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source: branches/publications/ORCHIDEE_CAMEO_gmd_2022/src_sechiba/chemistry.f90 @ 7693

Last change on this file since 7693 was 5973, checked in by josefine.ghattas, 5 years ago
Use area instead of resolution. See ticket #563
Property svn:keywords set to `Date Revision HeadURL`
File size: 103.0 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
36	IMPLICIT NONE
37
38	PRIVATE
39	PUBLIC :: chemistry_xios_initialize, chemistry_initialize, chemistry_bvoc, chemistry_flux_interface, chemistry_clear
40
41
42	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_iso !! Isoprene emissions from vegetation (kgC.m^{-2}.s^{-1})
43	!$OMP THREADPRIVATE(flx_iso)
44	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_mono !! Monoterpene emissions from vegetation (kgC.m^{-2}.s^{-1})
45	!$OMP THREADPRIVATE(flx_mono)
46	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_ORVOC !! Other Volatile Organic Compound emissions from vegetation (kgC.m^{-2}.s^{-1})
47	!$OMP THREADPRIVATE(flx_ORVOC)
48	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_MBO !! 2-methyl-3-buten-2-ol emissions from vegetation (mainly pines in America) (kgC.m^{-2}.s^{-1})
49	!$OMP THREADPRIVATE(flx_MBO)
50	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_methanol !! Methanol emissions from vegetation (kgC.m^{-2}.s^{-1})
51	!$OMP THREADPRIVATE(flx_methanol)
52	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_acetone !! Acetone emissions from vegetation (kgC.m^{-2}.s^{-1})
53	!$OMP THREADPRIVATE(flx_acetone)
54	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_acetal !! Acetaldehyde emissions from vegetation (kgC.m^{-2}.s^{-1})
55	!$OMP THREADPRIVATE(flx_acetal)
56	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_formal !! Formaldehyde emissions from vegetation (kgC.m^{-2}.s^{-1})
57	!$OMP THREADPRIVATE(flx_formal)
58	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_acetic !! Acetic acid emissions from vegetation (kgC.m^{-2}.s^{-1})
59	!$OMP THREADPRIVATE(flx_acetic)
60	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_formic !! Formic acid emissions from vegetation (kgC.m^{-2}.s^{-1})
61	!$OMP THREADPRIVATE(flx_formic)
62	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_apinen !! Alpha pinene emissions from vegetation (kgC.m^{-2}.s^{-1})
63	!$OMP THREADPRIVATE(flx_apinen)
64	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_bpinen !! Beta pinene emissions from vegetation (kgC.m^{-2}.s^{-1})
65	!$OMP THREADPRIVATE(flx_bpinen)
66	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_limonen !! Limonene emissions from vegetation (kgC.m^{-2}.s^{-1})
67	!$OMP THREADPRIVATE(flx_limonen)
68	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_myrcen !! Myrcene emissions from vegetation (kgC.m^{-2}.s^{-1})
69	!$OMP THREADPRIVATE(flx_myrcen)
70	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_sabinen !! Sabinene emissions from vegetation (kgC.m^{-2}.s^{-1})
71	!$OMP THREADPRIVATE(flx_sabinen)
72	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_camphen !! Camphene emissions from vegetation (kgC.m^{-2}.s^{-1})
73	!$OMP THREADPRIVATE(flx_camphen)
74	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_3caren !! 3-Carene emissions from vegetation (kgC.m^{-2}.s^{-1})
75	!$OMP THREADPRIVATE(flx_3caren)
76	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_tbocimen !! T-beta Ocimene emissions from vegetation (kgC.m^{-2}.s^{-1})
77	!$OMP THREADPRIVATE(flx_tbocimen)
78	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_othermono !! Emissions of other monoterpenes from vegetation (kgC.m^{-2}.s^{-1})
79	!$OMP THREADPRIVATE(flx_othermono)
80	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_sesquiter !! Sesquiterpene emissions from vegetation (kgC.m^{-2}.s^{-1})
81	!$OMP THREADPRIVATE(flx_sesquiter)
82	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_fertil_no !! Biogenic nitrogen oxide soil emission due to N-fertilisation (ngN.m^{-2}.s^{-1})
83	!$OMP THREADPRIVATE(flx_fertil_no)
84	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_no_soil !! Nitrogen Oxide emissions from soil, before deposition on canopy
85	!! (ngN.m^{-2}.s^{-1})
86	!$OMP THREADPRIVATE(flx_no_soil)
87	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_no !! Net nitrogen Oxide emissions from soil, after deposition on canopy
88	!$OMP THREADPRIVATE(flx_no)
89	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: CRF !! Canopy reduction factor for net NO flux calculation (kjpindex,nvm)
90	!$OMP THREADPRIVATE(CRF)
91
92	! variables used inside diffuco_inca module
93	LOGICAL, ALLOCATABLE, SAVE, DIMENSION(:) :: ok_siesta !! Flag for controlling post-pulse period (true/false)
94	!$OMP THREADPRIVATE(ok_siesta)
95	LOGICAL, ALLOCATABLE, SAVE, DIMENSION(:) :: allow_pulse !! Flag for controlling pulse period (true/false)
96	!$OMP THREADPRIVATE(allow_pulse)
97	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: pulse !! Pulse fonction
98	!$OMP THREADPRIVATE(pulse)
99	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: pulseday !! Counter for pulse period
100	!$OMP THREADPRIVATE(pulseday)
101	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: siestaday !! Counter for post-pulse period
102	!$OMP THREADPRIVATE(siestaday)
103	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: pulselim !! Pulse period length
104	!$OMP THREADPRIVATE(pulselim)
105	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: siestalim !! Post-pulse period length
106	!$OMP THREADPRIVATE(siestalim)
107	REAL(r_std), SAVE :: nbre_precip
108	!$OMP THREADPRIVATE(nbre_precip)
109	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: flx_co2_bbg_year !! CO2 emissions from biomass burning
110	!! Read in an input file (kgC.m^{-2}.year^{-1})
111	!$OMP THREADPRIVATE(flx_co2_bbg_year)
112	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: N_qt_WRICE_year !! N fertilizers applied on wetland rice
113	!! Read in an input file (kgN.yr^{-1})
114	!$OMP THREADPRIVATE(N_qt_WRICE_year)
115	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: N_qt_OTHER_year !! N fertilizers applied on other crops and grasses
116	!! Read in an input file (kgN.yr^{-1})
117	!$OMP THREADPRIVATE(N_qt_OTHER_year)
118	LOGICAL, SAVE :: l_first_chemistry_inca=.TRUE. !! Initialisation for chemistry_flux_interface
119	!$OMP THREADPRIVATE(l_first_chemistry_inca)
120
121
122
123	CONTAINS
124
125
126	!! =============================================================================================================================
127	!! SUBROUTINE: chemistry_xios_initialize
128	!!
129	!>\BRIEF Initialize xios dependant defintion before closing context defintion
130	!!
131	!! DESCRIPTION: Initialize xios dependant defintion before closing context defintion
132	!!
133	!! \n
134	!_ ==============================================================================================================================
135
136	SUBROUTINE chemistry_xios_initialize
137
138	CHARACTER(LEN=255) :: filename, name
139
140
141	!! 1. Treat the file for fertilzation needed for option ok_cropsfertil_Nox
142
143	! Read the input file name from run.def
144	filename = 'orchidee_fertilizer_1995.nc'
145	CALL getin_p('N_FERTIL_FILE',filename)
146
147	! Remove suffix .nc from filename
148	name = filename(1:LEN_TRIM(FILENAME)-3)
149	CALL xios_orchidee_set_file_attr("fertilizer_file",name=name)
150
151	! Check if the file will be read by XIOS, by IOIPSL or not at all
152	IF (xios_interpolation .AND. ok_cropsfertil_Nox) THEN
153	IF (printlev>=2) WRITE (numout,*) 'The fertilizer file will be read later by XIOS'
154	ELSE
155	IF (ok_cropsfertil_Nox) THEN
156	IF (printlev>=2) WRITE (numout,*) 'The fertilizer file will be read later by IOIPSL'
157	ELSE
158	IF (printlev>=2) WRITE (numout,*) 'The fertilizer file will not be read'
159	END IF
160
161	! The fertilizer file will not be read by XIOS. Now deactivate it for XIOS.
162	CALL xios_orchidee_set_file_attr("fertilizer_file",enabled=.FALSE.)
163	CALL xios_orchidee_set_field_attr("N_qt_WRICE_year_interp",enabled=.FALSE.)
164	CALL xios_orchidee_set_field_attr("N_qt_OTHER_year_interp",enabled=.FALSE.)
165	END IF
166
167
168	!! 2. Treat the file for bbg fertil needed for option ok_bbgfertil_Nox
169
170	! Read the input file name from run.def
171	filename = 'orchidee_bbg_clim.nc'
172	CALL getin_p('CO2_BBG_FILE',filename)
173
174	! Remove suffix .nc from filename
175	name = filename(1:LEN_TRIM(FILENAME)-3)
176	CALL xios_orchidee_set_file_attr("bbg_clim_file",name=name)
177
178	! Check if the file will be read by XIOS, by IOIPSL or not at all
179	IF (xios_interpolation .AND. ok_bbgfertil_Nox) THEN
180	IF (printlev>=2) WRITE (numout,*) 'The bbgfertil file will be read later by XIOS'
181	ELSE
182	IF (ok_bbgfertil_Nox) THEN
183	IF (printlev>=2) WRITE (numout,*) 'The bbgfertil file will be read later by IOIPSL'
184	ELSE
185	IF (printlev>=2) WRITE (numout,*) 'The bbgfertil file will not be read'
186	END IF
187
188	! This file will not be read by XIOS. Now deactivate it for XIOS.
189	CALL xios_orchidee_set_file_attr("bbg_clim_file",enabled=.FALSE.)
190	CALL xios_orchidee_set_field_attr("flx_co2_bbg_year_interp",enabled=.FALSE.)
191	END IF
192
193
194	END SUBROUTINE chemistry_xios_initialize
195
196	!! ================================================================================================================================
197	!! SUBROUTINE : chemistry_initialize
198	!!
199	!>\BRIEF This subroutine initializes the chemistry module
200	!!
201	!! DESCRIPTION : Some of the variables and flags used chemistry_bvoc are allocated and initialised here.
202	!!
203	!! RECENT CHANGE(S): Changed name from diffuco_inca_init to chemistry_initialize
204	!!
205	!! MAIN OUTPUT VARIABLE(S): None
206	!!
207	!! REFERENCE(S) : None
208	!!
209	!! FLOWCHART : None
210	!_ ================================================================================================================================
211	SUBROUTINE chemistry_initialize(kjpindex, lalo, neighbours, resolution)
212
213	USE interpweight
214
215	IMPLICIT NONE
216
217	!! 0. Variables and parameter declaration
218
219	!! 0.1 Input variables
220
221	INTEGER(i_std), INTENT(in) :: kjpindex !! Domain size (unitless)
222	REAL(r_std), DIMENSION(kjpindex,2), INTENT (in) :: lalo !! Geographical coordinates
223	INTEGER(i_std), DIMENSION(kjpindex,8), INTENT (in) :: neighbours !! Vector of neighbours for each
224	!! grid point (1=N, 2=E, 3=S, 4=W)
225	REAL(r_std),DIMENSION (kjpindex,2), INTENT(in) :: resolution !! The size in km of each grid-box in X and Y
226
227	!! 0.2 Output variables
228	REAL(r_std), DIMENSION(kjpindex) :: achem_wrice !! Availability of data for the interpolation
229	REAL(r_std), DIMENSION(kjpindex) :: achem_other !! Availability of data for the interpolation
230	REAL(r_std), DIMENSION(kjpindex) :: achem_co2 !! Availability of data for the interpolation
231
232	!! 0.3 Modified variables
233
234	!! 0.4 Local variables
235	LOGICAL :: allow_weathergen
236	CHARACTER(LEN=80) :: filename, fieldname
237	INTEGER(i_std) :: iml, jml, lml, tml, force_id
238	INTEGER(i_std) :: ier
239	REAL(r_std) :: vmin, vmax !! min/max values to use for the
240	!! renormalization
241	CHARACTER(LEN=250) :: maskvname !! Variable to read the mask from
242	!! the file
243	CHARACTER(LEN=80) :: lonname, latname !! lon, lat names in input file
244	REAL(r_std), DIMENSION(:), ALLOCATABLE :: variabletypevals !! Values for all the types of the variable
245	!! (variabletypevals(1) = -un, not used)
246	CHARACTER(LEN=50) :: fractype !! method of calculation of fraction
247	!! 'XYKindTime': Input values are kinds
248	!! of something with a temporal
249	!! evolution on the dx*dy matrix'
250	LOGICAL :: nonegative !! whether negative values should be removed
251	CHARACTER(LEN=50) :: maskingtype !! Type of masking
252	!! 'nomask': no-mask is applied
253	!! 'mbelow': take values below maskvals(1)
254	!! 'mabove': take values above maskvals(1)
255	!! 'msumrange': take values within 2 ranges;
256	!! maskvals(2) <= SUM(vals(k)) <= maskvals(1)
257	!! maskvals(1) < SUM(vals(k)) <= maskvals(3)
258	!! (normalized by maskvals(3))
259	!! 'var': mask values are taken from a
260	!! variable inside the file (>0)
261	REAL(r_std), DIMENSION(3) :: maskvals !! values to use to mask (according to
262	!! `maskingtype')
263	CHARACTER(LEN=250) :: namemaskvar !! name of the variable to use to mask
264	REAL(r_std) :: chem_norefinf !! No value
265	REAL(r_std) :: chem_default !! Default value
266
267	!_ ================================================================================================================================
268
269	ALLOCATE (pulse(kjpindex),stat=ier)
270	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable pulse','','')
271	pulse(:) = un
272
273	! If we acount for NOx pulse emissions
274	IF (ok_pulse_NOx) THEN
275
276	ALLOCATE (ok_siesta(kjpindex),stat=ier)
277	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable ok_siesta','','')
278	ok_siesta(:) = .FALSE.
279
280	ALLOCATE (allow_pulse(kjpindex),stat=ier)
281	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable allow_pulse','','')
282	allow_pulse(:) = .FALSE.
283
284	ALLOCATE (pulseday(kjpindex),stat=ier)
285	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable pulseday','','')
286	pulseday(:) = zero
287
288	ALLOCATE (siestaday(kjpindex),stat=ier)
289	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable siestaday','','')
290	siestaday(:) = zero
291
292	ALLOCATE (pulselim(kjpindex),stat=ier)
293	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable pulselim','','')
294	pulselim(:) = zero
295
296	ALLOCATE (siestalim(kjpindex),stat=ier)
297	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable siestalim','','')
298	siestalim(:) = zero
299
300	END IF ! (ok_pulse_NOx)
301
302	! If we acount for NOx emissions by N-fertilizers
303	IF (ok_cropsfertil_NOx) THEN
304
305	ALLOCATE (N_qt_WRICE_year(kjpindex),stat=ier) !! N fertilizers on wetland rice, read in file
306	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable N_qt_WRICE_year','','')
307	N_qt_WRICE_year(:) = zero
308
309	ALLOCATE (N_qt_OTHER_year(kjpindex),stat=ier) !! N fertilizers on other crops and grasses, read in file
310	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable N_qt_OTHER_year','','')
311	N_qt_OTHER_year(:) = zero
312
313	WRITE (numout,) ' ********************** Interpolating N fertilizers files for NOx emissions... '
314
315	!Config Key = N_FERTIL_FILE
316	!Config Desc = File name
317	!Config If = CHEMISTRY_BVOC and NOx_FERTILIZERS_USE
318	!Config Def = orchidee_fertilizer_1995.nc
319	!Config Help =
320	!Config Units = -
321	filename = 'orchidee_fertilizer_1995.nc'
322	CALL getin_p('N_FERTIL_FILE',filename)
323
324	IF ( xios_interpolation ) THEN
325
326	CALL xios_orchidee_recv_field('N_qt_WRICE_year_interp',N_qt_WRICE_year)
327	CALL xios_orchidee_recv_field('N_qt_OTHER_year_interp',N_qt_OTHER_year)
328
329	achem_wrice(:)=1
330	achem_other(:)=1
331	ELSE
332
333	!! Variables for interpweight
334	vmin = 0.
335	vmax = 0.
336	! Type of calculation of cell fractions
337	fractype = 'default'
338	! Name of the longitude and latitude in the input file
339	lonname = 'lon'
340	latname = 'lat'
341	! Default value when no value is get from input file
342	chem_default = 0.
343	! Reference value when no value is get from input file
344	chem_norefinf = 0.
345	! Should negative values be set to zero from input file?
346	nonegative = .TRUE.
347	! Type of mask to apply to the input data (see header for more details)
348	maskingtype = 'nomask'
349	! Values to use for the masking
350	maskvals = (/ min_sechiba, undef_sechiba, undef_sechiba /)
351	! Name of the variable with the values for the mask in the input file (only if maskkingtype='var') (here not used)
352	namemaskvar = ''
353
354	fieldname= 'N_qt_WRICE_year'
355	IF (printlev >= 1) WRITE(numout,*) "chemistry_initialize: Read and interpolate file " &
356	// TRIM(filename) //" for variable N_qt_WRICE_year"
357	CALL interpweight_2Dcont(kjpindex, 0, 0, lalo, resolution, neighbours, &
358	contfrac, filename, fieldname, lonname, latname, vmin, vmax, nonegative, maskingtype, &
359	maskvals, namemaskvar, -1, fractype, chem_default, chem_norefinf, &
360	N_qt_WRICE_year, achem_wrice)
361
362	fieldname= 'N_qt_OTHER_year'
363	IF (printlev >= 1) WRITE(numout,*) "chemistry_initialize: Read and interpolate file " &
364	// TRIM(filename) //" for variable N_qt_OTHER_year"
365	CALL interpweight_2Dcont(kjpindex, 0, 0, lalo, resolution, neighbours, &
366	contfrac, filename, fieldname, lonname, latname, vmin, vmax, nonegative, maskingtype, &
367	maskvals, namemaskvar, -1, fractype, chem_default, chem_norefinf, &
368	N_qt_OTHER_year, achem_other)
369	END IF
370	END IF
371
372	ALLOCATE (flx_iso(kjpindex,nvm), stat=ier)
373	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_iso','','')
374	flx_iso(:,:) = 0.
375
376	ALLOCATE (flx_mono(kjpindex,nvm), stat=ier)
377	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_mono','','')
378	flx_mono(:,:) = 0.
379
380	ALLOCATE (flx_ORVOC(kjpindex,nvm), stat=ier)
381	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_ORVOC ','','')
382	flx_ORVOC(:,:) = 0.
383
384	ALLOCATE (flx_MBO(kjpindex,nvm), stat=ier)
385	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_MBO','','')
386	flx_MBO(:,:) = 0.
387
388	ALLOCATE (flx_methanol(kjpindex,nvm), stat=ier)
389	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_methanol','','')
390	flx_methanol(:,:) = 0.
391
392	ALLOCATE (flx_acetone(kjpindex,nvm), stat=ier)
393	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_acetone','','')
394	flx_acetone(:,:) = 0.
395
396	ALLOCATE (flx_acetal(kjpindex,nvm), stat=ier)
397	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_acetal','','')
398	flx_acetal(:,:) = 0.
399
400	ALLOCATE (flx_formal(kjpindex,nvm), stat=ier)
401	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_formal','','')
402	flx_formal(:,:) = 0.
403
404	ALLOCATE (flx_acetic(kjpindex,nvm), stat=ier)
405	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_acetic','','')
406	flx_acetic(:,:) = 0.
407
408	ALLOCATE (flx_formic(kjpindex,nvm), stat=ier)
409	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_formic','','')
410	flx_formic(:,:) = 0.
411
412	ALLOCATE (flx_no_soil(kjpindex,nvm), stat=ier)
413	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_no_soil','','')
414	flx_no_soil(:,:) = 0.
415
416	ALLOCATE (flx_no(kjpindex,nvm), stat=ier)
417	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_no','','')
418	flx_no(:,:) = 0.
419
420	ALLOCATE (flx_fertil_no(kjpindex,nvm), stat=ier)
421	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_fertil_no','','')
422	flx_fertil_no(:,:) = 0.
423
424	ALLOCATE (flx_apinen(kjpindex,nvm), stat=ier)
425	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_apinen','','')
426	flx_apinen(:,:) = 0.
427
428	ALLOCATE (flx_bpinen (kjpindex,nvm), stat=ier)
429	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_bpinen','','')
430	flx_bpinen(:,:) = 0.
431
432	ALLOCATE (flx_limonen (kjpindex,nvm), stat=ier)
433	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_limonen','','')
434	flx_limonen(:,:) = 0.
435
436	ALLOCATE (flx_myrcen(kjpindex,nvm), stat=ier)
437	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_myrcen','','')
438	flx_myrcen(:,:) = 0.
439
440	ALLOCATE (flx_sabinen(kjpindex,nvm), stat=ier)
441	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_sabinen','','')
442	flx_sabinen(:,:) = 0.
443
444	ALLOCATE (flx_camphen(kjpindex,nvm), stat=ier)
445	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_camphen','','')
446	flx_camphen(:,:) = 0.
447
448	ALLOCATE (flx_3caren(kjpindex,nvm), stat=ier)
449	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_3caren','','')
450	flx_3caren(:,:) = 0.
451
452	ALLOCATE (flx_tbocimen(kjpindex,nvm), stat=ier)
453	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_tbocimen','','')
454	flx_tbocimen(:,:) = 0.
455
456	ALLOCATE (flx_othermono(kjpindex,nvm), stat=ier)
457	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_othermono','','')
458	flx_othermono(:,:) = 0.
459
460	ALLOCATE (flx_sesquiter(kjpindex,nvm), stat=ier)
461	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_sesquiter','','')
462	flx_sesquiter(:,:) = 0.
463
464	ALLOCATE(CRF(kjpindex,nvm), stat=ier)
465	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable CRF ','','')
466	CRF(:,:) = 0.
467
468
469	! If we acount for NOx emissions due to Biomass Burning
470	IF (ok_bbgfertil_NOx) THEN
471
472	ALLOCATE (flx_co2_bbg_year(kjpindex),stat=ier) !! CO2 emissions from bbg, read in file
473	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable flx_co2_bbg_year','','')
474	flx_co2_bbg_year(:) = zero
475
476	WRITE (numout,) ' ********************** Interpolating CO2 bbg files for NOx emissions... '
477	!Config Key = N_FERTIL_FILE
478	!Config Desc = File name
479	!Config If = CHEMISTRY_BVOC and NOx_FERTILIZERS_USE
480	!Config Def = orchidee_fertilizer_1995.nc
481	!Config Help = ...
482	!Config Units = -
483	filename = 'orchidee_bbg_clim.nc'
484	CALL getin_p('CO2_BBG_FILE',filename)
485
486	IF (xios_interpolation) THEN
487
488	CALL xios_orchidee_recv_field('flx_co2_bbg_year_interp',flx_co2_bbg_year)
489
490	achem_co2(:)=1
491	ELSE
492
493	!! Variables for interpweight
494	vmin = 0.
495	vmax = 0.
496	! Type of calculation of cell fractions
497	fractype = 'default'
498	! Name of the longitude and latitude in the input file
499	lonname = 'lon'
500	latname = 'lat'
501	! Default value when no value is get from input file
502	chem_default = 0.
503	! Reference value when no value is get from input file
504	chem_norefinf = 0.
505	! Should negative values be set to zero from input file?
506	nonegative = .TRUE.
507	! Type of mask to apply to the input data (see header for more details)
508	maskingtype = 'nomask'
509	! Values to use for the masking
510	maskvals = (/ min_sechiba, undef_sechiba, undef_sechiba /)
511	! Name of the variable with the values for the mask in the input file (only if maskkingtype='var') (here not used)
512	namemaskvar = ''
513
514	fieldname = 'flx_co2_bbg_year'
515	IF (printlev >= 1) WRITE(numout,*) "chemistry_initialize: Read and interpolate file " &
516	// TRIM(filename) //" for variable flx_co2_bbg_year"
517	CALL interpweight_2Dcont(kjpindex, 0, 0, lalo, resolution, neighbours, &
518	contfrac, filename, fieldname, lonname, latname, vmin, vmax, nonegative, maskingtype, &
519	maskvals, namemaskvar, -1, fractype, chem_default, chem_norefinf, &
520	flx_co2_bbg_year, achem_co2)
521	END IF
522	END IF
523
524	IF ( OFF_LINE_MODE ) THEN
525
526	!-
527	!- What are the alowed options for the temporal interpolation
528	!-
529	! ALLOW_WEATHERGEN : Allow weather generator to create data
530	! This parameter is already read in the driver
531	allow_weathergen = .FALSE.
532	CALL getin_p('ALLOW_WEATHERGEN',allow_weathergen)
533
534	! FORCING_FILE : Name of file containing the forcing data
535	! This parameter is already read in the driver
536	filename='forcing_file.nc'
537	CALL getin_p('FORCING_FILE',filename)
538	CALL flininfo(filename,iml, jml, lml, tml, force_id)
539	WRITE(numout,*) 'Number of data per year in forcing file :', tml
540	CALL flinclo(force_id)
541	WRITE(numout,*) 'Forcing file closed in chemistry_initialize'
542
543
544	IF ( allow_weathergen ) THEN
545	WRITE(numout,) '*chemistry_initialize: Using weather generator, careful to precip division for NOx '
546	nbre_precip = un
547	WRITE(numout,*) 'Division pour les precip, NOx:', nbre_precip
548	ELSE
549	WRITE(numout,*) 'DT_SECHIBA :', dt_sechiba
550	nbre_precip = (one_day/dt_sechiba)/(tml/one_year)
551	WRITE(numout,*) 'Division pour les precip, NOx:', nbre_precip
552	END IF
553
554	ELSE ! (in coupled mode)
555
556	nbre_precip = un
557
558	END IF ! (OFF_LINE_MODE)
559
560	! Write diagnostics
561	IF (ok_cropsfertil_NOx) THEN
562	CALL xios_orchidee_send_field("achem_wrice",achem_wrice)
563	CALL xios_orchidee_send_field("achem_other",achem_other)
564	CALL xios_orchidee_send_field("interp_diag_N_qt_WRICE_year",N_qt_WRICE_year)
565	CALL xios_orchidee_send_field("interp_diag_N_qt_OTHER_year",N_qt_OTHER_year)
566
567	END IF
568	IF (ok_bbgfertil_NOx) THEN
569	CALL xios_orchidee_send_field("achem_co2",achem_co2)
570	CALL xios_orchidee_send_field("interp_diag_flx_co2_bbg_year",flx_co2_bbg_year)
571	END IF
572
573
574	END SUBROUTINE chemistry_initialize
575
576
577	!! ================================================================================================================================
578	!! SUBROUTINE : chemistry_bvoc
579	!!
580	!>\BRIEF This subroutine computes biogenic emissions of reactive compounds, that is of
581	!! VOCs (volatile organic compounds) from vegetation and NOx (nitrogen oxides) from soils.
582	!! Calculation are mostly based on the works by Guenther et al. (1995) and Yienger and Levy (1995).\n
583	!!
584	!! DESCRIPTION : Biogenic VOC emissions from vegetation are based on the parameterisations developped by
585	!! Guenther et al. (1995). Biogenic VOCs considered here are: isoprene, monoterpenes, OVOC and ORVOC
586	!! as bulked emissions, methanol, acetone, acetaldehyde, formaldehyde, acetic acid, formic acid
587	!! as single emissions.\n
588	!! For every biogenic VOCs an emission factor (EF), depending on the PFT considered, is used.\n
589	!! Isoprene emissions depend on temperature and radiation. A partition between sunlit and shaded
590	!! leaves is taken into account and either one (if ok_multilayer = FALSE) or several layers
591	!! (if ok_multilayer = TRUE) in the canopy can be used.\n
592	!! When radiation extinction is considered, the canopy radiative transfer model takes into
593	!! account light extinction through canopy, calculating first need diffuse and direct radiation
594	!! based on Andrew Friend 2001 radiative model and Spitters et al. 1986. The calculation of lai,
595	!! parscat, parsh and parsun, laisun and laishabsed based on Guenther et al.(JGR, 1995) and Norman (1982).\n
596	!! Emissions for other BVOCs (monoterpenes, OVOC, ORVOC and other single compounds such as
597	!! methanol, acetone...) depend only on temperature.\n
598	!! The impact of leaf age, using an emission activity prescribed for each of the 4 leaf age
599	!! classes can also be considered for isoprene and methanol emissions when ok_leafage = TRUE.\n
600	!! NOx emissions from soils are based on Yienger and Levy (1995) and depend on soil moisture
601	!! and temperature and PFT. The pulse effect, related to significant rain occuring after severe
602	!! drought can also be considered (ok_pulse_NOx = TRUE), as well as the increase in emissions related to
603	!! biomass buring (ok_bbgfertil_NOx = TRUE) or use of fertilizers (ok_cropsfertil_NOx = TRUE).
604	!! A net NO flux is eventually calculated taking into account loss by deposition on the surface, using
605	!! a Canopy Reduction Factor (CRF) based on stomatal and leaf area.\n
606	!! This subroutine is called by diffuco_main only if biogenic emissions are activated
607	!! for sechiba (flag CHEMISTRY_BVOC=TRUE).\n
608	!!
609	!! RECENT CHANGE(S): Changed name from diffuco_inca to chemistry_bvoc
610	!!
611	!! MAIN OUTPUT VARIABLE(S): :: PAR, :: PARsun, :: PARsh, :: laisun, :: laish,
612	!! :: flx_iso, :: flx_mono, :: flx_ORVOC, :: flx_MBO,
613	!! :: flx_methanol, :: flx_acetone, :: flx_acetal, :: flx_formal,
614	!! :: flx_acetic, :: flx_formic, :: flx_no_soil, :: flx_no,
615	!! :: CRF, :: flx_fertil_no, :: Trans, :: Fdf,
616	!! :: PARdf, :: PARdr, :: PARsuntab, :: PARshtab
617	!!
618	!! REFERENCE(S) :
619	!! - Andrew Friend (2001), Modelling canopy CO2 fluxes: are 'big-leaf' simplifications justified?
620	!! Global Ecology and Biogeography, 10, 6, 603-619, doi: 10.1046/j.1466-822x.2001.00268.x
621	!! - Spitters, C.J.T, Toussaint, H.A.J.M, Groudriaan, J. (1986), Separating the diffuse and direct
622	!! component of global radiation and its implications for modeling canopy photosynthesis, Agricultural
623	!! and Forest Meteorology, 38, 1-3, 217-229, doi:10.1016/0168-1923(86)90060-2
624	!! - Norman JM (1982) Simulation of microclimates. In: Hatfield JL, Thomason IJ (eds)
625	!! Biometeorology in integrated pest management. Academic, New York, pp 65â99
626	!! - Guenther, A., Hewitt, C. N., Erickson, D., Fall, R., Geron, C., Graedel, T., Harley, P.,
627	!! Klinger, L., Lerdau, M., McKay, W. A., Pierce, T., Scholes, B., Steinbrecher, R., Tallamraju,
628	!! R., Taylor, J. et Zimmerman, P. (1995), A global model of natural volatile organic compound
629	!! emissions, J. Geophys. Res., 100, 8873-8892.
630	!! - MacDonald, R. et Fall, R. (1993), Detection of substantial emissions of methanol from
631	!! plants to the atmosphere, Atmos. Environ., 27A, 1709-1713.
632	!! - Guenther, A., Geron, C., Pierce, T., Lamb, B., Harley, P. et Fall, R. (2000), Natural emissions
633	!! of non-methane volatile organic compounds, carbon monoxide, and oxides of nitrogen from
634	!! North America, Atmos. Environ., 34, 2205-2230.
635	!! - Yienger, J. J. et Levy II, H. (1995), Empirical model of global soil-biogenic NOx emissions,
636	!! J. Geophys. Res., 100, 11,447-11,464.
637	!! - Lathiere, J., D.A. Hauglustaine, A. Friend, N. De Noblet-Ducoudre, N. Viovy, and
638	!! G. Folberth (2006), Impact of climate variability and land use changes on global biogenic volatile
639	!! organic compound emissions, Atmospheric Chemistry and Physics, 6, 2129-2146.
640	!! - Lathiere, J., D.A. Hauglustaine, N. De Noblet-Ducoudre, G. Krinner et G.A. Folberth (2005),
641	!! Past and future changes in biogenic volatile organic compound emissions simulated with a global
642	!! dynamic vegetation model, Geophysical Research Letters, 32, doi: 10.1029/2005GL024164.
643	!! - Lathiere, J. (2005), Evolution des emissions de composes organiques et azotes par la biosphere
644	!! continentale dans le modele LMDz-INCA-ORCHIDEE, These de doctorat, Universite Paris VI.
645	!!
646	!! FLOWCHART : None
647	!_ ================================================================================================================================
648
649	SUBROUTINE chemistry_bvoc (kjpindex, swdown, coszang, temp_air, &
650	temp_sol, ptnlev1, precip_rain, humrel, veget_max, lai, &
651	frac_age, lalo, ccanopy, cim, wind, snow, &
652	veget, hist_id, hist2_id,kjit, index, &
653	indexlai, indexveg)
654
655	!! 0. Variables and parameter declaration
656
657	!! 0.1 Input variables
658
659	INTEGER(i_std), INTENT(in) :: kjpindex !! Domain size - terrestrial pixels only (unitless)
660	INTEGER(i_std), INTENT(in) :: kjit !! Time step number (-)
661	INTEGER(i_std),INTENT (in) :: hist_id !! History file identifier (-)
662	INTEGER(i_std),INTENT (in) :: hist2_id !! History file 2 identifier (-)
663	INTEGER(i_std),DIMENSION (kjpindex), INTENT (in) :: index !! Indeces of the points on the map (-)
664	INTEGER(i_std),DIMENSION (kjpindex*(nlai+1)), INTENT (in) :: indexlai !! Indeces of the points on the 3D map
665	INTEGER(i_std),DIMENSION (kjpindex*nvm), INTENT (in) :: indexveg !! Indeces of the points on the 3D map (-)
666	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: swdown !! Down-welling surface short-wave flux
667	!! (W.m^{-2})
668	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: coszang !! Cosine of the solar zenith angle (unitless)
669	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: temp_air !! Air temperature (K)
670	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: temp_sol !! Skin temperature (K)
671	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: ptnlev1 !! 1st level of soil temperature (K)
672	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: precip_rain !! Rain precipitation !!?? init
673	REAL(r_std), DIMENSION(kjpindex,nvm), INTENT(in) :: humrel !! Soil moisture stress (0-1, unitless)
674	REAL(r_std), DIMENSION(kjpindex,nvm), INTENT(in) :: veget_max !! Max. vegetation fraction (0-1, unitless)
675	REAL(r_std),DIMENSION (kjpindex), INTENT (in) :: snow !! Snow mass (kg)
676	REAL(r_std),DIMENSION (kjpindex,nvm), INTENT (in) :: veget !! Fraction of vegetation type (-)
677	REAL(r_std), DIMENSION(kjpindex,nvm), INTENT(in) :: lai !! Leaf area index (m^2.m^{-2})
678	REAL(r_std), DIMENSION(kjpindex,nvm,nleafages), INTENT(in) :: frac_age !! Age efficacity from STOMATE for iso
679	REAL(r_std), DIMENSION(kjpindex,2), INTENT(in) :: lalo !! Geographical coordinates for pixels (degrees)
680	REAL(r_std),DIMENSION (kjpindex), INTENT (in) :: ccanopy !! CO2 concentration inside the canopy
681	REAL(r_std),DIMENSION (kjpindex,nvm), INTENT (in) :: cim !! Intercellular CO2 over nlai
682	REAL(r_std), DIMENSION (kjpindex), INTENT(in) :: wind !! Wind module (m s^{-1})
683
684	!! 0.2 Output variables
685
686	!! 0.3 Modified variables
687
688	!! 0.4 Local variables
689
690	INTEGER(i_std) :: ji, jv, jf, jl !! Indices (unitless)
691	REAL(r_std), DIMENSION(kjpindex,nvm) :: fol_dens !! foliar density (gDM.m^{-2})
692	REAL(r_std), DIMENSION(kjpindex) :: tleaf !! Foliar temperature (K)
693	REAL(r_std), DIMENSION(kjpindex) :: t_no !! Temperature used for soil NO emissions (C)
694	REAL(r_std), DIMENSION(kjpindex) :: exp_1 !! First exponential used in the calculation of
695	!! isoprene dependancy to Temperature
696	REAL(r_std), DIMENSION(kjpindex) :: exp_2 !! Second exponential used in the calculation of
697	!! Isoprene dependancy to Temperature
698	REAL(r_std), DIMENSION(kjpindex) :: Ct_iso !! Isoprene dependancy to Temperature
699	REAL(r_std), DIMENSION(kjpindex) :: Cl_iso !! Isoprene dependancy to Light
700	REAL(r_std), DIMENSION(kjpindex) :: Ct_mono !! Monoterpene dependancy to Temperature
701	REAL(r_std), DIMENSION(kjpindex) :: Ct_sesq !! Sesquiterpenes dependancy to Temperature
702	REAL(r_std), DIMENSION(kjpindex) :: Ct_meth !! Methanol dependancy to Temperature
703	REAL(r_std), DIMENSION(kjpindex) :: Ct_acet !! Acetone dependancy to Temperature
704	REAL(r_std), DIMENSION(kjpindex) :: Ct_oxyVOC !! Other oxygenated BVOC dependancy to Temperature
705	REAL(r_std) :: GAMMA_iso !! Temperature and light dependancy for isoprene and fo each PFT
706	REAL(r_std) :: GAMMA_iso_m !! Temperature and light dependancy for isoprene and fo each PFT for multilayer
707	REAL(r_std), DIMENSION(kjpindex) :: Ylt_mono !! Total Temperature and light dependancy for monoterpenes
708	REAL(r_std), DIMENSION(kjpindex) :: Ylt_sesq !! Total Temperature and light dependancy for sesquiterpens
709	REAL(r_std), DIMENSION(kjpindex) :: Ylt_meth !! Total Temperature and light dependancy for methanol
710	REAL(r_std), DIMENSION(kjpindex) :: Ylt_acet !! Total Temperature and light dependancy for acetone
711	REAL(r_std), DIMENSION(kjpindex) :: Ct_MBO !! MBO dependance to Temperature
712	REAL(r_std), DIMENSION(kjpindex) :: Cl_MBO !! MBO dependance to Light
713	REAL(r_std), DIMENSION(kjpindex) :: Xvar !! Parameter used in the calculation
714	!! of MBO dependance to Temperature
715	REAL(r_std), DIMENSION(kjpindex,nvm) :: flx_OVOC !! Biogenic OVOC emission -
716	!! Other Volatil Organic Components (kgC.m^{-2}.s^{-1})
717	!!Canopy radiative transfer model
718	REAL(r_std), DIMENSION(kjpindex) :: So !! Maximum radiation at the Earth surface (W.m^{-2})
719	REAL(r_std), DIMENSION(kjpindex) :: Rfrac !! Parameter in the regression of diffuse
720	!! share on transmission
721	REAL(r_std), DIMENSION(kjpindex) :: Kfrac !! Parameter in the regression of diffuse
722	!! share on transmission
723	REAL(r_std), DIMENSION(kjpindex) :: swdf !! Sw diffuse radiation (W.m^{-2})
724	REAL(r_std), DIMENSION(kjpindex) :: swdr !! Sw direct radiation (W.m^{-2})
725	REAL(r_std), DIMENSION(kjpindex,nvm) :: PARscat !! Scatter PAR @tex ($\mu mol m^{-2} s^{-1}$) @endtex
726	REAL(r_std), DIMENSION(kjpindex,nvm) :: Clsun_iso !! Isoprene dependance to light for sun leaves
727	REAL(r_std), DIMENSION(kjpindex,nvm) :: Clsh_iso !! Isoprene dependance to light for shaded leaves
728	!! for multilayer canopy model for iso flux
729	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARscattab !! Scatter PAR @tex ($\mu mol m^{-2} s^{-1}$) @endtex
730	REAL(r_std), DIMENSION(nlai+1) :: laitab !! LAI per layer (m^2.m^{-2})
731	REAL(r_std), DIMENSION(kjpindex,nlai) :: laisuntabdep !! LAI of sun leaves in each layer (m^2.m^{-2})
732	REAL(r_std), DIMENSION(kjpindex,nlai) :: laishtabdep !! LAI of shaded leaves in each layer
733	!! (m^2.m^{-2})
734	REAL(r_std) :: Clsun_iso_tab !! Isoprene dependance to light
735	!! for sun leaves and per layer
736	REAL(r_std) :: Clsh_iso_tab !! Isoprene dependance to light
737	!! for shaded leaves and per layer
738	!for multilayer canopy model Spitter et al. 1986
739	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARnotscat !! Not-Scattered PAR
740	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARabsdir !! Absorbed light of the PAR direct flux
741	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARabsdiff !! Absorbed light of the PAR diffuse flux
742	REAL(r_std), PARAMETER :: sigma = 0.20 !! scattering coefficient of single leaves and for visible radiation
743	REAL(r_std), PARAMETER :: cluster = 0.85 !! clustering coefficient for leaves, the same that is setting for default in MEGAN V2.10
744	REAL(r_std) :: rho !! reflection index of a green, closed vegetation
745	REAL(r_std) :: kbl !! extinction coefficient of black leaves
746	REAL(r_std) :: kdf !! extinction coefficient of diffuse flux
747	!!Leaf age
748	REAL(r_std), DIMENSION(kjpindex,nvm) :: Eff_age_iso !! Isoprene emission dependance to Leaf Age
749	REAL(r_std), DIMENSION(kjpindex,nvm) :: Eff_age_meth !! Methanol emission dependance to Leaf Age
750	REAL(r_std), DIMENSION(kjpindex,nvm) :: Eff_age_VOC !! Other VOC emission dependance to Leaf Age
751	!!BBG and Fertilizers for NOx soil emission
752	REAL(r_std), DIMENSION(kjpindex) :: veget_max_nowoody !! sum of veget_max for non-woody PFT
753	REAL(r_std), DIMENSION(kjpindex,nvm) :: N_qt_WRICE_pft !! N fertiliser on RICE
754	!! (kgN per year per grid cell)
755	REAL(r_std), DIMENSION(kjpindex,nvm) :: N_qt_OTHER_pft !! N fertiliser on other veg
756	!! (kgN per year per grid cell)
757	!! CO2 inhibition effect on isoprene
758	REAL(r_std),DIMENSION (kjpindex,nvm) :: fco2_wshort !! Wilkinson short term function for CO2 impact on BVOC (isoprene)
759	REAL(r_std),DIMENSION (kjpindex) :: fco2_wlong !! Wilkinson long term function for CO2 impact on BVOC (isoprene)
760	REAL(r_std) :: fco2_ctrl
761	REAL(r_std),DIMENSION (kjpindex,nvm) :: fco2 !! Function for CO2 impact on BVOC (isoprene)
762	REAL(r_std), DIMENSION(kjpindex) :: Ismax_short
763	REAL(r_std), DIMENSION(kjpindex) :: h_short
764	REAL(r_std), DIMENSION(kjpindex) :: Cstar_short
765	REAL(r_std) :: Ismax_long
766	REAL(r_std) :: h_long
767	REAL(r_std) :: Cstar_long
768
769	!! 0.5 Parameters values
770
771	REAL(r_std), PARAMETER :: CT1 = 95000.0 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(10)) (J.mol^{-1})
772	REAL(r_std), PARAMETER :: CT2 = 230000.0 !! Empirical coefficient (see Guenther .et. al, 1995, eq(10)) (J.mol^{-1})
773	REAL(r_std), PARAMETER :: TS = 303.0 !! Leaf temperature at standard condition
774	!! (see Guenther .et. al, 1995, eq(10)) (K)
775	REAL(r_std), PARAMETER :: TM = 314.0 !! Leaf temperature (see Guenther .et. al, 1995, eq(10)) (K)
776
777	REAL(r_std), PARAMETER :: alpha_ = 0.0027 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(9)) (unitless)
778	REAL(r_std), PARAMETER :: CL1 = 1.066 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(9)) (unitless)
779	REAL(r_std), PARAMETER :: beta = 0.09 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(11)) (K^{-1})
780	REAL(r_std), PARAMETER :: lai_threshold = 11. !! Lai threshold for the calculation of scattered radiation
781	!! based on Guenther .et. al (1995) (m^2.m^{-2})
782
783
784	! Biogenic emissions
785	REAL(r_std),DIMENSION(kjpindex) :: PAR !! Photosynthetic active radiation, half of swdown
786	!! @tex ($\mu mol photons. m^{-2} s^{-1}$) @endtex
787	REAL(r_std),DIMENSION(kjpindex,nvm) :: PARsun !! PAR received by sun leaves
788	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
789	REAL(r_std),DIMENSION(kjpindex,nvm) :: PARsh !! PAR received by shaded leaves
790	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
791	REAL(r_std),DIMENSION(kjpindex,nvm) :: laisun !! Leaf area index of Sun leaves (m^2.m^{-2})
792	REAL(r_std),DIMENSION(kjpindex,nvm) :: laish !! Leaf area index of Shaded leaves (m^2.m^{-2})
793
794	CHARACTER(LEN=14) :: tleafsun_name !! To store variables names for I/O
795	CHARACTER(LEN=13) :: tleafsh_name !! To store variables names for I/O
796	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: Tleafsun_temp !! temporary sunlit leaf temperature matrix for writing
797	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: Tleafsh_temp !! temporary shade leaf temperature matrix for writing
798	REAL(r_std),DIMENSION(kjpindex) :: Fdf !! Fraction of the radiation which is diffused (0-1, unitless)
799	REAL(r_std),DIMENSION(kjpindex,nlai+1) :: PARsuntab !! PAR received by sun leaves over LAI layers
800	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
801	REAL(r_std),DIMENSION(kjpindex,nlai+1) :: PARshtab !! PAR received by shaded leaves over LAI layers
802	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
803	REAL(r_std),DIMENSION(kjpindex) :: PARdf !! Diffuse photosynthetic active radiation
804	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
805	REAL(r_std),DIMENSION(kjpindex) :: PARdr !! Direct photosynthetic active radiation
806	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
807	REAL(r_std),DIMENSION(kjpindex) :: Trans !! Atmospheric Transmissivity (unitless)
808
809	!_ ================================================================================================================================
810	fco2 = 0.
811	fco2_wshort = 0.
812	fco2_wlong = 0.
813	Fdf(:) = 0.
814	PAR(:) = 0.
815	PARsun(:,:) = 0.
816	PARsh(:,:) = 0.
817	laisun(:,:) = 0.
818	laish(:,:) = 0.
819	CRF(:,:) = 0.
820	Trans(:) = 0.
821	PARdf(:) = 0.
822	PARdr(:) = 0.
823	PARsuntab(:,:) = 0.
824	PARshtab(:,:) = 0.
825
826
827	!! 1. Canopy radiative transfer model
828
829	!! Canopy radiative transfer model: takes into account light extinction through canopy
830	!! First need to calculate diffuse and direct radiation
831	!! Based on Andrew Friend radiative model (Global Ecology & Biogeography, 2001)
832	!! And Spitters et al. (Agricultural and Forest Meteorology, 1986)
833
834	IF ( ok_radcanopy ) THEN
835
836	DO ji = 1, kjpindex
837	IF (coszang(ji) .GT. zero) THEN
838	!! 1.1 Extra-terrestrial solar irradiance at a plan parallel to Earh's surface
839	So(ji) = Sct( un + 0.033COS(360.pi/180.julian_diff/365.))*coszang(ji)
840	!! 1.2 Atmospheric transmissivity
841	Trans(ji) = swdown(ji)/So(ji)
842	!! 1.3 Empirical calculation of fraction diffuse from transmission based on Spitters et al. (1986)
843	Rfrac(ji) = 0.847 - 1.61coszang(ji) + 1.04(coszang(ji)**2.)
844	Kfrac(ji) = (1.47 - Rfrac(ji))/1.66
845	IF (Trans(ji) .LE. 0.22) THEN
846	Fdf(ji) = un
847	ELSE IF (Trans(ji) .LE. 0.35) THEN
848	Fdf(ji) = un - 6.4((Trans(ji) - 0.22)*2.)
849	ELSE IF (Trans(ji) .LE. Kfrac(ji)) THEN
850	Fdf(ji) = 1.47 - 1.66*Trans(ji)
851	ELSE
852	Fdf(ji) = Rfrac(ji)
853	END IF
854	!! 1.4 Direct and diffuse sw radiation in W.m^{-2}
855	swdf(ji) = swdown(ji)*Fdf(ji)
856	swdr(ji) = swdown(ji)*(un-Fdf(ji))
857	ELSE
858	swdf(ji) = zero
859	swdr(ji) = zero
860	END IF
861
862	!! 1.5 PAR diffuse and direct in umol/m^2/s
863	PARdf(ji) = swdf(ji) * W_to_mol * RG_to_PAR
864	PARdr(ji) = swdr(ji) * W_to_mol * RG_to_PAR
865	END DO
866
867	!! 1.6 Calculation of lai, parscat, parsh and parsun, laisun and laish !!?? define the terms
868	!! Based on Guenther et al. (JGR, 1995) and Norman (1982)
869	! One-layer canopy model or multi-layer canopy model
870	IF (ok_multilayer) THEN
871
872
873	! Calculation PER LAYER
874	DO jl = nlai+1, 1, -1
875	laitab(jl) = laimax(EXP(lai_level_depth(jl-1) - un)/(EXP(lai_level_depth*nlai) - un))
876
877	!introduction of the Spitter way to calculate radiation over the levels !!!!!!!
878	DO ji = 1, kjpindex
879	kdf = cluster0.8SQRT((1 - sigma))
880	IF (ABS(ACOS(coszang(ji))) .LT. pi/2. .AND. coszang(ji) .NE. zero) THEN
881	! Coefficients calculation:
882	kbl = cluster*0.5/ABS(coszang(ji))
883	rho = ((1-SQRT((1 - sigma)))/(1+SQRT((1 - sigma))))(2/(1+1.6ABS(coszang(ji))))
884
885	PARnotscat(ji,jl) = (1 - sigma)PARdr(ji)kblEXP(-SQRT((1 - sigma))kbl*laitab(jl))
886	PARabsdir(ji,jl) = (1 - rho)SQRT((1 - sigma))PARdr(ji)kblEXP(-SQRT((1 - sigma))kbllaitab(jl))
887	PARabsdiff(ji,jl) = (1 - rho)PARdf(ji)kdfEXP(-kdflaitab(jl))
888	PARshtab(ji,jl) = (PARabsdiff(ji,jl) + (PARabsdir(ji,jl) - PARnotscat(ji,jl)))/(1 - sigma)
889	PARsuntab(ji,jl) = PARshtab(ji,jl) + (1-sigma)kblPARdr(ji)/(1 - sigma)
890
891	!correction using the equation (4) in Bodin et al 2012 and (7) or (8) in Spitter et al 1986
892	!using the extinction coefficient kbl = 0.5/coszang and not only 0.5
893	IF (jl .NE. nlai+1) THEN
894	laisuntabdep(ji,jl) =(laitab(jl+1)-laitab(jl))EXP(-kbllaitab(jl))
895	laishtabdep(ji,jl) =(laitab(jl+1)-laitab(jl))(1.-EXP(-kbllaitab(jl)))
896	ENDIF
897
898	ELSE
899
900	PARshtab(ji,jl) = PARdf(ji)kdfEXP(-kdf*laitab(jl))
901	PARsuntab(ji,jl) = 0.
902
903	IF (jl .NE. nlai+1) THEN
904	laisuntabdep(ji,jl) = 0.
905	laishtabdep(ji,jl) = laitab(jl+1)-laitab(jl)
906
907	ENDIF
908	END IF
909	END DO
910	END DO
911
912
913
914	! introduction of the Spitter way to calculate radiation over the levels !!!!!!!
915	ELSE
916	! Calculation FOR one layer
917	DO jv = 1, nvm
918	DO ji = 1, kjpindex
919	IF (lai(ji,jv) .LE. lai_threshold) THEN
920	PARscat(ji,jv) = 0.07PARdr(ji)(1.1 - 0.1lai(ji,jv))exp(-coszang(ji))
921	ELSE
922	PARscat(ji,jv) = zero
923	END IF
924
925	IF (coszang(ji) .NE. zero ) THEN
926	PARsh(ji,jv) = PARdf(ji)exp(-0.5((lai(ji,jv))**0.7)) + PARscat(ji,jv)
927	PARsun(ji,jv) = PARdr(ji)COS(60.pi/180.)/coszang(ji) + PARsh(ji,jv)
928	ELSE
929	PARsh(ji,jv) = PARdf(ji)exp(-0.5(lai(ji,jv)**0.7)) + PARscat(ji,jv)
930	PARsun(ji,jv) = zero
931	END IF
932	IF (ABS(ACOS(coszang(ji))) .LT. pi/2. .AND. ABS(coszang(ji)) .GT. min_sechiba) THEN
933	! calculation as in Lathiere (2005) = with correction removing lai in Guenther (1995)
934	laisun(ji,jv) = (un - exp(-0.5lai(ji,jv)/(coszang(ji))))coszang(ji)/COS(60.*pi/180.)
935	laish(ji,jv) = lai(ji,jv) - laisun(ji,jv)
936	ELSE
937	laisun(ji,jv) = zero
938	laish(ji,jv) = lai(ji,jv)
939	END IF
940	END DO
941	END DO
942	ENDIF
943	END IF
944
945
946	!! 2. Calculation of non-PFT dependant parameters used for VOC emissions
947	DO ji = 1, kjpindex ! (loop over # pixels)
948	!! 2.1 Calculation of Tleaf (based on Lathiere, 2005)
949
950
951	tleaf(ji) = temp_air(ji)
952
953	!! 2.2 Isoprene emission dependency - with no PARsun/PARshaded partitioning - Guenther et al. (1995) and Lathiere (2005)
954	!> @codeinc $$?? ecrire les equation en latex ?
955	exp_1(ji) = exp( (CT1 * ( tleaf(ji) - TS )) / (RRTStleaf(ji)) )
956	exp_2(ji) = exp( (CT2 ( tleaf(ji) - TM )) / (RRTS*tleaf(ji)) )
957	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
958	Ct_iso(ji) = exp_1(ji)/(un + exp_2(ji)) ! temperature dependance
959	Cl_iso(ji) = alpha_CL1PAR(ji)/sqrt(un + (alpha_*2) (PAR(ji)**2) ) ! light dependance
960	!> @endcodeinc
961
962	!! 2.3 Monoterpene and oxy VOB emission dependency to Temperature
963	!! light independant fraction
964	!> @codeinc
965	!Ct_mono(ji) = exp(beta*(tleaf(ji) - TS)) ! Old method
966	Ct_mono(ji) = exp(beta_mono*(tleaf(ji) - TS))
967	Ct_sesq(ji) = exp(beta_sesq*(tleaf(ji) - TS))
968	Ct_meth(ji) = exp(beta_meth*(tleaf(ji) - TS))
969	Ct_acet(ji) = exp(beta_acet*(tleaf(ji) - TS))
970	Ct_oxyVOC(ji) = exp(beta_oxyVOC*(tleaf(ji) - TS))
971	!> @endcodeinc
972	!! 2.4 MBO biogenic emissions dependency, only from PFT7 and PFT4 for location of vegetation emitter
973	! but in fact MBO fluxes only in America (ponderosa and lodgepole pines only found in these areas)
974	!> @codeinc
975	Xvar(ji) = ((un/312.3) - (un/tleaf(ji)))/RR
976	!> @endcodeinc
977	!! 2.4.1 temperature dependency
978	!> @codeinc
979	Ct_MBO(ji) = (1.52209000.0exp(67000.0Xvar(ji)))/(209000.0 - 67000.0(un - exp(209000.0*Xvar(ji))))
980	!> @endcodeinc
981	!! 2.4.2 light dependency
982	Cl_MBO(ji) = (0.00111.44PAR(ji))/(sqrt(un + (0.0011*2)(PAR(ji)**2)))
983	!! 2.5 NO biogenic emissions given in ngN/m^2/s, emission factor in ngN/m^2/s too
984	!! calculation of temperature used for NO soil emissions
985	t_no(ji) = ptnlev1(ji) - ZeroCelsius !!temp must be in celsius to calculate no emissions
986	!! 2.6 calculation of non-woody veget_max fraction
987	IF (ok_cropsfertil_NOx) THEN
988	veget_max_nowoody(ji) = zero
989	DO jv = 1,nvm
990	IF ( (jv /= ibare_sechiba) .AND. .NOT.(is_tree(jv)) ) THEN
991	veget_max_nowoody(ji) = veget_max_nowoody(ji) + veget_max(ji,jv)
992	ENDIF
993	ENDDO
994	END IF
995	END DO ! (loop over # pixels)
996
997	!! 2bis. Calculation of CO2 function for inhibition effect on isoprene
998	! 2 approaches can be used: either Possell et al. (2005) or Wilkinson et al. (2006)
999
1000	!! 19/04/2010 and then implemented in version revised by Nicolas Vuichard, 08042014
1001	!! Impact of atmospheric CO2 on isoprene emissions
1002	!! Can be activated or not
1003	!! If considered, can use either Possell 2005 or Wilkinson 2009 parameterisation
1004	!! This is used to rescale the emission factor, considered to be measured at 350 ppm of CO2
1005	!! to the CO2 conditions of the run
1006
1007	IF ( ok_co2bvoc_poss ) THEN
1008	WRITE(numout,*) 'CO2 impact on isoprene: Possell calculation'
1009
1010	!! Possell function needs to be normalized (experiments at 400 ppm and EF before 1995)
1011	!! Normalized at 350 ppm
1012	fco2_ctrl = (-0.0123+(441.4795/350.)+(-1282.65/(350.**2)))
1013
1014	!! 2 tests: using the canopy (atmospheric) CO2 'ccanopy'
1015	!! or the intercellular CO2 over nlai 'cim'
1016	!! with cim = ccanopy*0.667
1017	!! in the end I go for ccanopy for the Possell function since too much differences
1018	!! when using cim and also the function has been derived based on atmospheric CO2
1019	DO ji = 1, kjpindex
1020
1021	fco2(ji,:) = (-0.0123+(441.4795/ccanopy(ji))+(-1282.65/(ccanopy(ji)*ccanopy(ji))))/fco2_ctrl
1022
1023	END DO
1024	ELSE IF ( ok_co2bvoc_wilk ) THEN
1025	WRITE(numout,*) 'CO2 impact on isoprene: Wilkinson calculation'
1026
1027	!! In the Wilkinson function, 2 impacts are considered:
1028	!! -short-term impact for CO2 variation during a single day (seconds/minutes)
1029	!! -long-term impact for CO2 variation during leaf-growth (weeks/month)
1030
1031
1032	!! Long-term parameters
1033	!! Constant
1034	Ismax_long = 1.344
1035	h_long = 1.4614
1036	Cstar_long = 585.
1037	!! Short-term parameters
1038	!! They have to be calculated based on atmospheric CO2
1039	!! 10/05/2010
1040	!! For atmospheric CO2 lower than 400 ppm or higher than 1200 ppm
1041	!! (min and max CO2 level tested for short-term effect in Wilkinson et al. 2009)
1042	!! we use the parameters calculated at 400/1200 ppm. For intermediate CO2 concentration,
1043	!! parameters are calculated.
1044	!! Linear interpolation
1045
1046	DO ji = 1, kjpindex
1047
1048	IF (ccanopy(ji) .LE. 400.) THEN
1049
1050	Ismax_short(ji) = 1.072
1051	h_short(ji) = 1.7
1052	Cstar_short(ji) = 1218.
1053
1054	ELSE IF (ccanopy(ji) .EQ. 600.) THEN
1055
1056	Ismax_short(ji) = 1.036
1057	h_short(ji) = 2.0125
1058	Cstar_short(ji) = 1150.
1059
1060	ELSE IF (ccanopy(ji) .EQ. 800.) THEN
1061
1062	Ismax_short(ji) = 1.046
1063	h_short(ji) = 1.5380
1064	Cstar_short(ji) = 2025.
1065
1066	ELSE IF (ccanopy(ji) .GE. 1200.) THEN
1067
1068	Ismax_short(ji) = 1.014
1069	h_short(ji) = 2.8610
1070	Cstar_short(ji) = 1525.
1071
1072
1073	ELSE IF ((ccanopy(ji) .GT. 400.) .AND. (ccanopy(ji) .LT. 600.)) THEN
1074
1075	Ismax_short(ji) = 1.036 + (ccanopy(ji)-600.)*(1.036-1.072)/(600.-400.)
1076	h_short(ji) = 2.0125 + (ccanopy(ji)-600.)*(2.0125-1.7)/(600.-400.)
1077	Cstar_short(ji) = 1150. + (ccanopy(ji)-600.)*(1150.-1218.)/(600.-400.)
1078
1079	ELSE IF ((ccanopy(ji) .GT. 600.) .AND. (ccanopy(ji) .LT. 800.)) THEN
1080
1081	Ismax_short(ji) = 1.046 + (ccanopy(ji)-800.)*(1.046-1.036)/(800.-600.)
1082	h_short(ji) = 1.5380 + (ccanopy(ji)-800.)*(1.5380-2.0125)/(800.-600.)
1083	Cstar_short(ji) = 2025. + (ccanopy(ji)-800.)*(2025.-1150.)/(800.-600.)
1084
1085	ELSE IF ((ccanopy(ji) .GT. 800.) .AND. (ccanopy(ji) .LT. 1200.)) THEN
1086
1087	Ismax_short(ji) = 1.014 + (ccanopy(ji)-1200.)*(1.014-1.046)/(1200.-800.)
1088	h_short(ji) = 2.8610 + (ccanopy(ji)-1200.)*(2.8610-1.5380)/(1200.-800.)
1089	Cstar_short(ji) = 1525. + (ccanopy(ji)-1200.)*(1525.-2025.)/(1200.-800.)
1090
1091
1092	END IF
1093
1094	END DO
1095
1096	WRITE(numout,) 'Wilkinson BVOC-CO2 function: parameters*'
1097	WRITE(numout,*) 'Ismax_long: ', Ismax_long
1098	WRITE(numout,*) 'h_long: ', h_long
1099	WRITE(numout,*) 'Cstar_long: ', Cstar_long
1100	WRITE(numout,*) 'Ismax_short: ', MAXVAL(Ismax_short(:)) , MINVAL(Ismax_short(:))
1101	WRITE(numout,*) 'h_short: ', MAXVAL(h_short(:)) , MINVAL(h_short(:))
1102	WRITE(numout,*) 'Cstar_short: ', MAXVAL(Cstar_short(:)) , MINVAL(Cstar_short(:))
1103	WRITE(numout,) '*****'
1104
1105	DO ji = 1, kjpindex
1106	fco2_wlong(ji) = (Ismax_long-((Ismax_long((0.667ccanopy(ji))**h_long))/&
1107	& ((Cstar_long*h_long)+(0.667ccanopy(ji))**h_long)))/1.06566
1108	DO jv = 1, nvm
1109	fco2_wshort(ji,jv) = (Ismax_short(ji)-((Ismax_short(ji)((cim(ji,jv))*h_short(ji)))/&
1110	& ((Cstar_short(ji)h_short(ji))+(cim(ji,jv))h_short(ji))))/1.010803
1111	END DO
1112	END DO
1113
1114	DO ji = 1, kjpindex
1115	DO jv = 1, nvm
1116	fco2(ji,jv) = fco2_wshort(ji,jv)*fco2_wlong(ji)
1117	END DO
1118	END DO
1119
1120	ELSE
1121	WRITE(numout,*) 'CO2 impact on isoprene not considered'
1122	fco2(:,:) = 1.
1123	END IF
1124
1125
1126	!! 3. Calculation of PFT dependant parameters and
1127	! Calculation of VOC emissions flux
1128
1129	Eff_age_iso(:,:) = zero
1130	Eff_age_meth(:,:) = zero
1131
1132
1133	DO jv = 1, nvm ! loop over the PDFs
1134	DO ji = 1, kjpindex ! loop over the grid cell
1135	! 6-Calculation of Leaf Age Function (Lathiere 2005)
1136	IF ( ok_leafage ) THEN
1137	DO jf = 1, nleafages
1138	!> @codeinc
1139	Eff_age_iso(ji,jv) = Eff_age_iso(ji,jv) + frac_age(ji,jv,jf)*iso_activity(jf)
1140	Eff_age_meth(ji,jv) = Eff_age_meth(ji,jv) + frac_age(ji,jv,jf)*methanol_activity(jf)
1141	!> @endcodeinc
1142	END DO
1143	!> @codeinc
1144	Eff_age_VOC(ji,jv) = un
1145	!> @endcodeinc
1146	ELSE
1147	Eff_age_iso(ji,jv) = un
1148	Eff_age_meth(ji,jv) = un
1149	Eff_age_VOC(ji,jv) = un
1150	END IF
1151	!! 5. Calculation of foliar density
1152	IF ( sla(jv) .eq. zero ) THEN
1153	fol_dens(ji,jv) = zero
1154	ELSE
1155	! 2 factor for conversion from gC to gDM
1156	fol_dens(ji,jv) = 2 * lai(ji,jv)/sla(jv)
1157	ENDIF
1158	!! 6. Calculation of VOC emissions from vegetation
1159	IF ( ok_radcanopy ) THEN
1160	! if multi-layer canopy model
1161	IF (ok_multilayer) THEN
1162
1163	laisun(ji,jv) = zero
1164	laish(ji,jv) = zero
1165	GAMMA_iso_m = zero
1166	flx_iso(ji,jv) = zero
1167	flx_mono(ji,jv) = zero
1168	flx_apinen(ji,jv) = zero
1169	flx_bpinen(ji,jv) = zero
1170	flx_limonen(ji,jv) = zero
1171	flx_myrcen(ji,jv) = zero
1172	flx_sabinen(ji,jv) = zero
1173	flx_camphen(ji,jv) = zero
1174	flx_3caren(ji,jv) = zero
1175	flx_tbocimen(ji,jv) = zero
1176	flx_othermono(ji,jv) = zero
1177	flx_sesquiter(ji,jv) = zero
1178	flx_methanol(ji,jv) = zero
1179	flx_acetone(ji,jv) = zero
1180	flx_acetal(ji,jv) = zero
1181	flx_formal(ji,jv) = zero
1182	flx_acetic(ji,jv) = zero
1183	flx_formic(ji,jv) = zero
1184	! loop over the NLAI canopy layers
1185	DO jl = 1, nlai
1186	IF ((laitab(jl) .LE. lai(ji,jv)).AND.(lai(ji,jv).NE.zero)) THEN
1187	!sunlit vegetation
1188	Clsun_iso_tab = alpha_CL1PARsuntab(ji,jl)/sqrt(un + (alpha_*2) (PARsuntab(ji,jl)**2) )
1189	! shaded vegetation
1190	Clsh_iso_tab = alpha_CL1PARshtab(ji,jl)/sqrt(un + (alpha_*2) (PARshtab(ji,jl)**2) )
1191	flx_iso(ji,jv) = flx_iso(ji,jv) + (laisuntabdep(ji,jl)*Clsun_iso_tab+ &
1192	& laishtabdep(ji,jl)Clsh_iso_tab) &
1193	& fol_dens(ji,jv)/lai(ji,jv)Ct_iso(ji)em_factor_isoprene(jv)* &
1194	& Eff_age_iso(ji,jv)fco2(ji,jv)1e-9/one_hour
1195
1196	GAMMA_iso_m = GAMMA_iso_m + (laisuntabdep(ji,jl)*Clsun_iso_tab+ &
1197	& laishtabdep(ji,jl)Clsh_iso_tab) &
1198	& fol_dens(ji,jv)/lai(ji,jv)Ct_iso(ji)1e-9/one_hour
1199
1200	laisun(ji,jv) = laisun(ji,jv) + laisuntabdep(ji,jl)
1201	laish(ji,jv) = laish(ji,jv) + laishtabdep(ji,jl)
1202	END IF
1203	END DO
1204
1205	!! 6.1 Calculation of monoterpene biogenic emissions
1206	flx_mono(ji,jv) = ((1-LDF_mono)Ct_mono(ji)1e-9/one_hourfol_dens(ji,jv) + LDF_monoGAMMA_iso_m)* &
1207	& em_factor_monoterpene(jv)*Eff_age_VOC(ji,jv)
1208	!! 6.12 Calculation of sesquiterpenes biogenic emission
1209	flx_sesquiter(ji,jv) = ((1-LDF_sesq)Ct_sesq(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_sesqGAMMA_iso_m)* &
1210	& em_factor_sesquiterp(jv)*Eff_age_VOC(ji,jv)
1211	!! 6.13 Calculation of methanol biogenic emissions
1212	flx_methanol(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1213	& em_factor_methanol(jv)*Eff_age_meth(ji,jv)
1214	!! 6.14 Calculation of acetone biogenic emissions
1215	flx_acetone(ji,jv) = ((1-LDF_acet)Ct_acet(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_acetGAMMA_iso_m)* &
1216	& em_factor_acetone(jv)*Eff_age_VOC(ji,jv)
1217	!! 6.14 Calculation of acetaldehyde biogenic emissions
1218	flx_acetal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1219	& em_factor_acetal(jv)*Eff_age_VOC(ji,jv)
1220	!! 6.16 Calculation of formaldehyde biogenic emissions
1221	flx_formal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1222	& em_factor_formal(jv)*Eff_age_VOC(ji,jv)
1223	!! 6.17 Calculation of acetic acid biogenic emissions
1224	flx_acetic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1225	& em_factor_acetic(jv)*Eff_age_VOC(ji,jv)
1226	!! 6.18 Calculation of formic acid biogenic emissions
1227	flx_formic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1228	& em_factor_formic(jv)*Eff_age_VOC(ji,jv)
1229
1230
1231	!! 6.3 Calculation of alfa pinene biogenic emission
1232	flx_apinen(ji,jv) = em_factor_apinene(jv)*flx_mono(ji,jv)
1233	!! 6.4 Calculation of beta pinene biogenic emission
1234	flx_bpinen(ji,jv) = em_factor_bpinene(jv)*flx_mono(ji,jv)
1235	!! 6.5 Calculation of limonene biogenic emission
1236	flx_limonen(ji,jv) = em_factor_limonene(jv)*flx_mono(ji,jv)
1237	!! 6.6 Calculation of myrcene biogenic emission !!
1238	flx_myrcen(ji,jv) = em_factor_myrcene(jv)*flx_mono(ji,jv)
1239	!! 6.7 Calculation of sabinene biogenic emission
1240	flx_sabinen(ji,jv) = em_factor_sabinene(jv)*flx_mono(ji,jv)
1241	!! 6.8 Calculation of camphene biogenic emission
1242	flx_camphen(ji,jv) = em_factor_camphene(jv)*flx_mono(ji,jv)
1243	!! 6.9 Calculation of 3-carene biogenic emission
1244	flx_3caren(ji,jv) = em_factor_3carene(jv)*flx_mono(ji,jv)
1245	!! 6.10 Calculation of t-beta-ocimene biogenic emission
1246	flx_tbocimen(ji,jv) = em_factor_tbocimene(jv)*flx_mono(ji,jv)
1247	!! 6.11 Calculation of other monoterpenes biogenic emission
1248	flx_othermono(ji,jv) = em_factor_othermonot(jv)*flx_mono(ji,jv)
1249
1250	! if mono-layer canopy model
1251	ELSE
1252	!sunlit vegetation
1253	Clsun_iso(ji,jv) = alpha_CL1PARsun(ji,jv)/sqrt(un + (alpha_*2) (PARsun(ji,jv)**2) )
1254	! shaded vegetation
1255	Clsh_iso(ji,jv) = alpha_CL1PARsh(ji,jv)/sqrt(un + (alpha_*2) (PARsh(ji,jv)**2) )
1256	IF (lai(ji,jv) .NE. zero) THEN
1257	!! 6.1 Calculation of isoprene biogenic emissions
1258	GAMMA_iso = (laisun(ji,jv)Clsun_iso(ji,jv) + laish(ji,jv)Clsh_iso(ji,jv))/lai(ji,jv)*Ct_iso(ji)
1259	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
1260	!! 6.2 Calculation of monoterpene biogenic emissions
1261	flx_mono(ji,jv) = ((1-LDF_mono)Ct_mono(ji)+LDF_monoGAMMA_iso)fol_dens(ji,jv) &
1262	& em_factor_monoterpene(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1263	!! 6.3 Calculation of alfa pinene biogenic emission
1264	flx_apinen(ji,jv) = em_factor_apinene(jv)*flx_mono(ji,jv)
1265	!! 6.4 Calculation of beta pinene biogenic emission
1266	flx_bpinen(ji,jv) = em_factor_bpinene(jv)*flx_mono(ji,jv)
1267	!! 6.5 Calculation of limonene biogenic emission
1268	flx_limonen(ji,jv) = em_factor_limonene(jv)*flx_mono(ji,jv)
1269	!! 6.6 Calculation of myrcene biogenic emission
1270	flx_myrcen(ji,jv) = em_factor_myrcene(jv)*flx_mono(ji,jv)
1271	!! 6.7 Calculation of sabinene biogenic emission
1272	flx_sabinen(ji,jv) = em_factor_sabinene(jv)*flx_mono(ji,jv)
1273	!! 6.8 Calculation of camphene biogenic emission
1274	flx_camphen(ji,jv) = em_factor_camphene(jv)*flx_mono(ji,jv)
1275	!! 6.9 Calculation of 3-carene biogenic emission
1276	flx_3caren(ji,jv) = em_factor_3carene(jv)*flx_mono(ji,jv)
1277	!! 6.10 Calculation of t-beta-ocimene biogenic emission
1278	flx_tbocimen(ji,jv) = em_factor_tbocimene(jv)*flx_mono(ji,jv)
1279	!! 6.11 Calculation of other monoterpenes biogenic emission
1280	flx_othermono(ji,jv) = em_factor_othermonot(jv)*flx_mono(ji,jv)
1281	!! 6.12 Calculation of sesquiterpenes biogenic emission
1282	flx_sesquiter(ji,jv) = ((1-LDF_sesq)Ct_sesq(ji)+LDF_sesqGAMMA_iso)fol_dens(ji,jv) &
1283	& em_factor_sesquiterp(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1284	!! 6.13 Calculation of methanol biogenic emissions
1285	flx_methanol(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1286	& em_factor_methanol(jv)Eff_age_meth(ji,jv)1e-9/one_hour
1287	!! 6.14 Calculation of acetone biogenic emissions
1288	flx_acetone(ji,jv) = ((1-LDF_acet)Ct_acet(ji)+LDF_acetGAMMA_iso)fol_dens(ji,jv) &
1289	& em_factor_acetone(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1290	!! 6.15 Calculation of acetaldehyde biogenic emissions
1291	flx_acetal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1292	& em_factor_acetal(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1293	!! 6.16 Calculation of formaldehyde biogenic emissions
1294	flx_formal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1295	& em_factor_formal(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1296	!! 6.17 Calculation of acetic acid biogenic emissions
1297	flx_acetic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1298	& em_factor_acetic(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1299	!! 6.18 Calculation of formic acid biogenic emissions
1300	flx_formic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1301	& em_factor_formic(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1302
1303	ELSE
1304	!
1305	flx_iso(ji,jv) = zero
1306	flx_mono(ji,jv) = zero
1307	flx_apinen(ji,jv) = zero
1308	flx_bpinen(ji,jv) = zero
1309	flx_limonen(ji,jv) = zero
1310	flx_myrcen(ji,jv) = zero
1311	flx_sabinen(ji,jv) = zero
1312	flx_camphen(ji,jv) = zero
1313	flx_3caren(ji,jv) = zero
1314	flx_tbocimen(ji,jv) = zero
1315	flx_othermono(ji,jv) = zero
1316	flx_sesquiter(ji,jv) = zero
1317	flx_methanol(ji,jv) = zero
1318	flx_acetone(ji,jv) = zero
1319	flx_acetal(ji,jv) = zero
1320	flx_formal(ji,jv) = zero
1321	flx_acetic(ji,jv) = zero
1322	flx_formic(ji,jv) = zero
1323	END IF
1324	END IF
1325	! if no light extinction due to vegetation
1326	ELSE
1327	!! Isoprene emissions - general equation
1328	flx_iso(ji,jv) = fol_dens(ji,jv)Ct_iso(ji)Cl_iso(ji)Eff_age_iso(ji,jv)fco2(ji,jv)* &
1329	em_factor_isoprene(jv)*1e-9/one_hour
1330	!! 6.2 Calculation of monoterpene biogenic emissions
1331	Ylt_mono(ji) = ((1-LDF_mono)Ct_mono(ji)+LDF_monoCt_iso(ji)*Cl_iso(ji))
1332	flx_mono(ji,jv) = fol_dens(ji,jv)em_factor_monoterpene(jv)Ylt_mono(ji)Eff_age_VOC(ji,jv)&
1333	1e-9/one_hour
1334	!! 6.3 Calculation of alfa pinene biogenic emission
1335	flx_apinen(ji,jv) = em_factor_apinene(jv)*flx_mono(ji,jv)
1336	!! 6.4 Calculation of beta pinene biogenic emission
1337	flx_bpinen(ji,jv) = em_factor_bpinene(jv)*flx_mono(ji,jv)
1338	!! 6.5 Calculation of limonene biogenic emission
1339	flx_limonen(ji,jv) = em_factor_limonene(jv)*flx_mono(ji,jv)
1340	!! 6.6 Calculation of myrcene biogenic emission
1341	flx_myrcen(ji,jv) = em_factor_myrcene(jv)*flx_mono(ji,jv)
1342	!! 6.7 Calculation of sabinene biogenic emission
1343	flx_sabinen(ji,jv) = em_factor_sabinene(jv)*flx_mono(ji,jv)
1344	!! 6.8 Calculation of camphene biogenic emission
1345	flx_camphen(ji,jv) = em_factor_camphene(jv)*flx_mono(ji,jv)
1346	!! 6.9 Calculation of 3-carene biogenic emission
1347	flx_3caren(ji,jv) = em_factor_3carene(jv)*flx_mono(ji,jv)
1348	!! 6.10 Calculation of t-beta-ocimene biogenic emission
1349	flx_tbocimen(ji,jv) = em_factor_tbocimene(jv)*flx_mono(ji,jv)
1350	!! 6.11 Calculation of other monoterpenes biogenic emission
1351	flx_othermono(ji,jv) = em_factor_othermonot(jv)*flx_mono(ji,jv)
1352	!! 6.12 Calculation of sesquiterpenes biogenic emission
1353	Ylt_sesq(ji) = ((1-LDF_sesq)Ct_sesq(ji)+LDF_sesqCt_iso(ji)*Cl_iso(ji))
1354	flx_sesquiter(ji,jv) = fol_dens(ji,jv)em_factor_sesquiterp(jv)Ylt_sesq(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1355	!! 6.16 Calculation of methanol biogenic emissions
1356	Ylt_meth(ji) = ((1-LDF_meth)Ct_meth(ji)+LDF_methCt_iso(ji)*Cl_iso(ji))
1357	flx_methanol(ji,jv) = fol_dens(ji,jv)em_factor_methanol(jv)Ylt_meth(ji)Eff_age_meth(ji,jv)1e-9/one_hour
1358	!! 6.17 Calculation of acetone biogenic emissions
1359	Ylt_acet(ji) = ((1-LDF_acet)Ct_acet(ji)+LDF_acetCt_iso(ji)*Cl_iso(ji))
1360	flx_acetone(ji,jv) = fol_dens(ji,jv)em_factor_acetone(jv)Ylt_acet(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1361	!! 6.18 Calculation of acetaldehyde biogenic emissions
1362	flx_acetal(ji,jv) = fol_dens(ji,jv)em_factor_acetal(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1363	!! 6.19 Calculation of formaldehyde biogenic emissions
1364	flx_formal(ji,jv) = fol_dens(ji,jv)em_factor_formal(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1365	!! 6.20 Calculation of acetic acid biogenic emissions
1366	flx_acetic(ji,jv) = fol_dens(ji,jv)em_factor_acetic(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1367	!! 6.21 Calculation of formic acid biogenic emissions
1368	flx_formic(ji,jv) = fol_dens(ji,jv)em_factor_formic(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1369
1370	END IF
1371
1372	!! 6.22 Calculation of ORVOC biogenic emissions
1373	!! Other Reactive Volatile Organic Compounds
1374	!> @codeinc
1375	flx_ORVOC(ji,jv) = fol_dens(ji,jv)em_factor_ORVOC(jv)Ct_mono(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1376	!> @endcodeinc
1377	!! 6.4 Calculation of OVOC biogenic emissions
1378	!! Other Volatile Organic Compounds
1379	flx_OVOC(ji,jv) = fol_dens(ji,jv)em_factor_OVOC(jv)Ct_mono(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1380	!! 6.5 Calculation of MBO biogenic emissions
1381	!! 2-Methyl-3-Buten-2-ol
1382	IF(lalo(ji,1) .GE. 20. .AND. lalo(ji,2) .LE. -100) THEN
1383	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
1384	ELSE
1385	flx_MBO(ji,jv) = zero
1386	END IF
1387	END DO
1388
1389	END DO
1390
1391
1392	!! 7. Calculation of NOx emissions from soils
1393	! Based on Yienger & Levy (1995) and Lathiere (2005, chapter 3)
1394	DO ji = 1, kjpindex
1395	!! 7.1 Precipitation-related pulse function
1396	IF (ok_pulse_NOx) THEN
1397	! if we are during a period where pulses are not allowed
1398	IF (ok_siesta(ji)) THEN
1399	! if this period is not over
1400	IF (FLOOR(siestaday(ji)) .LE. siestalim(ji)) THEN
1401	siestaday(ji) = siestaday(ji) + (dt_sechiba/one_day)
1402	! if this period is over
1403	ELSE
1404	ok_siesta(ji) = .FALSE.
1405	siestaday(ji) = zero
1406	END IF
1407	END IF
1408	! if we are during a period where pulses are allowed
1409	IF ((.NOT. ok_siesta(ji)) .AND. (.NOT. allow_pulse(ji))) THEN
1410	IF (humrel(ji,1) .LT. 0.15) THEN
1411	! if precip exceeds 1 mm/day over one time step => a pulse occurs
1412	IF(precip_rain(ji)/nbre_precip .GE. un/(one_day/dt_sechiba)) THEN
1413	! if precip is up to 5 mm/day => pulse length is 3 days
1414	IF (precip_rain(ji)/nbre_precip .LT. 5./(one_day/dt_sechiba)) THEN
1415	pulselim(ji) = 3.
1416	! if precip is up to 15 mm/day => pulse length is 7 days
1417	ELSE IF (precip_rain(ji)/nbre_precip .LT. 15./(one_day/dt_sechiba)) THEN
1418	pulselim(ji) = 7.
1419	! if precip is upper than 15 mm/day => pulse length is 14 days
1420	ELSE IF (precip_rain(ji)/nbre_precip .GE. 15./(one_day/dt_sechiba)) THEN
1421	pulselim(ji) = 14.
1422	END IF
1423	allow_pulse(ji)=.TRUE.
1424	pulseday(ji) = un
1425	END IF
1426	END IF
1427	END IF
1428	! if we were during a pulse period
1429	IF (allow_pulse(ji)) THEN
1430	! if we are still during the pulse period
1431	! 16/06/2010 We assume a (pulselim-1) days for the pulse length (NVui+Jlath)
1432	IF(FLOOR(pulseday(ji)) .LT. pulselim(ji)) THEN
1433	! calculation of the pulse function
1434	IF (pulselim(ji).EQ.3) THEN
1435	pulse(ji) = 11.19exp(-0.805pulseday(ji))
1436	ELSE IF (pulselim(ji).EQ.7) THEN
1437	pulse(ji) = 14.68exp(-0.384pulseday(ji))
1438	ELSE IF (pulselim(ji).EQ.14) THEN
1439	pulse(ji) = 18.46exp(-0.208pulseday(ji))
1440	END IF
1441	pulseday(ji) = pulseday(ji) + (dt_sechiba/one_day)
1442	! if the pulse period is over
1443	ELSE
1444	! pulse function is set to 1
1445	pulse(ji) = un
1446	allow_pulse(ji) = .FALSE.
1447	siestaday(ji) = un
1448	siestalim(ji) = pulselim(ji)
1449	ok_siesta(ji) = .TRUE.
1450	END IF
1451	END IF
1452	! no precipitation-related pulse function
1453	ELSE
1454	pulse(ji) = un
1455	END IF
1456	END DO
1457
1458	!! 7.2 Calculation of NO basal emissions including pulse effect
1459	DO jv = 1, nvm
1460	DO ji = 1, kjpindex
1461	!Tropical forests
1462	IF ( is_tropical(jv) .AND. is_evergreen(jv) ) THEN
1463	! Wet soils
1464	IF (humrel(ji,1) .GT. 0.3) THEN
1465	flx_no_soil(ji,jv) = 2.6*pulse(ji)
1466	! Dry soils
1467	ELSE
1468	flx_no_soil(ji,jv) = 8.6*pulse(ji)
1469	END IF
1470	!Else If agricultural lands OR Wet soils
1471	ELSE IF ( ( .NOT.(natural(jv)) ) .OR. ( humrel(ji,1) .GT. 0.3 ) ) THEN
1472	! Calculation of NO emissions depending of Temperature
1473	IF (t_no(ji) .LT. zero) THEN
1474	flx_no_soil(ji,jv) = zero
1475	ELSE IF (t_no(ji) .LE. 10.) THEN
1476	flx_no_soil(ji,jv) = 0.28em_factor_no_wet(jv)t_no(ji)*pulse(ji)
1477	ELSE IF (t_no(ji) .LE. 30.) THEN
1478	flx_no_soil(ji,jv) = em_factor_no_wet(jv)exp(0.103t_no(ji))*pulse(ji)
1479	ELSE
1480	flx_no_soil(ji,jv) = 21.97em_factor_no_wet(jv)pulse(ji)
1481	END IF
1482	!Else if Temp negative
1483	ELSE IF (t_no(ji) .LT. zero) THEN
1484	flx_no_soil(ji,jv) = zero
1485	!Else if Temp <= 30
1486	ELSE IF (t_no(ji) .LE. 30.) THEN
1487	flx_no_soil(ji,jv) = (em_factor_no_dry(jv)t_no(ji))/30.pulse(ji)
1488	ELSE
1489	flx_no_soil(ji,jv) = em_factor_no_dry(jv)*pulse(ji)
1490	END IF
1491
1492	!! 7.3 IF ACTIVATED (ok_bbgfertil_NOx = TRUE) calculation of NOx soil emission increase due to biomass burning
1493	! Calculation of Biomass-Burning-induced NOx emissions (Lathiere, 2005)
1494	! => NOx emissions 3-fold increase
1495	IF (ok_bbgfertil_NOx) THEN
1496	IF ( natural(jv) ) THEN
1497	! North Tropical zone from May to June
1498	IF ((lalo(ji,1) .LE. 30. .AND. lalo(ji,1) .GE. zero).AND. &
1499	(julian_diff .GE. 121. .AND. julian_diff .LE. 181).AND.(flx_co2_bbg_year(ji) .GT. 0.1)) THEN
1500	flx_no_soil(ji,jv) = flx_no_soil(ji,jv)*3.
1501	! South Tropical zone from November to December
1502	ELSE IF ((lalo(ji,1) .GE. -30. .AND. lalo(ji,1) .LT. zero).AND.(julian_diff .GE. 305.).AND. &
1503	(flx_co2_bbg_year(ji) .GT. 0.1)) THEN
1504	flx_no_soil(ji,jv) = flx_no_soil(ji,jv)*3.
1505	END IF
1506	END IF
1507	END IF
1508
1509	!! 7.4 IF ACTIVATED (ok_cropsfertil_NOx = TRUE) calculation of NOx soil emission increase due to fertilizer use
1510	! Calculation of N-fertiliser-induced NOx emissions
1511	flx_fertil_no(ji,jv) = zero
1512	IF (ok_cropsfertil_NOx) THEN
1513	IF (veget_max_nowoody(ji) .NE. zero) THEN
1514	! Non-agricultural lands
1515	IF ( (jv == ibare_sechiba) .OR. is_tree(jv) ) THEN
1516	N_qt_WRICE_pft(ji,jv) = zero
1517	N_qt_OTHER_pft(ji,jv) = zero
1518	! Grasslands or Croplands
1519	ELSE
1520	N_qt_WRICE_pft(ji,jv) = N_qt_WRICE_year(ji)*veget_max(ji,jv)/veget_max_nowoody(ji)
1521	N_qt_OTHER_pft(ji,jv) = N_qt_OTHER_year(ji)*veget_max(ji,jv)/veget_max_nowoody(ji)
1522	END IF
1523	ELSE
1524	N_qt_WRICE_pft(ji,jv) = zero
1525	N_qt_OTHER_pft(ji,jv) = zero
1526	END IF
1527
1528	! North temperate regions from May to August
1529	! OR South Temperate regions from November to February
1530	IF (((lalo(ji,1) .GT. 30.) .AND. (julian_diff .GE. 121. .AND. julian_diff .LE. 243.).AND. &
1531	(veget_max(ji,jv) .GT. min_sechiba)) .OR. &
1532	((lalo(ji,1) .LT. -30.) .AND. (julian_diff .GE. 305. .OR. julian_diff .LE. 59.) .AND.&
1533	(veget_max(ji,jv) .GT. min_sechiba))) THEN
1534	! 1e12 for conversion from kg to Ng
1535	! 1/(365/122460604) for conversion from year to seconds corrected for 4 months of emissions
1536	flx_fertil_no(ji,jv) = (N_qt_WRICE_pft(ji,jv)(1/30.)+N_qt_OTHER_pft(ji,jv))(2.5/100.) &
1537	& 1e12/(3652460604/12)/(area(ji)veget_max(ji,jv))
1538	! OR Tropical regions all the year
1539	ELSE IF ((lalo(ji,1) .GE. -30.).AND.(lalo(ji,1) .LE. 30.).AND.(veget_max(ji,jv) .GT. min_sechiba)) THEN
1540	flx_fertil_no(ji,jv) = (N_qt_WRICE_pft(ji,jv)(1/30.)+N_qt_OTHER_pft(ji,jv))(2.5/100.) &
1541	& 1e12/(365246060)/(area(ji)*veget_max(ji,jv))
1542	END IF
1543	flx_no_soil(ji,jv) = flx_no_soil(ji,jv) + flx_fertil_no(ji,jv)
1544	END IF
1545
1546	!! 7.5 Calculation of net NO flux above soil accounting for surface deposition,
1547	!! based on the Canopy Reduction Factor (CRF), calculated using Leaf Area and Stomatal Area
1548	!kc=cuticle absorptivity = 0.24m^2/m^2
1549	!ks=stomatal absorptivity = 8.75m^2/m^2
1550	!Larch=Larcher SAI/LAI ratio given in Larcher 1991
1551	!> @codeinc
1552	CRF(ji,jv) = (exp(-8.75Larch(jv)lai(ji,jv)) + exp(-0.24*lai(ji,jv)))/2.
1553	flx_no(ji,jv) = flx_no_soil(ji,jv)*CRF(ji,jv)
1554	!> @endcodeinc
1555	END DO
1556	END DO
1557
1558
1559	! Write output with XIOS
1560	CALL xios_orchidee_send_field("PAR",PAR)
1561	CALL xios_orchidee_send_field("flx_fertil_no",flx_fertil_no)
1562	CALL xios_orchidee_send_field("flx_iso",flx_iso)
1563	CALL xios_orchidee_send_field("flx_mono",flx_mono)
1564	CALL xios_orchidee_send_field("flx_ORVOC",flx_ORVOC)
1565	CALL xios_orchidee_send_field("flx_MBO",flx_MBO)
1566	CALL xios_orchidee_send_field("flx_methanol",flx_methanol)
1567	CALL xios_orchidee_send_field("flx_acetone",flx_acetone)
1568	CALL xios_orchidee_send_field("flx_acetal",flx_acetal)
1569	CALL xios_orchidee_send_field("flx_formal",flx_formal)
1570	CALL xios_orchidee_send_field("flx_acetic",flx_acetic)
1571	CALL xios_orchidee_send_field("flx_formic",flx_formic)
1572	CALL xios_orchidee_send_field("flx_no_soil",flx_no_soil)
1573	CALL xios_orchidee_send_field("flx_no",flx_no)
1574	CALL xios_orchidee_send_field('flx_apinen' , flx_apinen)
1575	CALL xios_orchidee_send_field('flx_bpinen' , flx_bpinen)
1576	CALL xios_orchidee_send_field('flx_limonen' ,flx_limonen)
1577	CALL xios_orchidee_send_field('flx_myrcen' , flx_myrcen)
1578	CALL xios_orchidee_send_field('flx_sabinen' ,flx_sabinen)
1579	CALL xios_orchidee_send_field('flx_camphen' ,flx_camphen)
1580	CALL xios_orchidee_send_field('flx_3caren' , flx_3caren)
1581	CALL xios_orchidee_send_field('flx_tbocimen' ,flx_tbocimen)
1582	CALL xios_orchidee_send_field('flx_othermono',flx_othermono)
1583	CALL xios_orchidee_send_field('flx_sesquiter',flx_sesquiter)
1584	CALL xios_orchidee_send_field("CRF",CRF)
1585	CALL xios_orchidee_send_field('fco2', fco2)
1586
1587	IF ( ok_radcanopy ) THEN
1588	CALL xios_orchidee_send_field("PARdf",PARdf)
1589	CALL xios_orchidee_send_field("PARdr",PARdr)
1590
1591	IF (ok_multilayer) THEN
1592	CALL xios_orchidee_send_field("PARsuntab",PARsuntab)
1593	CALL xios_orchidee_send_field("PARshtab",PARshtab)
1594	ELSE
1595	CALL xios_orchidee_send_field("PARsun",PARsun)
1596	CALL xios_orchidee_send_field("PARsh",PARsh)
1597	CALL xios_orchidee_send_field("laisun",laisun)
1598	CALL xios_orchidee_send_field("laish",laish)
1599	ENDIF
1600	ENDIF
1601
1602	IF ( ok_bbgfertil_Nox ) THEN
1603	CALL xios_orchidee_send_field("flx_co2_bbg_year",flx_co2_bbg_year)
1604	END IF
1605
1606	IF ( ok_cropsfertil_Nox ) THEN
1607	CALL xios_orchidee_send_field("N_qt_WRICE_year",N_qt_WRICE_year)
1608	CALL xios_orchidee_send_field("N_qt_OTHER_year",N_qt_OTHER_year)
1609	END IF
1610
1611
1612	! Write output with IOIPSL
1613	IF ( .NOT. almaoutput ) THEN
1614
1615	CALL histwrite_p(hist_id, 'PAR', kjit, PAR, kjpindex, index)
1616	IF ( ok_radcanopy ) THEN
1617	CALL histwrite_p(hist_id, 'laisun', kjit, laisun, kjpindex*nvm, indexveg)
1618	CALL histwrite_p(hist_id, 'laish', kjit, laish, kjpindex*nvm, indexveg)
1619	CALL histwrite_p(hist_id, 'Fdf', kjit, Fdf, kjpindex, index)
1620	IF (ok_multilayer) THEN
1621	CALL histwrite_p(hist_id, 'PARsuntab', kjit, PARsuntab, kjpindex*(nlai+1), indexlai)
1622	CALL histwrite_p(hist_id, 'PARshtab', kjit, PARshtab, kjpindex*(nlai+1), indexlai)
1623	ELSE
1624	CALL histwrite_p(hist_id, 'PARsun', kjit, PARsun, kjpindex*nvm, indexveg)
1625	CALL histwrite_p(hist_id, 'PARsh', kjit, PARsh, kjpindex*nvm, indexveg)
1626	END IF
1627	CALL histwrite_p(hist_id, 'coszang', kjit, coszang, kjpindex, index)
1628	CALL histwrite_p(hist_id, 'PARdf', kjit, PARdf, kjpindex, index)
1629	CALL histwrite_p(hist_id, 'PARdr', kjit, PARdr, kjpindex, index)
1630	CALL histwrite_p(hist_id, 'Trans', kjit, Trans, kjpindex, index)
1631	END IF
1632	CALL histwrite_p(hist_id, 'flx_fertil_no', kjit, flx_fertil_no, kjpindex*nvm, indexveg)
1633	CALL histwrite_p(hist_id, 'CRF', kjit, CRF, kjpindex*nvm, indexveg)
1634	CALL histwrite_p(hist_id, 'fco2', kjit, fco2, kjpindex*nvm, indexveg)
1635
1636	IF ( ok_bbgfertil_Nox ) THEN
1637	CALL histwrite_p(hist_id, 'flx_co2_bbg_year', 1, flx_co2_bbg_year, kjpindex, index)
1638	ENDIF
1639	IF ( ok_cropsfertil_Nox ) THEN
1640	CALL histwrite_p(hist_id, 'N_qt_WRICE_year', 1, N_qt_WRICE_year, kjpindex, index)
1641	CALL histwrite_p(hist_id, 'N_qt_OTHER_year', 1, N_qt_OTHER_year, kjpindex, index)
1642	ENDIF
1643	CALL histwrite_p(hist_id, 'flx_iso', kjit, flx_iso, kjpindex*nvm, indexveg)
1644	CALL histwrite_p(hist_id, 'flx_mono', kjit, flx_mono, kjpindex*nvm, indexveg)
1645	CALL histwrite_p(hist_id, 'flx_apinen', kjit, flx_apinen, kjpindex*nvm, indexveg)
1646	CALL histwrite_p(hist_id, 'flx_bpinen', kjit, flx_bpinen, kjpindex*nvm, indexveg)
1647	CALL histwrite_p(hist_id, 'flx_limonen', kjit, flx_limonen, kjpindex*nvm, indexveg)
1648	CALL histwrite_p(hist_id, 'flx_myrcen', kjit, flx_myrcen, kjpindex*nvm, indexveg)
1649	CALL histwrite_p(hist_id, 'flx_sabinen', kjit, flx_sabinen, kjpindex*nvm, indexveg)
1650	CALL histwrite_p(hist_id, 'flx_camphen', kjit, flx_camphen, kjpindex*nvm, indexveg)
1651	CALL histwrite_p(hist_id, 'flx_3caren', kjit, flx_3caren, kjpindex*nvm, indexveg)
1652	CALL histwrite_p(hist_id, 'flx_tbocimen', kjit, flx_tbocimen, kjpindex*nvm, indexveg)
1653	CALL histwrite_p(hist_id, 'flx_othermono', kjit, flx_othermono, kjpindex*nvm, indexveg)
1654	CALL histwrite_p(hist_id, 'flx_sesquiter', kjit, flx_sesquiter, kjpindex*nvm, indexveg)
1655	CALL histwrite_p(hist_id, 'flx_ORVOC', kjit, flx_ORVOC, kjpindex*nvm, indexveg)
1656	CALL histwrite_p(hist_id, 'flx_MBO', kjit, flx_MBO, kjpindex*nvm, indexveg)
1657	CALL histwrite_p(hist_id, 'flx_methanol', kjit, flx_methanol, kjpindex*nvm, indexveg)
1658	CALL histwrite_p(hist_id, 'flx_acetone', kjit, flx_acetone, kjpindex*nvm, indexveg)
1659	CALL histwrite_p(hist_id, 'flx_acetal', kjit, flx_acetal, kjpindex*nvm, indexveg)
1660	CALL histwrite_p(hist_id, 'flx_formal', kjit, flx_formal, kjpindex*nvm, indexveg)
1661	CALL histwrite_p(hist_id, 'flx_acetic', kjit, flx_acetic, kjpindex*nvm, indexveg)
1662	CALL histwrite_p(hist_id, 'flx_formic', kjit, flx_formic, kjpindex*nvm, indexveg)
1663	CALL histwrite_p(hist_id, 'flx_no_soil', kjit, flx_no_soil, kjpindex*nvm, indexveg)
1664	CALL histwrite_p(hist_id, 'flx_no', kjit, flx_no, kjpindex*nvm, indexveg)
1665
1666	IF ( hist2_id > 0 ) THEN
1667	CALL histwrite_p(hist2_id, 'PAR', kjit, PAR, kjpindex, index)
1668	IF ( ok_radcanopy ) THEN
1669	CALL histwrite_p(hist2_id, 'PARsun', kjit, PARsun, kjpindex*nvm, indexveg)
1670	CALL histwrite_p(hist2_id, 'PARsh', kjit, PARsh, kjpindex*nvm, indexveg)
1671	CALL histwrite_p(hist2_id, 'laisun', kjit, laisun, kjpindex*nvm, indexveg)
1672	CALL histwrite_p(hist2_id, 'laish', kjit, laish, kjpindex*nvm, indexveg)
1673	ENDIF
1674	CALL histwrite_p(hist2_id, 'flx_fertil_no', kjit, flx_fertil_no, kjpindex*nvm, indexveg)
1675	CALL histwrite_p(hist2_id, 'CRF', kjit, CRF, kjpindex*nvm, indexveg)
1676	IF ( ok_bbgfertil_Nox ) THEN
1677	CALL histwrite_p(hist2_id, 'flx_co2_bbg_year', 1, flx_co2_bbg_year, kjpindex, index)
1678	ENDIF
1679	IF ( ok_cropsfertil_Nox ) THEN
1680	CALL histwrite_p(hist2_id, 'N_qt_WRICE_year', 1, N_qt_WRICE_year, kjpindex, index)
1681	CALL histwrite_p(hist2_id, 'N_qt_OTHER_year', 1, N_qt_OTHER_year, kjpindex, index)
1682	ENDIF
1683	CALL histwrite_p(hist2_id, 'flx_iso', kjit, flx_iso, kjpindex*nvm, indexveg)
1684	CALL histwrite_p(hist2_id, 'flx_mono', kjit, flx_mono, kjpindex*nvm, indexveg)
1685	CALL histwrite_p(hist2_id, 'flx_apinen', kjit, flx_apinen, kjpindex*nvm, indexveg)
1686	CALL histwrite_p(hist2_id, 'flx_bpinen', kjit, flx_bpinen, kjpindex*nvm, indexveg)
1687	CALL histwrite_p(hist2_id, 'flx_limonen', kjit, flx_limonen, kjpindex*nvm, indexveg)
1688	CALL histwrite_p(hist2_id, 'flx_myrcen', kjit, flx_myrcen, kjpindex*nvm, indexveg)
1689	CALL histwrite_p(hist2_id, 'flx_sabinen', kjit, flx_sabinen, kjpindex*nvm, indexveg)
1690	CALL histwrite_p(hist2_id, 'flx_camphen', kjit, flx_camphen, kjpindex*nvm, indexveg)
1691	CALL histwrite_p(hist2_id, 'flx_3caren', kjit, flx_3caren, kjpindex*nvm, indexveg)
1692	CALL histwrite_p(hist2_id, 'flx_tbocimen', kjit, flx_tbocimen, kjpindex*nvm, indexveg)
1693	CALL histwrite_p(hist2_id, 'flx_othermono', kjit, flx_othermono, kjpindex*nvm, indexveg)
1694	CALL histwrite_p(hist2_id, 'flx_sesquiter', kjit, flx_sesquiter, kjpindex*nvm, indexveg)
1695	CALL histwrite_p(hist2_id, 'flx_ORVOC', kjit, flx_ORVOC, kjpindex*nvm, indexveg)
1696	CALL histwrite_p(hist2_id, 'flx_MBO', kjit, flx_MBO, kjpindex*nvm, indexveg)
1697	CALL histwrite_p(hist2_id, 'flx_methanol', kjit, flx_methanol, kjpindex*nvm, indexveg)
1698	CALL histwrite_p(hist2_id, 'flx_acetone', kjit, flx_acetone, kjpindex*nvm, indexveg)
1699	CALL histwrite_p(hist2_id, 'flx_acetal', kjit, flx_acetal, kjpindex*nvm, indexveg)
1700	CALL histwrite_p(hist2_id, 'flx_formal', kjit, flx_formal, kjpindex*nvm, indexveg)
1701	CALL histwrite_p(hist2_id, 'flx_acetic', kjit, flx_acetic, kjpindex*nvm, indexveg)
1702	CALL histwrite_p(hist2_id, 'flx_formic', kjit, flx_formic, kjpindex*nvm, indexveg)
1703	CALL histwrite_p(hist2_id, 'flx_no_soil', kjit, flx_no_soil, kjpindex*nvm, indexveg)
1704	CALL histwrite_p(hist2_id, 'flx_no', kjit, flx_no, kjpindex*nvm, indexveg)
1705	ENDIF
1706	ENDIF
1707
1708	IF (printlev>=3) WRITE(numout,*) 'OK chemistry_bvoc'
1709
1710	END SUBROUTINE chemistry_bvoc
1711
1712	!! ================================================================================================================================
1713	!! SUBROUTINE : chemistry_flux_interface
1714	!!
1715	!>\BRIEF This subroutine will give to the interface between inca model and orchidee model in sechiba all the flux ask by inca
1716	!!
1717	!! DESCRIPTION : This subroutine allow the transfer of fluxes between surface and atmospheric chemistry. It is called from sechiba
1718	!!
1719	!! RECENT CHANGE(S): None
1720	!!
1721	!! MAIN OUTPUT VARIABLE(S): ::
1722	!!
1723	!! REFERENCE(S) : None
1724	!!
1725	!! FLOWCHART : None
1726	!_ ================================================================================================================================
1727
1728	SUBROUTINE chemistry_flux_interface( field_out_names, fields_out, field_in_names, fields_in)
1729
1730	!
1731	! Optional arguments
1732	!
1733	! Names and fields for emission variables : to be transport by Orchidee to Inca
1734	CHARACTER(LEN=*),DIMENSION(:), OPTIONAL, INTENT(IN) :: field_out_names
1735	REAL(r_std),DIMENSION(:,:,:), OPTIONAL, INTENT(OUT) :: fields_out
1736	!
1737	! Names and fields for deposit variables : to be transport from chemistry model by INCA to ORCHIDEE.
1738	CHARACTER(LEN=*),DIMENSION(:), OPTIONAL, INTENT(IN) :: field_in_names
1739	REAL(r_std),DIMENSION(:,:), OPTIONAL, INTENT(IN) :: fields_in
1740	!
1741	! Number of fields to give (nb_fields_out) or get from (nb_fields_in) INCA :
1742	INTEGER(i_std), SAVE :: nb_fields_out, nb_fields_in
1743	!$OMP THREADPRIVATE(nb_fields_out, nb_fields_in)
1744
1745	! Id of fields to give (nb_fields_out) or get from (nb_fields_in) INCA :
1746	INTEGER(i_std) :: i_fields_out, i_fields_in
1747
1748	IF (l_first_chemistry_inca) THEN
1749
1750	! il faut verifier que ok_bvoc (chemistry_ok_bvoc) est bien active sinon on arrete tout
1751	if (.not.ok_bvoc) then
1752	CALL ipslerr_p (3,'chemistry_inca', &
1753	& 'you need to activate chemistry_ok_bvoc in orchidee.def',&
1754	& 'This model won''t be able to continue.', &
1755	& '')
1756	endif
1757
1758	! Prepare fieds out/in for interface with INCA.
1759	IF (PRESENT(field_out_names)) THEN
1760	nb_fields_out=SIZE(field_out_names)
1761	ELSE
1762	nb_fields_out=0
1763	ENDIF
1764
1765	IF (PRESENT(field_in_names)) THEN
1766	nb_fields_in=SIZE(field_in_names)
1767	ELSE
1768	nb_fields_in=0
1769	ENDIF
1770	l_first_chemistry_inca = .FALSE.
1771
1772	ENDIF
1773
1774
1775
1776	IF (ok_bvoc) THEN
1777	! Fields for deposit variables : to be transport from chemistry model by INCA to ORCHIDEE.
1778	DO i_fields_in=1,nb_fields_in
1779	SELECT CASE(TRIM(field_in_names(i_fields_in)))
1780	CASE DEFAULT
1781	CALL ipslerr_p (3,'chemistry_inca', &
1782	& 'You ask in INCA an unknown field '//TRIM(field_in_names(i_fields_in))//&
1783	& ' to give to ORCHIDEE for this specific version.',&
1784	& 'This model won''t be able to continue.', &
1785	& '(check your tracer parameters in INCA)')
1786	END SELECT
1787	ENDDO
1788
1789	! Fields for Biogenic emissions : to be transport by Orchidee to Inca
1790	DO i_fields_out=1,nb_fields_out
1791	SELECT CASE(TRIM(field_out_names(i_fields_out)))
1792	CASE("flx_iso")
1793	fields_out(:,:,i_fields_out)=flx_iso(:,:)
1794	CASE("flx_mono")
1795	fields_out(:,:,i_fields_out)=flx_mono(:,:)
1796	CASE("flx_ORVOC")
1797	fields_out(:,:,i_fields_out)=flx_ORVOC(:,:)
1798	CASE("flx_MBO")
1799	fields_out(:,:,i_fields_out)=flx_MBO(:,:)
1800	CASE("flx_methanol")
1801	fields_out(:,:,i_fields_out)=flx_methanol(:,:)
1802	CASE("flx_acetone")
1803	fields_out(:,:,i_fields_out)=flx_acetone(:,:)
1804	CASE("flx_acetal")
1805	fields_out(:,:,i_fields_out)=flx_acetal(:,:)
1806	CASE("flx_formal")
1807	fields_out(:,:,i_fields_out)=flx_formal(:,:)
1808	CASE("flx_acetic")
1809	fields_out(:,:,i_fields_out)=flx_acetic(:,:)
1810	CASE("flx_formic")
1811	fields_out(:,:,i_fields_out)=flx_formic(:,:)
1812	CASE("flx_no_soil")
1813	fields_out(:,:,i_fields_out)=flx_no_soil(:,:)
1814	CASE("flx_nox")
1815	fields_out(:,:,i_fields_out)=flx_no(:,:)
1816	CASE("flx_fertil_no")
1817	fields_out(:,:,i_fields_out)=flx_fertil_no(:,:)
1818	CASE("flx_apinen")
1819	fields_out(:,:,i_fields_out)=flx_apinen(:,:)
1820	CASE("flx_bpinen")
1821	fields_out(:,:,i_fields_out)=flx_bpinen(:,:)
1822	CASE("flx_limonen")
1823	fields_out(:,:,i_fields_out)=flx_limonen(:,:)
1824	CASE("flx_myrcen")
1825	fields_out(:,:,i_fields_out)=flx_myrcen(:,:)
1826	CASE("flx_sabinen")
1827	fields_out(:,:,i_fields_out)=flx_sabinen(:,:)
1828	CASE("flx_camphen")
1829	fields_out(:,:,i_fields_out)=flx_camphen(:,:)
1830	CASE("flx_3caren")
1831	fields_out(:,:,i_fields_out)=flx_3caren(:,:)
1832	CASE("flx_tbocimen")
1833	fields_out(:,:,i_fields_out)=flx_tbocimen(:,:)
1834	CASE("flx_othermono")
1835	fields_out(:,:,i_fields_out)=flx_othermono(:,:)
1836	CASE("flx_sesquiter")
1837	fields_out(:,:,i_fields_out)=flx_sesquiter(:,:)
1838
1839	CASE DEFAULT
1840	CALL ipslerr_p (3,'chemistry_inca', &
1841	& 'You ask from INCA an unknown field '//TRIM(field_out_names(i_fields_out))//&
1842	& ' to ORCHIDEE for this specific version.',&
1843	& 'This model won''t be able to continue.', &
1844	& '(check your tracer parameters in INCA)')
1845	END SELECT
1846	ENDDO
1847
1848	ENDIF
1849	END SUBROUTINE chemistry_flux_interface
1850
1851	!! ================================================================================================================================
1852	!! SUBROUTINE : chemistry_clear
1853	!!
1854	!>\BRIEF Clear chemistry module
1855	!!
1856	!! DESCRIPTION : Deallocate memory and reset initialization variables to there original values
1857	!!
1858	!_ ================================================================================================================================
1859	SUBROUTINE chemistry_clear
1860
1861	!! 1. Initialize as for first run
1862	l_first_chemistry_inca = .TRUE.
1863
1864	!! 2. Deallocate dynamic variables
1865	IF (ALLOCATED(pulse)) DEALLOCATE (pulse)
1866	IF (ALLOCATED (ok_siesta)) DEALLOCATE (ok_siesta)
1867	IF (ALLOCATED (allow_pulse)) DEALLOCATE (allow_pulse)
1868	IF (ALLOCATED (pulseday)) DEALLOCATE (pulseday)
1869	IF (ALLOCATED (siestaday)) DEALLOCATE (siestaday)
1870	IF (ALLOCATED (pulselim)) DEALLOCATE (pulselim)
1871	IF (ALLOCATED (siestalim)) DEALLOCATE (siestalim)
1872	IF (ALLOCATED (N_qt_WRICE_year)) DEALLOCATE (N_qt_WRICE_year)
1873	IF (ALLOCATED (N_qt_OTHER_year)) DEALLOCATE (N_qt_OTHER_year)
1874	IF (ALLOCATED (flx_iso)) DEALLOCATE (flx_iso)
1875	IF (ALLOCATED (flx_mono)) DEALLOCATE (flx_mono)
1876	IF (ALLOCATED (flx_ORVOC)) DEALLOCATE (flx_ORVOC)
1877	IF (ALLOCATED (flx_MBO)) DEALLOCATE (flx_MBO)
1878	IF (ALLOCATED (flx_methanol)) DEALLOCATE (flx_methanol)
1879	IF (ALLOCATED (flx_acetone)) DEALLOCATE (flx_acetone)
1880	IF (ALLOCATED (flx_acetal)) DEALLOCATE (flx_acetal)
1881	IF (ALLOCATED (flx_formal)) DEALLOCATE (flx_formal)
1882	IF (ALLOCATED (flx_acetic)) DEALLOCATE (flx_acetic)
1883	IF (ALLOCATED (flx_formic)) DEALLOCATE (flx_formic)
1884	IF (ALLOCATED (flx_no_soil)) DEALLOCATE (flx_no_soil)
1885	IF (ALLOCATED (flx_no)) DEALLOCATE (flx_no)
1886	IF (ALLOCATED (flx_fertil_no)) DEALLOCATE (flx_fertil_no)
1887	IF (ALLOCATED (flx_apinen)) DEALLOCATE (flx_apinen)
1888	IF (ALLOCATED (flx_bpinen)) DEALLOCATE (flx_bpinen)
1889	IF (ALLOCATED (flx_limonen)) DEALLOCATE (flx_limonen)
1890	IF (ALLOCATED (flx_myrcen)) DEALLOCATE (flx_myrcen)
1891	IF (ALLOCATED (flx_sabinen)) DEALLOCATE (flx_sabinen)
1892	IF (ALLOCATED (flx_camphen)) DEALLOCATE (flx_camphen)
1893	IF (ALLOCATED (flx_3caren)) DEALLOCATE (flx_3caren)
1894	IF (ALLOCATED (flx_tbocimen)) DEALLOCATE (flx_tbocimen)
1895	IF (ALLOCATED (flx_othermono)) DEALLOCATE (flx_othermono)
1896	IF (ALLOCATED (flx_sesquiter)) DEALLOCATE (flx_sesquiter)
1897	IF (ALLOCATED (CRF)) DEALLOCATE (CRF)
1898	IF (ALLOCATED (flx_co2_bbg_year)) DEALLOCATE (flx_co2_bbg_year)
1899
1900	END SUBROUTINE chemistry_clear
1901
1902	END MODULE chemistry

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