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source: branches/publications/ORCHIDEE_GLUC_r6545/src_sechiba/chemistry.f90 @ 6737

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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 xios_orchidee
27	USE constantes
28	USE qsat_moisture
29	USE sechiba_io_p
30	USE ioipsl
31	USE pft_parameters
32	USE grid
33	USE time, ONLY : one_day, dt_sechiba, julian_diff, one_hour, one_year
34	USE ioipsl_para
35	USE xios_orchidee
36
37	IMPLICIT NONE
38
39	PRIVATE
40	PUBLIC :: chemistry_initialize, chemistry_bvoc, chemistry_flux_interface, chemistry_clear
41
42
43	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_iso !! Isoprene emissions from vegetation (kgC.m^{-2}.s^{-1})
44	!$OMP THREADPRIVATE(flx_iso)
45	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_mono !! Monoterpene emissions from vegetation (kgC.m^{-2}.s^{-1})
46	!$OMP THREADPRIVATE(flx_mono)
47	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_ORVOC !! Other Volatile Organic Compound emissions from vegetation (kgC.m^{-2}.s^{-1})
48	!$OMP THREADPRIVATE(flx_ORVOC)
49	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_MBO !! 2-methyl-3-buten-2-ol emissions from vegetation (mainly pines in America) (kgC.m^{-2}.s^{-1})
50	!$OMP THREADPRIVATE(flx_MBO)
51	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_methanol !! Methanol emissions from vegetation (kgC.m^{-2}.s^{-1})
52	!$OMP THREADPRIVATE(flx_methanol)
53	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_acetone !! Acetone emissions from vegetation (kgC.m^{-2}.s^{-1})
54	!$OMP THREADPRIVATE(flx_acetone)
55	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_acetal !! Acetaldehyde emissions from vegetation (kgC.m^{-2}.s^{-1})
56	!$OMP THREADPRIVATE(flx_acetal)
57	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_formal !! Formaldehyde emissions from vegetation (kgC.m^{-2}.s^{-1})
58	!$OMP THREADPRIVATE(flx_formal)
59	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_acetic !! Acetic acid emissions from vegetation (kgC.m^{-2}.s^{-1})
60	!$OMP THREADPRIVATE(flx_acetic)
61	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_formic !! Formic acid emissions from vegetation (kgC.m^{-2}.s^{-1})
62	!$OMP THREADPRIVATE(flx_formic)
63	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_apinen !! Alpha pinene emissions from vegetation (kgC.m^{-2}.s^{-1})
64	!$OMP THREADPRIVATE(flx_apinen)
65	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_bpinen !! Beta pinene emissions from vegetation (kgC.m^{-2}.s^{-1})
66	!$OMP THREADPRIVATE(flx_bpinen)
67	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_limonen !! Limonene emissions from vegetation (kgC.m^{-2}.s^{-1})
68	!$OMP THREADPRIVATE(flx_limonen)
69	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_myrcen !! Myrcene emissions from vegetation (kgC.m^{-2}.s^{-1})
70	!$OMP THREADPRIVATE(flx_myrcen)
71	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_sabinen !! Sabinene emissions from vegetation (kgC.m^{-2}.s^{-1})
72	!$OMP THREADPRIVATE(flx_sabinen)
73	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_camphen !! Camphene emissions from vegetation (kgC.m^{-2}.s^{-1})
74	!$OMP THREADPRIVATE(flx_camphen)
75	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_3caren !! 3-Carene emissions from vegetation (kgC.m^{-2}.s^{-1})
76	!$OMP THREADPRIVATE(flx_3caren)
77	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_tbocimen !! T-beta Ocimene emissions from vegetation (kgC.m^{-2}.s^{-1})
78	!$OMP THREADPRIVATE(flx_tbocimen)
79	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_othermono !! Emissions of other monoterpenes from vegetation (kgC.m^{-2}.s^{-1})
80	!$OMP THREADPRIVATE(flx_othermono)
81	REAL(r_std),ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_sesquiter !! Sesquiterpene emissions from vegetation (kgC.m^{-2}.s^{-1})
82	!$OMP THREADPRIVATE(flx_sesquiter)
83	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_fertil_no !! Biogenic nitrogen oxide soil emission due to N-fertilisation (ngN.m^{-2}.s^{-1})
84	!$OMP THREADPRIVATE(flx_fertil_no)
85	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_no_soil !! Nitrogen Oxide emissions from soil, before deposition on canopy
86	!! (ngN.m^{-2}.s^{-1})
87	!$OMP THREADPRIVATE(flx_no_soil)
88	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: flx_no !! Net nitrogen Oxide emissions from soil, after deposition on canopy
89	!$OMP THREADPRIVATE(flx_no)
90	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:,:) :: CRF !! Canopy reduction factor for net NO flux calculation (kjpindex,nvm)
91	!$OMP THREADPRIVATE(CRF)
92
93	! variables used inside diffuco_inca module
94	LOGICAL, ALLOCATABLE, SAVE, DIMENSION(:) :: ok_siesta !! Flag for controlling post-pulse period (true/false)
95	!$OMP THREADPRIVATE(ok_siesta)
96	LOGICAL, ALLOCATABLE, SAVE, DIMENSION(:) :: allow_pulse !! Flag for controlling pulse period (true/false)
97	!$OMP THREADPRIVATE(allow_pulse)
98	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: pulse !! Pulse fonction
99	!$OMP THREADPRIVATE(pulse)
100	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: pulseday !! Counter for pulse period
101	!$OMP THREADPRIVATE(pulseday)
102	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: siestaday !! Counter for post-pulse period
103	!$OMP THREADPRIVATE(siestaday)
104	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: pulselim !! Pulse period length
105	!$OMP THREADPRIVATE(pulselim)
106	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: siestalim !! Post-pulse period length
107	!$OMP THREADPRIVATE(siestalim)
108	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: area2 !! Grid cell area (m^2)
109	!$OMP THREADPRIVATE(area2)
110	REAL(r_std), SAVE :: nbre_precip
111	!$OMP THREADPRIVATE(nbre_precip)
112	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: flx_co2_bbg_year !! CO2 emissions from biomass burning
113	!! Read in an input file (kgC.m^{-2}.year^{-1})
114	!$OMP THREADPRIVATE(flx_co2_bbg_year)
115	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: N_qt_WRICE_year !! N fertilizers applied on wetland rice
116	!! Read in an input file (kgN.yr^{-1})
117	!$OMP THREADPRIVATE(N_qt_WRICE_year)
118	REAL(r_std), ALLOCATABLE, SAVE, DIMENSION(:) :: N_qt_OTHER_year !! N fertilizers applied on other crops and grasses
119	!! Read in an input file (kgN.yr^{-1})
120	!$OMP THREADPRIVATE(N_qt_OTHER_year)
121	LOGICAL, SAVE :: l_first_chemistry_inca=.TRUE. !! Initialisation for chemistry_flux_interface
122	!$OMP THREADPRIVATE(l_first_chemistry_inca)
123
124
125
126	CONTAINS
127
128	!! ================================================================================================================================
129	!! SUBROUTINE : chemistry_initialize
130	!!
131	!>\BRIEF This subroutine initializes the chemistry module
132	!!
133	!! DESCRIPTION : Some of the variables and flags used chemistry_bvoc are allocated and initialised here.
134	!!
135	!! RECENT CHANGE(S): Changed name from diffuco_inca_init to chemistry_initialize
136	!!
137	!! MAIN OUTPUT VARIABLE(S): None
138	!!
139	!! REFERENCE(S) : None
140	!!
141	!! FLOWCHART : None
142	!_ ================================================================================================================================
143	SUBROUTINE chemistry_initialize(kjpindex, lalo, neighbours, resolution)
144
145	USE interpweight
146
147	IMPLICIT NONE
148
149	!! 0. Variables and parameter declaration
150
151	!! 0.1 Input variables
152
153	INTEGER(i_std), INTENT(in) :: kjpindex !! Domain size (unitless)
154	REAL(r_std), DIMENSION(kjpindex,2), INTENT (in) :: lalo !! Geographical coordinates
155	INTEGER(i_std), DIMENSION(kjpindex,8), INTENT (in) :: neighbours !! Vector of neighbours for each
156	!! grid point (1=N, 2=E, 3=S, 4=W)
157	REAL(r_std),DIMENSION (kjpindex,2), INTENT(in) :: resolution !! The size in km of each grid-box in X and Y
158
159	!! 0.2 Output variables
160	REAL(r_std), DIMENSION(kjpindex) :: achem_wrice !! Availability of data for the interpolation
161	REAL(r_std), DIMENSION(kjpindex) :: achem_other !! Availability of data for the interpolation
162	REAL(r_std), DIMENSION(kjpindex) :: achem_co2 !! Availability of data for the interpolation
163
164	!! 0.3 Modified variables
165
166	!! 0.4 Local variables
167	LOGICAL :: allow_weathergen
168	CHARACTER(LEN=80) :: filename, fieldname
169	INTEGER(i_std) :: iml, jml, lml, tml, force_id
170	INTEGER(i_std) :: ier
171	REAL(r_std) :: vmin, vmax !! min/max values to use for the
172	!! renormalization
173	CHARACTER(LEN=250) :: maskvname !! Variable to read the mask from
174	!! the file
175	CHARACTER(LEN=80) :: lonname, latname !! lon, lat names in input file
176	REAL(r_std), DIMENSION(:), ALLOCATABLE :: variabletypevals !! Values for all the types of the variable
177	!! (variabletypevals(1) = -un, not used)
178	CHARACTER(LEN=50) :: fractype !! method of calculation of fraction
179	!! 'XYKindTime': Input values are kinds
180	!! of something with a temporal
181	!! evolution on the dx*dy matrix'
182	LOGICAL :: nonegative !! whether negative values should be removed
183	CHARACTER(LEN=50) :: maskingtype !! Type of masking
184	!! 'nomask': no-mask is applied
185	!! 'mbelow': take values below maskvals(1)
186	!! 'mabove': take values above maskvals(1)
187	!! 'msumrange': take values within 2 ranges;
188	!! maskvals(2) <= SUM(vals(k)) <= maskvals(1)
189	!! maskvals(1) < SUM(vals(k)) <= maskvals(3)
190	!! (normalized by maskvals(3))
191	!! 'var': mask values are taken from a
192	!! variable inside the file (>0)
193	REAL(r_std), DIMENSION(3) :: maskvals !! values to use to mask (according to
194	!! `maskingtype')
195	CHARACTER(LEN=250) :: namemaskvar !! name of the variable to use to mask
196	REAL(r_std) :: chem_norefinf !! No value
197	REAL(r_std) :: chem_default !! Default value
198
199	!_ ================================================================================================================================
200
201	ALLOCATE (pulse(kjpindex),stat=ier)
202	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable pulse','','')
203	pulse(:) = un
204
205	! If we acount for NOx pulse emissions
206	IF (ok_pulse_NOx) THEN
207
208	ALLOCATE (ok_siesta(kjpindex),stat=ier)
209	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable ok_siesta','','')
210	ok_siesta(:) = .FALSE.
211
212	ALLOCATE (allow_pulse(kjpindex),stat=ier)
213	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable allow_pulse','','')
214	allow_pulse(:) = .FALSE.
215
216	ALLOCATE (pulseday(kjpindex),stat=ier)
217	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable pulseday','','')
218	pulseday(:) = zero
219
220	ALLOCATE (siestaday(kjpindex),stat=ier)
221	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable siestaday','','')
222	siestaday(:) = zero
223
224	ALLOCATE (pulselim(kjpindex),stat=ier)
225	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable pulselim','','')
226	pulselim(:) = zero
227
228	ALLOCATE (siestalim(kjpindex),stat=ier)
229	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable siestalim','','')
230	siestalim(:) = zero
231
232	END IF ! (ok_pulse_NOx)
233
234	! If we acount for NOx emissions by N-fertilizers
235	IF (ok_cropsfertil_NOx) THEN
236
237	ALLOCATE (area2(kjpindex),stat=ier)
238	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable area2','','')
239	area2(:) = resolution(:,1)*resolution(:,2)
240
241	ALLOCATE (N_qt_WRICE_year(kjpindex),stat=ier) !! N fertilizers on wetland rice, read in file
242	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable N_qt_WRICE_year','','')
243	N_qt_WRICE_year(:) = zero
244
245	ALLOCATE (N_qt_OTHER_year(kjpindex),stat=ier) !! N fertilizers on other crops and grasses, read in file
246	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable N_qt_OTHER_year','','')
247	N_qt_OTHER_year(:) = zero
248
249	WRITE (numout,) ' ********************** Interpolating N fertilizers files for NOx emissions... '
250
251	!Config Key = N_FERTIL_FILE
252	!Config Desc = File name
253	!Config If = CHEMISTRY_BVOC and NOx_FERTILIZERS_USE
254	!Config Def = orchidee_fertilizer_1995.nc
255	!Config Help =
256	!Config Units = -
257	filename = 'orchidee_fertilizer_1995.nc'
258	CALL getin_p('N_FERTIL_FILE',filename)
259
260	!! Variables for interpweight
261	vmin = 0.
262	vmax = 0.
263	! Type of calculation of cell fractions
264	fractype = 'default'
265	! Name of the longitude and latitude in the input file
266	lonname = 'lon'
267	latname = 'lat'
268	! Default value when no value is get from input file
269	chem_default = 0.
270	! Reference value when no value is get from input file
271	chem_norefinf = 0.
272	! Should negative values be set to zero from input file?
273	nonegative = .TRUE.
274	! Type of mask to apply to the input data (see header for more details)
275	maskingtype = 'nomask'
276	! Values to use for the masking
277	maskvals = (/ min_sechiba, undef_sechiba, undef_sechiba /)
278	! Name of the variable with the values for the mask in the input file (only if maskkingtype='var') (here not used)
279	namemaskvar = ''
280
281	fieldname= 'N_qt_WRICE_year'
282	IF (printlev >= 1) WRITE(numout,*) "chemistry_initialize: Read and interpolate file " &
283	// TRIM(filename) //" for variable N_qt_WRICE_year"
284	CALL interpweight_2Dcont(kjpindex, 0, 0, lalo, resolution, neighbours, &
285	contfrac, filename, fieldname, lonname, latname, vmin, vmax, nonegative, maskingtype, &
286	maskvals, namemaskvar, -1, fractype, chem_default, chem_norefinf, &
287	N_qt_WRICE_year, achem_wrice)
288
289	fieldname= 'N_qt_OTHER_year'
290	IF (printlev >= 1) WRITE(numout,*) "chemistry_initialize: Read and interpolate file " &
291	// TRIM(filename) //" for variable N_qt_OTHER_year"
292	CALL interpweight_2Dcont(kjpindex, 0, 0, lalo, resolution, neighbours, &
293	contfrac, filename, fieldname, lonname, latname, vmin, vmax, nonegative, maskingtype, &
294	maskvals, namemaskvar, -1, fractype, chem_default, chem_norefinf, &
295	N_qt_OTHER_year, achem_other)
296
297	END IF
298
299	ALLOCATE (flx_iso(kjpindex,nvm), stat=ier)
300	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_iso','','')
301	flx_iso(:,:) = 0.
302
303	ALLOCATE (flx_mono(kjpindex,nvm), stat=ier)
304	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_mono','','')
305	flx_mono(:,:) = 0.
306
307	ALLOCATE (flx_ORVOC(kjpindex,nvm), stat=ier)
308	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_ORVOC ','','')
309	flx_ORVOC(:,:) = 0.
310
311	ALLOCATE (flx_MBO(kjpindex,nvm), stat=ier)
312	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_MBO','','')
313	flx_MBO(:,:) = 0.
314
315	ALLOCATE (flx_methanol(kjpindex,nvm), stat=ier)
316	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_methanol','','')
317	flx_methanol(:,:) = 0.
318
319	ALLOCATE (flx_acetone(kjpindex,nvm), stat=ier)
320	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_acetone','','')
321	flx_acetone(:,:) = 0.
322
323	ALLOCATE (flx_acetal(kjpindex,nvm), stat=ier)
324	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_acetal','','')
325	flx_acetal(:,:) = 0.
326
327	ALLOCATE (flx_formal(kjpindex,nvm), stat=ier)
328	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_formal','','')
329	flx_formal(:,:) = 0.
330
331	ALLOCATE (flx_acetic(kjpindex,nvm), stat=ier)
332	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_acetic','','')
333	flx_acetic(:,:) = 0.
334
335	ALLOCATE (flx_formic(kjpindex,nvm), stat=ier)
336	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_formic','','')
337	flx_formic(:,:) = 0.
338
339	ALLOCATE (flx_no_soil(kjpindex,nvm), stat=ier)
340	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_no_soil','','')
341	flx_no_soil(:,:) = 0.
342
343	ALLOCATE (flx_no(kjpindex,nvm), stat=ier)
344	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_no','','')
345	flx_no(:,:) = 0.
346
347	ALLOCATE (flx_fertil_no(kjpindex,nvm), stat=ier)
348	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_fertil_no','','')
349	flx_fertil_no(:,:) = 0.
350
351	ALLOCATE (flx_apinen(kjpindex,nvm), stat=ier)
352	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_apinen','','')
353	flx_apinen(:,:) = 0.
354
355	ALLOCATE (flx_bpinen (kjpindex,nvm), stat=ier)
356	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_bpinen','','')
357	flx_bpinen(:,:) = 0.
358
359	ALLOCATE (flx_limonen (kjpindex,nvm), stat=ier)
360	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_limonen','','')
361	flx_limonen(:,:) = 0.
362
363	ALLOCATE (flx_myrcen(kjpindex,nvm), stat=ier)
364	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_myrcen','','')
365	flx_myrcen(:,:) = 0.
366
367	ALLOCATE (flx_sabinen(kjpindex,nvm), stat=ier)
368	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_sabinen','','')
369	flx_sabinen(:,:) = 0.
370
371	ALLOCATE (flx_camphen(kjpindex,nvm), stat=ier)
372	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_camphen','','')
373	flx_camphen(:,:) = 0.
374
375	ALLOCATE (flx_3caren(kjpindex,nvm), stat=ier)
376	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_3caren','','')
377	flx_3caren(:,:) = 0.
378
379	ALLOCATE (flx_tbocimen(kjpindex,nvm), stat=ier)
380	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_tbocimen','','')
381	flx_tbocimen(:,:) = 0.
382
383	ALLOCATE (flx_othermono(kjpindex,nvm), stat=ier)
384	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_othermono','','')
385	flx_othermono(:,:) = 0.
386
387	ALLOCATE (flx_sesquiter(kjpindex,nvm), stat=ier)
388	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable flx_sesquiter','','')
389	flx_sesquiter(:,:) = 0.
390
391	ALLOCATE(CRF(kjpindex,nvm), stat=ier)
392	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_init','Problem in allocate of variable CRF ','','')
393	CRF(:,:) = 0.
394
395
396	! If we acount for NOx emissions due to Biomass Burning
397	IF (ok_bbgfertil_NOx) THEN
398
399	ALLOCATE (flx_co2_bbg_year(kjpindex),stat=ier) !! CO2 emissions from bbg, read in file
400	IF (ier /= 0) CALL ipslerr_p(3,'chemistry_initialize','Problem in allocate of variable flx_co2_bbg_year','','')
401	flx_co2_bbg_year(:) = zero
402
403	WRITE (numout,) ' ********************** Interpolating CO2 bbg files for NOx emissions... '
404	!Config Key = N_FERTIL_FILE
405	!Config Desc = File name
406	!Config If = CHEMISTRY_BVOC and NOx_FERTILIZERS_USE
407	!Config Def = orchidee_fertilizer_1995.nc
408	!Config Help = ...
409	!Config Units = -
410	filename = 'orchidee_bbg_clim.nc'
411	CALL getin_p('CO2_BBG_FILE',filename)
412
413	!! Variables for interpweight
414	vmin = 0.
415	vmax = 0.
416	! Type of calculation of cell fractions
417	fractype = 'default'
418	! Name of the longitude and latitude in the input file
419	lonname = 'lon'
420	latname = 'lat'
421	! Default value when no value is get from input file
422	chem_default = 0.
423	! Reference value when no value is get from input file
424	chem_norefinf = 0.
425	! Should negative values be set to zero from input file?
426	nonegative = .TRUE.
427	! Type of mask to apply to the input data (see header for more details)
428	maskingtype = 'nomask'
429	! Values to use for the masking
430	maskvals = (/ min_sechiba, undef_sechiba, undef_sechiba /)
431	! Name of the variable with the values for the mask in the input file (only if maskkingtype='var') (here not used)
432	namemaskvar = ''
433
434	fieldname = 'flx_co2_bbg_year'
435	IF (printlev >= 1) WRITE(numout,*) "chemistry_initialize: Read and interpolate file " &
436	// TRIM(filename) //" for variable flx_co2_bbg_year"
437	CALL interpweight_2Dcont(kjpindex, 0, 0, lalo, resolution, neighbours, &
438	contfrac, filename, fieldname, lonname, latname, vmin, vmax, nonegative, maskingtype, &
439	maskvals, namemaskvar, -1, fractype, chem_default, chem_norefinf, &
440	flx_co2_bbg_year, achem_co2)
441	END IF
442
443	IF ( OFF_LINE_MODE ) THEN
444
445	!-
446	!- What are the alowed options for the temporal interpolation
447	!-
448	! ALLOW_WEATHERGEN : Allow weather generator to create data
449	! This parameter is already read in the driver
450	allow_weathergen = .FALSE.
451	CALL getin_p('ALLOW_WEATHERGEN',allow_weathergen)
452
453	! FORCING_FILE : Name of file containing the forcing data
454	! This parameter is already read in the driver
455	filename='forcing_file.nc'
456	CALL getin_p('FORCING_FILE',filename)
457	CALL flininfo(filename,iml, jml, lml, tml, force_id)
458	WRITE(numout,*) 'Number of data per year in forcing file :', tml
459	CALL flinclo(force_id)
460	WRITE(numout,*) 'Forcing file closed in chemistry_initialize'
461
462
463	IF ( allow_weathergen ) THEN
464	WRITE(numout,) '*chemistry_initialize: Using weather generator, careful to precip division for NOx '
465	nbre_precip = un
466	WRITE(numout,*) 'Division pour les precip, NOx:', nbre_precip
467	ELSE
468	WRITE(numout,*) 'DT_SECHIBA :', dt_sechiba
469	nbre_precip = (one_day/dt_sechiba)/(tml/one_year)
470	WRITE(numout,*) 'Division pour les precip, NOx:', nbre_precip
471	END IF
472
473	ELSE ! (in coupled mode)
474
475	nbre_precip = un
476
477	END IF ! (OFF_LINE_MODE)
478
479	! Write diagnostics
480	IF (ok_cropsfertil_NOx) THEN
481	CALL xios_orchidee_send_field("achem_wrice",achem_wrice)
482	CALL xios_orchidee_send_field("achem_other",achem_other)
483	END IF
484	IF (ok_bbgfertil_NOx) THEN
485	CALL xios_orchidee_send_field("achem_co2",achem_co2)
486	END IF
487
488
489	END SUBROUTINE chemistry_initialize
490
491
492	!! ================================================================================================================================
493	!! SUBROUTINE : chemistry_bvoc
494	!!
495	!>\BRIEF This subroutine computes biogenic emissions of reactive compounds, that is of
496	!! VOCs (volatile organic compounds) from vegetation and NOx (nitrogen oxides) from soils.
497	!! Calculation are mostly based on the works by Guenther et al. (1995) and Yienger and Levy (1995).\n
498	!!
499	!! DESCRIPTION : Biogenic VOC emissions from vegetation are based on the parameterisations developped by
500	!! Guenther et al. (1995). Biogenic VOCs considered here are: isoprene, monoterpenes, OVOC and ORVOC
501	!! as bulked emissions, methanol, acetone, acetaldehyde, formaldehyde, acetic acid, formic acid
502	!! as single emissions.\n
503	!! For every biogenic VOCs an emission factor (EF), depending on the PFT considered, is used.\n
504	!! Isoprene emissions depend on temperature and radiation. A partition between sunlit and shaded
505	!! leaves is taken into account and either one (if ok_multilayer = FALSE) or several layers
506	!! (if ok_multilayer = TRUE) in the canopy can be used.\n
507	!! When radiation extinction is considered, the canopy radiative transfer model takes into
508	!! account light extinction through canopy, calculating first need diffuse and direct radiation
509	!! based on Andrew Friend 2001 radiative model and Spitters et al. 1986. The calculation of lai,
510	!! parscat, parsh and parsun, laisun and laishabsed based on Guenther et al.(JGR, 1995) and Norman (1982).\n
511	!! Emissions for other BVOCs (monoterpenes, OVOC, ORVOC and other single compounds such as
512	!! methanol, acetone...) depend only on temperature.\n
513	!! The impact of leaf age, using an emission activity prescribed for each of the 4 leaf age
514	!! classes can also be considered for isoprene and methanol emissions when ok_leafage = TRUE.\n
515	!! NOx emissions from soils are based on Yienger and Levy (1995) and depend on soil moisture
516	!! and temperature and PFT. The pulse effect, related to significant rain occuring after severe
517	!! drought can also be considered (ok_pulse_NOx = TRUE), as well as the increase in emissions related to
518	!! biomass buring (ok_bbgfertil_NOx = TRUE) or use of fertilizers (ok_cropsfertil_NOx = TRUE).
519	!! A net NO flux is eventually calculated taking into account loss by deposition on the surface, using
520	!! a Canopy Reduction Factor (CRF) based on stomatal and leaf area.\n
521	!! This subroutine is called by diffuco_main only if biogenic emissions are activated
522	!! for sechiba (flag CHEMISTRY_BVOC=TRUE).\n
523	!!
524	!! RECENT CHANGE(S): Changed name from diffuco_inca to chemistry_bvoc
525	!!
526	!! MAIN OUTPUT VARIABLE(S): :: PAR, :: PARsun, :: PARsh, :: laisun, :: laish,
527	!! :: flx_iso, :: flx_mono, :: flx_ORVOC, :: flx_MBO,
528	!! :: flx_methanol, :: flx_acetone, :: flx_acetal, :: flx_formal,
529	!! :: flx_acetic, :: flx_formic, :: flx_no_soil, :: flx_no,
530	!! :: CRF, :: flx_fertil_no, :: Trans, :: Fdf,
531	!! :: PARdf, :: PARdr, :: PARsuntab, :: PARshtab
532	!!
533	!! REFERENCE(S) :
534	!! - Andrew Friend (2001), Modelling canopy CO2 fluxes: are 'big-leaf' simplifications justified?
535	!! Global Ecology and Biogeography, 10, 6, 603-619, doi: 10.1046/j.1466-822x.2001.00268.x
536	!! - Spitters, C.J.T, Toussaint, H.A.J.M, Groudriaan, J. (1986), Separating the diffuse and direct
537	!! component of global radiation and its implications for modeling canopy photosynthesis, Agricultural
538	!! and Forest Meteorology, 38, 1-3, 217-229, doi:10.1016/0168-1923(86)90060-2
539	!! - Norman JM (1982) Simulation of microclimates. In: Hatfield JL, Thomason IJ (eds)
540	!! Biometeorology in integrated pest management. Academic, New York, pp 65â99
541	!! - Guenther, A., Hewitt, C. N., Erickson, D., Fall, R., Geron, C., Graedel, T., Harley, P.,
542	!! Klinger, L., Lerdau, M., McKay, W. A., Pierce, T., Scholes, B., Steinbrecher, R., Tallamraju,
543	!! R., Taylor, J. et Zimmerman, P. (1995), A global model of natural volatile organic compound
544	!! emissions, J. Geophys. Res., 100, 8873-8892.
545	!! - MacDonald, R. et Fall, R. (1993), Detection of substantial emissions of methanol from
546	!! plants to the atmosphere, Atmos. Environ., 27A, 1709-1713.
547	!! - Guenther, A., Geron, C., Pierce, T., Lamb, B., Harley, P. et Fall, R. (2000), Natural emissions
548	!! of non-methane volatile organic compounds, carbon monoxide, and oxides of nitrogen from
549	!! North America, Atmos. Environ., 34, 2205-2230.
550	!! - Yienger, J. J. et Levy II, H. (1995), Empirical model of global soil-biogenic NOx emissions,
551	!! J. Geophys. Res., 100, 11,447-11,464.
552	!! - Lathiere, J., D.A. Hauglustaine, A. Friend, N. De Noblet-Ducoudre, N. Viovy, and
553	!! G. Folberth (2006), Impact of climate variability and land use changes on global biogenic volatile
554	!! organic compound emissions, Atmospheric Chemistry and Physics, 6, 2129-2146.
555	!! - Lathiere, J., D.A. Hauglustaine, N. De Noblet-Ducoudre, G. Krinner et G.A. Folberth (2005),
556	!! Past and future changes in biogenic volatile organic compound emissions simulated with a global
557	!! dynamic vegetation model, Geophysical Research Letters, 32, doi: 10.1029/2005GL024164.
558	!! - Lathiere, J. (2005), Evolution des emissions de composes organiques et azotes par la biosphere
559	!! continentale dans le modele LMDz-INCA-ORCHIDEE, These de doctorat, Universite Paris VI.
560	!!
561	!! FLOWCHART : None
562	!_ ================================================================================================================================
563
564	SUBROUTINE chemistry_bvoc (kjpindex, swdown, coszang, temp_air, &
565	temp_sol, ptnlev1, precip_rain, humrel, veget_max, lai, &
566	frac_age, lalo, ccanopy, cim, wind, snow, &
567	veget, hist_id, hist2_id,kjit, index, &
568	indexlai, indexveg)
569
570	!! 0. Variables and parameter declaration
571
572	!! 0.1 Input variables
573
574	INTEGER(i_std), INTENT(in) :: kjpindex !! Domain size - terrestrial pixels only (unitless)
575	INTEGER(i_std), INTENT(in) :: kjit !! Time step number (-)
576	INTEGER(i_std),INTENT (in) :: hist_id !! History file identifier (-)
577	INTEGER(i_std),INTENT (in) :: hist2_id !! History file 2 identifier (-)
578	INTEGER(i_std),DIMENSION (kjpindex), INTENT (in) :: index !! Indeces of the points on the map (-)
579	INTEGER(i_std),DIMENSION (kjpindex*(nlai+1)), INTENT (in) :: indexlai !! Indeces of the points on the 3D map
580	INTEGER(i_std),DIMENSION (kjpindex*nvm), INTENT (in) :: indexveg !! Indeces of the points on the 3D map (-)
581	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: swdown !! Down-welling surface short-wave flux
582	!! (W.m^{-2})
583	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: coszang !! Cosine of the solar zenith angle (unitless)
584	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: temp_air !! Air temperature (K)
585	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: temp_sol !! Skin temperature (K)
586	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: ptnlev1 !! 1st level of soil temperature (K)
587	REAL(r_std), DIMENSION(kjpindex), INTENT(in) :: precip_rain !! Rain precipitation !!?? init
588	REAL(r_std), DIMENSION(kjpindex,nvm), INTENT(in) :: humrel !! Soil moisture stress (0-1, unitless)
589	REAL(r_std), DIMENSION(kjpindex,nvm), INTENT(in) :: veget_max !! Max. vegetation fraction (0-1, unitless)
590	REAL(r_std),DIMENSION (kjpindex), INTENT (in) :: snow !! Snow mass (kg)
591	REAL(r_std),DIMENSION (kjpindex,nvm), INTENT (in) :: veget !! Fraction of vegetation type (-)
592	REAL(r_std), DIMENSION(kjpindex,nvm), INTENT(in) :: lai !! Leaf area index (m^2.m^{-2})
593	REAL(r_std), DIMENSION(kjpindex,nvm,nleafages), INTENT(in) :: frac_age !! Age efficacity from STOMATE for iso
594	REAL(r_std), DIMENSION(kjpindex,2), INTENT(in) :: lalo !! Geographical coordinates for pixels (degrees)
595	REAL(r_std),DIMENSION (kjpindex), INTENT (in) :: ccanopy !! CO2 concentration inside the canopy
596	REAL(r_std),DIMENSION (kjpindex,nvm), INTENT (in) :: cim !! Intercellular CO2 over nlai
597	REAL(r_std), DIMENSION (kjpindex), INTENT(in) :: wind !! Wind module (m s^{-1})
598
599	!! 0.2 Output variables
600
601	!! 0.3 Modified variables
602
603	!! 0.4 Local variables
604
605	INTEGER(i_std) :: ji, jv, jf, jl !! Indices (unitless)
606	REAL(r_std), DIMENSION(kjpindex,nvm) :: fol_dens !! foliar density (gDM.m^{-2})
607	REAL(r_std), DIMENSION(kjpindex) :: tleaf !! Foliar temperature (K)
608	REAL(r_std), DIMENSION(kjpindex) :: t_no !! Temperature used for soil NO emissions (C)
609	REAL(r_std), DIMENSION(kjpindex) :: exp_1 !! First exponential used in the calculation of
610	!! isoprene dependancy to Temperature
611	REAL(r_std), DIMENSION(kjpindex) :: exp_2 !! Second exponential used in the calculation of
612	!! Isoprene dependancy to Temperature
613	REAL(r_std), DIMENSION(kjpindex) :: Ct_iso !! Isoprene dependancy to Temperature
614	REAL(r_std), DIMENSION(kjpindex) :: Cl_iso !! Isoprene dependancy to Light
615	REAL(r_std), DIMENSION(kjpindex) :: Ct_mono !! Monoterpene dependancy to Temperature
616	REAL(r_std), DIMENSION(kjpindex) :: Ct_sesq !! Sesquiterpenes dependancy to Temperature
617	REAL(r_std), DIMENSION(kjpindex) :: Ct_meth !! Methanol dependancy to Temperature
618	REAL(r_std), DIMENSION(kjpindex) :: Ct_acet !! Acetone dependancy to Temperature
619	REAL(r_std), DIMENSION(kjpindex) :: Ct_oxyVOC !! Other oxygenated BVOC dependancy to Temperature
620	REAL(r_std) :: GAMMA_iso !! Temperature and light dependancy for isoprene and fo each PFT
621	REAL(r_std) :: GAMMA_iso_m !! Temperature and light dependancy for isoprene and fo each PFT for multilayer
622	REAL(r_std), DIMENSION(kjpindex) :: Ylt_mono !! Total Temperature and light dependancy for monoterpenes
623	REAL(r_std), DIMENSION(kjpindex) :: Ylt_sesq !! Total Temperature and light dependancy for sesquiterpens
624	REAL(r_std), DIMENSION(kjpindex) :: Ylt_meth !! Total Temperature and light dependancy for methanol
625	REAL(r_std), DIMENSION(kjpindex) :: Ylt_acet !! Total Temperature and light dependancy for acetone
626	REAL(r_std), DIMENSION(kjpindex) :: Ct_MBO !! MBO dependance to Temperature
627	REAL(r_std), DIMENSION(kjpindex) :: Cl_MBO !! MBO dependance to Light
628	REAL(r_std), DIMENSION(kjpindex) :: Xvar !! Parameter used in the calculation
629	!! of MBO dependance to Temperature
630	REAL(r_std), DIMENSION(kjpindex,nvm) :: flx_OVOC !! Biogenic OVOC emission -
631	!! Other Volatil Organic Components (kgC.m^{-2}.s^{-1})
632	!!Canopy radiative transfer model
633	REAL(r_std), DIMENSION(kjpindex) :: So !! Maximum radiation at the Earth surface (W.m^{-2})
634	REAL(r_std), DIMENSION(kjpindex) :: Rfrac !! Parameter in the regression of diffuse
635	!! share on transmission
636	REAL(r_std), DIMENSION(kjpindex) :: Kfrac !! Parameter in the regression of diffuse
637	!! share on transmission
638	REAL(r_std), DIMENSION(kjpindex) :: swdf !! Sw diffuse radiation (W.m^{-2})
639	REAL(r_std), DIMENSION(kjpindex) :: swdr !! Sw direct radiation (W.m^{-2})
640	REAL(r_std), DIMENSION(kjpindex,nvm) :: PARscat !! Scatter PAR @tex ($\mu mol m^{-2} s^{-1}$) @endtex
641	REAL(r_std), DIMENSION(kjpindex,nvm) :: Clsun_iso !! Isoprene dependance to light for sun leaves
642	REAL(r_std), DIMENSION(kjpindex,nvm) :: Clsh_iso !! Isoprene dependance to light for shaded leaves
643	!! for multilayer canopy model for iso flux
644	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARscattab !! Scatter PAR @tex ($\mu mol m^{-2} s^{-1}$) @endtex
645	REAL(r_std), DIMENSION(nlai+1) :: laitab !! LAI per layer (m^2.m^{-2})
646	REAL(r_std), DIMENSION(kjpindex,nlai) :: laisuntabdep !! LAI of sun leaves in each layer (m^2.m^{-2})
647	REAL(r_std), DIMENSION(kjpindex,nlai) :: laishtabdep !! LAI of shaded leaves in each layer
648	!! (m^2.m^{-2})
649	REAL(r_std) :: Clsun_iso_tab !! Isoprene dependance to light
650	!! for sun leaves and per layer
651	REAL(r_std) :: Clsh_iso_tab !! Isoprene dependance to light
652	!! for shaded leaves and per layer
653	!for multilayer canopy model Spitter et al. 1986
654	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARnotscat !! Not-Scattered PAR
655	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARabsdir !! Absorbed light of the PAR direct flux
656	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: PARabsdiff !! Absorbed light of the PAR diffuse flux
657	REAL(r_std), PARAMETER :: sigma = 0.20 !! scattering coefficient of single leaves and for visible radiation
658	REAL(r_std), PARAMETER :: cluster = 0.85 !! clustering coefficient for leaves, the same that is setting for default in MEGAN V2.10
659	REAL(r_std) :: rho !! reflection index of a green, closed vegetation
660	REAL(r_std) :: kbl !! extinction coefficient of black leaves
661	REAL(r_std) :: kdf !! extinction coefficient of diffuse flux
662	!!Leaf age
663	REAL(r_std), DIMENSION(kjpindex,nvm) :: Eff_age_iso !! Isoprene emission dependance to Leaf Age
664	REAL(r_std), DIMENSION(kjpindex,nvm) :: Eff_age_meth !! Methanol emission dependance to Leaf Age
665	REAL(r_std), DIMENSION(kjpindex,nvm) :: Eff_age_VOC !! Other VOC emission dependance to Leaf Age
666	!!BBG and Fertilizers for NOx soil emission
667	REAL(r_std), DIMENSION(kjpindex) :: veget_max_nowoody !! sum of veget_max for non-woody PFT
668	REAL(r_std), DIMENSION(kjpindex,nvm) :: N_qt_WRICE_pft !! N fertiliser on RICE
669	!! (kgN per year per grid cell)
670	REAL(r_std), DIMENSION(kjpindex,nvm) :: N_qt_OTHER_pft !! N fertiliser on other veg
671	!! (kgN per year per grid cell)
672	!! CO2 inhibition effect on isoprene
673	REAL(r_std),DIMENSION (kjpindex,nvm) :: fco2_wshort !! Wilkinson short term function for CO2 impact on BVOC (isoprene)
674	REAL(r_std),DIMENSION (kjpindex) :: fco2_wlong !! Wilkinson long term function for CO2 impact on BVOC (isoprene)
675	REAL(r_std) :: fco2_ctrl
676	REAL(r_std),DIMENSION (kjpindex,nvm) :: fco2 !! Function for CO2 impact on BVOC (isoprene)
677	REAL(r_std), DIMENSION(kjpindex) :: Ismax_short
678	REAL(r_std), DIMENSION(kjpindex) :: h_short
679	REAL(r_std), DIMENSION(kjpindex) :: Cstar_short
680	REAL(r_std) :: Ismax_long
681	REAL(r_std) :: h_long
682	REAL(r_std) :: Cstar_long
683
684	!! 0.5 Parameters values
685
686	REAL(r_std), PARAMETER :: CT1 = 95000.0 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(10)) (J.mol^{-1})
687	REAL(r_std), PARAMETER :: CT2 = 230000.0 !! Empirical coefficient (see Guenther .et. al, 1995, eq(10)) (J.mol^{-1})
688	REAL(r_std), PARAMETER :: TS = 303.0 !! Leaf temperature at standard condition
689	!! (see Guenther .et. al, 1995, eq(10)) (K)
690	REAL(r_std), PARAMETER :: TM = 314.0 !! Leaf temperature (see Guenther .et. al, 1995, eq(10)) (K)
691
692	REAL(r_std), PARAMETER :: alpha_ = 0.0027 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(9)) (unitless)
693	REAL(r_std), PARAMETER :: CL1 = 1.066 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(9)) (unitless)
694	REAL(r_std), PARAMETER :: beta = 0.09 !! Empirical coeffcient (see Guenther .et. al, 1995, eq(11)) (K^{-1})
695	REAL(r_std), PARAMETER :: lai_threshold = 11. !! Lai threshold for the calculation of scattered radiation
696	!! based on Guenther .et. al (1995) (m^2.m^{-2})
697
698
699	! Biogenic emissions
700	REAL(r_std),DIMENSION(kjpindex) :: PAR !! Photosynthetic active radiation, half of swdown
701	!! @tex ($\mu mol photons. m^{-2} s^{-1}$) @endtex
702	REAL(r_std),DIMENSION(kjpindex,nvm) :: PARsun !! PAR received by sun leaves
703	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
704	REAL(r_std),DIMENSION(kjpindex,nvm) :: PARsh !! PAR received by shaded leaves
705	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
706	REAL(r_std),DIMENSION(kjpindex,nvm) :: laisun !! Leaf area index of Sun leaves (m^2.m^{-2})
707	REAL(r_std),DIMENSION(kjpindex,nvm) :: laish !! Leaf area index of Shaded leaves (m^2.m^{-2})
708
709	CHARACTER(LEN=14) :: tleafsun_name !! To store variables names for I/O
710	CHARACTER(LEN=13) :: tleafsh_name !! To store variables names for I/O
711	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: Tleafsun_temp !! temporary sunlit leaf temperature matrix for writing
712	REAL(r_std), DIMENSION(kjpindex,nlai+1) :: Tleafsh_temp !! temporary shade leaf temperature matrix for writing
713	REAL(r_std),DIMENSION(kjpindex) :: Fdf !! Fraction of the radiation which is diffused (0-1, unitless)
714	REAL(r_std),DIMENSION(kjpindex,nlai+1) :: PARsuntab !! PAR received by sun leaves over LAI layers
715	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
716	REAL(r_std),DIMENSION(kjpindex,nlai+1) :: PARshtab !! PAR received by shaded leaves over LAI layers
717	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
718	REAL(r_std),DIMENSION(kjpindex) :: PARdf !! Diffuse photosynthetic active radiation
719	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
720	REAL(r_std),DIMENSION(kjpindex) :: PARdr !! Direct photosynthetic active radiation
721	!! @tex ($\mu mol m^{-2} s^{-1}$) @endtex
722	REAL(r_std),DIMENSION(kjpindex) :: Trans !! Atmospheric Transmissivity (unitless)
723
724	!_ ================================================================================================================================
725	fco2 = 0.
726	fco2_wshort = 0.
727	fco2_wlong = 0.
728	Fdf(:) = 0.
729	PAR(:) = 0.
730	PARsun(:,:) = 0.
731	PARsh(:,:) = 0.
732	laisun(:,:) = 0.
733	laish(:,:) = 0.
734	CRF(:,:) = 0.
735	Trans(:) = 0.
736	PARdf(:) = 0.
737	PARdr(:) = 0.
738	PARsuntab(:,:) = 0.
739	PARshtab(:,:) = 0.
740
741
742	!! 1. Canopy radiative transfer model
743
744	!! Canopy radiative transfer model: takes into account light extinction through canopy
745	!! First need to calculate diffuse and direct radiation
746	!! Based on Andrew Friend radiative model (Global Ecology & Biogeography, 2001)
747	!! And Spitters et al. (Agricultural and Forest Meteorology, 1986)
748
749	IF ( ok_radcanopy ) THEN
750
751	DO ji = 1, kjpindex
752	IF (coszang(ji) .GT. zero) THEN
753	!! 1.1 Extra-terrestrial solar irradiance at a plan parallel to Earh's surface
754	So(ji) = Sct( un + 0.033COS(360.pi/180.julian_diff/365.))*coszang(ji)
755	!! 1.2 Atmospheric transmissivity
756	Trans(ji) = swdown(ji)/So(ji)
757	!! 1.3 Empirical calculation of fraction diffuse from transmission based on Spitters et al. (1986)
758	Rfrac(ji) = 0.847 - 1.61coszang(ji) + 1.04(coszang(ji)**2.)
759	Kfrac(ji) = (1.47 - Rfrac(ji))/1.66
760	IF (Trans(ji) .LE. 0.22) THEN
761	Fdf(ji) = un
762	ELSE IF (Trans(ji) .LE. 0.35) THEN
763	Fdf(ji) = un - 6.4((Trans(ji) - 0.22)*2.)
764	ELSE IF (Trans(ji) .LE. Kfrac(ji)) THEN
765	Fdf(ji) = 1.47 - 1.66*Trans(ji)
766	ELSE
767	Fdf(ji) = Rfrac(ji)
768	END IF
769	!! 1.4 Direct and diffuse sw radiation in W.m^{-2}
770	swdf(ji) = swdown(ji)*Fdf(ji)
771	swdr(ji) = swdown(ji)*(un-Fdf(ji))
772	ELSE
773	swdf(ji) = zero
774	swdr(ji) = zero
775	END IF
776
777	!! 1.5 PAR diffuse and direct in umol/m^2/s
778	PARdf(ji) = swdf(ji) * W_to_mol * RG_to_PAR
779	PARdr(ji) = swdr(ji) * W_to_mol * RG_to_PAR
780	END DO
781
782	!! 1.6 Calculation of lai, parscat, parsh and parsun, laisun and laish !!?? define the terms
783	!! Based on Guenther et al. (JGR, 1995) and Norman (1982)
784	! One-layer canopy model or multi-layer canopy model
785	IF (ok_multilayer) THEN
786
787
788	! Calculation PER LAYER
789	DO jl = nlai+1, 1, -1
790	laitab(jl) = laimax(EXP(lai_level_depth(jl-1) - un)/(EXP(lai_level_depth*nlai) - un))
791
792	!introduction of the Spitter way to calculate radiation over the levels !!!!!!!
793	DO ji = 1, kjpindex
794	kdf = cluster0.8SQRT((1 - sigma))
795	IF (ABS(ACOS(coszang(ji))) .LT. pi/2. .AND. coszang(ji) .NE. zero) THEN
796	! Coefficients calculation:
797	kbl = cluster*0.5/ABS(coszang(ji))
798	rho = ((1-SQRT((1 - sigma)))/(1+SQRT((1 - sigma))))(2/(1+1.6ABS(coszang(ji))))
799
800	PARnotscat(ji,jl) = (1 - sigma)PARdr(ji)kblEXP(-SQRT((1 - sigma))kbl*laitab(jl))
801	PARabsdir(ji,jl) = (1 - rho)SQRT((1 - sigma))PARdr(ji)kblEXP(-SQRT((1 - sigma))kbllaitab(jl))
802	PARabsdiff(ji,jl) = (1 - rho)PARdf(ji)kdfEXP(-kdflaitab(jl))
803	PARshtab(ji,jl) = (PARabsdiff(ji,jl) + (PARabsdir(ji,jl) - PARnotscat(ji,jl)))/(1 - sigma)
804	PARsuntab(ji,jl) = PARshtab(ji,jl) + (1-sigma)kblPARdr(ji)/(1 - sigma)
805
806	!correction using the equation (4) in Bodin et al 2012 and (7) or (8) in Spitter et al 1986
807	!using the extinction coefficient kbl = 0.5/coszang and not only 0.5
808	IF (jl .NE. nlai+1) THEN
809	laisuntabdep(ji,jl) =(laitab(jl+1)-laitab(jl))EXP(-kbllaitab(jl))
810	laishtabdep(ji,jl) =(laitab(jl+1)-laitab(jl))(1.-EXP(-kbllaitab(jl)))
811	ENDIF
812
813	ELSE
814
815	PARshtab(ji,jl) = PARdf(ji)kdfEXP(-kdf*laitab(jl))
816	PARsuntab(ji,jl) = 0.
817
818	IF (jl .NE. nlai+1) THEN
819	laisuntabdep(ji,jl) = 0.
820	laishtabdep(ji,jl) = laitab(jl+1)-laitab(jl)
821
822	ENDIF
823	END IF
824	END DO
825	END DO
826
827
828
829	! introduction of the Spitter way to calculate radiation over the levels !!!!!!!
830	ELSE
831	! Calculation FOR one layer
832	DO jv = 1, nvm
833	DO ji = 1, kjpindex
834	IF (lai(ji,jv) .LE. lai_threshold) THEN
835	PARscat(ji,jv) = 0.07PARdr(ji)(1.1 - 0.1lai(ji,jv))exp(-coszang(ji))
836	ELSE
837	PARscat(ji,jv) = zero
838	END IF
839
840	IF (coszang(ji) .NE. zero ) THEN
841	PARsh(ji,jv) = PARdf(ji)exp(-0.5((lai(ji,jv))**0.7)) + PARscat(ji,jv)
842	PARsun(ji,jv) = PARdr(ji)COS(60.pi/180.)/coszang(ji) + PARsh(ji,jv)
843	ELSE
844	PARsh(ji,jv) = PARdf(ji)exp(-0.5(lai(ji,jv)**0.7)) + PARscat(ji,jv)
845	PARsun(ji,jv) = zero
846	END IF
847	IF (ABS(ACOS(coszang(ji))) .LT. pi/2. .AND. ABS(coszang(ji)) .GT. min_sechiba) THEN
848	! calculation as in Lathiere (2005) = with correction removing lai in Guenther (1995)
849	laisun(ji,jv) = (un - exp(-0.5lai(ji,jv)/(coszang(ji))))coszang(ji)/COS(60.*pi/180.)
850	laish(ji,jv) = lai(ji,jv) - laisun(ji,jv)
851	ELSE
852	laisun(ji,jv) = zero
853	laish(ji,jv) = lai(ji,jv)
854	END IF
855	END DO
856	END DO
857	ENDIF
858	END IF
859
860
861	!! 2. Calculation of non-PFT dependant parameters used for VOC emissions
862	DO ji = 1, kjpindex ! (loop over # pixels)
863	!! 2.1 Calculation of Tleaf (based on Lathiere, 2005)
864
865
866	tleaf(ji) = temp_air(ji)
867
868	!! 2.2 Isoprene emission dependency - with no PARsun/PARshaded partitioning - Guenther et al. (1995) and Lathiere (2005)
869	!> @codeinc $$?? ecrire les equation en latex ?
870	exp_1(ji) = exp( (CT1 * ( tleaf(ji) - TS )) / (RRTStleaf(ji)) )
871	exp_2(ji) = exp( (CT2 ( tleaf(ji) - TM )) / (RRTS*tleaf(ji)) )
872	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
873	Ct_iso(ji) = exp_1(ji)/(un + exp_2(ji)) ! temperature dependance
874	Cl_iso(ji) = alpha_CL1PAR(ji)/sqrt(un + (alpha_*2) (PAR(ji)**2) ) ! light dependance
875	!> @endcodeinc
876
877	!! 2.3 Monoterpene and oxy VOB emission dependency to Temperature
878	!! light independant fraction
879	!> @codeinc
880	!Ct_mono(ji) = exp(beta*(tleaf(ji) - TS)) ! Old method
881	Ct_mono(ji) = exp(beta_mono*(tleaf(ji) - TS))
882	Ct_sesq(ji) = exp(beta_sesq*(tleaf(ji) - TS))
883	Ct_meth(ji) = exp(beta_meth*(tleaf(ji) - TS))
884	Ct_acet(ji) = exp(beta_acet*(tleaf(ji) - TS))
885	Ct_oxyVOC(ji) = exp(beta_oxyVOC*(tleaf(ji) - TS))
886	!> @endcodeinc
887	!! 2.4 MBO biogenic emissions dependency, only from PFT7 and PFT4 for location of vegetation emitter
888	! but in fact MBO fluxes only in America (ponderosa and lodgepole pines only found in these areas)
889	!> @codeinc
890	Xvar(ji) = ((un/312.3) - (un/tleaf(ji)))/RR
891	!> @endcodeinc
892	!! 2.4.1 temperature dependency
893	!> @codeinc
894	Ct_MBO(ji) = (1.52209000.0exp(67000.0Xvar(ji)))/(209000.0 - 67000.0(un - exp(209000.0*Xvar(ji))))
895	!> @endcodeinc
896	!! 2.4.2 light dependency
897	Cl_MBO(ji) = (0.00111.44PAR(ji))/(sqrt(un + (0.0011*2)(PAR(ji)**2)))
898	!! 2.5 NO biogenic emissions given in ngN/m^2/s, emission factor in ngN/m^2/s too
899	!! calculation of temperature used for NO soil emissions
900	t_no(ji) = ptnlev1(ji) - ZeroCelsius !!temp must be in celsius to calculate no emissions
901	!! 2.6 calculation of non-woody veget_max fraction
902	IF (ok_cropsfertil_NOx) THEN
903	veget_max_nowoody(ji) = zero
904	DO jv = 1,nvm
905	IF ( (jv /= ibare_sechiba) .AND. .NOT.(is_tree(jv)) ) THEN
906	veget_max_nowoody(ji) = veget_max_nowoody(ji) + veget_max(ji,jv)
907	ENDIF
908	ENDDO
909	END IF
910	END DO ! (loop over # pixels)
911
912	!! 2bis. Calculation of CO2 function for inhibition effect on isoprene
913	! 2 approaches can be used: either Possell et al. (2005) or Wilkinson et al. (2006)
914
915	!! 19/04/2010 and then implemented in version revised by Nicolas Vuichard, 08042014
916	!! Impact of atmospheric CO2 on isoprene emissions
917	!! Can be activated or not
918	!! If considered, can use either Possell 2005 or Wilkinson 2009 parameterisation
919	!! This is used to rescale the emission factor, considered to be measured at 350 ppm of CO2
920	!! to the CO2 conditions of the run
921
922	IF ( ok_co2bvoc_poss ) THEN
923	WRITE(numout,*) 'CO2 impact on isoprene: Possell calculation'
924
925	!! Possell function needs to be normalized (experiments at 400 ppm and EF before 1995)
926	!! Normalized at 350 ppm
927	fco2_ctrl = (-0.0123+(441.4795/350.)+(-1282.65/(350.**2)))
928
929	!! 2 tests: using the canopy (atmospheric) CO2 'ccanopy'
930	!! or the intercellular CO2 over nlai 'cim'
931	!! with cim = ccanopy*0.667
932	!! in the end I go for ccanopy for the Possell function since too much differences
933	!! when using cim and also the function has been derived based on atmospheric CO2
934	DO ji = 1, kjpindex
935
936	fco2(ji,:) = (-0.0123+(441.4795/ccanopy(ji))+(-1282.65/(ccanopy(ji)*ccanopy(ji))))/fco2_ctrl
937
938	END DO
939	ELSE IF ( ok_co2bvoc_wilk ) THEN
940	WRITE(numout,*) 'CO2 impact on isoprene: Wilkinson calculation'
941
942	!! In the Wilkinson function, 2 impacts are considered:
943	!! -short-term impact for CO2 variation during a single day (seconds/minutes)
944	!! -long-term impact for CO2 variation during leaf-growth (weeks/month)
945
946
947	!! Long-term parameters
948	!! Constant
949	Ismax_long = 1.344
950	h_long = 1.4614
951	Cstar_long = 585.
952	!! Short-term parameters
953	!! They have to be calculated based on atmospheric CO2
954	!! 10/05/2010
955	!! For atmospheric CO2 lower than 400 ppm or higher than 1200 ppm
956	!! (min and max CO2 level tested for short-term effect in Wilkinson et al. 2009)
957	!! we use the parameters calculated at 400/1200 ppm. For intermediate CO2 concentration,
958	!! parameters are calculated.
959	!! Linear interpolation
960
961	DO ji = 1, kjpindex
962
963	IF (ccanopy(ji) .LE. 400.) THEN
964
965	Ismax_short(ji) = 1.072
966	h_short(ji) = 1.7
967	Cstar_short(ji) = 1218.
968
969	ELSE IF (ccanopy(ji) .EQ. 600.) THEN
970
971	Ismax_short(ji) = 1.036
972	h_short(ji) = 2.0125
973	Cstar_short(ji) = 1150.
974
975	ELSE IF (ccanopy(ji) .EQ. 800.) THEN
976
977	Ismax_short(ji) = 1.046
978	h_short(ji) = 1.5380
979	Cstar_short(ji) = 2025.
980
981	ELSE IF (ccanopy(ji) .GE. 1200.) THEN
982
983	Ismax_short(ji) = 1.014
984	h_short(ji) = 2.8610
985	Cstar_short(ji) = 1525.
986
987
988	ELSE IF ((ccanopy(ji) .GT. 400.) .AND. (ccanopy(ji) .LT. 600.)) THEN
989
990	Ismax_short(ji) = 1.036 + (ccanopy(ji)-600.)*(1.036-1.072)/(600.-400.)
991	h_short(ji) = 2.0125 + (ccanopy(ji)-600.)*(2.0125-1.7)/(600.-400.)
992	Cstar_short(ji) = 1150. + (ccanopy(ji)-600.)*(1150.-1218.)/(600.-400.)
993
994	ELSE IF ((ccanopy(ji) .GT. 600.) .AND. (ccanopy(ji) .LT. 800.)) THEN
995
996	Ismax_short(ji) = 1.046 + (ccanopy(ji)-800.)*(1.046-1.036)/(800.-600.)
997	h_short(ji) = 1.5380 + (ccanopy(ji)-800.)*(1.5380-2.0125)/(800.-600.)
998	Cstar_short(ji) = 2025. + (ccanopy(ji)-800.)*(2025.-1150.)/(800.-600.)
999
1000	ELSE IF ((ccanopy(ji) .GT. 800.) .AND. (ccanopy(ji) .LT. 1200.)) THEN
1001
1002	Ismax_short(ji) = 1.014 + (ccanopy(ji)-1200.)*(1.014-1.046)/(1200.-800.)
1003	h_short(ji) = 2.8610 + (ccanopy(ji)-1200.)*(2.8610-1.5380)/(1200.-800.)
1004	Cstar_short(ji) = 1525. + (ccanopy(ji)-1200.)*(1525.-2025.)/(1200.-800.)
1005
1006
1007	END IF
1008
1009	END DO
1010
1011	WRITE(numout,) 'Wilkinson BVOC-CO2 function: parameters*'
1012	WRITE(numout,*) 'Ismax_long: ', Ismax_long
1013	WRITE(numout,*) 'h_long: ', h_long
1014	WRITE(numout,*) 'Cstar_long: ', Cstar_long
1015	WRITE(numout,*) 'Ismax_short: ', MAXVAL(Ismax_short(:)) , MINVAL(Ismax_short(:))
1016	WRITE(numout,*) 'h_short: ', MAXVAL(h_short(:)) , MINVAL(h_short(:))
1017	WRITE(numout,*) 'Cstar_short: ', MAXVAL(Cstar_short(:)) , MINVAL(Cstar_short(:))
1018	WRITE(numout,) '*****'
1019
1020	DO ji = 1, kjpindex
1021	fco2_wlong(ji) = (Ismax_long-((Ismax_long((0.667ccanopy(ji))**h_long))/&
1022	& ((Cstar_long*h_long)+(0.667ccanopy(ji))**h_long)))/1.06566
1023	DO jv = 1, nvm
1024	fco2_wshort(ji,jv) = (Ismax_short(ji)-((Ismax_short(ji)((cim(ji,jv))*h_short(ji)))/&
1025	& ((Cstar_short(ji)h_short(ji))+(cim(ji,jv))h_short(ji))))/1.010803
1026	END DO
1027	END DO
1028
1029	DO ji = 1, kjpindex
1030	DO jv = 1, nvm
1031	fco2(ji,jv) = fco2_wshort(ji,jv)*fco2_wlong(ji)
1032	END DO
1033	END DO
1034
1035	ELSE
1036	WRITE(numout,*) 'CO2 impact on isoprene not considered'
1037	fco2(:,:) = 1.
1038	END IF
1039
1040
1041	!! 3. Calculation of PFT dependant parameters and
1042	! Calculation of VOC emissions flux
1043
1044	Eff_age_iso(:,:) = zero
1045	Eff_age_meth(:,:) = zero
1046
1047
1048	DO jv = 1, nvm ! loop over the PDFs
1049	DO ji = 1, kjpindex ! loop over the grid cell
1050	! 6-Calculation of Leaf Age Function (Lathiere 2005)
1051	IF ( ok_leafage ) THEN
1052	DO jf = 1, nleafages
1053	!> @codeinc
1054	Eff_age_iso(ji,jv) = Eff_age_iso(ji,jv) + frac_age(ji,jv,jf)*iso_activity(jf)
1055	Eff_age_meth(ji,jv) = Eff_age_meth(ji,jv) + frac_age(ji,jv,jf)*methanol_activity(jf)
1056	!> @endcodeinc
1057	END DO
1058	!> @codeinc
1059	Eff_age_VOC(ji,jv) = un
1060	!> @endcodeinc
1061	ELSE
1062	Eff_age_iso(ji,jv) = un
1063	Eff_age_meth(ji,jv) = un
1064	Eff_age_VOC(ji,jv) = un
1065	END IF
1066	!! 5. Calculation of foliar density
1067	IF ( sla(jv) .eq. zero ) THEN
1068	fol_dens(ji,jv) = zero
1069	ELSE
1070	! 2 factor for conversion from gC to gDM
1071	fol_dens(ji,jv) = 2 * lai(ji,jv)/sla(jv)
1072	ENDIF
1073	!! 6. Calculation of VOC emissions from vegetation
1074	IF ( ok_radcanopy ) THEN
1075	! if multi-layer canopy model
1076	IF (ok_multilayer) THEN
1077
1078	laisun(ji,jv) = zero
1079	laish(ji,jv) = zero
1080	GAMMA_iso_m = zero
1081	flx_iso(ji,jv) = zero
1082	flx_mono(ji,jv) = zero
1083	flx_apinen(ji,jv) = zero
1084	flx_bpinen(ji,jv) = zero
1085	flx_limonen(ji,jv) = zero
1086	flx_myrcen(ji,jv) = zero
1087	flx_sabinen(ji,jv) = zero
1088	flx_camphen(ji,jv) = zero
1089	flx_3caren(ji,jv) = zero
1090	flx_tbocimen(ji,jv) = zero
1091	flx_othermono(ji,jv) = zero
1092	flx_sesquiter(ji,jv) = zero
1093	flx_methanol(ji,jv) = zero
1094	flx_acetone(ji,jv) = zero
1095	flx_acetal(ji,jv) = zero
1096	flx_formal(ji,jv) = zero
1097	flx_acetic(ji,jv) = zero
1098	flx_formic(ji,jv) = zero
1099	! loop over the NLAI canopy layers
1100	DO jl = 1, nlai
1101	IF ((laitab(jl) .LE. lai(ji,jv)).AND.(lai(ji,jv).NE.zero)) THEN
1102	!sunlit vegetation
1103	Clsun_iso_tab = alpha_CL1PARsuntab(ji,jl)/sqrt(un + (alpha_*2) (PARsuntab(ji,jl)**2) )
1104	! shaded vegetation
1105	Clsh_iso_tab = alpha_CL1PARshtab(ji,jl)/sqrt(un + (alpha_*2) (PARshtab(ji,jl)**2) )
1106	flx_iso(ji,jv) = flx_iso(ji,jv) + (laisuntabdep(ji,jl)*Clsun_iso_tab+ &
1107	& laishtabdep(ji,jl)Clsh_iso_tab) &
1108	& fol_dens(ji,jv)/lai(ji,jv)Ct_iso(ji)em_factor_isoprene(jv)* &
1109	& Eff_age_iso(ji,jv)fco2(ji,jv)1e-9/one_hour
1110
1111	GAMMA_iso_m = GAMMA_iso_m + (laisuntabdep(ji,jl)*Clsun_iso_tab+ &
1112	& laishtabdep(ji,jl)Clsh_iso_tab) &
1113	& fol_dens(ji,jv)/lai(ji,jv)Ct_iso(ji)1e-9/one_hour
1114
1115	laisun(ji,jv) = laisun(ji,jv) + laisuntabdep(ji,jl)
1116	laish(ji,jv) = laish(ji,jv) + laishtabdep(ji,jl)
1117	END IF
1118	END DO
1119
1120	!! 6.1 Calculation of monoterpene biogenic emissions
1121	flx_mono(ji,jv) = ((1-LDF_mono)Ct_mono(ji)1e-9/one_hourfol_dens(ji,jv) + LDF_monoGAMMA_iso_m)* &
1122	& em_factor_monoterpene(jv)*Eff_age_VOC(ji,jv)
1123	!! 6.12 Calculation of sesquiterpenes biogenic emission
1124	flx_sesquiter(ji,jv) = ((1-LDF_sesq)Ct_sesq(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_sesqGAMMA_iso_m)* &
1125	& em_factor_sesquiterp(jv)*Eff_age_VOC(ji,jv)
1126	!! 6.13 Calculation of methanol biogenic emissions
1127	flx_methanol(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1128	& em_factor_methanol(jv)*Eff_age_meth(ji,jv)
1129	!! 6.14 Calculation of acetone biogenic emissions
1130	flx_acetone(ji,jv) = ((1-LDF_acet)Ct_acet(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_acetGAMMA_iso_m)* &
1131	& em_factor_acetone(jv)*Eff_age_VOC(ji,jv)
1132	!! 6.14 Calculation of acetaldehyde biogenic emissions
1133	flx_acetal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1134	& em_factor_acetal(jv)*Eff_age_VOC(ji,jv)
1135	!! 6.16 Calculation of formaldehyde biogenic emissions
1136	flx_formal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1137	& em_factor_formal(jv)*Eff_age_VOC(ji,jv)
1138	!! 6.17 Calculation of acetic acid biogenic emissions
1139	flx_acetic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1140	& em_factor_acetic(jv)*Eff_age_VOC(ji,jv)
1141	!! 6.18 Calculation of formic acid biogenic emissions
1142	flx_formic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)1e-9/one_hourfol_dens(ji,jv) +LDF_methGAMMA_iso_m)* &
1143	& em_factor_formic(jv)*Eff_age_VOC(ji,jv)
1144
1145
1146	!! 6.3 Calculation of alfa pinene biogenic emission
1147	flx_apinen(ji,jv) = em_factor_apinene(jv)*flx_mono(ji,jv)
1148	!! 6.4 Calculation of beta pinene biogenic emission
1149	flx_bpinen(ji,jv) = em_factor_bpinene(jv)*flx_mono(ji,jv)
1150	!! 6.5 Calculation of limonene biogenic emission
1151	flx_limonen(ji,jv) = em_factor_limonene(jv)*flx_mono(ji,jv)
1152	!! 6.6 Calculation of myrcene biogenic emission !!
1153	flx_myrcen(ji,jv) = em_factor_myrcene(jv)*flx_mono(ji,jv)
1154	!! 6.7 Calculation of sabinene biogenic emission
1155	flx_sabinen(ji,jv) = em_factor_sabinene(jv)*flx_mono(ji,jv)
1156	!! 6.8 Calculation of camphene biogenic emission
1157	flx_camphen(ji,jv) = em_factor_camphene(jv)*flx_mono(ji,jv)
1158	!! 6.9 Calculation of 3-carene biogenic emission
1159	flx_3caren(ji,jv) = em_factor_3carene(jv)*flx_mono(ji,jv)
1160	!! 6.10 Calculation of t-beta-ocimene biogenic emission
1161	flx_tbocimen(ji,jv) = em_factor_tbocimene(jv)*flx_mono(ji,jv)
1162	!! 6.11 Calculation of other monoterpenes biogenic emission
1163	flx_othermono(ji,jv) = em_factor_othermonot(jv)*flx_mono(ji,jv)
1164
1165	! if mono-layer canopy model
1166	ELSE
1167	!sunlit vegetation
1168	Clsun_iso(ji,jv) = alpha_CL1PARsun(ji,jv)/sqrt(un + (alpha_*2) (PARsun(ji,jv)**2) )
1169	! shaded vegetation
1170	Clsh_iso(ji,jv) = alpha_CL1PARsh(ji,jv)/sqrt(un + (alpha_*2) (PARsh(ji,jv)**2) )
1171	IF (lai(ji,jv) .NE. zero) THEN
1172	!! 6.1 Calculation of isoprene biogenic emissions
1173	GAMMA_iso = (laisun(ji,jv)Clsun_iso(ji,jv) + laish(ji,jv)Clsh_iso(ji,jv))/lai(ji,jv)*Ct_iso(ji)
1174	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
1175	!! 6.2 Calculation of monoterpene biogenic emissions
1176	flx_mono(ji,jv) = ((1-LDF_mono)Ct_mono(ji)+LDF_monoGAMMA_iso)fol_dens(ji,jv) &
1177	& em_factor_monoterpene(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1178	!! 6.3 Calculation of alfa pinene biogenic emission
1179	flx_apinen(ji,jv) = em_factor_apinene(jv)*flx_mono(ji,jv)
1180	!! 6.4 Calculation of beta pinene biogenic emission
1181	flx_bpinen(ji,jv) = em_factor_bpinene(jv)*flx_mono(ji,jv)
1182	!! 6.5 Calculation of limonene biogenic emission
1183	flx_limonen(ji,jv) = em_factor_limonene(jv)*flx_mono(ji,jv)
1184	!! 6.6 Calculation of myrcene biogenic emission
1185	flx_myrcen(ji,jv) = em_factor_myrcene(jv)*flx_mono(ji,jv)
1186	!! 6.7 Calculation of sabinene biogenic emission
1187	flx_sabinen(ji,jv) = em_factor_sabinene(jv)*flx_mono(ji,jv)
1188	!! 6.8 Calculation of camphene biogenic emission
1189	flx_camphen(ji,jv) = em_factor_camphene(jv)*flx_mono(ji,jv)
1190	!! 6.9 Calculation of 3-carene biogenic emission
1191	flx_3caren(ji,jv) = em_factor_3carene(jv)*flx_mono(ji,jv)
1192	!! 6.10 Calculation of t-beta-ocimene biogenic emission
1193	flx_tbocimen(ji,jv) = em_factor_tbocimene(jv)*flx_mono(ji,jv)
1194	!! 6.11 Calculation of other monoterpenes biogenic emission
1195	flx_othermono(ji,jv) = em_factor_othermonot(jv)*flx_mono(ji,jv)
1196	!! 6.12 Calculation of sesquiterpenes biogenic emission
1197	flx_sesquiter(ji,jv) = ((1-LDF_sesq)Ct_sesq(ji)+LDF_sesqGAMMA_iso)fol_dens(ji,jv) &
1198	& em_factor_sesquiterp(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1199	!! 6.13 Calculation of methanol biogenic emissions
1200	flx_methanol(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1201	& em_factor_methanol(jv)Eff_age_meth(ji,jv)1e-9/one_hour
1202	!! 6.14 Calculation of acetone biogenic emissions
1203	flx_acetone(ji,jv) = ((1-LDF_acet)Ct_acet(ji)+LDF_acetGAMMA_iso)fol_dens(ji,jv) &
1204	& em_factor_acetone(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1205	!! 6.15 Calculation of acetaldehyde biogenic emissions
1206	flx_acetal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1207	& em_factor_acetal(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1208	!! 6.16 Calculation of formaldehyde biogenic emissions
1209	flx_formal(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1210	& em_factor_formal(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1211	!! 6.17 Calculation of acetic acid biogenic emissions
1212	flx_acetic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1213	& em_factor_acetic(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1214	!! 6.18 Calculation of formic acid biogenic emissions
1215	flx_formic(ji,jv) = ((1-LDF_meth)Ct_meth(ji)+LDF_methGAMMA_iso)fol_dens(ji,jv) &
1216	& em_factor_formic(jv)Eff_age_VOC(ji,jv)1e-9/one_hour
1217
1218	ELSE
1219	!
1220	flx_iso(ji,jv) = zero
1221	flx_mono(ji,jv) = zero
1222	flx_apinen(ji,jv) = zero
1223	flx_bpinen(ji,jv) = zero
1224	flx_limonen(ji,jv) = zero
1225	flx_myrcen(ji,jv) = zero
1226	flx_sabinen(ji,jv) = zero
1227	flx_camphen(ji,jv) = zero
1228	flx_3caren(ji,jv) = zero
1229	flx_tbocimen(ji,jv) = zero
1230	flx_othermono(ji,jv) = zero
1231	flx_sesquiter(ji,jv) = zero
1232	flx_methanol(ji,jv) = zero
1233	flx_acetone(ji,jv) = zero
1234	flx_acetal(ji,jv) = zero
1235	flx_formal(ji,jv) = zero
1236	flx_acetic(ji,jv) = zero
1237	flx_formic(ji,jv) = zero
1238	END IF
1239	END IF
1240	! if no light extinction due to vegetation
1241	ELSE
1242	!! Isoprene emissions - general equation
1243	flx_iso(ji,jv) = fol_dens(ji,jv)Ct_iso(ji)Cl_iso(ji)Eff_age_iso(ji,jv)fco2(ji,jv)* &
1244	em_factor_isoprene(jv)*1e-9/one_hour
1245	!! 6.2 Calculation of monoterpene biogenic emissions
1246	Ylt_mono(ji) = ((1-LDF_mono)Ct_mono(ji)+LDF_monoCt_iso(ji)*Cl_iso(ji))
1247	flx_mono(ji,jv) = fol_dens(ji,jv)em_factor_monoterpene(jv)Ylt_mono(ji)Eff_age_VOC(ji,jv)&
1248	1e-9/one_hour
1249	!! 6.3 Calculation of alfa pinene biogenic emission
1250	flx_apinen(ji,jv) = em_factor_apinene(jv)*flx_mono(ji,jv)
1251	!! 6.4 Calculation of beta pinene biogenic emission
1252	flx_bpinen(ji,jv) = em_factor_bpinene(jv)*flx_mono(ji,jv)
1253	!! 6.5 Calculation of limonene biogenic emission
1254	flx_limonen(ji,jv) = em_factor_limonene(jv)*flx_mono(ji,jv)
1255	!! 6.6 Calculation of myrcene biogenic emission
1256	flx_myrcen(ji,jv) = em_factor_myrcene(jv)*flx_mono(ji,jv)
1257	!! 6.7 Calculation of sabinene biogenic emission
1258	flx_sabinen(ji,jv) = em_factor_sabinene(jv)*flx_mono(ji,jv)
1259	!! 6.8 Calculation of camphene biogenic emission
1260	flx_camphen(ji,jv) = em_factor_camphene(jv)*flx_mono(ji,jv)
1261	!! 6.9 Calculation of 3-carene biogenic emission
1262	flx_3caren(ji,jv) = em_factor_3carene(jv)*flx_mono(ji,jv)
1263	!! 6.10 Calculation of t-beta-ocimene biogenic emission
1264	flx_tbocimen(ji,jv) = em_factor_tbocimene(jv)*flx_mono(ji,jv)
1265	!! 6.11 Calculation of other monoterpenes biogenic emission
1266	flx_othermono(ji,jv) = em_factor_othermonot(jv)*flx_mono(ji,jv)
1267	!! 6.12 Calculation of sesquiterpenes biogenic emission
1268	Ylt_sesq(ji) = ((1-LDF_sesq)Ct_sesq(ji)+LDF_sesqCt_iso(ji)*Cl_iso(ji))
1269	flx_sesquiter(ji,jv) = fol_dens(ji,jv)em_factor_sesquiterp(jv)Ylt_sesq(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1270	!! 6.16 Calculation of methanol biogenic emissions
1271	Ylt_meth(ji) = ((1-LDF_meth)Ct_meth(ji)+LDF_methCt_iso(ji)*Cl_iso(ji))
1272	flx_methanol(ji,jv) = fol_dens(ji,jv)em_factor_methanol(jv)Ylt_meth(ji)Eff_age_meth(ji,jv)1e-9/one_hour
1273	!! 6.17 Calculation of acetone biogenic emissions
1274	Ylt_acet(ji) = ((1-LDF_acet)Ct_acet(ji)+LDF_acetCt_iso(ji)*Cl_iso(ji))
1275	flx_acetone(ji,jv) = fol_dens(ji,jv)em_factor_acetone(jv)Ylt_acet(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1276	!! 6.18 Calculation of acetaldehyde biogenic emissions
1277	flx_acetal(ji,jv) = fol_dens(ji,jv)em_factor_acetal(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1278	!! 6.19 Calculation of formaldehyde biogenic emissions
1279	flx_formal(ji,jv) = fol_dens(ji,jv)em_factor_formal(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1280	!! 6.20 Calculation of acetic acid biogenic emissions
1281	flx_acetic(ji,jv) = fol_dens(ji,jv)em_factor_acetic(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1282	!! 6.21 Calculation of formic acid biogenic emissions
1283	flx_formic(ji,jv) = fol_dens(ji,jv)em_factor_formic(jv)Ylt_meth(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1284
1285	END IF
1286
1287	!! 6.22 Calculation of ORVOC biogenic emissions
1288	!! Other Reactive Volatile Organic Compounds
1289	!> @codeinc
1290	flx_ORVOC(ji,jv) = fol_dens(ji,jv)em_factor_ORVOC(jv)Ct_mono(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1291	!> @endcodeinc
1292	!! 6.4 Calculation of OVOC biogenic emissions
1293	!! Other Volatile Organic Compounds
1294	flx_OVOC(ji,jv) = fol_dens(ji,jv)em_factor_OVOC(jv)Ct_mono(ji)Eff_age_VOC(ji,jv)1e-9/one_hour
1295	!! 6.5 Calculation of MBO biogenic emissions
1296	!! 2-Methyl-3-Buten-2-ol
1297	IF(lalo(ji,1) .GE. 20. .AND. lalo(ji,2) .LE. -100) THEN
1298	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
1299	ELSE
1300	flx_MBO(ji,jv) = zero
1301	END IF
1302	END DO
1303
1304	END DO
1305
1306
1307	!! 7. Calculation of NOx emissions from soils
1308	! Based on Yienger & Levy (1995) and Lathiere (2005, chapter 3)
1309	DO ji = 1, kjpindex
1310	!! 7.1 Precipitation-related pulse function
1311	IF (ok_pulse_NOx) THEN
1312	! if we are during a period where pulses are not allowed
1313	IF (ok_siesta(ji)) THEN
1314	! if this period is not over
1315	IF (FLOOR(siestaday(ji)) .LE. siestalim(ji)) THEN
1316	siestaday(ji) = siestaday(ji) + (dt_sechiba/one_day)
1317	! if this period is over
1318	ELSE
1319	ok_siesta(ji) = .FALSE.
1320	siestaday(ji) = zero
1321	END IF
1322	END IF
1323	! if we are during a period where pulses are allowed
1324	IF ((.NOT. ok_siesta(ji)) .AND. (.NOT. allow_pulse(ji))) THEN
1325	IF (humrel(ji,1) .LT. 0.15) THEN
1326	! if precip exceeds 1 mm/day over one time step => a pulse occurs
1327	IF(precip_rain(ji)/nbre_precip .GE. un/(one_day/dt_sechiba)) THEN
1328	! if precip is up to 5 mm/day => pulse length is 3 days
1329	IF (precip_rain(ji)/nbre_precip .LT. 5./(one_day/dt_sechiba)) THEN
1330	pulselim(ji) = 3.
1331	! if precip is up to 15 mm/day => pulse length is 7 days
1332	ELSE IF (precip_rain(ji)/nbre_precip .LT. 15./(one_day/dt_sechiba)) THEN
1333	pulselim(ji) = 7.
1334	! if precip is upper than 15 mm/day => pulse length is 14 days
1335	ELSE IF (precip_rain(ji)/nbre_precip .GE. 15./(one_day/dt_sechiba)) THEN
1336	pulselim(ji) = 14.
1337	END IF
1338	allow_pulse(ji)=.TRUE.
1339	pulseday(ji) = un
1340	END IF
1341	END IF
1342	END IF
1343	! if we were during a pulse period
1344	IF (allow_pulse(ji)) THEN
1345	! if we are still during the pulse period
1346	! 16/06/2010 We assume a (pulselim-1) days for the pulse length (NVui+Jlath)
1347	IF(FLOOR(pulseday(ji)) .LT. pulselim(ji)) THEN
1348	! calculation of the pulse function
1349	IF (pulselim(ji).EQ.3) THEN
1350	pulse(ji) = 11.19exp(-0.805pulseday(ji))
1351	ELSE IF (pulselim(ji).EQ.7) THEN
1352	pulse(ji) = 14.68exp(-0.384pulseday(ji))
1353	ELSE IF (pulselim(ji).EQ.14) THEN
1354	pulse(ji) = 18.46exp(-0.208pulseday(ji))
1355	END IF
1356	pulseday(ji) = pulseday(ji) + (dt_sechiba/one_day)
1357	! if the pulse period is over
1358	ELSE
1359	! pulse function is set to 1
1360	pulse(ji) = un
1361	allow_pulse(ji) = .FALSE.
1362	siestaday(ji) = un
1363	siestalim(ji) = pulselim(ji)
1364	ok_siesta(ji) = .TRUE.
1365	END IF
1366	END IF
1367	! no precipitation-related pulse function
1368	ELSE
1369	pulse(ji) = un
1370	END IF
1371	END DO
1372
1373	!! 7.2 Calculation of NO basal emissions including pulse effect
1374	DO jv = 1, nvm
1375	DO ji = 1, kjpindex
1376	!Tropical forests
1377	IF ( is_tropical(jv) .AND. is_evergreen(jv) ) THEN
1378	! Wet soils
1379	IF (humrel(ji,1) .GT. 0.3) THEN
1380	flx_no_soil(ji,jv) = 2.6*pulse(ji)
1381	! Dry soils
1382	ELSE
1383	flx_no_soil(ji,jv) = 8.6*pulse(ji)
1384	END IF
1385	!Else If agricultural lands OR Wet soils
1386	ELSE IF ( ( .NOT.(natural(jv)) ) .OR. ( humrel(ji,1) .GT. 0.3 ) ) THEN
1387	! Calculation of NO emissions depending of Temperature
1388	IF (t_no(ji) .LT. zero) THEN
1389	flx_no_soil(ji,jv) = zero
1390	ELSE IF (t_no(ji) .LE. 10.) THEN
1391	flx_no_soil(ji,jv) = 0.28em_factor_no_wet(jv)t_no(ji)*pulse(ji)
1392	ELSE IF (t_no(ji) .LE. 30.) THEN
1393	flx_no_soil(ji,jv) = em_factor_no_wet(jv)exp(0.103t_no(ji))*pulse(ji)
1394	ELSE
1395	flx_no_soil(ji,jv) = 21.97em_factor_no_wet(jv)pulse(ji)
1396	END IF
1397	!Else if Temp negative
1398	ELSE IF (t_no(ji) .LT. zero) THEN
1399	flx_no_soil(ji,jv) = zero
1400	!Else if Temp <= 30
1401	ELSE IF (t_no(ji) .LE. 30.) THEN
1402	flx_no_soil(ji,jv) = (em_factor_no_dry(jv)t_no(ji))/30.pulse(ji)
1403	ELSE
1404	flx_no_soil(ji,jv) = em_factor_no_dry(jv)*pulse(ji)
1405	END IF
1406
1407	!! 7.3 IF ACTIVATED (ok_bbgfertil_NOx = TRUE) calculation of NOx soil emission increase due to biomass burning
1408	! Calculation of Biomass-Burning-induced NOx emissions (Lathiere, 2005)
1409	! => NOx emissions 3-fold increase
1410	IF (ok_bbgfertil_NOx) THEN
1411	IF ( natural(jv) ) THEN
1412	! North Tropical zone from May to June
1413	IF ((lalo(ji,1) .LE. 30. .AND. lalo(ji,1) .GE. zero).AND. &
1414	(julian_diff .GE. 121. .AND. julian_diff .LE. 181).AND.(flx_co2_bbg_year(ji) .GT. 0.1)) THEN
1415	flx_no_soil(ji,jv) = flx_no_soil(ji,jv)*3.
1416	! South Tropical zone from November to December
1417	ELSE IF ((lalo(ji,1) .GE. -30. .AND. lalo(ji,1) .LT. zero).AND.(julian_diff .GE. 305.).AND. &
1418	(flx_co2_bbg_year(ji) .GT. 0.1)) THEN
1419	flx_no_soil(ji,jv) = flx_no_soil(ji,jv)*3.
1420	END IF
1421	END IF
1422	END IF
1423
1424	!! 7.4 IF ACTIVATED (ok_cropsfertil_NOx = TRUE) calculation of NOx soil emission increase due to fertilizer use
1425	! Calculation of N-fertiliser-induced NOx emissions
1426	flx_fertil_no(ji,jv) = zero
1427	IF (ok_cropsfertil_NOx) THEN
1428	IF (veget_max_nowoody(ji) .NE. zero) THEN
1429	! Non-agricultural lands
1430	IF ( (jv == ibare_sechiba) .OR. is_tree(jv) ) THEN
1431	N_qt_WRICE_pft(ji,jv) = zero
1432	N_qt_OTHER_pft(ji,jv) = zero
1433	! Grasslands or Croplands
1434	ELSE
1435	N_qt_WRICE_pft(ji,jv) = N_qt_WRICE_year(ji)*veget_max(ji,jv)/veget_max_nowoody(ji)
1436	N_qt_OTHER_pft(ji,jv) = N_qt_OTHER_year(ji)*veget_max(ji,jv)/veget_max_nowoody(ji)
1437	END IF
1438	ELSE
1439	N_qt_WRICE_pft(ji,jv) = zero
1440	N_qt_OTHER_pft(ji,jv) = zero
1441	END IF
1442
1443	! North temperate regions from May to August
1444	! OR South Temperate regions from November to February
1445	IF (((lalo(ji,1) .GT. 30.) .AND. (julian_diff .GE. 121. .AND. julian_diff .LE. 243.).AND. &
1446	(veget_max(ji,jv) .GT. min_sechiba)) .OR. &
1447	((lalo(ji,1) .LT. -30.) .AND. (julian_diff .GE. 305. .OR. julian_diff .LE. 59.) .AND.&
1448	(veget_max(ji,jv) .GT. min_sechiba))) THEN
1449	! 1e12 for conversion from kg to Ng
1450	! 1/(365/122460604) for conversion from year to seconds corrected for 4 months of emissions
1451	flx_fertil_no(ji,jv) = (N_qt_WRICE_pft(ji,jv)(1/30.)+N_qt_OTHER_pft(ji,jv))(2.5/100.) &
1452	& 1e12/(3652460604/12)/(area2(ji)veget_max(ji,jv))
1453	! OR Tropical regions all the year
1454	ELSE IF ((lalo(ji,1) .GE. -30.).AND.(lalo(ji,1) .LE. 30.).AND.(veget_max(ji,jv) .GT. min_sechiba)) THEN
1455	flx_fertil_no(ji,jv) = (N_qt_WRICE_pft(ji,jv)(1/30.)+N_qt_OTHER_pft(ji,jv))(2.5/100.) &
1456	& 1e12/(365246060)/(area2(ji)*veget_max(ji,jv))
1457	END IF
1458	flx_no_soil(ji,jv) = flx_no_soil(ji,jv) + flx_fertil_no(ji,jv)
1459	END IF
1460
1461	!! 7.5 Calculation of net NO flux above soil accounting for surface deposition,
1462	!! based on the Canopy Reduction Factor (CRF), calculated using Leaf Area and Stomatal Area
1463	!kc=cuticle absorptivity = 0.24m^2/m^2
1464	!ks=stomatal absorptivity = 8.75m^2/m^2
1465	!Larch=Larcher SAI/LAI ratio given in Larcher 1991
1466	!> @codeinc
1467	CRF(ji,jv) = (exp(-8.75Larch(jv)lai(ji,jv)) + exp(-0.24*lai(ji,jv)))/2.
1468	flx_no(ji,jv) = flx_no_soil(ji,jv)*CRF(ji,jv)
1469	!> @endcodeinc
1470	END DO
1471	END DO
1472
1473
1474	! Write output with XIOS
1475	CALL xios_orchidee_send_field("PAR",PAR)
1476	CALL xios_orchidee_send_field("flx_fertil_no",flx_fertil_no)
1477	CALL xios_orchidee_send_field("flx_iso",flx_iso)
1478	CALL xios_orchidee_send_field("flx_mono",flx_mono)
1479	CALL xios_orchidee_send_field("flx_ORVOC",flx_ORVOC)
1480	CALL xios_orchidee_send_field("flx_MBO",flx_MBO)
1481	CALL xios_orchidee_send_field("flx_methanol",flx_methanol)
1482	CALL xios_orchidee_send_field("flx_acetone",flx_acetone)
1483	CALL xios_orchidee_send_field("flx_acetal",flx_acetal)
1484	CALL xios_orchidee_send_field("flx_formal",flx_formal)
1485	CALL xios_orchidee_send_field("flx_acetic",flx_acetic)
1486	CALL xios_orchidee_send_field("flx_formic",flx_formic)
1487	CALL xios_orchidee_send_field("flx_no_soil",flx_no_soil)
1488	CALL xios_orchidee_send_field("flx_no",flx_no)
1489	CALL xios_orchidee_send_field('flx_apinen' , flx_apinen)
1490	CALL xios_orchidee_send_field('flx_bpinen' , flx_bpinen)
1491	CALL xios_orchidee_send_field('flx_limonen' ,flx_limonen)
1492	CALL xios_orchidee_send_field('flx_myrcen' , flx_myrcen)
1493	CALL xios_orchidee_send_field('flx_sabinen' ,flx_sabinen)
1494	CALL xios_orchidee_send_field('flx_camphen' ,flx_camphen)
1495	CALL xios_orchidee_send_field('flx_3caren' , flx_3caren)
1496	CALL xios_orchidee_send_field('flx_tbocimen' ,flx_tbocimen)
1497	CALL xios_orchidee_send_field('flx_othermono',flx_othermono)
1498	CALL xios_orchidee_send_field('flx_sesquiter',flx_sesquiter)
1499	CALL xios_orchidee_send_field("CRF",CRF)
1500	CALL xios_orchidee_send_field('fco2', fco2)
1501
1502	IF ( ok_radcanopy ) THEN
1503	CALL xios_orchidee_send_field("PARdf",PARdf)
1504	CALL xios_orchidee_send_field("PARdr",PARdr)
1505
1506	IF (ok_multilayer) THEN
1507	CALL xios_orchidee_send_field("PARsuntab",PARsuntab)
1508	CALL xios_orchidee_send_field("PARshtab",PARshtab)
1509	ELSE
1510	CALL xios_orchidee_send_field("PARsun",PARsun)
1511	CALL xios_orchidee_send_field("PARsh",PARsh)
1512	CALL xios_orchidee_send_field("laisun",laisun)
1513	CALL xios_orchidee_send_field("laish",laish)
1514	ENDIF
1515	ENDIF
1516
1517	IF ( ok_bbgfertil_Nox ) THEN
1518	CALL xios_orchidee_send_field("flx_co2_bbg_year",flx_co2_bbg_year)
1519	END IF
1520
1521	IF ( ok_cropsfertil_Nox ) THEN
1522	CALL xios_orchidee_send_field("N_qt_WRICE_year",N_qt_WRICE_year)
1523	CALL xios_orchidee_send_field("N_qt_OTHER_year",N_qt_OTHER_year)
1524	END IF
1525
1526
1527	! Write output with IOIPSL
1528	IF ( .NOT. almaoutput ) THEN
1529
1530	CALL histwrite_p(hist_id, 'PAR', kjit, PAR, kjpindex, index)
1531	IF ( ok_radcanopy ) THEN
1532	CALL histwrite_p(hist_id, 'laisun', kjit, laisun, kjpindex*nvm, indexveg)
1533	CALL histwrite_p(hist_id, 'laish', kjit, laish, kjpindex*nvm, indexveg)
1534	CALL histwrite_p(hist_id, 'Fdf', kjit, Fdf, kjpindex, index)
1535	IF (ok_multilayer) THEN
1536	CALL histwrite_p(hist_id, 'PARsuntab', kjit, PARsuntab, kjpindex*(nlai+1), indexlai)
1537	CALL histwrite_p(hist_id, 'PARshtab', kjit, PARshtab, kjpindex*(nlai+1), indexlai)
1538	ELSE
1539	CALL histwrite_p(hist_id, 'PARsun', kjit, PARsun, kjpindex*nvm, indexveg)
1540	CALL histwrite_p(hist_id, 'PARsh', kjit, PARsh, kjpindex*nvm, indexveg)
1541	END IF
1542	CALL histwrite_p(hist_id, 'coszang', kjit, coszang, kjpindex, index)
1543	CALL histwrite_p(hist_id, 'PARdf', kjit, PARdf, kjpindex, index)
1544	CALL histwrite_p(hist_id, 'PARdr', kjit, PARdr, kjpindex, index)
1545	CALL histwrite_p(hist_id, 'Trans', kjit, Trans, kjpindex, index)
1546	END IF
1547	CALL histwrite_p(hist_id, 'flx_fertil_no', kjit, flx_fertil_no, kjpindex*nvm, indexveg)
1548	CALL histwrite_p(hist_id, 'CRF', kjit, CRF, kjpindex*nvm, indexveg)
1549	CALL histwrite_p(hist_id, 'fco2', kjit, fco2, kjpindex*nvm, indexveg)
1550
1551	IF ( ok_bbgfertil_Nox ) THEN
1552	CALL histwrite_p(hist_id, 'flx_co2_bbg_year', 1, flx_co2_bbg_year, kjpindex, index)
1553	ENDIF
1554	IF ( ok_cropsfertil_Nox ) THEN
1555	CALL histwrite_p(hist_id, 'N_qt_WRICE_year', 1, N_qt_WRICE_year, kjpindex, index)
1556	CALL histwrite_p(hist_id, 'N_qt_OTHER_year', 1, N_qt_OTHER_year, kjpindex, index)
1557	ENDIF
1558	CALL histwrite_p(hist_id, 'flx_iso', kjit, flx_iso, kjpindex*nvm, indexveg)
1559	CALL histwrite_p(hist_id, 'flx_mono', kjit, flx_mono, kjpindex*nvm, indexveg)
1560	CALL histwrite_p(hist_id, 'flx_apinen', kjit, flx_apinen, kjpindex*nvm, indexveg)
1561	CALL histwrite_p(hist_id, 'flx_bpinen', kjit, flx_bpinen, kjpindex*nvm, indexveg)
1562	CALL histwrite_p(hist_id, 'flx_limonen', kjit, flx_limonen, kjpindex*nvm, indexveg)
1563	CALL histwrite_p(hist_id, 'flx_myrcen', kjit, flx_myrcen, kjpindex*nvm, indexveg)
1564	CALL histwrite_p(hist_id, 'flx_sabinen', kjit, flx_sabinen, kjpindex*nvm, indexveg)
1565	CALL histwrite_p(hist_id, 'flx_camphen', kjit, flx_camphen, kjpindex*nvm, indexveg)
1566	CALL histwrite_p(hist_id, 'flx_3caren', kjit, flx_3caren, kjpindex*nvm, indexveg)
1567	CALL histwrite_p(hist_id, 'flx_tbocimen', kjit, flx_tbocimen, kjpindex*nvm, indexveg)
1568	CALL histwrite_p(hist_id, 'flx_othermono', kjit, flx_othermono, kjpindex*nvm, indexveg)
1569	CALL histwrite_p(hist_id, 'flx_sesquiter', kjit, flx_sesquiter, kjpindex*nvm, indexveg)
1570	CALL histwrite_p(hist_id, 'flx_ORVOC', kjit, flx_ORVOC, kjpindex*nvm, indexveg)
1571	CALL histwrite_p(hist_id, 'flx_MBO', kjit, flx_MBO, kjpindex*nvm, indexveg)
1572	CALL histwrite_p(hist_id, 'flx_methanol', kjit, flx_methanol, kjpindex*nvm, indexveg)
1573	CALL histwrite_p(hist_id, 'flx_acetone', kjit, flx_acetone, kjpindex*nvm, indexveg)
1574	CALL histwrite_p(hist_id, 'flx_acetal', kjit, flx_acetal, kjpindex*nvm, indexveg)
1575	CALL histwrite_p(hist_id, 'flx_formal', kjit, flx_formal, kjpindex*nvm, indexveg)
1576	CALL histwrite_p(hist_id, 'flx_acetic', kjit, flx_acetic, kjpindex*nvm, indexveg)
1577	CALL histwrite_p(hist_id, 'flx_formic', kjit, flx_formic, kjpindex*nvm, indexveg)
1578	CALL histwrite_p(hist_id, 'flx_no_soil', kjit, flx_no_soil, kjpindex*nvm, indexveg)
1579	CALL histwrite_p(hist_id, 'flx_no', kjit, flx_no, kjpindex*nvm, indexveg)
1580
1581	IF ( hist2_id > 0 ) THEN
1582	CALL histwrite_p(hist2_id, 'PAR', kjit, PAR, kjpindex, index)
1583	IF ( ok_radcanopy ) THEN
1584	CALL histwrite_p(hist2_id, 'PARsun', kjit, PARsun, kjpindex*nvm, indexveg)
1585	CALL histwrite_p(hist2_id, 'PARsh', kjit, PARsh, kjpindex*nvm, indexveg)
1586	CALL histwrite_p(hist2_id, 'laisun', kjit, laisun, kjpindex*nvm, indexveg)
1587	CALL histwrite_p(hist2_id, 'laish', kjit, laish, kjpindex*nvm, indexveg)
1588	ENDIF
1589	CALL histwrite_p(hist2_id, 'flx_fertil_no', kjit, flx_fertil_no, kjpindex*nvm, indexveg)
1590	CALL histwrite_p(hist2_id, 'CRF', kjit, CRF, kjpindex*nvm, indexveg)
1591	IF ( ok_bbgfertil_Nox ) THEN
1592	CALL histwrite_p(hist2_id, 'flx_co2_bbg_year', 1, flx_co2_bbg_year, kjpindex, index)
1593	ENDIF
1594	IF ( ok_cropsfertil_Nox ) THEN
1595	CALL histwrite_p(hist2_id, 'N_qt_WRICE_year', 1, N_qt_WRICE_year, kjpindex, index)
1596	CALL histwrite_p(hist2_id, 'N_qt_OTHER_year', 1, N_qt_OTHER_year, kjpindex, index)
1597	ENDIF
1598	CALL histwrite_p(hist2_id, 'flx_iso', kjit, flx_iso, kjpindex*nvm, indexveg)
1599	CALL histwrite_p(hist2_id, 'flx_mono', kjit, flx_mono, kjpindex*nvm, indexveg)
1600	CALL histwrite_p(hist2_id, 'flx_apinen', kjit, flx_apinen, kjpindex*nvm, indexveg)
1601	CALL histwrite_p(hist2_id, 'flx_bpinen', kjit, flx_bpinen, kjpindex*nvm, indexveg)
1602	CALL histwrite_p(hist2_id, 'flx_limonen', kjit, flx_limonen, kjpindex*nvm, indexveg)
1603	CALL histwrite_p(hist2_id, 'flx_myrcen', kjit, flx_myrcen, kjpindex*nvm, indexveg)
1604	CALL histwrite_p(hist2_id, 'flx_sabinen', kjit, flx_sabinen, kjpindex*nvm, indexveg)
1605	CALL histwrite_p(hist2_id, 'flx_camphen', kjit, flx_camphen, kjpindex*nvm, indexveg)
1606	CALL histwrite_p(hist2_id, 'flx_3caren', kjit, flx_3caren, kjpindex*nvm, indexveg)
1607	CALL histwrite_p(hist2_id, 'flx_tbocimen', kjit, flx_tbocimen, kjpindex*nvm, indexveg)
1608	CALL histwrite_p(hist2_id, 'flx_othermono', kjit, flx_othermono, kjpindex*nvm, indexveg)
1609	CALL histwrite_p(hist2_id, 'flx_sesquiter', kjit, flx_sesquiter, kjpindex*nvm, indexveg)
1610	CALL histwrite_p(hist2_id, 'flx_ORVOC', kjit, flx_ORVOC, kjpindex*nvm, indexveg)
1611	CALL histwrite_p(hist2_id, 'flx_MBO', kjit, flx_MBO, kjpindex*nvm, indexveg)
1612	CALL histwrite_p(hist2_id, 'flx_methanol', kjit, flx_methanol, kjpindex*nvm, indexveg)
1613	CALL histwrite_p(hist2_id, 'flx_acetone', kjit, flx_acetone, kjpindex*nvm, indexveg)
1614	CALL histwrite_p(hist2_id, 'flx_acetal', kjit, flx_acetal, kjpindex*nvm, indexveg)
1615	CALL histwrite_p(hist2_id, 'flx_formal', kjit, flx_formal, kjpindex*nvm, indexveg)
1616	CALL histwrite_p(hist2_id, 'flx_acetic', kjit, flx_acetic, kjpindex*nvm, indexveg)
1617	CALL histwrite_p(hist2_id, 'flx_formic', kjit, flx_formic, kjpindex*nvm, indexveg)
1618	CALL histwrite_p(hist2_id, 'flx_no_soil', kjit, flx_no_soil, kjpindex*nvm, indexveg)
1619	CALL histwrite_p(hist2_id, 'flx_no', kjit, flx_no, kjpindex*nvm, indexveg)
1620	ENDIF
1621	ENDIF
1622
1623	IF (printlev>=3) WRITE(numout,*) 'OK chemistry_bvoc'
1624
1625	END SUBROUTINE chemistry_bvoc
1626
1627	!! ================================================================================================================================
1628	!! SUBROUTINE : chemistry_flux_interface
1629	!!
1630	!>\BRIEF This subroutine will give to the interface between inca model and orchidee model in sechiba all the flux ask by inca
1631	!!
1632	!! DESCRIPTION : This subroutine allow the transfer of fluxes between surface and atmospheric chemistry. It is called from sechiba
1633	!!
1634	!! RECENT CHANGE(S): None
1635	!!
1636	!! MAIN OUTPUT VARIABLE(S): ::
1637	!!
1638	!! REFERENCE(S) : None
1639	!!
1640	!! FLOWCHART : None
1641	!_ ================================================================================================================================
1642
1643	SUBROUTINE chemistry_flux_interface( field_out_names, fields_out, field_in_names, fields_in)
1644
1645	!
1646	! Optional arguments
1647	!
1648	! Names and fields for emission variables : to be transport by Orchidee to Inca
1649	CHARACTER(LEN=*),DIMENSION(:), OPTIONAL, INTENT(IN) :: field_out_names
1650	REAL(r_std),DIMENSION(:,:,:), OPTIONAL, INTENT(OUT) :: fields_out
1651	!
1652	! Names and fields for deposit variables : to be transport from chemistry model by INCA to ORCHIDEE.
1653	CHARACTER(LEN=*),DIMENSION(:), OPTIONAL, INTENT(IN) :: field_in_names
1654	REAL(r_std),DIMENSION(:,:), OPTIONAL, INTENT(IN) :: fields_in
1655	!
1656	! Number of fields to give (nb_fields_out) or get from (nb_fields_in) INCA :
1657	INTEGER(i_std), SAVE :: nb_fields_out, nb_fields_in
1658	!$OMP THREADPRIVATE(nb_fields_out, nb_fields_in)
1659
1660	! Id of fields to give (nb_fields_out) or get from (nb_fields_in) INCA :
1661	INTEGER(i_std) :: i_fields_out, i_fields_in
1662
1663	IF (l_first_chemistry_inca) THEN
1664
1665	! il faut verifier que ok_bvoc (chemistry_ok_bvoc) est bien active sinon on arrete tout
1666	if (.not.ok_bvoc) then
1667	CALL ipslerr_p (3,'chemistry_inca', &
1668	& 'you need to activate chemistry_ok_bvoc in orchidee.def',&
1669	& 'This model won''t be able to continue.', &
1670	& '')
1671	endif
1672
1673	! Prepare fieds out/in for interface with INCA.
1674	IF (PRESENT(field_out_names)) THEN
1675	nb_fields_out=SIZE(field_out_names)
1676	ELSE
1677	nb_fields_out=0
1678	ENDIF
1679
1680	IF (PRESENT(field_in_names)) THEN
1681	nb_fields_in=SIZE(field_in_names)
1682	ELSE
1683	nb_fields_in=0
1684	ENDIF
1685	l_first_chemistry_inca = .FALSE.
1686
1687	ENDIF
1688
1689
1690
1691	IF (ok_bvoc) THEN
1692	! Fields for deposit variables : to be transport from chemistry model by INCA to ORCHIDEE.
1693	DO i_fields_in=1,nb_fields_in
1694	SELECT CASE(TRIM(field_in_names(i_fields_in)))
1695	CASE DEFAULT
1696	CALL ipslerr_p (3,'chemistry_inca', &
1697	& 'You ask in INCA an unknown field '//TRIM(field_in_names(i_fields_in))//&
1698	& ' to give to ORCHIDEE for this specific version.',&
1699	& 'This model won''t be able to continue.', &
1700	& '(check your tracer parameters in INCA)')
1701	END SELECT
1702	ENDDO
1703
1704	! Fields for Biogenic emissions : to be transport by Orchidee to Inca
1705	DO i_fields_out=1,nb_fields_out
1706	SELECT CASE(TRIM(field_out_names(i_fields_out)))
1707	CASE("flx_iso")
1708	fields_out(:,:,i_fields_out)=flx_iso(:,:)
1709	CASE("flx_mono")
1710	fields_out(:,:,i_fields_out)=flx_mono(:,:)
1711	CASE("flx_ORVOC")
1712	fields_out(:,:,i_fields_out)=flx_ORVOC(:,:)
1713	CASE("flx_MBO")
1714	fields_out(:,:,i_fields_out)=flx_MBO(:,:)
1715	CASE("flx_methanol")
1716	fields_out(:,:,i_fields_out)=flx_methanol(:,:)
1717	CASE("flx_acetone")
1718	fields_out(:,:,i_fields_out)=flx_acetone(:,:)
1719	CASE("flx_acetal")
1720	fields_out(:,:,i_fields_out)=flx_acetal(:,:)
1721	CASE("flx_formal")
1722	fields_out(:,:,i_fields_out)=flx_formal(:,:)
1723	CASE("flx_acetic")
1724	fields_out(:,:,i_fields_out)=flx_acetic(:,:)
1725	CASE("flx_formic")
1726	fields_out(:,:,i_fields_out)=flx_formic(:,:)
1727	CASE("flx_no_soil")
1728	fields_out(:,:,i_fields_out)=flx_no_soil(:,:)
1729	CASE("flx_nox")
1730	fields_out(:,:,i_fields_out)=flx_no(:,:)
1731	CASE("flx_fertil_no")
1732	fields_out(:,:,i_fields_out)=flx_fertil_no(:,:)
1733	CASE("flx_apinen")
1734	fields_out(:,:,i_fields_out)=flx_apinen(:,:)
1735	CASE("flx_bpinen")
1736	fields_out(:,:,i_fields_out)=flx_bpinen(:,:)
1737	CASE("flx_limonen")
1738	fields_out(:,:,i_fields_out)=flx_limonen(:,:)
1739	CASE("flx_myrcen")
1740	fields_out(:,:,i_fields_out)=flx_myrcen(:,:)
1741	CASE("flx_sabinen")
1742	fields_out(:,:,i_fields_out)=flx_sabinen(:,:)
1743	CASE("flx_camphen")
1744	fields_out(:,:,i_fields_out)=flx_camphen(:,:)
1745	CASE("flx_3caren")
1746	fields_out(:,:,i_fields_out)=flx_3caren(:,:)
1747	CASE("flx_tbocimen")
1748	fields_out(:,:,i_fields_out)=flx_tbocimen(:,:)
1749	CASE("flx_othermono")
1750	fields_out(:,:,i_fields_out)=flx_othermono(:,:)
1751	CASE("flx_sesquiter")
1752	fields_out(:,:,i_fields_out)=flx_sesquiter(:,:)
1753
1754	CASE DEFAULT
1755	CALL ipslerr_p (3,'chemistry_inca', &
1756	& 'You ask from INCA an unknown field '//TRIM(field_out_names(i_fields_out))//&
1757	& ' to ORCHIDEE for this specific version.',&
1758	& 'This model won''t be able to continue.', &
1759	& '(check your tracer parameters in INCA)')
1760	END SELECT
1761	ENDDO
1762
1763	ENDIF
1764	END SUBROUTINE chemistry_flux_interface
1765
1766	!! ================================================================================================================================
1767	!! SUBROUTINE : chemistry_clear
1768	!!
1769	!>\BRIEF Clear chemistry module
1770	!!
1771	!! DESCRIPTION : Deallocate memory and reset initialization variables to there original values
1772	!!
1773	!_ ================================================================================================================================
1774	SUBROUTINE chemistry_clear
1775
1776	!! 1. Initialize as for first run
1777	l_first_chemistry_inca = .TRUE.
1778
1779	!! 2. Deallocate dynamic variables
1780	IF (ALLOCATED(pulse)) DEALLOCATE (pulse)
1781	IF (ALLOCATED (ok_siesta)) DEALLOCATE (ok_siesta)
1782	IF (ALLOCATED (allow_pulse)) DEALLOCATE (allow_pulse)
1783	IF (ALLOCATED (pulseday)) DEALLOCATE (pulseday)
1784	IF (ALLOCATED (siestaday)) DEALLOCATE (siestaday)
1785	IF (ALLOCATED (pulselim)) DEALLOCATE (pulselim)
1786	IF (ALLOCATED (siestalim)) DEALLOCATE (siestalim)
1787	IF (ALLOCATED (area2)) DEALLOCATE (area2)
1788	IF (ALLOCATED (N_qt_WRICE_year)) DEALLOCATE (N_qt_WRICE_year)
1789	IF (ALLOCATED (N_qt_OTHER_year)) DEALLOCATE (N_qt_OTHER_year)
1790	IF (ALLOCATED (flx_iso)) DEALLOCATE (flx_iso)
1791	IF (ALLOCATED (flx_mono)) DEALLOCATE (flx_mono)
1792	IF (ALLOCATED (flx_ORVOC)) DEALLOCATE (flx_ORVOC)
1793	IF (ALLOCATED (flx_MBO)) DEALLOCATE (flx_MBO)
1794	IF (ALLOCATED (flx_methanol)) DEALLOCATE (flx_methanol)
1795	IF (ALLOCATED (flx_acetone)) DEALLOCATE (flx_acetone)
1796	IF (ALLOCATED (flx_acetal)) DEALLOCATE (flx_acetal)
1797	IF (ALLOCATED (flx_formal)) DEALLOCATE (flx_formal)
1798	IF (ALLOCATED (flx_acetic)) DEALLOCATE (flx_acetic)
1799	IF (ALLOCATED (flx_formic)) DEALLOCATE (flx_formic)
1800	IF (ALLOCATED (flx_no_soil)) DEALLOCATE (flx_no_soil)
1801	IF (ALLOCATED (flx_no)) DEALLOCATE (flx_no)
1802	IF (ALLOCATED (flx_fertil_no)) DEALLOCATE (flx_fertil_no)
1803	IF (ALLOCATED (flx_apinen)) DEALLOCATE (flx_apinen)
1804	IF (ALLOCATED (flx_bpinen)) DEALLOCATE (flx_bpinen)
1805	IF (ALLOCATED (flx_limonen)) DEALLOCATE (flx_limonen)
1806	IF (ALLOCATED (flx_myrcen)) DEALLOCATE (flx_myrcen)
1807	IF (ALLOCATED (flx_sabinen)) DEALLOCATE (flx_sabinen)
1808	IF (ALLOCATED (flx_camphen)) DEALLOCATE (flx_camphen)
1809	IF (ALLOCATED (flx_3caren)) DEALLOCATE (flx_3caren)
1810	IF (ALLOCATED (flx_tbocimen)) DEALLOCATE (flx_tbocimen)
1811	IF (ALLOCATED (flx_othermono)) DEALLOCATE (flx_othermono)
1812	IF (ALLOCATED (flx_sesquiter)) DEALLOCATE (flx_sesquiter)
1813	IF (ALLOCATED (CRF)) DEALLOCATE (CRF)
1814	IF (ALLOCATED (flx_co2_bbg_year)) DEALLOCATE (flx_co2_bbg_year)
1815
1816	END SUBROUTINE chemistry_clear
1817
1818	END MODULE chemistry

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