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source: palm/trunk/SOURCE/chemistry_model_mod.f90 @ 3430

Last change on this file since 3430 was 3373, checked in by kanani, 6 years ago
Fix cpp directives and error messages
Property svn:keywords set to `Id`
File size: 95.5 KB

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1	!> @file chemistry_model_mod.f90
2	!------------------------------------------------------------------------------!
3	! This file is part of the PALM model system.
4	!
5	! PALM is free software: you can redistribute it and/or modify it under the
6	! terms of the GNU General Public License as published by the Free Software
7	! Foundation, either version 3 of the License, or (at your option) any later
8	! version.
9	!
10	! PALM is distributed in the hope that it will be useful, but WITHOUT ANY
11	! WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
12	! A PARTICULAR PURPOSE. See the GNU General Public License for more details.
13	!
14	! You should have received a copy of the GNU General Public License along with
15	! PALM. If not, see <http://www.gnu.org/licenses/>.
16	!
17	! Copyright 2017-2018 Leibniz Universitaet Hannover
18	! Copyright 2017-2018 Karlsruhe Institute of Technology
19	! Copyright 2017-2018 Freie Universitaet Berlin
20	!------------------------------------------------------------------------------!
21	!
22	! Current revisions:
23	! -----------------
24	!
25	!
26	! Former revisions:
27	! -----------------
28	! $Id: chemistry_model_mod.f90 3373 2018-10-18 15:25:56Z maronga $
29	! Remove MPI_Abort, replace by message
30	!
31	! 3318 2018-10-08 11:43:01Z sward
32	! Fixed faulty syntax of message string
33	!
34	! 3298 2018-10-02 12:21:11Z kanani
35	! Add remarks (kanani)
36	! Merge with trunk, replaced cloud_physics by bulk_cloud_model 28.09.2018 forkel
37	! Subroutines header and chem_check_parameters added 25.09.2018 basit
38	! Removed chem_emission routine now declared in chem_emissions.f90 30.07.2018 ERUSSO
39	! Introduced emissions namelist parameters 30.07.2018 ERUSSO
40	!
41	! Timestep steering added in subroutine chem_integrate_ij and
42	! output of chosen solver in chem_parin added 30.07.2018 ketelsen
43	!
44	! chem_check_data_output_pr: added unit for PM compounds 20.07.2018 forkel
45	! replaced : by nzb+1:nzt for pt,q,ql (found by kk) 18.07.2018 forkel
46	! debugged restart run for chem species 06.07.2018 basit
47	! reorganized subroutines in alphabetical order. 27.06.2018 basit
48	! subroutine chem_parin updated for profile output 27.06.2018 basit
49	! Added humidity arrays to USE section and tmp_qvap in chem_integrate 26.6.2018 forkel
50	! Merged chemistry with with trunk (nzb_do and nzt_do in 3d output) 26.6.2018 forkel
51	!
52	! reorganized subroutines in alphabetical order. basit 22.06.2018
53	! subroutine chem_parin updated for profile output basit 22.06.2018
54	! subroutine chem_statistics added
55	! subroutine chem_check_data_output_pr add 21.06.2018 basit
56	! subroutine chem_data_output_mask added 20.05.2018 basit
57	! subroutine chem_data_output_2d added 20.05.2018 basit
58	! subroutine chem_statistics added 04.06.2018 basit
59	! subroutine chem_emissions: Set cssws to zero before setting values 20.03.2018 forkel
60	! subroutine chem_emissions: Introduced different conversion factors
61	! for PM and gaseous compounds 15.03.2018 forkel
62	! subroutine chem_emissions updated to take variable number of chem_spcs and
63	! emission factors. 13.03.2018 basit
64	! chem_boundary_conds_decycle improved. 05.03.2018 basit
65	! chem_boundary_conds_decycle subroutine added 21.02.2018 basit
66	! chem_init_profiles subroutines re-activated after correction 21.02.2018 basit
67	!
68	!
69	! 3293 2018-09-28 12:45:20Z forkel
70	! Modularization of all bulk cloud physics code components
71	!
72	! 3248 2018-09-14 09:42:06Z sward
73	! Minor formating changes
74	!
75	! 3246 2018-09-13 15:14:50Z sward
76	! Added error handling for input namelist via parin_fail_message
77	!
78	! 3241 2018-09-12 15:02:00Z raasch
79	! +nest_chemistry
80	!
81	! 3209 2018-08-27 16:58:37Z suehring
82	! Rename flags indicating outflow boundary conditions
83	!
84	! 3182 2018-07-27 13:36:03Z suehring
85	! Revise output of surface quantities in case of overhanging structures
86	!
87	! 3045 2018-05-28 07:55:41Z Giersch
88	! error messages revised
89	!
90	! 3014 2018-05-09 08:42:38Z maronga
91	! Bugfix: nzb_do and nzt_do were not used for 3d data output
92	!
93	! 3004 2018-04-27 12:33:25Z Giersch
94	! Comment concerning averaged data output added
95	!
96	! 2932 2018-03-26 09:39:22Z maronga
97	! renamed chemistry_par to chemistry_parameters
98	!
99	! 2894 2018-03-15 09:17:58Z Giersch
100	! Calculations of the index range of the subdomain on file which overlaps with
101	! the current subdomain are already done in read_restart_data_mod,
102	! chem_last_actions was renamed to chem_wrd_local, chem_read_restart_data was
103	! renamed to chem_rrd_local, chem_write_var_list was renamed to
104	! chem_wrd_global, chem_read_var_list was renamed to chem_rrd_global,
105	! chem_skip_var_list has been removed, variable named found has been
106	! introduced for checking if restart data was found, reading of restart strings
107	! has been moved completely to read_restart_data_mod, chem_rrd_local is already
108	! inside the overlap loop programmed in read_restart_data_mod, todo list has
109	! bees extended, redundant characters in chem_wrd_local have been removed,
110	! the marker * end chemistry * is not necessary anymore, strings and their
111	! respective lengths are written out and read now in case of restart runs to
112	! get rid of prescribed character lengths
113	!
114	! 2815 2018-02-19 11:29:57Z suehring
115	! Bugfix in restart mechanism,
116	! rename chem_tendency to chem_prognostic_equations,
117	! implement vector-optimized version of chem_prognostic_equations,
118	! some clean up (incl. todo list)
119	!
120	! 2773 2018-01-30 14:12:54Z suehring
121	! Declare variables required for nesting as public
122	!
123	! 2772 2018-01-29 13:10:35Z suehring
124	! Bugfix in string handling
125	!
126	! 2768 2018-01-24 15:38:29Z kanani
127	! Shorten lines to maximum length of 132 characters
128	!
129	! 2766 2018-01-22 17:17:47Z kanani
130	! Removed preprocessor directive __chem
131	!
132	! 2756 2018-01-16 18:11:14Z suehring
133	! Fill values in 3D output introduced.
134	!
135	! 2718 2018-01-02 08:49:38Z maronga
136	! Initial revision
137	!
138	!
139	!
140	!
141	! Authors:
142	! --------
143	! @author Renate Forkel
144	! @author Farah Kanani-Suehring
145	! @author Klaus Ketelsen
146	! @author Basit Khan
147	!
148	!
149	!------------------------------------------------------------------------------!
150	! Description:
151	! ------------
152	!> Chemistry model for PALM-4U
153	!> @todo Adjust chem_rrd_local to CASE structure of others modules. It is not
154	!> allowed to use the chemistry model in a precursor run and additionally
155	!> not using it in a main run
156	!> @todo Update/clean-up todo list! (FK)
157	!> @todo Set proper fill values (/= 0) for chem output arrays! (FK)
158	!> @todo Add routine chem_check_parameters, add checks for inconsistent or
159	!> unallowed parameter settings.
160	!> CALL of chem_check_parameters from check_parameters. (FK)
161	!> @todo Make routine chem_header available, CALL from header.f90
162	!> (see e.g. how it is done in routine lsm_header in
163	!> land_surface_model_mod.f90). chem_header should include all setup
164	!> info about chemistry parameter settings. (FK)
165	!> @todo Implement turbulent inflow of chem spcs in inflow_turbulence.
166	!> @todo Separate boundary conditions for each chem spcs to be implemented
167	!> @todo Currently only total concentration are calculated. Resolved, parameterized
168	!> and chemistry fluxes although partially and some completely coded but
169	!> are not operational/activated in this version. bK.
170	!> @todo slight differences in passive scalar and chem spcs when chem reactions
171	!> turned off. Need to be fixed. bK
172	!> @todo test nesting for chem spcs, was implemented by suehring (kanani)
173	!> @todo chemistry error messages
174	!> @todo Format this module according to PALM coding standard (see e.g. module
175	!> template under http://palm.muk.uni-hannover.de/mosaik/downloads/8 or
176	!> D3_coding_standard.pdf under https://palm.muk.uni-hannover.de/trac/downloads/16)
177	!
178	!------------------------------------------------------------------------------!
179
180	MODULE chemistry_model_mod
181
182	USE kinds, ONLY: wp, iwp
183	USE indices, ONLY: nz, nzb,nzt,nysg,nyng,nxlg,nxrg, &
184	nys,nyn,nx,nxl,nxr,ny,wall_flags_0
185	USE pegrid, ONLY: myid, threads_per_task
186
187	USE bulk_cloud_model_mod, &
188	ONLY: bulk_cloud_model
189
190	USE control_parameters, ONLY: bc_lr_cyc, bc_ns_cyc, dt_3d, humidity, &
191	initializing_actions, message_string, &
192	omega, tsc, intermediate_timestep_count, &
193	intermediate_timestep_count_max, &
194	timestep_scheme, use_prescribed_profile_data, ws_scheme_sca
195	USE arrays_3d, ONLY: exner, hyp, pt, q, ql, rdf_sc, tend, zu
196	USE chem_gasphase_mod, ONLY: nspec, spc_names, nkppctrl, nmaxfixsteps, &
197	t_steps, chem_gasphase_integrate, vl_dim, &
198	nvar, nreact, atol, rtol, nphot, phot_names
199	USE cpulog, ONLY: cpu_log, log_point
200
201	USE chem_modules
202
203	USE statistics
204
205	IMPLICIT NONE
206	PRIVATE
207	SAVE
208
209	LOGICAL :: nest_chemistry = .TRUE. !< flag for nesting mode of chemical species, independent on parent or not
210	!
211	!- Define chemical variables
212	TYPE species_def
213	CHARACTER(LEN=8) :: name
214	CHARACTER(LEN=16) :: unit
215	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc
216	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_av
217	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_p
218	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: tconc_m
219	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: cssws_av
220	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: flux_s_cs
221	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: diss_s_cs
222	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: flux_l_cs
223	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: diss_l_cs
224	REAL(kind=wp),ALLOCATABLE,DIMENSION(:) :: conc_pr_init
225	END TYPE species_def
226
227
228	TYPE photols_def
229	CHARACTER(LEN=8) :: name
230	CHARACTER(LEN=16) :: unit
231	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: freq
232	END TYPE photols_def
233
234
235	PUBLIC species_def
236	PUBLIC photols_def
237
238
239	TYPE(species_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: chem_species
240	TYPE(photols_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: phot_frequen
241
242	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_1
243	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_2
244	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_3
245	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_av
246	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: freq_1
247
248	INTEGER,DIMENSION(nkppctrl) :: icntrl ! Fine tuning kpp
249	REAL(kind=wp),DIMENSION(nkppctrl) :: rcntrl ! Fine tuning kpp
250	LOGICAL :: decycle_chem_lr = .FALSE.
251	LOGICAL :: decycle_chem_ns = .FALSE.
252	CHARACTER (LEN=20), DIMENSION(4) :: decycle_method = &
253	(/'dirichlet','dirichlet','dirichlet','dirichlet'/)
254	!< Decycling method at horizontal boundaries,
255	!< 1=left, 2=right, 3=south, 4=north
256	!< dirichlet = initial size distribution and
257	!< chemical composition set for the ghost and
258	!< first three layers
259	!< neumann = zero gradient
260
261	REAL(kind=wp), PUBLIC :: cs_time_step
262	CHARACTER(10), PUBLIC :: photolysis_scheme
263	! 'constant',
264	! 'simple' (Simple parameterisation from MCM, Saunders et al., 2003, Atmos. Chem. Phys., 3, 161-180
265	! 'fastj' (Wild et al., 2000, J. Atmos. Chem., 37, 245-282) STILL NOT IMPLEMENTED
266
267	PUBLIC nest_chemistry
268	PUBLIC nspec
269	PUBLIC nreact
270	PUBLIC nvar
271	PUBLIC spc_names
272	PUBLIC spec_conc_2
273
274	!- Interface section
275	INTERFACE chem_3d_data_averaging
276	MODULE PROCEDURE chem_3d_data_averaging
277	END INTERFACE chem_3d_data_averaging
278
279	INTERFACE chem_boundary_conds
280	MODULE PROCEDURE chem_boundary_conds
281	MODULE PROCEDURE chem_boundary_conds_decycle
282	END INTERFACE chem_boundary_conds
283
284	INTERFACE chem_check_data_output
285	MODULE PROCEDURE chem_check_data_output
286	END INTERFACE chem_check_data_output
287
288	INTERFACE chem_data_output_2d
289	MODULE PROCEDURE chem_data_output_2d
290	END INTERFACE chem_data_output_2d
291
292	INTERFACE chem_data_output_3d
293	MODULE PROCEDURE chem_data_output_3d
294	END INTERFACE chem_data_output_3d
295
296	INTERFACE chem_data_output_mask
297	MODULE PROCEDURE chem_data_output_mask
298	END INTERFACE chem_data_output_mask
299
300	INTERFACE chem_check_data_output_pr
301	MODULE PROCEDURE chem_check_data_output_pr
302	END INTERFACE chem_check_data_output_pr
303
304	INTERFACE chem_check_parameters
305	MODULE PROCEDURE chem_check_parameters
306	END INTERFACE chem_check_parameters
307
308	INTERFACE chem_define_netcdf_grid
309	MODULE PROCEDURE chem_define_netcdf_grid
310	END INTERFACE chem_define_netcdf_grid
311
312	INTERFACE chem_header
313	MODULE PROCEDURE chem_header
314	END INTERFACE chem_header
315
316	INTERFACE chem_init
317	MODULE PROCEDURE chem_init
318	END INTERFACE chem_init
319
320	INTERFACE chem_init_profiles
321	MODULE PROCEDURE chem_init_profiles
322	END INTERFACE chem_init_profiles
323
324	INTERFACE chem_integrate
325	MODULE PROCEDURE chem_integrate_ij
326	END INTERFACE chem_integrate
327
328	INTERFACE chem_parin
329	MODULE PROCEDURE chem_parin
330	END INTERFACE chem_parin
331
332	INTERFACE chem_prognostic_equations
333	MODULE PROCEDURE chem_prognostic_equations
334	MODULE PROCEDURE chem_prognostic_equations_ij
335	END INTERFACE chem_prognostic_equations
336
337	INTERFACE chem_rrd_local
338	MODULE PROCEDURE chem_rrd_local
339	END INTERFACE chem_rrd_local
340
341	INTERFACE chem_statistics
342	MODULE PROCEDURE chem_statistics
343	END INTERFACE chem_statistics
344
345	INTERFACE chem_swap_timelevel
346	MODULE PROCEDURE chem_swap_timelevel
347	END INTERFACE chem_swap_timelevel
348
349	INTERFACE chem_wrd_local
350	MODULE PROCEDURE chem_wrd_local
351	END INTERFACE chem_wrd_local
352
353
354	PUBLIC chem_3d_data_averaging, chem_boundary_conds, chem_check_data_output, &
355	chem_check_data_output_pr, chem_check_parameters, &
356	chem_data_output_2d, chem_data_output_3d, chem_data_output_mask, &
357	chem_define_netcdf_grid, chem_header, chem_init, &
358	chem_init_profiles, chem_integrate, chem_parin, &
359	chem_prognostic_equations, chem_rrd_local, &
360	chem_statistics, chem_swap_timelevel, chem_wrd_local
361
362
363
364	CONTAINS
365
366	!
367	!------------------------------------------------------------------------------!
368	!
369	! Description:
370	! ------------
371	!> Subroutine for averaging 3D data of chemical species. Due to the fact that
372	!> the averaged chem arrays are allocated in chem_init, no if-query concerning
373	!> the allocation is required (in any mode). Attention: If you just specify an
374	!> averaged output quantity in the _p3dr file during restarts the first output
375	!> includes the time between the beginning of the restart run and the first
376	!> output time (not necessarily the whole averaging_interval you have
377	!> specified in your _p3d/_p3dr file )
378	!------------------------------------------------------------------------------!
379
380	SUBROUTINE chem_3d_data_averaging ( mode, variable )
381
382	USE control_parameters
383
384	USE indices
385
386	USE kinds
387
388	USE surface_mod, &
389	ONLY: surf_def_h, surf_lsm_h, surf_usm_h
390
391	IMPLICIT NONE
392
393	CHARACTER (LEN=*) :: mode !<
394	CHARACTER (LEN=*) :: variable !<
395
396	LOGICAL :: match_def !< flag indicating natural-type surface
397	LOGICAL :: match_lsm !< flag indicating natural-type surface
398	LOGICAL :: match_usm !< flag indicating urban-type surface
399
400	INTEGER(iwp) :: i !< grid index x direction
401	INTEGER(iwp) :: j !< grid index y direction
402	INTEGER(iwp) :: k !< grid index z direction
403	INTEGER(iwp) :: m !< running index surface type
404	INTEGER(iwp) :: lsp !< running index for chem spcs
405
406
407	IF ( mode == 'allocate' ) THEN
408	DO lsp = 1, nspec
409	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
410	chem_species(lsp)%conc_av = 0.0_wp
411
412	ENDIF
413	ENDDO
414
415	ELSEIF ( mode == 'sum' ) THEN
416
417
418	DO lsp = 1, nspec
419	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
420	DO i = nxlg, nxrg
421	DO j = nysg, nyng
422	DO k = nzb, nzt+1
423	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) + &
424	chem_species(lsp)%conc(k,j,i)
425	ENDDO
426	ENDDO
427	ENDDO
428	ELSEIF ( TRIM(variable(4:)) == TRIM('cssws*') ) THEN
429	DO i = nxl, nxr
430	DO j = nys, nyn
431	match_def = surf_def_h(0)%start_index(j,i) <= &
432	surf_def_h(0)%end_index(j,i)
433	match_lsm = surf_lsm_h%start_index(j,i) <= &
434	surf_lsm_h%end_index(j,i)
435	match_usm = surf_usm_h%start_index(j,i) <= &
436	surf_usm_h%end_index(j,i)
437
438	IF ( match_def ) THEN
439	m = surf_def_h(0)%end_index(j,i)
440	chem_species(lsp)%cssws_av(j,i) = &
441	chem_species(lsp)%cssws_av(j,i) + &
442	surf_def_h(0)%cssws(lsp,m)
443	ELSEIF ( match_lsm .AND. .NOT. match_usm ) THEN
444	m = surf_lsm_h%end_index(j,i)
445	chem_species(lsp)%cssws_av(j,i) = &
446	chem_species(lsp)%cssws_av(j,i) + &
447	surf_lsm_h%cssws(lsp,m)
448	ELSEIF ( match_usm ) THEN
449	m = surf_usm_h%end_index(j,i)
450	chem_species(lsp)%cssws_av(j,i) = &
451	chem_species(lsp)%cssws_av(j,i) + &
452	surf_usm_h%cssws(lsp,m)
453	ENDIF
454	ENDDO
455	ENDDO
456	ENDIF
457	ENDDO
458
459	ELSEIF ( mode == 'average' ) THEN
460	DO lsp = 1, nspec
461	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
462	DO i = nxlg, nxrg
463	DO j = nysg, nyng
464	DO k = nzb, nzt+1
465	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) / REAL( average_count_3d, KIND=wp )
466	ENDDO
467	ENDDO
468	ENDDO
469
470	ELSEIF (TRIM(variable(4:)) == TRIM('cssws*') ) THEN
471	DO i = nxlg, nxrg
472	DO j = nysg, nyng
473	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) / REAL( average_count_3d, KIND=wp )
474	ENDDO
475	ENDDO
476	CALL exchange_horiz_2d( chem_species(lsp)%cssws_av, nbgp )
477	ENDIF
478	ENDDO
479
480	ENDIF
481
482	END SUBROUTINE chem_3d_data_averaging
483
484	!
485	!------------------------------------------------------------------------------!
486	!
487	! Description:
488	! ------------
489	!> Subroutine to initialize and set all boundary conditions for chemical species
490	!------------------------------------------------------------------------------!
491
492	SUBROUTINE chem_boundary_conds( mode )
493
494	USE control_parameters, &
495	ONLY: air_chemistry, bc_radiation_l, bc_radiation_n, bc_radiation_r, &
496	bc_radiation_s
497	USE indices, &
498	ONLY: nxl, nxr, nxlg, nxrg, nyng, nysg, nzt
499
500
501	USE arrays_3d, &
502	ONLY: dzu
503	USE surface_mod, &
504	ONLY: bc_h
505
506	CHARACTER (len=*), INTENT(IN) :: mode
507	INTEGER(iwp) :: i !< grid index x direction.
508	INTEGER(iwp) :: j !< grid index y direction.
509	INTEGER(iwp) :: k !< grid index z direction.
510	INTEGER(iwp) :: kb !< variable to set respective boundary value, depends on facing.
511	INTEGER(iwp) :: l !< running index boundary type, for up- and downward-facing walls.
512	INTEGER(iwp) :: m !< running index surface elements.
513	INTEGER(iwp) :: lsp !< running index for chem spcs.
514	INTEGER(iwp) :: lph !< running index for photolysis frequencies
515
516
517	SELECT CASE ( TRIM( mode ) )
518	CASE ( 'init' )
519
520	IF ( bc_cs_b == 'dirichlet' ) THEN
521	ibc_cs_b = 0
522	ELSEIF ( bc_cs_b == 'neumann' ) THEN
523	ibc_cs_b = 1
524	ELSE
525	message_string = 'unknown boundary condition: bc_cs_b ="' // TRIM( bc_cs_b ) // '"'
526	CALL message( 'chem_boundary_conds', 'CM0429', 1, 2, 0, 6, 0 ) !<
527	ENDIF
528	!
529	!-- Set Integer flags and check for possible erroneous settings for top
530	!-- boundary condition.
531	IF ( bc_cs_t == 'dirichlet' ) THEN
532	ibc_cs_t = 0
533	ELSEIF ( bc_cs_t == 'neumann' ) THEN
534	ibc_cs_t = 1
535	ELSEIF ( bc_cs_t == 'initial_gradient' ) THEN
536	ibc_cs_t = 2
537	ELSEIF ( bc_cs_t == 'nested' ) THEN
538	ibc_cs_t = 3
539	ELSE
540	message_string = 'unknown boundary condition: bc_c_t ="' // TRIM( bc_cs_t ) // '"'
541	CALL message( 'check_parameters', 'CM0430', 1, 2, 0, 6, 0 )
542	ENDIF
543
544
545	CASE ( 'set_bc_bottomtop' )
546	!-- Bottom boundary condtions for chemical species
547	DO lsp = 1, nspec
548	IF ( ibc_cs_b == 0 ) THEN
549	DO l = 0, 1
550	!-- Set index kb: For upward-facing surfaces (l=0), kb=-1, i.e.
551	!-- the chem_species(nspec)%conc_p value at the topography top (k-1)
552	!-- is set; for downward-facing surfaces (l=1), kb=1, i.e. the
553	!-- value at the topography bottom (k+1) is set.
554
555	kb = MERGE( -1, 1, l == 0 )
556	!$OMP PARALLEL DO PRIVATE( i, j, k )
557	DO m = 1, bc_h(l)%ns
558	i = bc_h(l)%i(m)
559	j = bc_h(l)%j(m)
560	k = bc_h(l)%k(m)
561	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc(k+kb,j,i)
562	ENDDO
563	ENDDO
564
565	ELSEIF ( ibc_cs_b == 1 ) THEN
566	!-- in boundary_conds there is som extra loop over m here for passive tracer
567	DO l = 0, 1
568	kb = MERGE( -1, 1, l == 0 )
569	!$OMP PARALLEL DO PRIVATE( i, j, k )
570	DO m = 1, bc_h(l)%ns
571	i = bc_h(l)%i(m)
572	j = bc_h(l)%j(m)
573	k = bc_h(l)%k(m)
574	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc_p(k,j,i)
575
576	ENDDO
577	ENDDO
578	ENDIF
579	ENDDO ! end lsp loop
580
581	!-- Top boundary conditions for chemical species - Should this not be done for all species?
582	IF ( ibc_cs_t == 0 ) THEN
583	DO lsp = 1, nspec
584	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc(nzt+1,:,:)
585	ENDDO
586	ELSEIF ( ibc_cs_t == 1 ) THEN
587	DO lsp = 1, nspec
588	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:)
589	ENDDO
590	ELSEIF ( ibc_cs_t == 2 ) THEN
591	DO lsp = 1, nspec
592	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:) + bc_cs_t_val(lsp) * dzu(nzt+1)
593	ENDDO
594	ENDIF
595	!
596	CASE ( 'set_bc_lateral' )
597	!-- Lateral boundary conditions for chem species at inflow boundary
598	!-- are automatically set when chem_species concentration is
599	!-- initialized. The initially set value at the inflow boundary is not
600	!-- touched during time integration, hence, this boundary value remains
601	!-- at a constant value, which is the concentration that flows into the
602	!-- domain.
603	!-- Lateral boundary conditions for chem species at outflow boundary
604
605	IF ( bc_radiation_s ) THEN
606	DO lsp = 1, nspec
607	chem_species(lsp)%conc_p(:,nys-1,:) = chem_species(lsp)%conc_p(:,nys,:)
608	ENDDO
609	ELSEIF ( bc_radiation_n ) THEN
610	DO lsp = 1, nspec
611	chem_species(lsp)%conc_p(:,nyn+1,:) = chem_species(lsp)%conc_p(:,nyn,:)
612	ENDDO
613	ELSEIF ( bc_radiation_l ) THEN
614	DO lsp = 1, nspec
615	chem_species(lsp)%conc_p(:,:,nxl-1) = chem_species(lsp)%conc_p(:,:,nxl)
616	ENDDO
617	ELSEIF ( bc_radiation_r ) THEN
618	DO lsp = 1, nspec
619	chem_species(lsp)%conc_p(:,:,nxr+1) = chem_species(lsp)%conc_p(:,:,nxr)
620	ENDDO
621	ENDIF
622
623	END SELECT
624
625	END SUBROUTINE chem_boundary_conds
626
627	!
628	!------------------------------------------------------------------------------!
629	! Description:
630	! ------------
631	!> Boundary conditions for prognostic variables in chemistry: decycling in the
632	!> x-direction
633	!-----------------------------------------------------------------------------
634	SUBROUTINE chem_boundary_conds_decycle (cs_3d, cs_pr_init )
635	USE pegrid, &
636	ONLY: myid
637
638	IMPLICIT NONE
639	INTEGER(iwp) :: boundary !<
640	INTEGER(iwp) :: ee !<
641	INTEGER(iwp) :: copied !<
642	INTEGER(iwp) :: i !<
643	INTEGER(iwp) :: j !<
644	INTEGER(iwp) :: k !<
645	INTEGER(iwp) :: ss !<
646	REAL(wp), DIMENSION(nzb:nzt+1) :: cs_pr_init
647	REAL(wp), DIMENSION(nzb:nzt+1,nysg:nyng,nxlg:nxrg) :: cs_3d
648	REAL(wp) :: flag !< flag to mask topography grid points
649
650	flag = 0.0_wp
651
652
653	!-- Left and right boundaries
654	IF ( decycle_chem_lr .AND. bc_lr_cyc ) THEN
655
656	DO boundary = 1, 2
657
658	IF ( decycle_method(boundary) == 'dirichlet' ) THEN
659	!
660	!-- Initial profile is copied to ghost and first three layers
661	ss = 1
662	ee = 0
663	IF ( boundary == 1 .AND. nxl == 0 ) THEN
664	ss = nxlg
665	ee = nxl+2
666	ELSEIF ( boundary == 2 .AND. nxr == nx ) THEN
667	ss = nxr-2
668	ee = nxrg
669	ENDIF
670
671	DO i = ss, ee
672	DO j = nysg, nyng
673	DO k = nzb+1, nzt
674	flag = MERGE( 1.0_wp, 0.0_wp, &
675	BTEST( wall_flags_0(k,j,i), 0 ) )
676	cs_3d(k,j,i) = cs_pr_init(k) * flag
677	ENDDO
678	ENDDO
679	ENDDO
680
681	ELSEIF ( decycle_method(boundary) == 'neumann' ) THEN
682	!
683	!-- The value at the boundary is copied to the ghost layers to simulate
684	!-- an outlet with zero gradient
685	ss = 1
686	ee = 0
687	IF ( boundary == 1 .AND. nxl == 0 ) THEN
688	ss = nxlg
689	ee = nxl-1
690	copied = nxl
691	ELSEIF ( boundary == 2 .AND. nxr == nx ) THEN
692	ss = nxr+1
693	ee = nxrg
694	copied = nxr
695	ENDIF
696
697	DO i = ss, ee
698	DO j = nysg, nyng
699	DO k = nzb+1, nzt
700	flag = MERGE( 1.0_wp, 0.0_wp, &
701	BTEST( wall_flags_0(k,j,i), 0 ) )
702	cs_3d(k,j,i) = cs_3d(k,j,copied) * flag
703	ENDDO
704	ENDDO
705	ENDDO
706
707	ELSE
708	WRITE(message_string,*) &
709	'unknown decycling method: decycle_method (', &
710	boundary, ') ="' // TRIM( decycle_method(boundary) ) // '"'
711	CALL message( 'chem_boundary_conds_decycle', 'CM0431', &
712	1, 2, 0, 6, 0 )
713	ENDIF
714	ENDDO
715	ENDIF
716
717
718	!-- South and north boundaries
719	IF ( decycle_chem_ns .AND. bc_ns_cyc ) THEN
720
721	DO boundary = 3, 4
722
723	IF ( decycle_method(boundary) == 'dirichlet' ) THEN
724	!
725	!-- Initial profile is copied to ghost and first three layers
726	ss = 1
727	ee = 0
728	IF ( boundary == 3 .AND. nys == 0 ) THEN
729	ss = nysg
730	ee = nys+2
731	ELSEIF ( boundary == 4 .AND. nyn == ny ) THEN
732	ss = nyn-2
733	ee = nyng
734	ENDIF
735
736	DO i = nxlg, nxrg
737	DO j = ss, ee
738	DO k = nzb+1, nzt
739	flag = MERGE( 1.0_wp, 0.0_wp, &
740	BTEST( wall_flags_0(k,j,i), 0 ) )
741	cs_3d(k,j,i) = cs_pr_init(k) * flag
742	ENDDO
743	ENDDO
744	ENDDO
745
746
747	ELSEIF ( decycle_method(boundary) == 'neumann' ) THEN
748	!
749	!-- The value at the boundary is copied to the ghost layers to simulate
750	!-- an outlet with zero gradient
751	ss = 1
752	ee = 0
753	IF ( boundary == 3 .AND. nys == 0 ) THEN
754	ss = nysg
755	ee = nys-1
756	copied = nys
757	ELSEIF ( boundary == 4 .AND. nyn == ny ) THEN
758	ss = nyn+1
759	ee = nyng
760	copied = nyn
761	ENDIF
762
763	DO i = nxlg, nxrg
764	DO j = ss, ee
765	DO k = nzb+1, nzt
766	flag = MERGE( 1.0_wp, 0.0_wp, &
767	BTEST( wall_flags_0(k,j,i), 0 ) )
768	cs_3d(k,j,i) = cs_3d(k,copied,i) * flag
769	ENDDO
770	ENDDO
771	ENDDO
772
773	ELSE
774	WRITE(message_string,*) &
775	'unknown decycling method: decycle_method (', &
776	boundary, ') ="' // TRIM( decycle_method(boundary) ) // '"'
777	CALL message( 'chem_boundary_conds_decycle', 'CM0432', &
778	1, 2, 0, 6, 0 )
779	ENDIF
780	ENDDO
781	ENDIF
782	END SUBROUTINE chem_boundary_conds_decycle
783	!
784	!------------------------------------------------------------------------------!
785	!
786	! Description:
787	! ------------
788	!> Subroutine for checking data output for chemical species
789	!------------------------------------------------------------------------------!
790
791	SUBROUTINE chem_check_data_output( var, unit, i, ilen, k )
792
793
794	USE control_parameters, &
795	ONLY: data_output, message_string
796
797	IMPLICIT NONE
798
799	CHARACTER (LEN=*) :: unit !<
800	CHARACTER (LEN=*) :: var !<
801
802	INTEGER(iwp) :: i, lsp
803	INTEGER(iwp) :: ilen
804	INTEGER(iwp) :: k
805
806	CHARACTER(len=16) :: spec_name
807
808	unit = 'illegal'
809
810	spec_name = TRIM(var(4:)) !< var 1:3 is 'kc_'.
811
812	DO lsp=1,nspec
813	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
814	unit = 'ppm'
815	ENDIF
816	! It is possible to plant PM10 and PM25 into the gasphase chemistry code
817	! as passive species (e.g. 'passive' in GASPHASE_PREPROC/mechanisms):
818	! set unit to micrograms per m**3 for PM10 and PM25 (PM2.5)
819	IF (spec_name(1:2) == 'PM') THEN
820	unit = 'kg m-3'
821	ENDIF
822	ENDDO
823
824	DO lsp=1,nphot
825	IF (TRIM(spec_name) == TRIM(phot_frequen(lsp)%name)) THEN
826	unit = 'sec-1'
827	ENDIF
828	ENDDO
829
830
831	RETURN
832	END SUBROUTINE chem_check_data_output
833	!
834	!------------------------------------------------------------------------------!
835	!
836	! Description:
837	! ------------
838	!> Subroutine for checking data output of profiles for chemistry model
839	!------------------------------------------------------------------------------!
840
841	SUBROUTINE chem_check_data_output_pr( variable, var_count, unit, dopr_unit )
842
843	USE arrays_3d
844	USE control_parameters, &
845	ONLY: data_output_pr, message_string, air_chemistry
846	USE indices
847	USE profil_parameter
848	USE statistics
849
850
851	IMPLICIT NONE
852
853	CHARACTER (LEN=*) :: unit !<
854	CHARACTER (LEN=*) :: variable !<
855	CHARACTER (LEN=*) :: dopr_unit
856	CHARACTER(len=16) :: spec_name
857
858	INTEGER(iwp) :: var_count, lsp !<
859
860
861	spec_name = TRIM(variable(4:))
862
863	IF ( .NOT. air_chemistry ) THEN
864	message_string = 'data_output_pr = ' // &
865	TRIM( data_output_pr(var_count) ) // ' is not imp' // &
866	'lemented for air_chemistry = .FALSE.'
867	CALL message( 'chem_check_parameters', 'CM0433', 1, 2, 0, 6, 0 )
868
869	ELSE
870	DO lsp = 1, nspec
871	IF (TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
872	cs_pr_count = cs_pr_count+1
873	cs_pr_index(cs_pr_count) = lsp
874	dopr_index(var_count) = pr_palm+cs_pr_count
875	dopr_unit = 'ppm'
876	IF (spec_name(1:2) == 'PM') THEN
877	dopr_unit = 'kg m-3'
878	ENDIF
879	hom(:,2, dopr_index(var_count),:) = SPREAD( zu, 2, statistic_regions+1 )
880	unit = dopr_unit
881	ENDIF
882	ENDDO
883	ENDIF
884
885	END SUBROUTINE chem_check_data_output_pr
886
887	!
888	!------------------------------------------------------------------------------!
889	! Description:
890	! ------------
891	!> Check parameters routine for chemistry_model_mod
892	!------------------------------------------------------------------------------!
893	SUBROUTINE chem_check_parameters
894
895	IMPLICIT NONE
896
897	LOGICAL :: found
898	INTEGER (iwp) :: lsp_usr !< running index for user defined chem spcs
899	INTEGER (iwp) :: lsp !< running index for chem spcs.
900
901
902	!!-- check for chemical reactions status
903	IF ( chem_gasphase_on ) THEN
904	message_string = 'Chemical reactions: ON'
905	CALL message( 'chem_check_parameters', 'CM0421', 0, 0, 0, 6, 0 )
906	ELSEIF ( .not. (chem_gasphase_on) ) THEN
907	message_string = 'Chemical reactions: OFF'
908	CALL message( 'chem_check_parameters', 'CM0422', 0, 0, 0, 6, 0 )
909	ENDIF
910
911	!-- check for chemistry time-step
912	IF ( call_chem_at_all_substeps ) THEN
913	message_string = 'Chemistry is calculated at all meteorology time-step'
914	CALL message( 'chem_check_parameters', 'CM0423', 0, 0, 0, 6, 0 )
915	ELSEIF ( .not. (call_chem_at_all_substeps) ) THEN
916	message_string = 'Sub-time-steps are skipped for chemistry time-steps'
917	CALL message( 'chem_check_parameters', 'CM0424', 0, 0, 0, 6, 0 )
918	ENDIF
919
920	!-- check for photolysis scheme
921	IF ( (photolysis_scheme /= 'simple') .AND. (photolysis_scheme /= 'constant') ) THEN
922	message_string = 'Incorrect photolysis scheme selected, please check spelling'
923	CALL message( 'chem_check_parameters', 'CM0425', 1, 2, 0, 6, 0 )
924	ENDIF
925
926	!-- check for decycling of chem species
927	IF ( (.not. any(decycle_method == 'neumann') ) .AND. (.not. any(decycle_method == 'dirichlet') ) ) THEN
928	message_string = 'Incorrect boundary conditions. Only neumann or ' &
929	// 'dirichlet &available for decycling chemical species '
930	CALL message( 'chem_check_parameters', 'CM0426', 1, 2, 0, 6, 0 )
931	ENDIF
932
933	!-- check for initial chem species input
934	lsp_usr = 1
935	lsp = 1
936	DO WHILE ( cs_name (lsp_usr) /= 'novalue')
937	found = .FALSE.
938	DO lsp = 1, nvar
939	IF ( TRIM(cs_name (lsp_usr)) == TRIM(chem_species(lsp)%name) ) THEN
940	found = .TRUE.
941	EXIT
942	ENDIF
943	ENDDO
944	IF ( .not. found ) THEN
945	message_string = 'Incorrect input for initial surface vaue: ' // TRIM(cs_name(lsp_usr))
946	CALL message( 'chem_check_parameters', 'CM0427', 0, 1, 0, 6, 0 )
947	ENDIF
948	lsp_usr = lsp_usr + 1
949	ENDDO
950
951	!-- check for surface emission flux chem species
952
953	lsp_usr = 1
954	lsp = 1
955	DO WHILE ( surface_csflux_name (lsp_usr) /= 'novalue')
956	found = .FALSE.
957	DO lsp = 1, nvar
958	IF ( TRIM(surface_csflux_name (lsp_usr)) == TRIM(chem_species(lsp)%name) ) THEN
959	found = .TRUE.
960	EXIT
961	ENDIF
962	ENDDO
963	IF ( .not. found ) THEN
964	message_string = 'Incorrect input of chemical species for surface emission fluxes: ' &
965	// TRIM(surface_csflux_name(lsp_usr))
966	CALL message( 'chem_check_parameters', 'CM0428', 0, 1, 0, 6, 0 )
967	ENDIF
968	lsp_usr = lsp_usr + 1
969	ENDDO
970
971	END SUBROUTINE chem_check_parameters
972
973	!
974	!------------------------------------------------------------------------------!
975	!
976	! Description:
977	! ------------
978	!> Subroutine defining 2D output variables for chemical species
979	!> @todo: Remove "mode" from argument list, not used.
980	!------------------------------------------------------------------------------!
981
982	SUBROUTINE chem_data_output_2d( av, variable, found, grid, mode, local_pf, &
983	two_d, nzb_do, nzt_do, fill_value )
984
985	USE indices
986
987	USE kinds
988
989	USE pegrid, ONLY: myid, threads_per_task
990
991	IMPLICIT NONE
992
993	CHARACTER (LEN=*) :: grid !<
994	CHARACTER (LEN=*) :: mode !<
995	CHARACTER (LEN=*) :: variable !<
996	INTEGER(iwp) :: av !< flag to control data output of instantaneous or time-averaged data
997	INTEGER(iwp) :: nzb_do !< lower limit of the domain (usually nzb)
998	INTEGER(iwp) :: nzt_do !< upper limit of the domain (usually nzt+1)
999	LOGICAL :: found !<
1000	LOGICAL :: two_d !< flag parameter that indicates 2D variables (horizontal cross sections)
1001	REAL(wp) :: fill_value
1002	REAL(wp), DIMENSION(nxl:nxr,nys:nyn,nzb:nzt+1) :: local_pf !<
1003
1004	!-- local variables.
1005	CHARACTER(len=16) :: spec_name
1006	INTEGER(iwp) :: lsp
1007	INTEGER(iwp) :: i !< grid index along x-direction
1008	INTEGER(iwp) :: j !< grid index along y-direction
1009	INTEGER(iwp) :: k !< grid index along z-direction
1010	INTEGER(iwp) :: m !< running index surface elements
1011	INTEGER(iwp) :: char_len !< length of a character string
1012	found = .TRUE.
1013	char_len = LEN_TRIM(variable)
1014
1015	spec_name = TRIM( variable(4:char_len-3) )
1016
1017	DO lsp=1,nspec
1018	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name) .AND. &
1019	( (variable(char_len-2:) == '_xy') .OR. &
1020	(variable(char_len-2:) == '_xz') .OR. &
1021	(variable(char_len-2:) == '_yz') ) ) THEN
1022	!
1023	!-- todo: remove or replace by "CALL message" mechanism (kanani)
1024	! IF(myid == 0) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
1025	! TRIM(chem_species(lsp)%name)
1026	IF (av == 0) THEN
1027	DO i = nxl, nxr
1028	DO j = nys, nyn
1029	DO k = nzb_do, nzt_do
1030	local_pf(i,j,k) = MERGE( &
1031	chem_species(lsp)%conc(k,j,i), &
1032	REAL( fill_value, KIND = wp ), &
1033	BTEST( wall_flags_0(k,j,i), 0 ) )
1034
1035
1036	ENDDO
1037	ENDDO
1038	ENDDO
1039
1040	ELSE
1041	DO i = nxl, nxr
1042	DO j = nys, nyn
1043	DO k = nzb_do, nzt_do
1044	local_pf(i,j,k) = MERGE( &
1045	chem_species(lsp)%conc(k,j,i), &
1046	REAL( fill_value, KIND = wp ), &
1047	BTEST( wall_flags_0(k,j,i), 0 ) )
1048	ENDDO
1049	ENDDO
1050	ENDDO
1051	ENDIF
1052	grid = 'zu'
1053	ENDIF
1054	ENDDO
1055
1056	RETURN
1057
1058	END SUBROUTINE chem_data_output_2d
1059
1060	!
1061	!------------------------------------------------------------------------------!
1062	!
1063	! Description:
1064	! ------------
1065	!> Subroutine defining 3D output variables for chemical species
1066	!------------------------------------------------------------------------------!
1067
1068	SUBROUTINE chem_data_output_3d( av, variable, found, local_pf, fill_value, nzb_do, nzt_do )
1069
1070
1071	USE indices
1072
1073	USE kinds
1074
1075
1076	IMPLICIT NONE
1077
1078	CHARACTER (LEN=*) :: variable !<
1079	INTEGER(iwp) :: av !<
1080	INTEGER(iwp) :: nzb_do !< lower limit of the data output (usually 0)
1081	INTEGER(iwp) :: nzt_do !< vertical upper limit of the data output (usually nz_do3d)
1082
1083	LOGICAL :: found !<
1084
1085	REAL(wp) :: fill_value !<
1086	REAL(sp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) :: local_pf
1087
1088
1089	!-- local variables
1090
1091	INTEGER :: i, j, k, lsp
1092	CHARACTER(len=16) :: spec_name
1093
1094
1095	found = .FALSE.
1096
1097	spec_name = TRIM(variable(4:))
1098
1099	DO lsp=1,nspec
1100	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
1101	!
1102	!-- todo: remove or replace by "CALL message" mechanism (kanani)
1103	! IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
1104	! TRIM(chem_species(lsp)%name)
1105
1106	IF (av == 0) THEN
1107	DO i = nxl, nxr
1108	DO j = nys, nyn
1109	DO k = nzb_do, nzt_do
1110	local_pf(i,j,k) = MERGE( &
1111	chem_species(lsp)%conc(k,j,i), &
1112	REAL( fill_value, KIND = wp ), &
1113	BTEST( wall_flags_0(k,j,i), 0 ) )
1114	ENDDO
1115	ENDDO
1116	ENDDO
1117
1118	ELSE
1119	DO i = nxl, nxr
1120	DO j = nys, nyn
1121	DO k = nzb_do, nzt_do
1122	local_pf(i,j,k) = MERGE( &
1123	chem_species(lsp)%conc_av(k,j,i),&
1124	REAL( fill_value, KIND = wp ), &
1125	BTEST( wall_flags_0(k,j,i), 0 ) )
1126	ENDDO
1127	ENDDO
1128	ENDDO
1129	ENDIF
1130
1131	found = .TRUE.
1132	ENDIF
1133	ENDDO
1134
1135	RETURN
1136	END SUBROUTINE chem_data_output_3d
1137	!
1138	!------------------------------------------------------------------------------!
1139	!
1140	! Description:
1141	! ------------
1142	!> Subroutine defining mask output variables for chemical species
1143	!------------------------------------------------------------------------------!
1144
1145	SUBROUTINE chem_data_output_mask( av, variable, found, local_pf )
1146
1147	USE control_parameters
1148	USE indices
1149	USE kinds
1150	USE pegrid, ONLY: myid, threads_per_task
1151
1152
1153	IMPLICIT NONE
1154
1155	CHARACTER (LEN=*):: variable !<
1156	INTEGER(iwp) :: av !< flag to control data output of instantaneous or time-averaged data
1157	LOGICAL :: found !<
1158	REAL(wp), DIMENSION(mask_size_l(mid,1),mask_size_l(mid,2),mask_size_l(mid,3)) :: &
1159	local_pf !<
1160
1161
1162	!-- local variables.
1163	CHARACTER(len=16) :: spec_name
1164	INTEGER(iwp) :: lsp
1165	INTEGER(iwp) :: i !< grid index along x-direction
1166	INTEGER(iwp) :: j !< grid index along y-direction
1167	INTEGER(iwp) :: k !< grid index along z-direction
1168	found = .TRUE.
1169
1170	spec_name = TRIM( variable(4:) )
1171	!av == 0
1172
1173	DO lsp=1,nspec
1174	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name) ) THEN
1175	!
1176	!-- todo: remove or replace by "CALL message" mechanism (kanani)
1177	! IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
1178	! TRIM(chem_species(lsp)%name)
1179	IF (av == 0) THEN
1180	DO i = 1, mask_size_l(mid,1)
1181	DO j = 1, mask_size_l(mid,2)
1182	DO k = 1, mask_size(mid,3)
1183	local_pf(i,j,k) = chem_species(lsp)%conc(mask_k(mid,k), &
1184	mask_j(mid,j), mask_i(mid,i))
1185	ENDDO
1186	ENDDO
1187	ENDDO
1188
1189	ELSE
1190	DO i = 1, mask_size_l(mid,1)
1191	DO j = 1, mask_size_l(mid,2)
1192	DO k = 1, mask_size_l(mid,3)
1193	local_pf(i,j,k) = chem_species(lsp)%conc_av(mask_k(mid,k), &
1194	mask_j(mid,j), mask_i(mid,i))
1195	ENDDO
1196	ENDDO
1197	ENDDO
1198	ENDIF
1199	found = .FALSE.
1200	ENDIF
1201	ENDDO
1202
1203	RETURN
1204
1205	END SUBROUTINE chem_data_output_mask
1206
1207	!
1208	!------------------------------------------------------------------------------!
1209	!
1210	! Description:
1211	! ------------
1212	!> Subroutine defining appropriate grid for netcdf variables.
1213	!> It is called out from subroutine netcdf.
1214	!------------------------------------------------------------------------------!
1215	SUBROUTINE chem_define_netcdf_grid( var, found, grid_x, grid_y, grid_z )
1216
1217	IMPLICIT NONE
1218
1219	CHARACTER (LEN=*), INTENT(IN) :: var !<
1220	LOGICAL, INTENT(OUT) :: found !<
1221	CHARACTER (LEN=*), INTENT(OUT) :: grid_x !<
1222	CHARACTER (LEN=*), INTENT(OUT) :: grid_y !<
1223	CHARACTER (LEN=*), INTENT(OUT) :: grid_z !<
1224
1225	found = .TRUE.
1226
1227	IF (var(1:3) == 'kc_') THEN !< always the same grid for chemistry variables
1228	grid_x = 'x'
1229	grid_y = 'y'
1230	grid_z = 'zu'
1231	ELSE
1232	found = .FALSE.
1233	grid_x = 'none'
1234	grid_y = 'none'
1235	grid_z = 'none'
1236	ENDIF
1237
1238
1239	END SUBROUTINE chem_define_netcdf_grid
1240	!
1241	!------------------------------------------------------------------------------!
1242	!
1243	! Description:
1244	! ------------
1245	!> Subroutine defining header output for chemistry model
1246	!------------------------------------------------------------------------------!
1247	SUBROUTINE chem_header ( io )
1248
1249	IMPLICIT NONE
1250
1251	INTEGER(iwp), INTENT(IN) :: io !< Unit of the output file
1252	INTEGER(iwp) :: lsp !< running index for chem spcs
1253	INTEGER(iwp) :: cs_fixed
1254	CHARACTER (LEN=80) :: docsflux_chr
1255	CHARACTER (LEN=80) :: docsinit_chr
1256
1257	!
1258	!-- Write chemistry model header
1259	WRITE( io, 1 )
1260
1261	!-- Gasphase reaction status
1262	IF ( chem_gasphase_on ) THEN
1263	WRITE( io, 2 )
1264	ELSE
1265	WRITE( io, 3 )
1266	ENDIF
1267
1268	! Chemistry time-step
1269	WRITE ( io, 4 ) cs_time_step
1270
1271	!-- Emission mode info
1272	IF ( mode_emis == "DEFAULT" ) THEN
1273	WRITE( io, 5 )
1274	ELSEIF ( mode_emis == "PARAMETERIZED" ) THEN
1275	WRITE( io, 6 )
1276	ELSEIF ( mode_emis == "PRE-PROCESSED" ) THEN
1277	WRITE( io, 7 )
1278	ENDIF
1279
1280	!-- Photolysis scheme info
1281	IF ( photolysis_scheme == "simple" ) THEN
1282	WRITE( io, 8 )
1283	ELSEIF (photolysis_scheme == "conastant" ) THEN
1284	WRITE( io, 9 )
1285	ENDIF
1286
1287	!-- Emission flux info
1288	lsp = 1
1289	docsflux_chr ='Chemical species for surface emission flux: '
1290	DO WHILE ( surface_csflux_name(lsp) /= 'novalue' )
1291	docsflux_chr = TRIM( docsflux_chr ) // ' ' // TRIM( surface_csflux_name(lsp) ) // ','
1292	IF ( LEN_TRIM( docsflux_chr ) >= 75 ) THEN
1293	WRITE ( io, 10 ) docsflux_chr
1294	docsflux_chr = ' '
1295	ENDIF
1296	lsp = lsp + 1
1297	ENDDO
1298
1299	IF ( docsflux_chr /= '' ) THEN
1300	WRITE ( io, 10 ) docsflux_chr
1301	ENDIF
1302
1303
1304	!-- initializatoin of Surface and profile chemical species
1305
1306	lsp = 1
1307	docsinit_chr ='Chemical species for initial surface and profile emissions: '
1308	DO WHILE ( cs_name(lsp) /= 'novalue' )
1309	docsinit_chr = TRIM( docsinit_chr ) // ' ' // TRIM( cs_name(lsp) ) // ','
1310	IF ( LEN_TRIM( docsinit_chr ) >= 75 ) THEN
1311	WRITE ( io, 11 ) docsinit_chr
1312	docsinit_chr = ' '
1313	ENDIF
1314	lsp = lsp + 1
1315	ENDDO
1316
1317	IF ( docsinit_chr /= '' ) THEN
1318	WRITE ( io, 11 ) docsinit_chr
1319	ENDIF
1320
1321	!-- number of variable and fix chemical species and number of reactions
1322	cs_fixed = nspec - nvar
1323	WRITE ( io, * ) ' --> Chemical species, variable: ', nvar
1324	WRITE ( io, * ) ' --> Chemical species, fixed : ', cs_fixed
1325	WRITE ( io, * ) ' --> Total number of reactions : ', nreact
1326
1327
1328	1 FORMAT (//' Chemistry model information:'/ &
1329	' ----------------------------'/)
1330	2 FORMAT (' --> Chemical reactions are turned on')
1331	3 FORMAT (' --> Chemical reactions are turned off')
1332	4 FORMAT (' --> Time-step for chemical species: ',F6.2, ' s')
1333	5 FORMAT (' --> Emission mode = DEFAULT ')
1334	6 FORMAT (' --> Emission mode = PARAMETERIZED ')
1335	7 FORMAT (' --> Emission mode = PRE-PROCESSED ')
1336	8 FORMAT (' --> Photolysis scheme used = simple ')
1337	9 FORMAT (' --> Photolysis scheme used = constant ')
1338	10 FORMAT (/' ',A)
1339	11 FORMAT (/' ',A)
1340	!
1341	!
1342	END SUBROUTINE chem_header
1343
1344	!
1345	!------------------------------------------------------------------------------!
1346	!
1347	! Description:
1348	! ------------
1349	!> Subroutine initializating chemistry_model_mod
1350	!------------------------------------------------------------------------------!
1351	SUBROUTINE chem_init
1352
1353	USE control_parameters, &
1354	ONLY: message_string, io_blocks, io_group, turbulent_inflow
1355	USE arrays_3d, &
1356	ONLY: mean_inflow_profiles
1357	USE pegrid
1358
1359	IMPLICIT none
1360	!-- local variables
1361	INTEGER :: i,j !< running index for for horiz numerical grid points
1362	INTEGER :: lsp !< running index for chem spcs
1363	INTEGER :: lpr_lev !< running index for chem spcs profile level
1364	!
1365	!-- NOPOINTER version not implemented yet
1366	! #if defined( __nopointer )
1367	! message_string = 'The chemistry module only runs with POINTER version'
1368	! CALL message( 'chemistry_model_mod', 'CM0001', 1, 2, 0, 6, 0 )
1369	! #endif
1370	!
1371	!-- Allocate memory for chemical species
1372	ALLOCATE( chem_species(nspec) )
1373	ALLOCATE( spec_conc_1 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
1374	ALLOCATE( spec_conc_2 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
1375	ALLOCATE( spec_conc_3 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
1376	ALLOCATE( spec_conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
1377	ALLOCATE( phot_frequen(nphot) )
1378	ALLOCATE( freq_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nphot) )
1379	ALLOCATE( bc_cs_t_val(nspec) )
1380	!
1381	!-- Initialize arrays
1382	spec_conc_1 (:,:,:,:) = 0.0_wp
1383	spec_conc_2 (:,:,:,:) = 0.0_wp
1384	spec_conc_3 (:,:,:,:) = 0.0_wp
1385	spec_conc_av(:,:,:,:) = 0.0_wp
1386
1387
1388	DO lsp = 1, nspec
1389	chem_species(lsp)%name = spc_names(lsp)
1390
1391	chem_species(lsp)%conc (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1 (:,:,:,lsp)
1392	chem_species(lsp)%conc_p (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2 (:,:,:,lsp)
1393	chem_species(lsp)%tconc_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_3 (:,:,:,lsp)
1394	chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_av(:,:,:,lsp)
1395
1396	ALLOCATE (chem_species(lsp)%cssws_av(nysg:nyng,nxlg:nxrg))
1397	chem_species(lsp)%cssws_av = 0.0_wp
1398	!
1399	!-- The following block can be useful when emission module is not applied. &
1400	!-- if emission module is applied the following block will be overwritten.
1401	ALLOCATE (chem_species(lsp)%flux_s_cs(nzb+1:nzt,0:threads_per_task-1))
1402	ALLOCATE (chem_species(lsp)%diss_s_cs(nzb+1:nzt,0:threads_per_task-1))
1403	ALLOCATE (chem_species(lsp)%flux_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
1404	ALLOCATE (chem_species(lsp)%diss_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
1405	chem_species(lsp)%flux_s_cs = 0.0_wp
1406	chem_species(lsp)%flux_l_cs = 0.0_wp
1407	chem_species(lsp)%diss_s_cs = 0.0_wp
1408	chem_species(lsp)%diss_l_cs = 0.0_wp
1409	!
1410	!-- Allocate memory for initial concentration profiles
1411	!-- (concentration values come from namelist)
1412	!-- (@todo (FK): Because of this, chem_init is called in palm before
1413	!-- check_parameters, since conc_pr_init is used there.
1414	!-- We have to find another solution since chem_init should
1415	!-- eventually be called from init_3d_model!!)
1416	ALLOCATE ( chem_species(lsp)%conc_pr_init(0:nz+1) )
1417	chem_species(lsp)%conc_pr_init(:) = 0.0_wp
1418
1419	ENDDO
1420
1421	!
1422	!-- Initial concentration of profiles is prescribed by parameters cs_profile
1423	!-- and cs_heights in the namelist &chemistry_parameters
1424	CALL chem_init_profiles
1425
1426
1427	!
1428	!-- Initialize model variables
1429
1430
1431	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1432	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1433
1434
1435	!-- First model run of a possible job queue.
1436	!-- Initial profiles of the variables must be computed.
1437	IF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
1438	CALL location_message( 'initializing with 1D chemistry model profiles', .FALSE. )
1439	!
1440	!-- Transfer initial profiles to the arrays of the 3D model
1441	DO lsp = 1, nspec
1442	DO i = nxlg, nxrg
1443	DO j = nysg, nyng
1444	DO lpr_lev = 1, nz + 1
1445	chem_species(lsp)%conc(lpr_lev,j,i) = chem_species(lsp)%conc_pr_init(lpr_lev)
1446	ENDDO
1447	ENDDO
1448	ENDDO
1449	ENDDO
1450
1451	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
1452	THEN
1453	CALL location_message( 'initializing with constant chemistry profiles', .FALSE. )
1454
1455	DO lsp = 1, nspec
1456	DO i = nxlg, nxrg
1457	DO j = nysg, nyng
1458	chem_species(lsp)%conc(:,j,i) = chem_species(lsp)%conc_pr_init
1459	ENDDO
1460	ENDDO
1461	ENDDO
1462
1463	ENDIF
1464
1465	!
1466	!-- If required, change the surface chem spcs at the start of the 3D run
1467	IF ( cs_surface_initial_change(1) /= 0.0_wp ) THEN
1468	DO lsp = 1, nspec
1469	chem_species(lsp)%conc(nzb,:,:) = chem_species(lsp)%conc(nzb,:,:) + &
1470	cs_surface_initial_change(lsp)
1471	ENDDO
1472	ENDIF
1473	!
1474	!-- Initiale old and new time levels.
1475	DO lsp = 1, nvar
1476	chem_species(lsp)%tconc_m = 0.0_wp
1477	chem_species(lsp)%conc_p = chem_species(lsp)%conc
1478	ENDDO
1479
1480	ENDIF
1481
1482
1483
1484	!--- new code add above this line
1485	DO lsp = 1, nphot
1486	phot_frequen(lsp)%name = phot_names(lsp)
1487	!
1488	!-- todo: remove or replace by "CALL message" mechanism (kanani)
1489	! IF( myid == 0 ) THEN
1490	! WRITE(6,'(a,i4,3x,a)') 'Photolysis: ',lsp,trim(phot_names(lsp))
1491	! ENDIF
1492	phot_frequen(lsp)%freq(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => freq_1(:,:,:,lsp)
1493	ENDDO
1494
1495	RETURN
1496
1497	END SUBROUTINE chem_init
1498
1499	!
1500	!------------------------------------------------------------------------------!
1501	!
1502	! Description:
1503	! ------------
1504	!> Subroutine defining initial vertical profiles of chemical species (given by
1505	!> namelist parameters chem_profiles and chem_heights) --> which should work
1506	!> analogue to parameters u_profile, v_profile and uv_heights)
1507	!------------------------------------------------------------------------------!
1508	SUBROUTINE chem_init_profiles !< SUBROUTINE is called from chem_init in case of
1509	!< TRIM( initializing_actions ) /= 'read_restart_data'
1510	!< We still need to see what has to be done in case of restart run
1511	USE chem_modules
1512
1513	IMPLICIT NONE
1514
1515	!-- Local variables
1516	INTEGER :: lsp !< running index for number of species in derived data type species_def
1517	INTEGER :: lsp_usr !< running index for number of species (user defined) in cs_names, cs_profiles etc
1518	INTEGER :: lpr_lev !< running index for profile level for each chem spcs.
1519	INTEGER :: npr_lev !< the next available profile lev
1520
1521	!-----------------
1522	!-- Parameter "cs_profile" and "cs_heights" are used to prescribe user defined initial profiles
1523	!-- and heights. If parameter "cs_profile" is not prescribed then initial surface values
1524	!-- "cs_surface" are used as constant initial profiles for each species. If "cs_profile" and
1525	!-- "cs_heights" are prescribed, their values will!override the constant profile given by
1526	!-- "cs_surface".
1527	!
1528	IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1529	lsp_usr = 1
1530	DO WHILE ( TRIM( cs_name( lsp_usr ) ) /= 'novalue' ) !'novalue' is the default
1531	DO lsp = 1, nspec !
1532	!-- create initial profile (conc_pr_init) for each chemical species
1533	IF ( TRIM( chem_species(lsp)%name ) == TRIM( cs_name(lsp_usr) ) ) THEN !
1534	IF ( cs_profile(lsp_usr,1) == 9999999.9_wp ) THEN
1535	!-- set a vertically constant profile based on the surface conc (cs_surface(lsp_usr)) of each species
1536	DO lpr_lev = 0, nzt+1
1537	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_surface(lsp_usr)
1538	ENDDO
1539	ELSE
1540	IF ( cs_heights(1,1) /= 0.0_wp ) THEN
1541	message_string = 'The surface value of cs_heights must be 0.0'
1542	CALL message( 'chem_check_parameters', 'CM0434', 1, 2, 0, 6, 0 )
1543	ENDIF
1544
1545	use_prescribed_profile_data = .TRUE.
1546
1547	npr_lev = 1
1548	! chem_species(lsp)%conc_pr_init(0) = 0.0_wp
1549	DO lpr_lev = 1, nz+1
1550	IF ( npr_lev < 100 ) THEN
1551	DO WHILE ( cs_heights(lsp_usr, npr_lev+1) <= zu(lpr_lev) )
1552	npr_lev = npr_lev + 1
1553	IF ( npr_lev == 100 ) THEN
1554	message_string = 'number of chem spcs exceeding the limit'
1555	CALL message( 'chem_check_parameters', 'CM0435', 1, 2, 0, 6, 0 )
1556	EXIT
1557	ENDIF
1558	ENDDO
1559	ENDIF
1560	IF ( npr_lev < 100 .AND. cs_heights(lsp_usr, npr_lev + 1) /= 9999999.9_wp ) THEN
1561	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp_usr, npr_lev) + &
1562	( zu(lpr_lev) - cs_heights(lsp_usr, npr_lev) ) / &
1563	( cs_heights(lsp_usr, (npr_lev + 1)) - cs_heights(lsp_usr, npr_lev ) ) * &
1564	( cs_profile(lsp_usr, (npr_lev + 1)) - cs_profile(lsp_usr, npr_lev ) )
1565	ELSE
1566	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp_usr, npr_lev)
1567	ENDIF
1568	ENDDO
1569	ENDIF
1570	!-- If a profile is prescribed explicity using cs_profiles and cs_heights, then
1571	!-- chem_species(lsp)%conc_pr_init is populated with the specific "lsp" based
1572	!-- on the cs_profiles(lsp_usr,:) and cs_heights(lsp_usr,:).
1573	ENDIF
1574	ENDDO
1575	lsp_usr = lsp_usr + 1
1576	ENDDO
1577	ENDIF
1578
1579	END SUBROUTINE chem_init_profiles
1580	!
1581	!------------------------------------------------------------------------------!
1582	!
1583	! Description:
1584	! ------------
1585	!> Subroutine to integrate chemical species in the given chemical mechanism
1586	!------------------------------------------------------------------------------!
1587
1588	SUBROUTINE chem_integrate_ij (i, j)
1589
1590	USE cpulog, &
1591	ONLY: cpu_log, log_point
1592	USE statistics, &
1593	ONLY: weight_pres
1594	USE control_parameters, &
1595	ONLY: dt_3d, intermediate_timestep_count,simulated_time
1596
1597	IMPLICIT none
1598	INTEGER,INTENT(IN) :: i,j
1599
1600	!-- local variables
1601	INTEGER(iwp) :: lsp !< running index for chem spcs.
1602	INTEGER(iwp) :: lph !< running index for photolysis frequencies
1603	INTEGER :: k,m,istatf
1604	INTEGER,DIMENSION(20) :: istatus
1605	REAL(kind=wp),DIMENSION(nzb+1:nzt,nspec) :: tmp_conc
1606	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_temp
1607	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_qvap
1608	REAL(kind=wp),DIMENSION(nzb+1:nzt,nphot) :: tmp_phot
1609	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_fact
1610	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_fact_i !< conversion factor between
1611	!< molecules cm^{-3} and ppm
1612
1613	INTEGER,DIMENSION(nzb+1:nzt) :: nacc !< Number of accepted steps
1614	INTEGER,DIMENSION(nzb+1:nzt) :: nrej !< Number of rejected steps
1615
1616	REAL(wp) :: conv !< conversion factor
1617	REAL(wp), PARAMETER :: ppm2fr = 1.0e-6_wp !< Conversion factor ppm to fraction
1618	REAL(wp), PARAMETER :: xm_air = 28.96_wp !< Mole mass of dry air
1619	REAL(wp), PARAMETER :: xm_h2o = 18.01528_wp !< Mole mass of water vapor
1620	REAL(wp), PARAMETER :: pref_i = 1._wp / 100000.0_wp !< inverse reference pressure (1/Pa)
1621	REAL(wp), PARAMETER :: t_std = 273.15_wp !< standard pressure (Pa)
1622	REAL(wp), PARAMETER :: p_std = 101325.0_wp !< standard pressure (Pa)
1623	REAL(wp), PARAMETER :: vmolcm = 22.414e3_wp !< Mole volume (22.414 l) in cm^{-3}
1624	REAL(wp), PARAMETER :: xna = 6.022e23_wp !< Avogadro number (molecules/mol)
1625
1626	REAL(wp),DIMENSION(size(rcntrl)) :: rcntrl_local
1627
1628
1629	REAL(kind=wp) :: dt_chem
1630
1631	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'start' )
1632	!< set chem_gasphase_on to .FALSE. if you want to skip computation of gas phase chemistry
1633	IF (chem_gasphase_on) THEN
1634	nacc = 0
1635	nrej = 0
1636
1637	tmp_temp(:) = pt(nzb+1:nzt,j,i) * exner(nzb+1:nzt)
1638	! ppm to molecules/cm**3
1639	! tmp_fact = 1.e-6_wp6.022e23_wp/(22.414_wp1000._wp) * 273.15_wp * hyp(nzb+1:nzt)/( 101300.0_wp * tmp_temp )
1640	conv = ppm2fr * xna / vmolcm
1641	tmp_fact(:) = conv * t_std * hyp(nzb+1:nzt) / (tmp_temp(:) * p_std)
1642	tmp_fact_i = 1.0_wp/tmp_fact
1643
1644	IF ( humidity ) THEN
1645	IF ( bulk_cloud_model ) THEN
1646	tmp_qvap(:) = ( q(nzb+1:nzt,j,i) - ql(nzb+1:nzt,j,i) ) * xm_air/xm_h2o * tmp_fact(:)
1647	ELSE
1648	tmp_qvap(:) = q(nzb+1:nzt,j,i) * xm_air/xm_h2o * tmp_fact(:)
1649	ENDIF
1650	ELSE
1651	tmp_qvap(:) = 0.01 * tmp_fact(:) !< Constant value for q if water vapor is not computed
1652	ENDIF
1653
1654	DO lsp = 1,nspec
1655	tmp_conc(:,lsp) = chem_species(lsp)%conc(nzb+1:nzt,j,i) * tmp_fact(:)
1656	ENDDO
1657
1658	DO lph = 1,nphot
1659	tmp_phot(:,lph) = phot_frequen(lph)%freq(nzb+1:nzt,j,i)
1660	ENDDO
1661	!
1662	!-- todo: remove (kanani)
1663	! IF(myid == 0 .AND. chem_debug0 ) THEN
1664	! IF (i == 10 .and. j == 10) WRITE(0,*) 'begin chemics step ',dt_3d
1665	! ENDIF
1666
1667	!-- Compute length of time step
1668	IF ( call_chem_at_all_substeps ) THEN
1669	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
1670	ELSE
1671	dt_chem = dt_3d
1672	ENDIF
1673
1674	cs_time_step = dt_chem
1675
1676	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'start' )
1677
1678	IF(maxval(rcntrl) > 0.0) THEN ! Only if rcntrl is set
1679	IF( simulated_time <= 2*dt_3d) THEN
1680	rcntrl_local = 0
1681	!
1682	!-- todo: remove (kanani)
1683	! WRITE(9,'(a,2f10.3)') 'USE Default rcntrl in the first steps ',simulated_time,dt_3d
1684	ELSE
1685	rcntrl_local = rcntrl
1686	ENDIF
1687	ELSE
1688	rcntrl_local = 0
1689	END IF
1690
1691	CALL chem_gasphase_integrate (dt_chem, tmp_conc, tmp_temp, tmp_qvap, tmp_fact, tmp_phot, &
1692	icntrl_i = icntrl, rcntrl_i = rcntrl_local, xnacc = nacc, xnrej = nrej, istatus=istatus)
1693
1694	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'stop' )
1695
1696	DO lsp = 1,nspec
1697	chem_species(lsp)%conc (nzb+1:nzt,j,i) = tmp_conc(:,lsp) * tmp_fact_i(:)
1698	ENDDO
1699
1700
1701	ENDIF
1702	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'stop' )
1703
1704	RETURN
1705	END SUBROUTINE chem_integrate_ij
1706	!
1707	!------------------------------------------------------------------------------!
1708	!
1709	! Description:
1710	! ------------
1711	!> Subroutine defining parin for &chemistry_parameters for chemistry model
1712	!------------------------------------------------------------------------------!
1713	SUBROUTINE chem_parin
1714
1715	USE chem_modules
1716	USE control_parameters
1717
1718	USE kinds
1719	USE pegrid
1720	USE statistics
1721
1722	IMPLICIT NONE
1723
1724	CHARACTER (LEN=80) :: line !< dummy string that contains the current line of the parameter file
1725	CHARACTER (LEN=3) :: cs_prefix
1726
1727	REAL(wp), DIMENSION(nmaxfixsteps) :: my_steps !< List of fixed timesteps my_step(1) = 0.0 automatic stepping
1728	INTEGER(iwp) :: i !<
1729	INTEGER(iwp) :: j !<
1730	INTEGER(iwp) :: max_pr_cs_tmp !<
1731
1732
1733	NAMELIST /chemistry_parameters/ bc_cs_b, &
1734	bc_cs_t, &
1735	call_chem_at_all_substeps, &
1736	chem_debug0, &
1737	chem_debug1, &
1738	chem_debug2, &
1739	chem_gasphase_on, &
1740	cs_heights, &
1741	cs_name, &
1742	cs_profile, &
1743	cs_profile_name, &
1744	cs_surface, &
1745	decycle_chem_lr, &
1746	decycle_chem_ns, &
1747	decycle_method, &
1748	emiss_factor_main, &
1749	emiss_factor_side, &
1750	icntrl, &
1751	main_street_id, &
1752	max_street_id, &
1753	my_steps, &
1754	nest_chemistry, &
1755	rcntrl, &
1756	side_street_id, &
1757	photolysis_scheme, &
1758	wall_csflux, &
1759	cs_vertical_gradient, &
1760	top_csflux, &
1761	surface_csflux, &
1762	surface_csflux_name, &
1763	cs_surface_initial_change, &
1764	cs_vertical_gradient_level, &
1765	! namelist parameters for emissions
1766	mode_emis, &
1767	time_fac_type, &
1768	daytype_mdh, &
1769	do_emis
1770
1771	!-- analogue to chem_names(nspj) we could invent chem_surfaceflux(nspj) and chem_topflux(nspj)
1772	!-- so this way we could prescribe a specific flux value for each species
1773	!> chemistry_parameters for initial profiles
1774	!> cs_names = 'O3', 'NO2', 'NO', ... to set initial profiles)
1775	!> cs_heights(1,:) = 0.0, 100.0, 500.0, 2000.0, .... (height levels where concs will be prescribed for O3)
1776	!> cs_heights(2,:) = 0.0, 200.0, 400.0, 1000.0, .... (same for NO2 etc.)
1777	!> cs_profiles(1,:) = 10.0, 20.0, 20.0, 30.0, ..... (chem spcs conc at height lvls chem_heights(1,:)) etc.
1778	!> If the respective concentration profile should be constant with height, then use "cs_surface( number of spcs)"
1779	!> then write these cs_surface values to chem_species(lsp)%conc_pr_init(:)
1780
1781	!
1782	!-- Read chem namelist
1783
1784	INTEGER :: ier
1785	CHARACTER(LEN=64) :: text
1786	CHARACTER(LEN=8) :: solver_type
1787
1788	icntrl = 0
1789	rcntrl = 0.0_wp
1790	my_steps = 0.0_wp
1791	photolysis_scheme = 'simple'
1792	atol = 1.0_wp
1793	rtol = 0.01_wp
1794	!
1795	!-- Try to find chemistry package
1796	REWIND ( 11 )
1797	line = ' '
1798	DO WHILE ( INDEX( line, '&chemistry_parameters' ) == 0 )
1799	READ ( 11, '(A)', END=20 ) line
1800	ENDDO
1801	BACKSPACE ( 11 )
1802	!
1803	!-- Read chemistry namelist
1804	READ ( 11, chemistry_parameters, ERR = 10, END = 20 )
1805	!
1806	!-- Enable chemistry model
1807	air_chemistry = .TRUE.
1808	GOTO 20
1809
1810	10 BACKSPACE( 11 )
1811	READ( 11 , '(A)') line
1812	CALL parin_fail_message( 'chemistry_parameters', line )
1813
1814	20 CONTINUE
1815
1816	!
1817	!-- check for emission mode for chem species
1818	IF ( (mode_emis /= 'PARAMETERIZED') .AND. ( mode_emis /= 'DEFAULT') .AND. (mode_emis /= 'PRE-PROCESSED' ) ) THEN
1819	message_string = 'Incorrect mode_emiss option select. Please check spelling'
1820	CALL message( 'chem_check_parameters', 'CM0436', 1, 2, 0, 6, 0 )
1821	ENDIF
1822
1823	t_steps = my_steps
1824
1825	!-- Determine the number of user-defined profiles and append them to the
1826	!-- standard data output (data_output_pr)
1827	max_pr_cs_tmp = 0
1828	i = 1
1829
1830	DO WHILE ( data_output_pr(i) /= ' ' .AND. i <= 100 )
1831	IF ( TRIM( data_output_pr(i)(1:3)) == 'kc_' ) THEN
1832	max_pr_cs_tmp = max_pr_cs_tmp+1
1833	ENDIF
1834	i = i +1
1835	ENDDO
1836
1837	IF ( max_pr_cs_tmp > 0 ) THEN
1838	cs_pr_namelist_found = .TRUE.
1839	max_pr_cs = max_pr_cs_tmp
1840	ENDIF
1841
1842	! Set Solver Type
1843	IF(icntrl(3) == 0) THEN
1844	solver_type = 'rodas3' !Default
1845	ELSE IF(icntrl(3) == 1) THEN
1846	solver_type = 'ros2'
1847	ELSE IF(icntrl(3) == 2) THEN
1848	solver_type = 'ros3'
1849	ELSE IF(icntrl(3) == 3) THEN
1850	solver_type = 'ro4'
1851	ELSE IF(icntrl(3) == 4) THEN
1852	solver_type = 'rodas3'
1853	ELSE IF(icntrl(3) == 5) THEN
1854	solver_type = 'rodas4'
1855	ELSE IF(icntrl(3) == 6) THEN
1856	solver_type = 'Rang3'
1857	ELSE
1858	message_string = 'illegal solver type'
1859	CALL message( 'chem_parin', 'PA0506', 1, 2, 0, 6, 0 )
1860	END IF
1861
1862	!
1863	!-- todo: remove or replace by "CALL message" mechanism (kanani)
1864	! write(text,*) 'gas_phase chemistry: solver_type = ',trim(solver_type)
1865	!kk Has to be changed to right calling sequence
1866	!kk CALL location_message( trim(text), .FALSE. )
1867	! IF(myid == 0) THEN
1868	! write(9,*) ' '
1869	! write(9,*) 'kpp setup '
1870	! write(9,*) ' '
1871	! write(9,*) ' gas_phase chemistry: solver_type = ',trim(solver_type)
1872	! write(9,*) ' '
1873	! write(9,*) ' Hstart = ',rcntrl(3)
1874	! write(9,*) ' FacMin = ',rcntrl(4)
1875	! write(9,*) ' FacMax = ',rcntrl(5)
1876	! write(9,*) ' '
1877	! IF(vl_dim > 1) THEN
1878	! write(9,*) ' Vector mode vektor length = ',vl_dim
1879	! ELSE
1880	! write(9,*) ' Scalar mode'
1881	! ENDIF
1882	! write(9,*) ' '
1883	! END IF
1884
1885	RETURN
1886
1887	END SUBROUTINE chem_parin
1888
1889	!
1890	!------------------------------------------------------------------------------!
1891	!
1892	! Description:
1893	! ------------
1894	!> Subroutine calculating prognostic equations for chemical species
1895	!> (vector-optimized).
1896	!> Routine is called separately for each chemical species over a loop from
1897	!> prognostic_equations.
1898	!------------------------------------------------------------------------------!
1899	SUBROUTINE chem_prognostic_equations ( cs_scalar_p, cs_scalar, tcs_scalar_m, &
1900	pr_init_cs, ilsp )
1901
1902	USE advec_s_pw_mod, &
1903	ONLY: advec_s_pw
1904	USE advec_s_up_mod, &
1905	ONLY: advec_s_up
1906	USE advec_ws, &
1907	ONLY: advec_s_ws
1908	USE diffusion_s_mod, &
1909	ONLY: diffusion_s
1910	USE indices, &
1911	ONLY: nxl, nxr, nyn, nys, wall_flags_0
1912	USE pegrid
1913	USE surface_mod, &
1914	ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
1915	surf_usm_v
1916
1917	IMPLICIT NONE
1918
1919	INTEGER :: i !< running index
1920	INTEGER :: j !< running index
1921	INTEGER :: k !< running index
1922
1923	INTEGER(iwp),INTENT(IN) :: ilsp !<
1924
1925	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
1926
1927	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar !<
1928	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p !<
1929	REAL(wp), DIMENSION(:,:,:), POINTER :: tcs_scalar_m !<
1930
1931
1932	!
1933	!-- Tendency terms for chemical species
1934	tend = 0.0_wp
1935	!
1936	!-- Advection terms
1937	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1938	IF ( ws_scheme_sca ) THEN
1939	CALL advec_s_ws( cs_scalar, 'kc' )
1940	ELSE
1941	CALL advec_s_pw( cs_scalar )
1942	ENDIF
1943	ELSE
1944	CALL advec_s_up( cs_scalar )
1945	ENDIF
1946	!
1947	!-- Diffusion terms (the last three arguments are zero)
1948	CALL diffusion_s( cs_scalar, &
1949	surf_def_h(0)%cssws(ilsp,:), &
1950	surf_def_h(1)%cssws(ilsp,:), &
1951	surf_def_h(2)%cssws(ilsp,:), &
1952	surf_lsm_h%cssws(ilsp,:), &
1953	surf_usm_h%cssws(ilsp,:), &
1954	surf_def_v(0)%cssws(ilsp,:), &
1955	surf_def_v(1)%cssws(ilsp,:), &
1956	surf_def_v(2)%cssws(ilsp,:), &
1957	surf_def_v(3)%cssws(ilsp,:), &
1958	surf_lsm_v(0)%cssws(ilsp,:), &
1959	surf_lsm_v(1)%cssws(ilsp,:), &
1960	surf_lsm_v(2)%cssws(ilsp,:), &
1961	surf_lsm_v(3)%cssws(ilsp,:), &
1962	surf_usm_v(0)%cssws(ilsp,:), &
1963	surf_usm_v(1)%cssws(ilsp,:), &
1964	surf_usm_v(2)%cssws(ilsp,:), &
1965	surf_usm_v(3)%cssws(ilsp,:) )
1966	!
1967	!-- Prognostic equation for chemical species
1968	DO i = nxl, nxr
1969	DO j = nys, nyn
1970	DO k = nzb+1, nzt
1971	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) &
1972	+ ( dt_3d * &
1973	( tsc(2) * tend(k,j,i) &
1974	+ tsc(3) * tcs_scalar_m(k,j,i) &
1975	) &
1976	- tsc(5) * rdf_sc(k) &
1977	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
1978	) &
1979	* MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_0(k,j,i), 0 ) )
1980
1981	IF ( cs_scalar_p(k,j,i) < 0.0_wp ) cs_scalar_p(k,j,i) = 0.1_wp * cs_scalar(k,j,i)
1982	ENDDO
1983	ENDDO
1984	ENDDO
1985	!
1986	!-- Calculate tendencies for the next Runge-Kutta step
1987	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1988	IF ( intermediate_timestep_count == 1 ) THEN
1989	DO i = nxl, nxr
1990	DO j = nys, nyn
1991	DO k = nzb+1, nzt
1992	tcs_scalar_m(k,j,i) = tend(k,j,i)
1993	ENDDO
1994	ENDDO
1995	ENDDO
1996	ELSEIF ( intermediate_timestep_count < &
1997	intermediate_timestep_count_max ) THEN
1998	DO i = nxl, nxr
1999	DO j = nys, nyn
2000	DO k = nzb+1, nzt
2001	tcs_scalar_m(k,j,i) = - 9.5625_wp * tend(k,j,i) &
2002	+ 5.3125_wp * tcs_scalar_m(k,j,i)
2003	ENDDO
2004	ENDDO
2005	ENDDO
2006	ENDIF
2007	ENDIF
2008
2009	END SUBROUTINE chem_prognostic_equations
2010
2011	!------------------------------------------------------------------------------!
2012	!
2013	! Description:
2014	! ------------
2015	!> Subroutine calculating prognostic equations for chemical species
2016	!> (cache-optimized).
2017	!> Routine is called separately for each chemical species over a loop from
2018	!> prognostic_equations.
2019	!------------------------------------------------------------------------------!
2020	SUBROUTINE chem_prognostic_equations_ij ( cs_scalar_p, cs_scalar, tcs_scalar_m, pr_init_cs, &
2021	i, j, i_omp_start, tn, ilsp, flux_s_cs, diss_s_cs, &
2022	flux_l_cs, diss_l_cs )
2023	USE pegrid
2024	USE advec_ws, ONLY: advec_s_ws
2025	USE advec_s_pw_mod, ONLY: advec_s_pw
2026	USE advec_s_up_mod, ONLY: advec_s_up
2027	USE diffusion_s_mod, ONLY: diffusion_s
2028	USE indices, ONLY: wall_flags_0
2029	USE surface_mod, ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
2030	surf_usm_v
2031
2032
2033	IMPLICIT NONE
2034
2035	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p, cs_scalar, tcs_scalar_m
2036
2037	INTEGER(iwp),INTENT(IN) :: i, j, i_omp_start, tn, ilsp
2038	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: flux_s_cs !<
2039	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: diss_s_cs !<
2040	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: flux_l_cs !<
2041	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: diss_l_cs !<
2042	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
2043
2044	!-- local variables
2045
2046	INTEGER :: k
2047	!
2048	!-- Tendency-terms for chem spcs.
2049	tend(:,j,i) = 0.0_wp
2050	!
2051	!-- Advection terms
2052	IF ( timestep_scheme(1:5) == 'runge' ) THEN
2053	IF ( ws_scheme_sca ) THEN
2054	CALL advec_s_ws( i, j, cs_scalar, 'kc', flux_s_cs, diss_s_cs, &
2055	flux_l_cs, diss_l_cs, i_omp_start, tn )
2056	ELSE
2057	CALL advec_s_pw( i, j, cs_scalar )
2058	ENDIF
2059	ELSE
2060	CALL advec_s_up( i, j, cs_scalar )
2061	ENDIF
2062
2063	!
2064
2065	!-- Diffusion terms (the last three arguments are zero)
2066
2067	CALL diffusion_s( i, j, cs_scalar, &
2068	surf_def_h(0)%cssws(ilsp,:), surf_def_h(1)%cssws(ilsp,:), &
2069	surf_def_h(2)%cssws(ilsp,:), &
2070	surf_lsm_h%cssws(ilsp,:), surf_usm_h%cssws(ilsp,:), &
2071	surf_def_v(0)%cssws(ilsp,:), surf_def_v(1)%cssws(ilsp,:), &
2072	surf_def_v(2)%cssws(ilsp,:), surf_def_v(3)%cssws(ilsp,:), &
2073	surf_lsm_v(0)%cssws(ilsp,:), surf_lsm_v(1)%cssws(ilsp,:), &
2074	surf_lsm_v(2)%cssws(ilsp,:), surf_lsm_v(3)%cssws(ilsp,:), &
2075	surf_usm_v(0)%cssws(ilsp,:), surf_usm_v(1)%cssws(ilsp,:), &
2076	surf_usm_v(2)%cssws(ilsp,:), surf_usm_v(3)%cssws(ilsp,:) )
2077
2078	!
2079	!-- Prognostic equation for chem spcs
2080	DO k = nzb+1, nzt
2081	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) + ( dt_3d * &
2082	( tsc(2) * tend(k,j,i) + &
2083	tsc(3) * tcs_scalar_m(k,j,i) ) &
2084	- tsc(5) * rdf_sc(k) &
2085	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
2086	) &
2087	* MERGE( 1.0_wp, 0.0_wp, &
2088	BTEST( wall_flags_0(k,j,i), 0 ) &
2089	)
2090
2091	IF ( cs_scalar_p(k,j,i) < 0.0_wp ) cs_scalar_p(k,j,i) = 0.1_wp * cs_scalar(k,j,i) !FKS6
2092	ENDDO
2093
2094	!
2095	!-- Calculate tendencies for the next Runge-Kutta step
2096	IF ( timestep_scheme(1:5) == 'runge' ) THEN
2097	IF ( intermediate_timestep_count == 1 ) THEN
2098	DO k = nzb+1, nzt
2099	tcs_scalar_m(k,j,i) = tend(k,j,i)
2100	ENDDO
2101	ELSEIF ( intermediate_timestep_count < &
2102	intermediate_timestep_count_max ) THEN
2103	DO k = nzb+1, nzt
2104	tcs_scalar_m(k,j,i) = -9.5625_wp * tend(k,j,i) + &
2105	5.3125_wp * tcs_scalar_m(k,j,i)
2106	ENDDO
2107	ENDIF
2108	ENDIF
2109
2110	END SUBROUTINE chem_prognostic_equations_ij
2111
2112	!
2113	!------------------------------------------------------------------------------!
2114	!
2115	! Description:
2116	! ------------
2117	!> Subroutine to read restart data of chemical species
2118	!------------------------------------------------------------------------------!
2119
2120	SUBROUTINE chem_rrd_local( i, k, nxlf, nxlc, nxl_on_file, nxrf, nxrc, &
2121	nxr_on_file, nynf, nync, nyn_on_file, nysf, nysc, &
2122	nys_on_file, tmp_3d, found )
2123
2124	USE control_parameters
2125
2126	USE indices
2127
2128	USE pegrid
2129
2130	IMPLICIT NONE
2131
2132	CHARACTER (LEN=20) :: spc_name_av !<
2133
2134	INTEGER(iwp) :: i, lsp !<
2135	INTEGER(iwp) :: k !<
2136	INTEGER(iwp) :: nxlc !<
2137	INTEGER(iwp) :: nxlf !<
2138	INTEGER(iwp) :: nxl_on_file !<
2139	INTEGER(iwp) :: nxrc !<
2140	INTEGER(iwp) :: nxrf !<
2141	INTEGER(iwp) :: nxr_on_file !<
2142	INTEGER(iwp) :: nync !<
2143	INTEGER(iwp) :: nynf !<
2144	INTEGER(iwp) :: nyn_on_file !<
2145	INTEGER(iwp) :: nysc !<
2146	INTEGER(iwp) :: nysf !<
2147	INTEGER(iwp) :: nys_on_file !<
2148
2149	LOGICAL, INTENT(OUT) :: found
2150
2151	REAL(wp), DIMENSION(nzb:nzt+1,nys_on_file-nbgp:nyn_on_file+nbgp,nxl_on_file-nbgp:nxr_on_file+nbgp) :: tmp_3d !< 3D array to temp store data
2152
2153
2154	found = .FALSE.
2155
2156
2157	IF ( ALLOCATED(chem_species) ) THEN
2158
2159	DO lsp = 1, nspec
2160
2161	!< for time-averaged chemical conc.
2162	spc_name_av = TRIM(chem_species(lsp)%name)//'_av'
2163
2164	IF (restart_string(1:length) == TRIM(chem_species(lsp)%name) ) &
2165	THEN
2166	!< read data into tmp_3d
2167	IF ( k == 1 ) READ ( 13 ) tmp_3d
2168	!< fill ..%conc in the restart run
2169	chem_species(lsp)%conc(:,nysc-nbgp:nync+nbgp, &
2170	nxlc-nbgp:nxrc+nbgp) = &
2171	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
2172	found = .TRUE.
2173	ELSEIF (restart_string(1:length) == spc_name_av ) THEN
2174	IF ( k == 1 ) READ ( 13 ) tmp_3d
2175	chem_species(lsp)%conc_av(:,nysc-nbgp:nync+nbgp, &
2176	nxlc-nbgp:nxrc+nbgp) = &
2177	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
2178	found = .TRUE.
2179	ENDIF
2180
2181	ENDDO
2182
2183	ENDIF
2184
2185
2186	END SUBROUTINE chem_rrd_local
2187	!
2188	!-------------------------------------------------------------------------------!
2189	!> Description:
2190	!> Calculation of horizontally averaged profiles
2191	!> This routine is called for every statistic region (sr) defined by the user,
2192	!> but at least for the region "total domain" (sr=0).
2193	!> quantities.
2194	!------------------------------------------------------------------------------!
2195	SUBROUTINE chem_statistics( mode, sr, tn )
2196
2197
2198	USE arrays_3d
2199	USE indices
2200	USE kinds
2201	USE pegrid
2202	USE statistics
2203
2204	USE user
2205
2206	IMPLICIT NONE
2207
2208	CHARACTER (LEN=*) :: mode !<
2209
2210	INTEGER(iwp) :: i !< running index on x-axis
2211	INTEGER(iwp) :: j !< running index on y-axis
2212	INTEGER(iwp) :: k !< vertical index counter
2213	INTEGER(iwp) :: sr !< statistical region
2214	INTEGER(iwp) :: tn !< thread number
2215	INTEGER(iwp) :: n !<
2216	INTEGER(iwp) :: m !<
2217	INTEGER(iwp) :: lpr !< running index chem spcs
2218	! REAL(wp), &
2219	! DIMENSION(dots_num_palm+1:dots_max) :: &
2220	! ts_value_l !<
2221
2222	IF ( mode == 'profiles' ) THEN
2223	!
2224	!-- Sample on how to calculate horizontally averaged profiles of user-
2225	!-- defined quantities. Each quantity is identified by the index
2226	!-- "pr_palm+#" where "#" is an integer starting from 1. These
2227	!-- user-profile-numbers must also be assigned to the respective strings
2228	!-- given by data_output_pr_cs in routine user_check_data_output_pr.
2229	!-- hom(:,:,:,:) = dim-1 = vertical level, dim-2= 1: met-species,2:zu/zw, dim-3 = quantity( e.g.
2230	! wpt), dim-4 = statistical region.
2231
2232	!$OMP DO
2233	DO i = nxl, nxr
2234	DO j = nys, nyn
2235	DO k = nzb, nzt+1
2236	DO lpr = 1, cs_pr_count
2237
2238	sums_l(k,pr_palm+lpr,tn) = sums_l(k,pr_palm+lpr,tn) + &
2239	chem_species(cs_pr_index(lpr))%conc(k,j,i) * &
2240	rmask(j,i,sr) * &
2241	MERGE( 1.0_wp, 0.0_wp, &
2242	BTEST( wall_flags_0(k,j,i), 22 ) )
2243	ENDDO
2244	ENDDO
2245	ENDDO
2246	ENDDO
2247	ELSEIF ( mode == 'time_series' ) THEN
2248	CALL location_message( 'Time series not calculated for chemistry', .TRUE. )
2249	ENDIF
2250
2251	END SUBROUTINE chem_statistics
2252	!
2253	!------------------------------------------------------------------------------!
2254	!
2255	! Description:
2256	! ------------
2257	!> Subroutine for swapping of timelevels for chemical species
2258	!> called out from subroutine swap_timelevel
2259	!------------------------------------------------------------------------------!
2260
2261	SUBROUTINE chem_swap_timelevel (level)
2262
2263	IMPLICIT none
2264
2265	INTEGER,INTENT(IN) :: level
2266	!-- local variables
2267	INTEGER :: lsp
2268
2269
2270	IF ( level == 0 ) THEN
2271	DO lsp=1, nvar
2272	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
2273	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
2274	ENDDO
2275	ELSE
2276	DO lsp=1, nvar
2277	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
2278	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
2279	ENDDO
2280	ENDIF
2281
2282	RETURN
2283	END SUBROUTINE chem_swap_timelevel
2284	!
2285	!------------------------------------------------------------------------------!
2286	!
2287	! Description:
2288	! ------------
2289	!> Subroutine to write restart data for chemistry model
2290	!------------------------------------------------------------------------------!
2291	SUBROUTINE chem_wrd_local
2292
2293	IMPLICIT NONE
2294
2295	INTEGER(iwp) :: lsp !<
2296
2297	DO lsp = 1, nspec
2298	CALL wrd_write_string( TRIM( chem_species(lsp)%name ))
2299	WRITE ( 14 ) chem_species(lsp)%conc
2300	CALL wrd_write_string( TRIM( chem_species(lsp)%name )//'_av' )
2301	WRITE ( 14 ) chem_species(lsp)%conc_av
2302	ENDDO
2303
2304	END SUBROUTINE chem_wrd_local
2305	END MODULE chemistry_model_mod
2306

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