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source: palm/trunk/SOURCE/chemistry_model_mod.f90 @ 3173

Last change on this file since 3173 was 3173, checked in by suehring, 6 years ago
Further revision of 2D surface output for radiation and chemistry quantities; bugfix for commit 3170
Property svn:keywords set to `Id`
File size: 76.2 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 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 3173 2018-07-26 12:55:23Z suehring $
29	! Revise output of surface quantities in case of overhanging structures
30	!
31	! 3045 2018-05-28 07:55:41Z Giersch
32	! error messages revised
33	!
34	! 3014 2018-05-09 08:42:38Z maronga
35	! Bugfix: nzb_do and nzt_do were not used for 3d data output
36	!
37	! 3004 2018-04-27 12:33:25Z Giersch
38	! Comment concerning averaged data output added
39	!
40	! 2932 2018-03-26 09:39:22Z maronga
41	! renamed chemistry_par to chemistry_parameters
42	!
43	! 2894 2018-03-15 09:17:58Z Giersch
44	! Calculations of the index range of the subdomain on file which overlaps with
45	! the current subdomain are already done in read_restart_data_mod,
46	! chem_last_actions was renamed to chem_wrd_local, chem_read_restart_data was
47	! renamed to chem_rrd_local, chem_write_var_list was renamed to
48	! chem_wrd_global, chem_read_var_list was renamed to chem_rrd_global,
49	! chem_skip_var_list has been removed, variable named found has been
50	! introduced for checking if restart data was found, reading of restart strings
51	! has been moved completely to read_restart_data_mod, chem_rrd_local is already
52	! inside the overlap loop programmed in read_restart_data_mod, todo list has
53	! bees extended, redundant characters in chem_wrd_local have been removed,
54	! the marker * end chemistry * is not necessary anymore, strings and their
55	! respective lengths are written out and read now in case of restart runs to
56	! get rid of prescribed character lengths
57	!
58	! 2815 2018-02-19 11:29:57Z suehring
59	! Bugfix in restart mechanism,
60	! rename chem_tendency to chem_prognostic_equations,
61	! implement vector-optimized version of chem_prognostic_equations,
62	! some clean up (incl. todo list)
63	!
64	! 2773 2018-01-30 14:12:54Z suehring
65	! Declare variables required for nesting as public
66	!
67	! 2772 2018-01-29 13:10:35Z suehring
68	! Bugfix in string handling
69	!
70	! 2768 2018-01-24 15:38:29Z kanani
71	! Shorten lines to maximum length of 132 characters
72	!
73	! 2766 2018-01-22 17:17:47Z kanani
74	! Removed preprocessor directive __chem
75	!
76	! 2756 2018-01-16 18:11:14Z suehring
77	! Fill values in 3D output introduced.
78	!
79	! 2718 2018-01-02 08:49:38Z maronga
80	! Initial revision
81	!
82	!
83	!
84	!
85	! Authors:
86	! --------
87	! @author Renate Forkel
88	! @author Farah Kanani-Suehring
89	! @author Klaus Ketelsen
90	! @author Basit Khan
91	!
92	!
93	!------------------------------------------------------------------------------!
94	! Description:
95	! ------------
96	!> Chemistry model for PALM-4U
97	!> @todo Adjust chem_rrd_local to CASE structure of others modules. It is not
98	!> allowed to use the chemistry model in a precursor run and additionally
99	!> not using it in a main run
100	!> @todo Update/clean-up todo list! (FK)
101	!> @todo Set proper fill values (/= 0) for chem output arrays! (FK)
102	!> @todo Add routine chem_check_parameters, add checks for inconsistent or
103	!> unallowed parameter settings.
104	!> CALL of chem_check_parameters from check_parameters. (FK)
105	!> @todo Make routine chem_header available, CALL from header.f90
106	!> (see e.g. how it is done in routine lsm_header in
107	!> land_surface_model_mod.f90). chem_header should include all setup
108	!> info about chemistry parameter settings. (FK)
109	!> @todo Implement turbulent inflow of chem spcs in inflow_turbulence.
110	!> @todo Separate boundary conditions for each chem spcs to be implemented
111	!> @todo Currently only total concentration are calculated. Resolved, parameterized
112	!> and chemistry fluxes although partially and some completely coded but
113	!> are not operational/activated in this version. bK.
114	!> @todo slight differences in passive scalar and chem spcs when chem reactions
115	!> turned off. Need to be fixed. bK
116	!> @todo test nesting for chem spcs, was implemented by suehring (kanani)
117	!> @todo subroutine set_const_initial_values to be taken out from chemistry_model_mod !bK.
118	!> @todo chemistry error messages
119	!> @todo Format this module according to PALM coding standard (see e.g. module
120	!> template under http://palm.muk.uni-hannover.de/mosaik/downloads/8 or
121	!> D3_coding_standard.pdf under https://palm.muk.uni-hannover.de/trac/downloads/16)
122	!
123	!------------------------------------------------------------------------------!
124
125	MODULE chemistry_model_mod
126
127	USE kinds, ONLY: wp, iwp
128	USE indices, ONLY: nz, nzb,nzt,nysg,nyng,nxlg,nxrg,nys,nyn
129	USE pegrid, ONLY: myid, threads_per_task
130	USE control_parameters, ONLY: dt_3d, ws_scheme_sca, initializing_actions, message_string, &
131	omega, tsc, intermediate_timestep_count, &
132	intermediate_timestep_count_max, &
133	timestep_scheme, use_prescribed_profile_data
134	USE arrays_3d, ONLY: hyp, pt, rdf_sc, tend, zu
135	USE chem_gasphase_mod, ONLY: nspec, spc_names, nkppctrl, nmaxfixsteps, &
136	t_steps, fill_temp, chem_gasphase_integrate, &
137	nvar, atol, rtol, nphot, phot_names
138	USE cpulog, ONLY: cpu_log, log_point
139
140	USE chem_modules
141
142
143	IMPLICIT NONE
144	PRIVATE
145	SAVE
146
147	!- Define chemical variables
148
149	TYPE species_def
150	CHARACTER(LEN=8) :: name
151	CHARACTER(LEN=16) :: unit
152	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc
153	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_av
154	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_p
155	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: tconc_m
156	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: cssws_av
157	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: flux_s_cs
158	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: diss_s_cs
159	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: flux_l_cs
160	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: diss_l_cs
161	REAL(kind=wp),ALLOCATABLE,DIMENSION(:) :: conc_pr_init
162	END TYPE species_def
163
164
165	TYPE photols_def
166	CHARACTER(LEN=8) :: name
167	CHARACTER(LEN=16) :: unit
168	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: freq
169	END TYPE photols_def
170
171
172	PUBLIC species_def
173	PUBLIC photols_def
174
175
176	TYPE(species_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: chem_species
177	TYPE(photols_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: phot_frequen
178
179	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_1
180	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_2
181	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_3
182	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_av
183	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: freq_1
184
185	INTEGER,DIMENSION(nkppctrl) :: icntrl ! Fine tuning kpp
186	REAL(kind=wp),DIMENSION(nkppctrl) :: rcntrl ! Fine tuning kpp
187
188	CHARACTER(10), PUBLIC :: photolysis_scheme
189	! 'constant',
190	! 'simple' (Simple parameterisation from MCM, Saunders et al., 2003, Atmos. Chem. Phys., 3, 161-180
191	! 'fastj' (Wild et al., 2000, J. Atmos. Chem., 37, 245-282) STILL NOT IMPLEMENTED
192
193	PUBLIC nspec
194	PUBLIC nvar
195	PUBLIC spc_names
196	PUBLIC spec_conc_2
197
198	!- Interface section
199	INTERFACE chem_boundary_conds
200	MODULE PROCEDURE chem_boundary_conds
201	END INTERFACE chem_boundary_conds
202
203	INTERFACE chem_init
204	MODULE PROCEDURE chem_init
205	END INTERFACE chem_init
206
207	INTERFACE chem_init_profiles
208	MODULE PROCEDURE chem_init_profiles
209	END INTERFACE chem_init_profiles
210
211	INTERFACE chem_parin
212	MODULE PROCEDURE chem_parin
213	END INTERFACE chem_parin
214
215	INTERFACE chem_integrate
216	MODULE PROCEDURE chem_integrate_ij
217	END INTERFACE chem_integrate
218
219	INTERFACE chem_swap_timelevel
220	MODULE PROCEDURE chem_swap_timelevel
221	END INTERFACE chem_swap_timelevel
222
223	INTERFACE chem_define_netcdf_grid
224	MODULE PROCEDURE chem_define_netcdf_grid
225	END INTERFACE chem_define_netcdf_grid
226
227	INTERFACE chem_data_output_3d
228	MODULE PROCEDURE chem_data_output_3d
229	END INTERFACE chem_data_output_3d
230
231	INTERFACE chem_check_data_output
232	MODULE PROCEDURE chem_check_data_output
233	END INTERFACE chem_check_data_output
234
235	INTERFACE chem_check_data_output_pr
236	MODULE PROCEDURE chem_check_data_output_pr
237	END INTERFACE chem_check_data_output_pr
238
239	INTERFACE chem_3d_data_averaging
240	MODULE PROCEDURE chem_3d_data_averaging
241	END INTERFACE chem_3d_data_averaging
242
243	INTERFACE chem_wrd_local
244	MODULE PROCEDURE chem_wrd_local
245	END INTERFACE chem_wrd_local
246
247	INTERFACE chem_rrd_local
248	MODULE PROCEDURE chem_rrd_local
249	END INTERFACE chem_rrd_local
250
251	INTERFACE chem_prognostic_equations
252	MODULE PROCEDURE chem_prognostic_equations
253	MODULE PROCEDURE chem_prognostic_equations_ij
254	END INTERFACE chem_prognostic_equations
255
256	INTERFACE chem_header
257	MODULE PROCEDURE chem_header
258	END INTERFACE chem_header
259
260	INTERFACE chem_emissions
261	MODULE PROCEDURE chem_emissions
262	END INTERFACE chem_emissions
263
264	! INTERFACE chem_wrd_global
265	! MODULE PROCEDURE chem_wrd_global
266	! END INTERFACE chem_wrd_global
267	!
268	! INTERFACE chem_rrd_global
269	! MODULE PROCEDURE chem_rrd_global
270	! END INTERFACE chem_rrd_global
271
272
273	PUBLIC chem_3d_data_averaging, chem_boundary_conds, chem_check_data_output, &
274	chem_check_data_output_pr, chem_data_output_3d, &
275	chem_define_netcdf_grid, chem_emissions, chem_header, chem_init, &
276	chem_init_profiles, chem_integrate, chem_wrd_local, &
277	chem_parin, chem_prognostic_equations, &
278	chem_rrd_local, chem_swap_timelevel
279
280
281	CONTAINS
282
283	!------------------------------------------------------------------------------!
284	!
285	! Description:
286	! ------------
287	!> Subroutine to initialize and set all boundary conditions for chemical species
288	!------------------------------------------------------------------------------!
289
290	SUBROUTINE chem_boundary_conds( mode )
291
292	USE control_parameters, &
293	ONLY: air_chemistry, outflow_l, outflow_n, outflow_r, outflow_s
294	USE indices, &
295	ONLY: nxl, nxr, nxlg, nxrg, nyng, nysg, nzt
296
297	! USE prognostic_equations_mod, &
298
299	USE arrays_3d, &
300	ONLY: dzu
301	USE surface_mod, &
302	ONLY: bc_h
303
304	CHARACTER (len=*), INTENT(IN) :: mode
305	INTEGER(iwp) :: i !< grid index x direction.
306	INTEGER(iwp) :: j !< grid index y direction.
307	INTEGER(iwp) :: k !< grid index z direction.
308	INTEGER(iwp) :: kb !< variable to set respective boundary value, depends on facing.
309	INTEGER(iwp) :: l !< running index boundary type, for up- and downward-facing walls.
310	INTEGER(iwp) :: m !< running index surface elements.
311	INTEGER(iwp) :: lsp !< running index for chem spcs.
312	INTEGER(iwp) :: lph !< running index for photolysis frequencies
313
314
315	SELECT CASE ( TRIM( mode ) )
316	CASE ( 'init' )
317	DO lsp = 1, nspec
318	IF ( surface_csflux(lsp) == 9999999.9_wp ) THEN
319	constant_csflux(lsp) = .FALSE.
320	ENDIF
321	ENDDO
322
323	IF ( bc_cs_b == 'dirichlet' ) THEN
324	ibc_cs_b = 0
325	ELSEIF ( bc_cs_b == 'neumann' ) THEN
326	ibc_cs_b = 1
327	ELSE
328	! message_string = 'unknown boundary condition: bc_cs_b ="' // TRIM( bc_cs_b ) // '"' ! bK commented
329	CALL message( 'chem_boundary_conds', 'CM0010', 1, 2, 0, 6, 0 ) !< chemistry_model_mod should have special error numbers --> "CHEM###",
330	ENDIF
331	!
332	!-- Set Integer flags and check for possible erroneous settings for top
333	!-- boundary condition. bK added _cs_ here.
334	IF ( bc_cs_t == 'dirichlet' ) THEN
335	ibc_cs_t = 0
336	ELSEIF ( bc_cs_t == 'neumann' ) THEN
337	ibc_cs_t = 1
338	ELSEIF ( bc_cs_t == 'initial_gradient' ) THEN
339	ibc_cs_t = 2
340	ELSEIF ( bc_cs_t == 'nested' ) THEN
341	ibc_cs_t = 3
342	ELSE
343	! message_string = 'unknown boundary condition: bc_c_t ="' // TRIM( bc_cs_t ) // '"'
344	CALL message( 'check_parameters', 'CM0011', 1, 2, 0, 6, 0 )
345	ENDIF
346
347
348	CASE ( 'set_bc_bottomtop' )
349	!-- Bottom boundary condtions for chemical species
350	DO lsp = 1, nspec
351	IF ( ibc_cs_b == 0 ) THEN
352	DO l = 0, 1
353	!-- Set index kb: For upward-facing surfaces (l=0), kb=-1, i.e.
354	!-- the chem_species(nsp)%conc_p value at the topography top (k-1)
355	!-- is set; for downward-facing surfaces (l=1), kb=1, i.e. the
356	!-- value at the topography bottom (k+1) is set.
357
358	kb = MERGE( -1, 1, l == 0 )
359	!$OMP PARALLEL DO PRIVATE( i, j, k )
360	DO m = 1, bc_h(l)%ns
361	i = bc_h(l)%i(m)
362	j = bc_h(l)%j(m)
363	k = bc_h(l)%k(m)
364	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc(k+kb,j,i)
365	ENDDO
366	ENDDO
367
368	ELSEIF ( ibc_cs_b == 1 ) THEN
369	! in boundary_conds there is som extra loop over m here for passive tracer
370	DO l = 0, 1
371	kb = MERGE( -1, 1, l == 0 )
372	!$OMP PARALLEL DO PRIVATE( i, j, k )
373	DO m = 1, bc_h(l)%ns
374	i = bc_h(l)%i(m)
375	j = bc_h(l)%j(m)
376	k = bc_h(l)%k(m)
377	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc_p(k,j,i)
378
379	!< @todo: chem_species(nsp)%conc_p(k+kb,j,i) = chem_species(nsp)%conc(k+kb,j,i), &
380	!< pls loop over nsp=1, NSPEC.
381	!< @todo: We should also think about the possibility to have &
382	!< individual boundary conditions for each species? This means, bc_cs_b, &
383	!< bc_cs_t, ibc_cs_b, ibc_cs_t would need to be added to TYPE chem_species(nsp)%, &
384	!< and the loop over nsp would have to be put outside of this IF-clause.
385	!< i think its better we keep the same bonundary cond i.e. dirichlet or neumann
386	!< for all chem spcs. ... !bK
387
388	ENDDO
389	ENDDO
390	ENDIF
391	ENDDO ! end lsp loop
392
393	!-- Top boundary conditions for chemical species - Should this not be done for all species?
394	IF ( ibc_cs_t == 0 ) THEN
395	DO lsp = 1, nspec
396	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc(nzt+1,:,:)
397	ENDDO
398	ELSEIF ( ibc_cs_t == 1 ) THEN
399	DO lsp = 1, nspec
400	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:)
401	ENDDO
402	ELSEIF ( ibc_cs_t == 2 ) THEN
403	DO lsp = 1, nspec
404	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:) + bc_cs_t_val(lsp) * dzu(nzt+1)
405	ENDDO
406	!@todo: bc_cs_t_val needs to be calculated,
407	!see bc_pt_t_val = ( pt_init(nzt+1) - pt_init(nzt) ) / dzu(nzt+1)
408	!(in time_integration). pt_init would be the counterpart to
409	!chem_species(i)%conc_pr_init (see kchem_driver_FKa1408.f90 of my
410	!"Hints: prescribing initial concentration.
411	ENDIF
412	!
413	CASE ( 'set_bc_lateral' ) ! bK commented it
414	!-- Lateral boundary conditions for chem species at inflow boundary
415	!-- are automatically set when chem_species concentration is
416	!-- initialized. The initially set value at the inflow boundary is not
417	!-- touched during time integration, hence, this boundary value remains
418	!-- at a constant value, which is the concentration that flows into the
419	!-- domain.
420	!-- Lateral boundary conditions for chem species at outflow boundary
421
422	IF ( outflow_s ) THEN
423	DO lsp = 1, nspec
424	chem_species(lsp)%conc_p(:,nys-1,:) = chem_species(lsp)%conc_p(:,nys,:)
425	ENDDO
426	ELSEIF ( outflow_n ) THEN
427	DO lsp = 1, nspec
428	chem_species(lsp)%conc_p(:,nyn+1,:) = chem_species(lsp)%conc_p(:,nyn,:)
429	ENDDO
430	ELSEIF ( outflow_l ) THEN
431	DO lsp = 1, nspec
432	chem_species(lsp)%conc_p(:,:,nxl-1) = chem_species(lsp)%conc_p(:,:,nxl)
433	ENDDO
434	ELSEIF ( outflow_r ) THEN
435	DO lsp = 1, nspec
436	chem_species(lsp)%conc_p(:,:,nxr+1) = chem_species(lsp)%conc_p(:,:,nxr)
437	ENDDO
438	ENDIF
439
440	END SELECT
441
442	END SUBROUTINE chem_boundary_conds
443	!
444	!------------------------------------------------------------------------------!
445	!
446	! Description:
447	! ------------
448	!> Subroutine defining initial vertical profiles of chemical species (given by
449	!> namelist parameters chem_profiles and chem_heights) --> which should work
450	!> analogue to parameters u_profile, v_profile and uv_heights)
451	!------------------------------------------------------------------------------!
452	SUBROUTINE chem_init_profiles !< SUBROUTINE is called from chem_init in case of
453	!< TRIM( initializing_actions ) /= 'read_restart_data'
454	!< We still need to see what has to be done in case of restart run
455	USE chem_modules
456
457	IMPLICIT NONE
458
459	!-- Local variables
460	INTEGER :: lsp !< running index for number of species in derived data type species_def
461	INTEGER :: lsp_pr !< running index for number of species in cs_names, cs_profiles etc
462	INTEGER :: lpr_lev !< running index for profile level for each chem spcs.
463	INTEGER :: npr_lev !< the next available profile lev
464
465	!-----------------
466	!-- To prescribe/initialize a vertically constant 'cs_profile', another parameter
467	!-- "cs_surface" is introduced. If "cs_profile" and "cs_heights" are prescribed,
468	!-- their values will override the constant profile given by "cs_surface".
469
470	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
471	lsp_pr = 1
472	DO WHILE ( TRIM( cs_name( lsp_pr ) ) /= 'novalue' ) !'novalue' is the default
473	DO lsp = 1, nspec !
474	!-- Create initial profile (conc_pr_init) for each chemical species
475	IF ( TRIM( chem_species(lsp)%name ) == TRIM( cs_name(lsp_pr) ) ) THEN !
476	! IF ( cs_profile(1,1) == 9999999.9_wp ) THEN
477	!-- Set a vertically constant profile based on the surface conc (cs_surface(lsp_pr)) of each species
478	DO lpr_lev = 0, nzt+1
479	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_surface(lsp_pr)
480	ENDDO
481
482	! ELSE
483	! IF ( cs_heights(lsp,1) /= 0.0_wp ) THEN
484	! message_string = 'cs_heights(1,1) must be 0.0'
485	! CALL message( 'chem_check_parameters', 'CM0012', 1, 2, 0, 6, 0 )
486	! ENDIF
487	!
488	! IF ( omega /= 0.0_wp ) THEN
489	! message_string = 'Coriolis force must be switched off (by setting omega=0.0)' // &
490	! ' when prescribing the forcing by u_profile and v_profile'
491	! CALL message( 'check_parameters', 'PA0347', 1, 2, 0, 6, 0 )
492	! ENDIF
493	!
494	! use_prescribed_profile_data = .TRUE.
495	!
496	! npr_lev = 1
497	! ! chem_sddpecies(lsp)%conc_pr_init(0) = 0.0_wp
498	! DO lpr_lev = 1, nz+1
499	! IF ( npr_lev < 100 ) THEN
500	! DO WHILE ( cs_heights(lsp, npr_lev+1) <= zu(lpr_lev) )
501	! npr_lev = npr_lev + 1
502	! IF ( npr_lev == 100 ) EXIT
503	! ENDDO
504	! ENDIF
505	!
506	! IF ( npr_lev < 100 .AND. cs_heights(lsp, npr_lev + 1) /= 9999999.9_wp ) THEN
507	! chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp, npr_lev) + &
508	! ( zu(lpr_lev) - cs_heights(lsp, npr_lev) ) / &
509	! ( cs_heights(lsp, npr_lev + 1) - cs_heights(lsp, npr_lev ) ) * &
510	! ( cs_profile(lsp, npr_lev + 1) - cs_profile(lsp, npr_lev ) )
511	! ELSE
512	! chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp, npr_lev)
513	! ENDIF
514	! ENDDO
515	! ENDIF
516	!-- If a profile is prescribed explicity using cs_profiles and cs_heights, we then have to fill the
517	!-- chem_species(lsp)%conc_pr_init for the specific "lsp" based on the cs_profiles(lsp_pr,:)
518	!-- and cs_heights(lsp_pr,:).
519	ENDIF
520	ENDDO
521	lsp_pr = lsp_pr + 1
522	ENDDO
523	! ELSE
524	! IF (chem_debug1 ) print*,'code to be added for initializing_actions == read_restart_data' !bK
525	! ENDIF
526
527	!-- Now, go back to chem_init and use the contents of chem_species(lsp)%conc_pr_init to
528	!-- initialize the 3D conc arrays, as it is currently taken care of in chem_set_constant_values.
529	!-- After initializing the 3D arrays, these can be used to set the boundary conditions in the
530	!-- subroutine kchem_boundary_conds, which should be called from boundary_conds.f90.
531
532
533	END SUBROUTINE chem_init_profiles
534	!
535	!------------------------------------------------------------------------------!
536	!
537	! Description:
538	! ------------
539	!> Subroutine initializating chemistry_model_mod
540	!------------------------------------------------------------------------------!
541	SUBROUTINE chem_init
542
543
544	USE control_parameters, &
545	ONLY: message_string, io_blocks, io_group, turbulent_inflow
546
547	USE arrays_3d, &
548	ONLY: mean_inflow_profiles
549
550	USE pegrid
551
552	IMPLICIT none
553	!-- local variables
554	INTEGER :: i,j !< running index for for horiz numerical grid points
555	INTEGER :: lsp !< running index for chem spcs
556	INTEGER :: lpr_lev !< running index for chem spcs profile level
557	!
558	!-- NOPOINTER version not implemented yet
559	! #if defined( __nopointer )
560	! message_string = 'The chemistry module only runs with POINTER version'
561	! CALL message( 'chemistry_model_mod', 'CM0001', 1, 2, 0, 6, 0 )
562	! #endif
563	!
564	!-- Allocate memory for chemical species
565	ALLOCATE( chem_species(nspec) )
566	ALLOCATE( spec_conc_1 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
567	ALLOCATE( spec_conc_2 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
568	ALLOCATE( spec_conc_3 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
569	ALLOCATE( spec_conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
570	ALLOCATE( phot_frequen(nphot) )
571	ALLOCATE( freq_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nphot) )
572	ALLOCATE( bc_cs_t_val(nspec) )
573	!
574	!-- Initialize arrays
575	spec_conc_1 (:,:,:,:) = 0.0_wp
576	spec_conc_2 (:,:,:,:) = 0.0_wp
577	spec_conc_3 (:,:,:,:) = 0.0_wp
578	spec_conc_av(:,:,:,:) = 0.0_wp
579
580
581	DO lsp = 1, nspec
582	chem_species(lsp)%name = spc_names(lsp)
583
584	chem_species(lsp)%conc (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1 (:,:,:,lsp)
585	chem_species(lsp)%conc_p (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2 (:,:,:,lsp)
586	chem_species(lsp)%tconc_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_3 (:,:,:,lsp)
587	chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_av(:,:,:,lsp)
588
589	ALLOCATE (chem_species(lsp)%cssws_av(nysg:nyng,nxlg:nxrg))
590	chem_species(lsp)%cssws_av = 0.0_wp
591	!
592	!-- (todo (FK): This needs to be revised. This block must go somewhere else)
593	! IF ( ws_scheme_sca ) THEN
594	ALLOCATE (chem_species(lsp)%flux_s_cs(nzb+1:nzt,0:threads_per_task-1))
595	ALLOCATE (chem_species(lsp)%diss_s_cs(nzb+1:nzt,0:threads_per_task-1))
596	ALLOCATE (chem_species(lsp)%flux_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
597	ALLOCATE (chem_species(lsp)%diss_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
598	chem_species(lsp)%flux_s_cs = 0.0_wp
599	chem_species(lsp)%flux_l_cs = 0.0_wp
600	chem_species(lsp)%diss_s_cs = 0.0_wp
601	chem_species(lsp)%diss_l_cs = 0.0_wp
602	! ENDIF
603	!
604	!-- Allocate memory for initial concentration profiles
605	!-- (concentration values come from namelist)
606	!-- (todo (FK): Because of this, chem_init is called in palm before
607	!-- check_parameters, since conc_pr_init is used there.
608	!-- We have to find another solution since chem_init should
609	!-- eventually be called from init_3d_model!!)
610	ALLOCATE ( chem_species(lsp)%conc_pr_init(0:nz+1) )
611	chem_species(lsp)%conc_pr_init(:) = 0.0_wp
612
613	ENDDO
614
615	!
616	!-- Set initial concentration of profiles prescribed by parameters cs_profile
617	!-- and cs_heights in the namelist &chemistry_parameters
618	!-- (todo (FK): chem_init_profiles not ready yet, has some bugs)
619	! CALL chem_init_profiles
620	!
621	!-- Initialize model variables
622
623
624	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
625	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
626
627
628	!-- First model run of a possible job queue.
629	!-- Initial profiles of the variables must be computes.
630	IF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
631	! CALL location_message( 'initializing with 1D model profiles', .FALSE. )
632	!
633	! CALL init_1d_model ...... decide to call or not later !bK
634
635	!-- Transfer initial profiles to the arrays of the 3D model
636	DO lsp = 1, nspec
637	DO i = nxlg, nxrg
638	DO j = nysg, nyng
639	DO lpr_lev = 1, nz + 1
640	chem_species(lsp)%conc(lpr_lev,j,i) = chem_species(lsp)%conc_pr_init(lpr_lev)
641	ENDDO
642	ENDDO
643	ENDDO
644	ENDDO
645
646	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
647	THEN
648	! CALL location_message( 'initializing with constant profiles', .FALSE. )
649
650
651
652	!-- Set initial horizontal velocities at the lowest computational grid
653	!-- levels to zero in order to avoid too small time steps caused by the
654	!-- diffusion limit in the initial phase of a run (at k=1, dz/2 occurs
655	!-- in the limiting formula!).
656
657	DO lsp = 1, nspec
658	DO i = nxlg, nxrg
659	DO j = nysg, nyng
660	chem_species(lsp)%conc(:,j,i) = chem_species(lsp)%conc_pr_init !ITS THERE bK
661	ENDDO
662	ENDDO
663	ENDDO
664
665	! ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) &
666	! THEN
667	! CALL location_message( 'initializing by user', .FALSE. )
668	!
669	!-- Initialization will completely be done by the user
670	!-- (FK: This should be called only once, in init_3d_model, i.e. remove it here)
671	! CALL user_init_3d_model
672	! CALL location_message( 'finished', .TRUE. )
673
674	ENDIF
675
676	!-- Store initial chem spcs profile
677	! DO lsp = 1, nvar
678	! hom_cs(:,1,115,:) = SPREAD( chem_species(lsp)%conc(:,nys,nxl), 2, statistic_regions+1 )
679	! ENDDO
680	!
681	!-- If required, change the surface chem spcs at the start of the 3D run
682	IF ( cs_surface_initial_change(1) /= 0.0_wp ) THEN
683	DO lsp = 1, nspec
684	chem_species(lsp)%conc(nzb,:,:) = chem_species(lsp)%conc(nzb,:,:) + &
685	cs_surface_initial_change(lsp)
686	ENDDO
687	ENDIF
688	!
689	!-- Initiale old and new time levels.
690	DO lsp = 1, nvar
691	chem_species(lsp)%tconc_m = 0.0_wp
692	chem_species(lsp)%conc_p = chem_species(lsp)%conc
693	ENDDO
694
695	ENDIF
696
697
698
699	!--- new code add above this line
700	DO lsp = 1, nphot
701	phot_frequen(lsp)%name = phot_names(lsp)
702	! IF( myid == 0 ) THEN
703	! WRITE(6,'(a,i4,3x,a)') 'Photolysis: ',lsp,trim(phot_names(lsp))
704	! ENDIF
705	phot_frequen(lsp)%freq(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => freq_1(:,:,:,lsp)
706	ENDDO
707
708	!-- Set initial values
709	! Not required any more, this can now be done with the namelist by setting cs_surface
710	! and cs_name without specifying cs_profile (Nevertheless, we still want to keep it for a while)
711	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
712	! CALL set_const_initial_values
713	! ENDIF
714
715	RETURN
716
717	CONTAINS
718	!------------------------------------------------------------------------------!
719	!
720	! Description:
721	! ------------
722	!> Subroutine setting constant initial values of chemical species
723	!------------------------------------------------------------------------------!
724	SUBROUTINE set_const_initial_values
725	! Not required any more, this can now be done with the namelist by setting cs_surface
726	! and cs_name without specifying cs_profile (Nevertheless, we still want to keep it for a while)
727	IMPLICIT none
728
729	!-- local variables
730	INTEGER :: lsp
731
732	IF(myid == 0) THEN
733	write(6,'(/,a,/)') ' chemics >>>> Set constant Initial Values: '
734	ENDIF
735
736	! Default values are taken from smog.def from supplied kpp example
737	DO lsp = 1, nspec
738	IF(trim(chem_species(lsp)%name) == 'NO') THEN
739	! chem_species(lsp)%conc = 8.725*1.0E+08
740	! chem_species(lsp)%conc = 0.05_wp !added by bK
741	chem_species(lsp)%conc = 0.01_wp !added by RFo
742	ELSEIF (trim(chem_species(lsp)%name) == 'NO2') THEN
743	! chem_species(lsp)%conc = 2.240*1.0E+08
744	! chem_species(lsp)%conc = 0.01_wp !added by bK
745	chem_species(lsp)%conc = 0.05_wp !added by RFo
746	ELSEIF( trim( chem_species(lsp)%name ) == 'O3' ) THEN
747	chem_species(lsp)%conc = 0.05_wp !added by bK
748	ELSEIF(trim(chem_species(lsp)%name) == 'H2O') THEN
749	! chem_species(lsp)%conc = 5.326*1.0E+11
750	chem_species(lsp)%conc = 1.30*1.0E+4_wp !added by bK
751	ELSEIF(trim(chem_species(lsp)%name) == 'O2') THEN
752	chem_species(lsp)%conc = 2.0*1.0E+5_wp !added by bK
753	ELSEIF(trim(chem_species(lsp)%name) == 'RH') THEN
754	chem_species(lsp)%conc = 0.001_wp !added by RFo
755	ELSEIF(trim(chem_species(lsp)%name) == 'CO') THEN
756	chem_species(lsp)%conc = 0.5_wp !added by RFo
757	ELSEIF(trim(chem_species(lsp)%name) == 'RCHO') THEN
758	! chem_species(lsp)%conc = 2.0_wp !added by bK
759	chem_species(lsp)%conc = 0.01_wp !added by RFo
760	! ELSEIF(trim(chem_species(lsp)%name) == 'OH') THEN
761	! chem_species(lsp)%conc = 1.0*1.0E-07_wp !added by bK
762	! ELSEIF(trim(chem_species(lsp)%name) == 'HO2') THEN
763	! chem_species(lsp)%conc = 1*1.0E-7_wp !added by bK
764	! ELSEIF(trim(chem_species(lsp)%name) == 'RCOO2') THEN ! corrected RFo
765	! chem_species(lsp)%conc = 1.0*1.0E-7_wp !added by bK
766	! ELSEIF(trim(chem_species(lsp)%name) == 'RCOO2NO2') THEN
767	! chem_species(lsp)%conc = 1.0*1.0E-7_wp !added by bK
768	ELSE
769	! H2O = 2.0e+04;
770	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) = 0.0_wp
771	ENDIF
772
773	IF(myid == 0) THEN
774	WRITE(6,'(a,3x,a,3x,a,e12.4)') ' Species: ',chem_species(lsp)%name(1:7), &
775	'Initial Value = ',chem_species(lsp)%conc(nzb,nysg,nxlg)
776	ENDIF
777	ENDDO
778
779	! #if defined( __nopointer )
780	! !kk Hier mit message abbrechen
781	! if(myid == 0) then
782	! write(6,*) ' KPP does only run with POINTER Version'
783	! end if
784	! stop 'error'
785	! #endif
786
787	RETURN
788	END SUBROUTINE set_const_initial_values
789
790
791	END SUBROUTINE chem_init
792	!
793	!------------------------------------------------------------------------------!
794	!
795	! Description:
796	! ------------
797	!> Subroutine defining parin for &chemistry_parameters for chemistry model
798	!------------------------------------------------------------------------------!
799	SUBROUTINE chem_parin
800
801	USE control_parameters, &
802	ONLY: air_chemistry
803
804	USE chem_modules
805
806	USE kinds
807
808	IMPLICIT none
809
810	CHARACTER (LEN=80) :: line !< dummy string that contains the current line of the parameter file
811
812	REAL(wp), DIMENSION(nmaxfixsteps) :: my_steps !< List of fixed timesteps my_step(1) = 0.0 automatic stepping
813
814	NAMELIST /chemistry_parameters/ bc_cs_b, &
815	bc_cs_t, &
816	call_chem_at_all_substeps, &
817	chem_debug0, &
818	chem_debug1, &
819	chem_debug2, &
820	chem_gasphase_on, &
821	cs_heights, &
822	cs_name, &
823	cs_profile, &
824	cs_profile_name, &
825	cs_surface, &
826	emiss_factor_main, &
827	emiss_factor_side, &
828	icntrl, &
829	main_street_id, &
830	max_street_id, &
831	my_steps, &
832	rcntrl, &
833	side_street_id, &
834	photolysis_scheme, &
835	wall_csflux, &
836	cs_vertical_gradient, &
837	top_csflux, &
838	surface_csflux, &
839	surface_csflux_name, &
840	cs_surface_initial_change, &
841	cs_vertical_gradient_level
842
843	!-- analogue to chem_names(nspj) we could invent chem_surfaceflux(nspj) and chem_topflux(nspj)
844	!-- so this way we could prescribe a specific flux value for each species
845	!> chemistry_parameters for initial profiles
846	!> cs_names = 'O3', 'NO2', 'NO', ... to set initial profiles)
847	!> cs_heights(1,:) = 0.0, 100.0, 500.0, 2000.0, .... (height levels where concs will be prescribed for O3)
848	!> cs_heights(2,:) = 0.0, 200.0, 400.0, 1000.0, .... (same for NO2 etc.)
849	!> cs_profiles(1,:) = 10.0, 20.0, 20.0, 30.0, ..... (chem spcs conc at height lvls chem_heights(1,:)) etc.
850	!> If the respective concentration profile should be constant with height, then use "cs_surface( number of spcs)"
851	!> then write these cs_surface values to chem_species(lsp)%conc_pr_init(:)
852
853	!
854	!-- Read chem namelist
855	!-- (todo: initialize these parameters in declaration part, do this for
856	!-- all chemistry_parameters namelist parameters)
857	icntrl = 0
858	rcntrl = 0.0_wp
859	my_steps = 0.0_wp
860	icntrl(2) = 1
861	photolysis_scheme = 'simple'
862	atol = 1.0_wp
863	rtol = 0.01_wp
864	!
865	!-- Try to find chemistry package
866	REWIND ( 11 )
867	line = ' '
868	DO WHILE ( INDEX( line, '&chemistry_parameters' ) == 0 )
869	READ ( 11, '(A)', END=10 ) line
870	ENDDO
871	BACKSPACE ( 11 )
872	!
873	!-- Read chemistry namelist
874	READ ( 11, chemistry_parameters )
875	!
876	!-- Enable chemistry model
877	air_chemistry = .TRUE.
878
879
880	10 CONTINUE
881
882	t_steps = my_steps !(todo: Why not directly make t_steps a
883	! namelist parameter?)
884
885	END SUBROUTINE chem_parin
886
887	!
888	!------------------------------------------------------------------------------!
889	!
890	! Description:
891	! ------------
892	!> Subroutine to integrate chemical species in the given chemical mechanism
893	!------------------------------------------------------------------------------!
894
895	SUBROUTINE chem_integrate_ij (i, j)
896
897	USE cpulog, &
898	ONLY: cpu_log, log_point
899	USE statistics, & ! ## RFo
900	ONLY: weight_pres
901	USE control_parameters, & ! ## RFo
902	ONLY: dt_3d, intermediate_timestep_count
903
904	IMPLICIT none
905	INTEGER,INTENT(IN) :: i,j
906
907	!-- local variables
908	INTEGER(iwp) :: lsp !< running index for chem spcs.
909	INTEGER(iwp) :: lph !< running index for photolysis frequencies
910	INTEGER :: k,m,istatf
911	INTEGER,dimension(20) :: istatus
912	REAL(kind=wp),dimension(nzb+1:nzt,nspec) :: tmp_conc
913	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_temp
914	REAL(kind=wp),dimension(nzb+1:nzt,nphot) :: tmp_phot
915	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_fact
916	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_fact_i !< conversion factor between molecules cm^{-3} and ppm
917	REAL(wp) :: conv !< conversion factor
918	REAL(wp), PARAMETER :: ppm2fr = 1.0e-6_wp !< Conversion factor ppm to fraction
919	REAL(wp), PARAMETER :: pref_i = 1._wp / 100000.0_wp !< inverse reference pressure (1/Pa)
920	REAL(wp), PARAMETER :: t_std = 273.15_wp !< standard pressure (Pa)
921	REAL(wp), PARAMETER :: p_std = 101325.0_wp !< standard pressure (Pa)
922	REAL(wp), PARAMETER :: r_cp = 0.286_wp !< R / cp (exponent for potential temperature)
923	REAL(wp), PARAMETER :: vmolcm = 22.414e3_wp !< Mole volume (22.414 l) in cm^{-3}
924	REAL(wp), PARAMETER :: xna = 6.022e23_wp !< Avogadro number (molecules/mol)
925
926
927	REAL(kind=wp) :: dt_chem
928
929	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'start' )
930	!< Set chem_gasphase_on to .FALSE. if you want to skip computation of gas phase chemistry
931	IF (chem_gasphase_on) THEN
932
933	tmp_temp(:) = pt(:,j,i) * ( hyp(nzb+1:nzt) / 100000.0_wp )**0.286_wp
934	! ppm to molecules/cm**3
935	! tmp_fact = 1.e-6_wp6.022e23_wp/(22.414_wp1000._wp) * 273.15_wp * hyp(nzb+1:nzt)/( 101300.0_wp * tmp_temp )
936	conv = ppm2fr * xna / vmolcm
937	tmp_fact(:) = conv * t_std * hyp(nzb+1:nzt) / (tmp_temp(:) * p_std)
938	tmp_fact_i = 1.0_wp/tmp_fact
939
940	CALL fill_temp (istatf, tmp_temp) !< Load constant temperature into kpp context
941	! CALL fill_temp (istatf, pt(nzb+1:nzt,j,i)) !< Load temperature into kpp context
942
943	DO lsp = 1,nspec
944	tmp_conc(:,lsp) = chem_species(lsp)%conc(nzb+1:nzt,j,i) * tmp_fact(:)
945	ENDDO
946
947	DO lph = 1,nphot
948	tmp_phot(:,lph) = phot_frequen(lph)%freq(nzb+1:nzt,j,i)
949	ENDDO
950
951	IF(myid == 0 .AND. chem_debug0 ) THEN
952	IF (i == 10 .and. j == 10) WRITE(0,*) 'begin chemics step ',dt_3d
953	ENDIF
954
955	!-- Compute length of time step # RFo
956	IF ( call_chem_at_all_substeps ) THEN
957	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
958	ELSE
959	dt_chem = dt_3d
960	ENDIF
961
962	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'start' )
963
964
965	CALL chem_gasphase_integrate (dt_chem, tmp_conc, tmp_temp, tmp_phot, istatus=istatus)
966
967
968	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'stop' )
969
970	DO lsp = 1,nspec
971	chem_species(lsp)%conc (nzb+1:nzt,j,i) = tmp_conc(:,lsp) * tmp_fact_i(:) ! RFo
972	ENDDO
973
974	! IF (myid == 0 .AND. chem_debug2 ) THEN
975	! IF (i == 10 .and. j == 10) WRITE(6,'(a,8i7)') ' KPP Status ',istatus(1:8)
976	! write(6,'(a,8i7)') ' KPP Status ',istatus(1:8)
977	! ENDIF
978
979	ENDIF
980	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'stop' )
981
982	RETURN
983	END SUBROUTINE chem_integrate_ij
984	!
985	!------------------------------------------------------------------------------!
986	!
987	! Description:
988	! ------------
989	!> Subroutine for swapping of timelevels for chemical species
990	!> called out from subroutine swap_timelevel
991	!------------------------------------------------------------------------------!
992
993	SUBROUTINE chem_swap_timelevel (level)
994	IMPLICIT none
995
996	INTEGER,INTENT(IN) :: level
997
998	!-- local variables
999
1000	INTEGER :: lsp
1001
1002	! print,' entering chem_swap_timelevel *) '
1003	if(level == 0) then
1004	do lsp=1, nvar
1005	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
1006	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
1007	end do
1008	else
1009	do lsp=1, nvar
1010	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
1011	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
1012	end do
1013	end if
1014
1015	RETURN
1016	END SUBROUTINE chem_swap_timelevel
1017
1018	!------------------------------------------------------------------------------!
1019	!
1020	! Description:
1021	! ------------
1022	!> Subroutine defining appropriate grid for netcdf variables.
1023	!> It is called out from subroutine netcdf.
1024	!------------------------------------------------------------------------------!
1025	SUBROUTINE chem_define_netcdf_grid( var, found, grid_x, grid_y, grid_z )
1026
1027	IMPLICIT NONE
1028
1029	CHARACTER (LEN=*), INTENT(IN) :: var !<
1030	LOGICAL, INTENT(OUT) :: found !<
1031	CHARACTER (LEN=*), INTENT(OUT) :: grid_x !<
1032	CHARACTER (LEN=*), INTENT(OUT) :: grid_y !<
1033	CHARACTER (LEN=*), INTENT(OUT) :: grid_z !<
1034
1035	found = .TRUE.
1036
1037	if(var(1:3) == 'kc_') then !< always the same grid for chemistry variables
1038	grid_x = 'x'
1039	grid_y = 'y'
1040	grid_z = 'zu' !< kk Use same z axis as u variables. Has to be checked if OK
1041	else
1042	found = .FALSE.
1043	grid_x = 'none'
1044	grid_y = 'none'
1045	grid_z = 'none'
1046	end if
1047
1048	! write(6,*) 'chem_define_netcdf_grid ',TRIM(var),' ',trim(grid_x),' ',found
1049
1050	END SUBROUTINE chem_define_netcdf_grid
1051	!
1052	!------------------------------------------------------------------------------!
1053	!
1054	! Description:
1055	! ------------
1056	!> Subroutine for checking data output for chemical species
1057	!------------------------------------------------------------------------------!
1058
1059	SUBROUTINE chem_check_data_output( var, unit, i, ilen, k )
1060
1061
1062	USE control_parameters, &
1063	ONLY: data_output, message_string
1064
1065	IMPLICIT NONE
1066
1067	CHARACTER (LEN=*) :: unit !<
1068	CHARACTER (LEN=*) :: var !<
1069
1070	INTEGER(iwp) :: i, lsp
1071	INTEGER(iwp) :: ilen
1072	INTEGER(iwp) :: k
1073
1074	CHARACTER(len=16) :: spec_name
1075
1076	unit = 'illegal'
1077
1078	spec_name = TRIM(var(4:)) !< var 1:3 is 'kc_'.
1079
1080	DO lsp=1,nspec
1081	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
1082	unit = 'ppm'
1083	ENDIF
1084	! It is possible to plant PM10 and PM25 into the gasphase chemistry code
1085	! ! as passive species (e.g. 'passive' in GASPHASE_PREPROC/mechanisms):
1086	! ! set unit to micrograms per m**3 for PM10 and PM25 (PM2.5)
1087	IF (spec_name(1:2) == 'PM') THEN
1088	unit = 'ug m-3'
1089	ENDIF
1090	ENDDO
1091
1092	DO lsp=1,nphot
1093	IF (TRIM(spec_name) == TRIM(phot_frequen(lsp)%name)) THEN
1094	unit = 'sec-1'
1095	ENDIF
1096	ENDDO
1097
1098
1099	RETURN
1100	END SUBROUTINE chem_check_data_output
1101	!
1102	!------------------------------------------------------------------------------!
1103	!
1104	! Description:
1105	! ------------
1106	!> Subroutine for checking data output of profiles for chemistry model
1107	!------------------------------------------------------------------------------!
1108
1109	SUBROUTINE chem_check_data_output_pr( variable, var_count, unit, dopr_unit )
1110
1111
1112	USE arrays_3d, &
1113	ONLY: zu
1114
1115	USE control_parameters, &
1116	ONLY: data_output_pr, message_string, air_chemistry
1117
1118	USE indices
1119
1120	USE profil_parameter
1121
1122	USE statistics
1123
1124
1125	IMPLICIT NONE
1126
1127	CHARACTER (LEN=*) :: unit !<
1128	CHARACTER (LEN=*) :: variable !<
1129	CHARACTER (LEN=*) :: dopr_unit
1130	CHARACTER(len=16) :: spec_name
1131
1132	INTEGER(iwp) :: var_count, lsp !<
1133
1134
1135	spec_name = TRIM(variable(4:))
1136	! write(9,*) 'fm #32 .. air_chemistry ', air_chemistry
1137
1138	IF ( .NOT. air_chemistry ) THEN
1139	message_string = 'data_output_pr = ' // &
1140	TRIM( data_output_pr(var_count) ) // ' is not imp' // &
1141	'lemented for air_chemistry = .FALSE.'
1142	! CALL message( 'check_parameters', 'PA0XXX', 1, 2, 0, 6, 0 )
1143	ELSE
1144	DO lsp = 1, nspec
1145	IF (TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
1146	dopr_index(var_count) = 900
1147	dopr_unit = 'ppm'
1148	hom(:,2,900,:) = SPREAD( zu, 2, statistic_regions+1 )
1149	ENDIF
1150	ENDDO
1151	ENDIF
1152
1153	END SUBROUTINE chem_check_data_output_pr
1154	!
1155	!------------------------------------------------------------------------------!
1156	!
1157	! Description:
1158	! ------------
1159	!> Subroutine defining 3D output variables for chemical species
1160	!------------------------------------------------------------------------------!
1161
1162
1163	SUBROUTINE chem_data_output_3d( av, variable, found, local_pf, fill_value, nzb_do, nzt_do )
1164
1165
1166	USE indices
1167
1168	USE kinds
1169
1170
1171	IMPLICIT NONE
1172
1173	CHARACTER (LEN=*) :: variable !<
1174
1175	INTEGER(iwp) :: av !<
1176	INTEGER(iwp) :: nzb_do !< lower limit of the data output (usually 0)
1177	INTEGER(iwp) :: nzt_do !< vertical upper limit of the data output (usually nz_do3d)
1178
1179	LOGICAL :: found !<
1180
1181	REAL(wp) :: fill_value !<
1182	REAL(sp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) :: local_pf
1183
1184
1185	!-- local variables
1186
1187	INTEGER :: i, j, k, lsp
1188	CHARACTER(len=16) :: spec_name
1189
1190
1191	found = .FALSE.
1192
1193	spec_name = TRIM(variable(4:))
1194	!av == 0
1195
1196	DO lsp=1,nspec
1197	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
1198	IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
1199	TRIM(chem_species(lsp)%name)
1200
1201	IF (av == 0) THEN
1202	DO i = nxl, nxr
1203	DO j = nys, nyn
1204	DO k = nzb_do, nzt_do
1205	local_pf(i,j,k) = MERGE( &
1206	chem_species(lsp)%conc(k,j,i), &
1207	REAL( fill_value, KIND = wp ), &
1208	BTEST( wall_flags_0(k,j,i), 0 ) )
1209	ENDDO
1210	ENDDO
1211	ENDDO
1212
1213	ELSE
1214	DO i = nxl, nxr
1215	DO j = nys, nyn
1216	DO k = nzb_do, nzt_do
1217	local_pf(i,j,k) = MERGE( &
1218	chem_species(lsp)%conc_av(k,j,i),&
1219	REAL( fill_value, KIND = wp ), &
1220	BTEST( wall_flags_0(k,j,i), 0 ) )
1221	ENDDO
1222	ENDDO
1223	ENDDO
1224	ENDIF
1225
1226	found = .TRUE.
1227	ENDIF
1228	ENDDO
1229
1230	RETURN
1231	END SUBROUTINE chem_data_output_3d
1232	!
1233	!------------------------------------------------------------------------------!
1234	!
1235	! Description:
1236	! ------------
1237	!> Subroutine for averaging 3D data of chemical species. Due to the fact that
1238	!> the averaged chem arrays are allocated in chem_init, no if-query concerning
1239	!> the allocation is required (in any mode). Attention: If you just specify an
1240	!> averaged output quantity in the _p3dr file during restarts the first output
1241	!> includes the time between the beginning of the restart run and the first
1242	!> output time (not necessarily the whole averaging_interval you have
1243	!> specified in your _p3d/_p3dr file )
1244	!------------------------------------------------------------------------------!
1245
1246	SUBROUTINE chem_3d_data_averaging ( mode, variable )
1247
1248	USE control_parameters
1249
1250	USE indices
1251
1252	USE kinds
1253
1254	USE surface_mod, &
1255	ONLY: surf_def_h, surf_lsm_h, surf_usm_h
1256
1257	IMPLICIT NONE
1258
1259	CHARACTER (LEN=*) :: mode !<
1260	CHARACTER (LEN=*) :: variable !<
1261
1262	LOGICAL :: match_def !< flag indicating natural-type surface
1263	LOGICAL :: match_lsm !< flag indicating natural-type surface
1264	LOGICAL :: match_usm !< flag indicating urban-type surface
1265
1266	INTEGER(iwp) :: i !< grid index x direction
1267	INTEGER(iwp) :: j !< grid index y direction
1268	INTEGER(iwp) :: k !< grid index z direction
1269	INTEGER(iwp) :: m !< running index surface type
1270	INTEGER(iwp) :: lsp !< running index for chem spcs
1271	INTEGER(iwp) :: lsp_2 !< it looks like redundent .. will be delted ..bK
1272
1273	IF ( mode == 'allocate' ) THEN
1274	DO lsp = 1, nspec
1275	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
1276	! lsp_2 = lsp
1277	chem_species(lsp)%conc_av = 0.0_wp
1278
1279	ENDIF
1280	ENDDO
1281
1282	ELSEIF ( mode == 'sum' ) THEN
1283
1284	DO lsp = 1, nspec
1285	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
1286	! lsp_2 = lsp
1287	DO i = nxlg, nxrg
1288	DO j = nysg, nyng
1289	DO k = nzb, nzt+1
1290	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) + &
1291	chem_species(lsp)%conc(k,j,i)
1292	ENDDO
1293	ENDDO
1294	ENDDO
1295	ELSEIF ( TRIM(variable(4:)) == TRIM('cssws*') ) THEN
1296	DO i = nxl, nxr
1297	DO j = nys, nyn
1298	match_def = surf_def_h(0)%start_index(j,i) <= &
1299	surf_def_h(0)%end_index(j,i)
1300	match_lsm = surf_lsm_h%start_index(j,i) <= &
1301	surf_lsm_h%end_index(j,i)
1302	match_usm = surf_usm_h%start_index(j,i) <= &
1303	surf_usm_h%end_index(j,i)
1304
1305	IF ( match_def ) THEN
1306	m = surf_def_h(0)%end_index(j,i)
1307	chem_species(lsp)%cssws_av(j,i) = &
1308	chem_species(lsp)%cssws_av(j,i) + &
1309	surf_def_h(0)%cssws(lsp,m)
1310	ELSEIF ( match_lsm .AND. .NOT. match_usm ) THEN
1311	m = surf_lsm_h%end_index(j,i)
1312	chem_species(lsp)%cssws_av(j,i) = &
1313	chem_species(lsp)%cssws_av(j,i) + &
1314	surf_lsm_h%cssws(lsp,m)
1315	ELSEIF ( match_usm ) THEN
1316	m = surf_usm_h%end_index(j,i)
1317	chem_species(lsp)%cssws_av(j,i) = &
1318	chem_species(lsp)%cssws_av(j,i) + &
1319	surf_usm_h%cssws(lsp,m)
1320	ENDIF
1321	ENDDO
1322	ENDDO
1323	ENDIF
1324	ENDDO
1325
1326	ELSEIF ( mode == 'average' ) THEN
1327	DO lsp = 1, nspec
1328	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
1329	! lsp_2 = lsp
1330	DO i = nxlg, nxrg
1331	DO j = nysg, nyng
1332	DO k = nzb, nzt+1
1333	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) / REAL( average_count_3d, KIND=wp )
1334	ENDDO
1335	ENDDO
1336	ENDDO
1337
1338	ELSEIF (TRIM(variable(4:)) == TRIM('cssws*') ) THEN
1339	DO i = nxlg, nxrg
1340	DO j = nysg, nyng
1341	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) / REAL( average_count_3d, KIND=wp )
1342	ENDDO
1343	ENDDO
1344	CALL exchange_horiz_2d( chem_species(lsp)%cssws_av, nbgp )
1345	ENDIF
1346	ENDDO
1347
1348	ENDIF
1349
1350	END SUBROUTINE chem_3d_data_averaging
1351
1352	!------------------------------------------------------------------------------!
1353	!
1354	! Description:
1355	! ------------
1356	!> Subroutine to write restart data for chemistry model
1357	!------------------------------------------------------------------------------!
1358	SUBROUTINE chem_wrd_local
1359
1360
1361	IMPLICIT NONE
1362
1363	INTEGER(iwp) :: lsp !<
1364
1365	! REAL(kind=wp), DIMENSION(nzb:nzt+1,nysg:nyng,nxlg:nxrg) :: chems_conc
1366
1367
1368	DO lsp = 1, nspec
1369
1370	CALL wrd_write_string( TRIM( chem_species(lsp)%name ))
1371	WRITE ( 14 ) chem_species(lsp)%conc
1372
1373	CALL wrd_write_string( TRIM( chem_species(lsp)%name )//'_av' )
1374	WRITE ( 14 ) chem_species(lsp)%conc_av
1375
1376	ENDDO
1377
1378
1379	END SUBROUTINE chem_wrd_local
1380
1381	!------------------------------------------------------------------------------!
1382	!
1383	! Description:
1384	! ------------
1385	!> Subroutine to read restart data of chemical species
1386	!------------------------------------------------------------------------------!
1387
1388	SUBROUTINE chem_rrd_local( i, k, nxlf, nxlc, nxl_on_file, nxrf, nxrc, &
1389	nxr_on_file, nynf, nync, nyn_on_file, nysf, nysc, &
1390	nys_on_file, tmp_3d, found )
1391
1392	USE control_parameters
1393
1394	USE indices
1395
1396	USE pegrid
1397
1398	IMPLICIT NONE
1399
1400	CHARACTER (LEN=20) :: spc_name_av !<
1401
1402	INTEGER(iwp) :: i, lsp !<
1403	INTEGER(iwp) :: k !<
1404	INTEGER(iwp) :: nxlc !<
1405	INTEGER(iwp) :: nxlf !<
1406	INTEGER(iwp) :: nxl_on_file !<
1407	INTEGER(iwp) :: nxrc !<
1408	INTEGER(iwp) :: nxrf !<
1409	INTEGER(iwp) :: nxr_on_file !<
1410	INTEGER(iwp) :: nync !<
1411	INTEGER(iwp) :: nynf !<
1412	INTEGER(iwp) :: nyn_on_file !<
1413	INTEGER(iwp) :: nysc !<
1414	INTEGER(iwp) :: nysf !<
1415	INTEGER(iwp) :: nys_on_file !<
1416
1417	LOGICAL, INTENT(OUT) :: found
1418
1419	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
1420
1421
1422	found = .FALSE.
1423
1424
1425	IF ( ALLOCATED(chem_species) ) THEN
1426
1427	DO lsp = 1, nspec
1428
1429	!< for time-averaged chemical conc.
1430	spc_name_av = TRIM(chem_species(lsp)%name)//'_av'
1431
1432	IF (restart_string(1:length) == TRIM(chem_species(lsp)%name) ) &
1433	THEN
1434	!< read data into tmp_3d
1435	IF ( k == 1 ) READ ( 13 ) tmp_3d
1436	!< fill ..%conc in the restart run
1437	chem_species(lsp)%conc(:,nysc-nbgp:nync+nbgp, &
1438	nxlc-nbgp:nxrc+nbgp) = &
1439	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
1440	found = .TRUE.
1441	ELSEIF (restart_string(1:length) == spc_name_av ) THEN
1442	IF ( k == 1 ) READ ( 13 ) tmp_3d
1443	chem_species(lsp)%conc_av(:,nysc-nbgp:nync+nbgp, &
1444	nxlc-nbgp:nxrc+nbgp) = &
1445	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
1446	found = .TRUE.
1447	ENDIF
1448
1449	ENDDO
1450
1451	ENDIF
1452
1453
1454	END SUBROUTINE chem_rrd_local
1455
1456
1457	!------------------------------------------------------------------------------!
1458	!
1459	! Description:
1460	! ------------
1461	!> Subroutine calculating prognostic equations for chemical species
1462	!> (cache-optimized).
1463	!> Routine is called separately for each chemical species over a loop from
1464	!> prognostic_equations.
1465	!------------------------------------------------------------------------------!
1466	SUBROUTINE chem_prognostic_equations_ij ( cs_scalar_p, cs_scalar, tcs_scalar_m, pr_init_cs, &
1467	i, j, i_omp_start, tn, ilsp, flux_s_cs, diss_s_cs, &
1468	flux_l_cs, diss_l_cs )
1469	USE pegrid
1470	USE advec_ws, ONLY: advec_s_ws
1471	USE advec_s_pw_mod, ONLY: advec_s_pw
1472	USE advec_s_up_mod, ONLY: advec_s_up
1473	USE diffusion_s_mod, ONLY: diffusion_s
1474	USE indices, ONLY: wall_flags_0
1475	USE surface_mod, ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
1476	surf_usm_v
1477
1478
1479	IMPLICIT NONE
1480
1481	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p, cs_scalar, tcs_scalar_m
1482
1483	INTEGER(iwp),INTENT(IN) :: i, j, i_omp_start, tn, ilsp
1484	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: flux_s_cs !<
1485	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: diss_s_cs !<
1486	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: flux_l_cs !<
1487	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: diss_l_cs !<
1488	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
1489
1490	!-- local variables
1491
1492	INTEGER :: k
1493	!
1494	!-- Tendency-terms for chem spcs.
1495	tend(:,j,i) = 0.0_wp
1496	!
1497	!-- Advection terms
1498	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1499	IF ( ws_scheme_sca ) THEN
1500	CALL advec_s_ws( i, j, cs_scalar, 'kc', flux_s_cs, diss_s_cs, &
1501	flux_l_cs, diss_l_cs, i_omp_start, tn )
1502	ELSE
1503	CALL advec_s_pw( i, j, cs_scalar )
1504	ENDIF
1505	ELSE
1506	CALL advec_s_up( i, j, cs_scalar )
1507	ENDIF
1508
1509	!
1510
1511	!-- Diffusion terms (the last three arguments are zero)
1512
1513	CALL diffusion_s( i, j, cs_scalar, &
1514	surf_def_h(0)%cssws(ilsp,:), surf_def_h(1)%cssws(ilsp,:), &
1515	surf_def_h(2)%cssws(ilsp,:), &
1516	surf_lsm_h%cssws(ilsp,:), surf_usm_h%cssws(ilsp,:), &
1517	surf_def_v(0)%cssws(ilsp,:), surf_def_v(1)%cssws(ilsp,:), &
1518	surf_def_v(2)%cssws(ilsp,:), surf_def_v(3)%cssws(ilsp,:), &
1519	surf_lsm_v(0)%cssws(ilsp,:), surf_lsm_v(1)%cssws(ilsp,:), &
1520	surf_lsm_v(2)%cssws(ilsp,:), surf_lsm_v(3)%cssws(ilsp,:), &
1521	surf_usm_v(0)%cssws(ilsp,:), surf_usm_v(1)%cssws(ilsp,:), &
1522	surf_usm_v(2)%cssws(ilsp,:), surf_usm_v(3)%cssws(ilsp,:) )
1523
1524	!
1525	!-- Prognostic equation for chem spcs
1526	DO k = nzb+1, nzt
1527	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) + ( dt_3d * &
1528	( tsc(2) * tend(k,j,i) + &
1529	tsc(3) * tcs_scalar_m(k,j,i) ) &
1530	- tsc(5) * rdf_sc(k) &
1531	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
1532	) &
1533	* MERGE( 1.0_wp, 0.0_wp, &
1534	BTEST( wall_flags_0(k,j,i), 0 ) &
1535	)
1536
1537	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
1538	ENDDO
1539
1540	!
1541	!-- Calculate tendencies for the next Runge-Kutta step
1542	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1543	IF ( intermediate_timestep_count == 1 ) THEN
1544	DO k = nzb+1, nzt
1545	tcs_scalar_m(k,j,i) = tend(k,j,i)
1546	ENDDO
1547	ELSEIF ( intermediate_timestep_count < &
1548	intermediate_timestep_count_max ) THEN
1549	DO k = nzb+1, nzt
1550	tcs_scalar_m(k,j,i) = -9.5625_wp * tend(k,j,i) + &
1551	5.3125_wp * tcs_scalar_m(k,j,i)
1552	ENDDO
1553	ENDIF
1554	ENDIF
1555
1556	END SUBROUTINE chem_prognostic_equations_ij
1557
1558
1559	!------------------------------------------------------------------------------!
1560	!
1561	! Description:
1562	! ------------
1563	!> Subroutine calculating prognostic equations for chemical species
1564	!> (vector-optimized).
1565	!> Routine is called separately for each chemical species over a loop from
1566	!> prognostic_equations.
1567	!------------------------------------------------------------------------------!
1568	SUBROUTINE chem_prognostic_equations ( cs_scalar_p, cs_scalar, tcs_scalar_m, &
1569	pr_init_cs, ilsp )
1570
1571	USE advec_s_pw_mod, &
1572	ONLY: advec_s_pw
1573
1574	USE advec_s_up_mod, &
1575	ONLY: advec_s_up
1576
1577	USE advec_ws, &
1578	ONLY: advec_s_ws
1579
1580	USE diffusion_s_mod, &
1581	ONLY: diffusion_s
1582
1583	USE indices, &
1584	ONLY: nxl, nxr, nyn, nys, wall_flags_0
1585
1586	USE pegrid
1587
1588	USE surface_mod, &
1589	ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
1590	surf_usm_v
1591
1592	IMPLICIT NONE
1593
1594	INTEGER :: i !< running index
1595	INTEGER :: j !< running index
1596	INTEGER :: k !< running index
1597
1598	INTEGER(iwp),INTENT(IN) :: ilsp !<
1599
1600	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
1601
1602	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar !<
1603	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p !<
1604	REAL(wp), DIMENSION(:,:,:), POINTER :: tcs_scalar_m !<
1605
1606
1607	!
1608	!-- Tendency terms for chemical species
1609	tend = 0.0_wp
1610	!
1611	!-- Advection terms
1612	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1613	IF ( ws_scheme_sca ) THEN
1614	CALL advec_s_ws( cs_scalar, 'kc' )
1615	ELSE
1616	CALL advec_s_pw( cs_scalar )
1617	ENDIF
1618	ELSE
1619	CALL advec_s_up( cs_scalar )
1620	ENDIF
1621	!
1622	!-- Diffusion terms (the last three arguments are zero)
1623	CALL diffusion_s( cs_scalar, &
1624	surf_def_h(0)%cssws(ilsp,:), &
1625	surf_def_h(1)%cssws(ilsp,:), &
1626	surf_def_h(2)%cssws(ilsp,:), &
1627	surf_lsm_h%cssws(ilsp,:), &
1628	surf_usm_h%cssws(ilsp,:), &
1629	surf_def_v(0)%cssws(ilsp,:), &
1630	surf_def_v(1)%cssws(ilsp,:), &
1631	surf_def_v(2)%cssws(ilsp,:), &
1632	surf_def_v(3)%cssws(ilsp,:), &
1633	surf_lsm_v(0)%cssws(ilsp,:), &
1634	surf_lsm_v(1)%cssws(ilsp,:), &
1635	surf_lsm_v(2)%cssws(ilsp,:), &
1636	surf_lsm_v(3)%cssws(ilsp,:), &
1637	surf_usm_v(0)%cssws(ilsp,:), &
1638	surf_usm_v(1)%cssws(ilsp,:), &
1639	surf_usm_v(2)%cssws(ilsp,:), &
1640	surf_usm_v(3)%cssws(ilsp,:) )
1641	!
1642	!-- Prognostic equation for chemical species
1643	DO i = nxl, nxr
1644	DO j = nys, nyn
1645	DO k = nzb+1, nzt
1646	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) &
1647	+ ( dt_3d * &
1648	( tsc(2) * tend(k,j,i) &
1649	+ tsc(3) * tcs_scalar_m(k,j,i) &
1650	) &
1651	- tsc(5) * rdf_sc(k) &
1652	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
1653	) &
1654	* MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_0(k,j,i), 0 ) )
1655
1656	IF ( cs_scalar_p(k,j,i) < 0.0_wp ) cs_scalar_p(k,j,i) = 0.1_wp * cs_scalar(k,j,i)
1657	ENDDO
1658	ENDDO
1659	ENDDO
1660	!
1661	!-- Calculate tendencies for the next Runge-Kutta step
1662	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1663	IF ( intermediate_timestep_count == 1 ) THEN
1664	DO i = nxl, nxr
1665	DO j = nys, nyn
1666	DO k = nzb+1, nzt
1667	tcs_scalar_m(k,j,i) = tend(k,j,i)
1668	ENDDO
1669	ENDDO
1670	ENDDO
1671	ELSEIF ( intermediate_timestep_count < &
1672	intermediate_timestep_count_max ) THEN
1673	DO i = nxl, nxr
1674	DO j = nys, nyn
1675	DO k = nzb+1, nzt
1676	tcs_scalar_m(k,j,i) = - 9.5625_wp * tend(k,j,i) &
1677	+ 5.3125_wp * tcs_scalar_m(k,j,i)
1678	ENDDO
1679	ENDDO
1680	ENDDO
1681	ENDIF
1682	ENDIF
1683
1684	END SUBROUTINE chem_prognostic_equations
1685
1686
1687	!------------------------------------------------------------------------------!
1688	!
1689	! Description:
1690	! ------------
1691	!> Subroutine defining header output for chemistry model
1692	!------------------------------------------------------------------------------!
1693	SUBROUTINE chem_header ( io )
1694
1695	IMPLICIT NONE
1696
1697	INTEGER(iwp), INTENT(IN) :: io !< Unit of the output file
1698
1699	! print*,'the header subroutine is still not operational'
1700	!!
1701	!!-- Write chemistry model header
1702	! WRITE( io, 3 )
1703	!
1704	! IF ( radiation_scheme == "constant" ) THEN
1705	! WRITE( io, 4 ) net_radiation
1706	! ELSEIF ( radiation_scheme == "clear-sky" ) THEN
1707	! WRITE( io, 5 )
1708	! ELSEIF ( radiation_scheme == "rrtmg" ) THEN
1709	! WRITE( io, 6 )
1710	! IF ( .NOT. lw_radiation ) WRITE( io, 10 )
1711	! IF ( .NOT. sw_radiation ) WRITE( io, 11 )
1712	! ENDIF
1713	!
1714	! IF ( albedo_type == 0 ) THEN
1715	! WRITE( io, 7 ) albedo
1716	! ELSE
1717	! WRITE( io, 8 ) TRIM( albedo_type_name(albedo_type) )
1718	! ENDIF
1719	! IF ( constant_albedo ) THEN
1720	! WRITE( io, 9 )
1721	! ENDIF
1722	!
1723	! IF ( radiation .AND. radiation_scheme /= 'constant' ) THEN
1724	! WRITE ( io, 1 ) lambda
1725	! WRITE ( io, 2 ) day_init, time_utc_init
1726	! ENDIF
1727	!
1728	! WRITE( io, 12 ) dt_radiation
1729	!
1730	! 1 FORMAT (' Geograph. longitude : lambda = ',F4.1,' degr')
1731	! 2 FORMAT (' Day of the year at model start : day_init = ',I3 &
1732	! /' UTC time at model start : time_utc_init = ',F7.1' s')
1733	! 3 FORMAT (//' Radiation model information:'/ &
1734	! ' ----------------------------'/)
1735	! 4 FORMAT (' --> Using constant net radiation: net_radiation = ', F6.2, &
1736	! // 'W/m**2')
1737	! 5 FORMAT (' --> Simple radiation scheme for clear sky is used (no clouds,', &
1738	! ' default)')
1739	! 6 FORMAT (' --> RRTMG scheme is used')
1740	! 7 FORMAT (/' User-specific surface albedo: albedo =', F6.3)
1741	! 8 FORMAT (/' Albedo is set for land surface type: ', A)
1742	! 9 FORMAT (/' --> Albedo is fixed during the run')
1743	!10 FORMAT (/' --> Longwave radiation is disabled')
1744	!11 FORMAT (/' --> Shortwave radiation is disabled.')
1745	!12 FORMAT (' Timestep: dt_radiation = ', F6.2, ' s')
1746	!
1747	!
1748	END SUBROUTINE chem_header
1749
1750	!------------------------------------------------------------------------------
1751	! Description:
1752	! ------------
1753	!> Subroutine reading restart data for chemistry model input parameters
1754	! (FK: To make restarts work, I had to comment this routine. We actually
1755	! don't need it, since the namelist parameters are always read in,
1756	! also in case of a restart run)
1757	!------------------------------------------------------------------------------
1758	! SUBROUTINE chem_rrd_global
1759	!
1760	! USE chem_modules
1761	!
1762	! USE control_parameters, &
1763	! ONLY: length, message_string, restart_string
1764	!
1765	!
1766	! IMPLICIT NONE
1767	!
1768	!
1769	!
1770	! DO
1771	!
1772	! SELECT CASE ( restart_string(1:length) )
1773	!
1774	! CASE ( 'bc_cs_b' )
1775	! READ ( 13 ) bc_cs_b
1776	!
1777	! CASE DEFAULT
1778	!
1779	! EXIT
1780	!
1781	! END SELECT
1782	!
1783	!!
1784	!!-- Read next string and its length
1785	! READ ( 13 ) length
1786	! READ ( 13 ) restart_string(1:length)
1787	!
1788	! ENDDO
1789	!
1790	! END SUBROUTINE chem_rrd_global
1791
1792
1793	!------------------------------------------------------------------------------!
1794	!
1795	! Description:
1796	! ------------
1797	!> Subroutine writing restart data for chemistry model input parameters
1798	! (FK: To make restarts work, I had to comment this routine. We actually
1799	! don't need it, since the namelist parameters are always read in,
1800	! also in case of a restart run)
1801	!------------------------------------------------------------------------------!
1802	! SUBROUTINE chem_wrd_global
1803	!
1804	! USE chem_modules
1805	!
1806	! USE kinds
1807	!
1808	!
1809	! IMPLICIT NONE
1810	!
1811	! INTEGER(iwp) :: lsp !< running index for chem spcs
1812	!
1813	! !
1814	! !-- Writing out input parameters that are not part of chemistry_parameters
1815	! !-- namelist (namelist parameters are anyway read in again in case of restart)
1816	! DO lsp = 1, nvar
1817	! CALL wrd_write_string( 'conc_pr_init_'//chem_species(lsp)%name )
1818	! WRITE ( 14 ) chem_species(lsp)%conc_pr_init
1819	! ENDDO
1820	!
1821	!
1822	! END SUBROUTINE chem_wrd_global
1823
1824
1825	!------------------------------------------------------------------------------!
1826	!
1827	! Description:
1828	! ------------
1829	!> Subroutine for emission
1830	!------------------------------------------------------------------------------!
1831	SUBROUTINE chem_emissions
1832
1833	USE chem_modules
1834
1835	USE netcdf_data_input_mod, &
1836	ONLY: street_type_f
1837
1838	USE surface_mod, &
1839	ONLY: surf_lsm_h
1840
1841
1842	IMPLICIT NONE
1843
1844	INTEGER(iwp) :: i !< running index for grid in x-direction
1845	INTEGER(iwp) :: j !< running index for grid in y-direction
1846	INTEGER(iwp) :: m !< running index for horizontal surfaces
1847	INTEGER(iwp) :: lsp !< running index for chem spcs
1848
1849	!
1850	!-- Comment??? (todo)
1851	IF ( street_type_f%from_file ) THEN
1852	!
1853	!-- Streets are lsm surfaces, hence, no usm surface treatment required
1854	DO m = 1, surf_lsm_h%ns
1855	i = surf_lsm_h%i(m)
1856	j = surf_lsm_h%j(m)
1857
1858	IF ( street_type_f%var(j,i) >= main_street_id .AND. &
1859	street_type_f%var(j,i) < max_street_id ) THEN
1860	DO lsp = 1, nvar
1861	surf_lsm_h%cssws(lsp,m) = emiss_factor_main * surface_csflux(lsp)
1862	ENDDO
1863	ELSEIF ( street_type_f%var(j,i) >= side_street_id .AND. &
1864	street_type_f%var(j,i) < main_street_id ) THEN
1865	DO lsp = 1, nvar
1866	surf_lsm_h%cssws(lsp,m) = emiss_factor_side * surface_csflux(lsp)
1867	ENDDO
1868	ELSE
1869	surf_lsm_h%cssws(:,m) = 0.0_wp
1870	ENDIF
1871	ENDDO
1872
1873	ENDIF
1874
1875	END SUBROUTINE chem_emissions
1876
1877
1878	END MODULE chemistry_model_mod
1879

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