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chemistry_model_mod.f90

Last change on this file was 4901, checked in by banzhafs, 4 years ago
removed unnecessary informative message and unused code from chemistry_model_mod
Property svn:keywords set to `Id`
File size: 259.5 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 terms of the GNU General
6	! Public License as published by the Free Software Foundation, either version 3 of the License, or
7	! (at your option) any later version.
8	!
9	! PALM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
10	! implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
11	! Public License for more details.
12	!
13	! You should have received a copy of the GNU General Public License along with PALM. If not, see
14	! <http://www.gnu.org/licenses/>.
15	!
16	! Copyright 2017-2021 Leibniz Universitaet Hannover
17	! Copyright 2017-2021 Karlsruhe Institute of Technology
18	! Copyright 2017-2021 Freie Universitaet Berlin
19	!--------------------------------------------------------------------------------------------------!
20	!
21	! Current revisions:
22	! -----------------
23	!
24	!
25	! Former revisions:
26	! -----------------
27	! $Id: chemistry_model_mod.f90 4901 2021-03-04 21:24:08Z banzhafs $
28	! removed unnecessary informative messages,
29	! removed unused code in chem_depo subroutine
30	!
31	! 4899 2021-03-04 16:42:21Z raasch
32	! small adjustments regarding r4897
33	!
34	! 4897 2021-03-04 09:08:58Z forkel
35	! Few informative messages removed, small changes in comments and chemistry header
36	!
37	! 4895 2021-03-03 15:39:08Z suehring
38	! Remove offset in terrain-following masked output
39	!
40	! 4887 2021-02-26 16:22:32Z banzhafs
41	! Unnecessary comments removed
42	!
43	! 4881 2021-02-19 22:05:08Z forkel
44	! removed unnecessarty namelist parameters and commented output statements
45	! and cs_surface_initial_change
46	!
47	! 4860 2021-02-01 08:10:59Z raasch
48	! further re-numbering of message IDs
49	!
50	! 4852 2021-01-25 07:18:30Z raasch
51	! re-numbering of message IDs
52	!
53	! 4847 2021-01-19 13:44:45Z raasch
54	! error message IDs changed from CM to the default PA
55	!
56	! 4843 2021-01-15 15:22:11Z raasch
57	! local namelist parameter added to switch off the module although the respective module namelist
58	! appears in the namelist file
59	!
60	! 4833 2021-01-07 08:57:54Z raasch
61	! openmp bugfix for time measurements of non advective processes
62	!
63	! 4828 2021-01-05 11:21:41Z Giersch
64	! reading of namelist file and actions in case of namelist errors revised so that statement labels
65	! and goto statements are not required any more
66	!
67	! 4768 2020-11-02 19:11:23Z suehring
68	! Enable 3D data output also with 64-bit precision
69	!
70	! 4731 2020-10-07 13:25:11Z schwenkel
71	! Move exchange_horiz from time_integration to modules
72	!
73	! 4671 2020-09-09 20:27:58Z pavelkrc
74	! Implementation of downward facing USM and LSM surfaces
75	!
76	! 4637 2020-08-07 07:49:33Z suehring
77	! Avoid usage of omp_lib, instead declare omp_get_thread_num explicitly
78	!
79	! 4636 2020-08-06 14:10:12Z resler
80	! Fix bugs in OpenMP directives
81	!
82	! 4636 2020-08-06 14:10:12Z suehring
83	! - Bugfix in variable name separation in profile-output initialization
84	! - Bugfix in counting the number of chemistry profiles
85	!
86	! 4581 2020-06-29 08:49:58Z suehring
87	! Enable output of resolved-scale vertical fluxes of chemical species.
88	!
89	! 4577 2020-06-25 09:53:58Z raasch
90	! further re-formatting to follow the PALM coding standard
91	!
92	! 4559 2020-06-11 08:51:48Z raasch
93	! file re-formatted to follow the PALM coding standard
94	!
95	! 4550 2020-05-29 15:22:13Z raasch
96	! bugfix for reading local restart data
97	!
98	! 4544 2020-05-21 14:43:05Z raasch
99	! conc_av changed from pointer to allocatable array, array spec_conc_av removed
100	!
101	! 4542 2020-05-19 15:45:12Z raasch
102	! redundant if statement removed
103	!
104	! 4535 2020-05-15 12:07:23Z raasch
105	! bugfix for restart data format query
106	!
107	! 4517 2020-05-03 14:29:30Z raasch
108	! added restart with MPI-IO
109	!
110	! 4511 2020-04-30 12:20:40Z raasch
111	! decycling replaced by explicit setting of lateral boundary conditions
112	!
113	! 4487 2020-04-03 09:38:20Z raasch
114	! bugfix for subroutine calls that contain the decycle_chem switches as arguments
115	!
116	! 4481 2020-03-31 18:55:54Z maronga
117	! use statement for exchange horiz added,
118	! bugfix for call of exchange horiz 2d
119	!
120	! 4442 2020-03-04 19:21:13Z suehring
121	! Change order of dimension in surface array %frac to allow for better
122	! vectorization.
123	!
124	! 4441 2020-03-04 19:20:35Z suehring
125	! in subroutine chem_init (ECC)
126	! - allows different init paths emission data for legacy mode emission and on-demand mode in
127	! subroutine chem_init_internal (ECC)
128	! - reads netcdf file only when legacy mode is activated (i.e., emiss_read_legacy_mode = .TRUE.)
129	! otherwise file is read once at the beginning to obtain header information, and emission data
130	! are extracted on an on-demand basis
131	!
132	! 4372 2020-01-14 10:20:35Z banzhafs
133	! chem_parin : added handler for new namelist item emiss_legacy_read_mode (ECC) added messages
134	! CM0465 - legacy read mode selection
135	! CM0466 - legacy read mode force selection
136	! CM0467 - new read mode selection
137	!
138	! 4370 2020-01-10 14:00:44Z raasch
139	! vector directives added to force vectorization on Intel19 compiler
140	!
141	! 4346 2019-12-18 11:55:56Z motisi
142	! Introduction of wall_flags_total_0, which currently sets bits based on static topography
143	! information used in wall_flags_static_0
144	!
145	! 4329 2019-12-10 15:46:36Z motisi
146	! Renamed wall_flags_0 to wall_flags_static_0
147	!
148	! 4306 2019-11-25 12:04:48Z banzhafs
149	! Corretion for r4304 commit
150	!
151	! 4304 2019-11-25 10:43:03Z banzhafs
152	! Precision clean-up in drydepo_aero_zhang_vd subroutine
153	!
154	! 4292 2019-11-11 13:04:50Z banzhafs
155	! Bugfix for r4290
156	!
157	! 4290 2019-11-11 12:06:14Z banzhafs
158	! Bugfix in sedimentation resistance calculation in drydepo_aero_zhang_vd subroutine
159	!
160	! 4273 2019-10-24 13:40:54Z monakurppa
161	! Add logical switches nesting_chem and nesting_offline_chem (both .TRUE. by default)
162	!
163	! 4272 2019-10-23 15:18:57Z schwenkel
164	! Further modularization of boundary conditions: moved boundary conditions to respective modules
165	!
166	! 4268 2019-10-17 11:29:38Z schwenkel
167	! Moving module specific boundary conditions from time_integration to module
168	!
169	! 4230 2019-09-11 13:58:14Z suehring
170	! Bugfix, initialize mean profiles also in restart runs. Also initialize array used for Runge-Kutta
171	! tendecies in restart runs.
172	!
173	! 4227 2019-09-10 18:04:34Z gronemeier
174	! implement new palm_date_time_mod
175	!
176	! 4182 2019-08-22 15:20:23Z scharf
177	! Corrected "Former revisions" section
178	!
179	! 4167 2019-08-16 11:01:48Z suehring
180	! Changed behaviour of masked output over surface to follow terrain and ignore buildings
181	! (J.Resler, T.Gronemeier)
182	!
183	! 4166 2019-08-16 07:54:21Z resler
184	! Bugfix in decycling
185	!
186	! 4115 2019-07-24 12:50:49Z suehring
187	! Fix faulty IF statement in decycling initialization
188	!
189	! 4110 2019-07-22 17:05:21Z suehring
190	! - Decycling boundary conditions are only set at the ghost points not on the prognostic grid points
191	! - Allocation and initialization of special advection flags cs_advc_flags_s used for chemistry.
192	! These are exclusively used for chemical species in order to distinguish from the usually-used
193	! flags which might be different when decycling is applied in combination with cyclic boundary
194	! conditions.
195	! Moreover, cs_advc_flags_s considers extended zones around buildings where first-order upwind
196	! scheme is applied for the horizontal advection terms, in order to overcome high concentration
197	! peaks due to stationary numerical oscillations caused by horizontal advection discretization.
198	!
199	! 4109 2019-07-22 17:00:34Z suehring
200	! Slightly revise setting of boundary conditions at horizontal walls, use data-structure offset
201	! index instead of pre-calculate it for each facing
202	!
203	! 4080 2019-07-09 18:17:37Z suehring
204	! Restore accidantly removed limitation to positive values
205	!
206	! 4079 2019-07-09 18:04:41Z suehring
207	! Application of monotonic flux limiter for the vertical scalar advection up to the topography top
208	! (only for the cache-optimized version at the moment).
209	!
210	! 4069 2019-07-01 14:05:51Z Giersch
211	! Masked output running index mid has been introduced as a local variable to avoid runtime error
212	! (Loop variable has been modified) in time_integration
213	!
214	! 4029 2019-06-14 14:04:35Z raasch
215	! nest_chemistry option removed
216	!
217	! 4004 2019-05-24 11:32:38Z suehring
218	! in subroutine chem_parin check emiss_lod / mod_emis only when emissions_anthropogenic is activated
219	! in namelist (E.C. Chan)
220	!
221	! 3968 2019-05-13 11:04:01Z suehring
222	! - added "emiss_lod" which serves the same function as "mode_emis" both will be synchronized with
223	! emiss_lod having pirority over mode_emis (see informational messages)
224	! - modified existing error message and introduced new informational messages
225	! - CM0436 - now also applies to invalid LOD settings
226	! - CM0463 - emiss_lod take precedence in case of conflict with mod_emis
227	! - CM0464 - emiss_lod valued assigned based on mode_emis if undefined
228	!
229	! 3930 2019-04-24 14:57:18Z forkel
230	! Changed chem_non_transport_physics to chem_non_advective_processes
231	!
232	! 3929 2019-04-24 12:52:08Z banzhafs
233	! Correct/complete module_interface introduction for chemistry model
234	! Add subroutine chem_exchange_horiz_bounds
235	! Bug fix deposition
236	!
237	! 3784 2019-03-05 14:16:20Z banzhafs
238	! 2D output of emission fluxes
239	!
240	! 3784 2019-03-05 14:16:20Z banzhafs
241	! Bugfix, uncomment erroneous commented variable used for dry deposition.
242	! Bugfix in 3D emission output.
243	!
244	! 3784 2019-03-05 14:16:20Z banzhafs
245	! Changes related to global restructuring of location messages and introduction
246	! of additional debug messages
247	!
248	! 3784 2019-03-05 14:16:20Z banzhafs
249	! some formatting of the deposition code
250	!
251	! 3784 2019-03-05 14:16:20Z banzhafs
252	! some formatting
253	!
254	! 3784 2019-03-05 14:16:20Z banzhafs
255	! added cs_mech to USE chem_gasphase_mod
256	!
257	! 3784 2019-03-05 14:16:20Z banzhafs
258	! renamed get_mechanismname to get_mechanism_name
259	! renamed do_emiss to emissions_anthropogenic and do_depo to deposition_dry (ecc)
260	!
261	! 3784 2019-03-05 14:16:20Z banzhafs
262	! Unused variables removed/taken care of
263	!
264	! 3784 2019-03-05 14:16:20Z forkel
265	! Replaced READ from unit 10 by CALL get_mechanismname also in chem_header
266	!
267	! 3783 2019-03-05 13:23:50Z forkel
268	! Removed forgotte write statements an some unused variables (did not touch the parts related to
269	! deposition)
270	!
271	! 3780 2019-03-05 11:19:45Z forkel
272	! Removed READ from unit 10, added CALL get_mechanismname
273	!
274	! 3767 2019-02-27 08:18:02Z raasch
275	! unused variable for file index removed from rrd-subroutines parameter list
276	!
277	! 3738 2019-02-12 17:00:45Z suehring
278	! Clean-up debug prints
279	!
280	! 3737 2019-02-12 16:57:06Z suehring
281	! Enable mesoscale offline nesting for chemistry variables as well as initialization of chemistry
282	! via dynamic input file.
283	!
284	! 3719 2019-02-06 13:10:18Z kanani
285	! Resolved cpu logpoint overlap with all progn.equations, moved cpu_log call to prognostic_equations
286	! for better overview
287	!
288	! 3700 2019-01-26 17:03:42Z knoop
289	! Some interface calls moved to module_interface + cleanup
290	!
291	! 3664 2019-01-09 14:00:37Z forkel
292	! Replaced misplaced location message by @todo
293	!
294	! 3654 2019-01-07 16:31:57Z suehring
295	! Disable misplaced location message
296	!
297	! 3652 2019-01-07 15:29:59Z forkel
298	! Checks added for chemistry mechanism, parameter chem_mechanism added (basit)
299	!
300	! 2718 2018-01-02 08:49:38Z maronga
301	! Initial revision
302	!
303	!
304	!
305	!
306	! Authors:
307	! --------
308	! @author Renate Forkel
309	! @author Farah Kanani-Suehring
310	! @author Klaus Ketelsen
311	! @author Basit Khan
312	! @author Sabine Banzhaf
313	!
314	!
315	!--------------------------------------------------------------------------------------------------!
316	! Description:
317	! ------------
318	!> Chemistry model for PALM-4U
319	!> @todo Adjust chem_rrd_local to CASE structure of others modules. It is not allowed to use the
320	!> chemistry model in a precursor run and additionally not using it in a main run
321	!> @todo Implement turbulent inflow of chem spcs in inflow_turbulence. Do we need this? Not done for salsa either.
322	!
323	!--------------------------------------------------------------------------------------------------!
324
325	MODULE chemistry_model_mod
326
327	USE advec_s_pw_mod, &
328	ONLY: advec_s_pw
329
330	USE advec_s_up_mod, &
331	ONLY: advec_s_up
332
333	USE advec_ws, &
334	ONLY: advec_s_ws, ws_init_flags_scalar
335
336	USE diffusion_s_mod, &
337	ONLY: diffusion_s
338
339	USE kinds, &
340	ONLY: iwp, wp
341
342	USE indices, &
343	ONLY: advc_flags_s, &
344	nbgp, nx, nxl, nxlg, nxr, nxrg, ny, nyn, nyng, nys, nysg, nz, nzb, nzt, &
345	wall_flags_total_0
346
347	USE pegrid, &
348	ONLY: myid, threads_per_task
349
350	USE bulk_cloud_model_mod, &
351	ONLY: bulk_cloud_model
352
353	USE control_parameters, &
354	ONLY: air_chemistry, &
355	bc_dirichlet_l, &
356	bc_dirichlet_n, &
357	bc_dirichlet_r, &
358	bc_dirichlet_s, &
359	bc_radiation_l, &
360	bc_lr_cyc, &
361	bc_ns_cyc, &
362	bc_radiation_n, &
363	bc_radiation_r, &
364	bc_radiation_s, &
365	debug_output, &
366	dt_3d, &
367	humidity, &
368	initializing_actions, &
369	intermediate_timestep_count, &
370	intermediate_timestep_count_max, &
371	max_pr_user, &
372	message_string, &
373	monotonic_limiter_z, &
374	nesting_offline, &
375	omega, &
376	restart_data_format_output, &
377	scalar_advec, &
378	timestep_scheme, &
379	tsc, &
380	use_prescribed_profile_data, &
381	ws_scheme_sca
382
383	USE arrays_3d, &
384	ONLY: exner, hyp, pt, q, ql, rdf_sc, tend, zu
385
386	USE chem_gasphase_mod, &
387	ONLY: atol, chem_gasphase_integrate, cs_mech, get_mechanism_name, nkppctrl, &
388	nmaxfixsteps, nphot, nreact, nspec, nvar, phot_names, rtol, spc_names, t_steps, vl_dim
389
390	USE chem_modules
391
392	USE chem_photolysis_mod, &
393	ONLY: photolysis_control
394
395	USE cpulog, &
396	ONLY: cpu_log, log_point_s
397
398	USE restart_data_mpi_io_mod, &
399	ONLY: rrd_mpi_io, rd_mpi_io_check_array, wrd_mpi_io
400
401	USE statistics
402
403	USE surface_mod, &
404	ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, surf_usm_v
405
406	IMPLICIT NONE
407
408	PRIVATE
409	SAVE
410
411	INTEGER, DIMENSION(nkppctrl) :: icntrl !< 20 integer parameters for fine tuning KPP code
412
413	REAL(kind=wp), PUBLIC :: cs_time_step = 0._wp
414
415	REAL(kind=wp), DIMENSION(nkppctrl) :: rcntrl !< 20 real parameters for fine tuning of KPP code
416	!< (e.g starting internal timestep of solver)
417
418	REAL(kind=wp), ALLOCATABLE, DIMENSION(:,:,:,:), TARGET :: spec_conc_1 !< pointer for swapping of timelevels for conc
419	REAL(kind=wp), ALLOCATABLE, DIMENSION(:,:,:,:), TARGET :: spec_conc_2 !< pointer for swapping of timelevels for conc
420	REAL(kind=wp), ALLOCATABLE, DIMENSION(:,:,:,:), TARGET :: spec_conc_3 !< pointer for swapping of timelevels for conc
421	REAL(kind=wp), ALLOCATABLE, DIMENSION(:,:,:,:), TARGET :: freq_1 !< pointer for phtolysis frequncies
422	!< (only 1 timelevel required) (e.g. solver type)
423
424	!
425	!-- Parameter needed for Deposition calculation using DEPAC model (van Zanten et al., 2010)
426	INTEGER(iwp), PARAMETER :: nlu_dep = 15 !< Number of DEPAC landuse classes (lu's)
427	INTEGER(iwp), PARAMETER :: ncmp = 10 !< Number of DEPAC gas components
428	INTEGER(iwp), PARAMETER :: nposp = 69 !< Number of possible species for deposition
429	!
430	!-- DEPAC landuse classes as defined in LOTOS-EUROS model v2.1
431	INTEGER(iwp) :: ilu_grass = 1
432	INTEGER(iwp) :: ilu_arable = 2
433	INTEGER(iwp) :: ilu_permanent_crops = 3
434	INTEGER(iwp) :: ilu_coniferous_forest = 4
435	INTEGER(iwp) :: ilu_deciduous_forest = 5
436	INTEGER(iwp) :: ilu_water_sea = 6
437	INTEGER(iwp) :: ilu_urban = 7
438	INTEGER(iwp) :: ilu_other = 8
439	INTEGER(iwp) :: ilu_desert = 9
440	INTEGER(iwp) :: ilu_ice = 10
441	INTEGER(iwp) :: ilu_savanna = 11
442	INTEGER(iwp) :: ilu_tropical_forest = 12
443	INTEGER(iwp) :: ilu_water_inland = 13
444	INTEGER(iwp) :: ilu_mediterrean_scrub = 14
445	INTEGER(iwp) :: ilu_semi_natural_veg = 15
446
447	!
448	!-- NH3/SO2 ratio regimes:
449	INTEGER(iwp), PARAMETER :: iratns_low = 1 !< low ratio NH3/SO2
450	INTEGER(iwp), PARAMETER :: iratns_high = 2 !< high ratio NH3/SO2
451	INTEGER(iwp), PARAMETER :: iratns_very_low = 3 !< very low ratio NH3/SO2
452	!
453	!-- Default:
454	INTEGER, PARAMETER :: iratns_default = iratns_low
455	!
456	!-- Set alpha for f_light (4.57 is conversion factor from 1./(mumol m-2 s-1) to W m-2
457	REAL(wp), DIMENSION(nlu_dep), PARAMETER :: alpha = (/ 0.009, 0.009, 0.009, 0.006, 0.006, &
458	-999.0, -999., 0.009, -999.0, -999.0, 0.009, 0.006, -999.0, 0.009, 0.008 /)*4.57
459	!
460	!-- Set temperatures per land use for f_temp
461	REAL(wp), DIMENSION(nlu_dep), PARAMETER :: tmin = (/ 12.0, 12.0, 12.0, 0.0, 0.0, -999.0, &
462	-999.0, 12.0, -999.0, -999.0, 12.0, 0.0, -999.0, 12.0, 8.0/)
463	REAL(wp), DIMENSION(nlu_dep), PARAMETER :: topt = (/ 26.0, 26.0, 26.0, 18.0, 20.0, -999.0, &
464	-999.0, 26.0, -999.0, -999.0, 26.0, 20.0, -999.0, 26.0, 24.0 /)
465	REAL(wp), DIMENSION(nlu_dep), PARAMETER :: tmax = (/ 40.0, 40.0, 40.0, 36.0, 35.0, -999.0, &
466	-999.0, 40.0, -999.0, -999.0, 40.0, 35.0, -999.0, 40.0, 39.0 /)
467	!
468	!-- Set f_min:
469	REAL(wp), DIMENSION(nlu_dep), PARAMETER :: f_min = (/ 0.01, 0.01, 0.01, 0.1, 0.1, -999.0, &
470	-999.0, 0.01, -999.0, -999.0, 0.01, 0.1, -999.0, 0.01, 0.04/)
471
472	!
473	!-- Set maximal conductance (m/s)
474	!-- (R T/P) = 1/41000 mmol/m3 is given for 20 deg C to go from mmol O3/m2/s to m/s
475	REAL(wp), DIMENSION(nlu_dep), PARAMETER :: g_max = (/ 270.0, 300.0, 300.0, 140.0, 150.0, &
476	-999.0, -999.0, 270.0, -999.0, -999.0, 270.0, 150.0, -999.0, 300.0, 422.0 /) / 41000.0
477	!
478	!-- Set max, min for vapour pressure deficit vpd
479	REAL(wp), DIMENSION(nlu_dep), PARAMETER :: vpd_max = (/ 1.3, 0.9, 0.9, 0.5, 1.0, -999.0, &
480	-999.0, 1.3, -999.0, -999.0, 1.3, 1.0, -999.0, 0.9, 2.8/)
481	REAL(wp), DIMENSION(nlu_dep), PARAMETER :: vpd_min = (/ 3.0, 2.8, 2.8, 3.0, 3.25, -999.0, &
482	-999.0, 3.0, -999.0, -999.0, 3.0, 3.25, -999.0, 2.8, 4.5/)
483
484	PUBLIC nreact
485	PUBLIC nspec !< number of gas phase chemical species including constant compound (e.g. N2)
486	PUBLIC nvar !< number of variable gas phase chemical species (nvar <= nspec)
487	PUBLIC spc_names !< names of gas phase chemical species (come from KPP) (come from KPP)
488	PUBLIC spec_conc_2
489	!
490	!-- Interface section
491	INTERFACE chem_actions
492	MODULE PROCEDURE chem_actions
493	MODULE PROCEDURE chem_actions_ij
494	END INTERFACE chem_actions
495
496	INTERFACE chem_3d_data_averaging
497	MODULE PROCEDURE chem_3d_data_averaging
498	END INTERFACE chem_3d_data_averaging
499
500	INTERFACE chem_boundary_conditions
501	MODULE PROCEDURE chem_boundary_conditions
502	END INTERFACE chem_boundary_conditions
503
504	INTERFACE chem_check_data_output
505	MODULE PROCEDURE chem_check_data_output
506	END INTERFACE chem_check_data_output
507
508	INTERFACE chem_data_output_2d
509	MODULE PROCEDURE chem_data_output_2d
510	END INTERFACE chem_data_output_2d
511
512	INTERFACE chem_data_output_3d
513	MODULE PROCEDURE chem_data_output_3d
514	END INTERFACE chem_data_output_3d
515
516	INTERFACE chem_data_output_mask
517	MODULE PROCEDURE chem_data_output_mask
518	END INTERFACE chem_data_output_mask
519
520	INTERFACE chem_check_data_output_pr
521	MODULE PROCEDURE chem_check_data_output_pr
522	END INTERFACE chem_check_data_output_pr
523
524	INTERFACE chem_check_parameters
525	MODULE PROCEDURE chem_check_parameters
526	END INTERFACE chem_check_parameters
527
528	INTERFACE chem_define_netcdf_grid
529	MODULE PROCEDURE chem_define_netcdf_grid
530	END INTERFACE chem_define_netcdf_grid
531
532	INTERFACE chem_header
533	MODULE PROCEDURE chem_header
534	END INTERFACE chem_header
535
536	INTERFACE chem_init_arrays
537	MODULE PROCEDURE chem_init_arrays
538	END INTERFACE chem_init_arrays
539
540	INTERFACE chem_init
541	MODULE PROCEDURE chem_init
542	END INTERFACE chem_init
543
544	INTERFACE chem_init_profiles
545	MODULE PROCEDURE chem_init_profiles
546	END INTERFACE chem_init_profiles
547
548	INTERFACE chem_integrate
549	MODULE PROCEDURE chem_integrate_ij
550	END INTERFACE chem_integrate
551
552	INTERFACE chem_parin
553	MODULE PROCEDURE chem_parin
554	END INTERFACE chem_parin
555
556	INTERFACE chem_non_advective_processes
557	MODULE PROCEDURE chem_non_advective_processes
558	MODULE PROCEDURE chem_non_advective_processes_ij
559	END INTERFACE chem_non_advective_processes
560
561	INTERFACE chem_exchange_horiz_bounds
562	MODULE PROCEDURE chem_exchange_horiz_bounds
563	END INTERFACE chem_exchange_horiz_bounds
564
565	INTERFACE chem_prognostic_equations
566	MODULE PROCEDURE chem_prognostic_equations
567	MODULE PROCEDURE chem_prognostic_equations_ij
568	END INTERFACE chem_prognostic_equations
569
570	INTERFACE chem_rrd_local
571	MODULE PROCEDURE chem_rrd_local_ftn
572	MODULE PROCEDURE chem_rrd_local_mpi
573	END INTERFACE chem_rrd_local
574
575	INTERFACE chem_statistics
576	MODULE PROCEDURE chem_statistics
577	END INTERFACE chem_statistics
578
579	INTERFACE chem_swap_timelevel
580	MODULE PROCEDURE chem_swap_timelevel
581	END INTERFACE chem_swap_timelevel
582
583	INTERFACE chem_wrd_local
584	MODULE PROCEDURE chem_wrd_local
585	END INTERFACE chem_wrd_local
586
587	INTERFACE chem_depo
588	MODULE PROCEDURE chem_depo
589	END INTERFACE chem_depo
590
591	INTERFACE drydepos_gas_depac
592	MODULE PROCEDURE drydepos_gas_depac
593	END INTERFACE drydepos_gas_depac
594
595	INTERFACE rc_special
596	MODULE PROCEDURE rc_special
597	END INTERFACE rc_special
598
599	INTERFACE rc_gw
600	MODULE PROCEDURE rc_gw
601	END INTERFACE rc_gw
602
603	INTERFACE rw_so2
604	MODULE PROCEDURE rw_so2
605	END INTERFACE rw_so2
606
607	INTERFACE rw_nh3_sutton
608	MODULE PROCEDURE rw_nh3_sutton
609	END INTERFACE rw_nh3_sutton
610
611	INTERFACE rw_constant
612	MODULE PROCEDURE rw_constant
613	END INTERFACE rw_constant
614
615	INTERFACE rc_gstom
616	MODULE PROCEDURE rc_gstom
617	END INTERFACE rc_gstom
618
619	INTERFACE rc_gstom_emb
620	MODULE PROCEDURE rc_gstom_emb
621	END INTERFACE rc_gstom_emb
622
623	INTERFACE par_dir_diff
624	MODULE PROCEDURE par_dir_diff
625	END INTERFACE par_dir_diff
626
627	INTERFACE rc_get_vpd
628	MODULE PROCEDURE rc_get_vpd
629	END INTERFACE rc_get_vpd
630
631	INTERFACE rc_gsoil_eff
632	MODULE PROCEDURE rc_gsoil_eff
633	END INTERFACE rc_gsoil_eff
634
635	INTERFACE rc_rinc
636	MODULE PROCEDURE rc_rinc
637	END INTERFACE rc_rinc
638
639	INTERFACE rc_rctot
640	MODULE PROCEDURE rc_rctot
641	END INTERFACE rc_rctot
642
643	INTERFACE drydepo_aero_zhang_vd
644	MODULE PROCEDURE drydepo_aero_zhang_vd
645	END INTERFACE drydepo_aero_zhang_vd
646
647	INTERFACE get_rb_cell
648	MODULE PROCEDURE get_rb_cell
649	END INTERFACE get_rb_cell
650
651
652
653	PUBLIC chem_3d_data_averaging, chem_boundary_conditions, chem_check_data_output, &
654	chem_check_data_output_pr, chem_check_parameters, chem_data_output_2d, &
655	chem_data_output_3d, chem_data_output_mask, chem_define_netcdf_grid, chem_header, &
656	chem_init, chem_init_arrays, chem_init_profiles, chem_integrate, chem_parin, &
657	chem_actions, chem_prognostic_equations, chem_rrd_local, chem_statistics, &
658	chem_swap_timelevel, chem_wrd_local, chem_depo, chem_non_advective_processes, &
659	chem_exchange_horiz_bounds
660
661	CONTAINS
662
663
664	!--------------------------------------------------------------------------------------------------!
665	! Description:
666	! ------------
667	!> Subroutine for averaging 3D data of chemical species. Due to the fact that the averaged chem
668	!> arrays are allocated in chem_init, no if-query concerning the allocation is required (in any
669	!> mode). Attention: If you just specify an averaged output quantity in the _p3dr file during
670	!> restarts the first output includes the time between the beginning of the restart run and the
671	!> first output time (not necessarily the whole averaging_interval you have specified in your
672	!> _p3d/_p3dr file ).
673	!--------------------------------------------------------------------------------------------------!
674	SUBROUTINE chem_3d_data_averaging( mode, variable )
675
676	USE control_parameters
677
678	USE exchange_horiz_mod, &
679	ONLY: exchange_horiz_2d
680
681
682	CHARACTER (LEN=*) :: mode !<
683	CHARACTER (LEN=*) :: variable !<
684
685	LOGICAL :: match_def !< flag indicating default-type surface
686	LOGICAL :: match_lsm !< flag indicating natural-type surface
687	LOGICAL :: match_usm !< flag indicating urban-type surface
688
689	INTEGER(iwp) :: i !< grid index x direction
690	INTEGER(iwp) :: j !< grid index y direction
691	INTEGER(iwp) :: k !< grid index z direction
692	INTEGER(iwp) :: lsp !< running index for chem spcs
693	INTEGER(iwp) :: m !< running index surface type
694
695	IF ( ( variable(1:3) == 'kc_' .OR. variable(1:3) == 'em_' ) ) THEN
696
697	IF ( mode == 'allocate' ) THEN
698
699	DO lsp = 1, nspec
700	IF ( TRIM( variable(1:3) ) == 'kc_' .AND. &
701	TRIM( variable(4:) ) == TRIM( chem_species(lsp)%name ) ) THEN
702	IF ( .NOT. ALLOCATED( chem_species(lsp)%conc_av ) ) THEN
703	ALLOCATE( chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
704	chem_species(lsp)%conc_av = 0.0_wp
705	ENDIF
706	ENDIF
707	ENDDO
708
709	ELSEIF ( mode == 'sum' ) THEN
710
711	DO lsp = 1, nspec
712	IF ( TRIM( variable(1:3) ) == 'kc_' .AND. &
713	TRIM( variable(4:) ) == TRIM( chem_species(lsp)%name ) ) THEN
714	DO i = nxlg, nxrg
715	DO j = nysg, nyng
716	DO k = nzb, nzt+1
717	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) + &
718	chem_species(lsp)%conc(k,j,i)
719	ENDDO
720	ENDDO
721	ENDDO
722	ELSEIF ( TRIM( variable(4:) ) == TRIM( 'cssws*' ) ) THEN
723	DO i = nxl, nxr
724	DO j = nys, nyn
725	match_def = surf_def_h(0)%start_index(j,i) <= surf_def_h(0)%end_index(j,i)
726	match_lsm = surf_lsm_h(0)%start_index(j,i) <= surf_lsm_h(0)%end_index(j,i)
727	match_usm = surf_usm_h(0)%start_index(j,i) <= surf_usm_h(0)%end_index(j,i)
728
729	IF ( match_def ) THEN
730	m = surf_def_h(0)%end_index(j,i)
731	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) + &
732	surf_def_h(0)%cssws(lsp,m)
733	ELSEIF ( match_lsm .AND. .NOT. match_usm ) THEN
734	m = surf_lsm_h(0)%end_index(j,i)
735	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) + &
736	surf_lsm_h(0)%cssws(lsp,m)
737	ELSEIF ( match_usm ) THEN
738	m = surf_usm_h(0)%end_index(j,i)
739	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) + &
740	surf_usm_h(0)%cssws(lsp,m)
741	ENDIF
742	ENDDO
743	ENDDO
744	ENDIF
745	ENDDO
746
747	ELSEIF ( mode == 'average' ) THEN
748
749	DO lsp = 1, nspec
750	IF ( TRIM( variable(1:3) ) == 'kc_' .AND. &
751	TRIM( variable(4:) ) == TRIM( chem_species(lsp)%name ) ) THEN
752	DO i = nxlg, nxrg
753	DO j = nysg, nyng
754	DO k = nzb, nzt+1
755	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) / &
756	REAL( average_count_3d, KIND = wp )
757	ENDDO
758	ENDDO
759	ENDDO
760
761	ELSEIF ( TRIM( variable(4:) ) == TRIM( 'cssws*' ) ) THEN
762	DO i = nxlg, nxrg
763	DO j = nysg, nyng
764	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) / &
765	REAL( average_count_3d, KIND = wp )
766	ENDDO
767	ENDDO
768	CALL exchange_horiz_2d( chem_species(lsp)%cssws_av )
769	ENDIF
770	ENDDO
771	ENDIF
772
773	ENDIF
774
775	END SUBROUTINE chem_3d_data_averaging
776
777
778	!--------------------------------------------------------------------------------------------------!
779	! Description:
780	! ------------
781	!> Subroutine to initialize and set all boundary conditions for chemical species
782	!--------------------------------------------------------------------------------------------------!
783	SUBROUTINE chem_boundary_conditions( horizontal_conditions_only )
784
785	USE arrays_3d, &
786	ONLY: dzu
787
788	USE surface_mod, &
789	ONLY: bc_h
790
791	INTEGER(iwp) :: i !< grid index x direction.
792	INTEGER(iwp) :: j !< grid index y direction.
793	INTEGER(iwp) :: k !< grid index z direction.
794	INTEGER(iwp) :: l !< running index boundary type, for up- and downward-facing walls.
795	INTEGER(iwp) :: lsp !< running index for chem spcs.
796	INTEGER(iwp) :: m !< running index surface elements.
797
798	LOGICAL, OPTIONAL :: horizontal_conditions_only !< switch to set horizontal bc only
799
800
801	IF ( .NOT. PRESENT( horizontal_conditions_only ) ) THEN
802	!
803	!-- Boundary condtions for chemical species at horizontal walls
804	DO lsp = 1, nspec
805	!
806	!-- Surface conditions:
807	IF ( ibc_cs_b == 0 ) THEN
808	!
809	!-- Dirichlet:
810	!-- Run loop over all non-natural and natural walls. Note, in wall-datatype the k
811	!-- coordinate belongs to the atmospheric grid point, therefore, set s_p at k-1
812	DO l = 0, 1
813	!$OMP PARALLEL DO PRIVATE( i, j, k )
814	DO m = 1, bc_h(l)%ns
815	i = bc_h(l)%i(m)
816	j = bc_h(l)%j(m)
817	k = bc_h(l)%k(m)
818	chem_species(lsp)%conc_p(k+bc_h(l)%koff,j,i) = &
819	chem_species(lsp)%conc(k+bc_h(l)%koff,j,i)
820	ENDDO
821	ENDDO
822
823	ELSEIF ( ibc_cs_b == 1 ) THEN
824	!
825	!-- Neumann:
826	DO l = 0, 1
827	!$OMP PARALLEL DO PRIVATE( i, j, k )
828	DO m = 1, bc_h(l)%ns
829	i = bc_h(l)%i(m)
830	j = bc_h(l)%j(m)
831	k = bc_h(l)%k(m)
832	chem_species(lsp)%conc_p(k+bc_h(l)%koff,j,i) = chem_species(lsp)%conc_p(k,j,i)
833	ENDDO
834	ENDDO
835
836	ENDIF
837
838	ENDDO
839
840	!
841	!-- Top boundary conditions for chemical species
842	DO lsp = 1, nspec
843	IF ( ibc_cs_t == 0 ) THEN
844	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc(nzt+1,:,:)
845	ELSEIF ( ibc_cs_t == 1 ) THEN
846	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:)
847	ELSEIF ( ibc_cs_t == 2 ) THEN
848	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:) + &
849	bc_cs_t_val(lsp) * dzu(nzt+1)
850	ENDIF
851	ENDDO
852
853	!
854	!-- Lateral boundary conditions.
855	!-- Dirichlet conditions have been already set when chem_species concentration is initialized.
856	!-- The initially set value is not touched during time integration, hence, this boundary value
857	!-- remains at a constant value.
858	!-- Neumann conditions:
859	IF ( bc_radiation_cs_s ) THEN
860	DO lsp = 1, nspec
861	chem_species(lsp)%conc_p(:,nys-1,:) = chem_species(lsp)%conc_p(:,nys,:)
862	ENDDO
863	ENDIF
864	IF ( bc_radiation_cs_n ) THEN
865	DO lsp = 1, nspec
866	chem_species(lsp)%conc_p(:,nyn+1,:) = chem_species(lsp)%conc_p(:,nyn,:)
867	ENDDO
868	ENDIF
869	IF ( bc_radiation_cs_l ) THEN
870	DO lsp = 1, nspec
871	chem_species(lsp)%conc_p(:,:,nxl-1) = chem_species(lsp)%conc_p(:,:,nxl)
872	ENDDO
873	ENDIF
874	IF ( bc_radiation_cs_r ) THEN
875	DO lsp = 1, nspec
876	chem_species(lsp)%conc_p(:,:,nxr+1) = chem_species(lsp)%conc_p(:,:,nxr)
877	ENDDO
878	ENDIF
879
880	!-- For testing: set Dirichlet conditions for all boundaries
881	! IF ( bc_dirichlet_cs_s ) THEN
882	! DO lsp = 1, nspec
883	! DO i = nxlg, nxrg
884	! DO j = nysg, nys-1
885	! DO k = nzb, nzt
886	! IF ( k /= nzb ) THEN
887	! flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 0 ) )
888	! ELSE
889	! flag = 1.0
890	! ENDIF
891	! chem_species(lsp)%conc_p(k,j,i) = chem_species(lsp)%conc_pr_init(k) * flag
892	! ENDDO
893	! ENDDO
894	! ENDDO
895	! ENDDO
896	! ENDIF
897	! IF ( bc_dirichlet_cs_n ) THEN
898	! DO lsp = 1, nspec
899	! DO i = nxlg, nxrg
900	! DO j = nyn+1, nyng
901	! DO k = nzb, nzt
902	! IF ( k /= nzb ) THEN
903	! flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 0 ) )
904	! ELSE
905	! flag = 1.0
906	! ENDIF
907	! chem_species(lsp)%conc_p(k,j,i) = chem_species(lsp)%conc_pr_init(k) * flag
908	! ENDDO
909	! ENDDO
910	! ENDDO
911	! ENDDO
912	! ENDIF
913	! IF ( bc_dirichlet_cs_l ) THEN
914	! DO lsp = 1, nspec
915	! DO i = nxlg, nxl-1
916	! DO j = nysg, nyng
917	! DO k = nzb, nzt
918	! IF ( k /= nzb ) THEN
919	! flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 0 ) )
920	! ELSE
921	! flag = 1.0
922	! ENDIF
923	! chem_species(lsp)%conc_p(k,j,i) = chem_species(lsp)%conc_pr_init(k) * flag
924	! ENDDO
925	! ENDDO
926	! ENDDO
927	! ENDDO
928	! ENDIF
929	! IF ( bc_dirichlet_cs_r ) THEN
930	! DO lsp = 1, nspec
931	! DO i = nxr+1, nxrg
932	! DO j = nysg, nyng
933	! DO k = nzb, nzt
934	! IF ( k /= nzb ) THEN
935	! flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 0 ) )
936	! ELSE
937	! flag = 1.0
938	! ENDIF
939	! chem_species(lsp)%conc_p(k,j,i) = chem_species(lsp)%conc_pr_init(k) * flag
940	! ENDDO
941	! ENDDO
942	! ENDDO
943	! ENDDO
944	! ENDIF
945
946	ELSE
947	!
948	!-- Lateral Neumann booundary conditions for timelevel t.
949	!-- This branch is executed when routine is called after the non-advective processes / before the
950	!-- prognostic equations.
951	IF ( bc_radiation_cs_s ) THEN
952	DO lsp = 1, nspec
953	chem_species(lsp)%conc(:,nys-1,:) = chem_species(lsp)%conc(:,nys,:)
954	ENDDO
955	ENDIF
956	IF ( bc_radiation_cs_n ) THEN
957	DO lsp = 1, nspec
958	chem_species(lsp)%conc(:,nyn+1,:) = chem_species(lsp)%conc(:,nyn,:)
959	ENDDO
960	ENDIF
961	IF ( bc_radiation_cs_l ) THEN
962	DO lsp = 1, nspec
963	chem_species(lsp)%conc(:,:,nxl-1) = chem_species(lsp)%conc(:,:,nxl)
964	ENDDO
965	ENDIF
966	IF ( bc_radiation_cs_r ) THEN
967	DO lsp = 1, nspec
968	chem_species(lsp)%conc(:,:,nxr+1) = chem_species(lsp)%conc(:,:,nxr)
969	ENDDO
970	ENDIF
971
972	!-- For testing: set Dirichlet conditions for all boundaries
973	! IF ( bc_dirichlet_cs_s ) THEN
974	! DO lsp = 1, nspec
975	! DO i = nxlg, nxrg
976	! DO j = nysg, nys-1
977	! DO k = nzb, nzt
978	! IF ( k /= nzb ) THEN
979	! flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 0 ) )
980	! ELSE
981	! flag = 1.0
982	! ENDIF
983	! chem_species(lsp)%conc(k,j,i) = chem_species(lsp)%conc_pr_init(k) * flag
984	! ENDDO
985	! ENDDO
986	! ENDDO
987	! ENDDO
988	! ENDIF
989	! IF ( bc_dirichlet_cs_n ) THEN
990	! DO lsp = 1, nspec
991	! DO i = nxlg, nxrg
992	! DO j = nyn+1, nyng
993	! DO k = nzb, nzt
994	! IF ( k /= nzb ) THEN
995	! flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 0 ) )
996	! ELSE
997	! flag = 1.0
998	! ENDIF
999	! chem_species(lsp)%conc(k,j,i) = chem_species(lsp)%conc_pr_init(k) * flag
1000	! ENDDO
1001	! ENDDO
1002	! ENDDO
1003	! ENDDO
1004	! ENDIF
1005	! IF ( bc_dirichlet_cs_l ) THEN
1006	! DO lsp = 1, nspec
1007	! DO i = nxlg, nxl-1
1008	! DO j = nysg, nyng
1009	! DO k = nzb, nzt
1010	! IF ( k /= nzb ) THEN
1011	! flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 0 ) )
1012	! ELSE
1013	! flag = 1.0
1014	! ENDIF
1015	! chem_species(lsp)%conc(k,j,i) = chem_species(lsp)%conc_pr_init(k) * flag
1016	! ENDDO
1017	! ENDDO
1018	! ENDDO
1019	! ENDDO
1020	! ENDIF
1021	! IF ( bc_dirichlet_cs_r ) THEN
1022	! DO lsp = 1, nspec
1023	! DO i = nxr+1, nxrg
1024	! DO j = nysg, nyng
1025	! DO k = nzb, nzt
1026	! IF ( k /= nzb ) THEN
1027	! flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 0 ) )
1028	! ELSE
1029	! flag = 1.0
1030	! ENDIF
1031	! chem_species(lsp)%conc(k,j,i) = chem_species(lsp)%conc_pr_init(k) * flag
1032	! ENDDO
1033	! ENDDO
1034	! ENDDO
1035	! ENDDO
1036	! ENDIF
1037
1038	ENDIF
1039
1040	END SUBROUTINE chem_boundary_conditions
1041
1042
1043	!--------------------------------------------------------------------------------------------------!
1044	! Description:
1045	! ------------
1046	!> Subroutine for checking data output for chemical species
1047	!--------------------------------------------------------------------------------------------------!
1048	SUBROUTINE chem_check_data_output( var, unit, i, ilen, k )
1049
1050
1051	CHARACTER (LEN=*) :: unit !<
1052	CHARACTER (LEN=*) :: var !<
1053
1054	INTEGER(iwp) :: i
1055	INTEGER(iwp) :: ilen
1056	INTEGER(iwp) :: lsp
1057	INTEGER(iwp) :: k
1058
1059	CHARACTER(LEN=16) :: spec_name
1060
1061	!
1062	!-- Next statement is to avoid compiler warnings about unused variables
1063	IF ( ( i + ilen + k ) > 0 .OR. var(1:1) == ' ' ) CONTINUE
1064
1065	unit = 'illegal'
1066
1067	spec_name = TRIM( var(4:) ) !< var 1:3 is 'kc_' or 'em_'.
1068
1069	IF ( TRIM( var(1:3) ) == 'em_' ) THEN
1070	DO lsp=1,nspec
1071	IF ( TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
1072	unit = 'mol m-2 s-1'
1073	ENDIF
1074	!
1075	!-- It is possible to plant PM10 and PM25 into the gasphase chemistry code as passive species
1076	!-- (e.g. 'passive' in GASPHASE_PREPROC/mechanisms): set unit to micrograms per m**3 for PM10
1077	!-- and PM25 (PM2.5)
1078	IF (spec_name(1:2) == 'PM') THEN
1079	unit = 'kg m-2 s-1'
1080	ENDIF
1081	ENDDO
1082
1083	ELSE
1084
1085	DO lsp=1,nspec
1086	IF ( TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
1087	unit = 'ppm'
1088	ENDIF
1089	!
1090	!-- It is possible to plant PM10 and PM25 into the gasphase chemistry code as passive species
1091	!-- (e.g. 'passive' in GASPHASE_PREPROC/mechanisms): set unit to kilograms per m**3 for PM10
1092	!-- and PM25 (PM2.5)
1093	IF (spec_name(1:2) == 'PM') THEN
1094	unit = 'kg 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	ENDIF
1104
1105
1106	RETURN
1107	END SUBROUTINE chem_check_data_output
1108
1109
1110	!--------------------------------------------------------------------------------------------------!
1111	! Description:
1112	! ------------
1113	!> Subroutine for checking data output of profiles for chemistry model
1114	!--------------------------------------------------------------------------------------------------!
1115	SUBROUTINE chem_check_data_output_pr( variable, var_count, unit, dopr_unit )
1116
1117	USE arrays_3d
1118
1119	USE control_parameters, &
1120	ONLY: data_output_pr, message_string
1121
1122	USE profil_parameter
1123
1124	USE statistics
1125
1126
1127	CHARACTER (LEN=*) :: unit !< unit
1128	CHARACTER (LEN=*) :: variable !< variable name
1129	CHARACTER (LEN=*) :: dopr_unit !< unit
1130	CHARACTER (LEN=16) :: spec_name !< species name extracted from output string
1131
1132	INTEGER(iwp) :: index_start !< start index of the species name in data-output string
1133	INTEGER(iwp) :: index_end !< end index of the species name in data-output string
1134	INTEGER(iwp) :: var_count !< number of data-output quantity
1135	INTEGER(iwp) :: lsp !< running index over species
1136
1137	SELECT CASE ( TRIM( variable(1:3 ) ) )
1138
1139	CASE ( 'kc_' )
1140
1141	IF ( .NOT. air_chemistry ) THEN
1142	message_string = 'data_output_pr = ' // TRIM( data_output_pr(var_count) ) // &
1143	' is not implemented for air_chemistry = .FALSE.'
1144	CALL message( 'chem_check_data_output_pr', 'PA0293', 1, 2, 0, 6, 0 )
1145
1146	ENDIF
1147	!
1148	!-- Output of total fluxes is not allowed to date.
1149	IF ( TRIM( variable(1:4) ) == 'kc_w' ) THEN
1150	IF ( TRIM( variable(1:5) ) /= 'kc_w*' .AND. TRIM( variable(1:5) ) /= 'kc_w"' ) THEN
1151	message_string = 'data_output_pr = ' // TRIM( data_output_pr(var_count) ) // &
1152	' is currently not implemented. Please output resolved- and '// &
1153	'subgrid-scale fluxes individually to obtain the total flux.'
1154	CALL message( 'chem_check_data_output_pr', 'PA0487', 1, 2, 0, 6, 0 )
1155	ENDIF
1156	ENDIF
1157	!
1158	!-- Check for profile output of first-order moments, i.e. variable(4:) equals a species name.
1159	spec_name = TRIM( variable(4:) )
1160	DO lsp = 1, nspec
1161	IF ( TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
1162	cs_pr_count_sp = cs_pr_count_sp + 1
1163	cs_pr_index_sp(cs_pr_count_sp) = lsp
1164	dopr_index(var_count) = pr_palm + cs_pr_count_sp + &
1165	cs_pr_count_fl_sgs + cs_pr_count_fl_res
1166	dopr_unit = 'ppm'
1167	IF ( spec_name(1:2) == 'PM') THEN
1168	dopr_unit = 'kg m-3'
1169	ENDIF
1170	hom(:,2,dopr_index(var_count),:) = SPREAD( zu, 2, statistic_regions+1 )
1171	unit = dopr_unit
1172
1173	hom_index_spec(cs_pr_count_sp) = dopr_index(var_count)
1174	ENDIF
1175	ENDDO
1176	!
1177	!-- Check for profile output of fluxes. variable(index_start:index_end) equals a species name.
1178	!-- Start with SGS components.
1179	IF ( TRIM( variable(1:5) ) == 'kc_w"' ) THEN
1180	DO lsp = 1, nspec
1181	index_end = LEN( TRIM( variable ) ) - 1
1182	index_start = 6
1183	spec_name = TRIM( variable(index_start:index_end) )
1184	IF ( TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
1185	cs_pr_count_fl_sgs = cs_pr_count_fl_sgs + 1
1186	cs_pr_index_fl_sgs(cs_pr_count_fl_sgs) = lsp
1187	dopr_index(var_count) = pr_palm + cs_pr_count_sp + &
1188	cs_pr_count_fl_sgs + &
1189	cs_pr_count_fl_res
1190	dopr_unit = 'm ppm s-1'
1191	IF ( spec_name(1:2) == 'PM') THEN
1192	dopr_unit = 'kg m-2 s-1'
1193	ENDIF
1194	hom(:,2,dopr_index(var_count),:) = SPREAD( zu, 2, statistic_regions+1 )
1195	unit = dopr_unit
1196
1197	hom_index_fl_sgs(cs_pr_count_fl_sgs) = dopr_index(var_count)
1198	ENDIF
1199	ENDDO
1200	ENDIF
1201	!
1202	!-- Proceed with resolved-scale fluxes.
1203	IF ( TRIM( variable(1:5) ) == 'kc_w*' ) THEN
1204	spec_name = TRIM( variable(6:) )
1205	DO lsp = 1, nspec
1206	index_start = 6
1207	index_end = LEN( TRIM( variable ) ) - 1
1208	spec_name = TRIM( variable(index_start:index_end) )
1209	IF ( TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
1210	cs_pr_count_fl_res = cs_pr_count_fl_res + 1
1211	cs_pr_index_fl_res(cs_pr_count_fl_res) = lsp
1212	dopr_index(var_count) = pr_palm + cs_pr_count_sp + &
1213	cs_pr_count_fl_sgs + &
1214	cs_pr_count_fl_res
1215	dopr_unit = 'm ppm s-1'
1216	IF ( spec_name(1:2) == 'PM') THEN
1217	dopr_unit = 'kg m-2 s-1'
1218	ENDIF
1219	hom(:,2, dopr_index(var_count),:) = SPREAD( zu, 2, statistic_regions+1 )
1220	unit = dopr_unit
1221
1222	hom_index_fl_res(cs_pr_count_fl_res) = dopr_index(var_count)
1223	ENDIF
1224	ENDDO
1225	ENDIF
1226	CASE DEFAULT
1227	unit = 'illegal'
1228
1229	END SELECT
1230
1231	END SUBROUTINE chem_check_data_output_pr
1232
1233
1234	!--------------------------------------------------------------------------------------------------!
1235	! Description:
1236	! ------------
1237	!> Check parameters routine for chemistry_model_mod
1238	!--------------------------------------------------------------------------------------------------!
1239	SUBROUTINE chem_check_parameters
1240
1241	USE control_parameters, &
1242	ONLY: bc_lr, bc_ns
1243
1244	INTEGER (iwp) :: lsp !< running index for chem spcs.
1245	INTEGER (iwp) :: lsp_usr !< running index for user defined chem spcs
1246
1247	LOGICAL :: found
1248
1249	!
1250	!-- Check for chemistry time-step
1251	IF ( call_chem_at_all_substeps ) THEN
1252	message_string = &
1253	'call_chem_at_all_substeps should only be used for test purposes'
1254	CALL message( 'chem_check_parameters', 'PA0522', 0, 1, 0, 6, 0 )
1255	ENDIF
1256	!
1257	!-- Check for photolysis scheme
1258	IF ( ( photolysis_scheme /= 'simple' ) .AND. ( photolysis_scheme /= 'constant' ) ) THEN
1259	message_string = 'Incorrect photolysis scheme selected, please check spelling'
1260	CALL message( 'chem_check_parameters', 'PA0523', 1, 2, 0, 6, 0 )
1261	ENDIF
1262	!
1263	!-- Check for chemical mechanism used
1264	CALL get_mechanism_name
1265	IF ( chem_mechanism /= TRIM( cs_mech ) ) THEN
1266	message_string = &
1267	'Incorrect chemistry mechanism selected, check spelling in namelist and/or chem_gasphase_mod'
1268	CALL message( 'chem_check_parameters', 'PA0551', 1, 2, 0, 6, 0 )
1269	ENDIF
1270
1271	!
1272	!-- Check bottom boundary condition and set internal steering parameter
1273	IF ( bc_cs_b == 'dirichlet' ) THEN
1274	ibc_cs_b = 0
1275	ELSEIF ( bc_cs_b == 'neumann' ) THEN
1276	ibc_cs_b = 1
1277	ELSE
1278	message_string = 'unknown boundary condition: bc_cs_b ="' // TRIM( bc_cs_b ) // '"'
1279	CALL message( 'chem_check_parameters', 'PA0593', 1, 2, 0, 6, 0 )
1280	ENDIF
1281	!
1282	!-- Check top boundary condition and set internal steering parameter
1283	IF ( bc_cs_t == 'dirichlet' ) THEN
1284	ibc_cs_t = 0
1285	ELSEIF ( bc_cs_t == 'neumann' ) THEN
1286	ibc_cs_t = 1
1287	ELSEIF ( bc_cs_t == 'initial_gradient' ) THEN
1288	ibc_cs_t = 2
1289	ELSEIF ( bc_cs_t == 'nested' ) THEN
1290	ibc_cs_t = 3
1291	ELSE
1292	message_string = 'unknown boundary condition: bc_c_t ="' // TRIM( bc_cs_t ) // '"'
1293	CALL message( 'chem_check_parameters', 'PA0675', 1, 2, 0, 6, 0 )
1294	ENDIF
1295
1296	!
1297	!-- If nesting_chem = .F., set top boundary condition to its default value
1298	IF ( .NOT. nesting_chem .AND. ibc_cs_t == 3 ) THEN
1299	ibc_cs_t = 2
1300	bc_cs_t = 'initial_gradient'
1301	ENDIF
1302
1303	!
1304	!-- Check left and right boundary conditions. First set default value if not set by user.
1305	IF ( bc_cs_l == 'undefined' ) THEN
1306	IF ( bc_lr == 'cyclic' ) THEN
1307	bc_cs_l = 'cyclic'
1308	ELSEIF ( bc_lr == 'dirichlet/radiation' ) THEN
1309	bc_cs_l = 'dirichlet'
1310	ELSEIF ( bc_lr == 'radiation/dirichlet' ) THEN
1311	bc_cs_l = 'neumann'
1312	ENDIF
1313	ENDIF
1314	IF ( bc_cs_r == 'undefined' ) THEN
1315	IF ( bc_lr == 'cyclic' ) THEN
1316	bc_cs_r = 'cyclic'
1317	ELSEIF ( bc_lr == 'dirichlet/radiation' ) THEN
1318	bc_cs_r = 'neumann'
1319	ELSEIF ( bc_lr == 'radiation/dirichlet' ) THEN
1320	bc_cs_r = 'dirichlet'
1321	ENDIF
1322	ENDIF
1323	IF ( bc_cs_l /= 'dirichlet' .AND. bc_cs_l /= 'neumann' .AND. bc_cs_l /= 'cyclic' ) THEN
1324	message_string = 'unknown boundary condition: bc_cs_l = "' // TRIM( bc_cs_l ) // '"'
1325	CALL message( 'chem_check_parameters','PA0505', 1, 2, 0, 6, 0 )
1326	ENDIF
1327	IF ( bc_cs_r /= 'dirichlet' .AND. bc_cs_r /= 'neumann' .AND. bc_cs_r /= 'cyclic' ) THEN
1328	message_string = 'unknown boundary condition: bc_cs_r = "' // TRIM( bc_cs_r ) // '"'
1329	CALL message( 'chem_check_parameters','PA0505', 1, 2, 0, 6, 0 )
1330	ENDIF
1331	!
1332	!-- Check north and south boundary conditions. First set default value if not set by user.
1333	IF ( bc_cs_n == 'undefined' ) THEN
1334	IF ( bc_ns == 'cyclic' ) THEN
1335	bc_cs_n = 'cyclic'
1336	ELSEIF ( bc_ns == 'dirichlet/radiation' ) THEN
1337	bc_cs_n = 'dirichlet'
1338	ELSEIF ( bc_ns == 'radiation/dirichlet' ) THEN
1339	bc_cs_n = 'neumann'
1340	ENDIF
1341	ENDIF
1342	IF ( bc_cs_s == 'undefined' ) THEN
1343	IF ( bc_ns == 'cyclic' ) THEN
1344	bc_cs_s = 'cyclic'
1345	ELSEIF ( bc_ns == 'dirichlet/radiation' ) THEN
1346	bc_cs_s = 'neumann'
1347	ELSEIF ( bc_ns == 'radiation/dirichlet' ) THEN
1348	bc_cs_s = 'dirichlet'
1349	ENDIF
1350	ENDIF
1351	IF ( bc_cs_n /= 'dirichlet' .AND. bc_cs_n /= 'neumann' .AND. bc_cs_n /= 'cyclic' ) THEN
1352	message_string = 'unknown boundary condition: bc_cs_n = "' // TRIM( bc_cs_n ) // '"'
1353	CALL message( 'chem_check_parameters','PA0505', 1, 2, 0, 6, 0 )
1354	ENDIF
1355	IF ( bc_cs_s /= 'dirichlet' .AND. bc_cs_s /= 'neumann' .AND. bc_cs_s /= 'cyclic' ) THEN
1356	message_string = 'unknown boundary condition: bc_cs_s = "' // TRIM( bc_cs_s ) // '"'
1357	CALL message( 'chem_check_parameters','PA0505', 1, 2, 0, 6, 0 )
1358	ENDIF
1359	!
1360	!-- Cyclic conditions must be set identically at opposing boundaries
1361	IF ( ( bc_cs_l == 'cyclic' .AND. bc_cs_r /= 'cyclic' ) .OR. &
1362	( bc_cs_r == 'cyclic' .AND. bc_cs_l /= 'cyclic' ) ) THEN
1363	message_string = 'boundary conditions bc_cs_l and bc_cs_r must both be cyclic or non-cyclic'
1364	CALL message( 'chem_check_parameters','PA0714', 1, 2, 0, 6, 0 )
1365	ENDIF
1366	IF ( ( bc_cs_n == 'cyclic' .AND. bc_cs_s /= 'cyclic' ) .OR. &
1367	( bc_cs_s == 'cyclic' .AND. bc_cs_n /= 'cyclic' ) ) THEN
1368	message_string = 'boundary conditions bc_cs_n and bc_cs_s must both be cyclic or non-cyclic'
1369	CALL message( 'chem_check_parameters','PA0714', 1, 2, 0, 6, 0 )
1370	ENDIF
1371	!
1372	!-- Set the switches that control application of horizontal boundary conditions at the boundaries
1373	!-- of the total domain
1374	IF ( bc_cs_n == 'dirichlet' .AND. nyn == ny ) bc_dirichlet_cs_n = .TRUE.
1375	IF ( bc_cs_n == 'neumann' .AND. nyn == ny ) bc_radiation_cs_n = .TRUE.
1376	IF ( bc_cs_s == 'dirichlet' .AND. nys == 0 ) bc_dirichlet_cs_s = .TRUE.
1377	IF ( bc_cs_s == 'neumann' .AND. nys == 0 ) bc_radiation_cs_s = .TRUE.
1378	IF ( bc_cs_l == 'dirichlet' .AND. nxl == 0 ) bc_dirichlet_cs_l = .TRUE.
1379	IF ( bc_cs_l == 'neumann' .AND. nxl == 0 ) bc_radiation_cs_l = .TRUE.
1380	IF ( bc_cs_r == 'dirichlet' .AND. nxr == nx ) bc_dirichlet_cs_r = .TRUE.
1381	IF ( bc_cs_r == 'neumann' .AND. nxr == nx ) bc_radiation_cs_r = .TRUE.
1382
1383	!
1384	!-- Set the communicator to be used for ghost layer data exchange
1385	!-- 1: cyclic, 2: cyclic along x, 3: cyclic along y, 4: non-cyclic
1386	IF ( bc_cs_l == 'cyclic' ) THEN
1387	IF ( bc_cs_s == 'cyclic' ) THEN
1388	communicator_chem = 1
1389	ELSE
1390	communicator_chem = 2
1391	ENDIF
1392	ELSE
1393	IF ( bc_cs_s == 'cyclic' ) THEN
1394	communicator_chem = 3
1395	ELSE
1396	communicator_chem = 4
1397	ENDIF
1398	ENDIF
1399
1400	!
1401	!-- chem_check_parameters is called before the array chem_species is allocated!
1402	!-- temporary switch of this part of the check
1403	!> TODO: this workaround definitely needs to be removed from here!!!
1404	CALL chem_init_internal
1405	!
1406	!-- Check for initial chem species input
1407	lsp_usr = 1
1408	lsp = 1
1409	DO WHILE ( cs_name (lsp_usr) /= 'novalue')
1410	found = .FALSE.
1411	DO lsp = 1, nvar
1412	IF ( TRIM( cs_name (lsp_usr) ) == TRIM( chem_species(lsp)%name) ) THEN
1413	found = .TRUE.
1414	EXIT
1415	ENDIF
1416	ENDDO
1417	IF ( .NOT. found ) THEN
1418	message_string = 'Unused/incorrect input for initial surface value: ' // &
1419	TRIM( cs_name(lsp_usr) )
1420	CALL message( 'chem_check_parameters', 'PA0715', 1, 2, 0, 6, 0 )
1421	ENDIF
1422	lsp_usr = lsp_usr + 1
1423	ENDDO
1424	!
1425	!-- Check for surface emission flux chem species
1426	lsp_usr = 1
1427	lsp = 1
1428	DO WHILE ( surface_csflux_name (lsp_usr) /= 'novalue')
1429	found = .FALSE.
1430	DO lsp = 1, nvar
1431	IF ( TRIM( surface_csflux_name (lsp_usr) ) == TRIM( chem_species(lsp)%name ) ) THEN
1432	found = .TRUE.
1433	EXIT
1434	ENDIF
1435	ENDDO
1436	IF ( .NOT. found ) THEN
1437	message_string = 'Unused/incorrect input of chemical species for surface emission fluxes: ' &
1438	// TRIM( surface_csflux_name(lsp_usr) )
1439	CALL message( 'chem_check_parameters', 'PA0716', 1, 2, 0, 6, 0 )
1440	ENDIF
1441	lsp_usr = lsp_usr + 1
1442	ENDDO
1443
1444	END SUBROUTINE chem_check_parameters
1445
1446
1447	!--------------------------------------------------------------------------------------------------!
1448	! Description:
1449	! ------------
1450	!> Subroutine defining 2D output variables for chemical species
1451	!> @todo: Remove "mode" from argument list, not used.
1452	!--------------------------------------------------------------------------------------------------!
1453	SUBROUTINE chem_data_output_2d( av, variable, found, grid, mode, local_pf, two_d, nzb_do, nzt_do, &
1454	fill_value )
1455
1456
1457	CHARACTER (LEN=*) :: grid !<
1458	CHARACTER (LEN=*) :: mode !<
1459	CHARACTER (LEN=*) :: variable !<
1460
1461	INTEGER(iwp) :: av !< flag to control data output of instantaneous or
1462	!< time-averaged data
1463	INTEGER(iwp) :: nzb_do !< lower limit of the domain (usually nzb)
1464	INTEGER(iwp) :: nzt_do !< upper limit of the domain (usually nzt+1)
1465
1466	LOGICAL :: found !<
1467	LOGICAL :: two_d !< flag parameter that indicates 2D variables (horizontal cross
1468	!< sections)
1469
1470	REAL(wp) :: fill_value
1471
1472	REAL(wp), DIMENSION(nxl:nxr,nys:nyn,nzb:nzt+1) :: local_pf
1473
1474	!
1475	!-- local variables.
1476	CHARACTER(LEN=16) :: spec_name
1477	INTEGER(iwp) :: lsp
1478	INTEGER(iwp) :: i !< grid index along x-direction
1479	INTEGER(iwp) :: j !< grid index along y-direction
1480	INTEGER(iwp) :: k !< grid index along z-direction
1481	INTEGER(iwp) :: m !< running indices for surfaces
1482	INTEGER(iwp) :: char_len !< length of a character string
1483	!
1484	!-- Next statement is to avoid compiler warnings about unused variables
1485	IF ( mode(1:1) == ' ' .OR. two_d ) CONTINUE
1486
1487	found = .FALSE.
1488	char_len = LEN_TRIM( variable )
1489
1490	spec_name = TRIM( variable(4:char_len-3) )
1491	!
1492	!-- Output of emission values, i.e. surface fluxes cssws.
1493	IF ( variable(1:3) == 'em_' ) THEN
1494
1495	local_pf = 0.0_wp
1496
1497	DO lsp = 1, nvar
1498	IF ( TRIM( spec_name ) == TRIM( chem_species(lsp)%name) ) THEN
1499	!
1500	!-- No average output for now.
1501	!-- !!! IT NEEDS TO RETHINK - with fully 3D structure, only lower (upper)
1502	!-- !!! upward facing horizontal surfaces should be taken into account here
1503	DO m = 1, surf_lsm_h(0)%ns
1504	local_pf(surf_lsm_h(0)%i(m),surf_lsm_h(0)%j(m),nzb+1) = &
1505	local_pf(surf_lsm_h(0)%i(m),surf_lsm_h(0)%j(m),nzb+1) &
1506	+ surf_lsm_h(0)%cssws(lsp,m)
1507	ENDDO
1508	DO m = 1, surf_usm_h(0)%ns
1509	local_pf(surf_usm_h(0)%i(m),surf_usm_h(0)%j(m),nzb+1) = &
1510	local_pf(surf_usm_h(0)%i(m),surf_usm_h(0)%j(m),nzb+1) &
1511	+ surf_usm_h(0)%cssws(lsp,m)
1512	ENDDO
1513	grid = 'zu'
1514	found = .TRUE.
1515	ENDIF
1516	ENDDO
1517
1518	ELSE
1519
1520	DO lsp=1,nspec
1521	IF ( TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) .AND. &
1522	( (variable(char_len-2:) == '_xy') .OR. &
1523	(variable(char_len-2:) == '_xz') .OR. &
1524	(variable(char_len-2:) == '_yz') ) ) THEN
1525	IF (av == 0) THEN
1526	DO i = nxl, nxr
1527	DO j = nys, nyn
1528	DO k = nzb_do, nzt_do
1529	local_pf(i,j,k) = MERGE( &
1530	chem_species(lsp)%conc(k,j,i), &
1531	REAL( fill_value, KIND = wp ), &
1532	BTEST( wall_flags_total_0(k,j,i), 0 ) )
1533	ENDDO
1534	ENDDO
1535	ENDDO
1536
1537	ELSE
1538	DO i = nxl, nxr
1539	DO j = nys, nyn
1540	DO k = nzb_do, nzt_do
1541	local_pf(i,j,k) = MERGE( &
1542	chem_species(lsp)%conc_av(k,j,i), &
1543	REAL( fill_value, KIND = wp ), &
1544	BTEST( wall_flags_total_0(k,j,i), 0 ) )
1545	ENDDO
1546	ENDDO
1547	ENDDO
1548	ENDIF
1549	grid = 'zu'
1550	found = .TRUE.
1551	ENDIF
1552	ENDDO
1553	ENDIF
1554
1555	RETURN
1556
1557	END SUBROUTINE chem_data_output_2d
1558
1559
1560	!--------------------------------------------------------------------------------------------------!
1561	! Description:
1562	! ------------
1563	!> Subroutine defining 3D output variables for chemical species
1564	!--------------------------------------------------------------------------------------------------!
1565	SUBROUTINE chem_data_output_3d( av, variable, found, local_pf, fill_value, nzb_do, nzt_do )
1566
1567
1568	USE surface_mod
1569
1570	CHARACTER (LEN=*) :: variable !<
1571
1572	INTEGER(iwp) :: av !<
1573	INTEGER(iwp) :: nzb_do !< lower limit of the data output (usually 0)
1574	INTEGER(iwp) :: nzt_do !< vertical upper limit of the data output (usually nz_do3d)
1575
1576	LOGICAL :: found !<
1577
1578	REAL(wp) :: fill_value !<
1579
1580	REAL(wp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) :: local_pf
1581	!
1582	!-- Local variables
1583	CHARACTER(LEN=16) :: spec_name
1584
1585	INTEGER(iwp) :: i
1586	INTEGER(iwp) :: j
1587	INTEGER(iwp) :: k
1588	INTEGER(iwp) :: m !< running indices for surfaces
1589	INTEGER(iwp) :: l
1590	INTEGER(iwp) :: lsp !< running index for chem spcs
1591
1592
1593	found = .FALSE.
1594	IF ( .NOT. (variable(1:3) == 'kc_' .OR. variable(1:3) == 'em_' ) ) THEN
1595	RETURN
1596	ENDIF
1597
1598	spec_name = TRIM( variable(4:) )
1599
1600	IF ( variable(1:3) == 'em_' ) THEN
1601
1602	DO lsp = 1, nvar !!! cssws - nvar species, chem_species - nspec species !!!
1603	IF ( TRIM( spec_name ) == TRIM( chem_species(lsp)%name) ) THEN
1604
1605	local_pf = 0.0_wp
1606	!
1607	!-- no average for now
1608	DO l = 0, 1
1609	DO m = 1, surf_usm_h(l)%ns
1610	local_pf(surf_usm_h(l)%i(m),surf_usm_h(l)%j(m),surf_usm_h(l)%k(m)) = &
1611	local_pf(surf_usm_h(l)%i(m),surf_usm_h(l)%j(m),surf_usm_h(l)%k(m)) &
1612	+ surf_usm_h(l)%cssws(lsp,m)
1613	ENDDO
1614	DO m = 1, surf_lsm_h(l)%ns
1615	local_pf(surf_lsm_h(l)%i(m),surf_lsm_h(l)%j(m),surf_lsm_h(l)%k(m)) = &
1616	local_pf(surf_lsm_h(l)%i(m),surf_lsm_h(l)%j(m),surf_lsm_h(l)%k(m)) &
1617	+ surf_lsm_h(l)%cssws(lsp,m)
1618	ENDDO
1619	ENDDO
1620	DO l = 0, 3
1621	DO m = 1, surf_usm_v(l)%ns
1622	local_pf(surf_usm_v(l)%i(m),surf_usm_v(l)%j(m),surf_usm_v(l)%k(m)) = &
1623	local_pf(surf_usm_v(l)%i(m),surf_usm_v(l)%j(m),surf_usm_v(l)%k(m)) &
1624	+ surf_usm_v(l)%cssws(lsp,m)
1625	ENDDO
1626	DO m = 1, surf_lsm_v(l)%ns
1627	local_pf(surf_lsm_v(l)%i(m),surf_lsm_v(l)%j(m),surf_lsm_v(l)%k(m)) = &
1628	local_pf(surf_lsm_v(l)%i(m),surf_lsm_v(l)%j(m),surf_lsm_v(l)%k(m)) &
1629	+ surf_lsm_v(l)%cssws(lsp,m)
1630	ENDDO
1631	ENDDO
1632	found = .TRUE.
1633	ENDIF
1634	ENDDO
1635	ELSE
1636	DO lsp = 1, nspec
1637	IF ( TRIM( spec_name ) == TRIM( chem_species(lsp)%name) ) THEN
1638	IF (av == 0) THEN
1639	DO i = nxl, nxr
1640	DO j = nys, nyn
1641	DO k = nzb_do, nzt_do
1642	local_pf(i,j,k) = MERGE( &
1643	chem_species(lsp)%conc(k,j,i), &
1644	REAL( fill_value, KIND = wp ), &
1645	BTEST( wall_flags_total_0(k,j,i), 0 ) )
1646	ENDDO
1647	ENDDO
1648	ENDDO
1649
1650	ELSE
1651
1652	DO i = nxl, nxr
1653	DO j = nys, nyn
1654	DO k = nzb_do, nzt_do
1655	local_pf(i,j,k) = MERGE( &
1656	chem_species(lsp)%conc_av(k,j,i), &
1657	REAL( fill_value, KIND = wp ), &
1658	BTEST( wall_flags_total_0(k,j,i), 0 ) )
1659	ENDDO
1660	ENDDO
1661	ENDDO
1662	ENDIF
1663	found = .TRUE.
1664	ENDIF
1665	ENDDO
1666	ENDIF
1667
1668	RETURN
1669
1670	END SUBROUTINE chem_data_output_3d
1671
1672
1673	!--------------------------------------------------------------------------------------------------!
1674	! Description:
1675	! ------------
1676	!> Subroutine defining mask output variables for chemical species
1677	!--------------------------------------------------------------------------------------------------!
1678	SUBROUTINE chem_data_output_mask( av, variable, found, local_pf, mid )
1679
1680
1681	USE control_parameters
1682
1683	REAL(wp), PARAMETER :: fill_value = -9999.0_wp !< value for the _FillValue attribute
1684
1685	CHARACTER(LEN=16) :: spec_name
1686	CHARACTER(LEN=*) :: variable !<
1687
1688	INTEGER(iwp) :: av !< flag to control data output of instantaneous or
1689	!< time-averaged data
1690	INTEGER(iwp) :: i !< grid index along x-direction
1691	INTEGER(iwp) :: im !< loop index for masked variables
1692	INTEGER(iwp) :: j !< grid index along y-direction
1693	INTEGER(iwp) :: jm !< loop index for masked variables
1694	INTEGER(iwp) :: k !< grid index along z-direction
1695	INTEGER(iwp) :: kk !< masked output index along z-direction
1696	INTEGER(iwp) :: ktt !< k index of lowest non-terrain grid point
1697	INTEGER(iwp) :: lsp
1698	INTEGER(iwp) :: mid !< masked output running index
1699
1700	LOGICAL :: found
1701
1702	REAL(wp), DIMENSION(mask_size_l(mid,1),mask_size_l(mid,2),mask_size_l(mid,3)) :: local_pf !<
1703
1704
1705	!
1706	!-- Local variables.
1707
1708	spec_name = TRIM( variable(4:) )
1709	found = .FALSE.
1710
1711	DO lsp=1,nspec
1712	IF (TRIM( spec_name ) == TRIM( chem_species(lsp)%name) ) THEN
1713	IF (av == 0) THEN
1714	IF ( .NOT. mask_surface(mid) ) THEN
1715
1716	DO i = 1, mask_size_l(mid,1)
1717	DO j = 1, mask_size_l(mid,2)
1718	DO k = 1, mask_size(mid,3)
1719	local_pf(i,j,k) = chem_species(lsp)%conc( mask_k(mid,k), &
1720	mask_j(mid,j), &
1721	mask_i(mid,i) )
1722	ENDDO
1723	ENDDO
1724	ENDDO
1725
1726	ELSE
1727	!
1728	!-- Terrain-following masked output
1729	DO i = 1, mask_size_l(mid,1)
1730	DO j = 1, mask_size_l(mid,2)
1731	!
1732	!-- Get k index of the lowest non-terrain grid point
1733	im = mask_i(mid,i)
1734	jm = mask_j(mid,j)
1735	ktt = MINLOC( MERGE( 1, 0, BTEST( wall_flags_total_0(:,jm,im), 5 ) ), &
1736	DIM = 1 ) - 1
1737	DO k = 1, mask_size_l(mid,3)
1738	kk = MIN( ktt + mask_k(mid,k) - 1, nzt+1 )
1739	!
1740	!-- Set value if not in building, else set fill value
1741	IF ( BTEST( wall_flags_total_0(kk,jm,im), 6 ) ) THEN
1742	local_pf(i,j,k) = fill_value
1743	ELSE
1744	local_pf(i,j,k) = chem_species(lsp)%conc(kk,jm,im)
1745	ENDIF
1746	ENDDO
1747	ENDDO
1748	ENDDO
1749
1750	ENDIF
1751	ELSE
1752	IF ( .NOT. mask_surface(mid) ) THEN
1753
1754	DO i = 1, mask_size_l(mid,1)
1755	DO j = 1, mask_size_l(mid,2)
1756	DO k = 1, mask_size_l(mid,3)
1757	local_pf(i,j,k) = chem_species(lsp)%conc_av( mask_k(mid,k), &
1758	mask_j(mid,j), &
1759	mask_i(mid,i) )
1760	ENDDO
1761	ENDDO
1762	ENDDO
1763
1764	ELSE
1765	!
1766	!-- Terrain-following masked output
1767	DO i = 1, mask_size_l(mid,1)
1768	DO j = 1, mask_size_l(mid,2)
1769	!
1770	!-- Get k index of the lowest non-terrain grid point
1771	im = mask_i(mid,i)
1772	jm = mask_j(mid,j)
1773	ktt = MINLOC( MERGE( 1, 0, BTEST( wall_flags_total_0(:,jm,im), 5 )), &
1774	DIM = 1 ) - 1
1775	DO k = 1, mask_size_l(mid,3)
1776	kk = MIN( ktt + mask_k(mid,k) - 1, nzt+1 )
1777	!
1778	!-- Set value if not in building, else set fill value
1779	IF ( BTEST( wall_flags_total_0(kk,jm,im), 6 ) ) THEN
1780	local_pf(i,j,k) = fill_value
1781	ELSE
1782	local_pf(i,j,k) = chem_species(lsp)%conc_av(kk,jm,im)
1783	ENDIF
1784	ENDDO
1785	ENDDO
1786	ENDDO
1787
1788	ENDIF
1789
1790	ENDIF
1791	found = .TRUE.
1792	EXIT
1793	ENDIF
1794	ENDDO
1795
1796	RETURN
1797
1798	END SUBROUTINE chem_data_output_mask
1799
1800
1801	!--------------------------------------------------------------------------------------------------!
1802	! Description:
1803	! ------------
1804	!> Subroutine defining appropriate grid for netcdf variables.
1805	!> It is called out from subroutine netcdf.
1806	!--------------------------------------------------------------------------------------------------!
1807	SUBROUTINE chem_define_netcdf_grid( var, found, grid_x, grid_y, grid_z )
1808
1809
1810	CHARACTER (LEN=*), INTENT(IN) :: var !<
1811
1812	CHARACTER (LEN=*), INTENT(OUT) :: grid_x !<
1813	CHARACTER (LEN=*), INTENT(OUT) :: grid_y !<
1814	CHARACTER (LEN=*), INTENT(OUT) :: grid_z !<
1815
1816	LOGICAL, INTENT(OUT) :: found !<
1817
1818	found = .TRUE.
1819
1820	IF ( var(1:3) == 'kc_' .OR. var(1:3) == 'em_' ) THEN !< always the same grid for
1821	!< chemistry variables
1822	grid_x = 'x'
1823	grid_y = 'y'
1824	grid_z = 'zu'
1825	ELSE
1826	found = .FALSE.
1827	grid_x = 'none'
1828	grid_y = 'none'
1829	grid_z = 'none'
1830	ENDIF
1831
1832
1833	END SUBROUTINE chem_define_netcdf_grid
1834
1835
1836	!--------------------------------------------------------------------------------------------------!
1837	! Description:
1838	! ------------
1839	!> Subroutine defining header output for chemistry model
1840	!--------------------------------------------------------------------------------------------------!
1841	SUBROUTINE chem_header( io )
1842
1843	CHARACTER (LEN=80) :: docsflux_chr
1844	CHARACTER (LEN=80) :: docsinit_chr
1845
1846	INTEGER(iwp), INTENT(IN) :: io !< Unit of the output file
1847
1848	INTEGER(iwp) :: cs_fixed
1849	INTEGER(iwp) :: lsp !< running index for chem spcs
1850
1851	!
1852	!-- Get name of chemical mechanism from chem_gasphase_mod
1853	CALL get_mechanism_name
1854	!
1855	!-- Write chemistry model header
1856	WRITE( io, 1 )
1857	!
1858	!-- Gasphase reaction status
1859	IF ( chem_gasphase_on ) THEN
1860	WRITE( io, 2 )
1861	ELSE
1862	WRITE( io, 3 )
1863	ENDIF
1864	!
1865	!-- Emission mode info
1866	WRITE( io, 4 ) emiss_read_legacy_mode
1867	!
1868	!-- At the moment the evaluation is done with both emiss_lod and mode_emis but once salsa has been
1869	!-- migrated to emiss_lod the .OR. mode_emis conditions can be removed
1870	IF ( ( emiss_lod == 1 ) .OR. ( mode_emis == 'DEFAULT' ) ) THEN
1871	WRITE ( io, 5 )
1872	ELSEIF ( ( emiss_lod == 0 ) .OR. ( mode_emis == 'PARAMETERIZED' ) ) THEN
1873	WRITE ( io, 6 )
1874	ELSEIF ( ( emiss_lod == 2 ) .OR. ( mode_emis == 'PRE-PROCESSED' ) ) THEN
1875	WRITE ( io, 7 )
1876	ENDIF
1877	!
1878	!-- Photolysis scheme info
1879	IF ( photolysis_scheme == "simple" ) THEN
1880	WRITE( io, 8 )
1881	ELSEIF (photolysis_scheme == "constant" ) THEN
1882	WRITE( io, 9 )
1883	ENDIF
1884	!
1885	!-- Emission flux info
1886	lsp = 1
1887	docsflux_chr ='Chemical species for surface emission flux: '
1888	DO WHILE ( surface_csflux_name(lsp) /= 'novalue' )
1889	docsflux_chr = TRIM( docsflux_chr ) // ' ' // TRIM( surface_csflux_name(lsp) ) // ','
1890	IF ( LEN_TRIM( docsflux_chr ) >= 75 ) THEN
1891	WRITE ( io, 10 ) docsflux_chr
1892	docsflux_chr = ' '
1893	ENDIF
1894	lsp = lsp + 1
1895	ENDDO
1896
1897	IF ( docsflux_chr /= '' ) THEN
1898	WRITE ( io, 10 ) docsflux_chr
1899	ENDIF
1900	!
1901	!-- Initialization of Surface and profile chemical species
1902	lsp = 1
1903	docsinit_chr ='Chemical species for initial surface and profile emissions: '
1904	DO WHILE ( cs_name(lsp) /= 'novalue' )
1905	docsinit_chr = TRIM( docsinit_chr ) // ' ' // TRIM( cs_name(lsp) ) // ','
1906	IF ( LEN_TRIM( docsinit_chr ) >= 75 ) THEN
1907	WRITE ( io, 11 ) docsinit_chr
1908	docsinit_chr = ' '
1909	ENDIF
1910	lsp = lsp + 1
1911	ENDDO
1912
1913	IF ( docsinit_chr /= '' ) THEN
1914	WRITE ( io, 11 ) docsinit_chr
1915	ENDIF
1916
1917	IF ( nesting_chem ) WRITE( io, 12 ) nesting_chem
1918	IF ( nesting_offline_chem .AND. nesting_offline ) WRITE( io, 13 ) nesting_offline_chem
1919
1920	WRITE( io, 14 ) TRIM( bc_cs_b ), TRIM( bc_cs_t ), TRIM( bc_cs_s ), TRIM( bc_cs_n ), &
1921	TRIM( bc_cs_l ), TRIM( bc_cs_r )
1922
1923	!
1924	!-- Number of variable and fix chemical species and number of reactions
1925	cs_fixed = nspec - nvar
1926	WRITE ( io, * ) ' --> Chemical Mechanism : ', cs_mech
1927	WRITE ( io, * ) ' --> Chemical species, variable : ', nvar
1928	WRITE ( io, * ) ' --> Chemical species, fixed : ', cs_fixed
1929	WRITE ( io, * ) ' --> Total number of reactions : ', nreact
1930	WRITE ( io, * ) ' --> Gas phase chemistry solver : ', icntrl(3)
1931	WRITE ( io, * ) ' --> Vector length (vector mode if > 1): ', vl_dim
1932
1933
1934	1 FORMAT (//' Chemistry model information:'/' ----------------------------'/)
1935	2 FORMAT (' --> Chemical reactions are turned on')
1936	3 FORMAT (' --> Chemical reactions are turned off')
1937	4 FORMAT (' --> Legacy emission read mode: ',L3,/, &
1938	' All emissions data will be loaded prior to start of simulation')
1939	5 FORMAT (' --> Emission mode = DEFAULT ')
1940	6 FORMAT (' --> Emission mode = PARAMETERIZED (LOD 0)')
1941	7 FORMAT (' --> Emission mode = PRE-PROCESSED (LOD 2)')
1942	8 FORMAT (' --> Photolysis scheme used = simple ')
1943	9 FORMAT (' --> Photolysis scheme used = constant ')
1944	10 FORMAT (/' ',A)
1945	11 FORMAT (/' ',A)
1946	12 FORMAT (/' Self nesting for chemistry variables (if nested_run): ', L1 )
1947	13 FORMAT (/' Offline nesting for chemistry variables : ', L1 )
1948	14 FORMAT (/' Boundary conditions for chemical species:', / &
1949	' bottom/top: ',A10,' / ',A10, / &
1950	' north/south: ',A10,' / ',A10, / &
1951	' left/right: ',A10,' / ',A10)
1952
1953	END SUBROUTINE chem_header
1954
1955
1956	!--------------------------------------------------------------------------------------------------!
1957	! Description:
1958	! ------------
1959	!> Subroutine initializating chemistry_model_mod specific arrays
1960	!--------------------------------------------------------------------------------------------------!
1961	SUBROUTINE chem_init_arrays
1962	!
1963	!-- Please use this place to allocate required arrays
1964
1965	END SUBROUTINE chem_init_arrays
1966
1967
1968	!--------------------------------------------------------------------------------------------------!
1969	! Description:
1970	! ------------
1971	!> Subroutine initializating chemistry_model_mod
1972	!--------------------------------------------------------------------------------------------------!
1973	SUBROUTINE chem_init
1974
1975	!
1976	!-- NB introduced additional interfaces for on-demand emission update
1977
1978	! USE chem_emissions_mod, &
1979	! ONLY: chem_emissions_init
1980
1981	USE chem_emissions_mod, &
1982	ONLY: chem_emissions_header_init, chem_emissions_init
1983
1984	USE netcdf_data_input_mod, &
1985	ONLY: init_3d
1986
1987
1988	INTEGER(iwp) :: i !< running index x dimension
1989	INTEGER(iwp) :: j !< running index y dimension
1990	INTEGER(iwp) :: n !< running index for chemical species
1991
1992
1993	IF ( debug_output ) CALL debug_message( 'chem_init', 'start' )
1994	!
1995	!-- Next statement is to avoid compiler warning about unused variables
1996	IF ( ( ilu_arable + ilu_coniferous_forest + ilu_deciduous_forest + ilu_mediterrean_scrub + &
1997	ilu_permanent_crops + ilu_savanna + ilu_semi_natural_veg + ilu_tropical_forest + &
1998	ilu_urban ) == 0 ) CONTINUE
1999
2000	!
2001	!-- NB Calls specific emisisons initialization subroutines for legacy mode and on-demand mode
2002
2003	! IF ( emissions_anthropogenic ) CALL chem_emissions_init
2004
2005	IF ( emissions_anthropogenic ) THEN
2006
2007	IF ( emiss_read_legacy_mode ) THEN
2008	CALL chem_emissions_init
2009	ELSE
2010	CALL chem_emissions_header_init
2011	ENDIF
2012
2013	ENDIF
2014
2015
2016	!
2017	!-- Chemistry variables will be initialized if availabe from dynamic input file. Note, it is
2018	!-- possible to initialize only part of the chemistry variables from dynamic input.
2019	IF ( INDEX( initializing_actions, 'inifor' ) /= 0 ) THEN
2020	DO n = 1, nspec
2021	IF ( init_3d%from_file_chem(n) ) THEN
2022	DO i = nxlg, nxrg
2023	DO j = nysg, nyng
2024	chem_species(n)%conc(:,j,i) = init_3d%chem_init(:,n)
2025	ENDDO
2026	ENDDO
2027	ENDIF
2028	ENDDO
2029	ENDIF
2030
2031	IF ( debug_output ) CALL debug_message( 'chem_init', 'end' )
2032
2033	END SUBROUTINE chem_init
2034
2035
2036	!--------------------------------------------------------------------------------------------------!
2037	! Description:
2038	! ------------
2039	!> Subroutine initializating chemistry_model_mod
2040	!> internal workaround for chem_species dependency in chem_check_parameters
2041	!--------------------------------------------------------------------------------------------------!
2042	SUBROUTINE chem_init_internal
2043
2044	USE pegrid
2045
2046	USE netcdf_data_input_mod, &
2047	ONLY: chem_emis, chem_emis_att, input_pids_dynamic, init_3d, &
2048	netcdf_data_input_chemistry_data
2049
2050	!
2051	!-- Local variables
2052	INTEGER(iwp) :: i !< running index for for horiz numerical grid points
2053	INTEGER(iwp) :: j !< running index for for horiz numerical grid points
2054	INTEGER(iwp) :: lpr_lev !< running index for chem spcs profile level
2055	INTEGER(iwp) :: lsp !< running index for chem spcs
2056
2057	REAL(wp) :: flag !< flag for masking topography/building grid points
2058	!
2059	!-- NB reads netcdf data only under legacy mode
2060
2061	! IF ( emissions_anthropogenic ) THEN
2062	! CALL netcdf_data_input_chemistry_data( chem_emis_att, chem_emis )
2063	! ENDIF
2064
2065	IF ( emissions_anthropogenic ) THEN
2066	IF ( emiss_read_legacy_mode ) THEN
2067	CALL netcdf_data_input_chemistry_data( chem_emis_att, chem_emis )
2068	ENDIF
2069	ENDIF
2070
2071	!
2072	!-- Allocate memory for chemical species
2073	ALLOCATE( chem_species(nspec) )
2074	ALLOCATE( spec_conc_1 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
2075	ALLOCATE( spec_conc_2 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
2076	ALLOCATE( spec_conc_3 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
2077	ALLOCATE( phot_frequen(nphot) )
2078	ALLOCATE( freq_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nphot) )
2079	ALLOCATE( bc_cs_t_val(nspec) )
2080	!
2081	!-- Initialize arrays
2082	spec_conc_1 (:,:,:,:) = 0.0_wp
2083	spec_conc_2 (:,:,:,:) = 0.0_wp
2084	spec_conc_3 (:,:,:,:) = 0.0_wp
2085
2086	!
2087	!-- Allocate array to store locally summed-up resolved-scale vertical fluxes.
2088	IF ( scalar_advec == 'ws-scheme' ) THEN
2089	ALLOCATE( sums_ws_l(nzb:nzt+1,0:threads_per_task-1,nspec) )
2090	sums_ws_l = 0.0_wp
2091	ENDIF
2092
2093	DO lsp = 1, nspec
2094	chem_species(lsp)%name = spc_names(lsp)
2095
2096	chem_species(lsp)%conc (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1 (:,:,:,lsp)
2097	chem_species(lsp)%conc_p (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2 (:,:,:,lsp)
2098	chem_species(lsp)%tconc_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_3 (:,:,:,lsp)
2099
2100	ALLOCATE (chem_species(lsp)%cssws_av(nysg:nyng,nxlg:nxrg))
2101	chem_species(lsp)%cssws_av = 0.0_wp
2102	!
2103	!-- The following block can be useful when emission module is not applied. &
2104	!-- If emission module is applied the following block will be overwritten.
2105	ALLOCATE (chem_species(lsp)%flux_s_cs(nzb+1:nzt,0:threads_per_task-1))
2106	ALLOCATE (chem_species(lsp)%diss_s_cs(nzb+1:nzt,0:threads_per_task-1))
2107	ALLOCATE (chem_species(lsp)%flux_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
2108	ALLOCATE (chem_species(lsp)%diss_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
2109	chem_species(lsp)%flux_s_cs = 0.0_wp
2110	chem_species(lsp)%flux_l_cs = 0.0_wp
2111	chem_species(lsp)%diss_s_cs = 0.0_wp
2112	chem_species(lsp)%diss_l_cs = 0.0_wp
2113	!
2114	!-- Allocate memory for initial concentration profiles (concentration values come from namelist)
2115	!-- (@todo (FK): Because of this, chem_init is called in palm before check_parameters, since
2116	!-- conc_pr_init is used there.
2117	!-- We have to find another solution since chem_init should eventually be called from
2118	!-- init_3d_model!!)
2119	ALLOCATE ( chem_species(lsp)%conc_pr_init(0:nz+1) )
2120	chem_species(lsp)%conc_pr_init(:) = 0.0_wp
2121
2122	ENDDO
2123
2124	!
2125	!-- For chemistry variables lateral boundary conditions can be set non-cyclic while
2126	!-- the other scalars may have cyclic boundary conditions.
2127	!-- However, large gradients near the boundaries may produce stationary numerical
2128	!-- oscillations near the lateral boundaries when a higher-order scheme is
2129	!-- applied near these boundaries.
2130	!-- To get rid-off this, set-up additional flags that control the order of the scalar advection
2131	!-- scheme near the lateral boundaries for passive scalars with non-cyclic bcs
2132	IF ( scalar_advec == 'ws-scheme' ) THEN
2133	ALLOCATE( cs_advc_flags_s(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
2134	!
2135	!-- In case of non-cyclic boundary conditions set wall_flags_total_0 bit 31
2136	!-- Bit 31 is used to identify extended degradation zones.
2137	!-- Note, since several also other modules like Salsa or other future one may access this bit but
2138	!-- may have other boundary conditions, the original value of wall_flags_total_0 bit 31 must not
2139	!-- be modified. Hence, store the boundary conditions directly on cs_advc_flags_s.
2140	!-- cs_advc_flags_s will be later overwritten in ws_init_flags_scalar and bit 31 won't be used to
2141	!-- control the numerical order.
2142	!-- Initialize with flag 31 only.
2143	cs_advc_flags_s = 0
2144	cs_advc_flags_s = MERGE( IBSET( cs_advc_flags_s, 31 ), 0, BTEST( wall_flags_total_0, 31 ) )
2145
2146	IF ( bc_dirichlet_cs_n .OR. bc_dirichlet_cs_s ) THEN
2147	IF ( nys == 0 ) THEN
2148	DO i = 1, nbgp
2149	cs_advc_flags_s(:,nys-i,:) = MERGE( &
2150	IBSET( cs_advc_flags_s(:,nys,:), 31 ), &
2151	IBCLR( cs_advc_flags_s(:,nys,:), 31 ), &
2152	BTEST( cs_advc_flags_s(:,nys,:), 31 ) &
2153	)
2154	ENDDO
2155	ENDIF
2156	IF ( nyn == ny ) THEN
2157	DO i = 1, nbgp
2158	cs_advc_flags_s(:,nyn+i,:) = MERGE( &
2159	IBSET( cs_advc_flags_s(:,nyn,:), 31 ), &
2160	IBCLR( cs_advc_flags_s(:,nyn,:), 31 ), &
2161	BTEST( cs_advc_flags_s(:,nyn,:), 31 ) &
2162	)
2163	ENDDO
2164	ENDIF
2165	ENDIF
2166	IF ( bc_dirichlet_cs_l .OR. bc_dirichlet_cs_r ) THEN
2167	IF ( nxl == 0 ) THEN
2168	DO i = 1, nbgp
2169	cs_advc_flags_s(:,:,nxl-i) = MERGE( &
2170	IBSET( cs_advc_flags_s(:,:,nxl), 31 ), &
2171	IBCLR( cs_advc_flags_s(:,:,nxl), 31 ), &
2172	BTEST( cs_advc_flags_s(:,:,nxl), 31 ) &
2173	)
2174	ENDDO
2175	ENDIF
2176	IF ( nxr == nx ) THEN
2177	DO i = 1, nbgp
2178	cs_advc_flags_s(:,:,nxr+i) = MERGE( &
2179	IBSET( cs_advc_flags_s(:,:,nxr), 31 ), &
2180	IBCLR( cs_advc_flags_s(:,:,nxr), 31 ), &
2181	BTEST( cs_advc_flags_s(:,:,nxr), 31 ) &
2182	)
2183	ENDDO
2184	ENDIF
2185
2186	ENDIF
2187	!
2188	!-- To initialize advection flags appropriately, pass the boundary flags.
2189	!-- The last argument indicates that a passive scalar is treated, where the horizontal advection
2190	!-- terms are degraded already 2 grid points before the lateral boundary to avoid stationary
2191	!-- oscillations at large-gradients.
2192	!-- Also, extended degradation zones are applied, where horizontal advection of passive scalars
2193	!-- is discretized by first-order scheme at all grid points that in the vicinity of buildings
2194	!-- (<= 3 grid points). Even though no building is within the numerical stencil, first-order
2195	!-- scheme is used.
2196	!-- At fourth and fifth grid point the order of the horizontal advection scheme
2197	!-- is successively upgraded.
2198	!-- These extended degradation zones are used to avoid stationary numerical oscillations, which
2199	!-- are responsible for high concentration maxima that may appear under shear-free stable
2200	!-- conditions.
2201	CALL ws_init_flags_scalar( bc_dirichlet_cs_l .OR. bc_radiation_cs_l, &
2202	bc_dirichlet_cs_n .OR. bc_radiation_cs_n, &
2203	bc_dirichlet_cs_r .OR. bc_radiation_cs_r, &
2204	bc_dirichlet_cs_s .OR. bc_radiation_cs_s, &
2205	cs_advc_flags_s, .TRUE. )
2206	ENDIF
2207	!
2208	!-- Initial concentration of profiles is prescribed by parameters cs_profile and cs_heights in the
2209	!-- namelist &chemistry_parameters.
2210	CALL chem_init_profiles
2211	!
2212	!-- In case there is dynamic input file, create a list of names for chemistry initial input files.
2213	!-- Also, initialize array that indicates whether the respective variable is on file or not.
2214	IF ( input_pids_dynamic ) THEN
2215	ALLOCATE( init_3d%var_names_chem(1:nspec) )
2216	ALLOCATE( init_3d%from_file_chem(1:nspec) )
2217	init_3d%from_file_chem(:) = .FALSE.
2218
2219	DO lsp = 1, nspec
2220	init_3d%var_names_chem(lsp) = init_3d%init_char // TRIM( chem_species(lsp)%name )
2221	ENDDO
2222	ENDIF
2223	!
2224	!-- Initialize model variables
2225	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
2226	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
2227	!
2228	!-- First model run of a possible job queue.
2229	!-- Initial profiles of the variables must be computed.
2230	IF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
2231	!
2232	!-- Transfer initial profiles to the arrays of the 3D model
2233	!-- Concentrations within buildings are set to zero.
2234	DO lsp = 1, nspec
2235	DO i = nxlg, nxrg
2236	DO j = nysg, nyng
2237	DO lpr_lev = 1, nz + 1
2238	flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(lpr_lev,j,i), 0 ) )
2239	chem_species(lsp)%conc(lpr_lev,j,i) = chem_species(lsp)%conc_pr_init(lpr_lev)&
2240	* flag
2241	ENDDO
2242	ENDDO
2243	ENDDO
2244	ENDDO
2245
2246	ELSEIF ( INDEX( initializing_actions, 'set_constant_profiles') /= 0 ) THEN
2247
2248	DO lsp = 1, nspec
2249	DO i = nxlg, nxrg
2250	DO j = nysg, nyng
2251	DO lpr_lev = nzb, nz+1
2252	flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(lpr_lev,j,i), 0 ) )
2253	chem_species(lsp)%conc(lpr_lev,j,i) = chem_species(lsp)%conc_pr_init(lpr_lev)&
2254	* flag
2255	ENDDO
2256	ENDDO
2257	ENDDO
2258	ENDDO
2259
2260	ENDIF
2261	!
2262	ENDIF
2263	!
2264	!-- Initial old and new time levels. Note, this has to be done also in restart runs
2265	DO lsp = 1, nvar
2266	chem_species(lsp)%tconc_m = 0.0_wp
2267	chem_species(lsp)%conc_p = chem_species(lsp)%conc
2268	ENDDO
2269
2270	DO lsp = 1, nphot
2271	phot_frequen(lsp)%name = phot_names(lsp)
2272	phot_frequen(lsp)%freq(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => freq_1(:,:,:,lsp)
2273	ENDDO
2274
2275	! CALL photolysis_init ! probably also required for restart
2276
2277	RETURN
2278
2279	END SUBROUTINE chem_init_internal
2280
2281
2282	!--------------------------------------------------------------------------------------------------!
2283	! Description:
2284	! ------------
2285	!> Subroutine defining initial vertical profiles of chemical species (given by namelist parameters
2286	!> chem_profiles and chem_heights) --> which should work analogically to parameters u_profile,
2287	!> v_profile and uv_heights)
2288	!--------------------------------------------------------------------------------------------------!
2289	SUBROUTINE chem_init_profiles
2290
2291	USE chem_modules
2292
2293	!
2294	!-- Local variables
2295	INTEGER :: lpr_lev !< running index for profile level for each chem spcs.
2296	INTEGER :: lsp !< running index for number of species in derived data type species_def
2297	INTEGER :: lsp_usr !< running index for number of species (user defined) in cs_names,
2298	!< cs_profiles etc
2299	INTEGER :: npr_lev !< the next available profile lev
2300	!
2301	!-- Parameter "cs_profile" and "cs_heights" are used to prescribe user defined initial profiles
2302	!-- and heights. If parameter "cs_profile" is not prescribed then initial surface values
2303	!-- "cs_surface" are used as constant initial profiles for each species. If "cs_profile" and
2304	!-- "cs_heights" are prescribed, their values will!override the constant profile given by
2305	!-- "cs_surface".
2306	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
2307	lsp_usr = 1
2308	DO WHILE ( TRIM( cs_name( lsp_usr ) ) /= 'novalue' ) !'novalue' is the default
2309	DO lsp = 1, nspec !
2310	!
2311	!-- Create initial profile (conc_pr_init) for each chemical species
2312	IF ( TRIM( chem_species(lsp)%name ) == TRIM( cs_name(lsp_usr) ) ) THEN
2313	IF ( cs_profile(lsp_usr,1) == 9999999.9_wp ) THEN
2314	!
2315	!-- Set a vertically constant profile based on the surface conc (cs_surface(lsp_usr)) of
2316	!-- each species
2317	DO lpr_lev = 0, nzt+1
2318	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_surface(lsp_usr)
2319	ENDDO
2320	ELSE
2321	IF ( cs_heights(1,1) /= 0.0_wp ) THEN
2322	message_string = 'The surface value of cs_heights must be 0.0'
2323	CALL message( 'chem_check_parameters', 'PA0717', 1, 2, 0, 6, 0 )
2324	ENDIF
2325
2326	use_prescribed_profile_data = .TRUE.
2327
2328	npr_lev = 1
2329	! chem_species(lsp)%conc_pr_init(0) = 0.0_wp
2330	DO lpr_lev = 1, nz+1
2331	IF ( npr_lev < 100 ) THEN
2332	DO WHILE ( cs_heights(lsp_usr, npr_lev+1) <= zu(lpr_lev) )
2333	npr_lev = npr_lev + 1
2334	IF ( npr_lev == 100 ) THEN
2335	message_string = 'number of chem spcs exceeding the limit'
2336	CALL message( 'chem_check_parameters', 'PA0730', 1, 2, 0, 6, 0 )
2337	EXIT
2338	ENDIF
2339	ENDDO
2340	ENDIF
2341	IF ( npr_lev < 100 .AND. cs_heights(lsp_usr,npr_lev+1) /= 9999999.9_wp ) THEN
2342	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp_usr, npr_lev) + &
2343	( zu(lpr_lev) - cs_heights(lsp_usr, npr_lev) ) / &
2344	( cs_heights(lsp_usr, (npr_lev + 1)) - cs_heights(lsp_usr, npr_lev ) ) *&
2345	( cs_profile(lsp_usr, (npr_lev + 1)) - cs_profile(lsp_usr, npr_lev ) )
2346	ELSE
2347	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp_usr, npr_lev)
2348	ENDIF
2349	ENDDO
2350	ENDIF
2351	!
2352	!-- If a profile is prescribed explicity using cs_profiles and cs_heights, then
2353	!-- chem_species(lsp)%conc_pr_init is populated with the specific "lsp" based on the
2354	!-- cs_profiles(lsp_usr,:) and cs_heights(lsp_usr,:).
2355	ENDIF
2356
2357	ENDDO
2358
2359	lsp_usr = lsp_usr + 1
2360	ENDDO
2361	! ENDIF
2362
2363	END SUBROUTINE chem_init_profiles
2364
2365
2366	!--------------------------------------------------------------------------------------------------!
2367	! Description:
2368	! ------------
2369	!> Subroutine to integrate chemical species in the given chemical mechanism
2370	!--------------------------------------------------------------------------------------------------!
2371	SUBROUTINE chem_integrate_ij( i, j )
2372
2373	USE statistics, &
2374	ONLY: weight_pres
2375
2376	USE control_parameters, &
2377	ONLY: dt_3d, intermediate_timestep_count, time_since_reference_point
2378
2379	REAL(wp), PARAMETER :: fr2ppm = 1.0e6_wp !< Conversion factor fraction to ppm
2380	! REAL(wp), PARAMETER :: xm_air = 28.96_wp !< Mole mass of dry air
2381	! REAL(wp), PARAMETER :: xm_h2o = 18.01528_wp !< Mole mass of water vapor
2382	REAL(wp), PARAMETER :: p_std = 101325.0_wp !< standard pressure (Pa)
2383	REAL(wp), PARAMETER :: ppm2fr = 1.0e-6_wp !< Conversion factor ppm to fraction
2384	REAL(wp), PARAMETER :: t_std = 273.15_wp !< standard pressure (Pa)
2385	REAL(wp), PARAMETER :: vmolcm = 22.414e3_wp !< Mole volume (22.414 l) in cm^3
2386	REAL(wp), PARAMETER :: xna = 6.022e23_wp !< Avogadro number (molecules/mol)
2387
2388	INTEGER,INTENT(IN) :: i
2389	INTEGER,INTENT(IN) :: j
2390	!
2391	!-- Local variables
2392	INTEGER(iwp) :: lph !< running index for photolysis frequencies
2393	INTEGER(iwp) :: lsp !< running index for chem spcs.
2394
2395	INTEGER, DIMENSION(20) :: istatus
2396
2397	INTEGER,DIMENSION(nzb+1:nzt) :: nacc !< Number of accepted steps
2398	INTEGER,DIMENSION(nzb+1:nzt) :: nrej !< Number of rejected steps
2399
2400	REAL(wp) :: conv !< conversion factor
2401	REAL(kind=wp) :: dt_chem
2402
2403	REAL(wp),DIMENSION(size(rcntrl)) :: rcntrl_local
2404
2405	REAL(kind=wp), DIMENSION(nzb+1:nzt) :: tmp_fact
2406	REAL(kind=wp), DIMENSION(nzb+1:nzt) :: tmp_fact_i !< conversion factor between
2407	!< molecules cm^{-3} and ppm
2408	REAL(kind=wp), DIMENSION(nzb+1:nzt) :: tmp_qvap
2409	REAL(kind=wp), DIMENSION(nzb+1:nzt) :: tmp_temp
2410
2411	REAL(kind=wp), DIMENSION(nzb+1:nzt,nspec) :: tmp_conc
2412	REAL(kind=wp), DIMENSION(nzb+1:nzt,nphot) :: tmp_phot
2413
2414	!
2415	!-- Set chem_gasphase_on to .FALSE. if you want to skip computation of gas phase chemistry
2416	IF (chem_gasphase_on) THEN
2417	nacc = 0
2418	nrej = 0
2419
2420	tmp_temp(:) = pt(nzb+1:nzt,j,i) * exner(nzb+1:nzt)
2421	!
2422	!-- Convert ppm to molecules/cm**3
2423	!-- tmp_fact = 1.e-6_wp6.022e23_wp/(22.414_wp1000._wp) * 273.15_wp *
2424	!-- hyp(nzb+1:nzt)/( 101300.0_wp * tmp_temp )
2425	conv = ppm2fr * xna / vmolcm
2426	tmp_fact(:) = conv * t_std * hyp(nzb+1:nzt) / (tmp_temp(:) * p_std)
2427	tmp_fact_i = 1.0_wp/tmp_fact
2428
2429	IF ( humidity ) THEN
2430	IF ( bulk_cloud_model ) THEN
2431	tmp_qvap(:) = ( q(nzb+1:nzt,j,i) - ql(nzb+1:nzt,j,i) ) * &
2432	xm_air/xm_h2o * fr2ppm * tmp_fact(:)
2433	ELSE
2434	tmp_qvap(:) = q(nzb+1:nzt,j,i) * xm_air/xm_h2o * fr2ppm * tmp_fact(:)
2435	ENDIF
2436	ELSE
2437	tmp_qvap(:) = 0.01 * xm_air/xm_h2o * fr2ppm * tmp_fact(:) !< Constant value for q if
2438	!< water vapor is not computed
2439	ENDIF
2440
2441	DO lsp = 1,nspec
2442	tmp_conc(:,lsp) = chem_species(lsp)%conc(nzb+1:nzt,j,i) * tmp_fact(:)
2443	ENDDO
2444
2445	DO lph = 1,nphot
2446	tmp_phot(:,lph) = phot_frequen(lph)%freq(nzb+1:nzt,j,i)
2447	ENDDO
2448	!
2449	!-- Compute length of time step
2450	IF ( call_chem_at_all_substeps ) THEN
2451	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
2452	ELSE
2453	dt_chem = dt_3d
2454	ENDIF
2455
2456	cs_time_step = dt_chem
2457
2458	IF ( MAXVAL( rcntrl ) > 0.0 ) THEN ! Only if rcntrl is set
2459	IF( time_since_reference_point <= 2*dt_3d) THEN
2460	rcntrl_local = 0
2461	ELSE
2462	rcntrl_local = rcntrl
2463	ENDIF
2464	ELSE
2465	rcntrl_local = 0
2466	END IF
2467
2468	CALL chem_gasphase_integrate ( dt_chem, tmp_conc, tmp_temp, tmp_qvap, tmp_fact, tmp_phot, &
2469	icntrl_i = icntrl, rcntrl_i = rcntrl_local, xnacc = nacc, xnrej = nrej, istatus=istatus )
2470
2471	DO lsp = 1,nspec
2472	chem_species(lsp)%conc (nzb+1:nzt,j,i) = tmp_conc(:,lsp) * tmp_fact_i(:)
2473	ENDDO
2474
2475
2476	ENDIF
2477
2478	RETURN
2479	END SUBROUTINE chem_integrate_ij
2480
2481
2482	!--------------------------------------------------------------------------------------------------!
2483	! Description:
2484	! ------------
2485	!> Subroutine defining parin for &chemistry_parameters for chemistry model
2486	!--------------------------------------------------------------------------------------------------!
2487	SUBROUTINE chem_parin
2488
2489	USE chem_modules
2490	USE control_parameters
2491	USE pegrid
2492	USE statistics
2493
2494	CHARACTER(LEN=100) :: line !< dummy string that contains the current
2495	!< line of the parameter file
2496	CHARACTER(LEN=8) :: solver_type
2497
2498	INTEGER(iwp) :: i !<
2499	INTEGER(iwp) :: io_status !< Status after reading the namelist file
2500	INTEGER(iwp) :: max_pr_cs_tmp !<
2501
2502	LOGICAL :: switch_off_module = .FALSE. !< local namelist parameter to switch off the module
2503	!< although the respective module namelist appears in
2504	!< the namelist file
2505
2506	REAL(wp), DIMENSION(nmaxfixsteps) :: my_steps !< List of fixed timesteps my_step(1) = 0.0
2507	!< automatic stepping
2508
2509
2510	NAMELIST /chemistry_parameters/ &
2511	bc_cs_b, &
2512	bc_cs_l, &
2513	bc_cs_n, &
2514	bc_cs_r, &
2515	bc_cs_s, &
2516	bc_cs_t, &
2517	call_chem_at_all_substeps, &
2518	chem_gasphase_on, &
2519	chem_mechanism, &
2520	cs_heights, &
2521	cs_name, &
2522	cs_profile, &
2523	cs_surface, &
2524	daytype_mdh, &
2525	deposition_dry, &
2526	emissions_anthropogenic, &
2527	emiss_lod, &
2528	emiss_factor_main, &
2529	emiss_factor_side, &
2530	emiss_read_legacy_mode, &
2531	icntrl, &
2532	main_street_id, &
2533	max_street_id, &
2534	mode_emis, &
2535	my_steps, &
2536	nesting_chem, &
2537	nesting_offline_chem, &
2538	rcntrl, &
2539	side_street_id, &
2540	photolysis_scheme, &
2541	wall_csflux, &
2542	surface_csflux, &
2543	surface_csflux_name, &
2544	switch_off_module, &
2545	time_fac_type
2546	!
2547	!-- Analogically to chem_names(nspj) we could invent chem_surfaceflux(nspj) and chem_topflux(nspj)
2548	!-- so this way we could prescribe a specific flux value for each species
2549	!> chemistry_parameters for initial profiles
2550	!> cs_names = 'O3', 'NO2', 'NO', ... to set initial profiles)
2551	!> cs_heights(1,:) = 0.0, 100.0, 500.0, 2000.0, .... (height levels where concs will be prescribed for O3)
2552	!> cs_heights(2,:) = 0.0, 200.0, 400.0, 1000.0, .... (same for NO2 etc.)
2553	!> cs_profiles(1,:) = 10.0, 20.0, 20.0, 30.0, ..... (chem spcs conc at height lvls chem_heights(1,:)) etc.
2554	!> If the respective concentration profile should be constant with height, then use "cs_surface( number of spcs)"
2555	!> then write these cs_surface values to chem_species(lsp)%conc_pr_init(:)
2556
2557	!
2558	!-- Read chem namelist
2559	icntrl = 0
2560	rcntrl = 0.0_wp
2561	my_steps = 0.0_wp
2562	photolysis_scheme = 'simple'
2563	atol = 1.0_wp
2564	rtol = 0.01_wp
2565	!
2566	!-- Move to the beginning of the namelist file and try to find and read the namelist named
2567	!-- chemistry_parameters.
2568	REWIND( 11 )
2569	READ( 11, chemistry_parameters, IOSTAT=io_status )
2570	!
2571	!-- Action depending on the READ status
2572	IF ( io_status == 0 ) THEN
2573	!
2574	! chemistry_parameters namelist was found and read correctly. Switch on chemistry model.
2575	IF ( .NOT. switch_off_module ) air_chemistry = .TRUE.
2576
2577	ELSEIF ( io_status > 0 ) THEN
2578	!
2579	!-- chemistry_parameters namelist was found, but contained errors. Print an error message
2580	!-- including the line that caused the problem.
2581	BACKSPACE( 11 )
2582	READ( 11 , '(A)') line
2583	CALL parin_fail_message( 'chemistry_parameters', line )
2584
2585	ENDIF
2586
2587	!
2588	!-- Synchronize emiss_lod and mod_emis only if emissions_anthropogenic is activated in the namelist.
2589	!-- Otherwise their values are "don't care"
2590	IF ( emissions_anthropogenic ) THEN
2591
2592	!
2593	!-- Check for emission mode for chem species
2594	IF ( emiss_lod < 0 ) THEN !- if LOD not defined in namelist
2595	IF ( ( mode_emis /= 'PARAMETERIZED' ) .AND. &
2596	( mode_emis /= 'DEFAULT' ) .AND. &
2597	( mode_emis /= 'PRE-PROCESSED' ) ) THEN
2598	message_string = 'Incorrect mode_emiss option select. Please check spelling'
2599	CALL message( 'chem_parin', 'PA0731', 1, 2, 0, 6, 0 )
2600	ENDIF
2601	ELSE
2602	IF ( ( emiss_lod /= 0 ) .AND. &
2603	( emiss_lod /= 1 ) .AND. &
2604	( emiss_lod /= 2 ) ) THEN
2605	message_string = 'Invalid value for emiss_lod (0, 1, or 2)'
2606	CALL message( 'chem_parin', 'PA0732', 1, 2, 0, 6, 0 )
2607	ENDIF
2608	ENDIF
2609
2610	!
2611	!-- Conflict resolution for emiss_lod and mode_emis.
2612	!-- 1) if emiss_lod is defined, have mode_emis assume same setting as emiss_lod
2613	!-- 2) if emiss_lod it not defined, have emiss_lod assuem same setting as mode_emis
2614	!-- This check is in place to retain backward compatibility with salsa until the code is
2615	!-- migrated completely to emiss_lod.
2616	IF ( emiss_lod >= 0 ) THEN
2617
2618	SELECT CASE ( emiss_lod )
2619	!
2620	!-- Synchronize mode_emis to defined emiss_lod (mode_emis will be depreciated in
2621	!-- future releases)
2622	CASE (0) !- parameterized mode
2623	mode_emis = 'PARAMETERIZED'
2624	CASE (1) !- default mode
2625	mode_emis = 'DEFAULT'
2626	CASE (2) !- preprocessed mode
2627	mode_emis = 'PRE-PROCESSED'
2628	END SELECT
2629
2630	ELSE ! if emiss_lod is not set
2631
2632	SELECT CASE ( mode_emis )
2633	CASE ('PARAMETERIZED')
2634	emiss_lod = 0
2635	CASE ('DEFAULT')
2636	emiss_lod = 1
2637	CASE ('PRE-PROCESSED')
2638	emiss_lod = 2
2639	END SELECT
2640
2641	message_string = 'emiss_lod undefined. Using existing mod_emiss setting&' // &
2642	'NOTE - mode_emis will be depreciated in future releases&' // &
2643	'please use emiss_lod to define emission mode'
2644	CALL message( 'chem_parin', 'PA0734', 0, 0, 0, 6, 0 )
2645	ENDIF
2646
2647	!
2648	!-- NB input check for emission read mode.
2649	!-- legacy : business as usual (everything read / set up at start of run)
2650	!-- new : emission based on timestamp, and for lod2 data is loaded on an hourly basis
2651
2652	!
2653	!-- NB handler for emiss_read_legacy_mode
2654	!-- * emiss_read_legacy_mode is defaulted to TRUE
2655	!-- * if emiss_read_legacy_mode is TRUE and LOD is 0 or 1,
2656	!-- force emission_read_legacy_mode to TRUE (not yet implemented)
2657
2658	IF ( .NOT. emiss_read_legacy_mode ) THEN !< if new read mode selected
2659
2660	IF ( emiss_lod < 2 ) THEN !< check LOD compatibility
2661
2662	message_string = 'New emission read mode ' // &
2663	'currently unavailable for LODs 0 and 1.&' // &
2664	'Reverting to legacy emission read mode'
2665	CALL message( 'chem_parin', 'PA0736', 0, 0, 0, 6, 0 )
2666
2667	emiss_read_legacy_mode = .TRUE.
2668
2669	ELSE !< notify new read mode
2670
2671	message_string = 'New emission read mode activated&' // &
2672	'LOD 2 emissions will be updated on-demand ' // &
2673	'according to indicated timestamps'
2674	CALL message( 'chem_parin', 'PA0737', 0, 0, 0, 6, 0 )
2675
2676	ENDIF
2677
2678	ENDIF ! if emiss_read_legacy_mode
2679
2680
2681	ENDIF ! if emissions_anthropengic
2682
2683
2684	t_steps = my_steps
2685	!
2686	!-- Determine the number of user-defined profiles and append them to the standard data output
2687	!-- (data_output_pr)
2688	max_pr_cs_tmp = 0
2689	i = 1
2690
2691	DO WHILE ( data_output_pr(i) /= ' ' .AND. i <= SIZE( data_output_pr ) )
2692	IF ( TRIM( data_output_pr(i)(1:3) ) == 'kc_' ) THEN
2693	max_pr_cs_tmp = max_pr_cs_tmp+1
2694	ENDIF
2695	i = i +1
2696	ENDDO
2697
2698	IF ( max_pr_cs_tmp > 0 ) THEN
2699	cs_pr_namelist_found = .TRUE.
2700	max_pr_cs = max_pr_cs_tmp
2701	ENDIF
2702	!
2703	!-- Set Solver Type
2704	IF ( icntrl(3) == 0 ) THEN
2705	solver_type = 'rodas3' !Default
2706	ELSEIF ( icntrl(3) == 1 ) THEN
2707	solver_type = 'ros2'
2708	ELSEIF ( icntrl(3) == 2 ) THEN
2709	solver_type = 'ros3'
2710	ELSEIF ( icntrl(3) == 3 ) THEN
2711	solver_type = 'ro4'
2712	ELSEIF ( icntrl(3) == 4 ) THEN
2713	solver_type = 'rodas3'
2714	ELSEIF ( icntrl(3) == 5 ) THEN
2715	solver_type = 'rodas4'
2716	ELSEIF ( icntrl(3) == 6 ) THEN
2717	solver_type = 'Rang3'
2718	ELSE
2719	message_string = 'illegal Rosenbrock-solver type'
2720	CALL message( 'chem_parin', 'PA0506', 1, 2, 0, 6, 0 )
2721	END IF
2722
2723	RETURN
2724
2725	END SUBROUTINE chem_parin
2726
2727
2728	!--------------------------------------------------------------------------------------------------!
2729	! Description:
2730	! ------------
2731	!> Call for all grid points
2732	!--------------------------------------------------------------------------------------------------!
2733	SUBROUTINE chem_actions( location )
2734
2735
2736	CHARACTER (LEN=*), INTENT(IN) :: location !< call location string
2737
2738	SELECT CASE ( location )
2739
2740	CASE ( 'before_prognostic_equations' )
2741	!
2742	!-- Chemical reactions and deposition
2743	IF ( chem_gasphase_on ) THEN
2744	!
2745	!-- If required, calculate photolysis frequencies -
2746	!-- UNFINISHED: Why not before the intermediate timestep loop?
2747	IF ( intermediate_timestep_count == 1 ) THEN
2748	CALL photolysis_control
2749	ENDIF
2750
2751	ENDIF
2752
2753	CASE ( 'before_timestep' )
2754	!
2755	!-- Set array used to sum-up resolved scale fluxes to zero.
2756	IF ( ws_scheme_sca ) THEN
2757	sums_ws_l = 0.0_wp
2758	ENDIF
2759
2760	CASE DEFAULT
2761	CONTINUE
2762
2763	END SELECT
2764
2765	END SUBROUTINE chem_actions
2766
2767
2768	!--------------------------------------------------------------------------------------------------!
2769	! Description:
2770	! ------------
2771	!> Call for grid points i,j
2772	!--------------------------------------------------------------------------------------------------!
2773
2774	SUBROUTINE chem_actions_ij( i, j, location )
2775
2776	CHARACTER (LEN=*), INTENT(IN) :: location !< call location string
2777
2778	INTEGER(iwp) :: dummy !< call location string
2779
2780	INTEGER(iwp), INTENT(IN) :: i !< grid index in x-direction
2781	INTEGER(iwp), INTENT(IN) :: j !< grid index in y-direction
2782
2783	IF ( air_chemistry ) dummy = i + j
2784
2785	SELECT CASE ( location )
2786
2787	CASE DEFAULT
2788	CONTINUE
2789
2790	END SELECT
2791
2792
2793	END SUBROUTINE chem_actions_ij
2794
2795
2796	!--------------------------------------------------------------------------------------------------!
2797	! Description:
2798	! ------------
2799	!> Call for all grid points
2800	!--------------------------------------------------------------------------------------------------!
2801	SUBROUTINE chem_non_advective_processes()
2802
2803
2804	INTEGER(iwp) :: i !<
2805	INTEGER(iwp) :: j !<
2806
2807	!
2808	!-- Calculation of chemical reactions and deposition.
2809	IF ( intermediate_timestep_count == 1 .OR. call_chem_at_all_substeps ) THEN
2810
2811	IF ( chem_gasphase_on ) THEN
2812	CALL cpu_log( log_point_s(19), 'chem.reactions', 'start' )
2813	!$OMP PARALLEL PRIVATE (i,j)
2814	!$OMP DO schedule(static,1)
2815	DO i = nxl, nxr
2816	DO j = nys, nyn
2817	CALL chem_integrate( i, j )
2818	ENDDO
2819	ENDDO
2820	!$OMP END PARALLEL
2821	CALL cpu_log( log_point_s(19), 'chem.reactions', 'stop' )
2822	ENDIF
2823
2824	IF ( deposition_dry ) THEN
2825	CALL cpu_log( log_point_s(24), 'chem.deposition', 'start' )
2826	DO i = nxl, nxr
2827	DO j = nys, nyn
2828	CALL chem_depo( i, j )
2829	ENDDO
2830	ENDDO
2831	CALL cpu_log( log_point_s(24), 'chem.deposition', 'stop' )
2832	ENDIF
2833
2834	ENDIF
2835
2836	END SUBROUTINE chem_non_advective_processes
2837
2838
2839	!--------------------------------------------------------------------------------------------------!
2840	! Description:
2841	! ------------
2842	!> Call for grid points i,j
2843	!--------------------------------------------------------------------------------------------------!
2844	SUBROUTINE chem_non_advective_processes_ij( i, j )
2845
2846
2847	INTEGER(iwp), INTENT(IN) :: i !< grid index in x-direction
2848	INTEGER(iwp), INTENT(IN) :: j !< grid index in y-direction
2849
2850	!
2851	!-- Calculation of chemical reactions and deposition.
2852	!-- It would have been nice to have time measurements for chemistry and deposition here.
2853	!-- Unfortunately measurements within i,j loops degrade performance ince they are calles so often
2854	!-- and the counter for this measurement gets extremely huge values. Therefore, no measurements
2855	!-- here.
2856	IF ( intermediate_timestep_count == 1 .OR. call_chem_at_all_substeps ) THEN
2857
2858	IF ( chem_gasphase_on ) THEN
2859	CALL chem_integrate( i, j )
2860	ENDIF
2861
2862	IF ( deposition_dry ) THEN
2863	CALL chem_depo( i, j )
2864	ENDIF
2865
2866	ENDIF
2867
2868	END SUBROUTINE chem_non_advective_processes_ij
2869
2870
2871	!--------------------------------------------------------------------------------------------------!
2872	! Description:
2873	! ------------
2874	!> routine for exchange horiz of chemical quantities
2875	!--------------------------------------------------------------------------------------------------!
2876	SUBROUTINE chem_exchange_horiz_bounds( location )
2877
2878	USE exchange_horiz_mod, &
2879	ONLY: exchange_horiz
2880
2881	INTEGER(iwp) :: lsp !<
2882	INTEGER(iwp) :: n
2883
2884	CHARACTER (LEN=*), INTENT(IN) :: location !< call location string
2885
2886	SELECT CASE ( location )
2887
2888	CASE ( 'before_prognostic_equation' )
2889	!
2890	!-- Loop over chemical species
2891	CALL cpu_log( log_point_s(84), 'chem.exch-horiz', 'start' )
2892	DO lsp = 1, nvar
2893	CALL exchange_horiz( chem_species(lsp)%conc, nbgp, &
2894	alternative_communicator = communicator_chem )
2895	ENDDO
2896
2897	CALL chem_boundary_conditions( horizontal_conditions_only = .TRUE. )
2898
2899	CALL cpu_log( log_point_s(84), 'chem.exch-horiz', 'stop' )
2900
2901	CASE ( 'after_prognostic_equation' )
2902
2903	IF ( air_chemistry ) THEN
2904	DO n = 1, nvar
2905	CALL exchange_horiz( chem_species(n)%conc_p, nbgp, &
2906	alternative_communicator = communicator_chem )
2907	ENDDO
2908	ENDIF
2909
2910	CASE ( 'after_anterpolation' )
2911
2912	IF ( air_chemistry ) THEN
2913	DO n = 1, nvar
2914	CALL exchange_horiz( chem_species(n)%conc, nbgp, &
2915	alternative_communicator = communicator_chem )
2916	ENDDO
2917	ENDIF
2918
2919	END SELECT
2920
2921	END SUBROUTINE chem_exchange_horiz_bounds
2922
2923
2924	!--------------------------------------------------------------------------------------------------!
2925	! Description:
2926	! ------------
2927	!> Subroutine calculating prognostic equations for chemical species (vector-optimized).
2928	!> Routine is called separately for each chemical species over a loop from prognostic_equations.
2929	!--------------------------------------------------------------------------------------------------!
2930	SUBROUTINE chem_prognostic_equations()
2931
2932
2933	INTEGER :: i !< running index
2934	INTEGER :: j !< running index
2935	INTEGER :: k !< running index
2936
2937	INTEGER(iwp) :: ilsp !<
2938
2939
2940	CALL cpu_log( log_point_s(25), 'chem.advec+diff+prog', 'start' )
2941
2942	DO ilsp = 1, nvar
2943	!
2944	!-- Tendency terms for chemical species
2945	tend = 0.0_wp
2946	!
2947	!-- Advection terms
2948	IF ( timestep_scheme(1:5) == 'runge' ) THEN
2949	IF ( ws_scheme_sca ) THEN
2950	sums_wschs_ws_l(nzb:,0:) => sums_ws_l(:,:,ilsp)
2951	CALL advec_s_ws( cs_advc_flags_s, chem_species(ilsp)%conc, 'kc', &
2952	bc_dirichlet_cs_l .OR. bc_radiation_cs_l, &
2953	bc_dirichlet_cs_n .OR. bc_radiation_cs_n, &
2954	bc_dirichlet_cs_r .OR. bc_radiation_cs_r, &
2955	bc_dirichlet_cs_s .OR. bc_radiation_cs_s )
2956	ELSE
2957	CALL advec_s_pw( chem_species(ilsp)%conc )
2958	ENDIF
2959	ELSE
2960	CALL advec_s_up( chem_species(ilsp)%conc )
2961	ENDIF
2962	!
2963	!-- Diffusion terms (the last three arguments are zero)
2964	CALL diffusion_s( chem_species(ilsp)%conc, &
2965	surf_def_h(0)%cssws(ilsp,:), &
2966	surf_def_h(1)%cssws(ilsp,:), &
2967	surf_def_h(2)%cssws(ilsp,:), &
2968	surf_lsm_h(0)%cssws(ilsp,:), &
2969	surf_lsm_h(1)%cssws(ilsp,:), &
2970	surf_usm_h(0)%cssws(ilsp,:), &
2971	surf_usm_h(1)%cssws(ilsp,:), &
2972	surf_def_v(0)%cssws(ilsp,:), &
2973	surf_def_v(1)%cssws(ilsp,:), &
2974	surf_def_v(2)%cssws(ilsp,:), &
2975	surf_def_v(3)%cssws(ilsp,:), &
2976	surf_lsm_v(0)%cssws(ilsp,:), &
2977	surf_lsm_v(1)%cssws(ilsp,:), &
2978	surf_lsm_v(2)%cssws(ilsp,:), &
2979	surf_lsm_v(3)%cssws(ilsp,:), &
2980	surf_usm_v(0)%cssws(ilsp,:), &
2981	surf_usm_v(1)%cssws(ilsp,:), &
2982	surf_usm_v(2)%cssws(ilsp,:), &
2983	surf_usm_v(3)%cssws(ilsp,:) )
2984	!
2985	!-- Prognostic equation for chemical species
2986	DO i = nxl, nxr
2987	DO j = nys, nyn
2988	!following directive is required to vectorize on Intel19
2989	!DIR$ IVDEP
2990	DO k = nzb+1, nzt
2991	chem_species(ilsp)%conc_p(k,j,i) = chem_species(ilsp)%conc(k,j,i) &
2992	+ ( dt_3d * &
2993	( tsc(2) * tend(k,j,i) &
2994	+ tsc(3) * chem_species(ilsp)%tconc_m(k,j,i) &
2995	) &
2996	- tsc(5) * rdf_sc(k) &
2997	* ( chem_species(ilsp)%conc(k,j,i) - chem_species(ilsp)%conc_pr_init(k) ) &
2998	) &
2999	* MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 0 ) )
3000
3001	IF ( chem_species(ilsp)%conc_p(k,j,i) < 0.0_wp ) THEN
3002	chem_species(ilsp)%conc_p(k,j,i) = 0.1_wp * chem_species(ilsp)%conc(k,j,i)
3003	ENDIF
3004	ENDDO
3005	ENDDO
3006	ENDDO
3007	!
3008	!-- Calculate tendencies for the next Runge-Kutta step
3009	IF ( timestep_scheme(1:5) == 'runge' ) THEN
3010	IF ( intermediate_timestep_count == 1 ) THEN
3011	DO i = nxl, nxr
3012	DO j = nys, nyn
3013	DO k = nzb+1, nzt
3014	chem_species(ilsp)%tconc_m(k,j,i) = tend(k,j,i)
3015	ENDDO
3016	ENDDO
3017	ENDDO
3018	ELSEIF ( intermediate_timestep_count < &
3019	intermediate_timestep_count_max ) THEN
3020	DO i = nxl, nxr
3021	DO j = nys, nyn
3022	DO k = nzb+1, nzt
3023	chem_species(ilsp)%tconc_m(k,j,i) = - 9.5625_wp * tend(k,j,i) &
3024	+ 5.3125_wp * chem_species(ilsp)%tconc_m(k,j,i)
3025	ENDDO
3026	ENDDO
3027	ENDDO
3028	ENDIF
3029	ENDIF
3030
3031	ENDDO
3032
3033	CALL cpu_log( log_point_s(25), 'chem.advec+diff+prog', 'stop' )
3034
3035	END SUBROUTINE chem_prognostic_equations
3036
3037
3038	!--------------------------------------------------------------------------------------------------!
3039	! Description:
3040	! ------------
3041	!> Subroutine calculating prognostic equations for chemical species (cache-optimized).
3042	!> Routine is called separately for each chemical species over a loop from prognostic_equations.
3043	!--------------------------------------------------------------------------------------------------!
3044	SUBROUTINE chem_prognostic_equations_ij( i, j, i_omp_start, tn )
3045
3046
3047	INTEGER(iwp),INTENT(IN) :: i, j, i_omp_start, tn
3048
3049	INTEGER(iwp) :: ilsp
3050	!
3051	!-- local variables
3052
3053	INTEGER :: k
3054
3055	DO ilsp = 1, nvar
3056	!
3057	!-- Tendency-terms for chem spcs.
3058	tend(:,j,i) = 0.0_wp
3059	!
3060	!-- Advection terms
3061	IF ( timestep_scheme(1:5) == 'runge' ) THEN
3062	IF ( ws_scheme_sca ) THEN
3063	sums_wschs_ws_l(nzb:,0:) => sums_ws_l(nzb:nzt+1,0:threads_per_task-1,ilsp)
3064	CALL advec_s_ws( cs_advc_flags_s, &
3065	i, &
3066	j, &
3067	chem_species(ilsp)%conc, &
3068	'kc', &
3069	chem_species(ilsp)%flux_s_cs, &
3070	chem_species(ilsp)%diss_s_cs, &
3071	chem_species(ilsp)%flux_l_cs, &
3072	chem_species(ilsp)%diss_l_cs, &
3073	i_omp_start, &
3074	tn, &
3075	bc_dirichlet_cs_l .OR. bc_radiation_cs_l, &
3076	bc_dirichlet_cs_n .OR. bc_radiation_cs_n, &
3077	bc_dirichlet_cs_r .OR. bc_radiation_cs_r, &
3078	bc_dirichlet_cs_s .OR. bc_radiation_cs_s, &
3079	monotonic_limiter_z )
3080	ELSE
3081	CALL advec_s_pw( i, j, chem_species(ilsp)%conc )
3082	ENDIF
3083	ELSE
3084	CALL advec_s_up( i, j, chem_species(ilsp)%conc )
3085	ENDIF
3086	!
3087	!-- Diffusion terms (the last three arguments are zero)
3088	CALL diffusion_s( i, j, chem_species(ilsp)%conc, &
3089	surf_def_h(0)%cssws(ilsp,:), surf_def_h(1)%cssws(ilsp,:), &
3090	surf_def_h(2)%cssws(ilsp,:), &
3091	surf_lsm_h(0)%cssws(ilsp,:), surf_lsm_h(1)%cssws(ilsp,:), &
3092	surf_usm_h(0)%cssws(ilsp,:), surf_usm_h(1)%cssws(ilsp,:), &
3093	surf_def_v(0)%cssws(ilsp,:), surf_def_v(1)%cssws(ilsp,:), &
3094	surf_def_v(2)%cssws(ilsp,:), surf_def_v(3)%cssws(ilsp,:), &
3095	surf_lsm_v(0)%cssws(ilsp,:), surf_lsm_v(1)%cssws(ilsp,:), &
3096	surf_lsm_v(2)%cssws(ilsp,:), surf_lsm_v(3)%cssws(ilsp,:), &
3097	surf_usm_v(0)%cssws(ilsp,:), surf_usm_v(1)%cssws(ilsp,:), &
3098	surf_usm_v(2)%cssws(ilsp,:), surf_usm_v(3)%cssws(ilsp,:) )
3099	!
3100	!-- Prognostic equation for chem spcs
3101	DO k = nzb+1, nzt
3102	chem_species(ilsp)%conc_p(k,j,i) = chem_species(ilsp)%conc(k,j,i) + ( dt_3d * &
3103	( tsc(2) * tend(k,j,i) + &
3104	tsc(3) * chem_species(ilsp)%tconc_m(k,j,i) ) &
3105	- tsc(5) * rdf_sc(k) &
3106	* ( chem_species(ilsp)%conc(k,j,i) - chem_species(ilsp)%conc_pr_init(k) ) &
3107	) &
3108	* MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 0 ) &
3109	)
3110
3111	IF ( chem_species(ilsp)%conc_p(k,j,i) < 0.0_wp ) THEN
3112	chem_species(ilsp)%conc_p(k,j,i) = 0.1_wp * chem_species(ilsp)%conc(k,j,i) !FKS6
3113	ENDIF
3114	ENDDO
3115	!
3116	!-- Calculate tendencies for the next Runge-Kutta step
3117	IF ( timestep_scheme(1:5) == 'runge' ) THEN
3118	IF ( intermediate_timestep_count == 1 ) THEN
3119	DO k = nzb+1, nzt
3120	chem_species(ilsp)%tconc_m(k,j,i) = tend(k,j,i)
3121	ENDDO
3122	ELSEIF ( intermediate_timestep_count < &
3123	intermediate_timestep_count_max ) THEN
3124	DO k = nzb+1, nzt
3125	chem_species(ilsp)%tconc_m(k,j,i) = -9.5625_wp * tend(k,j,i) + &
3126	5.3125_wp * chem_species(ilsp)%tconc_m(k,j,i)
3127	ENDDO
3128	ENDIF
3129	ENDIF
3130
3131	ENDDO
3132
3133	END SUBROUTINE chem_prognostic_equations_ij
3134
3135
3136	!--------------------------------------------------------------------------------------------------!
3137	! Description:
3138	! ------------
3139	!> Read module-specific local restart data arrays (Fortran binary format).
3140	!--------------------------------------------------------------------------------------------------!
3141	SUBROUTINE chem_rrd_local_ftn( k, nxlf, nxlc, nxl_on_file, nxrf, nxrc, nxr_on_file, nynf, nync, &
3142	nyn_on_file, nysf, nysc, nys_on_file, tmp_3d, found )
3143
3144	USE control_parameters
3145
3146	INTEGER(iwp) :: k !<
3147	INTEGER(iwp) :: lsp !<
3148	INTEGER(iwp) :: nxlc !<
3149	INTEGER(iwp) :: nxlf !<
3150	INTEGER(iwp) :: nxl_on_file !<
3151	INTEGER(iwp) :: nxrc !<
3152	INTEGER(iwp) :: nxrf !<
3153	INTEGER(iwp) :: nxr_on_file !<
3154	INTEGER(iwp) :: nync !<
3155	INTEGER(iwp) :: nynf !<
3156	INTEGER(iwp) :: nyn_on_file !<
3157	INTEGER(iwp) :: nysc !<
3158	INTEGER(iwp) :: nysf !<
3159	INTEGER(iwp) :: nys_on_file !<
3160
3161	LOGICAL, INTENT(OUT) :: found
3162
3163	REAL(wp), DIMENSION(nzb:nzt+1,nys_on_file-nbgp:nyn_on_file+nbgp,nxl_on_file-nbgp:nxr_on_file+nbgp) &
3164	:: tmp_3d !< 3D array to temp store data
3165
3166
3167	found = .FALSE.
3168
3169
3170	IF ( ALLOCATED( chem_species ) ) THEN
3171
3172	DO lsp = 1, nspec
3173
3174	IF ( restart_string(1:length) == TRIM( chem_species(lsp)%name) ) THEN
3175
3176	IF ( k == 1 ) READ ( 13 ) tmp_3d
3177	chem_species(lsp)%conc(:,nysc-nbgp:nync+nbgp,nxlc-nbgp:nxrc+nbgp) = &
3178	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
3179	found = .TRUE.
3180
3181	ELSEIF (restart_string(1:length) == TRIM( chem_species(lsp)%name ) // '_av' ) THEN
3182
3183	IF ( .NOT. ALLOCATED( chem_species(lsp)%conc_av ) ) THEN
3184	ALLOCATE( chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg ) )
3185	ENDIF
3186	IF ( k == 1 ) READ ( 13 ) tmp_3d
3187	chem_species(lsp)%conc_av(:,nysc-nbgp:nync+nbgp,nxlc-nbgp:nxrc+nbgp) = &
3188	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
3189	found = .TRUE.
3190
3191	ENDIF
3192
3193	ENDDO
3194
3195	ENDIF
3196
3197	END SUBROUTINE chem_rrd_local_ftn
3198
3199
3200	!--------------------------------------------------------------------------------------------------!
3201	! Description:
3202	! ------------
3203	!> Read module-specific local restart data arrays (Fortran binary format).
3204	!--------------------------------------------------------------------------------------------------!
3205	SUBROUTINE chem_rrd_local_mpi
3206
3207	IMPLICIT NONE
3208
3209	INTEGER(iwp) :: lsp !<
3210
3211	LOGICAL :: array_found !<
3212
3213
3214	DO lsp = 1, nspec
3215
3216	CALL rrd_mpi_io( TRIM( chem_species(lsp)%name ), chem_species(lsp)%conc )
3217
3218	CALL rd_mpi_io_check_array( TRIM( chem_species(lsp)%name )//'_av' , found = array_found )
3219	IF ( array_found ) THEN
3220	IF ( .NOT. ALLOCATED( chem_species(lsp)%conc_av ) ) THEN
3221	ALLOCATE( chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
3222	ENDIF
3223	CALL rrd_mpi_io( TRIM( chem_species(lsp)%name )//'_av', chem_species(lsp)%conc_av )
3224	ENDIF
3225
3226	ENDDO
3227
3228	END SUBROUTINE chem_rrd_local_mpi
3229
3230
3231	!--------------------------------------------------------------------------------------------------!
3232	!> Description:
3233	!> Calculation of horizontally averaged profiles
3234	!> This routine is called for every statistic region (sr) defined by the user,
3235	!> but at least for the region "total domain" (sr=0).
3236	!> quantities.
3237	!--------------------------------------------------------------------------------------------------!
3238	SUBROUTINE chem_statistics( mode, sr, tn )
3239
3240
3241	USE arrays_3d
3242
3243	USE statistics
3244
3245	CHARACTER (LEN=*) :: mode !<
3246
3247	INTEGER(iwp) :: i !< running index on x-axis
3248	INTEGER(iwp) :: j !< running index on y-axis
3249	INTEGER(iwp) :: k !< vertical index counter
3250	INTEGER(iwp) :: l !< direction index counter
3251	INTEGER(iwp) :: lpr !< running index chem spcs
3252	INTEGER(iwp) :: m !< running index for surface elements
3253	!$ INTEGER(iwp) :: omp_get_thread_num !< intrinsic OMP function
3254	INTEGER(iwp) :: sr !< statistical region
3255	INTEGER(iwp) :: surf_e !< end surface index
3256	INTEGER(iwp) :: surf_s !< start surface index
3257	INTEGER(iwp) :: tn !< thread number
3258
3259	REAL(wp) :: flag !< topography masking flag
3260	REAL(wp), DIMENSION(nzb:nzt+1,0:threads_per_task-1) :: sums_tmp !< temporary array used to sum-up profiles
3261
3262	IF ( mode == 'profiles' ) THEN
3263	!
3264	!-- Sum-up profiles for the species
3265	tn = 0
3266	!$OMP PARALLEL PRIVATE( i, j, k, tn, lpr, sums_tmp )
3267	!$ tn = omp_get_thread_num()
3268	!$OMP DO
3269	DO lpr = 1, cs_pr_count_sp
3270	sums_tmp(:,tn) = 0.0_wp
3271	DO i = nxl, nxr
3272	DO j = nys, nyn
3273	DO k = nzb, nzt+1
3274	sums_tmp(k,tn) = sums_tmp(k,tn) + &
3275	chem_species(cs_pr_index_sp(lpr))%conc(k,j,i) * &
3276	rmask(j,i,sr) * &
3277	MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 22 ) )
3278	ENDDO
3279	ENDDO
3280	ENDDO
3281	sums_l(nzb:nzt+1,hom_index_spec(lpr),tn) = sums_tmp(nzb:nzt+1,tn)
3282	ENDDO
3283	!$OMP END PARALLEL
3284	!
3285	!-- Sum-up profiles for vertical fluxes of the the species. Note, in case of WS5 scheme the
3286	!-- profiles of resolved-scale fluxes have been already summed-up, while resolved-scale fluxes
3287	!-- need to be calculated in case of PW scheme.
3288	!-- For summation employ a temporary array.
3289	!$OMP PARALLEL PRIVATE( i, j, k, tn, lpr, sums_tmp, flag )
3290	!$ tn = omp_get_thread_num()
3291	!$OMP DO
3292	DO lpr = 1, cs_pr_count_fl_sgs
3293	sums_tmp(:,tn) = 0.0_wp
3294	DO i = nxl, nxr
3295	DO j = nys, nyn
3296	DO k = nzb, nzt
3297	flag = MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 23 ) ) * &
3298	MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 9 ) )
3299	sums_tmp(k,tn) = sums_tmp(k,tn) - &
3300	0.5_wp * ( kh(k,j,i) + kh(k+1,j,i) ) &
3301	* ( chem_species(cs_pr_index_fl_sgs(lpr))%conc(k+1,j,i) - &
3302	chem_species(cs_pr_index_fl_sgs(lpr))%conc(k,j,i) ) * &
3303	ddzu(k+1) * rmask(j,i,sr) * flag
3304	ENDDO
3305	!
3306	!-- Add surface fluxes (?Is the order mandatory or could it be done in one cycle?)
3307	DO l = 0, 1
3308	surf_s = surf_def_h(0)%start_index(j,i)
3309	surf_e = surf_def_h(0)%end_index(j,i)
3310	DO m = surf_s, surf_e
3311	k = surf_def_h(0)%k(m) + surf_def_h(0)%koff
3312	sums_tmp(k,tn) = sums_tmp(k,tn) + surf_def_h(0)%cssws(cs_pr_index_fl_sgs(lpr),m)
3313	ENDDO
3314	ENDDO
3315	DO l = 0, 1
3316	surf_s = surf_lsm_h(0)%start_index(j,i)
3317	surf_e = surf_lsm_h(0)%end_index(j,i)
3318	DO m = surf_s, surf_e
3319	k = surf_lsm_h(0)%k(m) + surf_lsm_h(0)%koff
3320	sums_tmp(k,tn) = sums_tmp(k,tn) + surf_lsm_h(0)%cssws(cs_pr_index_fl_sgs(lpr),m)
3321	ENDDO
3322	ENDDO
3323	DO l = 0, 1
3324	surf_s = surf_usm_h(0)%start_index(j,i)
3325	surf_e = surf_usm_h(0)%end_index(j,i)
3326	DO m = surf_s, surf_e
3327	k = surf_usm_h(0)%k(m) + surf_usm_h(0)%koff
3328	sums_tmp(k,tn) = sums_tmp(k,tn) + surf_usm_h(0)%cssws(cs_pr_index_fl_sgs(lpr),m)
3329	ENDDO
3330	ENDDO
3331	ENDDO
3332	ENDDO
3333	sums_l(nzb:nzt+1,hom_index_fl_sgs(lpr),tn) = sums_tmp(nzb:nzt+1,tn)
3334	ENDDO
3335	!$OMP END PARALLEL
3336	!
3337	!-- Resolved-scale fluxes from the WS5 scheme
3338	IF ( ws_scheme_sca ) THEN
3339	!$OMP PARALLEL PRIVATE( tn, lpr )
3340	!$ tn = omp_get_thread_num()
3341	!$OMP DO
3342	DO lpr = 1, cs_pr_count_fl_res
3343	sums_l(nzb:nzt+1,hom_index_fl_res(lpr),tn) = &
3344	sums_ws_l(nzb:nzt+1,tn,cs_pr_index_fl_res(lpr))
3345	ENDDO
3346	!$OMP END PARALLEL
3347	ENDIF
3348
3349	ELSEIF ( mode == 'time_series' ) THEN
3350	! @todo
3351	ENDIF
3352
3353	END SUBROUTINE chem_statistics
3354
3355
3356	!--------------------------------------------------------------------------------------------------!
3357	! Description:
3358	! ------------
3359	!> Subroutine for swapping of timelevels for chemical species called out from subroutine
3360	!> swap_timelevel
3361	!--------------------------------------------------------------------------------------------------!
3362
3363
3364	SUBROUTINE chem_swap_timelevel( level )
3365
3366
3367	INTEGER(iwp), INTENT(IN) :: level
3368	!
3369	!-- Local variables
3370	INTEGER(iwp) :: lsp
3371
3372
3373	IF ( level == 0 ) THEN
3374	DO lsp=1, nvar
3375	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
3376	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
3377	ENDDO
3378	ELSE
3379	DO lsp=1, nvar
3380	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
3381	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
3382	ENDDO
3383	ENDIF
3384
3385	RETURN
3386	END SUBROUTINE chem_swap_timelevel
3387
3388
3389	!--------------------------------------------------------------------------------------------------!
3390	! Description:
3391	! ------------
3392	!> Subroutine to write restart data for chemistry model
3393	!--------------------------------------------------------------------------------------------------!
3394	SUBROUTINE chem_wrd_local
3395
3396
3397	INTEGER(iwp) :: lsp !< running index for chem spcs.
3398
3399	IF ( TRIM( restart_data_format_output ) == 'fortran_binary' ) THEN
3400
3401	DO lsp = 1, nspec
3402	CALL wrd_write_string( TRIM( chem_species(lsp)%name ) )
3403	WRITE ( 14 ) chem_species(lsp)%conc
3404	IF ( ALLOCATED( chem_species(lsp)%conc_av ) ) THEN
3405	CALL wrd_write_string( TRIM( chem_species(lsp)%name )//'_av' )
3406	WRITE ( 14 ) chem_species(lsp)%conc_av
3407	ENDIF
3408	ENDDO
3409
3410	ELSEIF ( restart_data_format_output(1:3) == 'mpi' ) THEN
3411
3412	DO lsp = 1, nspec
3413	CALL wrd_mpi_io( TRIM( chem_species(lsp)%name ), chem_species(lsp)%conc )
3414	IF ( ALLOCATED( chem_species(lsp)%conc_av ) ) THEN
3415	CALL wrd_mpi_io( TRIM( chem_species(lsp)%name ) // '_av', chem_species(lsp)%conc_av )
3416	ENDIF
3417	ENDDO
3418
3419	ENDIF
3420
3421	END SUBROUTINE chem_wrd_local
3422
3423
3424	!--------------------------------------------------------------------------------------------------!
3425	! Description:
3426	! ------------
3427	!> Subroutine to calculate the deposition of gases and PMs. For now deposition only takes place on
3428	!> lsm and usm horizontal upward faceing surfaces. Default surfaces are NOT considered.
3429	!> The deposition of particlesis derived following Zhang et al., 2001, gases are deposited using
3430	!> the DEPAC module (van Zanten et al., 2010).
3431	!>
3432	!> @TODO: Consider deposition on vertical surfaces
3433	!> @TODO: Consider overlaying horizontal surfaces
3434	!> @TODO: Consider resolved vegetation
3435	!> @TODO: Check error messages
3436	!--------------------------------------------------------------------------------------------------!
3437	SUBROUTINE chem_depo( i, j )
3438
3439	USE control_parameters, &
3440	ONLY: dt_3d, intermediate_timestep_count, latitude, time_since_reference_point
3441
3442	USE arrays_3d, &
3443	ONLY: dzw, rho_air_zw
3444
3445	USE palm_date_time_mod, &
3446	ONLY: get_date_time
3447
3448	USE surface_mod, &
3449	ONLY: ind_pav_green, ind_veg_wall, ind_wat_win, surf_lsm_h, surf_type, surf_usm_h
3450
3451	USE radiation_model_mod, &
3452	ONLY: cos_zenith
3453
3454
3455	INTEGER(iwp) :: day_of_year !< current day of the year
3456	INTEGER(iwp), INTENT(IN) :: i
3457	INTEGER(iwp) :: i_pspec !< index for matching depac gas component
3458	INTEGER(iwp), INTENT(IN) :: j
3459	INTEGER(iwp) :: k !< matching k to surface m at i,j
3460	INTEGER(iwp) :: lsp !< running index for chem spcs.
3461	INTEGER(iwp) :: luv_palm !< index of PALM LSM vegetation_type at current
3462	!< surface element
3463	INTEGER(iwp) :: lup_palm !< index of PALM LSM pavement_type at current
3464	!< surface element
3465	INTEGER(iwp) :: luw_palm !< index of PALM LSM water_type at current
3466	!< surface element
3467	INTEGER(iwp) :: luu_palm !< index of PALM USM walls/roofs at current
3468	!< surface element
3469	INTEGER(iwp) :: lug_palm !< index of PALM USM green walls/roofs at current
3470	!< surface element
3471	INTEGER(iwp) :: lud_palm !< index of PALM USM windows at current surface
3472	!< element
3473	INTEGER(iwp) :: luv_dep !< matching DEPAC LU to luv_palm
3474	INTEGER(iwp) :: lup_dep !< matching DEPAC LU to lup_palm
3475	INTEGER(iwp) :: luw_dep !< matching DEPAC LU to luw_palm
3476	INTEGER(iwp) :: luu_dep !< matching DEPAC LU to luu_palm
3477	INTEGER(iwp) :: lug_dep !< matching DEPAC LU to lug_palm
3478	INTEGER(iwp) :: lud_dep !< matching DEPAC LU to lud_palm
3479	INTEGER(iwp) :: m !< index for horizontal surfaces
3480	INTEGER(iwp) :: pspec !< running index
3481	!
3482	!-- Vegetation !< Assign PALM classes to DEPAC land
3483	!< use classes
3484	INTEGER(iwp) :: ind_luv_user = 0 !< ERROR as no class given in PALM
3485	INTEGER(iwp) :: ind_luv_b_soil = 1 !< assigned to ilu_desert
3486	INTEGER(iwp) :: ind_luv_mixed_crops = 2 !< assigned to ilu_arable
3487	INTEGER(iwp) :: ind_luv_s_grass = 3 !< assigned to ilu_grass
3488	INTEGER(iwp) :: ind_luv_ev_needle_trees = 4 !< assigned to ilu_coniferous_forest
3489	INTEGER(iwp) :: ind_luv_de_needle_trees = 5 !< assigned to ilu_coniferous_forest
3490	INTEGER(iwp) :: ind_luv_ev_broad_trees = 6 !< assigned to ilu_tropical_forest
3491	INTEGER(iwp) :: ind_luv_de_broad_trees = 7 !< assigned to ilu_deciduous_forest
3492	INTEGER(iwp) :: ind_luv_t_grass = 8 !< assigned to ilu_grass
3493	INTEGER(iwp) :: ind_luv_desert = 9 !< assigned to ilu_desert
3494	INTEGER(iwp) :: ind_luv_tundra = 10 !< assigned to ilu_other
3495	INTEGER(iwp) :: ind_luv_irr_crops = 11 !< assigned to ilu_arable
3496	INTEGER(iwp) :: ind_luv_semidesert = 12 !< assigned to ilu_other
3497	INTEGER(iwp) :: ind_luv_ice = 13 !< assigned to ilu_ice
3498	INTEGER(iwp) :: ind_luv_marsh = 14 !< assigned to ilu_other
3499	INTEGER(iwp) :: ind_luv_ev_shrubs = 15 !< assigned to ilu_mediterrean_scrub
3500	INTEGER(iwp) :: ind_luv_de_shrubs = 16 !< assigned to ilu_mediterrean_scrub
3501	INTEGER(iwp) :: ind_luv_mixed_forest = 17 !< assigned to ilu_coniferous_forest(ave(decid+conif))
3502	INTEGER(iwp) :: ind_luv_intrup_forest = 18 !< assigned to ilu_other (ave(other+decid))
3503	!
3504	!-- Water
3505	INTEGER(iwp) :: ind_luw_user = 0 !< ERROR as no class given in PALM
3506	INTEGER(iwp) :: ind_luw_lake = 1 !< assigned to ilu_water_inland
3507	INTEGER(iwp) :: ind_luw_river = 2 !< assigned to ilu_water_inland
3508	INTEGER(iwp) :: ind_luw_ocean = 3 !< assigned to ilu_water_sea
3509	INTEGER(iwp) :: ind_luw_pond = 4 !< assigned to ilu_water_inland
3510	INTEGER(iwp) :: ind_luw_fountain = 5 !< assigned to ilu_water_inland
3511	!
3512	!-- Pavement
3513	INTEGER(iwp) :: ind_lup_user = 0 !< ERROR as no class given in PALM
3514	INTEGER(iwp) :: ind_lup_asph_conc = 1 !< assigned to ilu_desert
3515	INTEGER(iwp) :: ind_lup_asph = 2 !< assigned to ilu_desert
3516	INTEGER(iwp) :: ind_lup_conc = 3 !< assigned to ilu_desert
3517	INTEGER(iwp) :: ind_lup_sett = 4 !< assigned to ilu_desert
3518	INTEGER(iwp) :: ind_lup_pav_stones = 5 !< assigned to ilu_desert
3519	INTEGER(iwp) :: ind_lup_cobblest = 6 !< assigned to ilu_desert
3520	INTEGER(iwp) :: ind_lup_metal = 7 !< assigned to ilu_desert
3521	INTEGER(iwp) :: ind_lup_wood = 8 !< assigned to ilu_desert
3522	INTEGER(iwp) :: ind_lup_gravel = 9 !< assigned to ilu_desert
3523	INTEGER(iwp) :: ind_lup_f_gravel = 10 !< assigned to ilu_desert
3524	INTEGER(iwp) :: ind_lup_pebblest = 11 !< assigned to ilu_desert
3525	INTEGER(iwp) :: ind_lup_woodchips = 12 !< assigned to ilu_desert
3526	INTEGER(iwp) :: ind_lup_tartan = 13 !< assigned to ilu_desert
3527	INTEGER(iwp) :: ind_lup_art_turf = 14 !< assigned to ilu_desert
3528	INTEGER(iwp) :: ind_lup_clay = 15 !< assigned to ilu_desert
3529	!
3530	!-- Particle parameters according to the respective aerosol classes (PM25, PM10)
3531	INTEGER(iwp) :: ind_p_size = 1 !< index for partsize in particle_pars
3532	INTEGER(iwp) :: ind_p_dens = 2 !< index for rhopart in particle_pars
3533	INTEGER(iwp) :: ind_p_slip = 3 !< index for slipcor in particle_pars
3534	INTEGER(iwp) :: nwet !< wetness indicator dor DEPAC; nwet=0 -> dry; nwet=1 -> wet; nwet=9 -> snow
3535	INTEGER(iwp) :: part_type !< index for particle type (PM10 or PM25) in particle_pars
3536
3537
3538	REAL(wp) :: conc_ijk_ugm3 !< concentration at i, j, k in ug/m3
3539	REAL(wp) :: dens !< density at layer k at i,j
3540	REAL(wp) :: dh !< vertical grid size
3541	REAL(wp) :: diffusivity !< diffusivity
3542	REAL(wp) :: dt_chem !< length of chem time step
3543	REAL(wp) :: dt_dh !< dt_chem/dh
3544	REAL(wp) :: inv_dh !< inverse of vertical grid size
3545	REAL(wp) :: lai !< leaf area index at current surface element
3546	REAL(wp) :: ppm2ugm3 !< conversion factor from ppm to ug/m3
3547	REAL(wp) :: qv_tmp !< surface mixing ratio at current surface element
3548	REAL(wp) :: r_aero_surf !< aerodynamic resistance (s/m) at current surface element
3549	REAL(wp) :: rb !< quasi-laminar boundary layer resistance (s/m)
3550	REAL(wp) :: rc_tot !< total canopy resistance (s/m)
3551	REAL(wp) :: rh_surf !< relative humidity at current surface element
3552	REAL(wp) :: rs !< Sedimentaion resistance (s/m)
3553	REAL(wp) :: sai !< surface area index at current surface element assumed to be
3554	!< lai + 1
3555	REAL(wp) :: slinnfac
3556	REAL(wp) :: solar_rad !< solar radiation, direct and diffuse, at current surface
3557	!< element
3558	REAL(wp) :: temp_tmp !< temperatur at i,j,k
3559	REAL(wp) :: ts !< surface temperatur in degrees celsius
3560	REAL(wp) :: ustar_surf !< ustar at current surface element
3561	REAL(wp) :: vd_lu !< deposition velocity (m/s)
3562	REAL(wp) :: visc !< Viscosity
3563	REAL(wp) :: vs !< Sedimentation velocity
3564	REAL(wp) :: z0h_surf !< roughness length for heat at current surface element
3565
3566	REAL(wp), DIMENSION(nspec) :: bud !< overall budget at current surface element
3567	REAL(wp), DIMENSION(nspec) :: bud_lud !< budget for USM windows at current surface element
3568	REAL(wp), DIMENSION(nspec) :: bud_lug !< budget for USM green surfaces at current surface
3569	!< element
3570	REAL(wp), DIMENSION(nspec) :: bud_lup !< budget for LSM pavement type at current surface
3571	!< element
3572	REAL(wp), DIMENSION(nspec) :: bud_luu !< budget for USM walls/roofs at current surface
3573	!< element
3574	REAL(wp), DIMENSION(nspec) :: bud_luv !< budget for LSM vegetation type at current surface
3575	!< element
3576	REAL(wp), DIMENSION(nspec) :: bud_luw !< budget for LSM water type at current surface
3577	!< element
3578	REAL(wp), DIMENSION(nspec) :: ccomp_tot !< total compensation point (ug/m3), for now kept to
3579	!< zero for all species!
3580	REAL(wp), DIMENSION(nspec) :: conc_ijk !< concentration at i,j,k
3581
3582
3583	!
3584	!-- Particle parameters (PM10 (1), PM25 (2)) partsize (diameter in m), rhopart (density in kg/m3),
3585	!-- slipcor (slip correction factor dimensionless, Seinfeld and Pandis 2006, Table 9.3)
3586	REAL(wp), DIMENSION(1:3,1:2), PARAMETER :: particle_pars = RESHAPE( (/ &
3587	8.0e-6_wp, 1.14e3_wp, 1.016_wp, & !< 1
3588	0.7e-6_wp, 1.14e3_wp, 1.082_wp & !< 2
3589	/), (/ 3, 2 /) )
3590
3591	LOGICAL :: match_lsm !< flag indicating natural-type surface
3592	LOGICAL :: match_usm !< flag indicating urban-type surface
3593
3594	!
3595	!-- List of names of possible tracers
3596	CHARACTER(LEN=*), PARAMETER :: pspecnames(nposp) = (/ &
3597	'NO2 ', & !< NO2
3598	'NO ', & !< NO
3599	'O3 ', & !< O3
3600	'CO ', & !< CO
3601	'form ', & !< FORM
3602	'ald ', & !< ALD
3603	'pan ', & !< PAN
3604	'mgly ', & !< MGLY
3605	'par ', & !< PAR
3606	'ole ', & !< OLE
3607	'eth ', & !< ETH
3608	'tol ', & !< TOL
3609	'cres ', & !< CRES
3610	'xyl ', & !< XYL
3611	'SO4a_f ', & !< SO4a_f
3612	'SO2 ', & !< SO2
3613	'HNO2 ', & !< HNO2
3614	'CH4 ', & !< CH4
3615	'NH3 ', & !< NH3
3616	'NO3 ', & !< NO3
3617	'OH ', & !< OH
3618	'HO2 ', & !< HO2
3619	'N2O5 ', & !< N2O5
3620	'SO4a_c ', & !< SO4a_c
3621	'NH4a_f ', & !< NH4a_f
3622	'NO3a_f ', & !< NO3a_f
3623	'NO3a_c ', & !< NO3a_c
3624	'C2O3 ', & !< C2O3
3625	'XO2 ', & !< XO2
3626	'XO2N ', & !< XO2N
3627	'cro ', & !< CRO
3628	'HNO3 ', & !< HNO3
3629	'H2O2 ', & !< H2O2
3630	'iso ', & !< ISO
3631	'ispd ', & !< ISPD
3632	'to2 ', & !< TO2
3633	'open ', & !< OPEN
3634	'terp ', & !< TERP
3635	'ec_f ', & !< EC_f
3636	'ec_c ', & !< EC_c
3637	'pom_f ', & !< POM_f
3638	'pom_c ', & !< POM_c
3639	'ppm_f ', & !< PPM_f
3640	'ppm_c ', & !< PPM_c
3641	'na_ff ', & !< Na_ff
3642	'na_f ', & !< Na_f
3643	'na_c ', & !< Na_c
3644	'na_cc ', & !< Na_cc
3645	'na_ccc ', & !< Na_ccc
3646	'dust_ff ', & !< dust_ff
3647	'dust_f ', & !< dust_f
3648	'dust_c ', & !< dust_c
3649	'dust_cc ', & !< dust_cc
3650	'dust_ccc ', & !< dust_ccc
3651	'tpm10 ', & !< tpm10
3652	'tpm25 ', & !< tpm25
3653	'tss ', & !< tss
3654	'tdust ', & !< tdust
3655	'tc ', & !< tc
3656	'tcg ', & !< tcg
3657	'tsoa ', & !< tsoa
3658	'tnmvoc ', & !< tnmvoc
3659	'SOxa ', & !< SOxa
3660	'NOya ', & !< NOya
3661	'NHxa ', & !< NHxa
3662	'NO2_obs ', & !< NO2_obs
3663	'tpm10_biascorr', & !< tpm10_biascorr
3664	'tpm25_biascorr', & !< tpm25_biascorr
3665	'O3_biascorr ' /) !< o3_biascorr
3666	!
3667	!-- Tracer mole mass:
3668	REAL(wp), PARAMETER :: specmolm(nposp) = (/ &
3669	xm_O * 2 + xm_N, & !< NO2
3670	xm_O + xm_N, & !< NO
3671	xm_O * 3, & !< O3
3672	xm_C + xm_O, & !< CO
3673	xm_H * 2 + xm_C + xm_O, & !< FORM
3674	xm_H * 3 + xm_C * 2 + xm_O, & !< ALD
3675	xm_H * 3 + xm_C * 2 + xm_O * 5 + xm_N, & !< PAN
3676	xm_H * 4 + xm_C * 3 + xm_O * 2, & !< MGLY
3677	xm_H * 3 + xm_C, & !< PAR
3678	xm_H * 3 + xm_C * 2, & !< OLE
3679	xm_H * 4 + xm_C * 2, & !< ETH
3680	xm_H * 8 + xm_C * 7, & !< TOL
3681	xm_H * 8 + xm_C * 7 + xm_O, & !< CRES
3682	xm_H * 10 + xm_C * 8, & !< XYL
3683	xm_S + xm_O * 4, & !< SO4a_f
3684	xm_S + xm_O * 2, & !< SO2
3685	xm_H + xm_O * 2 + xm_N, & !< HNO2
3686	xm_H * 4 + xm_C, & !< CH4
3687	xm_H * 3 + xm_N, & !< NH3
3688	xm_O * 3 + xm_N, & !< NO3
3689	xm_H + xm_O, & !< OH
3690	xm_H + xm_O * 2, & !< HO2
3691	xm_O * 5 + xm_N * 2, & !< N2O5
3692	xm_S + xm_O * 4, & !< SO4a_c
3693	xm_H * 4 + xm_N, & !< NH4a_f
3694	xm_O * 3 + xm_N, & !< NO3a_f
3695	xm_O * 3 + xm_N, & !< NO3a_c
3696	xm_C * 2 + xm_O * 3, & !< C2O3
3697	xm_dummy, & !< XO2
3698	xm_dummy, & !< XO2N
3699	xm_dummy, & !< CRO
3700	xm_H + xm_O * 3 + xm_N, & !< HNO3
3701	xm_H * 2 + xm_O * 2, & !< H2O2
3702	xm_H * 8 + xm_C * 5, & !< ISO
3703	xm_dummy, & !< ISPD
3704	xm_dummy, & !< TO2
3705	xm_dummy, & !< OPEN
3706	xm_H * 16 + xm_C * 10, & !< TERP
3707	xm_dummy, & !< EC_f
3708	xm_dummy, & !< EC_c
3709	xm_dummy, & !< POM_f
3710	xm_dummy, & !< POM_c
3711	xm_dummy, & !< PPM_f
3712	xm_dummy, & !< PPM_c
3713	xm_Na, & !< Na_ff
3714	xm_Na, & !< Na_f
3715	xm_Na, & !< Na_c
3716	xm_Na, & !< Na_cc
3717	xm_Na, & !< Na_ccc
3718	xm_dummy, & !< dust_ff
3719	xm_dummy, & !< dust_f
3720	xm_dummy, & !< dust_c
3721	xm_dummy, & !< dust_cc
3722	xm_dummy, & !< dust_ccc
3723	xm_dummy, & !< tpm10
3724	xm_dummy, & !< tpm25
3725	xm_dummy, & !< tss
3726	xm_dummy, & !< tdust
3727	xm_dummy, & !< tc
3728	xm_dummy, & !< tcg
3729	xm_dummy, & !< tsoa
3730	xm_dummy, & !< tnmvoc
3731	xm_dummy, & !< SOxa
3732	xm_dummy, & !< NOya
3733	xm_dummy, & !< NHxa
3734	xm_O * 2 + xm_N, & !< NO2_obs
3735	xm_dummy, & !< tpm10_biascorr
3736	xm_dummy, & !< tpm25_biascorr
3737	xm_O * 3 /) !< o3_biascorr
3738	!
3739	!-- Get current day of the year
3740	CALL get_date_time( time_since_reference_point, day_of_year = day_of_year )
3741	!
3742	!-- Initialize surface element m
3743	m = 0
3744	k = 0
3745	!
3746	!-- LSM or USM horizintal upward facing surface present at i,j:
3747	!-- Default surfaces are NOT considered for deposition
3748	match_lsm = surf_lsm_h(0)%start_index(j,i) <= surf_lsm_h(0)%end_index(j,i)
3749	match_usm = surf_usm_h(0)%start_index(j,i) <= surf_usm_h(0)%end_index(j,i)
3750	!
3751	!--For LSM surfaces
3752	IF ( match_lsm ) THEN
3753	!
3754	!-- Get surface element information at i,j:
3755	m = surf_lsm_h(0)%start_index(j,i)
3756	k = surf_lsm_h(0)%k(m)
3757	!
3758	!-- Get needed variables for surface element m
3759	ustar_surf = surf_lsm_h(0)%us(m)
3760	z0h_surf = surf_lsm_h(0)%z0h(m)
3761	r_aero_surf = surf_lsm_h(0)%r_a(m)
3762	solar_rad = surf_lsm_h(0)%rad_sw_dir(m) + surf_lsm_h(0)%rad_sw_dif(m)
3763
3764	lai = surf_lsm_h(0)%lai(m)
3765	sai = lai + 1
3766	!
3767	!-- For small grid spacing neglect R_a
3768	IF ( dzw(k) <= 1.0 ) THEN
3769	r_aero_surf = 0.0_wp
3770	ENDIF
3771	!
3772	!-- Initialize lu's
3773	luv_palm = 0
3774	luv_dep = 0
3775	lup_palm = 0
3776	lup_dep = 0
3777	luw_palm = 0
3778	luw_dep = 0
3779	!
3780	!-- Initialize budgets
3781	bud_luv = 0.0_wp
3782	bud_lup = 0.0_wp
3783	bud_luw = 0.0_wp
3784	!
3785	!-- Get land use for i,j and assign to DEPAC lu
3786	IF ( surf_lsm_h(0)%frac(m,ind_veg_wall) > 0 ) THEN
3787	luv_palm = surf_lsm_h(0)%vegetation_type(m)
3788	IF ( luv_palm == ind_luv_user ) THEN
3789	message_string = 'No lsm-vegetation type defined. Please define vegetation type to' //&
3790	' enable deposition calculation'
3791	CALL message( 'chem_depo', 'PA0738', 1, 2, 0, 6, 0 )
3792	ELSEIF ( luv_palm == ind_luv_b_soil ) THEN
3793	luv_dep = 9
3794	ELSEIF ( luv_palm == ind_luv_mixed_crops ) THEN
3795	luv_dep = 2
3796	ELSEIF ( luv_palm == ind_luv_s_grass ) THEN
3797	luv_dep = 1
3798	ELSEIF ( luv_palm == ind_luv_ev_needle_trees ) THEN
3799	luv_dep = 4
3800	ELSEIF ( luv_palm == ind_luv_de_needle_trees ) THEN
3801	luv_dep = 4
3802	ELSEIF ( luv_palm == ind_luv_ev_broad_trees ) THEN
3803	luv_dep = 12
3804	ELSEIF ( luv_palm == ind_luv_de_broad_trees ) THEN
3805	luv_dep = 5
3806	ELSEIF ( luv_palm == ind_luv_t_grass ) THEN
3807	luv_dep = 1
3808	ELSEIF ( luv_palm == ind_luv_desert ) THEN
3809	luv_dep = 9
3810	ELSEIF ( luv_palm == ind_luv_tundra ) THEN
3811	luv_dep = 8
3812	ELSEIF ( luv_palm == ind_luv_irr_crops ) THEN
3813	luv_dep = 2
3814	ELSEIF ( luv_palm == ind_luv_semidesert ) THEN
3815	luv_dep = 8
3816	ELSEIF ( luv_palm == ind_luv_ice ) THEN
3817	luv_dep = 10
3818	ELSEIF ( luv_palm == ind_luv_marsh ) THEN
3819	luv_dep = 8
3820	ELSEIF ( luv_palm == ind_luv_ev_shrubs ) THEN
3821	luv_dep = 14
3822	ELSEIF ( luv_palm == ind_luv_de_shrubs ) THEN
3823	luv_dep = 14
3824	ELSEIF ( luv_palm == ind_luv_mixed_forest ) THEN
3825	luv_dep = 4
3826	ELSEIF ( luv_palm == ind_luv_intrup_forest ) THEN
3827	luv_dep = 8
3828	ENDIF
3829	ENDIF
3830
3831	IF ( surf_lsm_h(0)%frac(m,ind_pav_green) > 0 ) THEN
3832	lup_palm = surf_lsm_h(0)%pavement_type(m)
3833	IF ( lup_palm == ind_lup_user ) THEN
3834	message_string = 'No lsm-pavement type defined. Please define pavement type to ' // &
3835	'enable deposition calculation'
3836	CALL message( 'chem_depo', 'PA0738', 1, 2, 0, 6, 0 )
3837	ELSEIF ( lup_palm == ind_lup_asph_conc ) THEN
3838	lup_dep = 9
3839	ELSEIF ( lup_palm == ind_lup_asph ) THEN
3840	lup_dep = 9
3841	ELSEIF ( lup_palm == ind_lup_conc ) THEN
3842	lup_dep = 9
3843	ELSEIF ( lup_palm == ind_lup_sett ) THEN
3844	lup_dep = 9
3845	ELSEIF ( lup_palm == ind_lup_pav_stones ) THEN
3846	lup_dep = 9
3847	ELSEIF ( lup_palm == ind_lup_cobblest ) THEN
3848	lup_dep = 9
3849	ELSEIF ( lup_palm == ind_lup_metal ) THEN
3850	lup_dep = 9
3851	ELSEIF ( lup_palm == ind_lup_wood ) THEN
3852	lup_dep = 9
3853	ELSEIF ( lup_palm == ind_lup_gravel ) THEN
3854	lup_dep = 9
3855	ELSEIF ( lup_palm == ind_lup_f_gravel ) THEN
3856	lup_dep = 9
3857	ELSEIF ( lup_palm == ind_lup_pebblest ) THEN
3858	lup_dep = 9
3859	ELSEIF ( lup_palm == ind_lup_woodchips ) THEN
3860	lup_dep = 9
3861	ELSEIF ( lup_palm == ind_lup_tartan ) THEN
3862	lup_dep = 9
3863	ELSEIF ( lup_palm == ind_lup_art_turf ) THEN
3864	lup_dep = 9
3865	ELSEIF ( lup_palm == ind_lup_clay ) THEN
3866	lup_dep = 9
3867	ENDIF
3868	ENDIF
3869
3870	IF ( surf_lsm_h(0)%frac(m,ind_wat_win) > 0 ) THEN
3871	luw_palm = surf_lsm_h(0)%water_type(m)
3872	IF ( luw_palm == ind_luw_user ) THEN
3873	message_string = 'No lsm-water type defined. Please define water type to enable' // &
3874	' deposition calculation'
3875	CALL message( 'chem_depo', 'PA0738', 1, 2, 0, 6, 0 )
3876	ELSEIF ( luw_palm == ind_luw_lake ) THEN
3877	luw_dep = 13
3878	ELSEIF ( luw_palm == ind_luw_river ) THEN
3879	luw_dep = 13
3880	ELSEIF ( luw_palm == ind_luw_ocean ) THEN
3881	luw_dep = 6
3882	ELSEIF ( luw_palm == ind_luw_pond ) THEN
3883	luw_dep = 13
3884	ELSEIF ( luw_palm == ind_luw_fountain ) THEN
3885	luw_dep = 13
3886	ENDIF
3887	ENDIF
3888	!
3889	!-- Set wetness indicator to dry or wet for lsm vegetation or pavement
3890	IF ( surf_lsm_h(0)%c_liq(m) > 0 ) THEN
3891	nwet = 1
3892	ELSE
3893	nwet = 0
3894	ENDIF
3895	!
3896	!-- Compute length of time step
3897	IF ( call_chem_at_all_substeps ) THEN
3898	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
3899	ELSE
3900	dt_chem = dt_3d
3901	ENDIF
3902
3903	dh = dzw(k)
3904	inv_dh = 1.0_wp / dh
3905	dt_dh = dt_chem/dh
3906	!
3907	!-- Concentration at i,j,k
3908	DO lsp = 1, nspec
3909	conc_ijk(lsp) = chem_species(lsp)%conc(k,j,i)
3910	ENDDO
3911
3912	!-- Temperature at i,j,k
3913	temp_tmp = pt(k,j,i) * ( hyp(k) / 100000.0_wp )**0.286_wp
3914
3915	ts = temp_tmp - 273.15 !< in degrees celcius
3916	!
3917	!-- Viscosity of air
3918	visc = 1.496e-6 * temp_tmp**1.5 / (temp_tmp + 120.0)
3919	!
3920	!-- Air density at k
3921	dens = rho_air_zw(k)
3922	!
3923	!-- Calculate relative humidity from specific humidity for DEPAC
3924	qv_tmp = MAX( q(k,j,i), 0.0_wp)
3925	rh_surf = relativehumidity_from_specifichumidity(qv_tmp, temp_tmp, hyp(k) )
3926	!
3927	!-- Check if surface fraction (vegetation, pavement or water) > 0 and calculate vd and budget
3928	!-- for each surface fraction. Then derive overall budget taking into account the surface fractions.
3929	!
3930	!-- Vegetation
3931	IF ( surf_lsm_h(0)%frac(m,ind_veg_wall) > 0 ) THEN
3932
3933	!
3934	!-- No vegetation on bare soil, desert or ice:
3935	IF ( ( luv_palm == ind_luv_b_soil ) .OR. ( luv_palm == ind_luv_desert ) .OR. &
3936	( luv_palm == ind_luv_ice ) ) THEN
3937
3938	lai = 0.0_wp
3939	sai = 0.0_wp
3940
3941	ENDIF
3942
3943	slinnfac = 1.0_wp
3944	!
3945	!-- Get deposition velocity vd
3946	DO lsp = 1, nvar
3947	!
3948	!-- Initialize
3949	vs = 0.0_wp
3950	vd_lu = 0.0_wp
3951	rs = 0.0_wp
3952	rb = 0.0_wp
3953	rc_tot = 0.0_wp
3954	IF ( spc_names(lsp) == 'PM10' ) THEN
3955	part_type = 1
3956	!
3957	!-- Sedimentation velocity
3958	vs = slinnfac * sedimentation_velocity( particle_pars(ind_p_dens, part_type), &
3959	particle_pars(ind_p_size, part_type), &
3960	particle_pars(ind_p_slip, part_type), &
3961	visc)
3962
3963	CALL drydepo_aero_zhang_vd( vd_lu, rs, &
3964	vs, &
3965	particle_pars(ind_p_size, part_type), &
3966	particle_pars(ind_p_slip, part_type), &
3967	nwet, temp_tmp, dens, visc, &
3968	luv_dep, &
3969	r_aero_surf, ustar_surf )
3970
3971	bud_luv(lsp) = - conc_ijk(lsp) * ( 1.0_wp - EXP( - vd_lu * dt_dh ) ) * dh
3972
3973
3974	ELSEIF ( spc_names(lsp) == 'PM25' ) THEN
3975	part_type = 2
3976	!
3977	!-- Sedimentation velocity
3978	vs = slinnfac * sedimentation_velocity( particle_pars(ind_p_dens, part_type), &
3979	particle_pars(ind_p_size, part_type), &
3980	particle_pars(ind_p_slip, part_type), &
3981	visc)
3982
3983	CALL drydepo_aero_zhang_vd( vd_lu, rs, &
3984	vs, &
3985	particle_pars(ind_p_size, part_type), &
3986	particle_pars(ind_p_slip, part_type), &
3987	nwet, temp_tmp, dens, visc, &
3988	luv_dep , &
3989	r_aero_surf, ustar_surf )
3990
3991	bud_luv(lsp) = - conc_ijk(lsp) * ( 1.0_wp - EXP( - vd_lu * dt_dh ) ) * dh
3992
3993	ELSE !< GASES
3994	!
3995	!-- Read spc_name of current species for gas parameter
3996	IF ( ANY( pspecnames(:) == spc_names(lsp) ) ) THEN
3997	i_pspec = 0
3998	DO pspec = 1, nposp
3999	IF ( pspecnames(pspec) == spc_names(lsp) ) THEN
4000	i_pspec = pspec
4001	END IF
4002	ENDDO
4003
4004	ELSE
4005	!
4006	!-- For now species not deposited
4007	CYCLE
4008	ENDIF
4009	!
4010	!-- Factor used for conversion from ppb to ug/m3 :
4011	!-- ppb (mole tr)/(mole air)/ppb (kg tr)/(mole tr) (ug tr)/(kg tr) &
4012	!-- (mole air)/(kg air) (kg air)/(m3 air) (kg air(ug/m3)/ppb/(kg/mole) = / (kg/mole)
4013	!-- c 1e-9 xm_tracer 1e9 / xm_air dens
4014	!-- thus:
4015	!-- c_in_ppb * xm_tracer * [ dens / xm_air ] = c_in_ugm3
4016	!-- Use density at k:
4017	ppm2ugm3 = (dens/xm_air) * 0.001_wp !< (mole air)/m3
4018	!
4019	!-- Atmospheric concentration in DEPAC is requested in ug/m3:
4020	! ug/m3 ppm (ug/m3)/ppm/(kg/mole) kg/mole
4021	conc_ijk_ugm3 = conc_ijk(lsp) * ppm2ugm3 * specmolm(i_pspec) ! in ug/m3
4022	!
4023	!-- Diffusivity for DEPAC relevant gases
4024	!-- Use default value
4025	diffusivity = 0.11e-4
4026	!
4027	!-- Overwrite with known coefficients of diffusivity from Massman (1998)
4028	IF ( spc_names(lsp) == 'NO2' ) diffusivity = 0.136e-4
4029	IF ( spc_names(lsp) == 'NO' ) diffusivity = 0.199e-4
4030	IF ( spc_names(lsp) == 'O3' ) diffusivity = 0.144e-4
4031	IF ( spc_names(lsp) == 'CO' ) diffusivity = 0.176e-4
4032	IF ( spc_names(lsp) == 'SO2' ) diffusivity = 0.112e-4
4033	IF ( spc_names(lsp) == 'CH4' ) diffusivity = 0.191e-4
4034	IF ( spc_names(lsp) == 'NH3' ) diffusivity = 0.191e-4
4035	!
4036	!-- Get quasi-laminar boundary layer resistance rb:
4037	CALL get_rb_cell( ( luv_dep == ilu_water_sea ) .OR. &
4038	( luv_dep == ilu_water_inland ), z0h_surf, ustar_surf, &
4039	diffusivity, rb )
4040	!
4041	!-- Get rc_tot
4042	CALL drydepos_gas_depac( spc_names(lsp), day_of_year, latitude, ts, ustar_surf, &
4043	solar_rad, cos_zenith, rh_surf, lai, sai, nwet, luv_dep, &
4044	2, rc_tot, ccomp_tot(lsp), hyp(nzb), conc_ijk_ugm3, &
4045	diffusivity, r_aero_surf , rb )
4046	!
4047	!-- Calculate budget
4048	IF ( rc_tot <= 0.0 ) THEN
4049
4050	bud_luv(lsp) = 0.0_wp
4051
4052	ELSE
4053
4054	vd_lu = 1.0_wp / ( r_aero_surf + rb + rc_tot )
4055
4056	bud_luv(lsp) = - ( conc_ijk(lsp) - ccomp_tot(lsp) ) * &
4057	( 1.0_wp - EXP( -vd_lu * dt_dh ) ) * dh
4058	ENDIF
4059
4060	ENDIF
4061	ENDDO
4062	ENDIF
4063	!
4064	!-- Pavement
4065	IF ( surf_lsm_h(0)%frac(m,ind_pav_green) > 0 ) THEN
4066	!
4067	!-- No vegetation on pavements:
4068	lai = 0.0_wp
4069	sai = 0.0_wp
4070
4071	slinnfac = 1.0_wp
4072	!
4073	!-- Get vd
4074	DO lsp = 1, nvar
4075	!
4076	!-- Initialize
4077	vs = 0.0_wp
4078	vd_lu = 0.0_wp
4079	rs = 0.0_wp
4080	rb = 0.0_wp
4081	rc_tot = 0.0_wp
4082	IF ( spc_names(lsp) == 'PM10' ) THEN
4083	part_type = 1
4084	!
4085	!-- Sedimentation velocity:
4086	vs = slinnfac * sedimentation_velocity( particle_pars(ind_p_dens, part_type), &
4087	particle_pars(ind_p_size, part_type), &
4088	particle_pars(ind_p_slip, part_type), &
4089	visc)
4090
4091	CALL drydepo_aero_zhang_vd( vd_lu, rs, &
4092	vs, &
4093	particle_pars(ind_p_size, part_type), &
4094	particle_pars(ind_p_slip, part_type), &
4095	nwet, temp_tmp, dens, visc, &
4096	lup_dep, &
4097	r_aero_surf, ustar_surf )
4098
4099	bud_lup(lsp) = - conc_ijk(lsp) * ( 1.0_wp - EXP( - vd_lu * dt_dh ) ) * dh
4100
4101
4102	ELSEIF ( spc_names(lsp) == 'PM25' ) THEN
4103	part_type = 2
4104	!
4105	!-- Sedimentation velocity:
4106	vs = slinnfac * sedimentation_velocity( particle_pars(ind_p_dens, part_type), &
4107	particle_pars(ind_p_size, part_type), &
4108	particle_pars(ind_p_slip, part_type), &
4109	visc)
4110
4111	CALL drydepo_aero_zhang_vd( vd_lu, rs, &
4112	vs, &
4113	particle_pars(ind_p_size, part_type), &
4114	particle_pars(ind_p_slip, part_type), &
4115	nwet, temp_tmp, dens, visc, &
4116	lup_dep, &
4117	r_aero_surf, ustar_surf )
4118
4119	bud_lup(lsp) = - conc_ijk(lsp) * ( 1.0_wp - EXP( - vd_lu * dt_dh ) ) * dh
4120
4121	ELSE !<GASES
4122	!
4123	!-- Read spc_name of current species for gas parameter
4124	IF ( ANY( pspecnames(:) == spc_names(lsp) ) ) THEN
4125	i_pspec = 0
4126	DO pspec = 1, nposp
4127	IF ( pspecnames(pspec) == spc_names(lsp) ) THEN
4128	i_pspec = pspec
4129	END IF
4130	ENDDO
4131
4132	ELSE
4133	!
4134	!-- For now species not deposited
4135	CYCLE
4136	ENDIF
4137	!
4138	!-- Factor used for conversion from ppb to ug/m3 :
4139	!-- ppb (mole tr)/(mole air)/ppb (kg tr)/(mole tr) (ug tr)/(kg tr) &
4140	!-- (mole air)/(kg air) (kg air)/(m3 air) (kg air(ug/m3)/ppb/(kg/mole) = / (kg/mole)
4141	!-- c 1e-9 xm_tracer 1e9 / xm_air dens
4142	!-- thus:
4143	!-- c_in_ppb * xm_tracer * [ dens / xm_air ] = c_in_ugm3
4144	!-- Use density at lowest layer:
4145	ppm2ugm3 = (dens/xm_air) * 0.001_wp !< (mole air)/m3
4146	!
4147	!-- Atmospheric concentration in DEPAC is requested in ug/m3:
4148	! ug/m3 ppm (ug/m3)/ppm/(kg/mole) kg/mole
4149	conc_ijk_ugm3 = conc_ijk(lsp) * ppm2ugm3 * specmolm(i_pspec) ! in ug/m3
4150	!
4151	!-- Diffusivity for DEPAC relevant gases
4152	!-- Use default value
4153	diffusivity = 0.11e-4
4154	!
4155	!-- Overwrite with known coefficients of diffusivity from Massman (1998)
4156	IF ( spc_names(lsp) == 'NO2' ) diffusivity = 0.136e-4
4157	IF ( spc_names(lsp) == 'NO' ) diffusivity = 0.199e-4
4158	IF ( spc_names(lsp) == 'O3' ) diffusivity = 0.144e-4
4159	IF ( spc_names(lsp) == 'CO' ) diffusivity = 0.176e-4
4160	IF ( spc_names(lsp) == 'SO2' ) diffusivity = 0.112e-4
4161	IF ( spc_names(lsp) == 'CH4' ) diffusivity = 0.191e-4
4162	IF ( spc_names(lsp) == 'NH3' ) diffusivity = 0.191e-4
4163	!
4164	!-- Get quasi-laminar boundary layer resistance rb:
4165	CALL get_rb_cell( ( lup_dep == ilu_water_sea ) .OR. &
4166	( lup_dep == ilu_water_inland ), z0h_surf, ustar_surf, &
4167	diffusivity, rb )
4168	!
4169	!-- Get rc_tot
4170	CALL drydepos_gas_depac( spc_names(lsp), day_of_year, latitude, ts, ustar_surf, &
4171	solar_rad, cos_zenith, rh_surf, lai, sai, nwet, lup_dep, &
4172	2, rc_tot, ccomp_tot(lsp), hyp(nzb), conc_ijk_ugm3, &
4173	diffusivity, r_aero_surf , rb )
4174	!
4175	!-- Calculate budget
4176	IF ( rc_tot <= 0.0 ) THEN
4177	bud_lup(lsp) = 0.0_wp
4178	ELSE
4179	vd_lu = 1.0_wp / (r_aero_surf + rb + rc_tot )
4180	bud_lup(lsp) = - ( conc_ijk(lsp) - ccomp_tot(lsp) ) * &
4181	( 1.0_wp - EXP( - vd_lu * dt_dh ) ) * dh
4182	ENDIF
4183
4184	ENDIF
4185	ENDDO
4186	ENDIF
4187	!
4188	!-- Water
4189	IF ( surf_lsm_h(0)%frac(m,ind_wat_win) > 0 ) THEN
4190	!
4191	!-- No vegetation on water:
4192	lai = 0.0_wp
4193	sai = 0.0_wp
4194	slinnfac = 1.0_wp
4195	!
4196	!-- Get vd
4197	DO lsp = 1, nvar
4198	!
4199	!-- Initialize
4200	vs = 0.0_wp
4201	vd_lu = 0.0_wp
4202	rs = 0.0_wp
4203	rb = 0.0_wp
4204	rc_tot = 0.0_wp
4205	IF ( spc_names(lsp) == 'PM10' ) THEN
4206	part_type = 1
4207	!
4208	!-- Sedimentation velocity:
4209	vs = slinnfac * sedimentation_velocity( particle_pars(ind_p_dens, part_type), &
4210	particle_pars(ind_p_size, part_type), &
4211	particle_pars(ind_p_slip, part_type), &
4212	visc)
4213
4214	CALL drydepo_aero_zhang_vd( vd_lu, rs, &
4215	vs, &
4216	particle_pars(ind_p_size, part_type), &
4217	particle_pars(ind_p_slip, part_type), &
4218	nwet, temp_tmp, dens, visc, &
4219	luw_dep, &
4220	r_aero_surf, ustar_surf )
4221
4222	bud_luw(lsp) = - conc_ijk(lsp) * ( 1.0_wp - EXP( - vd_lu * dt_dh ) ) * dh
4223
4224	ELSEIF ( spc_names(lsp) == 'PM25' ) THEN
4225	part_type = 2
4226	!
4227	!-- Sedimentation velocity:
4228	vs = slinnfac * sedimentation_velocity( particle_pars(ind_p_dens, part_type), &
4229	particle_pars(ind_p_size, part_type), &
4230	particle_pars(ind_p_slip, part_type), &
4231	visc)
4232
4233	CALL drydepo_aero_zhang_vd( vd_lu, rs, &
4234	vs, &
4235	particle_pars(ind_p_size, part_type), &
4236	particle_pars(ind_p_slip, part_type), &
4237	nwet, temp_tmp, dens, visc, &
4238	luw_dep, &
4239	r_aero_surf, ustar_surf )
4240
4241	bud_luw(lsp) = - conc_ijk(lsp) * ( 1.0_wp - EXP( - vd_lu * dt_dh ) ) * dh
4242
4243	ELSE !<GASES
4244	!
4245	!-- Read spc_name of current species for gas PARAMETER
4246	IF ( ANY(pspecnames(:) == spc_names(lsp) ) ) THEN
4247	i_pspec = 0
4248	DO pspec = 1, nposp
4249	IF ( pspecnames(pspec) == spc_names(lsp) ) THEN
4250	i_pspec = pspec
4251	END IF
4252	ENDDO
4253
4254	ELSE
4255	!
4256	!-- For now species not deposited
4257	CYCLE
4258	ENDIF
4259	!
4260	!-- Factor used for conversion from ppb to ug/m3 :
4261	!-- ppb (mole tr)/(mole air)/ppb (kg tr)/(mole tr) (ug tr)/(kg tr) &
4262	!-- (mole air)/(kg air) (kg air)/(m3 air) (kg air(ug/m3)/ppb/(kg/mole) = / (kg/mole)
4263	!-- c 1e-9 xm_tracer 1e9 / xm_air dens
4264	!-- thus:
4265	!-- c_in_ppb * xm_tracer * [ dens / xm_air ] = c_in_ugm3
4266	!-- Use density at lowest layer:
4267	ppm2ugm3 = (dens/xm_air) * 0.001_wp !< (mole air)/m3
4268	!
4269	!-- Atmospheric concentration in DEPAC is requested in ug/m3:
4270	!-- ug/m3 ppm (ug/m3)/ppm/(kg/mole) kg/mole
4271	conc_ijk_ugm3 = conc_ijk(lsp) * ppm2ugm3 * specmolm(i_pspec) ! in ug/m3
4272	!
4273	!-- Diffusivity for DEPAC relevant gases
4274	!-- Use default value
4275	diffusivity = 0.11e-4
4276	!
4277	!-- Overwrite with known coefficients of diffusivity from Massman (1998)
4278	IF ( spc_names(lsp) == 'NO2' ) diffusivity = 0.136e-4
4279	IF ( spc_names(lsp) == 'NO' ) diffusivity = 0.199e-4
4280	IF ( spc_names(lsp) == 'O3' ) diffusivity = 0.144e-4
4281	IF ( spc_names(lsp) == 'CO' ) diffusivity = 0.176e-4
4282	IF ( spc_names(lsp) == 'SO2' ) diffusivity = 0.112e-4
4283	IF ( spc_names(lsp) == 'CH4' ) diffusivity = 0.191e-4
4284	IF ( spc_names(lsp) == 'NH3' ) diffusivity = 0.191e-4
4285	!
4286	!-- Get quasi-laminar boundary layer resistance rb:
4287	CALL get_rb_cell( ( luw_dep == ilu_water_sea ) .OR. &
4288	( luw_dep == ilu_water_inland ), z0h_surf, ustar_surf, &
4289	diffusivity, rb )
4290
4291	!-- Get rc_tot
4292	CALL drydepos_gas_depac( spc_names(lsp), day_of_year, latitude, ts, ustar_surf, &
4293	solar_rad, cos_zenith, rh_surf, lai, sai, nwet, luw_dep, &
4294	2, rc_tot, ccomp_tot(lsp), hyp(nzb), conc_ijk_ugm3, &
4295	diffusivity, r_aero_surf , rb )
4296	!
4297	!-- Calculate budget
4298	IF ( rc_tot <= 0.0 ) THEN
4299
4300	bud_luw(lsp) = 0.0_wp
4301
4302	ELSE
4303
4304	vd_lu = 1.0_wp / (r_aero_surf + rb + rc_tot )
4305
4306	bud_luw(lsp) = - ( conc_ijk(lsp) - ccomp_tot(lsp) ) * &
4307	( 1.0_wp - EXP(-vd_lu * dt_dh ) ) * dh
4308	ENDIF
4309
4310	ENDIF
4311	ENDDO
4312	ENDIF
4313
4314
4315	bud = 0.0_wp
4316	!
4317	!-- Calculate overall budget for surface m and adapt concentration
4318	DO lsp = 1, nspec
4319
4320	bud(lsp) = surf_lsm_h(0)%frac(m,ind_veg_wall) * bud_luv(lsp) + &
4321	surf_lsm_h(0)%frac(m,ind_pav_green) * bud_lup(lsp) + &
4322	surf_lsm_h(0)%frac(m,ind_wat_win) * bud_luw(lsp)
4323	!
4324	!-- Compute new concentration:
4325	conc_ijk(lsp) = conc_ijk(lsp) + bud(lsp) * inv_dh
4326
4327	chem_species(lsp)%conc(k,j,i) = MAX( 0.0_wp, conc_ijk(lsp) )
4328
4329	ENDDO
4330
4331	ENDIF
4332	!
4333	!-- For USM surfaces
4334	IF ( match_usm ) THEN
4335	!
4336	!-- Get surface element information at i,j:
4337	m = surf_usm_h(0)%start_index(j,i)
4338	k = surf_usm_h(0)%k(m)
4339	!
4340	!-- Get needed variables for surface element m
4341	ustar_surf = surf_usm_h(0)%us(m)
4342	z0h_surf = surf_usm_h(0)%z0h(m)
4343	r_aero_surf = surf_usm_h(0)%r_a(m)
4344	solar_rad = surf_usm_h(0)%rad_sw_dir(m) + surf_usm_h(0)%rad_sw_dif(m)
4345	lai = surf_usm_h(0)%lai(m)
4346	sai = lai + 1
4347	!
4348	!-- For small grid spacing neglect R_a
4349	IF ( dzw(k) <= 1.0 ) THEN
4350	r_aero_surf = 0.0_wp
4351	ENDIF
4352	!
4353	!-- Initialize lu's
4354	luu_palm = 0
4355	luu_dep = 0
4356	lug_palm = 0
4357	lug_dep = 0
4358	lud_palm = 0
4359	lud_dep = 0
4360	!
4361	!-- Initialize budgets
4362	bud_luu = 0.0_wp
4363	bud_lug = 0.0_wp
4364	bud_lud = 0.0_wp
4365	!
4366	!-- Get land use for i,j and assign to DEPAC lu
4367	IF ( surf_usm_h(0)%frac(m,ind_pav_green) > 0 ) THEN
4368	!
4369	!-- For green urban surfaces (e.g. green roofs assume LU short grass
4370	lug_palm = ind_luv_s_grass
4371	IF ( lug_palm == ind_luv_user ) THEN
4372	message_string = 'No usm-vegetation type defined. Please define vegetation type to' //&
4373	' enable deposition calculation'
4374	CALL message( 'chem_depo', 'PA0738', 1, 2, 0, 6, 0 )
4375	ELSEIF ( lug_palm == ind_luv_b_soil ) THEN
4376	lug_dep = 9
4377	ELSEIF ( lug_palm == ind_luv_mixed_crops ) THEN
4378	lug_dep = 2
4379	ELSEIF ( lug_palm == ind_luv_s_grass ) THEN
4380	lug_dep = 1
4381	ELSEIF ( lug_palm == ind_luv_ev_needle_trees ) THEN
4382	lug_dep = 4
4383	ELSEIF ( lug_palm == ind_luv_de_needle_trees ) THEN
4384	lug_dep = 4
4385	ELSEIF ( lug_palm == ind_luv_ev_broad_trees ) THEN
4386	lug_dep = 12
4387	ELSEIF ( lug_palm == ind_luv_de_broad_trees ) THEN
4388	lug_dep = 5
4389	ELSEIF ( lug_palm == ind_luv_t_grass ) THEN
4390	lug_dep = 1
4391	ELSEIF ( lug_palm == ind_luv_desert ) THEN
4392	lug_dep = 9
4393	ELSEIF ( lug_palm == ind_luv_tundra ) THEN
4394	lug_dep = 8
4395	ELSEIF ( lug_palm == ind_luv_irr_crops ) THEN
4396	lug_dep = 2
4397	ELSEIF ( lug_palm == ind_luv_semidesert ) THEN
4398	lug_dep = 8
4399	ELSEIF ( lug_palm == ind_luv_ice ) THEN
4400	lug_dep = 10
4401	ELSEIF ( lug_palm == ind_luv_marsh ) THEN
4402	lug_dep = 8
4403	ELSEIF ( lug_palm == ind_luv_ev_shrubs ) THEN
4404	lug_dep = 14
4405	ELSEIF ( lug_palm == ind_luv_de_shrubs ) THEN
4406	lug_dep = 14
4407	ELSEIF ( lug_palm == ind_luv_mixed_forest ) THEN
4408	lug_dep = 4
4409	ELSEIF ( lug_palm == ind_luv_intrup_forest ) THEN
4410	lug_dep = 8
4411	ENDIF
4412	ENDIF
4413
4414	IF ( surf_usm_h(0)%frac(m,ind_veg_wall) > 0 ) THEN
4415	!
4416	!-- For walls in USM assume concrete walls/roofs,
4417	!-- assumed LU class desert as also assumed for pavements in LSM
4418	luu_palm = ind_lup_conc
4419	IF ( luu_palm == ind_lup_user ) THEN
4420	message_string = 'No pavement type defined. Please define pavement type to enable' // &
4421	' deposition calculation'
4422	CALL message( 'chem_depo', 'PA0739', 1, 2, 0, 6, 0 )
4423	ELSEIF ( luu_palm == ind_lup_asph_conc ) THEN
4424	luu_dep = 9
4425	ELSEIF ( luu_palm == ind_lup_asph ) THEN
4426	luu_dep = 9
4427	ELSEIF ( luu_palm == ind_lup_conc ) THEN
4428	luu_dep = 9
4429	ELSEIF ( luu_palm == ind_lup_sett ) THEN
4430	luu_dep = 9
4431	ELSEIF ( luu_palm == ind_lup_pav_stones ) THEN
4432	luu_dep = 9
4433	ELSEIF ( luu_palm == ind_lup_cobblest ) THEN
4434	luu_dep = 9
4435	ELSEIF ( luu_palm == ind_lup_metal ) THEN
4436	luu_dep = 9
4437	ELSEIF ( luu_palm == ind_lup_wood ) THEN
4438	luu_dep = 9
4439	ELSEIF ( luu_palm == ind_lup_gravel ) THEN
4440	luu_dep = 9
4441	ELSEIF ( luu_palm == ind_lup_f_gravel ) THEN
4442	luu_dep = 9
4443	ELSEIF ( luu_palm == ind_lup_pebblest ) THEN
4444	luu_dep = 9
4445	ELSEIF ( luu_palm == ind_lup_woodchips ) THEN
4446	luu_dep = 9
4447	ELSEIF ( luu_palm == ind_lup_tartan ) THEN
4448	luu_dep = 9
4449	ELSEIF ( luu_palm == ind_lup_art_turf ) THEN
4450	luu_dep = 9
4451	ELSEIF ( luu_palm == ind_lup_clay ) THEN
4452	luu_dep = 9
4453	ENDIF
4454	ENDIF
4455
4456	IF ( surf_usm_h(0)%frac(m,ind_wat_win) > 0 ) THEN
4457	!
4458	!-- For windows in USM assume metal as this is as close as we get, assumed LU class desert as
4459	!-- also assumed for pavements in LSM.
4460	lud_palm = ind_lup_metal
4461	IF ( lud_palm == ind_lup_user ) THEN
4462	message_string = 'No usm-pavement type defined. Please define pavement type to ' // &
4463	'enable deposition calculation'
4464	CALL message( 'chem_depo', 'PA0738', 1, 2, 0, 6, 0 )
4465	ELSEIF ( lud_palm == ind_lup_asph_conc ) THEN
4466	lud_dep = 9
4467	ELSEIF ( lud_palm == ind_lup_asph ) THEN
4468	lud_dep = 9
4469	ELSEIF ( lud_palm == ind_lup_conc ) THEN
4470	lud_dep = 9
4471	ELSEIF ( lud_palm == ind_lup_sett ) THEN
4472	lud_dep = 9
4473	ELSEIF ( lud_palm == ind_lup_pav_stones ) THEN
4474	lud_dep = 9
4475	ELSEIF ( lud_palm == ind_lup_cobblest ) THEN
4476	lud_dep = 9
4477	ELSEIF ( lud_palm == ind_lup_metal ) THEN
4478	lud_dep = 9
4479	ELSEIF ( lud_palm == ind_lup_wood ) THEN
4480	lud_dep = 9
4481	ELSEIF ( lud_palm == ind_lup_gravel ) THEN
4482	lud_dep = 9
4483	ELSEIF ( lud_palm == ind_lup_f_gravel ) THEN
4484	lud_dep = 9
4485	ELSEIF ( lud_palm == ind_lup_pebblest ) THEN
4486	lud_dep = 9
4487	ELSEIF ( lud_palm == ind_lup_woodchips ) THEN
4488	lud_dep = 9
4489	ELSEIF ( lud_palm == ind_lup_tartan ) THEN
4490	lud_dep = 9
4491	ELSEIF ( lud_palm == ind_lup_art_turf ) THEN
4492	lud_dep = 9
4493	ELSEIF ( lud_palm == ind_lup_clay ) THEN
4494	lud_dep = 9
4495	ENDIF
4496	ENDIF
4497	!
4498	!-- @TODO: Activate these lines as soon as new ebsolver branch is merged:
4499	!-- Set wetness indicator to dry or wet for usm vegetation or pavement
4500	!IF ( surf_usm_h(0)%c_liq(m) > 0 ) THEN
4501	! nwet = 1
4502	!ELSE
4503	nwet = 0
4504	!ENDIF
4505	!
4506	!-- Compute length of time step
4507	IF ( call_chem_at_all_substeps ) THEN
4508	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
4509	ELSE
4510	dt_chem = dt_3d
4511	ENDIF
4512
4513	dh = dzw(k)
4514	inv_dh = 1.0_wp / dh
4515	dt_dh = dt_chem / dh
4516	!
4517	!-- Concentration at i,j,k
4518	DO lsp = 1, nspec
4519	conc_ijk(lsp) = chem_species(lsp)%conc(k,j,i)
4520	ENDDO
4521	!
4522	!-- Temperature at i,j,k
4523	temp_tmp = pt(k,j,i) * ( hyp(k) / 100000.0_wp )**0.286_wp
4524
4525	ts = temp_tmp - 273.15 !< in degrees celcius
4526	!
4527	!-- Viscosity of air
4528	visc = 1.496e-6 * temp_tmp**1.5 / ( temp_tmp + 120.0 )
4529	!
4530	!-- Air density at k
4531	dens = rho_air_zw(k)
4532	!
4533	!-- Calculate relative humidity from specific humidity for DEPAC
4534	qv_tmp = MAX( q(k,j,i), 0.0_wp )
4535	rh_surf = relativehumidity_from_specifichumidity( qv_tmp, temp_tmp, hyp(k) )
4536	!
4537	!-- Check if surface fraction (vegetation, pavement or water) > 0 and calculate vd and budget for
4538	!-- each surface fraction. Then derive overall budget taking into account the surface fractions.
4539
4540	!-- Walls/roofs
4541	IF ( surf_usm_h(0)%frac(m,ind_veg_wall) > 0 ) THEN
4542	!
4543	!-- No vegetation on non-green walls:
4544	lai = 0.0_wp
4545	sai = 0.0_wp
4546
4547	slinnfac = 1.0_wp
4548	!
4549	!-- Get vd
4550	DO lsp = 1, nvar
4551	!
4552	!-- Initialize
4553	vs = 0.0_wp
4554	vd_lu = 0.0_wp
4555	rs = 0.0_wp
4556	rb = 0.0_wp
4557	rc_tot = 0.0_wp
4558	IF (spc_names(lsp) == 'PM10' ) THEN
4559	part_type = 1
4560	!
4561	!-- Sedimentation velocity
4562	vs = slinnfac * sedimentation_velocity( particle_pars(ind_p_dens, part_type), &
4563	particle_pars(ind_p_size, part_type), &
4564	particle_pars(ind_p_slip, part_type), &
4565	visc)
4566
4567	CALL drydepo_aero_zhang_vd( vd_lu, rs, &
4568	vs, &
4569	particle_pars(ind_p_size, part_type), &
4570	particle_pars(ind_p_slip, part_type), &
4571	nwet, temp_tmp, dens, visc, &
4572	luu_dep, &
4573	r_aero_surf, ustar_surf )
4574
4575	bud_luu(lsp) = - conc_ijk(lsp) * ( 1.0_wp - EXP( - vd_lu * dt_dh ) ) * dh
4576
4577	ELSEIF ( spc_names(lsp) == 'PM25' ) THEN
4578	part_type = 2
4579	!
4580	!-- Sedimentation velocity
4581	vs = slinnfac * sedimentation_velocity( particle_pars(ind_p_dens, part_type), &
4582	particle_pars(ind_p_size, part_type), &
4583	particle_pars(ind_p_slip, part_type), &
4584	visc)
4585
4586	CALL drydepo_aero_zhang_vd( vd_lu, rs, &
4587	vs, &
4588	particle_pars(ind_p_size, part_type), &
4589	particle_pars(ind_p_slip, part_type), &
4590	nwet, temp_tmp, dens, visc, &
4591	luu_dep , &
4592	r_aero_surf, ustar_surf )
4593
4594	bud_luu(lsp) = - conc_ijk(lsp) * ( 1.0_wp - EXP( - vd_lu * dt_dh ) ) * dh
4595
4596	ELSE�