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source: palm/trunk/SOURCE/chemistry_model_mod.f90 @ 3209

Last change on this file since 3209 was 3209, checked in by suehring, 6 years ago
Additional namelist parameter to switch on/off the nesting of chemical species; Enable the input of soil data from dynamic input files independent on atmosphere in order to initialize soil properties in nested child domains from dynamic input; Revise error message number for static/dynamic input; Revise and add checks for static/dynamic input; Bugfix, add netcdf4_parallel directive for collective read operation
Property svn:keywords set to `Id`
File size: 76.5 KB

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

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