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source: palm/trunk/SOURCE/chemistry_model_mod.f90 @ 3226

Last change on this file since 3226 was 3215, checked in by suehring, 6 years ago
changes for commit 3209 documented
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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 1997-2018 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 3215 2018-08-29 09:58:59Z suehring $
29	! +nest_chemistry
30	!
31	! 3209 2018-08-27 16:58:37Z suehring
32	! Rename flags indicating outflow boundary conditions
33	!
34	! 3182 2018-07-27 13:36:03Z suehring
35	! Revise output of surface quantities in case of overhanging structures
36	!
37	! 3045 2018-05-28 07:55:41Z Giersch
38	! error messages revised
39	!
40	! 3014 2018-05-09 08:42:38Z maronga
41	! Bugfix: nzb_do and nzt_do were not used for 3d data output
42	!
43	! 3004 2018-04-27 12:33:25Z Giersch
44	! Comment concerning averaged data output added
45	!
46	! 2932 2018-03-26 09:39:22Z maronga
47	! renamed chemistry_par to chemistry_parameters
48	!
49	! 2894 2018-03-15 09:17:58Z Giersch
50	! Calculations of the index range of the subdomain on file which overlaps with
51	! the current subdomain are already done in read_restart_data_mod,
52	! chem_last_actions was renamed to chem_wrd_local, chem_read_restart_data was
53	! renamed to chem_rrd_local, chem_write_var_list was renamed to
54	! chem_wrd_global, chem_read_var_list was renamed to chem_rrd_global,
55	! chem_skip_var_list has been removed, variable named found has been
56	! introduced for checking if restart data was found, reading of restart strings
57	! has been moved completely to read_restart_data_mod, chem_rrd_local is already
58	! inside the overlap loop programmed in read_restart_data_mod, todo list has
59	! bees extended, redundant characters in chem_wrd_local have been removed,
60	! the marker * end chemistry * is not necessary anymore, strings and their
61	! respective lengths are written out and read now in case of restart runs to
62	! get rid of prescribed character lengths
63	!
64	! 2815 2018-02-19 11:29:57Z suehring
65	! Bugfix in restart mechanism,
66	! rename chem_tendency to chem_prognostic_equations,
67	! implement vector-optimized version of chem_prognostic_equations,
68	! some clean up (incl. todo list)
69	!
70	! 2773 2018-01-30 14:12:54Z suehring
71	! Declare variables required for nesting as public
72	!
73	! 2772 2018-01-29 13:10:35Z suehring
74	! Bugfix in string handling
75	!
76	! 2768 2018-01-24 15:38:29Z kanani
77	! Shorten lines to maximum length of 132 characters
78	!
79	! 2766 2018-01-22 17:17:47Z kanani
80	! Removed preprocessor directive __chem
81	!
82	! 2756 2018-01-16 18:11:14Z suehring
83	! Fill values in 3D output introduced.
84	!
85	! 2718 2018-01-02 08:49:38Z maronga
86	! Initial revision
87	!
88	!
89	!
90	!
91	! Authors:
92	! --------
93	! @author Renate Forkel
94	! @author Farah Kanani-Suehring
95	! @author Klaus Ketelsen
96	! @author Basit Khan
97	!
98	!
99	!------------------------------------------------------------------------------!
100	! Description:
101	! ------------
102	!> Chemistry model for PALM-4U
103	!> @todo Adjust chem_rrd_local to CASE structure of others modules. It is not
104	!> allowed to use the chemistry model in a precursor run and additionally
105	!> not using it in a main run
106	!> @todo Update/clean-up todo list! (FK)
107	!> @todo Set proper fill values (/= 0) for chem output arrays! (FK)
108	!> @todo Add routine chem_check_parameters, add checks for inconsistent or
109	!> unallowed parameter settings.
110	!> CALL of chem_check_parameters from check_parameters. (FK)
111	!> @todo Make routine chem_header available, CALL from header.f90
112	!> (see e.g. how it is done in routine lsm_header in
113	!> land_surface_model_mod.f90). chem_header should include all setup
114	!> info about chemistry parameter settings. (FK)
115	!> @todo Implement turbulent inflow of chem spcs in inflow_turbulence.
116	!> @todo Separate boundary conditions for each chem spcs to be implemented
117	!> @todo Currently only total concentration are calculated. Resolved, parameterized
118	!> and chemistry fluxes although partially and some completely coded but
119	!> are not operational/activated in this version. bK.
120	!> @todo slight differences in passive scalar and chem spcs when chem reactions
121	!> turned off. Need to be fixed. bK
122	!> @todo test nesting for chem spcs, was implemented by suehring (kanani)
123	!> @todo subroutine set_const_initial_values to be taken out from chemistry_model_mod !bK.
124	!> @todo chemistry error messages
125	!> @todo Format this module according to PALM coding standard (see e.g. module
126	!> template under http://palm.muk.uni-hannover.de/mosaik/downloads/8 or
127	!> D3_coding_standard.pdf under https://palm.muk.uni-hannover.de/trac/downloads/16)
128	!
129	!------------------------------------------------------------------------------!
130
131	MODULE chemistry_model_mod
132
133	USE kinds, ONLY: wp, iwp
134	USE indices, ONLY: nz, nzb,nzt,nysg,nyng,nxlg,nxrg,nys,nyn
135	USE pegrid, ONLY: myid, threads_per_task
136	USE control_parameters, ONLY: dt_3d, ws_scheme_sca, initializing_actions, message_string, &
137	omega, tsc, intermediate_timestep_count, &
138	intermediate_timestep_count_max, &
139	timestep_scheme, use_prescribed_profile_data
140	USE arrays_3d, ONLY: hyp, pt, rdf_sc, tend, zu
141	USE chem_gasphase_mod, ONLY: nspec, spc_names, nkppctrl, nmaxfixsteps, &
142	t_steps, fill_temp, chem_gasphase_integrate, &
143	nvar, atol, rtol, nphot, phot_names
144	USE cpulog, ONLY: cpu_log, log_point
145
146	USE chem_modules
147
148
149	IMPLICIT NONE
150	PRIVATE
151	SAVE
152
153	LOGICAL :: nest_chemistry = .TRUE. !< flag for nesting mode of chemical species, independent on parent or not
154	!
155	!- Define chemical variables
156	TYPE species_def
157	CHARACTER(LEN=8) :: name
158	CHARACTER(LEN=16) :: unit
159	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc
160	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_av
161	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_p
162	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: tconc_m
163	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: cssws_av
164	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: flux_s_cs
165	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: diss_s_cs
166	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: flux_l_cs
167	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: diss_l_cs
168	REAL(kind=wp),ALLOCATABLE,DIMENSION(:) :: conc_pr_init
169	END TYPE species_def
170
171
172	TYPE photols_def
173	CHARACTER(LEN=8) :: name
174	CHARACTER(LEN=16) :: unit
175	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: freq
176	END TYPE photols_def
177
178
179	PUBLIC species_def
180	PUBLIC photols_def
181
182
183	TYPE(species_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: chem_species
184	TYPE(photols_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: phot_frequen
185
186	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_1
187	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_2
188	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_3
189	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_av
190	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: freq_1
191
192	INTEGER,DIMENSION(nkppctrl) :: icntrl ! Fine tuning kpp
193	REAL(kind=wp),DIMENSION(nkppctrl) :: rcntrl ! Fine tuning kpp
194
195	CHARACTER(10), PUBLIC :: photolysis_scheme
196	! 'constant',
197	! 'simple' (Simple parameterisation from MCM, Saunders et al., 2003, Atmos. Chem. Phys., 3, 161-180
198	! 'fastj' (Wild et al., 2000, J. Atmos. Chem., 37, 245-282) STILL NOT IMPLEMENTED
199
200	PUBLIC nest_chemistry, nspec
201	PUBLIC nvar
202	PUBLIC spc_names
203	PUBLIC spec_conc_2
204
205	!- Interface section
206	INTERFACE chem_boundary_conds
207	MODULE PROCEDURE chem_boundary_conds
208	END INTERFACE chem_boundary_conds
209
210	INTERFACE chem_init
211	MODULE PROCEDURE chem_init
212	END INTERFACE chem_init
213
214	INTERFACE chem_init_profiles
215	MODULE PROCEDURE chem_init_profiles
216	END INTERFACE chem_init_profiles
217
218	INTERFACE chem_parin
219	MODULE PROCEDURE chem_parin
220	END INTERFACE chem_parin
221
222	INTERFACE chem_integrate
223	MODULE PROCEDURE chem_integrate_ij
224	END INTERFACE chem_integrate
225
226	INTERFACE chem_swap_timelevel
227	MODULE PROCEDURE chem_swap_timelevel
228	END INTERFACE chem_swap_timelevel
229
230	INTERFACE chem_define_netcdf_grid
231	MODULE PROCEDURE chem_define_netcdf_grid
232	END INTERFACE chem_define_netcdf_grid
233
234	INTERFACE chem_data_output_3d
235	MODULE PROCEDURE chem_data_output_3d
236	END INTERFACE chem_data_output_3d
237
238	INTERFACE chem_check_data_output
239	MODULE PROCEDURE chem_check_data_output
240	END INTERFACE chem_check_data_output
241
242	INTERFACE chem_check_data_output_pr
243	MODULE PROCEDURE chem_check_data_output_pr
244	END INTERFACE chem_check_data_output_pr
245
246	INTERFACE chem_3d_data_averaging
247	MODULE PROCEDURE chem_3d_data_averaging
248	END INTERFACE chem_3d_data_averaging
249
250	INTERFACE chem_wrd_local
251	MODULE PROCEDURE chem_wrd_local
252	END INTERFACE chem_wrd_local
253
254	INTERFACE chem_rrd_local
255	MODULE PROCEDURE chem_rrd_local
256	END INTERFACE chem_rrd_local
257
258	INTERFACE chem_prognostic_equations
259	MODULE PROCEDURE chem_prognostic_equations
260	MODULE PROCEDURE chem_prognostic_equations_ij
261	END INTERFACE chem_prognostic_equations
262
263	INTERFACE chem_header
264	MODULE PROCEDURE chem_header
265	END INTERFACE chem_header
266
267	INTERFACE chem_emissions
268	MODULE PROCEDURE chem_emissions
269	END INTERFACE chem_emissions
270
271	! INTERFACE chem_wrd_global
272	! MODULE PROCEDURE chem_wrd_global
273	! END INTERFACE chem_wrd_global
274	!
275	! INTERFACE chem_rrd_global
276	! MODULE PROCEDURE chem_rrd_global
277	! END INTERFACE chem_rrd_global
278
279
280	PUBLIC chem_3d_data_averaging, chem_boundary_conds, chem_check_data_output, &
281	chem_check_data_output_pr, chem_data_output_3d, &
282	chem_define_netcdf_grid, chem_emissions, chem_header, chem_init, &
283	chem_init_profiles, chem_integrate, chem_wrd_local, &
284	chem_parin, chem_prognostic_equations, &
285	chem_rrd_local, chem_swap_timelevel
286
287
288	CONTAINS
289
290	!------------------------------------------------------------------------------!
291	!
292	! Description:
293	! ------------
294	!> Subroutine to initialize and set all boundary conditions for chemical species
295	!------------------------------------------------------------------------------!
296
297	SUBROUTINE chem_boundary_conds( mode )
298
299	USE control_parameters, &
300	ONLY: air_chemistry, bc_radiation_l, bc_radiation_n, bc_radiation_r, &
301	bc_radiation_s
302	USE indices, &
303	ONLY: nxl, nxr, nxlg, nxrg, nyng, nysg, nzt
304
305	! USE prognostic_equations_mod, &
306
307	USE arrays_3d, &
308	ONLY: dzu
309	USE surface_mod, &
310	ONLY: bc_h
311
312	CHARACTER (len=*), INTENT(IN) :: mode
313	INTEGER(iwp) :: i !< grid index x direction.
314	INTEGER(iwp) :: j !< grid index y direction.
315	INTEGER(iwp) :: k !< grid index z direction.
316	INTEGER(iwp) :: kb !< variable to set respective boundary value, depends on facing.
317	INTEGER(iwp) :: l !< running index boundary type, for up- and downward-facing walls.
318	INTEGER(iwp) :: m !< running index surface elements.
319	INTEGER(iwp) :: lsp !< running index for chem spcs.
320	INTEGER(iwp) :: lph !< running index for photolysis frequencies
321
322
323	SELECT CASE ( TRIM( mode ) )
324	CASE ( 'init' )
325	DO lsp = 1, nspec
326	IF ( surface_csflux(lsp) == 9999999.9_wp ) THEN
327	constant_csflux(lsp) = .FALSE.
328	ENDIF
329	ENDDO
330
331	IF ( bc_cs_b == 'dirichlet' ) THEN
332	ibc_cs_b = 0
333	ELSEIF ( bc_cs_b == 'neumann' ) THEN
334	ibc_cs_b = 1
335	ELSE
336	! message_string = 'unknown boundary condition: bc_cs_b ="' // TRIM( bc_cs_b ) // '"' ! bK commented
337	CALL message( 'chem_boundary_conds', 'CM0010', 1, 2, 0, 6, 0 ) !< chemistry_model_mod should have special error numbers --> "CHEM###",
338	ENDIF
339	!
340	!-- Set Integer flags and check for possible erroneous settings for top
341	!-- boundary condition. bK added _cs_ here.
342	IF ( bc_cs_t == 'dirichlet' ) THEN
343	ibc_cs_t = 0
344	ELSEIF ( bc_cs_t == 'neumann' ) THEN
345	ibc_cs_t = 1
346	ELSEIF ( bc_cs_t == 'initial_gradient' ) THEN
347	ibc_cs_t = 2
348	ELSEIF ( bc_cs_t == 'nested' ) THEN
349	ibc_cs_t = 3
350	ELSE
351	! message_string = 'unknown boundary condition: bc_c_t ="' // TRIM( bc_cs_t ) // '"'
352	CALL message( 'check_parameters', 'CM0011', 1, 2, 0, 6, 0 )
353	ENDIF
354
355
356	CASE ( 'set_bc_bottomtop' )
357	!-- Bottom boundary condtions for chemical species
358	DO lsp = 1, nspec
359	IF ( ibc_cs_b == 0 ) THEN
360	DO l = 0, 1
361	!-- Set index kb: For upward-facing surfaces (l=0), kb=-1, i.e.
362	!-- the chem_species(nsp)%conc_p value at the topography top (k-1)
363	!-- is set; for downward-facing surfaces (l=1), kb=1, i.e. the
364	!-- value at the topography bottom (k+1) is set.
365
366	kb = MERGE( -1, 1, l == 0 )
367	!$OMP PARALLEL DO PRIVATE( i, j, k )
368	DO m = 1, bc_h(l)%ns
369	i = bc_h(l)%i(m)
370	j = bc_h(l)%j(m)
371	k = bc_h(l)%k(m)
372	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc(k+kb,j,i)
373	ENDDO
374	ENDDO
375
376	ELSEIF ( ibc_cs_b == 1 ) THEN
377	! in boundary_conds there is som extra loop over m here for passive tracer
378	DO l = 0, 1
379	kb = MERGE( -1, 1, l == 0 )
380	!$OMP PARALLEL DO PRIVATE( i, j, k )
381	DO m = 1, bc_h(l)%ns
382	i = bc_h(l)%i(m)
383	j = bc_h(l)%j(m)
384	k = bc_h(l)%k(m)
385	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc_p(k,j,i)
386
387	!< @todo: chem_species(nsp)%conc_p(k+kb,j,i) = chem_species(nsp)%conc(k+kb,j,i), &
388	!< pls loop over nsp=1, NSPEC.
389	!< @todo: We should also think about the possibility to have &
390	!< individual boundary conditions for each species? This means, bc_cs_b, &
391	!< bc_cs_t, ibc_cs_b, ibc_cs_t would need to be added to TYPE chem_species(nsp)%, &
392	!< and the loop over nsp would have to be put outside of this IF-clause.
393	!< i think its better we keep the same bonundary cond i.e. dirichlet or neumann
394	!< for all chem spcs. ... !bK
395
396	ENDDO
397	ENDDO
398	ENDIF
399	ENDDO ! end lsp loop
400
401	!-- Top boundary conditions for chemical species - Should this not be done for all species?
402	IF ( ibc_cs_t == 0 ) THEN
403	DO lsp = 1, nspec
404	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc(nzt+1,:,:)
405	ENDDO
406	ELSEIF ( ibc_cs_t == 1 ) THEN
407	DO lsp = 1, nspec
408	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:)
409	ENDDO
410	ELSEIF ( ibc_cs_t == 2 ) THEN
411	DO lsp = 1, nspec
412	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:) + bc_cs_t_val(lsp) * dzu(nzt+1)
413	ENDDO
414	!@todo: bc_cs_t_val needs to be calculated,
415	!see bc_pt_t_val = ( pt_init(nzt+1) - pt_init(nzt) ) / dzu(nzt+1)
416	!(in time_integration). pt_init would be the counterpart to
417	!chem_species(i)%conc_pr_init (see kchem_driver_FKa1408.f90 of my
418	!"Hints: prescribing initial concentration.
419	ENDIF
420	!
421	CASE ( 'set_bc_lateral' ) ! bK commented it
422	!-- Lateral boundary conditions for chem species at inflow boundary
423	!-- are automatically set when chem_species concentration is
424	!-- initialized. The initially set value at the inflow boundary is not
425	!-- touched during time integration, hence, this boundary value remains
426	!-- at a constant value, which is the concentration that flows into the
427	!-- domain.
428	!-- Lateral boundary conditions for chem species at outflow boundary
429
430	IF ( bc_radiation_s ) THEN
431	DO lsp = 1, nspec
432	chem_species(lsp)%conc_p(:,nys-1,:) = chem_species(lsp)%conc_p(:,nys,:)
433	ENDDO
434	ELSEIF ( bc_radiation_n ) THEN
435	DO lsp = 1, nspec
436	chem_species(lsp)%conc_p(:,nyn+1,:) = chem_species(lsp)%conc_p(:,nyn,:)
437	ENDDO
438	ELSEIF ( bc_radiation_l ) THEN
439	DO lsp = 1, nspec
440	chem_species(lsp)%conc_p(:,:,nxl-1) = chem_species(lsp)%conc_p(:,:,nxl)
441	ENDDO
442	ELSEIF ( bc_radiation_r ) THEN
443	DO lsp = 1, nspec
444	chem_species(lsp)%conc_p(:,:,nxr+1) = chem_species(lsp)%conc_p(:,:,nxr)
445	ENDDO
446	ENDIF
447
448	END SELECT
449
450	END SUBROUTINE chem_boundary_conds
451	!
452	!------------------------------------------------------------------------------!
453	!
454	! Description:
455	! ------------
456	!> Subroutine defining initial vertical profiles of chemical species (given by
457	!> namelist parameters chem_profiles and chem_heights) --> which should work
458	!> analogue to parameters u_profile, v_profile and uv_heights)
459	!------------------------------------------------------------------------------!
460	SUBROUTINE chem_init_profiles !< SUBROUTINE is called from chem_init in case of
461	!< TRIM( initializing_actions ) /= 'read_restart_data'
462	!< We still need to see what has to be done in case of restart run
463	USE chem_modules
464
465	IMPLICIT NONE
466
467	!-- Local variables
468	INTEGER :: lsp !< running index for number of species in derived data type species_def
469	INTEGER :: lsp_pr !< running index for number of species in cs_names, cs_profiles etc
470	INTEGER :: lpr_lev !< running index for profile level for each chem spcs.
471	INTEGER :: npr_lev !< the next available profile lev
472
473	!-----------------
474	!-- To prescribe/initialize a vertically constant 'cs_profile', another parameter
475	!-- "cs_surface" is introduced. If "cs_profile" and "cs_heights" are prescribed,
476	!-- their values will override the constant profile given by "cs_surface".
477
478	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
479	lsp_pr = 1
480	DO WHILE ( TRIM( cs_name( lsp_pr ) ) /= 'novalue' ) !'novalue' is the default
481	DO lsp = 1, nspec !
482	!-- Create initial profile (conc_pr_init) for each chemical species
483	IF ( TRIM( chem_species(lsp)%name ) == TRIM( cs_name(lsp_pr) ) ) THEN !
484	! IF ( cs_profile(1,1) == 9999999.9_wp ) THEN
485	!-- Set a vertically constant profile based on the surface conc (cs_surface(lsp_pr)) of each species
486	DO lpr_lev = 0, nzt+1
487	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_surface(lsp_pr)
488	ENDDO
489
490	! ELSE
491	! IF ( cs_heights(lsp,1) /= 0.0_wp ) THEN
492	! message_string = 'cs_heights(1,1) must be 0.0'
493	! CALL message( 'chem_check_parameters', 'CM0012', 1, 2, 0, 6, 0 )
494	! ENDIF
495	!
496	! IF ( omega /= 0.0_wp ) THEN
497	! message_string = 'Coriolis force must be switched off (by setting omega=0.0)' // &
498	! ' when prescribing the forcing by u_profile and v_profile'
499	! CALL message( 'check_parameters', 'PA0347', 1, 2, 0, 6, 0 )
500	! ENDIF
501	!
502	! use_prescribed_profile_data = .TRUE.
503	!
504	! npr_lev = 1
505	! ! chem_sddpecies(lsp)%conc_pr_init(0) = 0.0_wp
506	! DO lpr_lev = 1, nz+1
507	! IF ( npr_lev < 100 ) THEN
508	! DO WHILE ( cs_heights(lsp, npr_lev+1) <= zu(lpr_lev) )
509	! npr_lev = npr_lev + 1
510	! IF ( npr_lev == 100 ) EXIT
511	! ENDDO
512	! ENDIF
513	!
514	! IF ( npr_lev < 100 .AND. cs_heights(lsp, npr_lev + 1) /= 9999999.9_wp ) THEN
515	! chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp, npr_lev) + &
516	! ( zu(lpr_lev) - cs_heights(lsp, npr_lev) ) / &
517	! ( cs_heights(lsp, npr_lev + 1) - cs_heights(lsp, npr_lev ) ) * &
518	! ( cs_profile(lsp, npr_lev + 1) - cs_profile(lsp, npr_lev ) )
519	! ELSE
520	! chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp, npr_lev)
521	! ENDIF
522	! ENDDO
523	! ENDIF
524	!-- If a profile is prescribed explicity using cs_profiles and cs_heights, we then have to fill the
525	!-- chem_species(lsp)%conc_pr_init for the specific "lsp" based on the cs_profiles(lsp_pr,:)
526	!-- and cs_heights(lsp_pr,:).
527	ENDIF
528	ENDDO
529	lsp_pr = lsp_pr + 1
530	ENDDO
531	! ELSE
532	! IF (chem_debug1 ) print*,'code to be added for initializing_actions == read_restart_data' !bK
533	! ENDIF
534
535	!-- Now, go back to chem_init and use the contents of chem_species(lsp)%conc_pr_init to
536	!-- initialize the 3D conc arrays, as it is currently taken care of in chem_set_constant_values.
537	!-- After initializing the 3D arrays, these can be used to set the boundary conditions in the
538	!-- subroutine kchem_boundary_conds, which should be called from boundary_conds.f90.
539
540
541	END SUBROUTINE chem_init_profiles
542	!
543	!------------------------------------------------------------------------------!
544	!
545	! Description:
546	! ------------
547	!> Subroutine initializating chemistry_model_mod
548	!------------------------------------------------------------------------------!
549	SUBROUTINE chem_init
550
551
552	USE control_parameters, &
553	ONLY: message_string, io_blocks, io_group, turbulent_inflow
554
555	USE arrays_3d, &
556	ONLY: mean_inflow_profiles
557
558	USE pegrid
559
560	IMPLICIT none
561	!-- local variables
562	INTEGER :: i,j !< running index for for horiz numerical grid points
563	INTEGER :: lsp !< running index for chem spcs
564	INTEGER :: lpr_lev !< running index for chem spcs profile level
565	!
566	!-- NOPOINTER version not implemented yet
567	! #if defined( __nopointer )
568	! message_string = 'The chemistry module only runs with POINTER version'
569	! CALL message( 'chemistry_model_mod', 'CM0001', 1, 2, 0, 6, 0 )
570	! #endif
571	!
572	!-- Allocate memory for chemical species
573	ALLOCATE( chem_species(nspec) )
574	ALLOCATE( spec_conc_1 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
575	ALLOCATE( spec_conc_2 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
576	ALLOCATE( spec_conc_3 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
577	ALLOCATE( spec_conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
578	ALLOCATE( phot_frequen(nphot) )
579	ALLOCATE( freq_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nphot) )
580	ALLOCATE( bc_cs_t_val(nspec) )
581	!
582	!-- Initialize arrays
583	spec_conc_1 (:,:,:,:) = 0.0_wp
584	spec_conc_2 (:,:,:,:) = 0.0_wp
585	spec_conc_3 (:,:,:,:) = 0.0_wp
586	spec_conc_av(:,:,:,:) = 0.0_wp
587
588
589	DO lsp = 1, nspec
590	chem_species(lsp)%name = spc_names(lsp)
591
592	chem_species(lsp)%conc (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1 (:,:,:,lsp)
593	chem_species(lsp)%conc_p (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2 (:,:,:,lsp)
594	chem_species(lsp)%tconc_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_3 (:,:,:,lsp)
595	chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_av(:,:,:,lsp)
596
597	ALLOCATE (chem_species(lsp)%cssws_av(nysg:nyng,nxlg:nxrg))
598	chem_species(lsp)%cssws_av = 0.0_wp
599	!
600	!-- (todo (FK): This needs to be revised. This block must go somewhere else)
601	! IF ( ws_scheme_sca ) THEN
602	ALLOCATE (chem_species(lsp)%flux_s_cs(nzb+1:nzt,0:threads_per_task-1))
603	ALLOCATE (chem_species(lsp)%diss_s_cs(nzb+1:nzt,0:threads_per_task-1))
604	ALLOCATE (chem_species(lsp)%flux_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
605	ALLOCATE (chem_species(lsp)%diss_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
606	chem_species(lsp)%flux_s_cs = 0.0_wp
607	chem_species(lsp)%flux_l_cs = 0.0_wp
608	chem_species(lsp)%diss_s_cs = 0.0_wp
609	chem_species(lsp)%diss_l_cs = 0.0_wp
610	! ENDIF
611	!
612	!-- Allocate memory for initial concentration profiles
613	!-- (concentration values come from namelist)
614	!-- (todo (FK): Because of this, chem_init is called in palm before
615	!-- check_parameters, since conc_pr_init is used there.
616	!-- We have to find another solution since chem_init should
617	!-- eventually be called from init_3d_model!!)
618	ALLOCATE ( chem_species(lsp)%conc_pr_init(0:nz+1) )
619	chem_species(lsp)%conc_pr_init(:) = 0.0_wp
620
621	ENDDO
622
623	!
624	!-- Set initial concentration of profiles prescribed by parameters cs_profile
625	!-- and cs_heights in the namelist &chemistry_parameters
626	!-- (todo (FK): chem_init_profiles not ready yet, has some bugs)
627	! CALL chem_init_profiles
628	!
629	!-- Initialize model variables
630
631
632	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
633	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
634
635
636	!-- First model run of a possible job queue.
637	!-- Initial profiles of the variables must be computes.
638	IF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
639	! CALL location_message( 'initializing with 1D model profiles', .FALSE. )
640	!
641	! CALL init_1d_model ...... decide to call or not later !bK
642
643	!-- Transfer initial profiles to the arrays of the 3D model
644	DO lsp = 1, nspec
645	DO i = nxlg, nxrg
646	DO j = nysg, nyng
647	DO lpr_lev = 1, nz + 1
648	chem_species(lsp)%conc(lpr_lev,j,i) = chem_species(lsp)%conc_pr_init(lpr_lev)
649	ENDDO
650	ENDDO
651	ENDDO
652	ENDDO
653
654	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
655	THEN
656	! CALL location_message( 'initializing with constant profiles', .FALSE. )
657
658
659
660	!-- Set initial horizontal velocities at the lowest computational grid
661	!-- levels to zero in order to avoid too small time steps caused by the
662	!-- diffusion limit in the initial phase of a run (at k=1, dz/2 occurs
663	!-- in the limiting formula!).
664
665	DO lsp = 1, nspec
666	DO i = nxlg, nxrg
667	DO j = nysg, nyng
668	chem_species(lsp)%conc(:,j,i) = chem_species(lsp)%conc_pr_init !ITS THERE bK
669	ENDDO
670	ENDDO
671	ENDDO
672
673	! ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) &
674	! THEN
675	! CALL location_message( 'initializing by user', .FALSE. )
676	!
677	!-- Initialization will completely be done by the user
678	!-- (FK: This should be called only once, in init_3d_model, i.e. remove it here)
679	! CALL user_init_3d_model
680	! CALL location_message( 'finished', .TRUE. )
681
682	ENDIF
683
684	!-- Store initial chem spcs profile
685	! DO lsp = 1, nvar
686	! hom_cs(:,1,115,:) = SPREAD( chem_species(lsp)%conc(:,nys,nxl), 2, statistic_regions+1 )
687	! ENDDO
688	!
689	!-- If required, change the surface chem spcs at the start of the 3D run
690	IF ( cs_surface_initial_change(1) /= 0.0_wp ) THEN
691	DO lsp = 1, nspec
692	chem_species(lsp)%conc(nzb,:,:) = chem_species(lsp)%conc(nzb,:,:) + &
693	cs_surface_initial_change(lsp)
694	ENDDO
695	ENDIF
696	!
697	!-- Initiale old and new time levels.
698	DO lsp = 1, nvar
699	chem_species(lsp)%tconc_m = 0.0_wp
700	chem_species(lsp)%conc_p = chem_species(lsp)%conc
701	ENDDO
702
703	ENDIF
704
705
706
707	!--- new code add above this line
708	DO lsp = 1, nphot
709	phot_frequen(lsp)%name = phot_names(lsp)
710	! IF( myid == 0 ) THEN
711	! WRITE(6,'(a,i4,3x,a)') 'Photolysis: ',lsp,trim(phot_names(lsp))
712	! ENDIF
713	phot_frequen(lsp)%freq(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => freq_1(:,:,:,lsp)
714	ENDDO
715
716	!-- Set initial values
717	! Not required any more, this can now be done with the namelist by setting cs_surface
718	! and cs_name without specifying cs_profile (Nevertheless, we still want to keep it for a while)
719	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
720	! CALL set_const_initial_values
721	! ENDIF
722
723	RETURN
724
725	CONTAINS
726	!------------------------------------------------------------------------------!
727	!
728	! Description:
729	! ------------
730	!> Subroutine setting constant initial values of chemical species
731	!------------------------------------------------------------------------------!
732	SUBROUTINE set_const_initial_values
733	! Not required any more, this can now be done with the namelist by setting cs_surface
734	! and cs_name without specifying cs_profile (Nevertheless, we still want to keep it for a while)
735	IMPLICIT none
736
737	!-- local variables
738	INTEGER :: lsp
739
740	IF(myid == 0) THEN
741	write(6,'(/,a,/)') ' chemics >>>> Set constant Initial Values: '
742	ENDIF
743
744	! Default values are taken from smog.def from supplied kpp example
745	DO lsp = 1, nspec
746	IF(trim(chem_species(lsp)%name) == 'NO') THEN
747	! chem_species(lsp)%conc = 8.725*1.0E+08
748	! chem_species(lsp)%conc = 0.05_wp !added by bK
749	chem_species(lsp)%conc = 0.01_wp !added by RFo
750	ELSEIF (trim(chem_species(lsp)%name) == 'NO2') THEN
751	! chem_species(lsp)%conc = 2.240*1.0E+08
752	! chem_species(lsp)%conc = 0.01_wp !added by bK
753	chem_species(lsp)%conc = 0.05_wp !added by RFo
754	ELSEIF( trim( chem_species(lsp)%name ) == 'O3' ) THEN
755	chem_species(lsp)%conc = 0.05_wp !added by bK
756	ELSEIF(trim(chem_species(lsp)%name) == 'H2O') THEN
757	! chem_species(lsp)%conc = 5.326*1.0E+11
758	chem_species(lsp)%conc = 1.30*1.0E+4_wp !added by bK
759	ELSEIF(trim(chem_species(lsp)%name) == 'O2') THEN
760	chem_species(lsp)%conc = 2.0*1.0E+5_wp !added by bK
761	ELSEIF(trim(chem_species(lsp)%name) == 'RH') THEN
762	chem_species(lsp)%conc = 0.001_wp !added by RFo
763	ELSEIF(trim(chem_species(lsp)%name) == 'CO') THEN
764	chem_species(lsp)%conc = 0.5_wp !added by RFo
765	ELSEIF(trim(chem_species(lsp)%name) == 'RCHO') THEN
766	! chem_species(lsp)%conc = 2.0_wp !added by bK
767	chem_species(lsp)%conc = 0.01_wp !added by RFo
768	! ELSEIF(trim(chem_species(lsp)%name) == 'OH') THEN
769	! chem_species(lsp)%conc = 1.0*1.0E-07_wp !added by bK
770	! ELSEIF(trim(chem_species(lsp)%name) == 'HO2') THEN
771	! chem_species(lsp)%conc = 1*1.0E-7_wp !added by bK
772	! ELSEIF(trim(chem_species(lsp)%name) == 'RCOO2') THEN ! corrected RFo
773	! chem_species(lsp)%conc = 1.0*1.0E-7_wp !added by bK
774	! ELSEIF(trim(chem_species(lsp)%name) == 'RCOO2NO2') THEN
775	! chem_species(lsp)%conc = 1.0*1.0E-7_wp !added by bK
776	ELSE
777	! H2O = 2.0e+04;
778	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) = 0.0_wp
779	ENDIF
780
781	IF(myid == 0) THEN
782	WRITE(6,'(a,3x,a,3x,a,e12.4)') ' Species: ',chem_species(lsp)%name(1:7), &
783	'Initial Value = ',chem_species(lsp)%conc(nzb,nysg,nxlg)
784	ENDIF
785	ENDDO
786
787	! #if defined( __nopointer )
788	! !kk Hier mit message abbrechen
789	! if(myid == 0) then
790	! write(6,*) ' KPP does only run with POINTER Version'
791	! end if
792	! stop 'error'
793	! #endif
794
795	RETURN
796	END SUBROUTINE set_const_initial_values
797
798
799	END SUBROUTINE chem_init
800	!
801	!------------------------------------------------------------------------------!
802	!
803	! Description:
804	! ------------
805	!> Subroutine defining parin for &chemistry_parameters for chemistry model
806	!------------------------------------------------------------------------------!
807	SUBROUTINE chem_parin
808
809	USE control_parameters, &
810	ONLY: air_chemistry
811
812	USE chem_modules
813
814	USE kinds
815
816	IMPLICIT none
817
818	CHARACTER (LEN=80) :: line !< dummy string that contains the current line of the parameter file
819
820	REAL(wp), DIMENSION(nmaxfixsteps) :: my_steps !< List of fixed timesteps my_step(1) = 0.0 automatic stepping
821
822	NAMELIST /chemistry_parameters/ bc_cs_b, &
823	bc_cs_t, &
824	call_chem_at_all_substeps, &
825	chem_debug0, &
826	chem_debug1, &
827	chem_debug2, &
828	chem_gasphase_on, &
829	cs_heights, &
830	cs_name, &
831	cs_profile, &
832	cs_profile_name, &
833	cs_surface, &
834	emiss_factor_main, &
835	emiss_factor_side, &
836	icntrl, &
837	main_street_id, &
838	max_street_id, &
839	my_steps, &
840	nest_chemistry, &
841	rcntrl, &
842	side_street_id, &
843	photolysis_scheme, &
844	wall_csflux, &
845	cs_vertical_gradient, &
846	top_csflux, &
847	surface_csflux, &
848	surface_csflux_name, &
849	cs_surface_initial_change, &
850	cs_vertical_gradient_level
851
852	!-- analogue to chem_names(nspj) we could invent chem_surfaceflux(nspj) and chem_topflux(nspj)
853	!-- so this way we could prescribe a specific flux value for each species
854	!> chemistry_parameters for initial profiles
855	!> cs_names = 'O3', 'NO2', 'NO', ... to set initial profiles)
856	!> cs_heights(1,:) = 0.0, 100.0, 500.0, 2000.0, .... (height levels where concs will be prescribed for O3)
857	!> cs_heights(2,:) = 0.0, 200.0, 400.0, 1000.0, .... (same for NO2 etc.)
858	!> cs_profiles(1,:) = 10.0, 20.0, 20.0, 30.0, ..... (chem spcs conc at height lvls chem_heights(1,:)) etc.
859	!> If the respective concentration profile should be constant with height, then use "cs_surface( number of spcs)"
860	!> then write these cs_surface values to chem_species(lsp)%conc_pr_init(:)
861
862	!
863	!-- Read chem namelist
864	!-- (todo: initialize these parameters in declaration part, do this for
865	!-- all chemistry_parameters namelist parameters)
866	icntrl = 0
867	rcntrl = 0.0_wp
868	my_steps = 0.0_wp
869	icntrl(2) = 1
870	photolysis_scheme = 'simple'
871	atol = 1.0_wp
872	rtol = 0.01_wp
873	!
874	!-- Try to find chemistry package
875	REWIND ( 11 )
876	line = ' '
877	DO WHILE ( INDEX( line, '&chemistry_parameters' ) == 0 )
878	READ ( 11, '(A)', END=10 ) line
879	ENDDO
880	BACKSPACE ( 11 )
881	!
882	!-- Read chemistry namelist
883	READ ( 11, chemistry_parameters )
884	!
885	!-- Enable chemistry model
886	air_chemistry = .TRUE.
887
888
889	10 CONTINUE
890
891	t_steps = my_steps !(todo: Why not directly make t_steps a
892	! namelist parameter?)
893
894	END SUBROUTINE chem_parin
895
896	!
897	!------------------------------------------------------------------------------!
898	!
899	! Description:
900	! ------------
901	!> Subroutine to integrate chemical species in the given chemical mechanism
902	!------------------------------------------------------------------------------!
903
904	SUBROUTINE chem_integrate_ij (i, j)
905
906	USE cpulog, &
907	ONLY: cpu_log, log_point
908	USE statistics, & ! ## RFo
909	ONLY: weight_pres
910	USE control_parameters, & ! ## RFo
911	ONLY: dt_3d, intermediate_timestep_count
912
913	IMPLICIT none
914	INTEGER,INTENT(IN) :: i,j
915
916	!-- local variables
917	INTEGER(iwp) :: lsp !< running index for chem spcs.
918	INTEGER(iwp) :: lph !< running index for photolysis frequencies
919	INTEGER :: k,m,istatf
920	INTEGER,dimension(20) :: istatus
921	REAL(kind=wp),dimension(nzb+1:nzt,nspec) :: tmp_conc
922	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_temp
923	REAL(kind=wp),dimension(nzb+1:nzt,nphot) :: tmp_phot
924	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_fact
925	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_fact_i !< conversion factor between molecules cm^{-3} and ppm
926	REAL(wp) :: conv !< conversion factor
927	REAL(wp), PARAMETER :: ppm2fr = 1.0e-6_wp !< Conversion factor ppm to fraction
928	REAL(wp), PARAMETER :: pref_i = 1._wp / 100000.0_wp !< inverse reference pressure (1/Pa)
929	REAL(wp), PARAMETER :: t_std = 273.15_wp !< standard pressure (Pa)
930	REAL(wp), PARAMETER :: p_std = 101325.0_wp !< standard pressure (Pa)
931	REAL(wp), PARAMETER :: r_cp = 0.286_wp !< R / cp (exponent for potential temperature)
932	REAL(wp), PARAMETER :: vmolcm = 22.414e3_wp !< Mole volume (22.414 l) in cm^{-3}
933	REAL(wp), PARAMETER :: xna = 6.022e23_wp !< Avogadro number (molecules/mol)
934
935
936	REAL(kind=wp) :: dt_chem
937
938	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'start' )
939	!< Set chem_gasphase_on to .FALSE. if you want to skip computation of gas phase chemistry
940	IF (chem_gasphase_on) THEN
941
942	tmp_temp(:) = pt(:,j,i) * ( hyp(nzb+1:nzt) / 100000.0_wp )**0.286_wp
943	! ppm to molecules/cm**3
944	! tmp_fact = 1.e-6_wp6.022e23_wp/(22.414_wp1000._wp) * 273.15_wp * hyp(nzb+1:nzt)/( 101300.0_wp * tmp_temp )
945	conv = ppm2fr * xna / vmolcm
946	tmp_fact(:) = conv * t_std * hyp(nzb+1:nzt) / (tmp_temp(:) * p_std)
947	tmp_fact_i = 1.0_wp/tmp_fact
948
949	CALL fill_temp (istatf, tmp_temp) !< Load constant temperature into kpp context
950	! CALL fill_temp (istatf, pt(nzb+1:nzt,j,i)) !< Load temperature into kpp context
951
952	DO lsp = 1,nspec
953	tmp_conc(:,lsp) = chem_species(lsp)%conc(nzb+1:nzt,j,i) * tmp_fact(:)
954	ENDDO
955
956	DO lph = 1,nphot
957	tmp_phot(:,lph) = phot_frequen(lph)%freq(nzb+1:nzt,j,i)
958	ENDDO
959
960	IF(myid == 0 .AND. chem_debug0 ) THEN
961	IF (i == 10 .and. j == 10) WRITE(0,*) 'begin chemics step ',dt_3d
962	ENDIF
963
964	!-- Compute length of time step # RFo
965	IF ( call_chem_at_all_substeps ) THEN
966	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
967	ELSE
968	dt_chem = dt_3d
969	ENDIF
970
971	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'start' )
972
973
974	CALL chem_gasphase_integrate (dt_chem, tmp_conc, tmp_temp, tmp_phot, istatus=istatus)
975
976
977	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'stop' )
978
979	DO lsp = 1,nspec
980	chem_species(lsp)%conc (nzb+1:nzt,j,i) = tmp_conc(:,lsp) * tmp_fact_i(:) ! RFo
981	ENDDO
982
983	! IF (myid == 0 .AND. chem_debug2 ) THEN
984	! IF (i == 10 .and. j == 10) WRITE(6,'(a,8i7)') ' KPP Status ',istatus(1:8)
985	! write(6,'(a,8i7)') ' KPP Status ',istatus(1:8)
986	! ENDIF
987
988	ENDIF
989	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'stop' )
990
991	RETURN
992	END SUBROUTINE chem_integrate_ij
993	!
994	!------------------------------------------------------------------------------!
995	!
996	! Description:
997	! ------------
998	!> Subroutine for swapping of timelevels for chemical species
999	!> called out from subroutine swap_timelevel
1000	!------------------------------------------------------------------------------!
1001
1002	SUBROUTINE chem_swap_timelevel (level)
1003	IMPLICIT none
1004
1005	INTEGER,INTENT(IN) :: level
1006
1007	!-- local variables
1008
1009	INTEGER :: lsp
1010
1011	! print,' entering chem_swap_timelevel *) '
1012	if(level == 0) then
1013	do lsp=1, nvar
1014	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
1015	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
1016	end do
1017	else
1018	do lsp=1, nvar
1019	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
1020	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
1021	end do
1022	end if
1023
1024	RETURN
1025	END SUBROUTINE chem_swap_timelevel
1026
1027	!------------------------------------------------------------------------------!
1028	!
1029	! Description:
1030	! ------------
1031	!> Subroutine defining appropriate grid for netcdf variables.
1032	!> It is called out from subroutine netcdf.
1033	!------------------------------------------------------------------------------!
1034	SUBROUTINE chem_define_netcdf_grid( var, found, grid_x, grid_y, grid_z )
1035
1036	IMPLICIT NONE
1037
1038	CHARACTER (LEN=*), INTENT(IN) :: var !<
1039	LOGICAL, INTENT(OUT) :: found !<
1040	CHARACTER (LEN=*), INTENT(OUT) :: grid_x !<
1041	CHARACTER (LEN=*), INTENT(OUT) :: grid_y !<
1042	CHARACTER (LEN=*), INTENT(OUT) :: grid_z !<
1043
1044	found = .TRUE.
1045
1046	if(var(1:3) == 'kc_') then !< always the same grid for chemistry variables
1047	grid_x = 'x'
1048	grid_y = 'y'
1049	grid_z = 'zu' !< kk Use same z axis as u variables. Has to be checked if OK
1050	else
1051	found = .FALSE.
1052	grid_x = 'none'
1053	grid_y = 'none'
1054	grid_z = 'none'
1055	end if
1056
1057	! write(6,*) 'chem_define_netcdf_grid ',TRIM(var),' ',trim(grid_x),' ',found
1058
1059	END SUBROUTINE chem_define_netcdf_grid
1060	!
1061	!------------------------------------------------------------------------------!
1062	!
1063	! Description:
1064	! ------------
1065	!> Subroutine for checking data output for chemical species
1066	!------------------------------------------------------------------------------!
1067
1068	SUBROUTINE chem_check_data_output( var, unit, i, ilen, k )
1069
1070
1071	USE control_parameters, &
1072	ONLY: data_output, message_string
1073
1074	IMPLICIT NONE
1075
1076	CHARACTER (LEN=*) :: unit !<
1077	CHARACTER (LEN=*) :: var !<
1078
1079	INTEGER(iwp) :: i, lsp
1080	INTEGER(iwp) :: ilen
1081	INTEGER(iwp) :: k
1082
1083	CHARACTER(len=16) :: spec_name
1084
1085	unit = 'illegal'
1086
1087	spec_name = TRIM(var(4:)) !< var 1:3 is 'kc_'.
1088
1089	DO lsp=1,nspec
1090	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
1091	unit = 'ppm'
1092	ENDIF
1093	! It is possible to plant PM10 and PM25 into the gasphase chemistry code
1094	! ! as passive species (e.g. 'passive' in GASPHASE_PREPROC/mechanisms):
1095	! ! set unit to micrograms per m**3 for PM10 and PM25 (PM2.5)
1096	IF (spec_name(1:2) == 'PM') THEN
1097	unit = 'ug m-3'
1098	ENDIF
1099	ENDDO
1100
1101	DO lsp=1,nphot
1102	IF (TRIM(spec_name) == TRIM(phot_frequen(lsp)%name)) THEN
1103	unit = 'sec-1'
1104	ENDIF
1105	ENDDO
1106
1107
1108	RETURN
1109	END SUBROUTINE chem_check_data_output
1110	!
1111	!------------------------------------------------------------------------------!
1112	!
1113	! Description:
1114	! ------------
1115	!> Subroutine for checking data output of profiles for chemistry model
1116	!------------------------------------------------------------------------------!
1117
1118	SUBROUTINE chem_check_data_output_pr( variable, var_count, unit, dopr_unit )
1119
1120
1121	USE arrays_3d, &
1122	ONLY: zu
1123
1124	USE control_parameters, &
1125	ONLY: data_output_pr, message_string, air_chemistry
1126
1127	USE indices
1128
1129	USE profil_parameter
1130
1131	USE statistics
1132
1133
1134	IMPLICIT NONE
1135
1136	CHARACTER (LEN=*) :: unit !<
1137	CHARACTER (LEN=*) :: variable !<
1138	CHARACTER (LEN=*) :: dopr_unit
1139	CHARACTER(len=16) :: spec_name
1140
1141	INTEGER(iwp) :: var_count, lsp !<
1142
1143
1144	spec_name = TRIM(variable(4:))
1145	! write(9,*) 'fm #32 .. air_chemistry ', air_chemistry
1146
1147	IF ( .NOT. air_chemistry ) THEN
1148	message_string = 'data_output_pr = ' // &
1149	TRIM( data_output_pr(var_count) ) // ' is not imp' // &
1150	'lemented for air_chemistry = .FALSE.'
1151	! CALL message( 'check_parameters', 'PA0XXX', 1, 2, 0, 6, 0 )
1152	ELSE
1153	DO lsp = 1, nspec
1154	IF (TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
1155	dopr_index(var_count) = 900
1156	dopr_unit = 'ppm'
1157	hom(:,2,900,:) = SPREAD( zu, 2, statistic_regions+1 )
1158	ENDIF
1159	ENDDO
1160	ENDIF
1161
1162	END SUBROUTINE chem_check_data_output_pr
1163	!
1164	!------------------------------------------------------------------------------!
1165	!
1166	! Description:
1167	! ------------
1168	!> Subroutine defining 3D output variables for chemical species
1169	!------------------------------------------------------------------------------!
1170
1171
1172	SUBROUTINE chem_data_output_3d( av, variable, found, local_pf, fill_value, nzb_do, nzt_do )
1173
1174
1175	USE indices
1176
1177	USE kinds
1178
1179
1180	IMPLICIT NONE
1181
1182	CHARACTER (LEN=*) :: variable !<
1183
1184	INTEGER(iwp) :: av !<
1185	INTEGER(iwp) :: nzb_do !< lower limit of the data output (usually 0)
1186	INTEGER(iwp) :: nzt_do !< vertical upper limit of the data output (usually nz_do3d)
1187
1188	LOGICAL :: found !<
1189
1190	REAL(wp) :: fill_value !<
1191	REAL(sp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) :: local_pf
1192
1193
1194	!-- local variables
1195
1196	INTEGER :: i, j, k, lsp
1197	CHARACTER(len=16) :: spec_name
1198
1199
1200	found = .FALSE.
1201
1202	spec_name = TRIM(variable(4:))
1203	!av == 0
1204
1205	DO lsp=1,nspec
1206	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
1207	IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
1208	TRIM(chem_species(lsp)%name)
1209
1210	IF (av == 0) THEN
1211	DO i = nxl, nxr
1212	DO j = nys, nyn
1213	DO k = nzb_do, nzt_do
1214	local_pf(i,j,k) = MERGE( &
1215	chem_species(lsp)%conc(k,j,i), &
1216	REAL( fill_value, KIND = wp ), &
1217	BTEST( wall_flags_0(k,j,i), 0 ) )
1218	ENDDO
1219	ENDDO
1220	ENDDO
1221
1222	ELSE
1223	DO i = nxl, nxr
1224	DO j = nys, nyn
1225	DO k = nzb_do, nzt_do
1226	local_pf(i,j,k) = MERGE( &
1227	chem_species(lsp)%conc_av(k,j,i),&
1228	REAL( fill_value, KIND = wp ), &
1229	BTEST( wall_flags_0(k,j,i), 0 ) )
1230	ENDDO
1231	ENDDO
1232	ENDDO
1233	ENDIF
1234
1235	found = .TRUE.
1236	ENDIF
1237	ENDDO
1238
1239	RETURN
1240	END SUBROUTINE chem_data_output_3d
1241	!
1242	!------------------------------------------------------------------------------!
1243	!
1244	! Description:
1245	! ------------
1246	!> Subroutine for averaging 3D data of chemical species. Due to the fact that
1247	!> the averaged chem arrays are allocated in chem_init, no if-query concerning
1248	!> the allocation is required (in any mode). Attention: If you just specify an
1249	!> averaged output quantity in the _p3dr file during restarts the first output
1250	!> includes the time between the beginning of the restart run and the first
1251	!> output time (not necessarily the whole averaging_interval you have
1252	!> specified in your _p3d/_p3dr file )
1253	!------------------------------------------------------------------------------!
1254
1255	SUBROUTINE chem_3d_data_averaging ( mode, variable )
1256
1257	USE control_parameters
1258
1259	USE indices
1260
1261	USE kinds
1262
1263	USE surface_mod, &
1264	ONLY: surf_def_h, surf_lsm_h, surf_usm_h
1265
1266	IMPLICIT NONE
1267
1268	CHARACTER (LEN=*) :: mode !<
1269	CHARACTER (LEN=*) :: variable !<
1270
1271	LOGICAL :: match_def !< flag indicating natural-type surface
1272	LOGICAL :: match_lsm !< flag indicating natural-type surface
1273	LOGICAL :: match_usm !< flag indicating urban-type surface
1274
1275	INTEGER(iwp) :: i !< grid index x direction
1276	INTEGER(iwp) :: j !< grid index y direction
1277	INTEGER(iwp) :: k !< grid index z direction
1278	INTEGER(iwp) :: m !< running index surface type
1279	INTEGER(iwp) :: lsp !< running index for chem spcs
1280	INTEGER(iwp) :: lsp_2 !< it looks like redundent .. will be delted ..bK
1281
1282	IF ( mode == 'allocate' ) THEN
1283	DO lsp = 1, nspec
1284	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
1285	! lsp_2 = lsp
1286	chem_species(lsp)%conc_av = 0.0_wp
1287
1288	ENDIF
1289	ENDDO
1290
1291	ELSEIF ( mode == 'sum' ) THEN
1292
1293	DO lsp = 1, nspec
1294	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
1295	! lsp_2 = lsp
1296	DO i = nxlg, nxrg
1297	DO j = nysg, nyng
1298	DO k = nzb, nzt+1
1299	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) + &
1300	chem_species(lsp)%conc(k,j,i)
1301	ENDDO
1302	ENDDO
1303	ENDDO
1304	ELSEIF ( TRIM(variable(4:)) == TRIM('cssws*') ) THEN
1305	DO i = nxl, nxr
1306	DO j = nys, nyn
1307	match_def = surf_def_h(0)%start_index(j,i) <= &
1308	surf_def_h(0)%end_index(j,i)
1309	match_lsm = surf_lsm_h%start_index(j,i) <= &
1310	surf_lsm_h%end_index(j,i)
1311	match_usm = surf_usm_h%start_index(j,i) <= &
1312	surf_usm_h%end_index(j,i)
1313
1314	IF ( match_def ) THEN
1315	m = surf_def_h(0)%end_index(j,i)
1316	chem_species(lsp)%cssws_av(j,i) = &
1317	chem_species(lsp)%cssws_av(j,i) + &
1318	surf_def_h(0)%cssws(lsp,m)
1319	ELSEIF ( match_lsm .AND. .NOT. match_usm ) THEN
1320	m = surf_lsm_h%end_index(j,i)
1321	chem_species(lsp)%cssws_av(j,i) = &
1322	chem_species(lsp)%cssws_av(j,i) + &
1323	surf_lsm_h%cssws(lsp,m)
1324	ELSEIF ( match_usm ) THEN
1325	m = surf_usm_h%end_index(j,i)
1326	chem_species(lsp)%cssws_av(j,i) = &
1327	chem_species(lsp)%cssws_av(j,i) + &
1328	surf_usm_h%cssws(lsp,m)
1329	ENDIF
1330	ENDDO
1331	ENDDO
1332	ENDIF
1333	ENDDO
1334
1335	ELSEIF ( mode == 'average' ) THEN
1336	DO lsp = 1, nspec
1337	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
1338	! lsp_2 = lsp
1339	DO i = nxlg, nxrg
1340	DO j = nysg, nyng
1341	DO k = nzb, nzt+1
1342	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) / REAL( average_count_3d, KIND=wp )
1343	ENDDO
1344	ENDDO
1345	ENDDO
1346
1347	ELSEIF (TRIM(variable(4:)) == TRIM('cssws*') ) THEN
1348	DO i = nxlg, nxrg
1349	DO j = nysg, nyng
1350	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) / REAL( average_count_3d, KIND=wp )
1351	ENDDO
1352	ENDDO
1353	CALL exchange_horiz_2d( chem_species(lsp)%cssws_av, nbgp )
1354	ENDIF
1355	ENDDO
1356
1357	ENDIF
1358
1359	END SUBROUTINE chem_3d_data_averaging
1360
1361	!------------------------------------------------------------------------------!
1362	!
1363	! Description:
1364	! ------------
1365	!> Subroutine to write restart data for chemistry model
1366	!------------------------------------------------------------------------------!
1367	SUBROUTINE chem_wrd_local
1368
1369
1370	IMPLICIT NONE
1371
1372	INTEGER(iwp) :: lsp !<
1373
1374	! REAL(kind=wp), DIMENSION(nzb:nzt+1,nysg:nyng,nxlg:nxrg) :: chems_conc
1375
1376
1377	DO lsp = 1, nspec
1378
1379	CALL wrd_write_string( TRIM( chem_species(lsp)%name ))
1380	WRITE ( 14 ) chem_species(lsp)%conc
1381
1382	CALL wrd_write_string( TRIM( chem_species(lsp)%name )//'_av' )
1383	WRITE ( 14 ) chem_species(lsp)%conc_av
1384
1385	ENDDO
1386
1387
1388	END SUBROUTINE chem_wrd_local
1389
1390	!------------------------------------------------------------------------------!
1391	!
1392	! Description:
1393	! ------------
1394	!> Subroutine to read restart data of chemical species
1395	!------------------------------------------------------------------------------!
1396
1397	SUBROUTINE chem_rrd_local( i, k, nxlf, nxlc, nxl_on_file, nxrf, nxrc, &
1398	nxr_on_file, nynf, nync, nyn_on_file, nysf, nysc, &
1399	nys_on_file, tmp_3d, found )
1400
1401	USE control_parameters
1402
1403	USE indices
1404
1405	USE pegrid
1406
1407	IMPLICIT NONE
1408
1409	CHARACTER (LEN=20) :: spc_name_av !<
1410
1411	INTEGER(iwp) :: i, lsp !<
1412	INTEGER(iwp) :: k !<
1413	INTEGER(iwp) :: nxlc !<
1414	INTEGER(iwp) :: nxlf !<
1415	INTEGER(iwp) :: nxl_on_file !<
1416	INTEGER(iwp) :: nxrc !<
1417	INTEGER(iwp) :: nxrf !<
1418	INTEGER(iwp) :: nxr_on_file !<
1419	INTEGER(iwp) :: nync !<
1420	INTEGER(iwp) :: nynf !<
1421	INTEGER(iwp) :: nyn_on_file !<
1422	INTEGER(iwp) :: nysc !<
1423	INTEGER(iwp) :: nysf !<
1424	INTEGER(iwp) :: nys_on_file !<
1425
1426	LOGICAL, INTENT(OUT) :: found
1427
1428	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
1429
1430
1431	found = .FALSE.
1432
1433
1434	IF ( ALLOCATED(chem_species) ) THEN
1435
1436	DO lsp = 1, nspec
1437
1438	!< for time-averaged chemical conc.
1439	spc_name_av = TRIM(chem_species(lsp)%name)//'_av'
1440
1441	IF (restart_string(1:length) == TRIM(chem_species(lsp)%name) ) &
1442	THEN
1443	!< read data into tmp_3d
1444	IF ( k == 1 ) READ ( 13 ) tmp_3d
1445	!< fill ..%conc in the restart run
1446	chem_species(lsp)%conc(:,nysc-nbgp:nync+nbgp, &
1447	nxlc-nbgp:nxrc+nbgp) = &
1448	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
1449	found = .TRUE.
1450	ELSEIF (restart_string(1:length) == spc_name_av ) THEN
1451	IF ( k == 1 ) READ ( 13 ) tmp_3d
1452	chem_species(lsp)%conc_av(:,nysc-nbgp:nync+nbgp, &
1453	nxlc-nbgp:nxrc+nbgp) = &
1454	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
1455	found = .TRUE.
1456	ENDIF
1457
1458	ENDDO
1459
1460	ENDIF
1461
1462
1463	END SUBROUTINE chem_rrd_local
1464
1465
1466	!------------------------------------------------------------------------------!
1467	!
1468	! Description:
1469	! ------------
1470	!> Subroutine calculating prognostic equations for chemical species
1471	!> (cache-optimized).
1472	!> Routine is called separately for each chemical species over a loop from
1473	!> prognostic_equations.
1474	!------------------------------------------------------------------------------!
1475	SUBROUTINE chem_prognostic_equations_ij ( cs_scalar_p, cs_scalar, tcs_scalar_m, pr_init_cs, &
1476	i, j, i_omp_start, tn, ilsp, flux_s_cs, diss_s_cs, &
1477	flux_l_cs, diss_l_cs )
1478	USE pegrid
1479	USE advec_ws, ONLY: advec_s_ws
1480	USE advec_s_pw_mod, ONLY: advec_s_pw
1481	USE advec_s_up_mod, ONLY: advec_s_up
1482	USE diffusion_s_mod, ONLY: diffusion_s
1483	USE indices, ONLY: wall_flags_0
1484	USE surface_mod, ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
1485	surf_usm_v
1486
1487
1488	IMPLICIT NONE
1489
1490	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p, cs_scalar, tcs_scalar_m
1491
1492	INTEGER(iwp),INTENT(IN) :: i, j, i_omp_start, tn, ilsp
1493	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: flux_s_cs !<
1494	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: diss_s_cs !<
1495	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: flux_l_cs !<
1496	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: diss_l_cs !<
1497	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
1498
1499	!-- local variables
1500
1501	INTEGER :: k
1502	!
1503	!-- Tendency-terms for chem spcs.
1504	tend(:,j,i) = 0.0_wp
1505	!
1506	!-- Advection terms
1507	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1508	IF ( ws_scheme_sca ) THEN
1509	CALL advec_s_ws( i, j, cs_scalar, 'kc', flux_s_cs, diss_s_cs, &
1510	flux_l_cs, diss_l_cs, i_omp_start, tn )
1511	ELSE
1512	CALL advec_s_pw( i, j, cs_scalar )
1513	ENDIF
1514	ELSE
1515	CALL advec_s_up( i, j, cs_scalar )
1516	ENDIF
1517
1518	!
1519
1520	!-- Diffusion terms (the last three arguments are zero)
1521
1522	CALL diffusion_s( i, j, cs_scalar, &
1523	surf_def_h(0)%cssws(ilsp,:), surf_def_h(1)%cssws(ilsp,:), &
1524	surf_def_h(2)%cssws(ilsp,:), &
1525	surf_lsm_h%cssws(ilsp,:), surf_usm_h%cssws(ilsp,:), &
1526	surf_def_v(0)%cssws(ilsp,:), surf_def_v(1)%cssws(ilsp,:), &
1527	surf_def_v(2)%cssws(ilsp,:), surf_def_v(3)%cssws(ilsp,:), &
1528	surf_lsm_v(0)%cssws(ilsp,:), surf_lsm_v(1)%cssws(ilsp,:), &
1529	surf_lsm_v(2)%cssws(ilsp,:), surf_lsm_v(3)%cssws(ilsp,:), &
1530	surf_usm_v(0)%cssws(ilsp,:), surf_usm_v(1)%cssws(ilsp,:), &
1531	surf_usm_v(2)%cssws(ilsp,:), surf_usm_v(3)%cssws(ilsp,:) )
1532
1533	!
1534	!-- Prognostic equation for chem spcs
1535	DO k = nzb+1, nzt
1536	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) + ( dt_3d * &
1537	( tsc(2) * tend(k,j,i) + &
1538	tsc(3) * tcs_scalar_m(k,j,i) ) &
1539	- tsc(5) * rdf_sc(k) &
1540	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
1541	) &
1542	* MERGE( 1.0_wp, 0.0_wp, &
1543	BTEST( wall_flags_0(k,j,i), 0 ) &
1544	)
1545
1546	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
1547	ENDDO
1548
1549	!
1550	!-- Calculate tendencies for the next Runge-Kutta step
1551	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1552	IF ( intermediate_timestep_count == 1 ) THEN
1553	DO k = nzb+1, nzt
1554	tcs_scalar_m(k,j,i) = tend(k,j,i)
1555	ENDDO
1556	ELSEIF ( intermediate_timestep_count < &
1557	intermediate_timestep_count_max ) THEN
1558	DO k = nzb+1, nzt
1559	tcs_scalar_m(k,j,i) = -9.5625_wp * tend(k,j,i) + &
1560	5.3125_wp * tcs_scalar_m(k,j,i)
1561	ENDDO
1562	ENDIF
1563	ENDIF
1564
1565	END SUBROUTINE chem_prognostic_equations_ij
1566
1567
1568	!------------------------------------------------------------------------------!
1569	!
1570	! Description:
1571	! ------------
1572	!> Subroutine calculating prognostic equations for chemical species
1573	!> (vector-optimized).
1574	!> Routine is called separately for each chemical species over a loop from
1575	!> prognostic_equations.
1576	!------------------------------------------------------------------------------!
1577	SUBROUTINE chem_prognostic_equations ( cs_scalar_p, cs_scalar, tcs_scalar_m, &
1578	pr_init_cs, ilsp )
1579
1580	USE advec_s_pw_mod, &
1581	ONLY: advec_s_pw
1582
1583	USE advec_s_up_mod, &
1584	ONLY: advec_s_up
1585
1586	USE advec_ws, &
1587	ONLY: advec_s_ws
1588
1589	USE diffusion_s_mod, &
1590	ONLY: diffusion_s
1591
1592	USE indices, &
1593	ONLY: nxl, nxr, nyn, nys, wall_flags_0
1594
1595	USE pegrid
1596
1597	USE surface_mod, &
1598	ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
1599	surf_usm_v
1600
1601	IMPLICIT NONE
1602
1603	INTEGER :: i !< running index
1604	INTEGER :: j !< running index
1605	INTEGER :: k !< running index
1606
1607	INTEGER(iwp),INTENT(IN) :: ilsp !<
1608
1609	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
1610
1611	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar !<
1612	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p !<
1613	REAL(wp), DIMENSION(:,:,:), POINTER :: tcs_scalar_m !<
1614
1615
1616	!
1617	!-- Tendency terms for chemical species
1618	tend = 0.0_wp
1619	!
1620	!-- Advection terms
1621	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1622	IF ( ws_scheme_sca ) THEN
1623	CALL advec_s_ws( cs_scalar, 'kc' )
1624	ELSE
1625	CALL advec_s_pw( cs_scalar )
1626	ENDIF
1627	ELSE
1628	CALL advec_s_up( cs_scalar )
1629	ENDIF
1630	!
1631	!-- Diffusion terms (the last three arguments are zero)
1632	CALL diffusion_s( cs_scalar, &
1633	surf_def_h(0)%cssws(ilsp,:), &
1634	surf_def_h(1)%cssws(ilsp,:), &
1635	surf_def_h(2)%cssws(ilsp,:), &
1636	surf_lsm_h%cssws(ilsp,:), &
1637	surf_usm_h%cssws(ilsp,:), &
1638	surf_def_v(0)%cssws(ilsp,:), &
1639	surf_def_v(1)%cssws(ilsp,:), &
1640	surf_def_v(2)%cssws(ilsp,:), &
1641	surf_def_v(3)%cssws(ilsp,:), &
1642	surf_lsm_v(0)%cssws(ilsp,:), &
1643	surf_lsm_v(1)%cssws(ilsp,:), &
1644	surf_lsm_v(2)%cssws(ilsp,:), &
1645	surf_lsm_v(3)%cssws(ilsp,:), &
1646	surf_usm_v(0)%cssws(ilsp,:), &
1647	surf_usm_v(1)%cssws(ilsp,:), &
1648	surf_usm_v(2)%cssws(ilsp,:), &
1649	surf_usm_v(3)%cssws(ilsp,:) )
1650	!
1651	!-- Prognostic equation for chemical species
1652	DO i = nxl, nxr
1653	DO j = nys, nyn
1654	DO k = nzb+1, nzt
1655	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) &
1656	+ ( dt_3d * &
1657	( tsc(2) * tend(k,j,i) &
1658	+ tsc(3) * tcs_scalar_m(k,j,i) &
1659	) &
1660	- tsc(5) * rdf_sc(k) &
1661	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
1662	) &
1663	* MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_0(k,j,i), 0 ) )
1664
1665	IF ( cs_scalar_p(k,j,i) < 0.0_wp ) cs_scalar_p(k,j,i) = 0.1_wp * cs_scalar(k,j,i)
1666	ENDDO
1667	ENDDO
1668	ENDDO
1669	!
1670	!-- Calculate tendencies for the next Runge-Kutta step
1671	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1672	IF ( intermediate_timestep_count == 1 ) THEN
1673	DO i = nxl, nxr
1674	DO j = nys, nyn
1675	DO k = nzb+1, nzt
1676	tcs_scalar_m(k,j,i) = tend(k,j,i)
1677	ENDDO
1678	ENDDO
1679	ENDDO
1680	ELSEIF ( intermediate_timestep_count < &
1681	intermediate_timestep_count_max ) THEN
1682	DO i = nxl, nxr
1683	DO j = nys, nyn
1684	DO k = nzb+1, nzt
1685	tcs_scalar_m(k,j,i) = - 9.5625_wp * tend(k,j,i) &
1686	+ 5.3125_wp * tcs_scalar_m(k,j,i)
1687	ENDDO
1688	ENDDO
1689	ENDDO
1690	ENDIF
1691	ENDIF
1692
1693	END SUBROUTINE chem_prognostic_equations
1694
1695
1696	!------------------------------------------------------------------------------!
1697	!
1698	! Description:
1699	! ------------
1700	!> Subroutine defining header output for chemistry model
1701	!------------------------------------------------------------------------------!
1702	SUBROUTINE chem_header ( io )
1703
1704	IMPLICIT NONE
1705
1706	INTEGER(iwp), INTENT(IN) :: io !< Unit of the output file
1707
1708	! print*,'the header subroutine is still not operational'
1709	!!
1710	!!-- Write chemistry model header
1711	! WRITE( io, 3 )
1712	!
1713	! IF ( radiation_scheme == "constant" ) THEN
1714	! WRITE( io, 4 ) net_radiation
1715	! ELSEIF ( radiation_scheme == "clear-sky" ) THEN
1716	! WRITE( io, 5 )
1717	! ELSEIF ( radiation_scheme == "rrtmg" ) THEN
1718	! WRITE( io, 6 )
1719	! IF ( .NOT. lw_radiation ) WRITE( io, 10 )
1720	! IF ( .NOT. sw_radiation ) WRITE( io, 11 )
1721	! ENDIF
1722	!
1723	! IF ( albedo_type == 0 ) THEN
1724	! WRITE( io, 7 ) albedo
1725	! ELSE
1726	! WRITE( io, 8 ) TRIM( albedo_type_name(albedo_type) )
1727	! ENDIF
1728	! IF ( constant_albedo ) THEN
1729	! WRITE( io, 9 )
1730	! ENDIF
1731	!
1732	! IF ( radiation .AND. radiation_scheme /= 'constant' ) THEN
1733	! WRITE ( io, 1 ) lambda
1734	! WRITE ( io, 2 ) day_init, time_utc_init
1735	! ENDIF
1736	!
1737	! WRITE( io, 12 ) dt_radiation
1738	!
1739	! 1 FORMAT (' Geograph. longitude : lambda = ',F4.1,' degr')
1740	! 2 FORMAT (' Day of the year at model start : day_init = ',I3 &
1741	! /' UTC time at model start : time_utc_init = ',F7.1' s')
1742	! 3 FORMAT (//' Radiation model information:'/ &
1743	! ' ----------------------------'/)
1744	! 4 FORMAT (' --> Using constant net radiation: net_radiation = ', F6.2, &
1745	! // 'W/m**2')
1746	! 5 FORMAT (' --> Simple radiation scheme for clear sky is used (no clouds,', &
1747	! ' default)')
1748	! 6 FORMAT (' --> RRTMG scheme is used')
1749	! 7 FORMAT (/' User-specific surface albedo: albedo =', F6.3)
1750	! 8 FORMAT (/' Albedo is set for land surface type: ', A)
1751	! 9 FORMAT (/' --> Albedo is fixed during the run')
1752	!10 FORMAT (/' --> Longwave radiation is disabled')
1753	!11 FORMAT (/' --> Shortwave radiation is disabled.')
1754	!12 FORMAT (' Timestep: dt_radiation = ', F6.2, ' s')
1755	!
1756	!
1757	END SUBROUTINE chem_header
1758
1759	!------------------------------------------------------------------------------
1760	! Description:
1761	! ------------
1762	!> Subroutine reading restart data for chemistry model input parameters
1763	! (FK: To make restarts work, I had to comment this routine. We actually
1764	! don't need it, since the namelist parameters are always read in,
1765	! also in case of a restart run)
1766	!------------------------------------------------------------------------------
1767	! SUBROUTINE chem_rrd_global
1768	!
1769	! USE chem_modules
1770	!
1771	! USE control_parameters, &
1772	! ONLY: length, message_string, restart_string
1773	!
1774	!
1775	! IMPLICIT NONE
1776	!
1777	!
1778	!
1779	! DO
1780	!
1781	! SELECT CASE ( restart_string(1:length) )
1782	!
1783	! CASE ( 'bc_cs_b' )
1784	! READ ( 13 ) bc_cs_b
1785	!
1786	! CASE DEFAULT
1787	!
1788	! EXIT
1789	!
1790	! END SELECT
1791	!
1792	!!
1793	!!-- Read next string and its length
1794	! READ ( 13 ) length
1795	! READ ( 13 ) restart_string(1:length)
1796	!
1797	! ENDDO
1798	!
1799	! END SUBROUTINE chem_rrd_global
1800
1801
1802	!------------------------------------------------------------------------------!
1803	!
1804	! Description:
1805	! ------------
1806	!> Subroutine writing restart data for chemistry model input parameters
1807	! (FK: To make restarts work, I had to comment this routine. We actually
1808	! don't need it, since the namelist parameters are always read in,
1809	! also in case of a restart run)
1810	!------------------------------------------------------------------------------!
1811	! SUBROUTINE chem_wrd_global
1812	!
1813	! USE chem_modules
1814	!
1815	! USE kinds
1816	!
1817	!
1818	! IMPLICIT NONE
1819	!
1820	! INTEGER(iwp) :: lsp !< running index for chem spcs
1821	!
1822	! !
1823	! !-- Writing out input parameters that are not part of chemistry_parameters
1824	! !-- namelist (namelist parameters are anyway read in again in case of restart)
1825	! DO lsp = 1, nvar
1826	! CALL wrd_write_string( 'conc_pr_init_'//chem_species(lsp)%name )
1827	! WRITE ( 14 ) chem_species(lsp)%conc_pr_init
1828	! ENDDO
1829	!
1830	!
1831	! END SUBROUTINE chem_wrd_global
1832
1833
1834	!------------------------------------------------------------------------------!
1835	!
1836	! Description:
1837	! ------------
1838	!> Subroutine for emission
1839	!------------------------------------------------------------------------------!
1840	SUBROUTINE chem_emissions
1841
1842	USE chem_modules
1843
1844	USE netcdf_data_input_mod, &
1845	ONLY: street_type_f
1846
1847	USE surface_mod, &
1848	ONLY: surf_lsm_h
1849
1850
1851	IMPLICIT NONE
1852
1853	INTEGER(iwp) :: i !< running index for grid in x-direction
1854	INTEGER(iwp) :: j !< running index for grid in y-direction
1855	INTEGER(iwp) :: m !< running index for horizontal surfaces
1856	INTEGER(iwp) :: lsp !< running index for chem spcs
1857
1858	!
1859	!-- Comment??? (todo)
1860	IF ( street_type_f%from_file ) THEN
1861	!
1862	!-- Streets are lsm surfaces, hence, no usm surface treatment required
1863	DO m = 1, surf_lsm_h%ns
1864	i = surf_lsm_h%i(m)
1865	j = surf_lsm_h%j(m)
1866
1867	IF ( street_type_f%var(j,i) >= main_street_id .AND. &
1868	street_type_f%var(j,i) < max_street_id ) THEN
1869	DO lsp = 1, nvar
1870	surf_lsm_h%cssws(lsp,m) = emiss_factor_main * surface_csflux(lsp)
1871	ENDDO
1872	ELSEIF ( street_type_f%var(j,i) >= side_street_id .AND. &
1873	street_type_f%var(j,i) < main_street_id ) THEN
1874	DO lsp = 1, nvar
1875	surf_lsm_h%cssws(lsp,m) = emiss_factor_side * surface_csflux(lsp)
1876	ENDDO
1877	ELSE
1878	surf_lsm_h%cssws(:,m) = 0.0_wp
1879	ENDIF
1880	ENDDO
1881
1882	ENDIF
1883
1884	END SUBROUTINE chem_emissions
1885
1886
1887	END MODULE chemistry_model_mod
1888

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