s^{-1})
62	!$OMP THREADPRIVATE(flx_formic)
63	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_apinen !! Alpha pinene emissions from vegetation (kgC.m^{-2}.s^{-1})
64	!$OMP THREADPRIVATE(flx_apinen)
65	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_bpinen !! Beta pinene emissions from vegetation (kgC.m^{-2}.s^{-1})
66	!$OMP THREADPRIVATE(flx_bpinen)
67	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_limonen !! Limonene emissions from vegetation (kgC.m^{-2}.s^{-1})
68	!$OMP THREADPRIVATE(flx_limonen)
69	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_myrcen !! Myrcene emissions from vegetation (kgC.m^{-2}.s^{-1})
70	!$OMP THREADPRIVATE(flx_myrcen)
71	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_sabinen !! Sabinene emissions from vegetation (kgC.m^{-2}.s^{-1})
72	!$OMP THREADPRIVATE(flx_sabinen)
73	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_camphen !! Camphene emissions from vegetation (kgC.m^{-2}.s^{-1})
74	!$OMP THREADPRIVATE(flx_camphen)
75	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_3caren !! 3-Carene emissions from vegetation (kgC.m^{-2}.s^{-1})
76	!$OMP THREADPRIVATE(flx_3caren)
77	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_tbocimen !! T-beta Ocimene emissions from vegetation (kgC.m^{-2}.s^{-1})
78	!$OMP THREADPRIVATE(flx_tbocimen)
79	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_othermono !! Emissions of other monoterpenes from vegetation (kgC.m^{-2}.s^{-1})
80	!$OMP THREADPRIVATE(flx_othermono)
81	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_sesquiter !! Sesquiterpene emissions from vegetation (kgC.m^{-2}.s^{-1})
82	!$OMP THREADPRIVATE(flx_sesquiter)
83	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_fertil_no !! Biogenic nitrogen oxide soil emission due to N-fertilisation (ngN.m^{-2}.s^{-1})
84	!$OMP THREADPRIVATE(flx_fertil_no)
85	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_no_soil !! Nitrogen Oxide emissions from soil, before deposition on canopy
86	!! (ngN.m^{-2}.s^{-1})
87	!$OMP THREADPRIVATE(flx_no_soil)
88	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_no !! Net nitrogen Oxide emissions from soil, after deposition on canopy
89	!$OMP THREADPRIVATE(flx_no)
90	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: CRF !! Canopy reduction factor for net NO flux calculation (kjpindex,nvm)
91	!$OMP THREADPRIVATE(CRF)
92
93	! variables used inside diffuco_inca module
94	LOGICAL, ALLOCATABLE, SAVE, DIMENSION(:) :: ok_siesta !! Flag for controlling post-pulse period (true/false)
95	!$OMP THREADPRIVATE(ok_siesta)
96	LOGICAL, ALLOCATABLE, SAVE, DIMENSION(:) :: allow_pulse !! Flag for controlling pulse period (true/false)
97	!$OMP THREADPRIVATE(allow_pulse)
98	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: pulse !! Pulse fonction
99	!$OMP THREADPRIVATE(pulse)
100	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: pulseday !! Counter for pulse period
101	!$OMP THREADPRIVATE(pulseday)
102	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: siestaday !! Counter for post-pulse period
103	!$OMP THREADPRIVATE(siestaday)
104	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: pulselim !! Pulse period length
105	!$OMP THREADPRIVATE(pulselim)
106	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: siestalim !! Post-pulse period length
107	!$OMP THREADPRIVATE(siestalim)
108	REAL(r_std), SAVE :: nbre_precip
109	!$OMP THREADPRIVATE(nbre_precip)
110	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: flx_co2_bbg_year !! CO2 emissions from biomass burning
111	!! Read in an input file (kgC.m^{-2}.year^{-1})
112	!$OMP THREADPRIVATE(flx_co2_bbg_year)
113	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: N_qt_WRICE_year !! N fertilizers applied on wetland rice
114	!! Read in an input file (kgN.yr^{-1})
115	!$OMP THREADPRIVATE(N_qt_WRICE_year)
116	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: N_qt_OTHER_year !! N fertilizers applied on other crops and grasses
117	!! Read in an input file (kgN.yr^{-1})
118	!$OMP THREADPRIVATE(N_qt_OTHER_year)
119	LOGICAL, SAVE :: l_first_chemistry_inca=.TRUE. !! Initialisation for chemistry_flux_interface
120	!$OMP THREADPRIVATE(l_first_chemistry_inca)
121
122
123
124	CONTAINS
125
126
127	!! =============================================================================================================================
128	!! SUBROUTINE: chemistry_xios_initialize
129	!!
130	!>\BRIEF Initialize xios dependant defintion before closing context defintion
131	!!
132	!! DESCRIPTION: Initialize xios dependant defintion before closing context defintion
133	!!
134	!! \n
135	!_ ==============================================================================================================================
136
137	SUBROUTINE chemistry_xios_initialize
138
139	CHARACTER(LEN=255) :: filename, name
140
141
142	!! 1. Treat the file for fertilzation needed for option ok_cropsfertil_Nox
143
144	! Read the input file name from run.def
145	filename = 'orchidee_fertilizer_1995.nc'
146	CALL getin_p('N_FERTIL_FILE',filename)
147
148	! Remove suffix .nc from filename
149	name = filename(1:LEN_TRIM(FILENAME)-3)
150	CALL xios_orchidee_set_file_attr("fertilizer_file",name=name)
151
152	! Check if the file will be read by XIOS, by IOIPSL or not at all
153	IF (xios_interpolation .AND. ok_cropsfertil_Nox) THEN
154	IF (printlev>=2) WRITE (numout,*) 'The fertilizer file will be read later by XIOS'
155	ELSE
156	IF (ok_cropsfertil_Nox) THEN
157	IF (printlev>=2) WRITE (numout,*) 'The fertilizer file will be read later by IOIPSL'
158	ELSE
159	IF (printlev>=2) WRITE (numout,*) 'The fertilizer file will not be read'
160	END IF
161
162	! The fertilizer file will not be read by XIOS. Now deactivate it for XIOS.
163	CALL xios_orchidee_set_file_attr("fertilizer_file",enabled=.FALSE.)
164	CALL xios_orchidee_set_field_attr("N_qt_WRICE_year_interp",enabled=.FALSE.)
165	CALL xios_orchidee_set_field_attr("N_qt_OTHER_year_interp",enabled=.FALSE.)
166	END IF
167
168
169	!! 2. Treat the file for bbg fertil needed for option ok_bbgfertil_Nox
170
171	! Read the input file name from run.def
172	filename = 'orchidee_bbg_clim.nc'
173	CALL getin_p('CO2_BBG_FILE',filename)
174
175	! Remove suffix .nc from filename
176	name = filename(1:LEN_TRIM(FILENAME)-3)
177	CALL xios_orchidee_set_file_attr("bbg_clim_file",name=name)
178
179	! Check if the file will be read by XIOS, by IOIPSL or not at all
180	IF (xios_interpolation .AND. ok_bbgfertil_Nox) THEN
181	IF (printlev>=2) WRITE (numout,*) 'The bbgfertil file will be read later by XIOS'
182	ELSE
183	IF (ok_bbgfertil_Nox) THEN
184	IF (printlev>=2) WRITE (numout,*) 'The bbgfertil file will be read later by IOIPSL'
185	ELSE
186	IF (printlev>=2) WRITE (numout,*) 'The bbgfertil file will not be read'
187	END IF
188
189	! This file will not be read by XIOS. Now deactivate it for XIOS.
190	CALL xios_orchidee_set_file_attr("bbg_clim_file",enabled=.FALSE.)
191	CALL xios_orchidee_set_field_attr("flx_co2_bbg_year_interp",enabled=.FALSE.)
192	END IF
193
194
195	END SUBROUTINE chemistry_xios_initialize
196
197	!! ================================================================================================================================
198	!! SUBROUTINE : chemistry_initialize
199	!!
200	!>\BRIEF This subroutine initializes the chemistry module
201	!!
202	!! DESCRIPTION : Some of the variables and flags used chemistry_bvoc are allocated and initialised here.
203	!!
204	!! RECENT CHANGE(S): Changed name from diffuco_inca_init to chemistry_initialize
205	!!
206	!! MAIN OUTPUT VARIABLE(S): None
207	!!
208	!! REFERENCE(S) : None
209	!!
210	!! FLOWCHART : None
211	!_ ================================================================================================================================
212	SUBROUTINE chemistry_initialize(kjpindex, lalo, neighbours, resolution)
213
214	USE interpweight
215
216	IMPLICIT NONE
217
218	!! 0. Variables and parameter declaration
219
220	!! 0.1 Input variables
221
222	INTEGER(i_std), INTENT(in) :: kjpindex !! Domain size (unitless)
223	REAL(r_std), DIMENSION(kjpindex,2), INTENT (in) :: lalo !! Geographical coordinates
224	INTEGER(i_std), DIMENSION(kjpindex,8), INTENT (in) :: neighbours !! Vector of neighbours for each
225	!! grid point (1=N, 2=E, 3=S, 4=W)
226	REAL(r_std),DIMENSION (kjpindex,2), INTENT(in) :: resolution !! The size in km of each grid-box in X and Y
227
228	!! 0.2 Output variables
229	REAL(r_std), DIMENSION(kjpindex) :: achem_wrice !! Availability of data for the interpolation
230	REAL(r_std), DIMENSION(kjpindex) :: achem_other !! Availability of data for the interpolation
231	REAL(r_std), DIMENSION(kjpindex) :: achem_co2 !! Availability of data for the interpolation
232
233	!! 0.3 Modified variables
234
235	!! 0.4 Local variables
236	LOGICAL :: allow_weathergen
237	CHARACTER(LEN=80) :: filename, fieldname
238	INTEGER(i_std) :: iml, jml, lml, tml, force_id
239	INTEGER(i_std) :: ier
240	REAL(r_std) :: vmin, vmax !! min/max values to use for the
241	!! renormalization
242	CHARACTER(LEN=250) :: maskvname !! Variable to read the mask from
243	!! the file
244	CHARACTER(LEN=80) :: lonname, latname !! lon, lat names in input file
245	REAL(r_std), DIMENSION(:), ALLOCATABLE :: variabletypevals !! Values for all the types of the variable
246	!! (variabletypevals(1) = -un, not used)
247	CHARACTER(LEN=50) :: fractype !! method of calculation of fraction
248	!! 'XYKindTime': Input values are kinds
249	!! of something with a temporal
250	!! evolution on the dx*dy matrix'
251	LOGICAL :: nonegative !! whether negative values should be removed
252	CHARACTER(LEN=50) :: maskingtype !! Type of masking
253	!! 'nomask': no-mask is applied
254	!! 'mbelow': take values below maskvals(1)
255	!! 'mabove': take values above maskvals(1)
256	!! 'msumrange': take values within 2 ranges;
257	!! maskvals(2) <= SUM(vals(k)) <= maskvals(1)
258	!! maskvals(1) < SUM(vals(k)) <= maskvals(3)
259	!! (normalized by maskvals(3))
260	!! 'var': mask values are taken from a
261	!! variable inside the file (>0)
262	REAL(r_std), DIMENSION(3) :: maskvals !! values to use to mask (according to
263	!! `maskingtype')
264	CHARACTER(LEN=250) :: namemaskvar !! name of the variable to use to mask
265	REAL(r_std) :: chem_norefinf !! No value
266	REAL(r_std) :: chem_default !! Default value
267
268	!_ ================================================================================================================================
269
270	ALLOCATE (pulse(kjpindex),stat=ier)
271	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable pulse','','')
272	pulse(:) = un
273
274	! If we acount for NOx pulse emissions
275	IF (ok_pulse_NOx) THEN
276
277	ALLOCATE (ok_siesta(kjpindex),stat=ier)
278	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable ok_siesta','','')
279	ok_siesta(:) = .FALSE.
280
281	ALLOCATE (allow_pulse(kjpindex),stat=ier)
282	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable allow_pulse','','')
283	allow_pulse(:) = .FALSE.
284
285	ALLOCATE (pulseday(kjpindex),stat=ier)
286	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable pulseday','','')
287	pulseday(:) = zero
288
289	ALLOCATE (siestaday(kjpindex),stat=ier)
290	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable siestaday','','')
291	siestaday(:) = zero
292
293	ALLOCATE (pulselim(kjpindex),stat=ier)
294	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable pulselim','','')
295	pulselim(:) = zero
296
297	ALLOCATE (siestalim(kjpindex),stat=ier)
298	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable siestalim','','')
299	siestalim(:) = zero
300
301	END IF ! (ok_pulse_NOx)
302
303	! If we acount for NOx emissions by N-fertilizers
304	IF (ok_cropsfertil_NOx) THEN
305
306	ALLOCATE (N_qt_WRICE_year(kjpindex),stat=ier) !! N fertilizers on wetland rice, read in file
307	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable N_qt_WRICE_year','','')
308	N_qt_WRICE_year(:) = zero
309
310	ALLOCATE (N_qt_OTHER_year(kjpindex),stat=ier) !! N fertilizers on other crops and grasses, read in file
311	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable N_qt_OTHER_year','','')
312	N_qt_OTHER_year(:) = zero
313
314	WRITE (numout,) ' ********************** Interpolating N fertilizers files for NOx emissions... '
315
316	!Config Key = N_FERTIL_FILE
317	!Config Desc = File name
318	!Config If = CHEMISTRY_BVOC and NOx_FERTILIZERS_USE
319	!Config Def = orchidee_fertilizer_1995.nc
320	!Config Help =
321	!Config Units = -
322	filename = 'orchidee_fertilizer_1995.nc'
323	CALL getin_p('N_FERTIL_FILE',filename)
324
325	IF ( xios_interpolation ) THEN
326
327	CALL xios_orchidee_recv_field('N_qt_WRICE_year_interp',N_qt_WRICE_year)
328	CALL xios_orchidee_recv_field('N_qt_OTHER_year_interp',N_qt_OTHER_year)
329
330	achem_wrice(:)=1
331	achem_other(:)=1
332	ELSE
333
334	!! Variables for interpweight
335	vmin = 0.
336	vmax = 0.
337	! Type of calculation of cell fractions
338	fractype = 'default'
339	! Name of the longitude and latitude in the input file
340	lonname = 'lon'
341	latname = 'lat'
342	! Default value when no value is get from input file
343	chem_default = 0.
344	! Reference value when no value is get from input file
345	chem_norefinf = 0.
346	! Should negative values be set to zero from input file?
347	nonegative = .TRUE.
348	! Type of mask to apply to the input data (see header for more details)
349	maskingtype = 'nomask'
350	! Values to use for the masking
351	maskvals = (/ min_sechiba, undef_sechiba, undef_sechiba /)
352	! Name of the variable with the values for the mask in the input file (only if maskkingtype='var') (here not used)
353	namemaskvar = ''
354
355	fieldname= 'N_qt_WRICE_year'
356	IF (printlev >= 1) WRITE(numout,*) "chemistry_initialize: Read and interpolate file " &
357	// TRIM(filename) //" for variable N_qt_WRICE_year"
358	CALL interpweight_2Dcont(kjpindex, 0, 0, lalo, resolution, neighbours, &
359	contfrac, filename, fieldname, lonname, latname, vmin, vmax, nonegative, maskingtype, &
360	maskvals, namemaskvar, -1, fractype, chem_default, chem_norefinf, &
361	N_qt_WRICE_year, achem_wrice)
362
363	fieldname= 'N_qt_OTHER_year'
364	IF (printlev >= 1) WRITE(numout,*) "chemistry_initialize: Read and interpolate file " &
365	// TRIM(filename) //" for variable N_qt_OTHER_year"
366	CALL interpweight_2Dcont(kjpindex, 0, 0, lalo, resolution, neighbours, &
367	contfrac, filename, fieldname, lonname, latname, vmin, vmax, nonegative, maskingtype, &
368	maskvals, namemaskvar, -1, fractype, chem_default, chem_norefinf, &
369	N_qt_OTHER_year, achem_other)
370	END IF
371	END IF
372
373	ALLOCATE (flx_iso(kjpindex,nvm), stat=ier)
374	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_iso','','')
375	flx_iso(:,:) = 0.
376
377	ALLOCATE (flx_mono(kjpindex,nvm), stat=ier)
378	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_mono','','')
379	flx_mono(:,:) = 0.
380
381	ALLOCATE (flx_ORVOC(kjpindex,nvm), stat=ier)
382	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_ORVOC ','','')
383	flx_ORVOC(:,:) = 0.
384
385	ALLOCATE (flx_MBO(kjpindex,nvm), stat=ier)
386	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_MBO','','')
387	flx_MBO(:,:) = 0.
388
389	ALLOCATE (flx_methanol(kjpindex,nvm), stat=ier)
390	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_methanol','','')
391	flx_methanol(:,:) = 0.
392
393	ALLOCATE (flx_acetone(kjpindex,nvm), stat=ier)
394	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_acetone','','')
395	flx_acetone(:,:) = 0.
396
397	ALLOCATE (flx_acetal(kjpindex,nvm), stat=ier)
398	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_acetal','','')
399	flx_acetal(:,:) = 0.
400
401	ALLOCATE (flx_formal(kjpindex,nvm), stat=ier)
402	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_formal','','')
403	flx_formal(:,:) = 0.
404
405	ALLOCATE (flx_acetic(kjpindex,nvm), stat=ier)
406	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_acetic','','')
407	flx_acetic(:,:) = 0.
408
409	ALLOCATE (flx_formic(kjpindex,nvm), stat=ier)
410	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_formic','','')
411	flx_formic(:,:) = 0.
412
413	ALLOCATE (flx_no_soil(kjpindex,nvm), stat=ier)
414	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_no_soil','','')
415	flx_no_soil(:,:) = 0.
416
417	ALLOCATE (flx_no(kjpindex,nvm), stat=ier)
418	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_no','','')
419	flx_no(:,:) = 0.
420
421	ALLOCATE (flx_fertil_no(kjpindex,nvm), stat=ier)
422	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_fertil_no','','')
423	flx_fertil_no(:,:) = 0.
424
425	ALLOCATE (flx_apinen(kjpindex,nvm), stat=ier)
426	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_apinen','','')
427	flx_apinen(:,:) = 0.
428
429	ALLOCATE (flx_bpinen (kjpindex,nvm), stat=ier)
430	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_bpinen','','')
431	flx_bpinen(:,:) = 0.
432
433	ALLOCATE (flx_limonen (kjpindex,nvm), stat=ier)
434	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_limonen','','')
435	flx_limonen(:,:) = 0.
436
437	ALLOCATE (flx_myrcen(kjpindex,nvm), stat=ier)
438	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_myrcen','','')
439	flx_myrcen(:,:) = 0.
440
441	ALLOCATE (flx_sabinen(kjpindex,nvm), stat=ier)
442	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_sabinen','','')
443	flx_sabinen(:,:) = 0.
444
445	ALLOCATE (flx_camphen(kjpindex,nvm), stat=ier)
446	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_camphen','','')
447	flx_camphen(:,:) = 0.
448
449	ALLOCATE (flx_3caren(kjpindex,nvm), stat=ier)
450	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_3caren','','')
451	flx_3caren(:,:) = 0.
452
453	ALLOCATE (flx_tbocimen(kjpindex,nvm), stat=ier)
454	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_tbocimen','','')
455	flx_tbocimen(:,:) = 0.
456
457	ALLOCATE (flx_othermono(kjpindex,nvm), stat=ier)
458	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_othermono','','')
459	flx_othermono(:,:) = 0.
460
461	ALLOCATE (flx_sesquiter(kjpindex,nvm), stat=ier)
462	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_sesquiter','','')
463	flx_sesquiter(:,:) = 0.
464
465	ALLOCATE(CRF(kjpindex,nvm), stat=ier)
466	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable CRF ','','')
467	CRF(:,:) = 0.
468
469
470	! If we acount for NOx emissions due to Biomass Burning
471	IF (ok_bbgfertil_NOx) THEN
472
473	ALLOCATE (flx_co2_bbg_year(kjpindex),stat=ier) !! CO2 emissions from bbg, read in file
474	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable flx_co2_bbg_year','','')
475	flx_co2_bbg_year(:) = zero
476
477	WRITE (numout,) ' ********************** Interpolating CO2 bbg files for NOx emissions... '
478	!Config Key = N_FERTIL_FILE
479	!Config Desc = File name
480	!Config If = CHEMISTRY_BVOC and NOx_FERTILIZERS_USE
481	!Config Def = orchidee_fertilizer_1995.nc
482	!Config Help = ...
483	!Config Units = -
484	filename = 'orchidee_bbg_clim.nc'
485	CALL getin_p('CO2_BBG_FILE',filename)
486
487	IF (xios_interpolation) THEN
488
489	CALL xios_orchidee_recv_field('flx_co2_bbg_year_interp',flx_co2_bbg_year)
490
491	achem_co2(:)=1
492	ELSE
493
494	!! Variables for interpweight
495	vmin = 0.
496	vmax = 0.
497	! Type of calculation of cell fractions
498	fractype = 'default'
499	! Name of the longitude and latitude in the input file
500	lonname = 'lon'
501	latname = 'lat'
502	! Default value when no value is get from input file
503	chem_default = 0.
504	! Reference value when no value is get from input file
505	chem_norefinf = 0.
506	! Should negative values be set to zero from input file?
507	nonegative = .TRUE.
508	! Type of mask to apply to the input data (see header for more details)
509	maskingtype = 'nomask'
510	! Values to use for the masking
511	maskvals = (/ min_sechiba, undef_sechiba, undef_sechiba /)
512	! Name of the variable with the values for the mask in the input file (only if maskkingtype='var') (here not used)
513	namemaskvar = ''
514
515	fieldname = 'flx_co2_bbg_year'
516	IF (printlev >= 1) WRITE(numout,*) "chemistry_initialize: Read and interpolate file " &
517	// TRIM(filename) //" for variable flx_co2_bbg_year"
518	CALL interpweight_2Dcont(kjpindex, 0, 0, lalo, resolution, neighbours, &
519	contfrac, filename, fieldname, lonname, latname, vmin, vmax, nonegative, maskingtype, &
520	maskvals, namemaskvar, -1, fractype, chem_default, chem_norefinf, &
521	flx_co2_bbg_year, achem_co2)
522	END IF
523	END IF
524
525	IF ( OFF_LINE_MODE ) THEN
526
527	!-
528	!- What are the alowed options for the temporal interpolation
529	!-
530	! ALLOW_WEATHERGEN : Allow weather generator to create data
531	! This parameter is already read in the driver
532	allow_weathergen = .FALSE.
533	CALL getin_p('ALLOW_WEATHERGEN',allow_weathergen)
534
535	! FORCING_FILE : Name of file containing the forcing data
536	! This parameter is already read in the driver
537	filename='forcing_file.nc'
538	CALL getin_p('FORCING_FILE',filename)
539	CALL flininfo(filename,iml, jml, lml, tml, force_id)
540	WRITE(numout,*) 'Number of data per year in forcing file :', tml
541	CALL flinclo(force_id)
542	WRITE(numout,*) 'Forcing file closed in chemistry_initialize'
543
544
545	IF ( allow_weathergen ) THEN
546	WRITE(numout,) '*chemistry_initialize: Using weather generator, careful to precip division for NOx '
547	nbre_precip = un
548	WRITE(numout,*) 'Division pour les precip, NOx:', nbre_precip
549	ELSE
550	WRITE(numout,*) 'DT_SECHIBA :', dt_sechiba
551	nbre_precip = (one_day/dt_sechiba)/(tml/one_year)
552	WRITE(numout,*) 'Division pour les precip, NOx:', nbre_precip
553	END IF
554
555	ELSE ! (in coupled mode)
556
557	nbre_precip = un
558
559	END IF ! (OFF_LINE_MODE)
560
561	! Write diagnostics
562	IF (ok_cropsfertil_NOx) THEN
563	CALL xios_orchidee_send_field("interp_avail_achem_wrice",achem_wrice)
564	CALL xios_orchidee_send_field("interp_avail_achem_other",achem_other)
565	CALL xios_orchidee_send_field("interp_diag_N_qt_WRICE_year",N_qt_WRICE_year)
566	CALL xios_orchidee_send_field("interp_diag_N_qt_OTHER_year",N_qt_OTHER_year)
567
568	END IF
569	IF (ok_bbgfertil_NOx) THEN
570	CALL xios_orchidee_send_field("interp_avail_achem_co2",achem_co2)
571	CALL xios_orchidee_send_field("interp_diag_flx_co2_bbg_year",flx_co2_bbg_year)
572	END IF
573
574
575	END SUBROUTINE chemistry_initialize
576
577
578	!! ================================================================================================================================
579	!! SUBROUTINE : chemistry_bvoc
580	!!
581	!>\BRIEF This subroutine computes biogenic emissions of reactive compounds, that is of
582	!! VOCs (volatile organic compounds) from vegetation and NOx (nitrogen oxides) from soils.
583	!! Calculation are mostly based on the works by Guenther et al. (1995) and Yienger and Levy (1995).\n
584	!!
585	!! DESCRIPTION : Biogenic VOC emissions from vegetation are based on the parameterisations developped by
586	!! Guenther et al. (1995). Biogenic VOCs considered here are: isoprene, monoterpenes, OVOC and ORVOC
587	!! as bulked emissions, methanol, acetone, acetaldehyde, formaldehyde, acetic acid, formic acid
588	!! as single emissions.\n
589	!! For every biogenic VOCs an emission factor (EF), depending on the PFT considered, is used.\n
590	!! Isoprene emissions depend on temperature and radiation. A partition between sunlit and shaded
591	!! leaves is taken into account and either one (if ok_multilayer = FALSE) or several layers
592	!! (if ok_multilayer = TRUE) in the canopy can be used.\n
593	!! When radiation extinction is considered, the canopy radiative transfer model takes into
594	!! account light extinction through canopy, calculating first need diffuse and direct radiation
595	!! based on Andrew Friend 2001 radiative model and Spitters et al. 1986. The calculation of lai,
596	!! parscat, parsh and parsun, laisun and laishabsed based on Guenther et al.(JGR, 1995) and Norman (1982).\n
597	!! Emissions for other BVOCs (monoterpenes, OVOC, ORVOC and other single compounds such as
598	!! methanol, acetone...) depend only on temperature.\n
599	!! The impact of leaf age, using an emission activity prescribed for each of the 4 leaf age
600	!! classes can also be considered for isoprene and methanol emissions when ok_leafage = TRUE.\n
601	!! NOx emissions from soils are based on Yienger and Levy (1995) and depend on soil moisture
602	!! and temperature and PFT. The pulse effect, related to significant rain occuring after severe
603	!! drought can also be considered (ok_pulse_NOx = TRUE), as well as the increase in emissions related to
604	!! biomass buring (ok_bbgfertil_NOx = TRUE) or use of fertilizers (ok_cropsfertil_NOx = TRUE).
605	!! A net NO flux is eventually calculated taking into account loss by deposition on the surface, using
606	!! a Canopy Reduction Factor (CRF) based on stomatal and leaf area.\n
607	!! This subroutine is called by diffuco_main only if biogenic emissions are activated
608	!! for sechiba (flag CHEMISTRY_BVOC=TRUE).\n
609	!!
610	!! RECENT CHANGE(S): Changed name from diffuco_inca to chemistry_bvoc
611	!!
612	!! MAIN OUTPUT VARIABLE(S): :: PAR, :: PARsun, :: PARsh, :: laisun, :: laish,
613	!! :: flx_iso, :: flx_mono, :: flx_ORVOC, :: flx_MBO,
614	!! :: flx_methanol, :: flx_acetone, :: flx_acetal, :: flx_formal,
615	!! :: flx_acetic, :: flx_formic, :: flx_no_soil, :: flx_no,
616	!! :: CRF, :: flx_fertil_no, :: Trans, :: Fdf,
617	!! :: PARdf, :: PARdr, :: PARsuntab, :: PARshtab
618	!!
619	!! REFERENCE(S) :
620	!! - Andrew Friend (2001), Modelling canopy CO2 fluxes: are 'big-leaf' simplifications justified?
621	!! Global Ecology and Biogeography, 10, 6, 603-619, doi: 10.1046/j.1466-822x.2001.00268.x
622	!! - Spitters, C.J.T, Toussaint, H.A.J.M, Groudriaan, J. (1986), Separating the diffuse and direct
623	!! component of global radiation and its implications for modeling canopy photosynthesis, Agricultural
624	!! and Forest Meteorology, 38, 1-3, 217-229, doi:10.1016/0168-1923(86)90060-2
625	!! - Norman JM (1982) Simulation of microclimates. In: Hatfield JL, Thomason IJ (eds)
626	!! Biometeorology in integrated pest management. Academic, New York, pp 65â99
627	!! - Guenther, A., Hewitt, C. N., Erickson, D., Fall, R., Geron, C., Graedel, T., Harley, P.,
628	!! Klinger, L., Lerdau, M., McKay, W. A., Pierce, T., Scholes, B., Steinbrecher, R., Tallamraju,
629	!! R., Taylor, J. et Zimmerman, P. (1995), A global model of natural volatile organic compound
630	!! emissions, J. Geophys. Res., 100, 8873-8892.
631	!! - MacDonald, R. et Fall, R. (1993), Detection of substantial emissions of methanol from
632	!! plants to the atmosphere, Atmos. Environ., 27A, 1709-1713.
633	!! - Guenther, A., Geron, C., Pierce, T., Lamb, B., Harley, P. et Fall, R. (2000), Natural emissions
634	!! of non-methane volatile organic compounds, carbon monoxide, and oxides of nitrogen from
635	!! North America, Atmos. Environ., 34, 2205-2230.
636	!! - Yienger, J. J. et Levy II, H. (1995), Empirical model of global soil-biogenic NOx emissions,
637	!! J. Geophys. Res., 100, 11,447-11,464.
638	!! - Lathiere, J., D.A. Hauglustaine, A. Friend, N. De Noblet-Ducoudre, N. Viovy, and
639	!! G. Folberth (2006), Impact of climate variability and land use changes on global biogenic volatile
640	!! organic compound emissions, Atmospheric Chemistry and Physics, 6, 2129-2146.
641	!! - Lathiere, J., D.A. Hauglustaine, N. De Noblet-Ducoudre, G. Krinner et G.A. Folberth (2005),
642	!! Past and future changes in biogenic volatile organic compound emissions simulated with a global
643	!! dynamic vegetation model, Geophysical Research Letters, 32, doi: 10.1029/2005GL024164.
644	!! - Lathiere, J. (2005), Evolution des emissions de composes organiques et azotes par la biosphere
645	!! continentale dans le modele LMDz-INCA-ORCHIDEE, These de doctorat, Universite Paris VI.
646	!!
647	!! FLOWCHART : None
648	!_ ================================================================================================================================
649
650	SUBROUTINE chemistry_bvoc (kjpindex, swdown, coszang, temp_air, &
651	temp_sol, ptnlev1, precip_rain, humrel, veget_max, lai, &
652	frac_age, lalo, ccanopy, cim, wind, snow, &
653	veget, hist_id, hist2_id,kjit, index, &
654	indexlai, indexveg)
655
656	!! 0. Variables and parameter declaration
657
658	!! 0.1 Input variables
659
660	INTEGER(i_std), INTENT(in) :: kjpindex !! Domain size - terrestrial pixels only (unitless)
661	INTEGER(i_std), INTENT(in) :: kjit !! Time step number (-)
662	INTEGER(i_std),INTENT (in) :: hist_id !! History file identifier (-)
663	INTEGER(i_std),INTENT (in) :: hist2_id !! History file 2 identifier (-)
664	INTEGER(i_std),DIMENSION (kjpindex), INTENT (in) :: index !! Indeces of the points on the map (-)
665	INTEGER(i_std),DIMENSION (kjpindex*(nlai+1)), INTENT (in) :: indexlai !! Indeces of the points on the 3D map
666	INTEGER(i_std),DIMENSION (kjpindex*nvm), INTENT (in) :: indexveg !! Indeces of the points on the 3D map (-)
667	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: swdown !! Down-welling surface short-wave flux
668	!! (W.m^{-2})
669	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: coszang !! Cosine of the solar zenith angle (unitless)
670	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: temp_air !! Air temperature (K)
671	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: temp_sol !! Skin temperature (K)
672	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: ptnlev1 !! 1st level of soil temperature (K)
673	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: precip_rain !! Rain precipitation !!?? init
674	REAL(r_std), DIMENSION(kjpindex,nvm), INTENT(in) :: humrel !! Soil moisture stress (0-1, unitless)
675	REAL(r_std), DIMENSION(kjpindex,nvm), INTENT(in) :: veget_max !! Max. vegetation fraction (0-1, unitless)
676	REAL(r_std),DIMENSION (kjpindex), INTENT (in) :: snow !! Snow mass (kg)
677	REAL(r_std),DIMENSION (kjpindex,nvm), INTENT (in) :: veget !! Fraction of vegetation type (-)
678	REAL(r_std), DIMENSION(kjpindex,nvm), INTENT(in) :: lai !! Leaf area index (m^2.m^{-2})
679	REAL(r_std), DIMENSION(kjpindex,nvm,nleafages), INTENT(in) :: frac_age !! Age efficacity from STOMATE for iso
680	REAL(r_std), DIMENSION(kjpindex,2), INTENT(in) :: lalo !! Geographical coordinates for pixels (degrees)
681	REAL(r_std),DIMENSION (kjpindex), INTENT (in) :: ccanopy !! CO2 concentration inside the canopy
682	REAL(r_std),DIMENSION (kjpindex,nvm), INTENT (in) :: cim !! Intercellular CO2 over nlai
683	REAL(r_std), DIMENSION (kjpindex), INTENT(in) :: wind !! Wind module (m s^{-1})
684
685	!! 0.2 Output variables
686
687	!! 0.3 Modified variables
688
689	!! 0.4 Local variables
690
691	INTEGER(i_std) :: ji, jv, jf, jl !! Indices (unitless)
692	REAL(r_std), DIMENSION(kjpindex,nvm) :: fol_dens !! foliar density (gDM.m^{-2})
693	REAL(r_std), DIMENSION(kjpindex) :: tleaf !! Foliar temperature (K)
694	REAL(r_std), DIMENSION(kjpindex) :: t_no !! Temperature used for soil NO emissions (C)
695	REAL(r_std), DIMENSION(kjpindex) :: exp_1 !! First exponential used in the calculation of
696	!! isoprene dependancy to Temperature
697	REAL(r_std), DIMENSION(kjpindex) :: exp_2 !! Second exponential used in the calculation of
698	!! Isoprene dependancy to Temperature
699	REAL(r_std), DIMENSION(kjpindex) :: Ct_iso !! Isoprene dependancy to Temperature
700	REAL(r_std), DIMENSION(kjpindex) :: Cl_iso !! Isoprene dependancy to Light
701	REAL(r_std), DIMENSION(kjpindex) :: Ct_mono !! Monoterpene dependancy to Temperature
702	REAL(r_std), DIMENSION(kjpindex) :: Ct_sesq !! Sesquiterpenes dependancy to Temperature
703	REAL(r_std), DIMENSION(kjpindex) :: Ct_meth !! Methanol dependancy to Temperature
704	REAL(r_std), DIMENSION(kjpindex) :: Ct_acet !! Acetone dependancy to Temperature
705	REAL(r_std), DIMENSION(kjpindex) :: Ct_oxyVOC !! Other oxygenated BVOC dependancy to Temperature
706	REAL(r_std) :: GAMMA_iso !! Temperature and light dependancy for isoprene and fo each PFT
707	REAL(r_std) :: GAMMA_iso_m !! Temperature and light dependancy for isoprene and fo each PFT for multilayer
708	REAL(r_std), DIMENSION(kjpindex) :: Ylt_mono !! Total Temperature and light dependancy for monoterpenes
709	REAL(r_std), DIMENSION(kjpindex) :: Ylt_sesq !! Total Temperature and light dependancy for sesquiterpens
710	REAL(r_std), DIMENSION(kjpindex) :: Ylt_meth !! Total Temperature and light dependancy for methanol
711	REAL(r_std), DIMENSION(kjpindex) :: Ylt_acet !! Total Temperature and light dependancy for acetone
712	REAL(r_std), DIMENSION(kjpindex) :: Ct_MBO !! MBO dependance to Temperature
713	REAL(r_std), DIMENSION(kjpindex) :: Cl_MBO !! MBO dependance to Light
714	REAL(r_std), DIMENSION(kjpindex) :: Xvar !! Parameter used in the calculation
715	!! of MBO dependance to Temperature
716	REAL(r_std), DIMENSION(kjpindex,nvm) :: flx_OVOC !! Biogenic OVOC emission -
717	!! Other Volatil Organic Components (kgC.m^{-2}.s^{-1})
718	!!Canopy radiative transfer model
719	REAL(r_std), DIMENSION(kjpindex) :: So !! Maximum radiation at the Earth surface (W.m^{-2})
720	REAL(r_std), DIMENSION(kjpindex) :: Rfrac !! Parameter in the regression of diffuse
721	!! share on transmission
722	REAL(r_std), DIMENSION(kjpindex) :: Kfrac !! Parameter in the regression of diffuse
723	!! share on transmission
724	REAL(r_std), DIMENSION(kjpindex) :: swdf !! Sw diffuse radiation (W.m^{-2})
725	REAL(r_std), DIMENSION(kjpindex) :: swdr !! Sw direct radiation (W.m^{-2})
726	REAL(r_std), DIMENSION(kjpindex,nvm) :: PARscat !! Scatter PAR @tex ($\mu mol m^{-2} s^{-1}$) @endtex
727	REAL(r_std), DIMENSION(kjpindex,nvm) :: Clsun_iso !! Isoprene dependance to light for sun leaves
728	REAL(r_std), DIMENSION(kjpindex,nvm) :: Clsh_iso !! Isoprene dependance to light for shaded leaves
729	!! for multilayer canopy model for iso flux
730	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARscattab !! Scatter PAR @tex ($\mu mol m^{-2} s^{-1}$) @endtex
731	REAL(r_std), DIMENSION(nlai+1) :: laitab !! LAI per layer (m^2.m^{-2})
732	REAL(r_std), DIMENSION(kjpindex,nlai) :: laisuntabdep !! LAI of sun leaves in each layer (m^2.m^{-2})
733	REAL(r_std), DIMENSION(kjpindex,nlai) :: laishtabdep !! LAI of shaded leaves in each layer
734	!! (m^2.m^{-2})
735	REAL(r_std) :: Clsun_iso_tab !! Isoprene dependance to light
736	!! for sun leaves and per layer
737	REAL(r_std) :: Clsh_iso_tab !! Isoprene dependance to light
738	!! for shaded leaves and per layer
739	!for multilayer canopy model Spitter et al. 1986
740	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARnotscat !! Not-Scattered PAR
741	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARabsdir !! Absorbed light of the PAR direct flux
742	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARabsdiff !! Absorbed light of the PAR diffuse flux
743	REAL(r_std), PARAMETER :: sigma = 0.20 !! scattering coefficient of single leaves and for visible radiation
744	REAL(r_std), PARAMETER :: cluster = 0.85 !! clustering coefficient for leaves, the same that is setting for default in MEGAN V2.10
745	REAL(r_std) :: rho !! reflection index of a green, closed vegetation
746	REAL(r_std) :: kbl !! extinction coefficient of black leaves
747	REAL(r_std) :: kdf !! extinction coefficient of diffuse flux
748	!!Leaf age
749	REAL(r_std), DIMENSION(kjpindex,nvm) :: Eff_age_iso !! Isoprene emission dependance to Leaf Age
750	REAL(r_std), DIMENSION(kjpindex,nvm) :: Eff_age_meth !! Methanol emission dependance to Leaf Age
751	REAL(r_std), DIMENSION(kjpindex,nvm) :: Eff_age_VOC !! Other VOC emission dependance to Leaf Age
752	!!BBG and Fertilizers for NOx soil emission
753	REAL(r_std), DIMENSION(kjpindex) :: veget_max_nowoody !! sum of veget_max for non-woody PFT
754	REAL(r_std), DIMENSION(kjpindex,nvm) :: N_qt_WRICE_pft !! N fertiliser on RICE
755	!! (kgN per year per grid cell)
756	REAL(r_std), DIMENSION(kjpindex,nvm) :: N_qt_OTHER_pft !! N fertiliser on other veg
757	!! (kgN per year per grid cell)
758	!! CO2 inhibition effect on isoprene
759	REAL(r_std),DIMENSION (kjpindex,nvm) :: fco2_wshort !! Wilkinson short term function for CO2 impact on BVOC (isoprene)
760	REAL(r_std),DIMENSION (kjpindex) :: fco2_wlong !! Wilkinson long term function for CO2 impact on BVOC (isoprene)
761	REAL(r_std) :: fco2_ctrl
762	REAL(r_std),DIMENSION (kjpindex,nvm) :: fco2 !! Function for CO2 impact on BVOC (isoprene)
763	REAL(r_std), DIMENSION(kjpindex) :: Ismax_short
764	REAL(r_std), DIMENSION(kjpindex) :: h_short
765	REAL(r_std), DIMENSION(kjpindex) :: Cstar_short
766	REAL(r_std) :: Ismax_long
767	REAL(r_std) :: h_long
768	REAL(r_std) :: Cstar_long
769
770	!! 0.5 Parameters values
771
772	REAL(r_std), PARAMETER :: CT1 = 95000.0 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(10)) (J.mol^{-1})
773	REAL(r_std), PARAMETER :: CT2 = 230000.0 !! Empirical coefficient (see Guenther .et. al, 1995, eq(10)) (J.mol^{-1})
774	REAL(r_std), PARAMETER :: TS = 303.0 !! Leaf temperature at standard condition
775	!! (see Guenther .et. al, 1995, eq(10)) (K)
776	REAL(r_std), PARAMETER :: TM = 314.0 !! Leaf temperature (see Guenther .et. al, 1995, eq(10)) (K)
777
778	REAL(r_std), PARAMETER :: alpha_ = 0.0027 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(9)) (unitless)
779	REAL(r_std), PARAMETER :: CL1 = 1.066 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(9)) (unitless)
780	REAL(r_std), PARAMETER :: beta = 0.09 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(11)) (K^{-1})
781	REAL(r_std), PARAMETER :: lai_threshold = 11. !! Lai threshold for the calculation of scattered radiation
782	!! based on Guenther .et. al (1995) (m^2.m^{-2})
783
784
785	! Biogenic emissions
786	REAL(r_std),DIMENSION(kjpindex) :: PAR !! Photosynthetic active radiation, half of swdown
787	!! @tex ($\mu mol photons. m^{-2} s^{-1}$) @endtex
788	REAL(r_std),DIMENSION(kjpindex,nvm) :: PARsun !! PAR received by sun leaves
789	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
790	REAL(r_std),DIMENSION(kjpindex,nvm) :: PARsh !! PAR received by shaded leaves
791	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
792	REAL(r_std),DIMENSION(kjpindex,nvm) :: laisun !! Leaf area index of Sun leaves (m^2.m^{-2})
793	REAL(r_std),DIMENSION(kjpindex,nvm) :: laish !! Leaf area index of Shaded leaves (m^2.m^{-2})
794
795	CHARACTER(LEN=14) :: tleafsun_name !! To store variables names for I/O
796	CHARACTER(LEN=13) :: tleafsh_name !! To store variables names for I/O
797	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: Tleafsun_temp !! temporary sunlit leaf temperature matrix for writing
798	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: Tleafsh_temp !! temporary shade leaf temperature matrix for writing
799	REAL(r_std),DIMENSION(kjpindex) :: Fdf !! Fraction of the radiation which is diffused (0-1, unitless)
800	REAL(r_std),DIMENSION(kjpindex,nlai+1) :: PARsuntab !! PAR received by sun leaves over LAI layers
801	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
802	REAL(r_std),DIMENSION(kjpindex,nlai+1) :: PARshtab !! PAR received by shaded leaves over LAI layers
803	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
804	REAL(r_std),DIMENSION(kjpindex) :: PARdf !! Diffuse photosynthetic active radiation
805	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
806	REAL(r_std),DIMENSION(kjpindex) :: PARdr !! Direct photosynthetic active radiation
807	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
808	REAL(r_std),DIMENSION(kjpindex) :: Trans !! Atmospheric Transmissivity (unitless)
809
810	!_ ================================================================================================================================
811	fco2 = 0.
812	fco2_wshort = 0.
813	fco2_wlong = 0.
814	Fdf(:) = 0.
815	PAR(:) = 0.
816	PARsun(:,:) = 0.
817	PARsh(:,:) = 0.
818	laisun(:,:) = 0.
819	laish(:,:) = 0.
820	CRF(:,:) = 0.
821	Trans(:) = 0.
822	PARdf(:) = 0.
823	PARdr(:) = 0.
824	PARsuntab(:,:) = 0.
825	PARshtab(:,:) = 0.
826
827
828	!! 1. Canopy radiative transfer model
829
830	!! Canopy radiative transfer model: takes into account light extinction through canopy
831	!! First need to calculate diffuse and direct radiation
832	!! Based on Andrew Friend radiative model (Global Ecology & Biogeography, 2001)
833	!! And Spitters et al. (Agricultural and Forest Meteorology, 1986)
834
835	IF ( ok_radcanopy ) THEN
836
837	DO ji = 1, kjpindex
838	IF (coszang(ji) .GT. zero) THEN
839	!! 1.1 Extra-terrestrial solar irradiance at a plan parallel to Earh's surface
840	So(ji) = Sct( un + 0.033COS(360.pi/180.julian_diff/365.))*coszang(ji)
841	!! 1.2 Atmospheric transmissivity
842	Trans(ji) = swdown(ji)/So(ji)
843	!! 1.3 Empirical calculation of fraction diffuse from transmission based on Spitters et al. (1986)
844	Rfrac(ji) = 0.847 - 1.61coszang(ji) + 1.04(coszang(ji)**2.)
845	Kfrac(ji) = (1.47 - Rfrac(ji))/1.66
846	IF (Trans(ji) .LE. 0.22) THEN
847	Fdf(ji) = un
848	ELSE IF (Trans(ji) .LE. 0.35) THEN
849	Fdf(ji) = un - 6.4((Trans(ji) - 0.22)*2.)
850	ELSE IF (Trans(ji) .LE. Kfrac(ji)) THEN
851	Fdf(ji) = 1.47 - 1.66*Trans(ji)
852	ELSE
853	Fdf(ji) = Rfrac(ji)
854	END IF
855	!! 1.4 Direct and diffuse sw radiation in W.m^{-2}
856	swdf(ji) = swdown(ji)*Fdf(ji)
857	swdr(ji) = swdown(ji)*(un-Fdf(ji))
858	ELSE
859	swdf(ji) = zero
860	swdr(ji) = zero
861	END IF
862
863	!! 1.5 PAR diffuse and direct in umol/m^2/s
864	PARdf(ji) = swdf(ji) * W_to_mol * RG_to_PAR
865	PARdr(ji) = swdr(ji) * W_to_mol * RG_to_PAR
866	END DO
867
868	!! 1.6 Calculation of lai, parscat, parsh and parsun, laisun and laish !!?? define the terms
869	!! Based on Guenther et al. (JGR, 1995) and Norman (1982)
870	! One-layer canopy model or multi-layer canopy model
871	IF (ok_multilayer) THEN
872
873
874	! Calculation PER LAYER
875	DO jl = nlai+1, 1, -1
876	laitab(jl) = laimax(EXP(lai_level_depth(jl-1) - un)/(EXP(lai_level_depth*nlai) - un))
877
878	!introduction of the Spitter way to calculate radiation over the levels !!!!!!!
879	DO ji = 1, kjpindex
880	kdf = cluster0.8SQRT((1 - sigma))
881	IF (ABS(ACOS(coszang(ji))) .LT. pi/2. .AND. coszang(ji) .NE. zero) THEN
882	! Coefficients calculation:
883	kbl = cluster*0.5/ABS(coszang(ji))
884	rho = ((1-SQRT((1 - sigma)))/(1+SQRT((1 - sigma))))(2/(1+1.6ABS(coszang(ji))))
885
886	PARnotscat(ji,jl) = (1 - sigma)PARdr(ji)kblEXP(-SQRT((1 - sigma))kbl*laitab(jl))
887	PARabsdir(ji,jl) = (1 - rho)SQRT((1 - sigma))PARdr(ji)kblEXP(-SQRT((1 - sigma))kbllaitab(jl))
888	PARabsdiff(ji,jl) = (1 - rho)PARdf(ji)kdfEXP(-kdflaitab(jl))
889	PARshtab(ji,jl) = (PARabsdiff(ji,jl) + (PARabsdir(ji,jl) - PARnotscat(ji,jl)))/(1 - sigma)
890	PARsuntab(ji,jl) = PARshtab(ji,jl) + (1-sigma)kblPARdr(ji)/(1 - sigma)
891
892	!correction using the equation (4) in Bodin et al 2012 and (7) or (8) in Spitter et al 1986
893	!using the extinction coefficient kbl = 0.5/coszang and not only 0.5
894	IF (jl .NE. nlai+1) THEN
895	laisuntabdep(ji,jl) =(laitab(jl+1)-laitab(jl))EXP(-kbllaitab(jl))
896	laishtabdep(ji,jl) =(laitab(jl+1)-laitab(jl))(1.-EXP(-kbllaitab(jl)))
897	ENDIF
898
899	ELSE
900
901	PARshtab(ji,jl) = PARdf(ji)kdfEXP(-kdf*laitab(jl))
902	PARsuntab(ji,jl) = 0.
903
904	IF (jl .NE. nlai+1) THEN
905	laisuntabdep(ji,jl) = 0.
906	laishtabdep(ji,jl) = laitab(jl+1)-laitab(jl)
907
908	ENDIF
909	END IF
910	END DO
911	END DO
912
913
914
915	! introduction of the Spitter way to calculate radiation over the levels !!!!!!!
916	ELSE
917	! Calculation FOR one layer
918	DO jv = 1, nvm
919	DO ji = 1, kjpindex
920	IF (lai(ji,jv) .LE. lai_threshold) THEN
921	PARscat(ji,jv) = 0.07PARdr(ji)(1.1 - 0.1lai(ji,jv))exp(-coszang(ji))
922	ELSE
923	PARscat(ji,jv) = zero
924	END IF
925
926	IF (coszang(ji) .NE. zero ) THEN
927	PARsh(ji,jv) = PARdf(ji)exp(-0.5((lai(ji,jv))**0.7)) + PARscat(ji,jv)
928	PARsun(ji,jv) = PARdr(ji)COS(60.pi/180.)/coszang(ji) + PARsh(ji,jv)
929	ELSE
930	PARsh(ji,jv) = PARdf(ji)exp(-0.5(lai(ji,jv)**0.7)) + PARscat(ji,jv)
931	PARsun(ji,jv) = zero
932	END IF
933	IF (ABS(ACOS(coszang(ji))) .LT. pi/2. .AND. ABS(coszang(ji)) .GT. min_sechiba) THEN
934	! calculation as in Lathiere (2005) = with correction removing lai in Guenther (1995)
935	laisun(ji,jv) = (un - exp(-0.5lai(ji,jv)/(coszang(ji))))coszang(ji)/COS(60.*pi/180.)
936	laish(ji,jv) = lai(ji,jv) - laisun(ji,jv)
937	ELSE
938	laisun(ji,jv) = zero
939	laish(ji,jv) = lai(ji,jv)
940	END IF
941	END DO
942	END DO
943	ENDIF
944	END IF
945
946
947	!! 2. Calculation of non-PFT dependant parameters used for VOC emissions
948	DO ji = 1, kjpindex ! (loop over # pixels)
949	!! 2.1 Calculation of Tleaf (based on Lathiere, 2005)
950
951
952	tleaf(ji) = temp_air(ji)
953
954	!! 2.2 Isoprene emission dependency - with no PARsun/PARshaded partitioning - Guenther et al. (1995) and Lathiere (2005)
955	!> @codeinc $$?? ecrire les equation en latex ?
956	exp_1(ji) = exp( (CT1 * ( tleaf(ji) - TS )) / (RRTStleaf(ji)) )
957	exp_2(ji) = exp( (CT2 ( tleaf(ji) - TM )) / (RRTS*tleaf(ji)) )
958	PAR(ji) = swdown(ji) * W_to_mol * RG_to_PAR ! from W/m^2 to umol photons/m^2/s and half of sw for PAR
959	Ct_iso(ji) = exp_1(ji)/(un + exp_2(ji)) ! temperature dependance
960	Cl_iso(ji) = alpha_CL1PAR(ji)/sqrt(un + (alpha_*2) (PAR(ji)**2) ) ! light dependance
961	!> @endcodeinc
962
963	!! 2.3 Monoterpene and oxy VOB emission dependency to Temperature
964	!! light independant fraction
965	!> @codeinc
966	!Ct_mono(ji) = exp(beta*(tleaf(ji) - TS)) ! Old method
967	Ct_mono(ji) = exp(beta_mono*(tleaf(ji) - TS))
968	Ct_sesq(ji) = exp(beta_sesq*(tleaf(ji) - TS))
969	Ct_meth(ji) = exp(beta_meth*(tleaf(ji) - TS))
970	Ct_acet(ji) = exp(beta_acet*(tleaf(ji) - TS))
971	Ct_oxyVOC(ji) = exp(beta_oxyVOC*(tleaf(ji) - TS))
972	!> @endcodeinc
973	!! 2.4 MBO biogenic emissions dependency, only from PFT7 and PFT4 for location of vegetation emitter
974	! but in fact MBO fluxes only in America (ponderosa and lodgepole pines only found in these areas)
975	!> @codeinc
976	Xvar(ji) = ((un/312.3) - (un/tleaf(ji)))/RR
977	!> @endcodeinc
978	!! 2.4.1 temperature dependency
979	!> @codeinc
980	Ct_MBO(ji) = (1.52209000.0exp(67000.0Xvar(ji)))/(209000.0 - 67000.0(un - exp(209000.0*Xvar(ji))))
981	!> @endcodeinc
982	!! 2.4.2 light dependency
983	Cl_MBO(ji) = (0.00111.44PAR(ji))/(sqrt(un + (0.0011*2)(PAR(ji)**2)))
984	!! 2.5 NO biogenic emissions given in ngN/m^2/s, emission factor in ngN/m^2/s too
985	!! calculation of temperature used for NO soil emissions
986	t_no(ji) = ptnlev1(ji) - ZeroCelsius !!temp must be in celsius to calculate no emissions
987	!! 2.6 calculation of non-woody veget_max fraction
988	IF (ok_cropsfertil_NOx) THEN
989	veget_max_nowoody(ji) = zero
990	DO jv = 1,nvm
991	IF ( (jv /= ibare_sechiba) .AND. .NOT.(is_tree(jv)) ) THEN
992	veget_max_nowoody(ji) = veget_max_nowoody(ji) + veget_max(ji,jv)
993	ENDIF
994	ENDDO
995	END IF
996	END DO ! (loop over # pixels)
997
998	!! 2bis. Calculation of CO2 function for inhibition effect on isoprene
999	! 2 approaches can be used: either Possell et al. (2005) or Wilkinson et al. (2006)
1000
1001	!! 19/04/2010 and then implemented in version revised by Nicolas Vuichard, 08042014
1002	!! Impact of atmospheric CO2 on isoprene emissions
1003	!! Can be activated or not
1004	!! If considered, can use either Possell 2005 or Wilkinson 2009 parameterisation
1005	!! This is used to rescale the emission factor, considered to be measured at 350 ppm of CO2
1006	!! to the CO2 conditions of the run
1007
1008	IF ( ok_co2bvoc_poss ) THEN
1009	WRITE(numout,*) 'CO2 impact on isoprene: Possell calculation'
1010
1011	!! Possell function needs to be normalized (experiments at 400 ppm and EF before 1995)
1012	!! Normalized at 350 ppm
1013	fco2_ctrl = (-0.0123+(441.4795/350.)+(-1282.65/(350.**2)))
1014
1015	!! 2 tests: using the canopy (atmospheric) CO2 'ccanopy'
1016	!! or the intercellular CO2 over nlai 'cim'
1017	!! with cim = ccanopy*0.667
1018	!! in the end I go for ccanopy for the Possell function since too much differences
1019	!! when using cim and also the function has been derived based on atmospheric CO2
1020	DO ji = 1, kjpindex
1021
1022	fco2(ji,:) = (-0.0123+(441.4795/ccanopy(ji))+(-1282.65/(ccanopy(ji)*ccanopy(ji))))/fco2_ctrl
1023
1024	END DO
1025	ELSE IF ( ok_co2bvoc_wilk ) THEN
1026	WRITE(numout,*) 'CO2 impact on isoprene: Wilkinson calculation'
1027
1028	!! In the Wilkinson function, 2 impacts are considered:
1029	!! -short-term impact for CO2 variation during a single day (seconds/minutes)
1030	!! -long-term impact for CO2 variation during leaf-growth (weeks/month)
1031
1032
1033	!! Long-term parameters
1034	!! Constant
1035	Ismax_long = 1.344
1036	h_long = 1.4614
1037	Cstar_long = 585.
1038	!! Short-term parameters
1039	!! They have to be calculated based on atmospheric CO2
1040	!! 10/05/2010
1041	!! For atmospheric CO2 lower than 400 ppm or higher than 1200 ppm
1042	!! (min and max CO2 level tested for short-term effect in Wilkinson et al. 2009)
1043	!! we use the parameters calculated at 400/1200 ppm. For intermediate CO2 concentration,
1044	!! parameters are calculated.
1045	!! Linear interpolation
1046
1047	DO ji = 1, kjpindex
1048
1049	IF (ccanopy(ji) .LE. 400.) THEN
1050
1051	Ismax_short(ji) = 1.072
1052	h_short(ji) = 1.7
1053	Cstar_short(ji) = 1218.
1054
1055	ELSE IF (ccanopy(ji) .EQ. 600.) THEN
1056
1057	Ismax_short(ji) = 1.036
1058	h_short(ji) = 2.0125
1059	Cstar_short(ji) = 1150.
1060
1061	ELSE IF (ccanopy(ji) .EQ. 800.) THEN
1062
1063	Ismax_short(ji) = 1.046
1064	h_short(ji) = 1.5380
1065	Cstar_short(ji) = 2025.
1066
1067	ELSE IF (ccanopy(ji) .GE. 1200.) THEN
1068
1069	Ismax_short(ji) = 1.014
1070	h_short(ji) = 2.8610
1071	Cstar_short(ji) = 1525.
1072
1073
1074	ELSE IF ((ccanopy(ji) .GT. 400.) .AND. (ccanopy(ji) .LT. 600.)) THEN
1075
1076	Ismax_short(ji) = 1.036 + (ccanopy(ji)-600.)*(1.036-1.072)/(600.-400.)
1077	h_short(ji) = 2.0125 + (ccanopy(ji)-600.)*(2.0125-1.7)/(600.-400.)
1078	Cstar_short(ji) = 1150. + (ccanopy(ji)-600.)*(1150.-1218.)/(600.-400.)
1079
1080	ELSE IF ((ccanopy(ji) .GT. 600.) .AND. (ccanopy(ji) .LT. 800.)) THEN
1081
1082	Ismax_short(ji) = 1.046 + (ccanopy(ji)-800.)*(1.046-1.036)/(800.-600.)
1083	h_short(ji) = 1.5380 + (ccanopy(ji)-800.)*(1.5380-2.0125)/(800.-600.)
1084	Cstar_short(ji) = 2025. + (ccanopy(ji)-800.)*(2025.-1150.)/(800.-600.)
1085
1086	ELSE IF ((ccanopy(ji) .GT. 800.) .AND. (ccanopy(ji) .LT. 1200.)) THEN
1087
1088	Ismax_short(ji) = 1.014 + (ccanopy(ji)-1200.)*(1.014-1.046)/(1200.-800.)
1089	h_short(ji) = 2.8610 + (ccanopy(ji)-1200.)*(2.8610-1.5380)/(1200.-800.)
1090	Cstar_short(ji) = 1525. + (ccanopy(ji)-1200.)*(1525.-2025.)/(1200.-800.)
1091
1092
1093	END IF
1094
1095	END DO
1096
1097	WRITE(numout,) 'Wilkinson BVOC-CO2 function: parameters*'
1098	WRITE(numout,*) 'Ismax_long: ', Ismax_long
1099	WRITE(numout,*) 'h_long: ', h_long
1100	WRITE(numout,*) 'Cstar_long: ', Cstar_long
1101	WRITE(numout,*) 'Ismax_short: ', MAXVAL(Ismax_short(:)) , MINVAL(Ismax_short(:))
1102	WRITE(numout,*) 'h_short: ', MAXVAL(h_short(:)) , MINVAL(h_short(:))
1103	WRITE(numout,*) 'Cstar_short: ', MAXVAL(Cstar_short(:)) , MINVAL(Cstar_short(:))
1104	WRITE(numout,) '*****'
1105
1106	DO ji = 1, kjpindex
1107	fco2_wlong(ji) = (Ismax_long-((Ismax_long((0.667ccanopy(ji))**h_long))/&
1108	& ((Cstar_long*h_long)+(0.667ccanopy(ji))**h_long)))/1.06566
1109	DO jv = 1, nvm
1110	fco2_wshort(ji,jv) = (Ismax_short(ji)-((Ismax_short(ji)((cim(ji,jv))*h_short(ji)))/&
1111	& ((Cstar_short(ji)h_short(ji))+(cim(ji,jv))h_short(ji))))/1.010803
1112	END DO
1113	END DO
1114
1115	DO ji = 1, kjpindex
1116	DO jv = 1, nvm
1117	fco2(ji,jv) = fco2_wshort(ji,jv)*fco2_wlong(ji)
1118	END DO
1119	END DO
1120
1121	ELSE
1122	WRITE(numout,*) 'CO2 impact on isoprene not considered'
1123	fco2(:,:) = 1.
1124	END IF
1125
1126
1127	!! 3. Calculation of PFT dependant parameters and
1128	! Calculation of VOC emissions flux
1129
1130	Eff_age_iso(:,:) = zero
1131	Eff_age_meth(:,:) = zero
1132
1133
1134	DO jv = 1, nvm ! loop over the PDFs
1135	DO ji = 1, kjpindex ! loop over the grid cell
1136	! 6-Calculation of Leaf Age Function (Lathiere 2005)
1137	IF ( ok_leafage ) THEN
1138	DO jf = 1, nleafages
1139	!> @codeinc
1140	Eff_age_iso(ji,jv) = Eff_age_iso(ji,jv) + frac_age(ji,jv,jf)*iso_activity(jf)
1141	Eff_age_meth(ji,jv) = Eff_age_meth(ji,jv) + frac_age(ji,jv,jf)*methanol_activity(jf)
1142	!> @endcodeinc
1143	END DO
1144	!> @codeinc
1145	Eff_age_VOC(ji,jv) = un
1146	!> @endcodeinc
1147	ELSE
1148	Eff_age_iso(ji,jv) = un
1149	Eff_age_meth(ji,jv) = un
1150	Eff_age_VOC(ji,jv) = un
1151	END IF
1152	!! 5. Calculation of foliar density
1153	! Changes the IF-statement so it also works for
1154	! a dynamic sla
1155	!!$ IF ( sla(jv) .eq. zero ) THEN
1156	IF ( veget_max(ji,jv) .eq. zero ) THEN
1157	fol_dens(ji,jv) = zero
1158	ELSE
1159	! 2 factor for conversion from gC to gDM. Use
1160	! lai_to_biomass to account for dynamic sla
1161	fol_dens(ji,jv) = lai_to_biomass(2 * lai(ji,jv),jv)
1162	ENDIF
1163	!! 6. Calculation of VOC emissions from vegetation
1164	IF ( ok_radcanopy ) THEN
1165	! if multi-layer canopy model
1166	IF (ok_multilayer) THEN
1167
1168	laisun(ji,jv) = zero
1169	laish(ji,jv) = zero
1170	GAMMA_iso_m = zero
1171	flx_iso(ji,jv) = zero
1172	flx_mono(ji,jv) = zero
1173	flx_apinen(ji,jv) = zero
1174	flx_bpinen(ji,jv) = zero
1175	flx_limonen(ji,jv) = zero
1176	flx_myrcen(ji,jv) = zero
1177	flx_sabinen(ji,jv) = zero
1178	flx_camphen(ji,jv) = zero
1179	flx_3caren(ji,jv) = zero
1180	flx_tbocimen(ji,jv) = zero
1181	flx_othermono(ji,jv) = zero
1182	flx_sesquiter(ji,jv) = zero
1183	flx_methanol(ji,jv) = zero
1184	flx_acetone(ji,jv) = zero
1185	flx_acetal(ji,jv) = zero
1186	flx_formal(ji,jv) = zero
1187	flx_acetic(ji,jv) = zero
1188	flx_formic(ji,jv) = zero
1189	! loop over the NLAI canopy layers
1190	DO jl = 1, nlai
1191	IF ((laitab(jl) .LE. lai(ji,jv)).AND.(lai(ji,jv).NE.zero)) THEN
1192	!sunlit vegetation
1193	Clsun_iso_tab = alpha_CL1PARsuntab(ji,jl)/sqrt(un + (alpha_*2) (PARsuntab(ji,jl)**2) )
1194	! shaded vegetation
1195	Clsh_iso_tab = alpha_CL1PARshtab(ji,jl)/sqrt(un + (alpha_*2) (PARshtab(ji,jl)**2) )
1196	flx_iso(ji,jv) = flx_iso(ji,jv) + (laisuntabdep(ji,jl)*Clsun_iso_tab+ &
1197	& laishtabdep(ji,jl)Clsh_iso_tab) &
1198	& fol_dens(ji,jv)/lai(ji,jv)Ct_iso(ji)em_factor_isoprene(jv)* &
1199	& Eff_age_iso(ji,jv)fco2(ji,jv)1e-9/one_hour
1200
1201	GAMMA_iso_m = GAMMA_iso_m + (laisuntabdep(ji,jl)*Clsun_iso_tab+ &
1202	& laishtabdep(ji,jl)Clsh_iso_tab) &
1203	& fol_dens(ji,jv)/lai(ji,jv)Ct_iso(ji)1e-9/one_hour
1204
1205	laisun(ji,jv) = laisun(ji,jv) + laisuntabdep(ji,jl)
1206	laish(ji,jv) = laish(ji,jv) + laishtabdep(ji,jl)
1207	END IF
1208	END DO
1209
1210	!! 6.1 Calculation of monoterpene biogenic emissions
1211	flx_mono(ji,jv) = ((1-LDF_mono)Ct_mono(ji)1e-9/one_hourfol_dens(ji,jv) + LDF_monoGAMMA_iso_m)* &
1212	& em_factor_monoterpene(jv)*Eff_age_VOC(ji,jv)
1213	!! 6.12 Calculation of sesquiterpenes biogenic emission
1214	flx_sesquiter(ji,jv) = ((1-LDF_sesq)Ct_sesq(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_sesqGAMMA_iso_m)* &
1215	& em_factor_sesquiterp(jv)*Eff_age_VOC(ji,jv)
1216	!! 6.13 Calculation of methanol biogenic emissions
1217	flx_methanol(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1218	& em_factor_methanol(jv)*Eff_age_meth(ji,jv)
1219	!! 6.14 Calculation of acetone biogenic emissions
1220	flx_acetone(ji,jv) = ((1-LDF_acet)Ct_acet(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_acetGAMMA_iso_m)* &
1221	& em_factor_acetone(jv)*Eff_age_VOC(ji,jv)
1222	!! 6.14 Calculation of acetaldehyde biogenic emissions
1223	flx_acetal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1224	& em_factor_acetal(jv)*Eff_age_VOC(ji,jv)
1225	!! 6.16 Calculation of formaldehyde biogenic emissions
1226	flx_formal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1227	& em_factor_formal(jv)*Eff_age_VOC(ji,jv)
1228	!! 6.17 Calculation of acetic acid biogenic emissions
1229	flx_acetic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1230	& em_factor_acetic(jv)*Eff_age_VOC(ji,jv)
1231	!! 6.18 Calculation of formic acid biogenic emissions
1232	flx_formic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1233	& em_factor_formic(jv)*Eff_age_VOC(ji,jv)
1234
1235
1236	!! 6.3 Calculation of alfa pinene biogenic emission
1237	flx_apinen(ji,jv) = em_factor_apinene(jv)*flx_mono(ji,jv)
1238	!! 6.4 Calculation of beta pinene biogenic emission
1239	flx_bpinen(ji,jv) = em_factor_bpinene(jv)*flx_mono(ji,jv)
1240	!! 6.5 Calculation of limonene biogenic emission
1241	flx_limonen(ji,jv) = em_factor_limonene(jv)*flx_mono(ji,jv)
1242	!! 6.6 Calculation of myrcene biogenic emission !!
1243	flx_myrcen(ji,jv) = em_factor_myrcene(jv)*flx_mono(ji,jv)
1244	!! 6.7 Calculation of sabinene biogenic emission
1245	flx_sabinen(ji,jv) = em_factor_sabinene(jv)*flx_mono(ji,jv)
1246	!! 6.8 Calculation of camphene biogenic emission
1247	flx_camphen(ji,jv) = em_factor_camphene(jv)*flx_mono(ji,jv)
1248	!! 6.9 Calculation of 3-carene biogenic emission
1249	flx_3caren(ji,jv) = em_factor_3carene(jv)*flx_mono(ji,jv)
1250	!! 6.10 Calculation of t-beta-ocimene biogenic emission
1251	flx_tbocimen(ji,jv) = em_factor_tbocimene(jv)*flx_mono(ji,jv)
1252	!! 6.11 Calculation of other monoterpenes biogenic emission
1253	flx_othermono(ji,jv) = em_factor_othermonot(jv)*flx_mono(ji,jv)
1254
1255	! if mono-layer canopy model
1256	ELSE
1257	!sunlit vegetation
1258	Clsun_iso(ji,jv) = alpha_CL1PARsun(ji,jv)/sqrt(un + (alpha_*2) (PARsun(ji,jv)**2) )
1259	! shaded vegetation
1260	Clsh_iso(ji,jv) = alpha_CL1PARsh(ji,jv)/sqrt(un + (alpha_*2) (PARsh(ji,jv)**2) )
1261	IF (lai(ji,jv) .NE. zero) THEN
1262	!! 6.1 Calculation of isoprene biogenic emissions
1263	GAMMA_iso = (laisun(ji,jv)Clsun_iso(ji,jv) + laish(ji,jv)Clsh_iso(ji,jv))/lai(ji,jv)*Ct_iso(ji)
1264	flx_iso(ji,jv) = GAMMA_isofol_dens(ji,jv)em_factor_isoprene(jv)Eff_age_iso(ji,jv)fco2(ji,jv)*1e-9/one_hour
1265	!! 6.2 Calculation of monoterpene biogenic emissions
1266	flx_mono(ji,jv) = ((1-LDF_mono)Ct_mono(ji)+LDF_monoGAMMA_iso)fol_dens(ji,jv) &
1267	& em_factor_monoterpene(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1268	!! 6.3 Calculation of alfa pinene biogenic emission
1269	flx_apinen(ji,jv) = em_factor_apinene(jv)*flx_mono(ji,jv)
1270	!! 6.4 Calculation of beta pinene biogenic emission
1271	flx_bpinen(ji,jv) = em_factor_bpinene(jv)*flx_mono(ji,jv)
1272	!! 6.5 Calculation of limonene biogenic emission
1273	flx_limonen(ji,jv) = em_factor_limonene(jv)*flx_mono(ji,jv)
1274	!! 6.6 Calculation of myrcene biogenic emission
1275	flx_myrcen(ji,jv) = em_factor_myrcene(jv)*flx_mono(ji,jv)
1276	!! 6.7 Calculation of sabinene biogenic emission
1277	flx_sabinen(ji,jv) = em_factor_sabinene(jv)*flx_mono(ji,jv)
1278	!! 6.8 Calculation of camphene biogenic emission
1279	flx_camphen(ji,jv) = em_factor_camphene(jv)*flx_mono(ji,jv)
1280	!! 6.9 Calculation of 3-carene biogenic emission
1281	flx_3caren(ji,jv) = em_factor_3carene(jv)*flx_mono(ji,jv)
1282	!! 6.10 Calculation of t-beta-ocimene biogenic emission
1283	flx_tbocimen(ji,jv) = em_factor_tbocimene(jv)*flx_mono(ji,jv)
1284	!! 6.11 Calculation of other monoterpenes biogenic emission
1285	flx_othermono(ji,jv) = em_factor_othermonot(jv)*flx_mono(ji,jv)
1286	!! 6.12 Calculation of sesquiterpenes biogenic emission
1287	flx_sesquiter(ji,jv) = ((1-LDF_sesq)Ct_sesq(ji)+LDF_sesqGAMMA_iso)fol_dens(ji,jv) &
1288	& em_factor_sesquiterp(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1289	!! 6.13 Calculation of methanol biogenic emissions
1290	flx_methanol(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1291	& em_factor_methanol(jv)Eff_age_meth(ji,jv)1e-9/one_hour
1292	!! 6.14 Calculation of acetone biogenic emissions
1293	flx_acetone(ji,jv) = ((1-LDF_acet)Ct_acet(ji)+LDF_acetGAMMA_iso)fol_dens(ji,jv) &
1294	& em_factor_acetone(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1295	!! 6.15 Calculation of acetaldehyde biogenic emissions
1296	flx_acetal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1297	& em_factor_acetal(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1298	!! 6.16 Calculation of formaldehyde biogenic emissions
1299	flx_formal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1300	& em_factor_formal(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1301	!! 6.17 Calculation of acetic acid biogenic emissions
1302	flx_acetic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1303	& em_factor_acetic(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1304	!! 6.18 Calculation of formic acid biogenic emissions
1305	flx_formic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1306	& em_factor_formic(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1307
1308	ELSE
1309	!
1310	flx_iso(ji,jv) = zero
1311	flx_mono(ji,jv) = zero
1312	flx_apinen(ji,jv) = zero
1313	flx_bpinen(ji,jv) = zero
1314	flx_limonen(ji,jv) = zero
1315	flx_myrcen(ji,jv) = zero
1316	flx_sabinen(ji,jv) = zero
1317	flx_camphen(ji,jv) = zero
1318	flx_3caren(ji,jv) = zero
1319	flx_tbocimen(ji,jv) = zero
1320	flx_othermono(ji,jv) = zero
1321	flx_sesquiter(ji,jv) = zero
1322	flx_methanol(ji,jv) = zero
1323	flx_acetone(ji,jv) = zero
1324	flx_acetal(ji,jv) = zero
1325	flx_formal(ji,jv) = zero
1326	flx_acetic(ji,jv) = zero
1327	flx_formic(ji,jv) = zero
1328	END IF
1329	END IF
1330	! if no light extinction due to vegetation
1331	ELSE
1332	!! Isoprene emissions - general equation
1333	flx_iso(ji,jv) = fol_dens(ji,jv)Ct_iso(ji)Cl_iso(ji)Eff_age_iso(ji,jv)fco2(ji,jv)* &
1334	em_factor_isoprene(jv)*1e-9/one_hour
1335	!! 6.2 Calculation of monoterpene biogenic emissions
1336	Ylt_mono(ji) = ((1-LDF_mono)Ct_mono(ji)+LDF_monoCt_iso(ji)*Cl_iso(ji))
1337	flx_mono(ji,jv) = fol_dens(ji,jv)em_factor_monoterpene(jv)Ylt_mono(ji)Eff_age_VOC(ji,jv)&
1338	1e-9/one_hour
1339	!! 6.3 Calculation of alfa pinene biogenic emission
1340	flx_apinen(ji,jv) = em_factor_apinene(jv)*flx_mono(ji,jv)
1341	!! 6.4 Calculation of beta pinene biogenic emission
1342	flx_bpinen(ji,jv) = em_factor_bpinene(jv)*flx_mono(ji,jv)
1343	!! 6.5 Calculation of limonene biogenic emission
1344	flx_limonen(ji,jv) = em_factor_limonene(jv)*flx_mono(ji,jv)
1345	!! 6.6 Calculation of myrcene biogenic emission
1346	flx_myrcen(ji,jv) = em_factor_myrcene(jv)*flx_mono(ji,jv)
1347	!! 6.7 Calculation of sabinene biogenic emission
1348	flx_sabinen(ji,jv) = em_factor_sabinene(jv)*flx_mono(ji,jv)
1349	!! 6.8 Calculation of camphene biogenic emission
1350	flx_camphen(ji,jv) = em_factor_camphene(jv)*flx_mono(ji,jv)
1351	!! 6.9 Calculation of 3-carene biogenic emission
1352	flx_3caren(ji,jv) = em_factor_3carene(jv)*flx_mono(ji,jv)
1353	!! 6.10 Calculation of t-beta-ocimene biogenic emission
1354	flx_tbocimen(ji,jv) = em_factor_tbocimene(jv)*flx_mono(ji,jv)
1355	!! 6.11 Calculation of other monoterpenes biogenic emission
1356	flx_othermono(ji,jv) = em_factor_othermonot(jv)*flx_mono(ji,jv)
1357	!! 6.12 Calculation of sesquiterpenes biogenic emission
1358	Ylt_sesq(ji) = ((1-LDF_sesq)Ct_sesq(ji)+LDF_sesqCt_iso(ji)*Cl_iso(ji))
1359	flx_sesquiter(ji,jv) = fol_dens(ji,jv)em_factor_sesquiterp(jv)Ylt_sesq(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1360	!! 6.16 Calculation of methanol biogenic emissions
1361	Ylt_meth(ji) = ((1-LDF_meth)Ct_meth(ji)+LDF_methCt_iso(ji)*Cl_iso(ji))
1362	flx_methanol(ji,jv) = fol_dens(ji,jv)em_factor_methanol(jv)Ylt_meth(ji)Eff_age_meth(ji,jv)1e-9/one_hour
1363	!! 6.17 Calculation of acetone biogenic emissions
1364	Ylt_acet(ji) = ((1-LDF_acet)Ct_acet(ji)+LDF_acetCt_iso(ji)*Cl_iso(ji))
1365	flx_acetone(ji,jv) = fol_dens(ji,jv)em_factor_acetone(jv)Ylt_acet(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1366	!! 6.18 Calculation of acetaldehyde biogenic emissions
1367	flx_acetal(ji,jv) = fol_dens(ji,jv)em_factor_acetal(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1368	!! 6.19 Calculation of formaldehyde biogenic emissions
1369	flx_formal(ji,jv) = fol_dens(ji,jv)em_factor_formal(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1370	!! 6.20 Calculation of acetic acid biogenic emissions
1371	flx_acetic(ji,jv) = fol_dens(ji,jv)em_factor_acetic(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1372	!! 6.21 Calculation of formic acid biogenic emissions
1373	flx_formic(ji,jv) = fol_dens(ji,jv)em_factor_formic(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1374
1375	END IF
1376
1377	!! 6.22 Calculation of ORVOC biogenic emissions
1378	!! Other Reactive Volatile Organic Compounds
1379	!> @codeinc
1380	flx_ORVOC(ji,jv) = fol_dens(ji,jv)em_factor_ORVOC(jv)Ct_mono(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1381	!> @endcodeinc
1382	!! 6.4 Calculation of OVOC biogenic emissions
1383	!! Other Volatile Organic Compounds
1384	flx_OVOC(ji,jv) = fol_dens(ji,jv)em_factor_OVOC(jv)Ct_mono(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1385	!! 6.5 Calculation of MBO biogenic emissions
1386	!! 2-Methyl-3-Buten-2-ol
1387	IF(lalo(ji,1) .GE. 20. .AND. lalo(ji,2) .LE. -100) THEN
1388	flx_MBO(ji,jv) = fol_dens(ji,jv)em_factor_MBO(jv)Ct_MBO(ji)Cl_MBO(ji)Eff_age_VOC(ji,jv)*1e-9/one_hour
1389	ELSE
1390	flx_MBO(ji,jv) = zero
1391	END IF
1392	END DO
1393
1394	END DO
1395
1396
1397	!! 7. Calculation of NOx emissions from soils
1398	! Based on Yienger & Levy (1995) and Lathiere (2005, chapter 3)
1399	DO ji = 1, kjpindex
1400	!! 7.1 Precipitation-related pulse function
1401	IF (ok_pulse_NOx) THEN
1402	! if we are during a period where pulses are not allowed
1403	IF (ok_siesta(ji)) THEN
1404	! if this period is not over
1405	IF (FLOOR(siestaday(ji)) .LE. siestalim(ji)) THEN
1406	siestaday(ji) = siestaday(ji) + (dt_sechiba/one_day)
1407	! if this period is over
1408	ELSE
1409	ok_siesta(ji) = .FALSE.
1410	siestaday(ji) = zero
1411	END IF
1412	END IF
1413	! if we are during a period where pulses are allowed
1414	IF ((.NOT. ok_siesta(ji)) .AND. (.NOT. allow_pulse(ji))) THEN
1415	IF (humrel(ji,1) .LT. 0.15) THEN
1416	! if precip exceeds 1 mm/day over one time step => a pulse occurs
1417	IF(precip_rain(ji)/nbre_precip .GE. un/(one_day/dt_sechiba)) THEN
1418	! if precip is up to 5 mm/day => pulse length is 3 days
1419	IF (precip_rain(ji)/nbre_precip .LT. 5./(one_day/dt_sechiba)) THEN
1420	pulselim(ji) = 3.
1421	! if precip is up to 15 mm/day => pulse length is 7 days
1422	ELSE IF (precip_rain(ji)/nbre_precip .LT. 15./(one_day/dt_sechiba)) THEN
1423	pulselim(ji) = 7.
1424	! if precip is upper than 15 mm/day => pulse length is 14 days
1425	ELSE IF (precip_rain(ji)/nbre_precip .GE. 15./(one_day/dt_sechiba)) THEN
1426	pulselim(ji) = 14.
1427	END IF
1428	allow_pulse(ji)=.TRUE.
1429	pulseday(ji) = un
1430	END IF
1431	END IF
1432	END IF
1433	! if we were during a pulse period
1434	IF (allow_pulse(ji)) THEN
1435	! if we are still during the pulse period
1436	! 16/06/2010 We assume a (pulselim-1) days for the pulse length (NVui+Jlath)
1437	IF(FLOOR(pulseday(ji)) .LT. pulselim(ji)) THEN
1438	! calculation of the pulse function
1439	IF (pulselim(ji).EQ.3) THEN
1440	pulse(ji) = 11.19exp(-0.805pulseday(ji))
1441	ELSE IF (pulselim(ji).EQ.7) THEN
1442	pulse(ji) = 14.68exp(-0.384pulseday(ji))
1443	ELSE IF (pulselim(ji).EQ.14) THEN
1444	pulse(ji) = 18.46exp(-0.208pulseday(ji))
1445	END IF
1446	pulseday(ji) = pulseday(ji) + (dt_sechiba/one_day)
1447	! if the pulse period is over
1448	ELSE
1449	! pulse function is set to 1
1450	pulse(ji) = un
1451	allow_pulse(ji) = .FALSE.
1452	siestaday(ji) = un
1453	siestalim(ji) = pulselim(ji)
1454	ok_siesta(ji) = .TRUE.
1455	END IF
1456	END IF
1457	! no precipitation-related pulse function
1458	ELSE
1459	pulse(ji) = un
1460	END IF
1461	END DO
1462
1463	!! 7.2 Calculation of NO basal emissions including pulse effect
1464	DO jv = 1, nvm
1465	DO ji = 1, kjpindex
1466	!Tropical forests
1467	IF ( is_tropical(jv) .AND. is_evergreen(jv) ) THEN
1468	! Wet soils
1469	IF (humrel(ji,1) .GT. 0.3) THEN
1470	flx_no_soil(ji,jv) = 2.6*pulse(ji)
1471	! Dry soils
1472	ELSE
1473	flx_no_soil(ji,jv) = 8.6*pulse(ji)
1474	END IF
1475	!Else If agricultural lands OR Wet soils
1476	ELSE IF ( ( .NOT.(natural(jv)) ) .OR. ( humrel(ji,1) .GT. 0.3 ) ) THEN
1477	! Calculation of NO emissions depending of Temperature
1478	IF (t_no(ji) .LT. zero) THEN
1479	flx_no_soil(ji,jv) = zero
1480	ELSE IF (t_no(ji) .LE. 10.) THEN
1481	flx_no_soil(ji,jv) = 0.28em_factor_no_wet(jv)t_no(ji)*pulse(ji)
1482	ELSE IF (t_no(ji) .LE. 30.) THEN
1483	flx_no_soil(ji,jv) = em_factor_no_wet(jv)exp(0.103t_no(ji))*pulse(ji)
1484	ELSE
1485	flx_no_soil(ji,jv) = 21.97em_factor_no_wet(jv)pulse(ji)
1486	END IF
1487	!Else if Temp negative
1488	ELSE IF (t_no(ji) .LT. zero) THEN
1489	flx_no_soil(ji,jv) = zero
1490	!Else if Temp <= 30
1491	ELSE IF (t_no(ji) .LE. 30.) THEN
1492	flx_no_soil(ji,jv) = (em_factor_no_dry(jv)t_no(ji))/30.pulse(ji)
1493	ELSE
1494	flx_no_soil(ji,jv) = em_factor_no_dry(jv)*pulse(ji)
1495	END IF
1496
1497	!! 7.3 IF ACTIVATED (ok_bbgfertil_NOx = TRUE) calculation of NOx soil emission increase due to biomass burning
1498	! Calculation of Biomass-Burning-induced NOx emissions (Lathiere, 2005)
1499	! => NOx emissions 3-fold increase
1500	IF (ok_bbgfertil_NOx) THEN
1501	IF ( natural(jv) ) THEN
1502	! North Tropical zone from May to June
1503	IF ((lalo(ji,1) .LE. 30. .AND. lalo(ji,1) .GE. zero).AND. &
1504	(julian_diff .GE. 121. .AND. julian_diff .LE. 181).AND.(flx_co2_bbg_year(ji) .GT. 0.1)) THEN
1505	flx_no_soil(ji,jv) = flx_no_soil(ji,jv)*3.
1506	! South Tropical zone from November to December
1507	ELSE IF ((lalo(ji,1) .GE. -30. .AND. lalo(ji,1) .LT. zero).AND.(julian_diff .GE. 305.).AND. &
1508	(flx_co2_bbg_year(ji) .GT. 0.1)) THEN
1509	flx_no_soil(ji,jv) = flx_no_soil(ji,jv)*3.
1510	END IF
1511	END IF
1512	END IF
1513
1514	!! 7.4 IF ACTIVATED (ok_cropsfertil_NOx = TRUE) calculation of NOx soil emission increase due to fertilizer use
1515	! Calculation of N-fertiliser-induced NOx emissions
1516	flx_fertil_no(ji,jv) = zero
1517	IF (ok_cropsfertil_NOx) THEN
1518	IF (veget_max_nowoody(ji) .NE. zero) THEN
1519	! Non-agricultural lands
1520	IF ( (jv == ibare_sechiba) .OR. is_tree(jv) ) THEN
1521	N_qt_WRICE_pft(ji,jv) = zero
1522	N_qt_OTHER_pft(ji,jv) = zero
1523	! Grasslands or Croplands
1524	ELSE
1525	N_qt_WRICE_pft(ji,jv) = N_qt_WRICE_year(ji)*veget_max(ji,jv)/veget_max_nowoody(ji)
1526	N_qt_OTHER_pft(ji,jv) = N_qt_OTHER_year(ji)*veget_max(ji,jv)/veget_max_nowoody(ji)
1527	END IF
1528	ELSE
1529	N_qt_WRICE_pft(ji,jv) = zero
1530	N_qt_OTHER_pft(ji,jv) = zero
1531	END IF
1532
1533	! North temperate regions from May to August
1534	! OR South Temperate regions from November to February
1535	IF (((lalo(ji,1) .GT. 30.) .AND. (julian_diff .GE. 121. .AND. julian_diff .LE. 243.).AND. &
1536	(veget_max(ji,jv) .GT. min_sechiba)) .OR. &
1537	((lalo(ji,1) .LT. -30.) .AND. (julian_diff .GE. 305. .OR. julian_diff .LE. 59.) .AND.&
1538	(veget_max(ji,jv) .GT. min_sechiba))) THEN
1539	! 1e12 for conversion from kg to Ng
1540	! 1/(365/122460604) for conversion from year to seconds corrected for 4 months of emissions
1541	flx_fertil_no(ji,jv) = (N_qt_WRICE_pft(ji,jv)(1/30.)+N_qt_OTHER_pft(ji,jv))(2.5/100.) &
1542	& 1e12/(3652460604/12)/(area(ji)veget_max(ji,jv))
1543	! OR Tropical regions all the year
1544	ELSE IF ((lalo(ji,1) .GE. -30.).AND.(lalo(ji,1) .LE. 30.).AND.(veget_max(ji,jv) .GT. min_sechiba)) THEN
1545	flx_fertil_no(ji,jv) = (N_qt_WRICE_pft(ji,jv)(1/30.)+N_qt_OTHER_pft(ji,jv))(2.5/100.) &
1546	& 1e12/(365246060)/(area(ji)*veget_max(ji,jv))
1547	END IF
1548	flx_no_soil(ji,jv) = flx_no_soil(ji,jv) + flx_fertil_no(ji,jv)
1549	END IF
1550
1551	!! 7.5 Calculation of net NO flux above soil accounting for surface deposition,
1552	!! based on the Canopy Reduction Factor (CRF), calculated using Leaf Area and Stomatal Area
1553	!kc=cuticle absorptivity = 0.24m^2/m^2
1554	!ks=stomatal absorptivity = 8.75m^2/m^2
1555	!Larch=Larcher SAI/LAI ratio given in Larcher 1991
1556	!> @codeinc
1557	CRF(ji,jv) = (exp(-8.75Larch(jv)lai(ji,jv)) + exp(-0.24*lai(ji,jv)))/2.
1558	flx_no(ji,jv) = flx_no_soil(ji,jv)*CRF(ji,jv)
1559	!> @endcodeinc
1560	END DO
1561	END DO
1562
1563
1564	! Write output with XIOS
1565	CALL xios_orchidee_send_field("PAR",PAR)
1566	CALL xios_orchidee_send_field("flx_fertil_no",flx_fertil_no)
1567	CALL xios_orchidee_send_field("flx_iso",flx_iso)
1568	CALL xios_orchidee_send_field("flx_mono",flx_mono)
1569	CALL xios_orchidee_send_field("flx_ORVOC",flx_ORVOC)
1570	CALL xios_orchidee_send_field("flx_MBO",flx_MBO)
1571	CALL xios_orchidee_send_field("flx_methanol",flx_methanol)
1572	CALL xios_orchidee_send_field("flx_acetone",flx_acetone)
1573	CALL xios_orchidee_send_field("flx_acetal",flx_acetal)
1574	CALL xios_orchidee_send_field("flx_formal",flx_formal)
1575	CALL xios_orchidee_send_field("flx_acetic",flx_acetic)
1576	CALL xios_orchidee_send_field("flx_formic",flx_formic)
1577	CALL xios_orchidee_send_field("flx_no_soil",flx_no_soil)
1578	CALL xios_orchidee_send_field("flx_no",flx_no)
1579	CALL xios_orchidee_send_field('flx_apinen' , flx_apinen)
1580	CALL xios_orchidee_send_field('flx_bpinen' , flx_bpinen)
1581	CALL xios_orchidee_send_field('flx_limonen' ,flx_limonen)
1582	CALL xios_orchidee_send_field('flx_myrcen' , flx_myrcen)
1583	CALL xios_orchidee_send_field('flx_sabinen' ,flx_sabinen)
1584	CALL xios_orchidee_send_field('flx_camphen' ,flx_camphen)
1585	CALL xios_orchidee_send_field('flx_3caren' , flx_3caren)
1586	CALL xios_orchidee_send_field('flx_tbocimen' ,flx_tbocimen)
1587	CALL xios_orchidee_send_field('flx_othermono',flx_othermono)
1588	CALL xios_orchidee_send_field('flx_sesquiter',flx_sesquiter)
1589	CALL xios_orchidee_send_field("CRF",CRF)
1590	CALL xios_orchidee_send_field('fco2', fco2)
1591
1592	IF ( ok_radcanopy ) THEN
1593	CALL xios_orchidee_send_field("PARdf",PARdf)
1594	CALL xios_orchidee_send_field("PARdr",PARdr)
1595
1596	IF (ok_multilayer) THEN
1597	CALL xios_orchidee_send_field("PARsuntab",PARsuntab)
1598	CALL xios_orchidee_send_field("PARshtab",PARshtab)
1599	ELSE
1600	CALL xios_orchidee_send_field("PARsun",PARsun)
1601	CALL xios_orchidee_send_field("PARsh",PARsh)
1602	CALL xios_orchidee_send_field("laisun",laisun)
1603	CALL xios_orchidee_send_field("laish",laish)
1604	ENDIF
1605	ENDIF
1606
1607	IF ( ok_bbgfertil_Nox ) THEN
1608	CALL xios_orchidee_send_field("flx_co2_bbg_year",flx_co2_bbg_year)
1609	END IF
1610
1611	IF ( ok_cropsfertil_Nox ) THEN
1612	CALL xios_orchidee_send_field("N_qt_WRICE_year",N_qt_WRICE_year)
1613	CALL xios_orchidee_send_field("N_qt_OTHER_year",N_qt_OTHER_year)
1614	END IF
1615
1616
1617	! Write output with IOIPSL
1618	IF ( .NOT. almaoutput ) THEN
1619
1620	CALL histwrite_p(hist_id, 'PAR', kjit, PAR, kjpindex, index)
1621	IF ( ok_radcanopy ) THEN
1622	CALL histwrite_p(hist_id, 'laisun', kjit, laisun, kjpindex*nvm, indexveg)
1623	CALL histwrite_p(hist_id, 'laish', kjit, laish, kjpindex*nvm, indexveg)
1624	CALL histwrite_p(hist_id, 'Fdf', kjit, Fdf, kjpindex, index)
1625	IF (ok_multilayer) THEN
1626	CALL histwrite_p(hist_id, 'PARsuntab', kjit, PARsuntab, kjpindex*(nlai+1), indexlai)
1627	CALL histwrite_p(hist_id, 'PARshtab', kjit, PARshtab, kjpindex*(nlai+1), indexlai)
1628	ELSE
1629	CALL histwrite_p(hist_id, 'PARsun', kjit, PARsun, kjpindex*nvm, indexveg)
1630	CALL histwrite_p(hist_id, 'PARsh', kjit, PARsh, kjpindex*nvm, indexveg)
1631	END IF
1632	CALL histwrite_p(hist_id, 'coszang', kjit, coszang, kjpindex, index)
1633	CALL histwrite_p(hist_id, 'PARdf', kjit, PARdf, kjpindex, index)
1634	CALL histwrite_p(hist_id, 'PARdr', kjit, PARdr, kjpindex, index)
1635	CALL histwrite_p(hist_id, 'Trans', kjit, Trans, kjpindex, index)
1636	END IF
1637	CALL histwrite_p(hist_id, 'flx_fertil_no', kjit, flx_fertil_no, kjpindex*nvm, indexveg)
1638	CALL histwrite_p(hist_id, 'CRF', kjit, CRF, kjpindex*nvm, indexveg)
1639	CALL histwrite_p(hist_id, 'fco2', kjit, fco2, kjpindex*nvm, indexveg)
1640
1641	IF ( ok_bbgfertil_Nox ) THEN
1642	CALL histwrite_p(hist_id, 'flx_co2_bbg_year', 1, flx_co2_bbg_year, kjpindex, index)
1643	ENDIF
1644	IF ( ok_cropsfertil_Nox ) THEN
1645	CALL histwrite_p(hist_id, 'N_qt_WRICE_year', 1, N_qt_WRICE_year, kjpindex, index)
1646	CALL histwrite_p(hist_id, 'N_qt_OTHER_year', 1, N_qt_OTHER_year, kjpindex, index)
1647	ENDIF
1648	CALL histwrite_p(hist_id, 'flx_iso', kjit, flx_iso, kjpindex*nvm, indexveg)
1649	CALL histwrite_p(hist_id, 'flx_mono', kjit, flx_mono, kjpindex*nvm, indexveg)
1650	CALL histwrite_p(hist_id, 'flx_apinen', kjit, flx_apinen, kjpindex*nvm, indexveg)
1651	CALL histwrite_p(hist_id, 'flx_bpinen', kjit, flx_bpinen, kjpindex*nvm, indexveg)
1652	CALL histwrite_p(hist_id, 'flx_limonen', kjit, flx_limonen, kjpindex*nvm, indexveg)
1653	CALL histwrite_p(hist_id, 'flx_myrcen', kjit, flx_myrcen, kjpindex*nvm, indexveg)
1654	CALL histwrite_p(hist_id, 'flx_sabinen', kjit, flx_sabinen, kjpindex*nvm, indexveg)
1655	CALL histwrite_p(hist_id, 'flx_camphen', kjit, flx_camphen, kjpindex*nvm, indexveg)
1656	CALL histwrite_p(hist_id, 'flx_3caren', kjit, flx_3caren, kjpindex*nvm, indexveg)
1657	CALL histwrite_p(hist_id, 'flx_tbocimen', kjit, flx_tbocimen, kjpindex*nvm, indexveg)
1658	CALL histwrite_p(hist_id, 'flx_othermono', kjit, flx_othermono, kjpindex*nvm, indexveg)
1659	CALL histwrite_p(hist_id, 'flx_sesquiter', kjit, flx_sesquiter, kjpindex*nvm, indexveg)
1660	CALL histwrite_p(hist_id, 'flx_ORVOC', kjit, flx_ORVOC, kjpindex*nvm, indexveg)
1661	CALL histwrite_p(hist_id, 'flx_MBO', kjit, flx_MBO, kjpindex*nvm, indexveg)
1662	CALL histwrite_p(hist_id, 'flx_methanol', kjit, flx_methanol, kjpindex*nvm, indexveg)
1663	CALL histwrite_p(hist_id, 'flx_acetone', kjit, flx_acetone, kjpindex*nvm, indexveg)
1664	CALL histwrite_p(hist_id, 'flx_acetal', kjit, flx_acetal, kjpindex*nvm, indexveg)
1665	CALL histwrite_p(hist_id, 'flx_formal', kjit, flx_formal, kjpindex*nvm, indexveg)
1666	CALL histwrite_p(hist_id, 'flx_acetic', kjit, flx_acetic, kjpindex*nvm, indexveg)
1667	CALL histwrite_p(hist_id, 'flx_formic', kjit, flx_formic, kjpindex*nvm, indexveg)
1668	CALL histwrite_p(hist_id, 'flx_no_soil', kjit, flx_no_soil, kjpindex*nvm, indexveg)
1669	CALL histwrite_p(hist_id, 'flx_no', kjit, flx_no, kjpindex*nvm, indexveg)
1670
1671	IF ( hist2_id > 0 ) THEN
1672	CALL histwrite_p(hist2_id, 'PAR', kjit, PAR, kjpindex, index)
1673	IF ( ok_radcanopy ) THEN
1674	CALL histwrite_p(hist2_id, 'PARsun', kjit, PARsun, kjpindex*nvm, indexveg)
1675	CALL histwrite_p(hist2_id, 'PARsh', kjit, PARsh, kjpindex*nvm, indexveg)
1676	CALL histwrite_p(hist2_id, 'laisun', kjit, laisun, kjpindex*nvm, indexveg)
1677	CALL histwrite_p(hist2_id, 'laish', kjit, laish, kjpindex*nvm, indexveg)
1678	ENDIF
1679	CALL histwrite_p(hist2_id, 'flx_fertil_no', kjit, flx_fertil_no, kjpindex*nvm, indexveg)
1680	CALL histwrite_p(hist2_id, 'CRF', kjit, CRF, kjpindex*nvm, indexveg)
1681	IF ( ok_bbgfertil_Nox ) THEN
1682	CALL histwrite_p(hist2_id, 'flx_co2_bbg_year', 1, flx_co2_bbg_year, kjpindex, index)
1683	ENDIF
1684	IF ( ok_cropsfertil_Nox ) THEN
1685	CALL histwrite_p(hist2_id, 'N_qt_WRICE_year', 1, N_qt_WRICE_year, kjpindex, index)
1686	CALL histwrite_p(hist2_id, 'N_qt_OTHER_year', 1, N_qt_OTHER_year, kjpindex, index)
1687	ENDIF
1688	CALL histwrite_p(hist2_id, 'flx_iso', kjit, flx_iso, kjpindex*nvm, indexveg)
1689	CALL histwrite_p(hist2_id, 'flx_mono', kjit, flx_mono, kjpindex*nvm, indexveg)
1690	CALL histwrite_p(hist2_id, 'flx_apinen', kjit, flx_apinen, kjpindex*nvm, indexveg)
1691	CALL histwrite_p(hist2_id, 'flx_bpinen', kjit, flx_bpinen, kjpindex*nvm, indexveg)
1692	CALL histwrite_p(hist2_id, 'flx_limonen', kjit, flx_limonen, kjpindex*nvm, indexveg)
1693	CALL histwrite_p(hist2_id, 'flx_myrcen', kjit, flx_myrcen, kjpindex*nvm, indexveg)
1694	CALL histwrite_p(hist2_id, 'flx_sabinen', kjit, flx_sabinen, kjpindex*nvm, indexveg)
1695	CALL histwrite_p(hist2_id, 'flx_camphen', kjit, flx_camphen, kjpindex*nvm, indexveg)
1696	CALL histwrite_p(hist2_id, 'flx_3caren', kjit, flx_3caren, kjpindex*nvm, indexveg)
1697	CALL histwrite_p(hist2_id, 'flx_tbocimen', kjit, flx_tbocimen, kjpindex*nvm, indexveg)
1698	CALL histwrite_p(hist2_id, 'flx_othermono', kjit, flx_othermono, kjpindex*nvm, indexveg)
1699	CALL histwrite_p(hist2_id, 'flx_sesquiter', kjit, flx_sesquiter, kjpindex*nvm, indexveg)
1700	CALL histwrite_p(hist2_id, 'flx_ORVOC', kjit, flx_ORVOC, kjpindex*nvm, indexveg)
1701	CALL histwrite_p(hist2_id, 'flx_MBO', kjit, flx_MBO, kjpindex*nvm, indexveg)
1702	CALL histwrite_p(hist2_id, 'flx_methanol', kjit, flx_methanol, kjpindex*nvm, indexveg)
1703	CALL histwrite_p(hist2_id, 'flx_acetone', kjit, flx_acetone, kjpindex*nvm, indexveg)
1704	CALL histwrite_p(hist2_id, 'flx_acetal', kjit, flx_acetal, kjpindex*nvm, indexveg)
1705	CALL histwrite_p(hist2_id, 'flx_formal', kjit, flx_formal, kjpindex*nvm, indexveg)
1706	CALL histwrite_p(hist2_id, 'flx_acetic', kjit, flx_acetic, kjpindex*nvm, indexveg)
1707	CALL histwrite_p(hist2_id, 'flx_formic', kjit, flx_formic, kjpindex*nvm, indexveg)
1708	CALL histwrite_p(hist2_id, 'flx_no_soil', kjit, flx_no_soil, kjpindex*nvm, indexveg)
1709	CALL histwrite_p(hist2_id, 'flx_no', kjit, flx_no, kjpindex*nvm, indexveg)
1710	ENDIF
1711	ENDIF
1712
1713	IF (printlev>=3) WRITE(numout,*) 'OK chemistry_bvoc'
1714
1715	END SUBROUTINE chemistry_bvoc
1716
1717	!! ================================================================================================================================
1718	!! SUBROUTINE : chemistry_flux_interface
1719	!!
1720	!>\BRIEF This subroutine will give to the interface between inca model and orchidee model in sechiba all the flux ask by inca
1721	!!
1722	!! DESCRIPTION : This subroutine allow the transfer of fluxes between surface and atmospheric chemistry. It is called from sechiba
1723	!!
1724	!! RECENT CHANGE(S): None
1725	!!
1726	!! MAIN OUTPUT VARIABLE(S): ::
1727	!!
1728	!! REFERENCE(S) : None
1729	!!
1730	!! FLOWCHART : None
1731	!_ ================================================================================================================================
1732
1733	SUBROUTINE chemistry_flux_interface( field_out_names, fields_out, field_in_names, fields_in)
1734
1735	!
1736	! Optional arguments
1737	!
1738	! Names and fields for emission variables : to be transport by Orchidee to Inca
1739	CHARACTER(LEN=*),DIMENSION(:), OPTIONAL, INTENT(IN) :: field_out_names
1740	REAL(r_std),DIMENSION(:,:,:), OPTIONAL, INTENT(OUT) :: fields_out
1741	!
1742	! Names and fields for deposit variables : to be transport from chemistry model by INCA to ORCHIDEE.
1743	CHARACTER(LEN=*),DIMENSION(:), OPTIONAL, INTENT(IN) :: field_in_names
1744	REAL(r_std),DIMENSION(:,:), OPTIONAL, INTENT(IN) :: fields_in
1745	!
1746	! Number of fields to give (nb_fields_out) or get from (nb_fields_in) INCA :
1747	INTEGER(i_std), SAVE :: nb_fields_out, nb_fields_in
1748	!$OMP THREADPRIVATE(nb_fields_out, nb_fields_in)
1749
1750	! Id of fields to give (nb_fields_out) or get from (nb_fields_in) INCA :
1751	INTEGER(i_std) :: i_fields_out, i_fields_in
1752
1753	IF (l_first_chemistry_inca) THEN
1754
1755	! il faut verifier que ok_bvoc (chemistry_ok_bvoc) est bien active sinon on arrete tout
1756	if (.not.ok_bvoc) then
1757	CALL ipslerr_p (3,'chemistry_inca', &
1758	& 'you need to activate chemistry_ok_bvoc in orchidee.def',&
1759	& 'This model won''t be able to continue.', &
1760	& '')
1761	endif
1762
1763	! Prepare fieds out/in for interface with INCA.
1764	IF (PRESENT(field_out_names)) THEN
1765	nb_fields_out=SIZE(field_out_names)
1766	ELSE
1767	nb_fields_out=0
1768	ENDIF
1769
1770	IF (PRESENT(field_in_names)) THEN
1771	nb_fields_in=SIZE(field_in_names)
1772	ELSE
1773	nb_fields_in=0
1774	ENDIF
1775	l_first_chemistry_inca = .FALSE.
1776
1777	ENDIF
1778
1779
1780
1781	IF (ok_bvoc) THEN
1782	! Fields for deposit variables : to be transport from chemistry model by INCA to ORCHIDEE.
1783	DO i_fields_in=1,nb_fields_in
1784	SELECT CASE(TRIM(field_in_names(i_fields_in)))
1785	CASE DEFAULT
1786	CALL ipslerr_p (3,'chemistry_inca', &
1787	& 'You ask in INCA an unknown field '//TRIM(field_in_names(i_fields_in))//&
1788	& ' to give to ORCHIDEE for this specific version.',&
1789	& 'This model won''t be able to continue.', &
1790	& '(check your tracer parameters in INCA)')
1791	END SELECT
1792	ENDDO
1793
1794	! Fields for Biogenic emissions : to be transport by Orchidee to Inca
1795	DO i_fields_out=1,nb_fields_out
1796	SELECT CASE(TRIM(field_out_names(i_fields_out)))
1797	CASE("flx_iso")
1798	fields_out(:,:,i_fields_out)=flx_iso(:,:)
1799	CASE("flx_mono")
1800	fields_out(:,:,i_fields_out)=flx_mono(:,:)
1801	CASE("flx_ORVOC")
1802	fields_out(:,:,i_fields_out)=flx_ORVOC(:,:)
1803	CASE("flx_MBO")
1804	fields_out(:,:,i_fields_out)=flx_MBO(:,:)
1805	CASE("flx_methanol")
1806	fields_out(:,:,i_fields_out)=flx_methanol(:,:)
1807	CASE("flx_acetone")
1808	fields_out(:,:,i_fields_out)=flx_acetone(:,:)
1809	CASE("flx_acetal")
1810	fields_out(:,:,i_fields_out)=flx_acetal(:,:)
1811	CASE("flx_formal")
1812	fields_out(:,:,i_fields_out)=flx_formal(:,:)
1813	CASE("flx_acetic")
1814	fields_out(:,:,i_fields_out)=flx_acetic(:,:)
1815	CASE("flx_formic")
1816	fields_out(:,:,i_fields_out)=flx_formic(:,:)
1817	CASE("flx_no_soil")
1818	fields_out(:,:,i_fields_out)=flx_no_soil(:,:)
1819	CASE("flx_nox")
1820	fields_out(:,:,i_fields_out)=flx_no(:,:)
1821	CASE("flx_fertil_no")
1822	fields_out(:,:,i_fields_out)=flx_fertil_no(:,:)
1823	CASE("flx_apinen")
1824	fields_out(:,:,i_fields_out)=flx_apinen(:,:)
1825	CASE("flx_bpinen")
1826	fields_out(:,:,i_fields_out)=flx_bpinen(:,:)
1827	CASE("flx_limonen")
1828	fields_out(:,:,i_fields_out)=flx_limonen(:,:)
1829	CASE("flx_myrcen")
1830	fields_out(:,:,i_fields_out)=flx_myrcen(:,:)
1831	CASE("flx_sabinen")
1832	fields_out(:,:,i_fields_out)=flx_sabinen(:,:)
1833	CASE("flx_camphen")
1834	fields_out(:,:,i_fields_out)=flx_camphen(:,:)
1835	CASE("flx_3caren")
1836	fields_out(:,:,i_fields_out)=flx_3caren(:,:)
1837	CASE("flx_tbocimen")
1838	fields_out(:,:,i_fields_out)=flx_tbocimen(:,:)
1839	CASE("flx_othermono")
1840	fields_out(:,:,i_fields_out)=flx_othermono(:,:)
1841	CASE("flx_sesquiter")
1842	fields_out(:,:,i_fields_out)=flx_sesquiter(:,:)
1843
1844	CASE DEFAULT
1845	CALL ipslerr_p (3,'chemistry_inca', &
1846	& 'You ask from INCA an unknown field '//TRIM(field_out_names(i_fields_out))//&
1847	& ' to ORCHIDEE for this specific version.',&
1848	& 'This model won''t be able to continue.', &
1849	& '(check your tracer parameters in INCA)')
1850	END SELECT
1851	ENDDO
1852
1853	ENDIF
1854	END SUBROUTINE chemistry_flux_interface
1855
1856	!! ================================================================================================================================
1857	!! SUBROUTINE : chemistry_clear
1858	!!
1859	!>\BRIEF Clear chemistry module
1860	!!
1861	!! DESCRIPTION : Deallocate memory and reset initialization variables to there original values
1862	!!
1863	!_ ================================================================================================================================
1864	SUBROUTINE chemistry_clear
1865
1866	!! 1. Initialize as for first run
1867	l_first_chemistry_inca = .TRUE.
1868
1869	!! 2. Deallocate dynamic variables
1870	IF (ALLOCATED(pulse)) DEALLOCATE (pulse)
1871	IF (ALLOCATED (ok_siesta)) DEALLOCATE (ok_siesta)
1872	IF (ALLOCATED (allow_pulse)) DEALLOCATE (allow_pulse)
1873	IF (ALLOCATED (pulseday)) DEALLOCATE (pulseday)
1874	IF (ALLOCATED (siestaday)) DEALLOCATE (siestaday)
1875	IF (ALLOCATED (pulselim)) DEALLOCATE (pulselim)
1876	IF (ALLOCATED (siestalim)) DEALLOCATE (siestalim)
1877	IF (ALLOCATED (N_qt_WRICE_year)) DEALLOCATE (N_qt_WRICE_year)
1878	IF (ALLOCATED (N_qt_OTHER_year)) DEALLOCATE (N_qt_OTHER_year)
1879	IF (ALLOCATED (flx_iso)) DEALLOCATE (flx_iso)
1880	IF (ALLOCATED (flx_mono)) DEALLOCATE (flx_mono)
1881	IF (ALLOCATED (flx_ORVOC)) DEALLOCATE (flx_ORVOC)
1882	IF (ALLOCATED (flx_MBO)) DEALLOCATE (flx_MBO)
1883	IF (ALLOCATED (flx_methanol)) DEALLOCATE (flx_methanol)
1884	IF (ALLOCATED (flx_acetone)) DEALLOCATE (flx_acetone)
1885	IF (ALLOCATED (flx_acetal)) DEALLOCATE (flx_acetal)
1886	IF (ALLOCATED (flx_formal)) DEALLOCATE (flx_formal)
1887	IF (ALLOCATED (flx_acetic)) DEALLOCATE (flx_acetic)
1888	IF (ALLOCATED (flx_formic)) DEALLOCATE (flx_formic)
1889	IF (ALLOCATED (flx_no_soil)) DEALLOCATE (flx_no_soil)
1890	IF (ALLOCATED (flx_no)) DEALLOCATE (flx_no)
1891	IF (ALLOCATED (flx_fertil_no)) DEALLOCATE (flx_fertil_no)
1892	IF (ALLOCATED (flx_apinen)) DEALLOCATE (flx_apinen)
1893	IF (ALLOCATED (flx_bpinen)) DEALLOCATE (flx_bpinen)
1894	IF (ALLOCATED (flx_limonen)) DEALLOCATE (flx_limonen)
1895	IF (ALLOCATED (flx_myrcen)) DEALLOCATE (flx_myrcen)
1896	IF (ALLOCATED (flx_sabinen)) DEALLOCATE (flx_sabinen)
1897	IF (ALLOCATED (flx_camphen)) DEALLOCATE (flx_camphen)
1898	IF (ALLOCATED (flx_3caren)) DEALLOCATE (flx_3caren)
1899	IF (ALLOCATED (flx_tbocimen)) DEALLOCATE (flx_tbocimen)
1900	IF (ALLOCATED (flx_othermono)) DEALLOCATE (flx_othermono)
1901	IF (ALLOCATED (flx_sesquiter)) DEALLOCATE (flx_sesquiter)
1902	IF (ALLOCATED (CRF)) DEALLOCATE (CRF)
1903	IF (ALLOCATED (flx_co2_bbg_year)) DEALLOCATE (flx_co2_bbg_year)
1904
1905	END SUBROUTINE chemistry_clear
1906
1907	END MODULE chemistry

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