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source: palm/trunk/SOURCE/chemistry_model_mod.f90 @ 3435

Last change on this file since 3435 was 3435, checked in by gronemeier, 6 years ago
new: terrain-following masked output; bugfixes: increase vertical dimension of gamma_w_green_sat by 1, add checks for masked output for chemistry_model and radiation_model, reordered calls to xxx_define_netcdf_grid in masked output part
Property svn:keywords set to `Id`
File size: 98.4 KB

Rev	Line
[2425]	1	!> @file chemistry_model_mod.f90
	2	!------------------------------------------------------------------------------!
[2828]	3	! This file is part of the PALM model system.
[2425]	4	!
	5	! PALM is free software: you can redistribute it and/or modify it under the
	6	! terms of the GNU General Public License as published by the Free Software
	7	! Foundation, either version 3 of the License, or (at your option) any later
	8	! version.
	9	!
	10	! PALM is distributed in the hope that it will be useful, but WITHOUT ANY
	11	! WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
	12	! A PARTICULAR PURPOSE. See the GNU General Public License for more details.
	13	!
	14	! You should have received a copy of the GNU General Public License along with
	15	! PALM. If not, see <http://www.gnu.org/licenses/>.
	16	!
[3298]	17	! Copyright 2017-2018 Leibniz Universitaet Hannover
[2828]	18	! Copyright 2017-2018 Karlsruhe Institute of Technology
	19	! Copyright 2017-2018 Freie Universitaet Berlin
[2425]	20	!------------------------------------------------------------------------------!
	21	!
	22	! Current revisions:
	23	! -----------------
[3298]	24	!
	25	!
	26	! Former revisions:
	27	! -----------------
	28	! $Id: chemistry_model_mod.f90 3435 2018-10-26 18:25:44Z gronemeier $
[3435]	29	! Add terrain-following masked output
	30	!
	31	! 3373 2018-10-18 15:25:56Z kanani
[3373]	32	! Remove MPI_Abort, replace by message
	33	!
	34	! 3318 2018-10-08 11:43:01Z sward
[3318]	35	! Fixed faulty syntax of message string
	36	!
	37	! 3298 2018-10-02 12:21:11Z kanani
[3298]	38	! Add remarks (kanani)
[3292]	39	! Merge with trunk, replaced cloud_physics by bulk_cloud_model 28.09.2018 forkel
[3281]	40	! Subroutines header and chem_check_parameters added 25.09.2018 basit
[3190]	41	! Removed chem_emission routine now declared in chem_emissions.f90 30.07.2018 ERUSSO
	42	! Introduced emissions namelist parameters 30.07.2018 ERUSSO
[3188]	43	!
	44	! Timestep steering added in subroutine chem_integrate_ij and
	45	! output of chosen solver in chem_parin added 30.07.2018 ketelsen
	46	!
	47	! chem_check_data_output_pr: added unit for PM compounds 20.07.2018 forkel
	48	! replaced : by nzb+1:nzt for pt,q,ql (found by kk) 18.07.2018 forkel
[3140]	49	! debugged restart run for chem species 06.07.2018 basit
	50	! reorganized subroutines in alphabetical order. 27.06.2018 basit
	51	! subroutine chem_parin updated for profile output 27.06.2018 basit
[3114]	52	! Added humidity arrays to USE section and tmp_qvap in chem_integrate 26.6.2018 forkel
	53	! Merged chemistry with with trunk (nzb_do and nzt_do in 3d output) 26.6.2018 forkel
	54	!
[3140]	55	! reorganized subroutines in alphabetical order. basit 22.06.2018
	56	! subroutine chem_parin updated for profile output basit 22.06.2018
	57	! subroutine chem_statistics added
	58	! subroutine chem_check_data_output_pr add 21.06.2018 basit
	59	! subroutine chem_data_output_mask added 20.05.2018 basit
	60	! subroutine chem_data_output_2d added 20.05.2018 basit
	61	! subroutine chem_statistics added 04.06.2018 basit
[2914]	62	! subroutine chem_emissions: Set cssws to zero before setting values 20.03.2018 forkel
[2900]	63	! subroutine chem_emissions: Introduced different conversion factors
	64	! for PM and gaseous compounds 15.03.2018 forkel
[2888]	65	! subroutine chem_emissions updated to take variable number of chem_spcs and
[3140]	66	! emission factors. 13.03.2018 basit
	67	! chem_boundary_conds_decycle improved. 05.03.2018 basit
	68	! chem_boundary_conds_decycle subroutine added 21.02.2018 basit
[3188]	69	! chem_init_profiles subroutines re-activated after correction 21.02.2018 basit
[2616]	70	!
[2828]	71	!
[3298]	72	! 3293 2018-09-28 12:45:20Z forkel
[3287]	73	! Modularization of all bulk cloud physics code components
	74	!
	75	! 3248 2018-09-14 09:42:06Z sward
	76	! Minor formating changes
	77	!
	78	! 3246 2018-09-13 15:14:50Z sward
	79	! Added error handling for input namelist via parin_fail_message
	80	!
	81	! 3241 2018-09-12 15:02:00Z raasch
[3228]	82	! +nest_chemistry
	83	!
	84	! 3209 2018-08-27 16:58:37Z suehring
	85	! Rename flags indicating outflow boundary conditions
	86	!
	87	! 3182 2018-07-27 13:36:03Z suehring
	88	! Revise output of surface quantities in case of overhanging structures
	89	!
	90	! 3045 2018-05-28 07:55:41Z Giersch
[3114]	91	! error messages revised
	92	!
	93	! 3014 2018-05-09 08:42:38Z maronga
	94	! Bugfix: nzb_do and nzt_do were not used for 3d data output
	95	!
	96	! 3004 2018-04-27 12:33:25Z Giersch
	97	! Comment concerning averaged data output added
	98	!
	99	! 2932 2018-03-26 09:39:22Z maronga
[2981]	100	! renamed chemistry_par to chemistry_parameters
	101	!
	102	! 2894 2018-03-15 09:17:58Z Giersch
[2914]	103	! Calculations of the index range of the subdomain on file which overlaps with
	104	! the current subdomain are already done in read_restart_data_mod,
	105	! chem_last_actions was renamed to chem_wrd_local, chem_read_restart_data was
	106	! renamed to chem_rrd_local, chem_write_var_list was renamed to
	107	! chem_wrd_global, chem_read_var_list was renamed to chem_rrd_global,
	108	! chem_skip_var_list has been removed, variable named found has been
	109	! introduced for checking if restart data was found, reading of restart strings
	110	! has been moved completely to read_restart_data_mod, chem_rrd_local is already
	111	! inside the overlap loop programmed in read_restart_data_mod, todo list has
	112	! bees extended, redundant characters in chem_wrd_local have been removed,
	113	! the marker * end chemistry * is not necessary anymore, strings and their
	114	! respective lengths are written out and read now in case of restart runs to
	115	! get rid of prescribed character lengths
	116	!
	117	! 2815 2018-02-19 11:29:57Z suehring
[2828]	118	! Bugfix in restart mechanism,
	119	! rename chem_tendency to chem_prognostic_equations,
	120	! implement vector-optimized version of chem_prognostic_equations,
	121	! some clean up (incl. todo list)
[2656]	122	!
[2828]	123	! 2773 2018-01-30 14:12:54Z suehring
	124	! Declare variables required for nesting as public
[2656]	125	!
[2828]	126	! 2772 2018-01-29 13:10:35Z suehring
	127	! Bugfix in string handling
[2635]	128	!
[2828]	129	! 2768 2018-01-24 15:38:29Z kanani
	130	! Shorten lines to maximum length of 132 characters
[2633]	131	!
[2828]	132	! 2766 2018-01-22 17:17:47Z kanani
	133	! Removed preprocessor directive __chem
[2633]	134	!
[2828]	135	! 2756 2018-01-16 18:11:14Z suehring
	136	! Fill values in 3D output introduced.
[2627]	137	!
[2828]	138	! 2718 2018-01-02 08:49:38Z maronga
	139	! Initial revision
	140	!
[2452]	141	!
[2828]	142	!
	143	!
	144	! Authors:
	145	! --------
	146	! @author Renate Forkel
	147	! @author Farah Kanani-Suehring
	148	! @author Klaus Ketelsen
	149	! @author Basit Khan
	150	!
	151	!
[2426]	152	!------------------------------------------------------------------------------!
[2425]	153	! Description:
	154	! ------------
[2592]	155	!> Chemistry model for PALM-4U
[2914]	156	!> @todo Adjust chem_rrd_local to CASE structure of others modules. It is not
	157	!> allowed to use the chemistry model in a precursor run and additionally
	158	!> not using it in a main run
[2828]	159	!> @todo Update/clean-up todo list! (FK)
	160	!> @todo Set proper fill values (/= 0) for chem output arrays! (FK)
	161	!> @todo Add routine chem_check_parameters, add checks for inconsistent or
	162	!> unallowed parameter settings.
	163	!> CALL of chem_check_parameters from check_parameters. (FK)
	164	!> @todo Make routine chem_header available, CALL from header.f90
	165	!> (see e.g. how it is done in routine lsm_header in
	166	!> land_surface_model_mod.f90). chem_header should include all setup
	167	!> info about chemistry parameter settings. (FK)
[2592]	168	!> @todo Implement turbulent inflow of chem spcs in inflow_turbulence.
	169	!> @todo Separate boundary conditions for each chem spcs to be implemented
	170	!> @todo Currently only total concentration are calculated. Resolved, parameterized
	171	!> and chemistry fluxes although partially and some completely coded but
	172	!> are not operational/activated in this version. bK.
	173	!> @todo slight differences in passive scalar and chem spcs when chem reactions
	174	!> turned off. Need to be fixed. bK
[2828]	175	!> @todo test nesting for chem spcs, was implemented by suehring (kanani)
[2592]	176	!> @todo chemistry error messages
[2425]	177	!> @todo Format this module according to PALM coding standard (see e.g. module
	178	!> template under http://palm.muk.uni-hannover.de/mosaik/downloads/8 or
	179	!> D3_coding_standard.pdf under https://palm.muk.uni-hannover.de/trac/downloads/16)
[2482]	180	!
[2425]	181	!------------------------------------------------------------------------------!
	182
[3281]	183	MODULE chemistry_model_mod
[2828]	184
[3281]	185	USE kinds, ONLY: wp, iwp
[3282]	186	USE indices, ONLY: nz, nzb,nzt,nysg,nyng,nxlg,nxrg, &
[3114]	187	nys,nyn,nx,nxl,nxr,ny,wall_flags_0
[3281]	188	USE pegrid, ONLY: myid, threads_per_task
[3293]	189
	190	USE bulk_cloud_model_mod, &
	191	ONLY: bulk_cloud_model
	192
	193	USE control_parameters, ONLY: bc_lr_cyc, bc_ns_cyc, dt_3d, humidity, &
[3282]	194	initializing_actions, message_string, &
	195	omega, tsc, intermediate_timestep_count, &
	196	intermediate_timestep_count_max, &
[3287]	197	timestep_scheme, use_prescribed_profile_data, ws_scheme_sca
	198	USE arrays_3d, ONLY: exner, hyp, pt, q, ql, rdf_sc, tend, zu
[3282]	199	USE chem_gasphase_mod, ONLY: nspec, spc_names, nkppctrl, nmaxfixsteps, &
	200	t_steps, chem_gasphase_integrate, vl_dim, &
	201	nvar, nreact, atol, rtol, nphot, phot_names
[3281]	202	USE cpulog, ONLY: cpu_log, log_point
[2425]	203
[3281]	204	USE chem_modules
[2615]	205
[3281]	206	USE statistics
[2615]	207
[3281]	208	IMPLICIT NONE
	209	PRIVATE
	210	SAVE
[2425]	211
[3281]	212	LOGICAL :: nest_chemistry = .TRUE. !< flag for nesting mode of chemical species, independent on parent or not
[3228]	213	!
[2425]	214	!- Define chemical variables
[3281]	215	TYPE species_def
	216	CHARACTER(LEN=8) :: name
	217	CHARACTER(LEN=16) :: unit
	218	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc
	219	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_av
	220	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_p
	221	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: tconc_m
	222	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: cssws_av
	223	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: flux_s_cs
	224	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: diss_s_cs
	225	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: flux_l_cs
	226	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: diss_l_cs
	227	REAL(kind=wp),ALLOCATABLE,DIMENSION(:) :: conc_pr_init
	228	END TYPE species_def
[2425]	229
[2592]	230
[3281]	231	TYPE photols_def
	232	CHARACTER(LEN=8) :: name
	233	CHARACTER(LEN=16) :: unit
	234	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: freq
	235	END TYPE photols_def
[2425]	236
	237
[3281]	238	PUBLIC species_def
	239	PUBLIC photols_def
[2425]	240
[3228]	241
[3281]	242	TYPE(species_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: chem_species
	243	TYPE(photols_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: phot_frequen
[2425]	244
[3281]	245	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_1
	246	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_2
	247	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_3
	248	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_av
	249	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: freq_1
[2425]	250
[3281]	251	INTEGER,DIMENSION(nkppctrl) :: icntrl ! Fine tuning kpp
	252	REAL(kind=wp),DIMENSION(nkppctrl) :: rcntrl ! Fine tuning kpp
	253	LOGICAL :: decycle_chem_lr = .FALSE.
	254	LOGICAL :: decycle_chem_ns = .FALSE.
	255	CHARACTER (LEN=20), DIMENSION(4) :: decycle_method = &
[2854]	256	(/'dirichlet','dirichlet','dirichlet','dirichlet'/)
	257	!< Decycling method at horizontal boundaries,
	258	!< 1=left, 2=right, 3=south, 4=north
	259	!< dirichlet = initial size distribution and
	260	!< chemical composition set for the ghost and
	261	!< first three layers
	262	!< neumann = zero gradient
[2425]	263
[3282]	264	REAL(kind=wp), PUBLIC :: cs_time_step
[3281]	265	CHARACTER(10), PUBLIC :: photolysis_scheme
[3114]	266	! 'constant',
[2592]	267	! 'simple' (Simple parameterisation from MCM, Saunders et al., 2003, Atmos. Chem. Phys., 3, 161-180
	268	! 'fastj' (Wild et al., 2000, J. Atmos. Chem., 37, 245-282) STILL NOT IMPLEMENTED
[2535]	269
[3281]	270	PUBLIC nest_chemistry
	271	PUBLIC nspec
[3282]	272	PUBLIC nreact
[3281]	273	PUBLIC nvar
	274	PUBLIC spc_names
	275	PUBLIC spec_conc_2
[2425]	276
[3281]	277	!- Interface section
	278	INTERFACE chem_3d_data_averaging
	279	MODULE PROCEDURE chem_3d_data_averaging
	280	END INTERFACE chem_3d_data_averaging
[3228]	281
[3281]	282	INTERFACE chem_boundary_conds
	283	MODULE PROCEDURE chem_boundary_conds
	284	MODULE PROCEDURE chem_boundary_conds_decycle
	285	END INTERFACE chem_boundary_conds
[2425]	286
[3281]	287	INTERFACE chem_check_data_output
	288	MODULE PROCEDURE chem_check_data_output
	289	END INTERFACE chem_check_data_output
[2425]	290
[3281]	291	INTERFACE chem_data_output_2d
	292	MODULE PROCEDURE chem_data_output_2d
	293	END INTERFACE chem_data_output_2d
[2425]	294
[3281]	295	INTERFACE chem_data_output_3d
	296	MODULE PROCEDURE chem_data_output_3d
	297	END INTERFACE chem_data_output_3d
[2425]	298
[3281]	299	INTERFACE chem_data_output_mask
	300	MODULE PROCEDURE chem_data_output_mask
	301	END INTERFACE chem_data_output_mask
[3085]	302
[3281]	303	INTERFACE chem_check_data_output_pr
	304	MODULE PROCEDURE chem_check_data_output_pr
	305	END INTERFACE chem_check_data_output_pr
[3085]	306
[3281]	307	INTERFACE chem_check_parameters
	308	MODULE PROCEDURE chem_check_parameters
	309	END INTERFACE chem_check_parameters
[2425]	310
[3281]	311	INTERFACE chem_define_netcdf_grid
	312	MODULE PROCEDURE chem_define_netcdf_grid
	313	END INTERFACE chem_define_netcdf_grid
[2425]	314
[3281]	315	INTERFACE chem_header
	316	MODULE PROCEDURE chem_header
	317	END INTERFACE chem_header
[2425]	318
[3281]	319	INTERFACE chem_init
	320	MODULE PROCEDURE chem_init
	321	END INTERFACE chem_init
[2425]	322
[3281]	323	INTERFACE chem_init_profiles
	324	MODULE PROCEDURE chem_init_profiles
	325	END INTERFACE chem_init_profiles
[2425]	326
[3281]	327	INTERFACE chem_integrate
	328	MODULE PROCEDURE chem_integrate_ij
	329	END INTERFACE chem_integrate
[2425]	330
[3281]	331	INTERFACE chem_parin
	332	MODULE PROCEDURE chem_parin
	333	END INTERFACE chem_parin
[2425]	334
[3281]	335	INTERFACE chem_prognostic_equations
	336	MODULE PROCEDURE chem_prognostic_equations
	337	MODULE PROCEDURE chem_prognostic_equations_ij
	338	END INTERFACE chem_prognostic_equations
[3228]	339
[3281]	340	INTERFACE chem_rrd_local
	341	MODULE PROCEDURE chem_rrd_local
	342	END INTERFACE chem_rrd_local
[2467]	343
[3281]	344	INTERFACE chem_statistics
	345	MODULE PROCEDURE chem_statistics
	346	END INTERFACE chem_statistics
[3085]	347
[3281]	348	INTERFACE chem_swap_timelevel
	349	MODULE PROCEDURE chem_swap_timelevel
	350	END INTERFACE chem_swap_timelevel
	351
	352	INTERFACE chem_wrd_local
	353	MODULE PROCEDURE chem_wrd_local
	354	END INTERFACE chem_wrd_local
[2482]	355
[2615]	356
[3281]	357	PUBLIC chem_3d_data_averaging, chem_boundary_conds, chem_check_data_output, &
	358	chem_check_data_output_pr, chem_check_parameters, &
	359	chem_data_output_2d, chem_data_output_3d, chem_data_output_mask, &
	360	chem_define_netcdf_grid, chem_header, chem_init, &
	361	chem_init_profiles, chem_integrate, chem_parin, &
	362	chem_prognostic_equations, chem_rrd_local, &
	363	chem_statistics, chem_swap_timelevel, chem_wrd_local
[2425]	364
[3281]	365
	366
[2425]	367	CONTAINS
	368
[3228]	369	!
[2425]	370	!------------------------------------------------------------------------------!
[2535]	371	!
[2425]	372	! Description:
	373	! ------------
[3228]	374	!> Subroutine for averaging 3D data of chemical species. Due to the fact that
	375	!> the averaged chem arrays are allocated in chem_init, no if-query concerning
	376	!> the allocation is required (in any mode). Attention: If you just specify an
	377	!> averaged output quantity in the _p3dr file during restarts the first output
	378	!> includes the time between the beginning of the restart run and the first
	379	!> output time (not necessarily the whole averaging_interval you have
	380	!> specified in your _p3d/_p3dr file )
	381	!------------------------------------------------------------------------------!
	382
[3281]	383	SUBROUTINE chem_3d_data_averaging ( mode, variable )
[3228]	384
[3281]	385	USE control_parameters
[3228]	386
[3281]	387	USE indices
[3228]	388
[3281]	389	USE kinds
[3228]	390
[3281]	391	USE surface_mod, &
	392	ONLY: surf_def_h, surf_lsm_h, surf_usm_h
[3228]	393
[3281]	394	IMPLICIT NONE
[3228]	395
[3281]	396	CHARACTER (LEN=*) :: mode !<
	397	CHARACTER (LEN=*) :: variable !<
[3228]	398
[3281]	399	LOGICAL :: match_def !< flag indicating natural-type surface
	400	LOGICAL :: match_lsm !< flag indicating natural-type surface
	401	LOGICAL :: match_usm !< flag indicating urban-type surface
[3228]	402
[3281]	403	INTEGER(iwp) :: i !< grid index x direction
	404	INTEGER(iwp) :: j !< grid index y direction
	405	INTEGER(iwp) :: k !< grid index z direction
	406	INTEGER(iwp) :: m !< running index surface type
	407	INTEGER(iwp) :: lsp !< running index for chem spcs
[3228]	408
[3281]	409
	410	IF ( mode == 'allocate' ) THEN
	411	DO lsp = 1, nspec
	412	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	413	chem_species(lsp)%conc_av = 0.0_wp
	414
	415	ENDIF
	416	ENDDO
	417
	418	ELSEIF ( mode == 'sum' ) THEN
	419
	420
	421	DO lsp = 1, nspec
	422	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	423	DO i = nxlg, nxrg
	424	DO j = nysg, nyng
	425	DO k = nzb, nzt+1
	426	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) + &
	427	chem_species(lsp)%conc(k,j,i)
	428	ENDDO
[3228]	429	ENDDO
	430	ENDDO
[3281]	431	ELSEIF ( TRIM(variable(4:)) == TRIM('cssws*') ) THEN
	432	DO i = nxl, nxr
	433	DO j = nys, nyn
	434	match_def = surf_def_h(0)%start_index(j,i) <= &
	435	surf_def_h(0)%end_index(j,i)
	436	match_lsm = surf_lsm_h%start_index(j,i) <= &
	437	surf_lsm_h%end_index(j,i)
	438	match_usm = surf_usm_h%start_index(j,i) <= &
	439	surf_usm_h%end_index(j,i)
[3228]	440
[3281]	441	IF ( match_def ) THEN
	442	m = surf_def_h(0)%end_index(j,i)
	443	chem_species(lsp)%cssws_av(j,i) = &
	444	chem_species(lsp)%cssws_av(j,i) + &
	445	surf_def_h(0)%cssws(lsp,m)
	446	ELSEIF ( match_lsm .AND. .NOT. match_usm ) THEN
	447	m = surf_lsm_h%end_index(j,i)
	448	chem_species(lsp)%cssws_av(j,i) = &
	449	chem_species(lsp)%cssws_av(j,i) + &
	450	surf_lsm_h%cssws(lsp,m)
	451	ELSEIF ( match_usm ) THEN
	452	m = surf_usm_h%end_index(j,i)
	453	chem_species(lsp)%cssws_av(j,i) = &
	454	chem_species(lsp)%cssws_av(j,i) + &
	455	surf_usm_h%cssws(lsp,m)
	456	ENDIF
	457	ENDDO
[3228]	458	ENDDO
[3281]	459	ENDIF
	460	ENDDO
[3228]	461
[3281]	462	ELSEIF ( mode == 'average' ) THEN
	463	DO lsp = 1, nspec
	464	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	465	DO i = nxlg, nxrg
	466	DO j = nysg, nyng
	467	DO k = nzb, nzt+1
	468	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) / REAL( average_count_3d, KIND=wp )
	469	ENDDO
[3228]	470	ENDDO
	471	ENDDO
	472
[3281]	473	ELSEIF (TRIM(variable(4:)) == TRIM('cssws*') ) THEN
	474	DO i = nxlg, nxrg
	475	DO j = nysg, nyng
	476	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) / REAL( average_count_3d, KIND=wp )
	477	ENDDO
[3228]	478	ENDDO
[3281]	479	CALL exchange_horiz_2d( chem_species(lsp)%cssws_av, nbgp )
	480	ENDIF
	481	ENDDO
	482
	483	ENDIF
[3228]	484
[3281]	485	END SUBROUTINE chem_3d_data_averaging
	486
	487	!
[3228]	488	!------------------------------------------------------------------------------!
	489	!
	490	! Description:
	491	! ------------
[2535]	492	!> Subroutine to initialize and set all boundary conditions for chemical species
[2425]	493	!------------------------------------------------------------------------------!
	494
[3281]	495	SUBROUTINE chem_boundary_conds( mode )
	496
	497	USE control_parameters, &
	498	ONLY: air_chemistry, bc_radiation_l, bc_radiation_n, bc_radiation_r, &
	499	bc_radiation_s
	500	USE indices, &
	501	ONLY: nxl, nxr, nxlg, nxrg, nyng, nysg, nzt
	502
[2425]	503
[3281]	504	USE arrays_3d, &
	505	ONLY: dzu
	506	USE surface_mod, &
	507	ONLY: bc_h
[2425]	508
[3281]	509	CHARACTER (len=*), INTENT(IN) :: mode
	510	INTEGER(iwp) :: i !< grid index x direction.
	511	INTEGER(iwp) :: j !< grid index y direction.
	512	INTEGER(iwp) :: k !< grid index z direction.
	513	INTEGER(iwp) :: kb !< variable to set respective boundary value, depends on facing.
	514	INTEGER(iwp) :: l !< running index boundary type, for up- and downward-facing walls.
	515	INTEGER(iwp) :: m !< running index surface elements.
	516	INTEGER(iwp) :: lsp !< running index for chem spcs.
	517	INTEGER(iwp) :: lph !< running index for photolysis frequencies
[2425]	518
[2615]	519
[3281]	520	SELECT CASE ( TRIM( mode ) )
	521	CASE ( 'init' )
[2626]	522
[3281]	523	IF ( bc_cs_b == 'dirichlet' ) THEN
	524	ibc_cs_b = 0
	525	ELSEIF ( bc_cs_b == 'neumann' ) THEN
	526	ibc_cs_b = 1
	527	ELSE
	528	message_string = 'unknown boundary condition: bc_cs_b ="' // TRIM( bc_cs_b ) // '"'
	529	CALL message( 'chem_boundary_conds', 'CM0429', 1, 2, 0, 6, 0 ) !<
	530	ENDIF
[2425]	531	!
[3281]	532	!-- Set Integer flags and check for possible erroneous settings for top
	533	!-- boundary condition.
	534	IF ( bc_cs_t == 'dirichlet' ) THEN
	535	ibc_cs_t = 0
	536	ELSEIF ( bc_cs_t == 'neumann' ) THEN
	537	ibc_cs_t = 1
	538	ELSEIF ( bc_cs_t == 'initial_gradient' ) THEN
	539	ibc_cs_t = 2
	540	ELSEIF ( bc_cs_t == 'nested' ) THEN
	541	ibc_cs_t = 3
	542	ELSE
	543	message_string = 'unknown boundary condition: bc_c_t ="' // TRIM( bc_cs_t ) // '"'
	544	CALL message( 'check_parameters', 'CM0430', 1, 2, 0, 6, 0 )
	545	ENDIF
[2425]	546
[3281]	547
	548	CASE ( 'set_bc_bottomtop' )
	549	!-- Bottom boundary condtions for chemical species
	550	DO lsp = 1, nspec
	551	IF ( ibc_cs_b == 0 ) THEN
	552	DO l = 0, 1
	553	!-- Set index kb: For upward-facing surfaces (l=0), kb=-1, i.e.
[3282]	554	!-- the chem_species(nspec)%conc_p value at the topography top (k-1)
[3281]	555	!-- is set; for downward-facing surfaces (l=1), kb=1, i.e. the
	556	!-- value at the topography bottom (k+1) is set.
[2425]	557
[3281]	558	kb = MERGE( -1, 1, l == 0 )
	559	!$OMP PARALLEL DO PRIVATE( i, j, k )
	560	DO m = 1, bc_h(l)%ns
	561	i = bc_h(l)%i(m)
	562	j = bc_h(l)%j(m)
	563	k = bc_h(l)%k(m)
	564	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc(k+kb,j,i)
	565	ENDDO
	566	ENDDO
	567
	568	ELSEIF ( ibc_cs_b == 1 ) THEN
	569	!-- in boundary_conds there is som extra loop over m here for passive tracer
	570	DO l = 0, 1
	571	kb = MERGE( -1, 1, l == 0 )
	572	!$OMP PARALLEL DO PRIVATE( i, j, k )
	573	DO m = 1, bc_h(l)%ns
	574	i = bc_h(l)%i(m)
	575	j = bc_h(l)%j(m)
	576	k = bc_h(l)%k(m)
	577	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc_p(k,j,i)
[2535]	578
[3281]	579	ENDDO
[2615]	580	ENDDO
[3281]	581	ENDIF
[3287]	582	ENDDO ! end lsp loop
[3281]	583
[3287]	584	!-- Top boundary conditions for chemical species - Should this not be done for all species?
[3281]	585	IF ( ibc_cs_t == 0 ) THEN
	586	DO lsp = 1, nspec
	587	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc(nzt+1,:,:)
[2615]	588	ENDDO
[3281]	589	ELSEIF ( ibc_cs_t == 1 ) THEN
	590	DO lsp = 1, nspec
	591	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:)
	592	ENDDO
	593	ELSEIF ( ibc_cs_t == 2 ) THEN
	594	DO lsp = 1, nspec
	595	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:) + bc_cs_t_val(lsp) * dzu(nzt+1)
	596	ENDDO
[2615]	597	ENDIF
[2425]	598	!
[3281]	599	CASE ( 'set_bc_lateral' )
	600	!-- Lateral boundary conditions for chem species at inflow boundary
	601	!-- are automatically set when chem_species concentration is
	602	!-- initialized. The initially set value at the inflow boundary is not
	603	!-- touched during time integration, hence, this boundary value remains
	604	!-- at a constant value, which is the concentration that flows into the
	605	!-- domain.
	606	!-- Lateral boundary conditions for chem species at outflow boundary
[2535]	607
[3281]	608	IF ( bc_radiation_s ) THEN
	609	DO lsp = 1, nspec
	610	chem_species(lsp)%conc_p(:,nys-1,:) = chem_species(lsp)%conc_p(:,nys,:)
	611	ENDDO
	612	ELSEIF ( bc_radiation_n ) THEN
	613	DO lsp = 1, nspec
	614	chem_species(lsp)%conc_p(:,nyn+1,:) = chem_species(lsp)%conc_p(:,nyn,:)
	615	ENDDO
	616	ELSEIF ( bc_radiation_l ) THEN
	617	DO lsp = 1, nspec
	618	chem_species(lsp)%conc_p(:,:,nxl-1) = chem_species(lsp)%conc_p(:,:,nxl)
	619	ENDDO
	620	ELSEIF ( bc_radiation_r ) THEN
	621	DO lsp = 1, nspec
	622	chem_species(lsp)%conc_p(:,:,nxr+1) = chem_species(lsp)%conc_p(:,:,nxr)
	623	ENDDO
	624	ENDIF
	625
	626	END SELECT
[2535]	627
[3281]	628	END SUBROUTINE chem_boundary_conds
[2831]	629
[2425]	630	!
[2535]	631	!------------------------------------------------------------------------------!
[2831]	632	! Description:
	633	! ------------
	634	!> Boundary conditions for prognostic variables in chemistry: decycling in the
	635	!> x-direction
	636	!-----------------------------------------------------------------------------
[3281]	637	SUBROUTINE chem_boundary_conds_decycle (cs_3d, cs_pr_init )
	638	USE pegrid, &
	639	ONLY: myid
[2831]	640
[3281]	641	IMPLICIT NONE
	642	INTEGER(iwp) :: boundary !<
	643	INTEGER(iwp) :: ee !<
	644	INTEGER(iwp) :: copied !<
	645	INTEGER(iwp) :: i !<
	646	INTEGER(iwp) :: j !<
	647	INTEGER(iwp) :: k !<
	648	INTEGER(iwp) :: ss !<
	649	REAL(wp), DIMENSION(nzb:nzt+1) :: cs_pr_init
	650	REAL(wp), DIMENSION(nzb:nzt+1,nysg:nyng,nxlg:nxrg) :: cs_3d
	651	REAL(wp) :: flag !< flag to mask topography grid points
[2831]	652
[3281]	653	flag = 0.0_wp
[2854]	654
[3281]	655
	656	!-- Left and right boundaries
	657	IF ( decycle_chem_lr .AND. bc_lr_cyc ) THEN
[2854]	658
[3281]	659	DO boundary = 1, 2
[2854]	660
[3281]	661	IF ( decycle_method(boundary) == 'dirichlet' ) THEN
[2854]	662	!
[3281]	663	!-- Initial profile is copied to ghost and first three layers
	664	ss = 1
	665	ee = 0
	666	IF ( boundary == 1 .AND. nxl == 0 ) THEN
	667	ss = nxlg
	668	ee = nxl+2
	669	ELSEIF ( boundary == 2 .AND. nxr == nx ) THEN
	670	ss = nxr-2
	671	ee = nxrg
	672	ENDIF
[2854]	673
[3281]	674	DO i = ss, ee
	675	DO j = nysg, nyng
	676	DO k = nzb+1, nzt
	677	flag = MERGE( 1.0_wp, 0.0_wp, &
	678	BTEST( wall_flags_0(k,j,i), 0 ) )
	679	cs_3d(k,j,i) = cs_pr_init(k) * flag
	680	ENDDO
[2854]	681	ENDDO
[2831]	682	ENDDO
	683
[3281]	684	ELSEIF ( decycle_method(boundary) == 'neumann' ) THEN
[2854]	685	!
[3281]	686	!-- The value at the boundary is copied to the ghost layers to simulate
	687	!-- an outlet with zero gradient
	688	ss = 1
	689	ee = 0
	690	IF ( boundary == 1 .AND. nxl == 0 ) THEN
	691	ss = nxlg
	692	ee = nxl-1
	693	copied = nxl
	694	ELSEIF ( boundary == 2 .AND. nxr == nx ) THEN
	695	ss = nxr+1
	696	ee = nxrg
	697	copied = nxr
	698	ENDIF
[2854]	699
[3281]	700	DO i = ss, ee
	701	DO j = nysg, nyng
	702	DO k = nzb+1, nzt
	703	flag = MERGE( 1.0_wp, 0.0_wp, &
	704	BTEST( wall_flags_0(k,j,i), 0 ) )
	705	cs_3d(k,j,i) = cs_3d(k,j,copied) * flag
	706	ENDDO
[2854]	707	ENDDO
[2831]	708	ENDDO
[2854]	709
[3281]	710	ELSE
	711	WRITE(message_string,*) &
	712	'unknown decycling method: decycle_method (', &
	713	boundary, ') ="' // TRIM( decycle_method(boundary) ) // '"'
	714	CALL message( 'chem_boundary_conds_decycle', 'CM0431', &
	715	1, 2, 0, 6, 0 )
	716	ENDIF
	717	ENDDO
	718	ENDIF
[2831]	719
[3281]	720
	721	!-- South and north boundaries
	722	IF ( decycle_chem_ns .AND. bc_ns_cyc ) THEN
[2854]	723
[3281]	724	DO boundary = 3, 4
[2854]	725
[3281]	726	IF ( decycle_method(boundary) == 'dirichlet' ) THEN
[2854]	727	!
[3281]	728	!-- Initial profile is copied to ghost and first three layers
	729	ss = 1
	730	ee = 0
	731	IF ( boundary == 3 .AND. nys == 0 ) THEN
	732	ss = nysg
	733	ee = nys+2
	734	ELSEIF ( boundary == 4 .AND. nyn == ny ) THEN
	735	ss = nyn-2
	736	ee = nyng
	737	ENDIF
[2854]	738
[3281]	739	DO i = nxlg, nxrg
	740	DO j = ss, ee
	741	DO k = nzb+1, nzt
	742	flag = MERGE( 1.0_wp, 0.0_wp, &
	743	BTEST( wall_flags_0(k,j,i), 0 ) )
	744	cs_3d(k,j,i) = cs_pr_init(k) * flag
	745	ENDDO
[2854]	746	ENDDO
[2831]	747	ENDDO
[3281]	748
	749
	750	ELSEIF ( decycle_method(boundary) == 'neumann' ) THEN
[2854]	751	!
[3281]	752	!-- The value at the boundary is copied to the ghost layers to simulate
	753	!-- an outlet with zero gradient
	754	ss = 1
	755	ee = 0
	756	IF ( boundary == 3 .AND. nys == 0 ) THEN
	757	ss = nysg
	758	ee = nys-1
	759	copied = nys
	760	ELSEIF ( boundary == 4 .AND. nyn == ny ) THEN
	761	ss = nyn+1
	762	ee = nyng
	763	copied = nyn
	764	ENDIF
[2831]	765
[3281]	766	DO i = nxlg, nxrg
	767	DO j = ss, ee
	768	DO k = nzb+1, nzt
	769	flag = MERGE( 1.0_wp, 0.0_wp, &
	770	BTEST( wall_flags_0(k,j,i), 0 ) )
	771	cs_3d(k,j,i) = cs_3d(k,copied,i) * flag
	772	ENDDO
[2854]	773	ENDDO
[2831]	774	ENDDO
[2854]	775
[3281]	776	ELSE
	777	WRITE(message_string,*) &
	778	'unknown decycling method: decycle_method (', &
	779	boundary, ') ="' // TRIM( decycle_method(boundary) ) // '"'
	780	CALL message( 'chem_boundary_conds_decycle', 'CM0432', &
	781	1, 2, 0, 6, 0 )
	782	ENDIF
	783	ENDDO
	784	ENDIF
	785	END SUBROUTINE chem_boundary_conds_decycle
	786	!
[3085]	787	!------------------------------------------------------------------------------!
[2831]	788	!
[3085]	789	! Description:
	790	! ------------
	791	!> Subroutine for checking data output for chemical species
[2831]	792	!------------------------------------------------------------------------------!
[3085]	793
[3281]	794	SUBROUTINE chem_check_data_output( var, unit, i, ilen, k )
[3085]	795
	796
[3281]	797	USE control_parameters, &
	798	ONLY: data_output, message_string
[3085]	799
[3281]	800	IMPLICIT NONE
[3085]	801
[3281]	802	CHARACTER (LEN=*) :: unit !<
	803	CHARACTER (LEN=*) :: var !<
[3085]	804
[3281]	805	INTEGER(iwp) :: i, lsp
	806	INTEGER(iwp) :: ilen
	807	INTEGER(iwp) :: k
[3085]	808
[3281]	809	CHARACTER(len=16) :: spec_name
[3085]	810
[3281]	811	unit = 'illegal'
[3085]	812
[3281]	813	spec_name = TRIM(var(4:)) !< var 1:3 is 'kc_'.
[3085]	814
[3281]	815	DO lsp=1,nspec
	816	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
	817	unit = 'ppm'
	818	ENDIF
	819	! It is possible to plant PM10 and PM25 into the gasphase chemistry code
	820	! as passive species (e.g. 'passive' in GASPHASE_PREPROC/mechanisms):
	821	! set unit to micrograms per m**3 for PM10 and PM25 (PM2.5)
	822	IF (spec_name(1:2) == 'PM') THEN
[3276]	823	unit = 'kg m-3'
[3281]	824	ENDIF
	825	ENDDO
[3085]	826
[3281]	827	DO lsp=1,nphot
	828	IF (TRIM(spec_name) == TRIM(phot_frequen(lsp)%name)) THEN
	829	unit = 'sec-1'
	830	ENDIF
	831	ENDDO
[3085]	832
	833
	834	RETURN
[3281]	835	END SUBROUTINE chem_check_data_output
[2831]	836	!
[3085]	837	!------------------------------------------------------------------------------!
	838	!
[2535]	839	! Description:
	840	! ------------
[3085]	841	!> Subroutine for checking data output of profiles for chemistry model
[2535]	842	!------------------------------------------------------------------------------!
[2615]	843
[3281]	844	SUBROUTINE chem_check_data_output_pr( variable, var_count, unit, dopr_unit )
[3085]	845
[3281]	846	USE arrays_3d
	847	USE control_parameters, &
	848	ONLY: data_output_pr, message_string, air_chemistry
	849	USE indices
	850	USE profil_parameter
	851	USE statistics
[3085]	852
	853
[3281]	854	IMPLICIT NONE
[3085]	855
[3281]	856	CHARACTER (LEN=*) :: unit !<
	857	CHARACTER (LEN=*) :: variable !<
	858	CHARACTER (LEN=*) :: dopr_unit
	859	CHARACTER(len=16) :: spec_name
[3228]	860
[3281]	861	INTEGER(iwp) :: var_count, lsp !<
	862
[3085]	863
[3281]	864	spec_name = TRIM(variable(4:))
[3085]	865
	866	IF ( .NOT. air_chemistry ) THEN
[3281]	867	message_string = 'data_output_pr = ' // &
	868	TRIM( data_output_pr(var_count) ) // ' is not imp' // &
	869	'lemented for air_chemistry = .FALSE.'
	870	CALL message( 'chem_check_parameters', 'CM0433', 1, 2, 0, 6, 0 )
[3085]	871
	872	ELSE
	873	DO lsp = 1, nspec
	874	IF (TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
[3281]	875	cs_pr_count = cs_pr_count+1
	876	cs_pr_index(cs_pr_count) = lsp
	877	dopr_index(var_count) = pr_palm+cs_pr_count
	878	dopr_unit = 'ppm'
	879	IF (spec_name(1:2) == 'PM') THEN
[3276]	880	dopr_unit = 'kg m-3'
[3281]	881	ENDIF
[3085]	882	hom(:,2, dopr_index(var_count),:) = SPREAD( zu, 2, statistic_regions+1 )
	883	unit = dopr_unit
	884	ENDIF
	885	ENDDO
	886	ENDIF
	887
[3281]	888	END SUBROUTINE chem_check_data_output_pr
[3085]	889
[3281]	890	!
	891	!------------------------------------------------------------------------------!
	892	! Description:
	893	! ------------
	894	!> Check parameters routine for chemistry_model_mod
	895	!------------------------------------------------------------------------------!
	896	SUBROUTINE chem_check_parameters
[3085]	897
[3281]	898	IMPLICIT NONE
	899
	900	LOGICAL :: found
	901	INTEGER (iwp) :: lsp_usr !< running index for user defined chem spcs
	902	INTEGER (iwp) :: lsp !< running index for chem spcs.
	903
	904
	905	!!-- check for chemical reactions status
	906	IF ( chem_gasphase_on ) THEN
	907	message_string = 'Chemical reactions: ON'
	908	CALL message( 'chem_check_parameters', 'CM0421', 0, 0, 0, 6, 0 )
	909	ELSEIF ( .not. (chem_gasphase_on) ) THEN
	910	message_string = 'Chemical reactions: OFF'
	911	CALL message( 'chem_check_parameters', 'CM0422', 0, 0, 0, 6, 0 )
	912	ENDIF
	913
	914	!-- check for chemistry time-step
	915	IF ( call_chem_at_all_substeps ) THEN
	916	message_string = 'Chemistry is calculated at all meteorology time-step'
	917	CALL message( 'chem_check_parameters', 'CM0423', 0, 0, 0, 6, 0 )
	918	ELSEIF ( .not. (call_chem_at_all_substeps) ) THEN
	919	message_string = 'Sub-time-steps are skipped for chemistry time-steps'
	920	CALL message( 'chem_check_parameters', 'CM0424', 0, 0, 0, 6, 0 )
	921	ENDIF
	922
	923	!-- check for photolysis scheme
	924	IF ( (photolysis_scheme /= 'simple') .AND. (photolysis_scheme /= 'constant') ) THEN
	925	message_string = 'Incorrect photolysis scheme selected, please check spelling'
	926	CALL message( 'chem_check_parameters', 'CM0425', 1, 2, 0, 6, 0 )
	927	ENDIF
	928
	929	!-- check for decycling of chem species
	930	IF ( (.not. any(decycle_method == 'neumann') ) .AND. (.not. any(decycle_method == 'dirichlet') ) ) THEN
[3318]	931	message_string = 'Incorrect boundary conditions. Only neumann or ' &
	932	// 'dirichlet &available for decycling chemical species '
[3281]	933	CALL message( 'chem_check_parameters', 'CM0426', 1, 2, 0, 6, 0 )
	934	ENDIF
	935
	936	!-- check for initial chem species input
	937	lsp_usr = 1
	938	lsp = 1
	939	DO WHILE ( cs_name (lsp_usr) /= 'novalue')
	940	found = .FALSE.
	941	DO lsp = 1, nvar
	942	IF ( TRIM(cs_name (lsp_usr)) == TRIM(chem_species(lsp)%name) ) THEN
	943	found = .TRUE.
	944	EXIT
	945	ENDIF
	946	ENDDO
	947	IF ( .not. found ) THEN
	948	message_string = 'Incorrect input for initial surface vaue: ' // TRIM(cs_name(lsp_usr))
	949	CALL message( 'chem_check_parameters', 'CM0427', 0, 1, 0, 6, 0 )
	950	ENDIF
	951	lsp_usr = lsp_usr + 1
	952	ENDDO
	953
	954	!-- check for surface emission flux chem species
	955
	956	lsp_usr = 1
	957	lsp = 1
	958	DO WHILE ( surface_csflux_name (lsp_usr) /= 'novalue')
	959	found = .FALSE.
	960	DO lsp = 1, nvar
	961	IF ( TRIM(surface_csflux_name (lsp_usr)) == TRIM(chem_species(lsp)%name) ) THEN
	962	found = .TRUE.
	963	EXIT
	964	ENDIF
	965	ENDDO
	966	IF ( .not. found ) THEN
	967	message_string = 'Incorrect input of chemical species for surface emission fluxes: ' &
	968	// TRIM(surface_csflux_name(lsp_usr))
	969	CALL message( 'chem_check_parameters', 'CM0428', 0, 1, 0, 6, 0 )
	970	ENDIF
	971	lsp_usr = lsp_usr + 1
	972	ENDDO
	973
	974	END SUBROUTINE chem_check_parameters
	975
[3085]	976	!
	977	!------------------------------------------------------------------------------!
	978	!
	979	! Description:
	980	! ------------
	981	!> Subroutine defining 2D output variables for chemical species
[3298]	982	!> @todo: Remove "mode" from argument list, not used.
[3085]	983	!------------------------------------------------------------------------------!
	984
[3281]	985	SUBROUTINE chem_data_output_2d( av, variable, found, grid, mode, local_pf, &
	986	two_d, nzb_do, nzt_do, fill_value )
	987
	988	USE indices
[3085]	989
[3281]	990	USE kinds
[3085]	991
[3281]	992	USE pegrid, ONLY: myid, threads_per_task
[3085]	993
[3281]	994	IMPLICIT NONE
[3085]	995
[3281]	996	CHARACTER (LEN=*) :: grid !<
	997	CHARACTER (LEN=*) :: mode !<
	998	CHARACTER (LEN=*) :: variable !<
[3282]	999	INTEGER(iwp) :: av !< flag to control data output of instantaneous or time-averaged data
[3281]	1000	INTEGER(iwp) :: nzb_do !< lower limit of the domain (usually nzb)
	1001	INTEGER(iwp) :: nzt_do !< upper limit of the domain (usually nzt+1)
	1002	LOGICAL :: found !<
	1003	LOGICAL :: two_d !< flag parameter that indicates 2D variables (horizontal cross sections)
	1004	REAL(wp) :: fill_value
	1005	REAL(wp), DIMENSION(nxl:nxr,nys:nyn,nzb:nzt+1) :: local_pf !<
[3085]	1006
[3281]	1007	!-- local variables.
	1008	CHARACTER(len=16) :: spec_name
	1009	INTEGER(iwp) :: lsp
[3282]	1010	INTEGER(iwp) :: i !< grid index along x-direction
	1011	INTEGER(iwp) :: j !< grid index along y-direction
	1012	INTEGER(iwp) :: k !< grid index along z-direction
	1013	INTEGER(iwp) :: m !< running index surface elements
	1014	INTEGER(iwp) :: char_len !< length of a character string
[3281]	1015	found = .TRUE.
	1016	char_len = LEN_TRIM(variable)
[3085]	1017
[3281]	1018	spec_name = TRIM( variable(4:char_len-3) )
[3085]	1019
[3281]	1020	DO lsp=1,nspec
	1021	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name) .AND. &
	1022	( (variable(char_len-2:) == '_xy') .OR. &
	1023	(variable(char_len-2:) == '_xz') .OR. &
	1024	(variable(char_len-2:) == '_yz') ) ) THEN
[3373]	1025	!
	1026	!-- todo: remove or replace by "CALL message" mechanism (kanani)
	1027	! IF(myid == 0) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
	1028	! TRIM(chem_species(lsp)%name)
[3281]	1029	IF (av == 0) THEN
	1030	DO i = nxl, nxr
	1031	DO j = nys, nyn
	1032	DO k = nzb_do, nzt_do
	1033	local_pf(i,j,k) = MERGE( &
	1034	chem_species(lsp)%conc(k,j,i), &
	1035	REAL( fill_value, KIND = wp ), &
	1036	BTEST( wall_flags_0(k,j,i), 0 ) )
[3085]	1037
	1038
[3281]	1039	ENDDO
[3085]	1040	ENDDO
	1041	ENDDO
[3281]	1042
	1043	ELSE
	1044	DO i = nxl, nxr
	1045	DO j = nys, nyn
	1046	DO k = nzb_do, nzt_do
	1047	local_pf(i,j,k) = MERGE( &
	1048	chem_species(lsp)%conc(k,j,i), &
	1049	REAL( fill_value, KIND = wp ), &
	1050	BTEST( wall_flags_0(k,j,i), 0 ) )
	1051	ENDDO
[3085]	1052	ENDDO
	1053	ENDDO
[3281]	1054	ENDIF
	1055	grid = 'zu'
[2535]	1056	ENDIF
[3281]	1057	ENDDO
[3085]	1058
[3281]	1059	RETURN
	1060
	1061	END SUBROUTINE chem_data_output_2d
[3085]	1062
	1063	!
	1064	!------------------------------------------------------------------------------!
	1065	!
	1066	! Description:
	1067	! ------------
	1068	!> Subroutine defining 3D output variables for chemical species
	1069	!------------------------------------------------------------------------------!
	1070
[3281]	1071	SUBROUTINE chem_data_output_3d( av, variable, found, local_pf, fill_value, nzb_do, nzt_do )
[3085]	1072
	1073
[3281]	1074	USE indices
[3228]	1075
[3281]	1076	USE kinds
[3085]	1077
	1078
[3281]	1079	IMPLICIT NONE
[3085]	1080
[3282]	1081	CHARACTER (LEN=*) :: variable !<
	1082	INTEGER(iwp) :: av !<
	1083	INTEGER(iwp) :: nzb_do !< lower limit of the data output (usually 0)
	1084	INTEGER(iwp) :: nzt_do !< vertical upper limit of the data output (usually nz_do3d)
[3085]	1085
[3282]	1086	LOGICAL :: found !<
[3085]	1087
[3281]	1088	REAL(wp) :: fill_value !<
	1089	REAL(sp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) :: local_pf
[3228]	1090
[3085]	1091
[3281]	1092	!-- local variables
[3085]	1093
[3281]	1094	INTEGER :: i, j, k, lsp
	1095	CHARACTER(len=16) :: spec_name
[3085]	1096
	1097
[3281]	1098	found = .FALSE.
[3085]	1099
[3281]	1100	spec_name = TRIM(variable(4:))
[3085]	1101
	1102	DO lsp=1,nspec
[3114]	1103	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
[3373]	1104	!
	1105	!-- todo: remove or replace by "CALL message" mechanism (kanani)
	1106	! IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
	1107	! TRIM(chem_species(lsp)%name)
[3228]	1108
[3085]	1109	IF (av == 0) THEN
	1110	DO i = nxl, nxr
	1111	DO j = nys, nyn
[3114]	1112	DO k = nzb_do, nzt_do
[3085]	1113	local_pf(i,j,k) = MERGE( &
	1114	chem_species(lsp)%conc(k,j,i), &
	1115	REAL( fill_value, KIND = wp ), &
	1116	BTEST( wall_flags_0(k,j,i), 0 ) )
	1117	ENDDO
	1118	ENDDO
	1119	ENDDO
	1120
	1121	ELSE
	1122	DO i = nxl, nxr
	1123	DO j = nys, nyn
[3114]	1124	DO k = nzb_do, nzt_do
[3085]	1125	local_pf(i,j,k) = MERGE( &
	1126	chem_species(lsp)%conc_av(k,j,i),&
	1127	REAL( fill_value, KIND = wp ), &
	1128	BTEST( wall_flags_0(k,j,i), 0 ) )
	1129	ENDDO
	1130	ENDDO
	1131	ENDDO
	1132	ENDIF
	1133
[3281]	1134	found = .TRUE.
[3085]	1135	ENDIF
	1136	ENDDO
	1137
	1138	RETURN
[3281]	1139	END SUBROUTINE chem_data_output_3d
[3085]	1140	!
	1141	!------------------------------------------------------------------------------!
	1142	!
	1143	! Description:
	1144	! ------------
	1145	!> Subroutine defining mask output variables for chemical species
	1146	!------------------------------------------------------------------------------!
	1147
[3281]	1148	SUBROUTINE chem_data_output_mask( av, variable, found, local_pf )
	1149
	1150	USE control_parameters
	1151	USE indices
	1152	USE kinds
	1153	USE pegrid, ONLY: myid, threads_per_task
[3435]	1154	USE surface_mod, ONLY: get_topography_top_index_ji
[3085]	1155
[3281]	1156	IMPLICIT NONE
[3085]	1157
[3435]	1158	CHARACTER(LEN=5) :: grid !< flag to distinquish between staggered grids
	1159
[3282]	1160	CHARACTER (LEN=*):: variable !<
	1161	INTEGER(iwp) :: av !< flag to control data output of instantaneous or time-averaged data
	1162	LOGICAL :: found !<
[3281]	1163	REAL(wp), DIMENSION(mask_size_l(mid,1),mask_size_l(mid,2),mask_size_l(mid,3)) :: &
	1164	local_pf !<
[3085]	1165
	1166
[3281]	1167	!-- local variables.
	1168	CHARACTER(len=16) :: spec_name
	1169	INTEGER(iwp) :: lsp
[3282]	1170	INTEGER(iwp) :: i !< grid index along x-direction
	1171	INTEGER(iwp) :: j !< grid index along y-direction
	1172	INTEGER(iwp) :: k !< grid index along z-direction
[3435]	1173	INTEGER(iwp) :: topo_top_ind !< k index of highest horizontal surface
	1174
[3281]	1175	found = .TRUE.
[3435]	1176	grid = 's'
[3085]	1177
[3281]	1178	spec_name = TRIM( variable(4:) )
	1179	!av == 0
[3085]	1180
	1181	DO lsp=1,nspec
	1182	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name) ) THEN
[3373]	1183	!
	1184	!-- todo: remove or replace by "CALL message" mechanism (kanani)
	1185	! IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
	1186	! TRIM(chem_species(lsp)%name)
[3085]	1187	IF (av == 0) THEN
[3435]	1188	IF ( .NOT. mask_surface(mid) ) THEN
	1189
	1190	DO i = 1, mask_size_l(mid,1)
	1191	DO j = 1, mask_size_l(mid,2)
	1192	DO k = 1, mask_size(mid,3)
	1193	local_pf(i,j,k) = chem_species(lsp)%conc( &
	1194	mask_k(mid,k), &
	1195	mask_j(mid,j), &
	1196	mask_i(mid,i) )
	1197	ENDDO
[3085]	1198	ENDDO
	1199	ENDDO
[3435]	1200
	1201	ELSE
	1202	!
	1203	!-- Terrain-following masked output
	1204	DO i = 1, mask_size_l(mid,1)
	1205	DO j = 1, mask_size_l(mid,2)
	1206	!
	1207	!-- Get k index of highest horizontal surface
	1208	topo_top_ind = get_topography_top_index_ji( &
	1209	mask_j(mid,j), &
	1210	mask_i(mid,i), &
	1211	grid )
	1212	!
	1213	!-- Save output array
	1214	DO k = 1, mask_size_l(mid,3)
	1215	local_pf(i,j,k) = chem_species(lsp)%conc( &
	1216	MIN( topo_top_ind+mask_k(mid,k), &
	1217	nzt+1 ), &
	1218	mask_j(mid,j), &
	1219	mask_i(mid,i) )
	1220	ENDDO
	1221	ENDDO
	1222	ENDDO
	1223
	1224	ENDIF
[3085]	1225	ELSE
[3435]	1226	IF ( .NOT. mask_surface(mid) ) THEN
	1227
	1228	DO i = 1, mask_size_l(mid,1)
	1229	DO j = 1, mask_size_l(mid,2)
	1230	DO k = 1, mask_size_l(mid,3)
	1231	local_pf(i,j,k) = chem_species(lsp)%conc_av( &
	1232	mask_k(mid,k), &
	1233	mask_j(mid,j), &
	1234	mask_i(mid,i) )
	1235	ENDDO
[3085]	1236	ENDDO
	1237	ENDDO
[3435]	1238
	1239	ELSE
	1240	!
	1241	!-- Terrain-following masked output
	1242	DO i = 1, mask_size_l(mid,1)
	1243	DO j = 1, mask_size_l(mid,2)
	1244	!
	1245	!-- Get k index of highest horizontal surface
	1246	topo_top_ind = get_topography_top_index_ji( &
	1247	mask_j(mid,j), &
	1248	mask_i(mid,i), &
	1249	grid )
	1250	!
	1251	!-- Save output array
	1252	DO k = 1, mask_size_l(mid,3)
	1253	local_pf(i,j,k) = chem_species(lsp)%conc_av( &
	1254	MIN( topo_top_ind+mask_k(mid,k), &
	1255	nzt+1 ), &
	1256	mask_j(mid,j), &
	1257	mask_i(mid,i) )
	1258	ENDDO
	1259	ENDDO
	1260	ENDDO
	1261
	1262	ENDIF
	1263
	1264
[3085]	1265	ENDIF
	1266	found = .FALSE.
	1267	ENDIF
	1268	ENDDO
	1269
	1270	RETURN
[3281]	1271
	1272	END SUBROUTINE chem_data_output_mask
[3085]	1273
	1274	!
	1275	!------------------------------------------------------------------------------!
	1276	!
	1277	! Description:
	1278	! ------------
	1279	!> Subroutine defining appropriate grid for netcdf variables.
	1280	!> It is called out from subroutine netcdf.
	1281	!------------------------------------------------------------------------------!
[3281]	1282	SUBROUTINE chem_define_netcdf_grid( var, found, grid_x, grid_y, grid_z )
[3085]	1283
[3281]	1284	IMPLICIT NONE
[3085]	1285
[3282]	1286	CHARACTER (LEN=*), INTENT(IN) :: var !<
	1287	LOGICAL, INTENT(OUT) :: found !<
	1288	CHARACTER (LEN=*), INTENT(OUT) :: grid_x !<
	1289	CHARACTER (LEN=*), INTENT(OUT) :: grid_y !<
	1290	CHARACTER (LEN=*), INTENT(OUT) :: grid_z !<
[3085]	1291
[3281]	1292	found = .TRUE.
[3085]	1293
[3281]	1294	IF (var(1:3) == 'kc_') THEN !< always the same grid for chemistry variables
	1295	grid_x = 'x'
	1296	grid_y = 'y'
	1297	grid_z = 'zu'
	1298	ELSE
	1299	found = .FALSE.
	1300	grid_x = 'none'
	1301	grid_y = 'none'
	1302	grid_z = 'none'
	1303	ENDIF
[3085]	1304
	1305
[3281]	1306	END SUBROUTINE chem_define_netcdf_grid
[3085]	1307	!
	1308	!------------------------------------------------------------------------------!
	1309	!
	1310	! Description:
	1311	! ------------
	1312	!> Subroutine defining header output for chemistry model
	1313	!------------------------------------------------------------------------------!
[3281]	1314	SUBROUTINE chem_header ( io )
[3085]	1315
[3281]	1316	IMPLICIT NONE
[3085]	1317
	1318	INTEGER(iwp), INTENT(IN) :: io !< Unit of the output file
[3281]	1319	INTEGER(iwp) :: lsp !< running index for chem spcs
[3282]	1320	INTEGER(iwp) :: cs_fixed
	1321	CHARACTER (LEN=80) :: docsflux_chr
	1322	CHARACTER (LEN=80) :: docsinit_chr
	1323
[3281]	1324	!
	1325	!-- Write chemistry model header
	1326	WRITE( io, 1 )
[3085]	1327
[3281]	1328	!-- Gasphase reaction status
	1329	IF ( chem_gasphase_on ) THEN
	1330	WRITE( io, 2 )
	1331	ELSE
	1332	WRITE( io, 3 )
	1333	ENDIF
	1334
	1335	! Chemistry time-step
	1336	WRITE ( io, 4 ) cs_time_step
	1337
	1338	!-- Emission mode info
	1339	IF ( mode_emis == "DEFAULT" ) THEN
	1340	WRITE( io, 5 )
	1341	ELSEIF ( mode_emis == "PARAMETERIZED" ) THEN
	1342	WRITE( io, 6 )
	1343	ELSEIF ( mode_emis == "PRE-PROCESSED" ) THEN
	1344	WRITE( io, 7 )
	1345	ENDIF
	1346
	1347	!-- Photolysis scheme info
	1348	IF ( photolysis_scheme == "simple" ) THEN
	1349	WRITE( io, 8 )
	1350	ELSEIF (photolysis_scheme == "conastant" ) THEN
	1351	WRITE( io, 9 )
	1352	ENDIF
	1353
	1354	!-- Emission flux info
	1355	lsp = 1
	1356	docsflux_chr ='Chemical species for surface emission flux: '
	1357	DO WHILE ( surface_csflux_name(lsp) /= 'novalue' )
	1358	docsflux_chr = TRIM( docsflux_chr ) // ' ' // TRIM( surface_csflux_name(lsp) ) // ','
	1359	IF ( LEN_TRIM( docsflux_chr ) >= 75 ) THEN
	1360	WRITE ( io, 10 ) docsflux_chr
	1361	docsflux_chr = ' '
	1362	ENDIF
	1363	lsp = lsp + 1
	1364	ENDDO
	1365
	1366	IF ( docsflux_chr /= '' ) THEN
	1367	WRITE ( io, 10 ) docsflux_chr
	1368	ENDIF
	1369
	1370
	1371	!-- initializatoin of Surface and profile chemical species
	1372
	1373	lsp = 1
	1374	docsinit_chr ='Chemical species for initial surface and profile emissions: '
	1375	DO WHILE ( cs_name(lsp) /= 'novalue' )
	1376	docsinit_chr = TRIM( docsinit_chr ) // ' ' // TRIM( cs_name(lsp) ) // ','
	1377	IF ( LEN_TRIM( docsinit_chr ) >= 75 ) THEN
	1378	WRITE ( io, 11 ) docsinit_chr
	1379	docsinit_chr = ' '
	1380	ENDIF
	1381	lsp = lsp + 1
	1382	ENDDO
	1383
	1384	IF ( docsinit_chr /= '' ) THEN
	1385	WRITE ( io, 11 ) docsinit_chr
	1386	ENDIF
	1387
	1388	!-- number of variable and fix chemical species and number of reactions
[3282]	1389	cs_fixed = nspec - nvar
	1390	WRITE ( io, * ) ' --> Chemical species, variable: ', nvar
	1391	WRITE ( io, * ) ' --> Chemical species, fixed : ', cs_fixed
	1392	WRITE ( io, * ) ' --> Total number of reactions : ', nreact
[3281]	1393
	1394
	1395	1 FORMAT (//' Chemistry model information:'/ &
	1396	' ----------------------------'/)
	1397	2 FORMAT (' --> Chemical reactions are turned on')
	1398	3 FORMAT (' --> Chemical reactions are turned off')
	1399	4 FORMAT (' --> Time-step for chemical species: ',F6.2, ' s')
	1400	5 FORMAT (' --> Emission mode = DEFAULT ')
	1401	6 FORMAT (' --> Emission mode = PARAMETERIZED ')
	1402	7 FORMAT (' --> Emission mode = PRE-PROCESSED ')
	1403	8 FORMAT (' --> Photolysis scheme used = simple ')
	1404	9 FORMAT (' --> Photolysis scheme used = constant ')
[3282]	1405	10 FORMAT (/' ',A)
	1406	11 FORMAT (/' ',A)
[3085]	1407	!
	1408	!
[3281]	1409	END SUBROUTINE chem_header
[3085]	1410
	1411	!
	1412	!------------------------------------------------------------------------------!
	1413	!
	1414	! Description:
	1415	! ------------
[2535]	1416	!> Subroutine initializating chemistry_model_mod
[2425]	1417	!------------------------------------------------------------------------------!
[3281]	1418	SUBROUTINE chem_init
[2535]	1419
[3281]	1420	USE control_parameters, &
	1421	ONLY: message_string, io_blocks, io_group, turbulent_inflow
	1422	USE arrays_3d, &
	1423	ONLY: mean_inflow_profiles
	1424	USE pegrid
[3085]	1425
[3281]	1426	IMPLICIT none
	1427	!-- local variables
	1428	INTEGER :: i,j !< running index for for horiz numerical grid points
	1429	INTEGER :: lsp !< running index for chem spcs
	1430	INTEGER :: lpr_lev !< running index for chem spcs profile level
[2535]	1431	!
	1432	!-- NOPOINTER version not implemented yet
[2828]	1433	! #if defined( __nopointer )
	1434	! message_string = 'The chemistry module only runs with POINTER version'
	1435	! CALL message( 'chemistry_model_mod', 'CM0001', 1, 2, 0, 6, 0 )
	1436	! #endif
	1437	!
	1438	!-- Allocate memory for chemical species
[3281]	1439	ALLOCATE( chem_species(nspec) )
	1440	ALLOCATE( spec_conc_1 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	1441	ALLOCATE( spec_conc_2 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	1442	ALLOCATE( spec_conc_3 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	1443	ALLOCATE( spec_conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	1444	ALLOCATE( phot_frequen(nphot) )
	1445	ALLOCATE( freq_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nphot) )
	1446	ALLOCATE( bc_cs_t_val(nspec) )
[2828]	1447	!
	1448	!-- Initialize arrays
[3281]	1449	spec_conc_1 (:,:,:,:) = 0.0_wp
	1450	spec_conc_2 (:,:,:,:) = 0.0_wp
	1451	spec_conc_3 (:,:,:,:) = 0.0_wp
	1452	spec_conc_av(:,:,:,:) = 0.0_wp
[2535]	1453
[2828]	1454
[3281]	1455	DO lsp = 1, nspec
	1456	chem_species(lsp)%name = spc_names(lsp)
[2535]	1457
[3281]	1458	chem_species(lsp)%conc (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1 (:,:,:,lsp)
	1459	chem_species(lsp)%conc_p (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2 (:,:,:,lsp)
	1460	chem_species(lsp)%tconc_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_3 (:,:,:,lsp)
	1461	chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_av(:,:,:,lsp)
[2425]	1462
[3281]	1463	ALLOCATE (chem_species(lsp)%cssws_av(nysg:nyng,nxlg:nxrg))
	1464	chem_species(lsp)%cssws_av = 0.0_wp
[2828]	1465	!
[3282]	1466	!-- The following block can be useful when emission module is not applied. &
	1467	!-- if emission module is applied the following block will be overwritten.
	1468	ALLOCATE (chem_species(lsp)%flux_s_cs(nzb+1:nzt,0:threads_per_task-1))
	1469	ALLOCATE (chem_species(lsp)%diss_s_cs(nzb+1:nzt,0:threads_per_task-1))
	1470	ALLOCATE (chem_species(lsp)%flux_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
	1471	ALLOCATE (chem_species(lsp)%diss_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
	1472	chem_species(lsp)%flux_s_cs = 0.0_wp
	1473	chem_species(lsp)%flux_l_cs = 0.0_wp
	1474	chem_species(lsp)%diss_s_cs = 0.0_wp
	1475	chem_species(lsp)%diss_l_cs = 0.0_wp
[2828]	1476	!
	1477	!-- Allocate memory for initial concentration profiles
	1478	!-- (concentration values come from namelist)
[3282]	1479	!-- (@todo (FK): Because of this, chem_init is called in palm before
[2828]	1480	!-- check_parameters, since conc_pr_init is used there.
	1481	!-- We have to find another solution since chem_init should
	1482	!-- eventually be called from init_3d_model!!)
[3281]	1483	ALLOCATE ( chem_species(lsp)%conc_pr_init(0:nz+1) )
	1484	chem_species(lsp)%conc_pr_init(:) = 0.0_wp
[2425]	1485
[3281]	1486	ENDDO
[2425]	1487
[2615]	1488	!
[3281]	1489	!-- Initial concentration of profiles is prescribed by parameters cs_profile
	1490	!-- and cs_heights in the namelist &chemistry_parameters
	1491	CALL chem_init_profiles
	1492
	1493
[2615]	1494	!
	1495	!-- Initialize model variables
[2425]	1496
[3114]	1497
[3281]	1498	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
	1499	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
[2425]	1500
[3228]	1501
[2615]	1502	!-- First model run of a possible job queue.
[3282]	1503	!-- Initial profiles of the variables must be computed.
[3281]	1504	IF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
[3282]	1505	CALL location_message( 'initializing with 1D chemistry model profiles', .FALSE. )
[2615]	1506	!
	1507	!-- Transfer initial profiles to the arrays of the 3D model
[3281]	1508	DO lsp = 1, nspec
	1509	DO i = nxlg, nxrg
	1510	DO j = nysg, nyng
	1511	DO lpr_lev = 1, nz + 1
	1512	chem_species(lsp)%conc(lpr_lev,j,i) = chem_species(lsp)%conc_pr_init(lpr_lev)
	1513	ENDDO
[2615]	1514	ENDDO
[3281]	1515	ENDDO
	1516	ENDDO
	1517
	1518	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
	1519	THEN
[3282]	1520	CALL location_message( 'initializing with constant chemistry profiles', .FALSE. )
[2425]	1521
[3281]	1522	DO lsp = 1, nspec
	1523	DO i = nxlg, nxrg
	1524	DO j = nysg, nyng
	1525	chem_species(lsp)%conc(:,j,i) = chem_species(lsp)%conc_pr_init
	1526	ENDDO
[2615]	1527	ENDDO
	1528	ENDDO
	1529
[3281]	1530	ENDIF
[2615]	1531
[2535]	1532	!
[3281]	1533	!-- If required, change the surface chem spcs at the start of the 3D run
	1534	IF ( cs_surface_initial_change(1) /= 0.0_wp ) THEN
	1535	DO lsp = 1, nspec
	1536	chem_species(lsp)%conc(nzb,:,:) = chem_species(lsp)%conc(nzb,:,:) + &
	1537	cs_surface_initial_change(lsp)
	1538	ENDDO
	1539	ENDIF
	1540	!
	1541	!-- Initiale old and new time levels.
	1542	DO lsp = 1, nvar
	1543	chem_species(lsp)%tconc_m = 0.0_wp
	1544	chem_species(lsp)%conc_p = chem_species(lsp)%conc
[2615]	1545	ENDDO
[2592]	1546
[3281]	1547	ENDIF
[2535]	1548
[3114]	1549
	1550
[3281]	1551	!--- new code add above this line
	1552	DO lsp = 1, nphot
	1553	phot_frequen(lsp)%name = phot_names(lsp)
[3373]	1554	!
	1555	!-- todo: remove or replace by "CALL message" mechanism (kanani)
[3281]	1556	! IF( myid == 0 ) THEN
	1557	! WRITE(6,'(a,i4,3x,a)') 'Photolysis: ',lsp,trim(phot_names(lsp))
	1558	! ENDIF
	1559	phot_frequen(lsp)%freq(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => freq_1(:,:,:,lsp)
	1560	ENDDO
[2425]	1561
[3281]	1562	RETURN
[2425]	1563
[3085]	1564	END SUBROUTINE chem_init
[2425]	1565
[2535]	1566	!
	1567	!------------------------------------------------------------------------------!
	1568	!
	1569	! Description:
	1570	! ------------
[3085]	1571	!> Subroutine defining initial vertical profiles of chemical species (given by
	1572	!> namelist parameters chem_profiles and chem_heights) --> which should work
	1573	!> analogue to parameters u_profile, v_profile and uv_heights)
[2535]	1574	!------------------------------------------------------------------------------!
[3281]	1575	SUBROUTINE chem_init_profiles !< SUBROUTINE is called from chem_init in case of
	1576	!< TRIM( initializing_actions ) /= 'read_restart_data'
	1577	!< We still need to see what has to be done in case of restart run
	1578	USE chem_modules
[2615]	1579
[3281]	1580	IMPLICIT NONE
[2425]	1581
[3281]	1582	!-- Local variables
	1583	INTEGER :: lsp !< running index for number of species in derived data type species_def
	1584	INTEGER :: lsp_usr !< running index for number of species (user defined) in cs_names, cs_profiles etc
	1585	INTEGER :: lpr_lev !< running index for profile level for each chem spcs.
	1586	INTEGER :: npr_lev !< the next available profile lev
[2425]	1587
[3085]	1588	!-----------------
	1589	!-- Parameter "cs_profile" and "cs_heights" are used to prescribe user defined initial profiles
	1590	!-- and heights. If parameter "cs_profile" is not prescribed then initial surface values
	1591	!-- "cs_surface" are used as constant initial profiles for each species. If "cs_profile" and
	1592	!-- "cs_heights" are prescribed, their values will!override the constant profile given by
	1593	!-- "cs_surface".
[3114]	1594	!
[3281]	1595	IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
	1596	lsp_usr = 1
	1597	DO WHILE ( TRIM( cs_name( lsp_usr ) ) /= 'novalue' ) !'novalue' is the default
	1598	DO lsp = 1, nspec !
[3282]	1599	!-- create initial profile (conc_pr_init) for each chemical species
[3281]	1600	IF ( TRIM( chem_species(lsp)%name ) == TRIM( cs_name(lsp_usr) ) ) THEN !
	1601	IF ( cs_profile(lsp_usr,1) == 9999999.9_wp ) THEN
[3282]	1602	!-- set a vertically constant profile based on the surface conc (cs_surface(lsp_usr)) of each species
	1603	DO lpr_lev = 0, nzt+1
	1604	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_surface(lsp_usr)
	1605	ENDDO
[3281]	1606	ELSE
	1607	IF ( cs_heights(1,1) /= 0.0_wp ) THEN
	1608	message_string = 'The surface value of cs_heights must be 0.0'
	1609	CALL message( 'chem_check_parameters', 'CM0434', 1, 2, 0, 6, 0 )
	1610	ENDIF
	1611
	1612	use_prescribed_profile_data = .TRUE.
	1613
	1614	npr_lev = 1
	1615	! chem_species(lsp)%conc_pr_init(0) = 0.0_wp
	1616	DO lpr_lev = 1, nz+1
	1617	IF ( npr_lev < 100 ) THEN
	1618	DO WHILE ( cs_heights(lsp_usr, npr_lev+1) <= zu(lpr_lev) )
	1619	npr_lev = npr_lev + 1
	1620	IF ( npr_lev == 100 ) THEN
	1621	message_string = 'number of chem spcs exceeding the limit'
	1622	CALL message( 'chem_check_parameters', 'CM0435', 1, 2, 0, 6, 0 )
	1623	EXIT
	1624	ENDIF
	1625	ENDDO
	1626	ENDIF
	1627	IF ( npr_lev < 100 .AND. cs_heights(lsp_usr, npr_lev + 1) /= 9999999.9_wp ) THEN
	1628	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp_usr, npr_lev) + &
	1629	( zu(lpr_lev) - cs_heights(lsp_usr, npr_lev) ) / &
	1630	( cs_heights(lsp_usr, (npr_lev + 1)) - cs_heights(lsp_usr, npr_lev ) ) * &
	1631	( cs_profile(lsp_usr, (npr_lev + 1)) - cs_profile(lsp_usr, npr_lev ) )
	1632	ELSE
	1633	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp_usr, npr_lev)
	1634	ENDIF
	1635	ENDDO
[3085]	1636	ENDIF
[3282]	1637	!-- If a profile is prescribed explicity using cs_profiles and cs_heights, then
	1638	!-- chem_species(lsp)%conc_pr_init is populated with the specific "lsp" based
	1639	!-- on the cs_profiles(lsp_usr,:) and cs_heights(lsp_usr,:).
[3281]	1640	ENDIF
	1641	ENDDO
	1642	lsp_usr = lsp_usr + 1
[3085]	1643	ENDDO
[3281]	1644	ENDIF
[2425]	1645
[3281]	1646	END SUBROUTINE chem_init_profiles
[2828]	1647	!
[2535]	1648	!------------------------------------------------------------------------------!
	1649	!
	1650	! Description:
	1651	! ------------
	1652	!> Subroutine to integrate chemical species in the given chemical mechanism
	1653	!------------------------------------------------------------------------------!
	1654
[3281]	1655	SUBROUTINE chem_integrate_ij (i, j)
[2425]	1656
[3281]	1657	USE cpulog, &
	1658	ONLY: cpu_log, log_point
[3287]	1659	USE statistics, &
[3281]	1660	ONLY: weight_pres
[3287]	1661	USE control_parameters, &
[3281]	1662	ONLY: dt_3d, intermediate_timestep_count,simulated_time
[2425]	1663
[3281]	1664	IMPLICIT none
	1665	INTEGER,INTENT(IN) :: i,j
[2425]	1666
[3281]	1667	!-- local variables
[3282]	1668	INTEGER(iwp) :: lsp !< running index for chem spcs.
	1669	INTEGER(iwp) :: lph !< running index for photolysis frequencies
[3281]	1670	INTEGER :: k,m,istatf
	1671	INTEGER,DIMENSION(20) :: istatus
	1672	REAL(kind=wp),DIMENSION(nzb+1:nzt,nspec) :: tmp_conc
	1673	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_temp
	1674	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_qvap
	1675	REAL(kind=wp),DIMENSION(nzb+1:nzt,nphot) :: tmp_phot
	1676	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_fact
	1677	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_fact_i !< conversion factor between
	1678	!< molecules cm^{-3} and ppm
[3185]	1679
[3281]	1680	INTEGER,DIMENSION(nzb+1:nzt) :: nacc !< Number of accepted steps
	1681	INTEGER,DIMENSION(nzb+1:nzt) :: nrej !< Number of rejected steps
[3185]	1682
[3281]	1683	REAL(wp) :: conv !< conversion factor
	1684	REAL(wp), PARAMETER :: ppm2fr = 1.0e-6_wp !< Conversion factor ppm to fraction
	1685	REAL(wp), PARAMETER :: xm_air = 28.96_wp !< Mole mass of dry air
	1686	REAL(wp), PARAMETER :: xm_h2o = 18.01528_wp !< Mole mass of water vapor
	1687	REAL(wp), PARAMETER :: pref_i = 1._wp / 100000.0_wp !< inverse reference pressure (1/Pa)
	1688	REAL(wp), PARAMETER :: t_std = 273.15_wp !< standard pressure (Pa)
	1689	REAL(wp), PARAMETER :: p_std = 101325.0_wp !< standard pressure (Pa)
	1690	REAL(wp), PARAMETER :: vmolcm = 22.414e3_wp !< Mole volume (22.414 l) in cm^{-3}
	1691	REAL(wp), PARAMETER :: xna = 6.022e23_wp !< Avogadro number (molecules/mol)
[2425]	1692
[3281]	1693	REAL(wp),DIMENSION(size(rcntrl)) :: rcntrl_local
[2615]	1694
[3185]	1695
[3281]	1696	REAL(kind=wp) :: dt_chem
[2425]	1697
[2535]	1698	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'start' )
[3282]	1699	!< set chem_gasphase_on to .FALSE. if you want to skip computation of gas phase chemistry
[3281]	1700	IF (chem_gasphase_on) THEN
	1701	nacc = 0
	1702	nrej = 0
[2635]	1703
[3287]	1704	tmp_temp(:) = pt(nzb+1:nzt,j,i) * exner(nzb+1:nzt)
[3282]	1705	! ppm to molecules/cm**3
[3287]	1706	! tmp_fact = 1.e-6_wp6.022e23_wp/(22.414_wp1000._wp) * 273.15_wp * hyp(nzb+1:nzt)/( 101300.0_wp * tmp_temp )
[3281]	1707	conv = ppm2fr * xna / vmolcm
	1708	tmp_fact(:) = conv * t_std * hyp(nzb+1:nzt) / (tmp_temp(:) * p_std)
	1709	tmp_fact_i = 1.0_wp/tmp_fact
[2615]	1710
[3281]	1711	IF ( humidity ) THEN
[3292]	1712	IF ( bulk_cloud_model ) THEN
[3281]	1713	tmp_qvap(:) = ( q(nzb+1:nzt,j,i) - ql(nzb+1:nzt,j,i) ) * xm_air/xm_h2o * tmp_fact(:)
	1714	ELSE
	1715	tmp_qvap(:) = q(nzb+1:nzt,j,i) * xm_air/xm_h2o * tmp_fact(:)
	1716	ENDIF
[3114]	1717	ELSE
[3281]	1718	tmp_qvap(:) = 0.01 * tmp_fact(:) !< Constant value for q if water vapor is not computed
[3114]	1719	ENDIF
	1720
[3281]	1721	DO lsp = 1,nspec
	1722	tmp_conc(:,lsp) = chem_species(lsp)%conc(nzb+1:nzt,j,i) * tmp_fact(:)
	1723	ENDDO
[2425]	1724
[3281]	1725	DO lph = 1,nphot
	1726	tmp_phot(:,lph) = phot_frequen(lph)%freq(nzb+1:nzt,j,i)
	1727	ENDDO
[3373]	1728	!
	1729	!-- todo: remove (kanani)
	1730	! IF(myid == 0 .AND. chem_debug0 ) THEN
	1731	! IF (i == 10 .and. j == 10) WRITE(0,*) 'begin chemics step ',dt_3d
	1732	! ENDIF
[2425]	1733
[3281]	1734	!-- Compute length of time step
	1735	IF ( call_chem_at_all_substeps ) THEN
	1736	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
	1737	ELSE
	1738	dt_chem = dt_3d
	1739	ENDIF
[2425]	1740
[3281]	1741	cs_time_step = dt_chem
[2425]	1742
[3281]	1743	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'start' )
[2425]	1744
[3281]	1745	IF(maxval(rcntrl) > 0.0) THEN ! Only if rcntrl is set
	1746	IF( simulated_time <= 2*dt_3d) THEN
	1747	rcntrl_local = 0
[3373]	1748	!
	1749	!-- todo: remove (kanani)
	1750	! WRITE(9,'(a,2f10.3)') 'USE Default rcntrl in the first steps ',simulated_time,dt_3d
[3281]	1751	ELSE
	1752	rcntrl_local = rcntrl
	1753	ENDIF
	1754	ELSE
	1755	rcntrl_local = 0
	1756	END IF
[2425]	1757
[3281]	1758	CALL chem_gasphase_integrate (dt_chem, tmp_conc, tmp_temp, tmp_qvap, tmp_fact, tmp_phot, &
	1759	icntrl_i = icntrl, rcntrl_i = rcntrl_local, xnacc = nacc, xnrej = nrej, istatus=istatus)
[2425]	1760
[3281]	1761	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'stop' )
[2425]	1762
[3281]	1763	DO lsp = 1,nspec
	1764	chem_species(lsp)%conc (nzb+1:nzt,j,i) = tmp_conc(:,lsp) * tmp_fact_i(:)
	1765	ENDDO
[3185]	1766
[2535]	1767
[3281]	1768	ENDIF
	1769	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'stop' )
	1770
[2615]	1771	RETURN
[3281]	1772	END SUBROUTINE chem_integrate_ij
[2535]	1773	!
	1774	!------------------------------------------------------------------------------!
	1775	!
	1776	! Description:
	1777	! ------------
[3085]	1778	!> Subroutine defining parin for &chemistry_parameters for chemistry model
[2535]	1779	!------------------------------------------------------------------------------!
[3281]	1780	SUBROUTINE chem_parin
[3085]	1781
[3281]	1782	USE chem_modules
	1783	USE control_parameters
[3287]	1784
[3281]	1785	USE kinds
	1786	USE pegrid
	1787	USE statistics
	1788
	1789	IMPLICIT NONE
[2425]	1790
[3282]	1791	CHARACTER (LEN=80) :: line !< dummy string that contains the current line of the parameter file
[3281]	1792	CHARACTER (LEN=3) :: cs_prefix
[2425]	1793
[3282]	1794	REAL(wp), DIMENSION(nmaxfixsteps) :: my_steps !< List of fixed timesteps my_step(1) = 0.0 automatic stepping
	1795	INTEGER(iwp) :: i !<
	1796	INTEGER(iwp) :: j !<
	1797	INTEGER(iwp) :: max_pr_cs_tmp !<
[2425]	1798
	1799
[3281]	1800	NAMELIST /chemistry_parameters/ bc_cs_b, &
[3085]	1801	bc_cs_t, &
	1802	call_chem_at_all_substeps, &
	1803	chem_debug0, &
	1804	chem_debug1, &
	1805	chem_debug2, &
	1806	chem_gasphase_on, &
	1807	cs_heights, &
	1808	cs_name, &
	1809	cs_profile, &
	1810	cs_profile_name, &
	1811	cs_surface, &
	1812	decycle_chem_lr, &
	1813	decycle_chem_ns, &
	1814	decycle_method, &
	1815	emiss_factor_main, &
	1816	emiss_factor_side, &
	1817	icntrl, &
	1818	main_street_id, &
	1819	max_street_id, &
	1820	my_steps, &
[3228]	1821	nest_chemistry, &
[3085]	1822	rcntrl, &
	1823	side_street_id, &
	1824	photolysis_scheme, &
	1825	wall_csflux, &
	1826	cs_vertical_gradient, &
	1827	top_csflux, &
	1828	surface_csflux, &
	1829	surface_csflux_name, &
	1830	cs_surface_initial_change, &
[3190]	1831	cs_vertical_gradient_level, &
[3282]	1832	! namelist parameters for emissions
[3190]	1833	mode_emis, &
	1834	time_fac_type, &
	1835	daytype_mdh, &
	1836	do_emis
[3085]	1837
	1838	!-- analogue to chem_names(nspj) we could invent chem_surfaceflux(nspj) and chem_topflux(nspj)
	1839	!-- so this way we could prescribe a specific flux value for each species
	1840	!> chemistry_parameters for initial profiles
	1841	!> cs_names = 'O3', 'NO2', 'NO', ... to set initial profiles)
	1842	!> cs_heights(1,:) = 0.0, 100.0, 500.0, 2000.0, .... (height levels where concs will be prescribed for O3)
	1843	!> cs_heights(2,:) = 0.0, 200.0, 400.0, 1000.0, .... (same for NO2 etc.)
	1844	!> cs_profiles(1,:) = 10.0, 20.0, 20.0, 30.0, ..... (chem spcs conc at height lvls chem_heights(1,:)) etc.
	1845	!> If the respective concentration profile should be constant with height, then use "cs_surface( number of spcs)"
	1846	!> then write these cs_surface values to chem_species(lsp)%conc_pr_init(:)
[2425]	1847
	1848	!
[3085]	1849	!-- Read chem namelist
[3185]	1850
[3281]	1851	INTEGER :: ier
	1852	CHARACTER(LEN=64) :: text
	1853	CHARACTER(LEN=8) :: solver_type
[3185]	1854
[3281]	1855	icntrl = 0
	1856	rcntrl = 0.0_wp
	1857	my_steps = 0.0_wp
	1858	photolysis_scheme = 'simple'
	1859	atol = 1.0_wp
	1860	rtol = 0.01_wp
	1861	!
	1862	!-- Try to find chemistry package
	1863	REWIND ( 11 )
	1864	line = ' '
	1865	DO WHILE ( INDEX( line, '&chemistry_parameters' ) == 0 )
[3287]	1866	READ ( 11, '(A)', END=20 ) line
[3281]	1867	ENDDO
	1868	BACKSPACE ( 11 )
	1869	!
	1870	!-- Read chemistry namelist
[3287]	1871	READ ( 11, chemistry_parameters, ERR = 10, END = 20 )
[3281]	1872	!
	1873	!-- Enable chemistry model
	1874	air_chemistry = .TRUE.
[3287]	1875	GOTO 20
	1876
	1877	10 BACKSPACE( 11 )
	1878	READ( 11 , '(A)') line
	1879	CALL parin_fail_message( 'chemistry_parameters', line )
	1880
	1881	20 CONTINUE
	1882
	1883	!
	1884	!-- check for emission mode for chem species
[3281]	1885	IF ( (mode_emis /= 'PARAMETERIZED') .AND. ( mode_emis /= 'DEFAULT') .AND. (mode_emis /= 'PRE-PROCESSED' ) ) THEN
	1886	message_string = 'Incorrect mode_emiss option select. Please check spelling'
	1887	CALL message( 'chem_check_parameters', 'CM0436', 1, 2, 0, 6, 0 )
	1888	ENDIF
[2425]	1889
[3282]	1890	t_steps = my_steps
	1891
	1892	!-- Determine the number of user-defined profiles and append them to the
	1893	!-- standard data output (data_output_pr)
[3085]	1894	max_pr_cs_tmp = 0
	1895	i = 1
[2425]	1896
[3085]	1897	DO WHILE ( data_output_pr(i) /= ' ' .AND. i <= 100 )
	1898	IF ( TRIM( data_output_pr(i)(1:3)) == 'kc_' ) THEN
	1899	max_pr_cs_tmp = max_pr_cs_tmp+1
[2615]	1900	ENDIF
[3085]	1901	i = i +1
[2615]	1902	ENDDO
[2425]	1903
[3085]	1904	IF ( max_pr_cs_tmp > 0 ) THEN
	1905	cs_pr_namelist_found = .TRUE.
	1906	max_pr_cs = max_pr_cs_tmp
[2914]	1907	ENDIF
[3185]	1908
	1909	! Set Solver Type
[3260]	1910	IF(icntrl(3) == 0) THEN
[3185]	1911	solver_type = 'rodas3' !Default
[3260]	1912	ELSE IF(icntrl(3) == 1) THEN
[3185]	1913	solver_type = 'ros2'
[3260]	1914	ELSE IF(icntrl(3) == 2) THEN
[3185]	1915	solver_type = 'ros3'
[3260]	1916	ELSE IF(icntrl(3) == 3) THEN
[3185]	1917	solver_type = 'ro4'
[3260]	1918	ELSE IF(icntrl(3) == 4) THEN
[3185]	1919	solver_type = 'rodas3'
[3260]	1920	ELSE IF(icntrl(3) == 5) THEN
[3185]	1921	solver_type = 'rodas4'
[3260]	1922	ELSE IF(icntrl(3) == 6) THEN
[3185]	1923	solver_type = 'Rang3'
[3260]	1924	ELSE
[3373]	1925	message_string = 'illegal solver type'
	1926	CALL message( 'chem_parin', 'PA0506', 1, 2, 0, 6, 0 )
[3260]	1927	END IF
[3185]	1928
[3373]	1929	!
	1930	!-- todo: remove or replace by "CALL message" mechanism (kanani)
	1931	! write(text,*) 'gas_phase chemistry: solver_type = ',trim(solver_type)
[3185]	1932	!kk Has to be changed to right calling sequence
	1933	!kk CALL location_message( trim(text), .FALSE. )
[3373]	1934	! IF(myid == 0) THEN
	1935	! write(9,*) ' '
	1936	! write(9,*) 'kpp setup '
	1937	! write(9,*) ' '
	1938	! write(9,*) ' gas_phase chemistry: solver_type = ',trim(solver_type)
	1939	! write(9,*) ' '
	1940	! write(9,*) ' Hstart = ',rcntrl(3)
	1941	! write(9,*) ' FacMin = ',rcntrl(4)
	1942	! write(9,*) ' FacMax = ',rcntrl(5)
	1943	! write(9,*) ' '
	1944	! IF(vl_dim > 1) THEN
	1945	! write(9,*) ' Vector mode vektor length = ',vl_dim
	1946	! ELSE
	1947	! write(9,*) ' Scalar mode'
	1948	! ENDIF
	1949	! write(9,*) ' '
	1950	! END IF
[3185]	1951
[3281]	1952	RETURN
[2491]	1953
[3281]	1954	END SUBROUTINE chem_parin
[2467]	1955
	1956	!
[2828]	1957	!------------------------------------------------------------------------------!
[2467]	1958	!
[2828]	1959	! Description:
	1960	! ------------
	1961	!> Subroutine calculating prognostic equations for chemical species
	1962	!> (vector-optimized).
	1963	!> Routine is called separately for each chemical species over a loop from
	1964	!> prognostic_equations.
	1965	!------------------------------------------------------------------------------!
[3281]	1966	SUBROUTINE chem_prognostic_equations ( cs_scalar_p, cs_scalar, tcs_scalar_m, &
	1967	pr_init_cs, ilsp )
[2467]	1968
[3281]	1969	USE advec_s_pw_mod, &
	1970	ONLY: advec_s_pw
	1971	USE advec_s_up_mod, &
	1972	ONLY: advec_s_up
	1973	USE advec_ws, &
	1974	ONLY: advec_s_ws
	1975	USE diffusion_s_mod, &
	1976	ONLY: diffusion_s
	1977	USE indices, &
	1978	ONLY: nxl, nxr, nyn, nys, wall_flags_0
	1979	USE pegrid
	1980	USE surface_mod, &
	1981	ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
	1982	surf_usm_v
[2828]	1983
[3281]	1984	IMPLICIT NONE
[2828]	1985
[3281]	1986	INTEGER :: i !< running index
	1987	INTEGER :: j !< running index
	1988	INTEGER :: k !< running index
[2828]	1989
[3281]	1990	INTEGER(iwp),INTENT(IN) :: ilsp !<
[2828]	1991
[3281]	1992	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
[2828]	1993
[3281]	1994	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar !<
	1995	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p !<
	1996	REAL(wp), DIMENSION(:,:,:), POINTER :: tcs_scalar_m !<
[2828]	1997
	1998
[3281]	1999	!
	2000	!-- Tendency terms for chemical species
	2001	tend = 0.0_wp
	2002	!
	2003	!-- Advection terms
	2004	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	2005	IF ( ws_scheme_sca ) THEN
	2006	CALL advec_s_ws( cs_scalar, 'kc' )
	2007	ELSE
	2008	CALL advec_s_pw( cs_scalar )
	2009	ENDIF
[2828]	2010	ELSE
[3281]	2011	CALL advec_s_up( cs_scalar )
[2828]	2012	ENDIF
[3281]	2013	!
	2014	!-- Diffusion terms (the last three arguments are zero)
	2015	CALL diffusion_s( cs_scalar, &
	2016	surf_def_h(0)%cssws(ilsp,:), &
	2017	surf_def_h(1)%cssws(ilsp,:), &
	2018	surf_def_h(2)%cssws(ilsp,:), &
	2019	surf_lsm_h%cssws(ilsp,:), &
	2020	surf_usm_h%cssws(ilsp,:), &
	2021	surf_def_v(0)%cssws(ilsp,:), &
	2022	surf_def_v(1)%cssws(ilsp,:), &
	2023	surf_def_v(2)%cssws(ilsp,:), &
	2024	surf_def_v(3)%cssws(ilsp,:), &
	2025	surf_lsm_v(0)%cssws(ilsp,:), &
	2026	surf_lsm_v(1)%cssws(ilsp,:), &
	2027	surf_lsm_v(2)%cssws(ilsp,:), &
	2028	surf_lsm_v(3)%cssws(ilsp,:), &
	2029	surf_usm_v(0)%cssws(ilsp,:), &
	2030	surf_usm_v(1)%cssws(ilsp,:), &
	2031	surf_usm_v(2)%cssws(ilsp,:), &
	2032	surf_usm_v(3)%cssws(ilsp,:) )
	2033	!
	2034	!-- Prognostic equation for chemical species
	2035	DO i = nxl, nxr
	2036	DO j = nys, nyn
	2037	DO k = nzb+1, nzt
	2038	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) &
	2039	+ ( dt_3d * &
	2040	( tsc(2) * tend(k,j,i) &
	2041	+ tsc(3) * tcs_scalar_m(k,j,i) &
	2042	) &
	2043	- tsc(5) * rdf_sc(k) &
	2044	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
	2045	) &
	2046	* MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_0(k,j,i), 0 ) )
[2828]	2047
[3281]	2048	IF ( cs_scalar_p(k,j,i) < 0.0_wp ) cs_scalar_p(k,j,i) = 0.1_wp * cs_scalar(k,j,i)
	2049	ENDDO
[2828]	2050	ENDDO
	2051	ENDDO
[3281]	2052	!
	2053	!-- Calculate tendencies for the next Runge-Kutta step
	2054	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	2055	IF ( intermediate_timestep_count == 1 ) THEN
	2056	DO i = nxl, nxr
	2057	DO j = nys, nyn
	2058	DO k = nzb+1, nzt
	2059	tcs_scalar_m(k,j,i) = tend(k,j,i)
	2060	ENDDO
[2828]	2061	ENDDO
	2062	ENDDO
[3281]	2063	ELSEIF ( intermediate_timestep_count < &
	2064	intermediate_timestep_count_max ) THEN
	2065	DO i = nxl, nxr
	2066	DO j = nys, nyn
	2067	DO k = nzb+1, nzt
	2068	tcs_scalar_m(k,j,i) = - 9.5625_wp * tend(k,j,i) &
	2069	+ 5.3125_wp * tcs_scalar_m(k,j,i)
	2070	ENDDO
[2828]	2071	ENDDO
	2072	ENDDO
[3281]	2073	ENDIF
[2828]	2074	ENDIF
	2075
[3281]	2076	END SUBROUTINE chem_prognostic_equations
[3228]	2077
[2482]	2078	!------------------------------------------------------------------------------!
[2535]	2079	!
[2482]	2080	! Description:
	2081	! ------------
[3085]	2082	!> Subroutine calculating prognostic equations for chemical species
	2083	!> (cache-optimized).
	2084	!> Routine is called separately for each chemical species over a loop from
	2085	!> prognostic_equations.
[2482]	2086	!------------------------------------------------------------------------------!
[3281]	2087	SUBROUTINE chem_prognostic_equations_ij ( cs_scalar_p, cs_scalar, tcs_scalar_m, pr_init_cs, &
	2088	i, j, i_omp_start, tn, ilsp, flux_s_cs, diss_s_cs, &
	2089	flux_l_cs, diss_l_cs )
	2090	USE pegrid
	2091	USE advec_ws, ONLY: advec_s_ws
	2092	USE advec_s_pw_mod, ONLY: advec_s_pw
	2093	USE advec_s_up_mod, ONLY: advec_s_up
	2094	USE diffusion_s_mod, ONLY: diffusion_s
	2095	USE indices, ONLY: wall_flags_0
	2096	USE surface_mod, ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
	2097	surf_usm_v
[3085]	2098
	2099
[3281]	2100	IMPLICIT NONE
[3085]	2101
[3281]	2102	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p, cs_scalar, tcs_scalar_m
[3085]	2103
[3281]	2104	INTEGER(iwp),INTENT(IN) :: i, j, i_omp_start, tn, ilsp
	2105	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: flux_s_cs !<
	2106	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: diss_s_cs !<
	2107	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: flux_l_cs !<
	2108	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: diss_l_cs !<
	2109	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
[3085]	2110
	2111	!-- local variables
	2112
[3281]	2113	INTEGER :: k
	2114	!
	2115	!-- Tendency-terms for chem spcs.
	2116	tend(:,j,i) = 0.0_wp
[3085]	2117	!
	2118	!-- Advection terms
[3281]	2119	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	2120	IF ( ws_scheme_sca ) THEN
	2121	CALL advec_s_ws( i, j, cs_scalar, 'kc', flux_s_cs, diss_s_cs, &
	2122	flux_l_cs, diss_l_cs, i_omp_start, tn )
	2123	ELSE
	2124	CALL advec_s_pw( i, j, cs_scalar )
	2125	ENDIF
[3085]	2126	ELSE
[3281]	2127	CALL advec_s_up( i, j, cs_scalar )
[3085]	2128	ENDIF
	2129
	2130	!
	2131
	2132	!-- Diffusion terms (the last three arguments are zero)
	2133
[3281]	2134	CALL diffusion_s( i, j, cs_scalar, &
	2135	surf_def_h(0)%cssws(ilsp,:), surf_def_h(1)%cssws(ilsp,:), &
	2136	surf_def_h(2)%cssws(ilsp,:), &
	2137	surf_lsm_h%cssws(ilsp,:), surf_usm_h%cssws(ilsp,:), &
	2138	surf_def_v(0)%cssws(ilsp,:), surf_def_v(1)%cssws(ilsp,:), &
	2139	surf_def_v(2)%cssws(ilsp,:), surf_def_v(3)%cssws(ilsp,:), &
	2140	surf_lsm_v(0)%cssws(ilsp,:), surf_lsm_v(1)%cssws(ilsp,:), &
	2141	surf_lsm_v(2)%cssws(ilsp,:), surf_lsm_v(3)%cssws(ilsp,:), &
	2142	surf_usm_v(0)%cssws(ilsp,:), surf_usm_v(1)%cssws(ilsp,:), &
	2143	surf_usm_v(2)%cssws(ilsp,:), surf_usm_v(3)%cssws(ilsp,:) )
	2144
[3085]	2145	!
	2146	!-- Prognostic equation for chem spcs
[3281]	2147	DO k = nzb+1, nzt
	2148	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) + ( dt_3d * &
	2149	( tsc(2) * tend(k,j,i) + &
	2150	tsc(3) * tcs_scalar_m(k,j,i) ) &
	2151	- tsc(5) * rdf_sc(k) &
	2152	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
	2153	) &
	2154	* MERGE( 1.0_wp, 0.0_wp, &
	2155	BTEST( wall_flags_0(k,j,i), 0 ) &
	2156	)
[2467]	2157
[3281]	2158	IF ( cs_scalar_p(k,j,i) < 0.0_wp ) cs_scalar_p(k,j,i) = 0.1_wp * cs_scalar(k,j,i) !FKS6
	2159	ENDDO
[3085]	2160
[2482]	2161	!
[3085]	2162	!-- Calculate tendencies for the next Runge-Kutta step
[3281]	2163	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	2164	IF ( intermediate_timestep_count == 1 ) THEN
	2165	DO k = nzb+1, nzt
	2166	tcs_scalar_m(k,j,i) = tend(k,j,i)
	2167	ENDDO
	2168	ELSEIF ( intermediate_timestep_count < &
	2169	intermediate_timestep_count_max ) THEN
	2170	DO k = nzb+1, nzt
	2171	tcs_scalar_m(k,j,i) = -9.5625_wp * tend(k,j,i) + &
	2172	5.3125_wp * tcs_scalar_m(k,j,i)
	2173	ENDDO
	2174	ENDIF
[3085]	2175	ENDIF
	2176
[3281]	2177	END SUBROUTINE chem_prognostic_equations_ij
[3085]	2178
[2482]	2179	!
[3085]	2180	!------------------------------------------------------------------------------!
	2181	!
	2182	! Description:
	2183	! ------------
	2184	!> Subroutine to read restart data of chemical species
	2185	!------------------------------------------------------------------------------!
[2828]	2186
[3281]	2187	SUBROUTINE chem_rrd_local( i, k, nxlf, nxlc, nxl_on_file, nxrf, nxrc, &
	2188	nxr_on_file, nynf, nync, nyn_on_file, nysf, nysc, &
	2189	nys_on_file, tmp_3d, found )
	2190
	2191	USE control_parameters
	2192
	2193	USE indices
	2194
	2195	USE pegrid
[3085]	2196
[3281]	2197	IMPLICIT NONE
[3085]	2198
[3281]	2199	CHARACTER (LEN=20) :: spc_name_av !<
	2200
	2201	INTEGER(iwp) :: i, lsp !<
	2202	INTEGER(iwp) :: k !<
	2203	INTEGER(iwp) :: nxlc !<
	2204	INTEGER(iwp) :: nxlf !<
	2205	INTEGER(iwp) :: nxl_on_file !<
	2206	INTEGER(iwp) :: nxrc !<
	2207	INTEGER(iwp) :: nxrf !<
	2208	INTEGER(iwp) :: nxr_on_file !<
	2209	INTEGER(iwp) :: nync !<
	2210	INTEGER(iwp) :: nynf !<
	2211	INTEGER(iwp) :: nyn_on_file !<
	2212	INTEGER(iwp) :: nysc !<
	2213	INTEGER(iwp) :: nysf !<
	2214	INTEGER(iwp) :: nys_on_file !<
[3085]	2215
[3281]	2216	LOGICAL, INTENT(OUT) :: found
[3085]	2217
[3281]	2218	REAL(wp), DIMENSION(nzb:nzt+1,nys_on_file-nbgp:nyn_on_file+nbgp,nxl_on_file-nbgp:nxr_on_file+nbgp) :: tmp_3d !< 3D array to temp store data
[3085]	2219
	2220
[3281]	2221	found = .FALSE.
[3085]	2222
	2223
[3281]	2224	IF ( ALLOCATED(chem_species) ) THEN
[3085]	2225
[3281]	2226	DO lsp = 1, nspec
[3085]	2227
[3281]	2228	!< for time-averaged chemical conc.
	2229	spc_name_av = TRIM(chem_species(lsp)%name)//'_av'
[3085]	2230
[3281]	2231	IF (restart_string(1:length) == TRIM(chem_species(lsp)%name) ) &
	2232	THEN
	2233	!< read data into tmp_3d
	2234	IF ( k == 1 ) READ ( 13 ) tmp_3d
	2235	!< fill ..%conc in the restart run
	2236	chem_species(lsp)%conc(:,nysc-nbgp:nync+nbgp, &
	2237	nxlc-nbgp:nxrc+nbgp) = &
	2238	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
	2239	found = .TRUE.
	2240	ELSEIF (restart_string(1:length) == spc_name_av ) THEN
	2241	IF ( k == 1 ) READ ( 13 ) tmp_3d
	2242	chem_species(lsp)%conc_av(:,nysc-nbgp:nync+nbgp, &
	2243	nxlc-nbgp:nxrc+nbgp) = &
	2244	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
	2245	found = .TRUE.
	2246	ENDIF
[3085]	2247
[3281]	2248	ENDDO
[3085]	2249
[3281]	2250	ENDIF
[3085]	2251
	2252
[3281]	2253	END SUBROUTINE chem_rrd_local
[3085]	2254	!
	2255	!-------------------------------------------------------------------------------!
	2256	!> Description:
	2257	!> Calculation of horizontally averaged profiles
	2258	!> This routine is called for every statistic region (sr) defined by the user,
	2259	!> but at least for the region "total domain" (sr=0).
	2260	!> quantities.
[2828]	2261	!------------------------------------------------------------------------------!
[3281]	2262	SUBROUTINE chem_statistics( mode, sr, tn )
[3085]	2263
	2264
[3281]	2265	USE arrays_3d
	2266	USE indices
	2267	USE kinds
	2268	USE pegrid
	2269	USE statistics
[3085]	2270
	2271	USE user
	2272
	2273	IMPLICIT NONE
	2274
	2275	CHARACTER (LEN=*) :: mode !<
	2276
	2277	INTEGER(iwp) :: i !< running index on x-axis
	2278	INTEGER(iwp) :: j !< running index on y-axis
	2279	INTEGER(iwp) :: k !< vertical index counter
	2280	INTEGER(iwp) :: sr !< statistical region
	2281	INTEGER(iwp) :: tn !< thread number
	2282	INTEGER(iwp) :: n !<
	2283	INTEGER(iwp) :: m !<
	2284	INTEGER(iwp) :: lpr !< running index chem spcs
	2285	! REAL(wp), &
	2286	! DIMENSION(dots_num_palm+1:dots_max) :: &
	2287	! ts_value_l !<
	2288
	2289	IF ( mode == 'profiles' ) THEN
[2615]	2290	!
[3085]	2291	!-- Sample on how to calculate horizontally averaged profiles of user-
	2292	!-- defined quantities. Each quantity is identified by the index
	2293	!-- "pr_palm+#" where "#" is an integer starting from 1. These
	2294	!-- user-profile-numbers must also be assigned to the respective strings
	2295	!-- given by data_output_pr_cs in routine user_check_data_output_pr.
	2296	!-- hom(:,:,:,:) = dim-1 = vertical level, dim-2= 1: met-species,2:zu/zw, dim-3 = quantity( e.g.
	2297	! wpt), dim-4 = statistical region.
	2298
	2299	!$OMP DO
	2300	DO i = nxl, nxr
	2301	DO j = nys, nyn
	2302	DO k = nzb, nzt+1
	2303	DO lpr = 1, cs_pr_count
	2304
	2305	sums_l(k,pr_palm+lpr,tn) = sums_l(k,pr_palm+lpr,tn) + &
	2306	chem_species(cs_pr_index(lpr))%conc(k,j,i) * &
	2307	rmask(j,i,sr) * &
	2308	MERGE( 1.0_wp, 0.0_wp, &
	2309	BTEST( wall_flags_0(k,j,i), 22 ) )
	2310	ENDDO
	2311	ENDDO
	2312	ENDDO
	2313	ENDDO
	2314	ELSEIF ( mode == 'time_series' ) THEN
[3282]	2315	CALL location_message( 'Time series not calculated for chemistry', .TRUE. )
	2316	ENDIF
[3085]	2317
[3281]	2318	END SUBROUTINE chem_statistics
[3085]	2319	!
	2320	!------------------------------------------------------------------------------!
	2321	!
[2828]	2322	! Description:
	2323	! ------------
[3085]	2324	!> Subroutine for swapping of timelevels for chemical species
	2325	!> called out from subroutine swap_timelevel
	2326	!------------------------------------------------------------------------------!
	2327
[3281]	2328	SUBROUTINE chem_swap_timelevel (level)
[3085]	2329
[3281]	2330	IMPLICIT none
[3085]	2331
[3281]	2332	INTEGER,INTENT(IN) :: level
	2333	!-- local variables
	2334	INTEGER :: lsp
[3085]	2335
[3298]	2336
[3281]	2337	IF ( level == 0 ) THEN
	2338	DO lsp=1, nvar
	2339	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
	2340	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
	2341	ENDDO
	2342	ELSE
	2343	DO lsp=1, nvar
	2344	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
	2345	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
	2346	ENDDO
	2347	ENDIF
[3085]	2348
[3281]	2349	RETURN
	2350	END SUBROUTINE chem_swap_timelevel
[3085]	2351	!
[2615]	2352	!------------------------------------------------------------------------------!
[3085]	2353	!
[2615]	2354	! Description:
	2355	! ------------
[3085]	2356	!> Subroutine to write restart data for chemistry model
[2615]	2357	!------------------------------------------------------------------------------!
[3281]	2358	SUBROUTINE chem_wrd_local
[2482]	2359
[3281]	2360	IMPLICIT NONE
[2615]	2361
[3281]	2362	INTEGER(iwp) :: lsp !<
[2615]	2363
[3281]	2364	DO lsp = 1, nspec
	2365	CALL wrd_write_string( TRIM( chem_species(lsp)%name ))
	2366	WRITE ( 14 ) chem_species(lsp)%conc
	2367	CALL wrd_write_string( TRIM( chem_species(lsp)%name )//'_av' )
	2368	WRITE ( 14 ) chem_species(lsp)%conc_av
	2369	ENDDO
[2615]	2370
[3281]	2371	END SUBROUTINE chem_wrd_local
[2615]	2372	END MODULE chemistry_model_mod
	2373

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