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source: palm/trunk/SOURCE/chemistry_model_mod.f90 @ 3449

Last change on this file since 3449 was 3449, checked in by suehring, 5 years ago
Branch resler -r 3439 re-integrated into current trunk: RTM 3.0, transpiration of plant canopy, output fixes in USM
Property svn:keywords set to `Id`
File size: 101.1 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 3449 2018-10-29 19:36:56Z suehring $
[3449]	29	! additional output - merged from branch resler
	30	!
	31	! 3438 2018-10-28 19:31:42Z pavelkrc
[3435]	32	! Add terrain-following masked output
	33	!
	34	! 3373 2018-10-18 15:25:56Z kanani
[3373]	35	! Remove MPI_Abort, replace by message
	36	!
	37	! 3318 2018-10-08 11:43:01Z sward
[3318]	38	! Fixed faulty syntax of message string
	39	!
	40	! 3298 2018-10-02 12:21:11Z kanani
[3298]	41	! Add remarks (kanani)
[3292]	42	! Merge with trunk, replaced cloud_physics by bulk_cloud_model 28.09.2018 forkel
[3281]	43	! Subroutines header and chem_check_parameters added 25.09.2018 basit
[3190]	44	! Removed chem_emission routine now declared in chem_emissions.f90 30.07.2018 ERUSSO
	45	! Introduced emissions namelist parameters 30.07.2018 ERUSSO
[3188]	46	!
	47	! Timestep steering added in subroutine chem_integrate_ij and
	48	! output of chosen solver in chem_parin added 30.07.2018 ketelsen
	49	!
	50	! chem_check_data_output_pr: added unit for PM compounds 20.07.2018 forkel
	51	! replaced : by nzb+1:nzt for pt,q,ql (found by kk) 18.07.2018 forkel
[3140]	52	! debugged restart run for chem species 06.07.2018 basit
	53	! reorganized subroutines in alphabetical order. 27.06.2018 basit
	54	! subroutine chem_parin updated for profile output 27.06.2018 basit
[3114]	55	! Added humidity arrays to USE section and tmp_qvap in chem_integrate 26.6.2018 forkel
	56	! Merged chemistry with with trunk (nzb_do and nzt_do in 3d output) 26.6.2018 forkel
	57	!
[3140]	58	! reorganized subroutines in alphabetical order. basit 22.06.2018
	59	! subroutine chem_parin updated for profile output basit 22.06.2018
	60	! subroutine chem_statistics added
	61	! subroutine chem_check_data_output_pr add 21.06.2018 basit
	62	! subroutine chem_data_output_mask added 20.05.2018 basit
	63	! subroutine chem_data_output_2d added 20.05.2018 basit
	64	! subroutine chem_statistics added 04.06.2018 basit
[2914]	65	! subroutine chem_emissions: Set cssws to zero before setting values 20.03.2018 forkel
[2900]	66	! subroutine chem_emissions: Introduced different conversion factors
	67	! for PM and gaseous compounds 15.03.2018 forkel
[2888]	68	! subroutine chem_emissions updated to take variable number of chem_spcs and
[3140]	69	! emission factors. 13.03.2018 basit
	70	! chem_boundary_conds_decycle improved. 05.03.2018 basit
	71	! chem_boundary_conds_decycle subroutine added 21.02.2018 basit
[3188]	72	! chem_init_profiles subroutines re-activated after correction 21.02.2018 basit
[2616]	73	!
[2828]	74	!
[3298]	75	! 3293 2018-09-28 12:45:20Z forkel
[3287]	76	! Modularization of all bulk cloud physics code components
	77	!
	78	! 3248 2018-09-14 09:42:06Z sward
	79	! Minor formating changes
	80	!
	81	! 3246 2018-09-13 15:14:50Z sward
	82	! Added error handling for input namelist via parin_fail_message
	83	!
	84	! 3241 2018-09-12 15:02:00Z raasch
[3228]	85	! +nest_chemistry
	86	!
	87	! 3209 2018-08-27 16:58:37Z suehring
	88	! Rename flags indicating outflow boundary conditions
	89	!
	90	! 3182 2018-07-27 13:36:03Z suehring
	91	! Revise output of surface quantities in case of overhanging structures
	92	!
	93	! 3045 2018-05-28 07:55:41Z Giersch
[3114]	94	! error messages revised
	95	!
	96	! 3014 2018-05-09 08:42:38Z maronga
	97	! Bugfix: nzb_do and nzt_do were not used for 3d data output
	98	!
	99	! 3004 2018-04-27 12:33:25Z Giersch
	100	! Comment concerning averaged data output added
	101	!
	102	! 2932 2018-03-26 09:39:22Z maronga
[2981]	103	! renamed chemistry_par to chemistry_parameters
	104	!
	105	! 2894 2018-03-15 09:17:58Z Giersch
[2914]	106	! Calculations of the index range of the subdomain on file which overlaps with
	107	! the current subdomain are already done in read_restart_data_mod,
	108	! chem_last_actions was renamed to chem_wrd_local, chem_read_restart_data was
	109	! renamed to chem_rrd_local, chem_write_var_list was renamed to
	110	! chem_wrd_global, chem_read_var_list was renamed to chem_rrd_global,
	111	! chem_skip_var_list has been removed, variable named found has been
	112	! introduced for checking if restart data was found, reading of restart strings
	113	! has been moved completely to read_restart_data_mod, chem_rrd_local is already
	114	! inside the overlap loop programmed in read_restart_data_mod, todo list has
	115	! bees extended, redundant characters in chem_wrd_local have been removed,
	116	! the marker * end chemistry * is not necessary anymore, strings and their
	117	! respective lengths are written out and read now in case of restart runs to
	118	! get rid of prescribed character lengths
	119	!
	120	! 2815 2018-02-19 11:29:57Z suehring
[2828]	121	! Bugfix in restart mechanism,
	122	! rename chem_tendency to chem_prognostic_equations,
	123	! implement vector-optimized version of chem_prognostic_equations,
	124	! some clean up (incl. todo list)
[2656]	125	!
[2828]	126	! 2773 2018-01-30 14:12:54Z suehring
	127	! Declare variables required for nesting as public
[2656]	128	!
[2828]	129	! 2772 2018-01-29 13:10:35Z suehring
	130	! Bugfix in string handling
[2635]	131	!
[2828]	132	! 2768 2018-01-24 15:38:29Z kanani
	133	! Shorten lines to maximum length of 132 characters
[2633]	134	!
[2828]	135	! 2766 2018-01-22 17:17:47Z kanani
	136	! Removed preprocessor directive __chem
[2633]	137	!
[2828]	138	! 2756 2018-01-16 18:11:14Z suehring
	139	! Fill values in 3D output introduced.
[2627]	140	!
[2828]	141	! 2718 2018-01-02 08:49:38Z maronga
	142	! Initial revision
	143	!
[2452]	144	!
[2828]	145	!
	146	!
	147	! Authors:
	148	! --------
	149	! @author Renate Forkel
	150	! @author Farah Kanani-Suehring
	151	! @author Klaus Ketelsen
	152	! @author Basit Khan
	153	!
	154	!
[2426]	155	!------------------------------------------------------------------------------!
[2425]	156	! Description:
	157	! ------------
[2592]	158	!> Chemistry model for PALM-4U
[2914]	159	!> @todo Adjust chem_rrd_local to CASE structure of others modules. It is not
	160	!> allowed to use the chemistry model in a precursor run and additionally
	161	!> not using it in a main run
[2828]	162	!> @todo Update/clean-up todo list! (FK)
	163	!> @todo Set proper fill values (/= 0) for chem output arrays! (FK)
	164	!> @todo Add routine chem_check_parameters, add checks for inconsistent or
	165	!> unallowed parameter settings.
	166	!> CALL of chem_check_parameters from check_parameters. (FK)
	167	!> @todo Make routine chem_header available, CALL from header.f90
	168	!> (see e.g. how it is done in routine lsm_header in
	169	!> land_surface_model_mod.f90). chem_header should include all setup
	170	!> info about chemistry parameter settings. (FK)
[2592]	171	!> @todo Implement turbulent inflow of chem spcs in inflow_turbulence.
	172	!> @todo Separate boundary conditions for each chem spcs to be implemented
	173	!> @todo Currently only total concentration are calculated. Resolved, parameterized
	174	!> and chemistry fluxes although partially and some completely coded but
	175	!> are not operational/activated in this version. bK.
	176	!> @todo slight differences in passive scalar and chem spcs when chem reactions
	177	!> turned off. Need to be fixed. bK
[2828]	178	!> @todo test nesting for chem spcs, was implemented by suehring (kanani)
[2592]	179	!> @todo chemistry error messages
[2425]	180	!> @todo Format this module according to PALM coding standard (see e.g. module
	181	!> template under http://palm.muk.uni-hannover.de/mosaik/downloads/8 or
	182	!> D3_coding_standard.pdf under https://palm.muk.uni-hannover.de/trac/downloads/16)
[2482]	183	!
[2425]	184	!------------------------------------------------------------------------------!
	185
[3281]	186	MODULE chemistry_model_mod
[2828]	187
[3281]	188	USE kinds, ONLY: wp, iwp
[3282]	189	USE indices, ONLY: nz, nzb,nzt,nysg,nyng,nxlg,nxrg, &
[3114]	190	nys,nyn,nx,nxl,nxr,ny,wall_flags_0
[3281]	191	USE pegrid, ONLY: myid, threads_per_task
[3293]	192
	193	USE bulk_cloud_model_mod, &
	194	ONLY: bulk_cloud_model
	195
	196	USE control_parameters, ONLY: bc_lr_cyc, bc_ns_cyc, dt_3d, humidity, &
[3282]	197	initializing_actions, message_string, &
	198	omega, tsc, intermediate_timestep_count, &
	199	intermediate_timestep_count_max, &
[3287]	200	timestep_scheme, use_prescribed_profile_data, ws_scheme_sca
	201	USE arrays_3d, ONLY: exner, hyp, pt, q, ql, rdf_sc, tend, zu
[3282]	202	USE chem_gasphase_mod, ONLY: nspec, spc_names, nkppctrl, nmaxfixsteps, &
	203	t_steps, chem_gasphase_integrate, vl_dim, &
	204	nvar, nreact, atol, rtol, nphot, phot_names
[3281]	205	USE cpulog, ONLY: cpu_log, log_point
[2425]	206
[3281]	207	USE chem_modules
[2615]	208
[3281]	209	USE statistics
[2615]	210
[3281]	211	IMPLICIT NONE
	212	PRIVATE
	213	SAVE
[2425]	214
[3281]	215	LOGICAL :: nest_chemistry = .TRUE. !< flag for nesting mode of chemical species, independent on parent or not
[3228]	216	!
[2425]	217	!- Define chemical variables
[3281]	218	TYPE species_def
	219	CHARACTER(LEN=8) :: name
	220	CHARACTER(LEN=16) :: unit
	221	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc
	222	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_av
	223	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_p
	224	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: tconc_m
	225	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: cssws_av
	226	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: flux_s_cs
	227	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: diss_s_cs
	228	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: flux_l_cs
	229	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: diss_l_cs
	230	REAL(kind=wp),ALLOCATABLE,DIMENSION(:) :: conc_pr_init
	231	END TYPE species_def
[2425]	232
[2592]	233
[3281]	234	TYPE photols_def
	235	CHARACTER(LEN=8) :: name
	236	CHARACTER(LEN=16) :: unit
	237	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: freq
	238	END TYPE photols_def
[2425]	239
	240
[3281]	241	PUBLIC species_def
	242	PUBLIC photols_def
[2425]	243
[3228]	244
[3281]	245	TYPE(species_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: chem_species
	246	TYPE(photols_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: phot_frequen
[2425]	247
[3281]	248	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_1
	249	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_2
	250	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_3
	251	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_av
	252	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: freq_1
[2425]	253
[3281]	254	INTEGER,DIMENSION(nkppctrl) :: icntrl ! Fine tuning kpp
	255	REAL(kind=wp),DIMENSION(nkppctrl) :: rcntrl ! Fine tuning kpp
	256	LOGICAL :: decycle_chem_lr = .FALSE.
	257	LOGICAL :: decycle_chem_ns = .FALSE.
	258	CHARACTER (LEN=20), DIMENSION(4) :: decycle_method = &
[2854]	259	(/'dirichlet','dirichlet','dirichlet','dirichlet'/)
	260	!< Decycling method at horizontal boundaries,
	261	!< 1=left, 2=right, 3=south, 4=north
	262	!< dirichlet = initial size distribution and
	263	!< chemical composition set for the ghost and
	264	!< first three layers
	265	!< neumann = zero gradient
[2425]	266
[3449]	267	REAL(kind=wp), PUBLIC :: cs_time_step = 0._wp
[3281]	268	CHARACTER(10), PUBLIC :: photolysis_scheme
[3114]	269	! 'constant',
[2592]	270	! 'simple' (Simple parameterisation from MCM, Saunders et al., 2003, Atmos. Chem. Phys., 3, 161-180
	271	! 'fastj' (Wild et al., 2000, J. Atmos. Chem., 37, 245-282) STILL NOT IMPLEMENTED
[2535]	272
[3281]	273	PUBLIC nest_chemistry
	274	PUBLIC nspec
[3282]	275	PUBLIC nreact
[3281]	276	PUBLIC nvar
	277	PUBLIC spc_names
	278	PUBLIC spec_conc_2
[2425]	279
[3281]	280	!- Interface section
	281	INTERFACE chem_3d_data_averaging
	282	MODULE PROCEDURE chem_3d_data_averaging
	283	END INTERFACE chem_3d_data_averaging
[3228]	284
[3281]	285	INTERFACE chem_boundary_conds
	286	MODULE PROCEDURE chem_boundary_conds
	287	MODULE PROCEDURE chem_boundary_conds_decycle
	288	END INTERFACE chem_boundary_conds
[2425]	289
[3281]	290	INTERFACE chem_check_data_output
	291	MODULE PROCEDURE chem_check_data_output
	292	END INTERFACE chem_check_data_output
[2425]	293
[3281]	294	INTERFACE chem_data_output_2d
	295	MODULE PROCEDURE chem_data_output_2d
	296	END INTERFACE chem_data_output_2d
[2425]	297
[3281]	298	INTERFACE chem_data_output_3d
	299	MODULE PROCEDURE chem_data_output_3d
	300	END INTERFACE chem_data_output_3d
[2425]	301
[3281]	302	INTERFACE chem_data_output_mask
	303	MODULE PROCEDURE chem_data_output_mask
	304	END INTERFACE chem_data_output_mask
[3085]	305
[3281]	306	INTERFACE chem_check_data_output_pr
	307	MODULE PROCEDURE chem_check_data_output_pr
	308	END INTERFACE chem_check_data_output_pr
[3085]	309
[3281]	310	INTERFACE chem_check_parameters
	311	MODULE PROCEDURE chem_check_parameters
	312	END INTERFACE chem_check_parameters
[2425]	313
[3281]	314	INTERFACE chem_define_netcdf_grid
	315	MODULE PROCEDURE chem_define_netcdf_grid
	316	END INTERFACE chem_define_netcdf_grid
[2425]	317
[3281]	318	INTERFACE chem_header
	319	MODULE PROCEDURE chem_header
	320	END INTERFACE chem_header
[2425]	321
[3281]	322	INTERFACE chem_init
	323	MODULE PROCEDURE chem_init
	324	END INTERFACE chem_init
[2425]	325
[3281]	326	INTERFACE chem_init_profiles
	327	MODULE PROCEDURE chem_init_profiles
	328	END INTERFACE chem_init_profiles
[2425]	329
[3281]	330	INTERFACE chem_integrate
	331	MODULE PROCEDURE chem_integrate_ij
	332	END INTERFACE chem_integrate
[2425]	333
[3281]	334	INTERFACE chem_parin
	335	MODULE PROCEDURE chem_parin
	336	END INTERFACE chem_parin
[2425]	337
[3281]	338	INTERFACE chem_prognostic_equations
	339	MODULE PROCEDURE chem_prognostic_equations
	340	MODULE PROCEDURE chem_prognostic_equations_ij
	341	END INTERFACE chem_prognostic_equations
[3228]	342
[3281]	343	INTERFACE chem_rrd_local
	344	MODULE PROCEDURE chem_rrd_local
	345	END INTERFACE chem_rrd_local
[2467]	346
[3281]	347	INTERFACE chem_statistics
	348	MODULE PROCEDURE chem_statistics
	349	END INTERFACE chem_statistics
[3085]	350
[3281]	351	INTERFACE chem_swap_timelevel
	352	MODULE PROCEDURE chem_swap_timelevel
	353	END INTERFACE chem_swap_timelevel
	354
	355	INTERFACE chem_wrd_local
	356	MODULE PROCEDURE chem_wrd_local
	357	END INTERFACE chem_wrd_local
[2482]	358
[2615]	359
[3281]	360	PUBLIC chem_3d_data_averaging, chem_boundary_conds, chem_check_data_output, &
	361	chem_check_data_output_pr, chem_check_parameters, &
	362	chem_data_output_2d, chem_data_output_3d, chem_data_output_mask, &
	363	chem_define_netcdf_grid, chem_header, chem_init, &
	364	chem_init_profiles, chem_integrate, chem_parin, &
	365	chem_prognostic_equations, chem_rrd_local, &
	366	chem_statistics, chem_swap_timelevel, chem_wrd_local
[2425]	367
[3281]	368
	369
[2425]	370	CONTAINS
	371
[3228]	372	!
[2425]	373	!------------------------------------------------------------------------------!
[2535]	374	!
[2425]	375	! Description:
	376	! ------------
[3228]	377	!> Subroutine for averaging 3D data of chemical species. Due to the fact that
	378	!> the averaged chem arrays are allocated in chem_init, no if-query concerning
	379	!> the allocation is required (in any mode). Attention: If you just specify an
	380	!> averaged output quantity in the _p3dr file during restarts the first output
	381	!> includes the time between the beginning of the restart run and the first
	382	!> output time (not necessarily the whole averaging_interval you have
	383	!> specified in your _p3d/_p3dr file )
	384	!------------------------------------------------------------------------------!
	385
[3281]	386	SUBROUTINE chem_3d_data_averaging ( mode, variable )
[3228]	387
[3281]	388	USE control_parameters
[3228]	389
[3281]	390	USE indices
[3228]	391
[3281]	392	USE kinds
[3228]	393
[3281]	394	USE surface_mod, &
	395	ONLY: surf_def_h, surf_lsm_h, surf_usm_h
[3228]	396
[3281]	397	IMPLICIT NONE
[3228]	398
[3281]	399	CHARACTER (LEN=*) :: mode !<
	400	CHARACTER (LEN=*) :: variable !<
[3228]	401
[3281]	402	LOGICAL :: match_def !< flag indicating natural-type surface
	403	LOGICAL :: match_lsm !< flag indicating natural-type surface
	404	LOGICAL :: match_usm !< flag indicating urban-type surface
[3228]	405
[3281]	406	INTEGER(iwp) :: i !< grid index x direction
	407	INTEGER(iwp) :: j !< grid index y direction
	408	INTEGER(iwp) :: k !< grid index z direction
	409	INTEGER(iwp) :: m !< running index surface type
	410	INTEGER(iwp) :: lsp !< running index for chem spcs
[3228]	411
[3281]	412
	413	IF ( mode == 'allocate' ) THEN
	414	DO lsp = 1, nspec
[3449]	415	IF ( TRIM(variable(1:3)) == 'kc_' .AND. &
	416	TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
[3281]	417	chem_species(lsp)%conc_av = 0.0_wp
	418	ENDIF
	419	ENDDO
	420
	421	ELSEIF ( mode == 'sum' ) THEN
	422
	423	DO lsp = 1, nspec
[3449]	424	IF ( TRIM(variable(1:3)) == 'kc_' .AND. &
	425	TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
[3281]	426	DO i = nxlg, nxrg
	427	DO j = nysg, nyng
	428	DO k = nzb, nzt+1
	429	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) + &
	430	chem_species(lsp)%conc(k,j,i)
	431	ENDDO
[3228]	432	ENDDO
	433	ENDDO
[3281]	434	ELSEIF ( TRIM(variable(4:)) == TRIM('cssws*') ) THEN
	435	DO i = nxl, nxr
	436	DO j = nys, nyn
	437	match_def = surf_def_h(0)%start_index(j,i) <= &
	438	surf_def_h(0)%end_index(j,i)
	439	match_lsm = surf_lsm_h%start_index(j,i) <= &
	440	surf_lsm_h%end_index(j,i)
	441	match_usm = surf_usm_h%start_index(j,i) <= &
	442	surf_usm_h%end_index(j,i)
[3228]	443
[3281]	444	IF ( match_def ) THEN
	445	m = surf_def_h(0)%end_index(j,i)
	446	chem_species(lsp)%cssws_av(j,i) = &
	447	chem_species(lsp)%cssws_av(j,i) + &
	448	surf_def_h(0)%cssws(lsp,m)
	449	ELSEIF ( match_lsm .AND. .NOT. match_usm ) THEN
	450	m = surf_lsm_h%end_index(j,i)
	451	chem_species(lsp)%cssws_av(j,i) = &
	452	chem_species(lsp)%cssws_av(j,i) + &
	453	surf_lsm_h%cssws(lsp,m)
	454	ELSEIF ( match_usm ) THEN
	455	m = surf_usm_h%end_index(j,i)
	456	chem_species(lsp)%cssws_av(j,i) = &
	457	chem_species(lsp)%cssws_av(j,i) + &
	458	surf_usm_h%cssws(lsp,m)
	459	ENDIF
	460	ENDDO
[3228]	461	ENDDO
[3281]	462	ENDIF
	463	ENDDO
[3228]	464
[3281]	465	ELSEIF ( mode == 'average' ) THEN
	466	DO lsp = 1, nspec
[3449]	467	IF ( TRIM(variable(1:3)) == 'kc_' .AND. &
	468	TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
[3281]	469	DO i = nxlg, nxrg
	470	DO j = nysg, nyng
	471	DO k = nzb, nzt+1
	472	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) / REAL( average_count_3d, KIND=wp )
	473	ENDDO
[3228]	474	ENDDO
	475	ENDDO
	476
[3281]	477	ELSEIF (TRIM(variable(4:)) == TRIM('cssws*') ) THEN
	478	DO i = nxlg, nxrg
	479	DO j = nysg, nyng
	480	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) / REAL( average_count_3d, KIND=wp )
	481	ENDDO
[3228]	482	ENDDO
[3281]	483	CALL exchange_horiz_2d( chem_species(lsp)%cssws_av, nbgp )
	484	ENDIF
	485	ENDDO
	486
	487	ENDIF
[3228]	488
[3281]	489	END SUBROUTINE chem_3d_data_averaging
	490
	491	!
[3228]	492	!------------------------------------------------------------------------------!
	493	!
	494	! Description:
	495	! ------------
[2535]	496	!> Subroutine to initialize and set all boundary conditions for chemical species
[2425]	497	!------------------------------------------------------------------------------!
	498
[3281]	499	SUBROUTINE chem_boundary_conds( mode )
	500
	501	USE control_parameters, &
	502	ONLY: air_chemistry, bc_radiation_l, bc_radiation_n, bc_radiation_r, &
	503	bc_radiation_s
	504	USE indices, &
	505	ONLY: nxl, nxr, nxlg, nxrg, nyng, nysg, nzt
	506
[2425]	507
[3281]	508	USE arrays_3d, &
	509	ONLY: dzu
	510	USE surface_mod, &
	511	ONLY: bc_h
[2425]	512
[3281]	513	CHARACTER (len=*), INTENT(IN) :: mode
	514	INTEGER(iwp) :: i !< grid index x direction.
	515	INTEGER(iwp) :: j !< grid index y direction.
	516	INTEGER(iwp) :: k !< grid index z direction.
	517	INTEGER(iwp) :: kb !< variable to set respective boundary value, depends on facing.
	518	INTEGER(iwp) :: l !< running index boundary type, for up- and downward-facing walls.
	519	INTEGER(iwp) :: m !< running index surface elements.
	520	INTEGER(iwp) :: lsp !< running index for chem spcs.
	521	INTEGER(iwp) :: lph !< running index for photolysis frequencies
[2425]	522
[2615]	523
[3281]	524	SELECT CASE ( TRIM( mode ) )
	525	CASE ( 'init' )
[2626]	526
[3281]	527	IF ( bc_cs_b == 'dirichlet' ) THEN
	528	ibc_cs_b = 0
	529	ELSEIF ( bc_cs_b == 'neumann' ) THEN
	530	ibc_cs_b = 1
	531	ELSE
	532	message_string = 'unknown boundary condition: bc_cs_b ="' // TRIM( bc_cs_b ) // '"'
	533	CALL message( 'chem_boundary_conds', 'CM0429', 1, 2, 0, 6, 0 ) !<
	534	ENDIF
[2425]	535	!
[3281]	536	!-- Set Integer flags and check for possible erroneous settings for top
	537	!-- boundary condition.
	538	IF ( bc_cs_t == 'dirichlet' ) THEN
	539	ibc_cs_t = 0
	540	ELSEIF ( bc_cs_t == 'neumann' ) THEN
	541	ibc_cs_t = 1
	542	ELSEIF ( bc_cs_t == 'initial_gradient' ) THEN
	543	ibc_cs_t = 2
	544	ELSEIF ( bc_cs_t == 'nested' ) THEN
	545	ibc_cs_t = 3
	546	ELSE
	547	message_string = 'unknown boundary condition: bc_c_t ="' // TRIM( bc_cs_t ) // '"'
	548	CALL message( 'check_parameters', 'CM0430', 1, 2, 0, 6, 0 )
	549	ENDIF
[2425]	550
[3281]	551
	552	CASE ( 'set_bc_bottomtop' )
	553	!-- Bottom boundary condtions for chemical species
	554	DO lsp = 1, nspec
	555	IF ( ibc_cs_b == 0 ) THEN
	556	DO l = 0, 1
	557	!-- Set index kb: For upward-facing surfaces (l=0), kb=-1, i.e.
[3282]	558	!-- the chem_species(nspec)%conc_p value at the topography top (k-1)
[3281]	559	!-- is set; for downward-facing surfaces (l=1), kb=1, i.e. the
	560	!-- value at the topography bottom (k+1) is set.
[2425]	561
[3281]	562	kb = MERGE( -1, 1, l == 0 )
	563	!$OMP PARALLEL DO PRIVATE( i, j, k )
	564	DO m = 1, bc_h(l)%ns
	565	i = bc_h(l)%i(m)
	566	j = bc_h(l)%j(m)
	567	k = bc_h(l)%k(m)
	568	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc(k+kb,j,i)
	569	ENDDO
	570	ENDDO
	571
	572	ELSEIF ( ibc_cs_b == 1 ) THEN
	573	!-- in boundary_conds there is som extra loop over m here for passive tracer
	574	DO l = 0, 1
	575	kb = MERGE( -1, 1, l == 0 )
	576	!$OMP PARALLEL DO PRIVATE( i, j, k )
	577	DO m = 1, bc_h(l)%ns
	578	i = bc_h(l)%i(m)
	579	j = bc_h(l)%j(m)
	580	k = bc_h(l)%k(m)
	581	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc_p(k,j,i)
[2535]	582
[3281]	583	ENDDO
[2615]	584	ENDDO
[3281]	585	ENDIF
[3287]	586	ENDDO ! end lsp loop
[3281]	587
[3287]	588	!-- Top boundary conditions for chemical species - Should this not be done for all species?
[3281]	589	IF ( ibc_cs_t == 0 ) THEN
	590	DO lsp = 1, nspec
	591	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc(nzt+1,:,:)
[2615]	592	ENDDO
[3281]	593	ELSEIF ( ibc_cs_t == 1 ) THEN
	594	DO lsp = 1, nspec
	595	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:)
	596	ENDDO
	597	ELSEIF ( ibc_cs_t == 2 ) THEN
	598	DO lsp = 1, nspec
	599	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:) + bc_cs_t_val(lsp) * dzu(nzt+1)
	600	ENDDO
[2615]	601	ENDIF
[2425]	602	!
[3281]	603	CASE ( 'set_bc_lateral' )
	604	!-- Lateral boundary conditions for chem species at inflow boundary
	605	!-- are automatically set when chem_species concentration is
	606	!-- initialized. The initially set value at the inflow boundary is not
	607	!-- touched during time integration, hence, this boundary value remains
	608	!-- at a constant value, which is the concentration that flows into the
	609	!-- domain.
	610	!-- Lateral boundary conditions for chem species at outflow boundary
[2535]	611
[3281]	612	IF ( bc_radiation_s ) THEN
	613	DO lsp = 1, nspec
	614	chem_species(lsp)%conc_p(:,nys-1,:) = chem_species(lsp)%conc_p(:,nys,:)
	615	ENDDO
	616	ELSEIF ( bc_radiation_n ) THEN
	617	DO lsp = 1, nspec
	618	chem_species(lsp)%conc_p(:,nyn+1,:) = chem_species(lsp)%conc_p(:,nyn,:)
	619	ENDDO
	620	ELSEIF ( bc_radiation_l ) THEN
	621	DO lsp = 1, nspec
	622	chem_species(lsp)%conc_p(:,:,nxl-1) = chem_species(lsp)%conc_p(:,:,nxl)
	623	ENDDO
	624	ELSEIF ( bc_radiation_r ) THEN
	625	DO lsp = 1, nspec
	626	chem_species(lsp)%conc_p(:,:,nxr+1) = chem_species(lsp)%conc_p(:,:,nxr)
	627	ENDDO
	628	ENDIF
	629
	630	END SELECT
[2535]	631
[3281]	632	END SUBROUTINE chem_boundary_conds
[2831]	633
[2425]	634	!
[2535]	635	!------------------------------------------------------------------------------!
[2831]	636	! Description:
	637	! ------------
	638	!> Boundary conditions for prognostic variables in chemistry: decycling in the
	639	!> x-direction
	640	!-----------------------------------------------------------------------------
[3281]	641	SUBROUTINE chem_boundary_conds_decycle (cs_3d, cs_pr_init )
	642	USE pegrid, &
	643	ONLY: myid
[2831]	644
[3281]	645	IMPLICIT NONE
	646	INTEGER(iwp) :: boundary !<
	647	INTEGER(iwp) :: ee !<
	648	INTEGER(iwp) :: copied !<
	649	INTEGER(iwp) :: i !<
	650	INTEGER(iwp) :: j !<
	651	INTEGER(iwp) :: k !<
	652	INTEGER(iwp) :: ss !<
	653	REAL(wp), DIMENSION(nzb:nzt+1) :: cs_pr_init
	654	REAL(wp), DIMENSION(nzb:nzt+1,nysg:nyng,nxlg:nxrg) :: cs_3d
	655	REAL(wp) :: flag !< flag to mask topography grid points
[2831]	656
[3281]	657	flag = 0.0_wp
[2854]	658
[3281]	659
	660	!-- Left and right boundaries
	661	IF ( decycle_chem_lr .AND. bc_lr_cyc ) THEN
[2854]	662
[3281]	663	DO boundary = 1, 2
[2854]	664
[3281]	665	IF ( decycle_method(boundary) == 'dirichlet' ) THEN
[2854]	666	!
[3281]	667	!-- Initial profile is copied to ghost and first three layers
	668	ss = 1
	669	ee = 0
	670	IF ( boundary == 1 .AND. nxl == 0 ) THEN
	671	ss = nxlg
	672	ee = nxl+2
	673	ELSEIF ( boundary == 2 .AND. nxr == nx ) THEN
	674	ss = nxr-2
	675	ee = nxrg
	676	ENDIF
[2854]	677
[3281]	678	DO i = ss, ee
	679	DO j = nysg, nyng
	680	DO k = nzb+1, nzt
	681	flag = MERGE( 1.0_wp, 0.0_wp, &
	682	BTEST( wall_flags_0(k,j,i), 0 ) )
	683	cs_3d(k,j,i) = cs_pr_init(k) * flag
	684	ENDDO
[2854]	685	ENDDO
[2831]	686	ENDDO
	687
[3281]	688	ELSEIF ( decycle_method(boundary) == 'neumann' ) THEN
[2854]	689	!
[3281]	690	!-- The value at the boundary is copied to the ghost layers to simulate
	691	!-- an outlet with zero gradient
	692	ss = 1
	693	ee = 0
	694	IF ( boundary == 1 .AND. nxl == 0 ) THEN
	695	ss = nxlg
	696	ee = nxl-1
	697	copied = nxl
	698	ELSEIF ( boundary == 2 .AND. nxr == nx ) THEN
	699	ss = nxr+1
	700	ee = nxrg
	701	copied = nxr
	702	ENDIF
[2854]	703
[3281]	704	DO i = ss, ee
	705	DO j = nysg, nyng
	706	DO k = nzb+1, nzt
	707	flag = MERGE( 1.0_wp, 0.0_wp, &
	708	BTEST( wall_flags_0(k,j,i), 0 ) )
	709	cs_3d(k,j,i) = cs_3d(k,j,copied) * flag
	710	ENDDO
[2854]	711	ENDDO
[2831]	712	ENDDO
[2854]	713
[3281]	714	ELSE
	715	WRITE(message_string,*) &
	716	'unknown decycling method: decycle_method (', &
	717	boundary, ') ="' // TRIM( decycle_method(boundary) ) // '"'
	718	CALL message( 'chem_boundary_conds_decycle', 'CM0431', &
	719	1, 2, 0, 6, 0 )
	720	ENDIF
	721	ENDDO
	722	ENDIF
[2831]	723
[3281]	724
	725	!-- South and north boundaries
	726	IF ( decycle_chem_ns .AND. bc_ns_cyc ) THEN
[2854]	727
[3281]	728	DO boundary = 3, 4
[2854]	729
[3281]	730	IF ( decycle_method(boundary) == 'dirichlet' ) THEN
[2854]	731	!
[3281]	732	!-- Initial profile is copied to ghost and first three layers
	733	ss = 1
	734	ee = 0
	735	IF ( boundary == 3 .AND. nys == 0 ) THEN
	736	ss = nysg
	737	ee = nys+2
	738	ELSEIF ( boundary == 4 .AND. nyn == ny ) THEN
	739	ss = nyn-2
	740	ee = nyng
	741	ENDIF
[2854]	742
[3281]	743	DO i = nxlg, nxrg
	744	DO j = ss, ee
	745	DO k = nzb+1, nzt
	746	flag = MERGE( 1.0_wp, 0.0_wp, &
	747	BTEST( wall_flags_0(k,j,i), 0 ) )
	748	cs_3d(k,j,i) = cs_pr_init(k) * flag
	749	ENDDO
[2854]	750	ENDDO
[2831]	751	ENDDO
[3281]	752
	753
	754	ELSEIF ( decycle_method(boundary) == 'neumann' ) THEN
[2854]	755	!
[3281]	756	!-- The value at the boundary is copied to the ghost layers to simulate
	757	!-- an outlet with zero gradient
	758	ss = 1
	759	ee = 0
	760	IF ( boundary == 3 .AND. nys == 0 ) THEN
	761	ss = nysg
	762	ee = nys-1
	763	copied = nys
	764	ELSEIF ( boundary == 4 .AND. nyn == ny ) THEN
	765	ss = nyn+1
	766	ee = nyng
	767	copied = nyn
	768	ENDIF
[2831]	769
[3281]	770	DO i = nxlg, nxrg
	771	DO j = ss, ee
	772	DO k = nzb+1, nzt
	773	flag = MERGE( 1.0_wp, 0.0_wp, &
	774	BTEST( wall_flags_0(k,j,i), 0 ) )
	775	cs_3d(k,j,i) = cs_3d(k,copied,i) * flag
	776	ENDDO
[2854]	777	ENDDO
[2831]	778	ENDDO
[2854]	779
[3281]	780	ELSE
	781	WRITE(message_string,*) &
	782	'unknown decycling method: decycle_method (', &
	783	boundary, ') ="' // TRIM( decycle_method(boundary) ) // '"'
	784	CALL message( 'chem_boundary_conds_decycle', 'CM0432', &
	785	1, 2, 0, 6, 0 )
	786	ENDIF
	787	ENDDO
	788	ENDIF
	789	END SUBROUTINE chem_boundary_conds_decycle
	790	!
[3085]	791	!------------------------------------------------------------------------------!
[2831]	792	!
[3085]	793	! Description:
	794	! ------------
	795	!> Subroutine for checking data output for chemical species
[2831]	796	!------------------------------------------------------------------------------!
[3085]	797
[3281]	798	SUBROUTINE chem_check_data_output( var, unit, i, ilen, k )
[3085]	799
	800
[3281]	801	USE control_parameters, &
	802	ONLY: data_output, message_string
[3085]	803
[3281]	804	IMPLICIT NONE
[3085]	805
[3281]	806	CHARACTER (LEN=*) :: unit !<
	807	CHARACTER (LEN=*) :: var !<
[3085]	808
[3281]	809	INTEGER(iwp) :: i, lsp
	810	INTEGER(iwp) :: ilen
	811	INTEGER(iwp) :: k
[3085]	812
[3281]	813	CHARACTER(len=16) :: spec_name
[3085]	814
[3281]	815	unit = 'illegal'
[3085]	816
[3449]	817	spec_name = TRIM(var(4:)) !< var 1:3 is 'kc_' or 'em_'.
[3085]	818
[3449]	819	IF ( TRIM(var(1:3)) == 'em_' ) THEN
[3281]	820	DO lsp=1,nspec
	821	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
[3449]	822	unit = 'mol m-2 s-1'
	823	ENDIF
	824	!-- It is possible to plant PM10 and PM25 into the gasphase chemistry code
	825	!-- as passive species (e.g. 'passive' in GASPHASE_PREPROC/mechanisms):
	826	!-- set unit to micrograms per m**3 for PM10 and PM25 (PM2.5)
	827	IF (spec_name(1:2) == 'PM') THEN
	828	unit = 'kg m-2 s-1'
	829	ENDIF
	830	ENDDO
	831
	832	ELSE
	833
	834	DO lsp=1,nspec
	835	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
[3281]	836	unit = 'ppm'
	837	ENDIF
	838	! It is possible to plant PM10 and PM25 into the gasphase chemistry code
	839	! as passive species (e.g. 'passive' in GASPHASE_PREPROC/mechanisms):
	840	! set unit to micrograms per m**3 for PM10 and PM25 (PM2.5)
	841	IF (spec_name(1:2) == 'PM') THEN
[3449]	842	unit = 'kg m-3'
[3281]	843	ENDIF
	844	ENDDO
[3085]	845
[3449]	846	DO lsp=1,nphot
[3281]	847	IF (TRIM(spec_name) == TRIM(phot_frequen(lsp)%name)) THEN
	848	unit = 'sec-1'
	849	ENDIF
	850	ENDDO
[3449]	851	ENDIF
[3085]	852
	853
[3449]	854	RETURN
[3281]	855	END SUBROUTINE chem_check_data_output
[2831]	856	!
[3085]	857	!------------------------------------------------------------------------------!
	858	!
[2535]	859	! Description:
	860	! ------------
[3085]	861	!> Subroutine for checking data output of profiles for chemistry model
[2535]	862	!------------------------------------------------------------------------------!
[2615]	863
[3281]	864	SUBROUTINE chem_check_data_output_pr( variable, var_count, unit, dopr_unit )
[3085]	865
[3281]	866	USE arrays_3d
	867	USE control_parameters, &
	868	ONLY: data_output_pr, message_string, air_chemistry
	869	USE indices
	870	USE profil_parameter
	871	USE statistics
[3085]	872
	873
[3281]	874	IMPLICIT NONE
[3085]	875
[3281]	876	CHARACTER (LEN=*) :: unit !<
	877	CHARACTER (LEN=*) :: variable !<
	878	CHARACTER (LEN=*) :: dopr_unit
	879	CHARACTER(len=16) :: spec_name
[3228]	880
[3281]	881	INTEGER(iwp) :: var_count, lsp !<
	882
[3085]	883
[3281]	884	spec_name = TRIM(variable(4:))
[3085]	885
	886	IF ( .NOT. air_chemistry ) THEN
[3281]	887	message_string = 'data_output_pr = ' // &
	888	TRIM( data_output_pr(var_count) ) // ' is not imp' // &
	889	'lemented for air_chemistry = .FALSE.'
	890	CALL message( 'chem_check_parameters', 'CM0433', 1, 2, 0, 6, 0 )
[3085]	891
	892	ELSE
	893	DO lsp = 1, nspec
	894	IF (TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
[3281]	895	cs_pr_count = cs_pr_count+1
	896	cs_pr_index(cs_pr_count) = lsp
	897	dopr_index(var_count) = pr_palm+cs_pr_count
	898	dopr_unit = 'ppm'
	899	IF (spec_name(1:2) == 'PM') THEN
[3276]	900	dopr_unit = 'kg m-3'
[3281]	901	ENDIF
[3085]	902	hom(:,2, dopr_index(var_count),:) = SPREAD( zu, 2, statistic_regions+1 )
	903	unit = dopr_unit
	904	ENDIF
	905	ENDDO
	906	ENDIF
	907
[3281]	908	END SUBROUTINE chem_check_data_output_pr
[3085]	909
[3281]	910	!
	911	!------------------------------------------------------------------------------!
	912	! Description:
	913	! ------------
	914	!> Check parameters routine for chemistry_model_mod
	915	!------------------------------------------------------------------------------!
	916	SUBROUTINE chem_check_parameters
[3085]	917
[3281]	918	IMPLICIT NONE
	919
	920	LOGICAL :: found
	921	INTEGER (iwp) :: lsp_usr !< running index for user defined chem spcs
	922	INTEGER (iwp) :: lsp !< running index for chem spcs.
	923
	924
	925	!!-- check for chemical reactions status
	926	IF ( chem_gasphase_on ) THEN
	927	message_string = 'Chemical reactions: ON'
	928	CALL message( 'chem_check_parameters', 'CM0421', 0, 0, 0, 6, 0 )
	929	ELSEIF ( .not. (chem_gasphase_on) ) THEN
	930	message_string = 'Chemical reactions: OFF'
	931	CALL message( 'chem_check_parameters', 'CM0422', 0, 0, 0, 6, 0 )
	932	ENDIF
	933
	934	!-- check for chemistry time-step
	935	IF ( call_chem_at_all_substeps ) THEN
	936	message_string = 'Chemistry is calculated at all meteorology time-step'
	937	CALL message( 'chem_check_parameters', 'CM0423', 0, 0, 0, 6, 0 )
	938	ELSEIF ( .not. (call_chem_at_all_substeps) ) THEN
	939	message_string = 'Sub-time-steps are skipped for chemistry time-steps'
	940	CALL message( 'chem_check_parameters', 'CM0424', 0, 0, 0, 6, 0 )
	941	ENDIF
	942
	943	!-- check for photolysis scheme
	944	IF ( (photolysis_scheme /= 'simple') .AND. (photolysis_scheme /= 'constant') ) THEN
	945	message_string = 'Incorrect photolysis scheme selected, please check spelling'
	946	CALL message( 'chem_check_parameters', 'CM0425', 1, 2, 0, 6, 0 )
	947	ENDIF
	948
	949	!-- check for decycling of chem species
	950	IF ( (.not. any(decycle_method == 'neumann') ) .AND. (.not. any(decycle_method == 'dirichlet') ) ) THEN
[3318]	951	message_string = 'Incorrect boundary conditions. Only neumann or ' &
	952	// 'dirichlet &available for decycling chemical species '
[3281]	953	CALL message( 'chem_check_parameters', 'CM0426', 1, 2, 0, 6, 0 )
	954	ENDIF
	955
[3449]	956	!---------------------
	957	!-- chem_check_parameters is called before the array chem_species is allocated!
	958	!-- temporary switch of this part of the check
	959	RETURN
	960	!---------------------
	961
[3281]	962	!-- check for initial chem species input
	963	lsp_usr = 1
	964	lsp = 1
	965	DO WHILE ( cs_name (lsp_usr) /= 'novalue')
	966	found = .FALSE.
	967	DO lsp = 1, nvar
	968	IF ( TRIM(cs_name (lsp_usr)) == TRIM(chem_species(lsp)%name) ) THEN
	969	found = .TRUE.
	970	EXIT
	971	ENDIF
	972	ENDDO
	973	IF ( .not. found ) THEN
	974	message_string = 'Incorrect input for initial surface vaue: ' // TRIM(cs_name(lsp_usr))
	975	CALL message( 'chem_check_parameters', 'CM0427', 0, 1, 0, 6, 0 )
	976	ENDIF
	977	lsp_usr = lsp_usr + 1
	978	ENDDO
	979
	980	!-- check for surface emission flux chem species
	981
	982	lsp_usr = 1
	983	lsp = 1
	984	DO WHILE ( surface_csflux_name (lsp_usr) /= 'novalue')
	985	found = .FALSE.
	986	DO lsp = 1, nvar
	987	IF ( TRIM(surface_csflux_name (lsp_usr)) == TRIM(chem_species(lsp)%name) ) THEN
	988	found = .TRUE.
	989	EXIT
	990	ENDIF
	991	ENDDO
	992	IF ( .not. found ) THEN
	993	message_string = 'Incorrect input of chemical species for surface emission fluxes: ' &
	994	// TRIM(surface_csflux_name(lsp_usr))
	995	CALL message( 'chem_check_parameters', 'CM0428', 0, 1, 0, 6, 0 )
	996	ENDIF
	997	lsp_usr = lsp_usr + 1
	998	ENDDO
	999
	1000	END SUBROUTINE chem_check_parameters
	1001
[3085]	1002	!
	1003	!------------------------------------------------------------------------------!
	1004	!
	1005	! Description:
	1006	! ------------
	1007	!> Subroutine defining 2D output variables for chemical species
[3298]	1008	!> @todo: Remove "mode" from argument list, not used.
[3085]	1009	!------------------------------------------------------------------------------!
	1010
[3281]	1011	SUBROUTINE chem_data_output_2d( av, variable, found, grid, mode, local_pf, &
	1012	two_d, nzb_do, nzt_do, fill_value )
	1013
	1014	USE indices
[3085]	1015
[3281]	1016	USE kinds
[3085]	1017
[3281]	1018	USE pegrid, ONLY: myid, threads_per_task
[3085]	1019
[3281]	1020	IMPLICIT NONE
[3085]	1021
[3281]	1022	CHARACTER (LEN=*) :: grid !<
	1023	CHARACTER (LEN=*) :: mode !<
	1024	CHARACTER (LEN=*) :: variable !<
[3282]	1025	INTEGER(iwp) :: av !< flag to control data output of instantaneous or time-averaged data
[3281]	1026	INTEGER(iwp) :: nzb_do !< lower limit of the domain (usually nzb)
	1027	INTEGER(iwp) :: nzt_do !< upper limit of the domain (usually nzt+1)
	1028	LOGICAL :: found !<
	1029	LOGICAL :: two_d !< flag parameter that indicates 2D variables (horizontal cross sections)
	1030	REAL(wp) :: fill_value
	1031	REAL(wp), DIMENSION(nxl:nxr,nys:nyn,nzb:nzt+1) :: local_pf !<
[3085]	1032
[3281]	1033	!-- local variables.
	1034	CHARACTER(len=16) :: spec_name
	1035	INTEGER(iwp) :: lsp
[3282]	1036	INTEGER(iwp) :: i !< grid index along x-direction
	1037	INTEGER(iwp) :: j !< grid index along y-direction
	1038	INTEGER(iwp) :: k !< grid index along z-direction
	1039	INTEGER(iwp) :: m !< running index surface elements
	1040	INTEGER(iwp) :: char_len !< length of a character string
[3281]	1041	found = .TRUE.
	1042	char_len = LEN_TRIM(variable)
[3085]	1043
[3281]	1044	spec_name = TRIM( variable(4:char_len-3) )
[3085]	1045
[3281]	1046	DO lsp=1,nspec
	1047	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name) .AND. &
	1048	( (variable(char_len-2:) == '_xy') .OR. &
	1049	(variable(char_len-2:) == '_xz') .OR. &
	1050	(variable(char_len-2:) == '_yz') ) ) THEN
[3373]	1051	!
	1052	!-- todo: remove or replace by "CALL message" mechanism (kanani)
	1053	! IF(myid == 0) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
	1054	! TRIM(chem_species(lsp)%name)
[3281]	1055	IF (av == 0) THEN
	1056	DO i = nxl, nxr
	1057	DO j = nys, nyn
	1058	DO k = nzb_do, nzt_do
	1059	local_pf(i,j,k) = MERGE( &
	1060	chem_species(lsp)%conc(k,j,i), &
	1061	REAL( fill_value, KIND = wp ), &
	1062	BTEST( wall_flags_0(k,j,i), 0 ) )
[3085]	1063
	1064
[3281]	1065	ENDDO
[3085]	1066	ENDDO
	1067	ENDDO
[3281]	1068
	1069	ELSE
	1070	DO i = nxl, nxr
	1071	DO j = nys, nyn
	1072	DO k = nzb_do, nzt_do
	1073	local_pf(i,j,k) = MERGE( &
	1074	chem_species(lsp)%conc(k,j,i), &
	1075	REAL( fill_value, KIND = wp ), &
	1076	BTEST( wall_flags_0(k,j,i), 0 ) )
	1077	ENDDO
[3085]	1078	ENDDO
	1079	ENDDO
[3281]	1080	ENDIF
	1081	grid = 'zu'
[2535]	1082	ENDIF
[3281]	1083	ENDDO
[3085]	1084
[3281]	1085	RETURN
	1086
	1087	END SUBROUTINE chem_data_output_2d
[3085]	1088
	1089	!
	1090	!------------------------------------------------------------------------------!
	1091	!
	1092	! Description:
	1093	! ------------
	1094	!> Subroutine defining 3D output variables for chemical species
	1095	!------------------------------------------------------------------------------!
	1096
[3281]	1097	SUBROUTINE chem_data_output_3d( av, variable, found, local_pf, fill_value, nzb_do, nzt_do )
[3085]	1098
	1099
[3281]	1100	USE indices
[3228]	1101
[3281]	1102	USE kinds
[3085]	1103
[3449]	1104	USE surface_mod
[3085]	1105
[3449]	1106	!USE chem_modules, ONLY: nvar
	1107
[3281]	1108	IMPLICIT NONE
[3085]	1109
[3282]	1110	CHARACTER (LEN=*) :: variable !<
	1111	INTEGER(iwp) :: av !<
	1112	INTEGER(iwp) :: nzb_do !< lower limit of the data output (usually 0)
	1113	INTEGER(iwp) :: nzt_do !< vertical upper limit of the data output (usually nz_do3d)
[3085]	1114
[3282]	1115	LOGICAL :: found !<
[3085]	1116
[3281]	1117	REAL(wp) :: fill_value !<
	1118	REAL(sp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) :: local_pf
[3228]	1119
[3085]	1120
[3281]	1121	!-- local variables
	1122	CHARACTER(len=16) :: spec_name
[3449]	1123	INTEGER(iwp) :: i, j, k
	1124	INTEGER(iwp) :: m, l !< running indices for surfaces
	1125	INTEGER(iwp) :: lsp !< running index for chem spcs
[3085]	1126
	1127
[3281]	1128	found = .FALSE.
[3449]	1129	IF ( .NOT. (variable(1:3) == 'kc_' .OR. variable(1:3) == 'em_' ) ) THEN
	1130	RETURN
	1131	ENDIF
[3085]	1132
[3281]	1133	spec_name = TRIM(variable(4:))
[3085]	1134
[3449]	1135	IF ( variable(1:3) == 'em_' ) THEN
	1136
	1137	local_pf = 0.0_wp
	1138
	1139	DO lsp = 1, nvar !!! cssws - nvar species, chem_species - nspec species !!!
	1140	IF ( TRIM(spec_name) == TRIM(chem_species(lsp)%name) ) THEN
	1141	! no average for now
	1142	DO m = 1, surf_usm_h%ns
	1143	local_pf(surf_usm_h%i(m),surf_usm_h%j(m),surf_usm_h%k(m)) = &
	1144	local_pf(surf_usm_h%i(m),surf_usm_h%j(m),surf_usm_h%k(m)) + surf_usm_h%cssws(lsp,m)
	1145	ENDDO
	1146	DO m = 1, surf_lsm_h%ns
	1147	local_pf(surf_lsm_h%i(m),surf_lsm_h%j(m),surf_lsm_h%k(m)) = &
	1148	local_pf(surf_lsm_h%i(m),surf_lsm_h%j(m),surf_lsm_h%k(m)) + surf_lsm_h%cssws(lsp,m)
	1149	ENDDO
	1150	DO l = 0, 3
	1151	DO m = 1, surf_usm_v(l)%ns
	1152	local_pf(surf_usm_v(l)%i(m),surf_usm_v(l)%j(m),surf_usm_v(l)%k(m)) = &
	1153	local_pf(surf_usm_v(l)%i(m),surf_usm_v(l)%j(m),surf_usm_v(l)%k(m)) + surf_usm_v(l)%cssws(lsp,m)
	1154	ENDDO
	1155	DO m = 1, surf_lsm_v(l)%ns
	1156	local_pf(surf_lsm_v(l)%i(m),surf_lsm_v(l)%j(m),surf_lsm_v(l)%k(m)) = &
	1157	local_pf(surf_lsm_v(l)%i(m),surf_lsm_v(l)%j(m),surf_lsm_v(l)%k(m)) + surf_lsm_v(l)%cssws(lsp,m)
	1158	ENDDO
	1159	ENDDO
	1160	found = .TRUE.
	1161	ENDIF
	1162	ENDDO
	1163	ELSE
	1164	DO lsp=1,nspec
	1165	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
[3373]	1166	!
	1167	!-- todo: remove or replace by "CALL message" mechanism (kanani)
	1168	! IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
	1169	! TRIM(chem_species(lsp)%name)
[3449]	1170	IF (av == 0) THEN
	1171	DO i = nxl, nxr
	1172	DO j = nys, nyn
	1173	DO k = nzb_do, nzt_do
	1174	local_pf(i,j,k) = MERGE( &
	1175	chem_species(lsp)%conc(k,j,i), &
	1176	REAL( fill_value, KIND = wp ), &
	1177	BTEST( wall_flags_0(k,j,i), 0 ) )
	1178	ENDDO
	1179	ENDDO
	1180	ENDDO
[3085]	1181
[3449]	1182	ELSE
	1183	DO i = nxl, nxr
	1184	DO j = nys, nyn
	1185	DO k = nzb_do, nzt_do
	1186	local_pf(i,j,k) = MERGE( &
	1187	chem_species(lsp)%conc_av(k,j,i),&
	1188	REAL( fill_value, KIND = wp ), &
	1189	BTEST( wall_flags_0(k,j,i), 0 ) )
	1190	ENDDO
	1191	ENDDO
	1192	ENDDO
	1193	ENDIF
	1194	found = .TRUE.
	1195	ENDIF
	1196	ENDDO
	1197	ENDIF
[3085]	1198
	1199	RETURN
[3449]	1200
[3281]	1201	END SUBROUTINE chem_data_output_3d
[3085]	1202	!
	1203	!------------------------------------------------------------------------------!
	1204	!
	1205	! Description:
	1206	! ------------
	1207	!> Subroutine defining mask output variables for chemical species
	1208	!------------------------------------------------------------------------------!
	1209
[3281]	1210	SUBROUTINE chem_data_output_mask( av, variable, found, local_pf )
	1211
	1212	USE control_parameters
	1213	USE indices
	1214	USE kinds
	1215	USE pegrid, ONLY: myid, threads_per_task
[3435]	1216	USE surface_mod, ONLY: get_topography_top_index_ji
[3085]	1217
[3281]	1218	IMPLICIT NONE
[3085]	1219
[3435]	1220	CHARACTER(LEN=5) :: grid !< flag to distinquish between staggered grids
	1221
[3282]	1222	CHARACTER (LEN=*):: variable !<
	1223	INTEGER(iwp) :: av !< flag to control data output of instantaneous or time-averaged data
	1224	LOGICAL :: found !<
[3281]	1225	REAL(wp), DIMENSION(mask_size_l(mid,1),mask_size_l(mid,2),mask_size_l(mid,3)) :: &
	1226	local_pf !<
[3085]	1227
	1228
[3281]	1229	!-- local variables.
	1230	CHARACTER(len=16) :: spec_name
	1231	INTEGER(iwp) :: lsp
[3282]	1232	INTEGER(iwp) :: i !< grid index along x-direction
	1233	INTEGER(iwp) :: j !< grid index along y-direction
	1234	INTEGER(iwp) :: k !< grid index along z-direction
[3435]	1235	INTEGER(iwp) :: topo_top_ind !< k index of highest horizontal surface
	1236
[3281]	1237	found = .TRUE.
[3435]	1238	grid = 's'
[3085]	1239
[3281]	1240	spec_name = TRIM( variable(4:) )
[3449]	1241	!av == 0
[3085]	1242
	1243	DO lsp=1,nspec
	1244	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name) ) THEN
[3373]	1245	!
	1246	!-- todo: remove or replace by "CALL message" mechanism (kanani)
	1247	! IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
	1248	! TRIM(chem_species(lsp)%name)
[3085]	1249	IF (av == 0) THEN
[3435]	1250	IF ( .NOT. mask_surface(mid) ) THEN
	1251
	1252	DO i = 1, mask_size_l(mid,1)
	1253	DO j = 1, mask_size_l(mid,2)
	1254	DO k = 1, mask_size(mid,3)
	1255	local_pf(i,j,k) = chem_species(lsp)%conc( &
	1256	mask_k(mid,k), &
	1257	mask_j(mid,j), &
	1258	mask_i(mid,i) )
	1259	ENDDO
[3085]	1260	ENDDO
	1261	ENDDO
[3435]	1262
	1263	ELSE
	1264	!
	1265	!-- Terrain-following masked output
	1266	DO i = 1, mask_size_l(mid,1)
	1267	DO j = 1, mask_size_l(mid,2)
	1268	!
	1269	!-- Get k index of highest horizontal surface
	1270	topo_top_ind = get_topography_top_index_ji( &
	1271	mask_j(mid,j), &
	1272	mask_i(mid,i), &
	1273	grid )
	1274	!
	1275	!-- Save output array
	1276	DO k = 1, mask_size_l(mid,3)
	1277	local_pf(i,j,k) = chem_species(lsp)%conc( &
	1278	MIN( topo_top_ind+mask_k(mid,k), &
	1279	nzt+1 ), &
	1280	mask_j(mid,j), &
	1281	mask_i(mid,i) )
	1282	ENDDO
	1283	ENDDO
	1284	ENDDO
	1285
	1286	ENDIF
[3085]	1287	ELSE
[3435]	1288	IF ( .NOT. mask_surface(mid) ) THEN
	1289
	1290	DO i = 1, mask_size_l(mid,1)
	1291	DO j = 1, mask_size_l(mid,2)
	1292	DO k = 1, mask_size_l(mid,3)
	1293	local_pf(i,j,k) = chem_species(lsp)%conc_av( &
	1294	mask_k(mid,k), &
	1295	mask_j(mid,j), &
	1296	mask_i(mid,i) )
	1297	ENDDO
[3085]	1298	ENDDO
	1299	ENDDO
[3435]	1300
	1301	ELSE
	1302	!
	1303	!-- Terrain-following masked output
	1304	DO i = 1, mask_size_l(mid,1)
	1305	DO j = 1, mask_size_l(mid,2)
	1306	!
	1307	!-- Get k index of highest horizontal surface
	1308	topo_top_ind = get_topography_top_index_ji( &
	1309	mask_j(mid,j), &
	1310	mask_i(mid,i), &
	1311	grid )
	1312	!
	1313	!-- Save output array
	1314	DO k = 1, mask_size_l(mid,3)
	1315	local_pf(i,j,k) = chem_species(lsp)%conc_av( &
	1316	MIN( topo_top_ind+mask_k(mid,k), &
	1317	nzt+1 ), &
	1318	mask_j(mid,j), &
	1319	mask_i(mid,i) )
	1320	ENDDO
	1321	ENDDO
	1322	ENDDO
	1323
	1324	ENDIF
	1325
	1326
[3085]	1327	ENDIF
	1328	found = .FALSE.
	1329	ENDIF
	1330	ENDDO
	1331
	1332	RETURN
[3281]	1333
	1334	END SUBROUTINE chem_data_output_mask
[3085]	1335
	1336	!
	1337	!------------------------------------------------------------------------------!
	1338	!
	1339	! Description:
	1340	! ------------
	1341	!> Subroutine defining appropriate grid for netcdf variables.
	1342	!> It is called out from subroutine netcdf.
	1343	!------------------------------------------------------------------------------!
[3281]	1344	SUBROUTINE chem_define_netcdf_grid( var, found, grid_x, grid_y, grid_z )
[3085]	1345
[3281]	1346	IMPLICIT NONE
[3085]	1347
[3282]	1348	CHARACTER (LEN=*), INTENT(IN) :: var !<
	1349	LOGICAL, INTENT(OUT) :: found !<
	1350	CHARACTER (LEN=*), INTENT(OUT) :: grid_x !<
	1351	CHARACTER (LEN=*), INTENT(OUT) :: grid_y !<
	1352	CHARACTER (LEN=*), INTENT(OUT) :: grid_z !<
[3085]	1353
[3281]	1354	found = .TRUE.
[3085]	1355
[3449]	1356	IF ( var(1:3) == 'kc_' .OR. var(1:3) == 'em_' ) THEN !< always the same grid for chemistry variables
[3281]	1357	grid_x = 'x'
	1358	grid_y = 'y'
	1359	grid_z = 'zu'
	1360	ELSE
	1361	found = .FALSE.
	1362	grid_x = 'none'
	1363	grid_y = 'none'
	1364	grid_z = 'none'
	1365	ENDIF
[3085]	1366
	1367
[3281]	1368	END SUBROUTINE chem_define_netcdf_grid
[3085]	1369	!
	1370	!------------------------------------------------------------------------------!
	1371	!
	1372	! Description:
	1373	! ------------
	1374	!> Subroutine defining header output for chemistry model
	1375	!------------------------------------------------------------------------------!
[3281]	1376	SUBROUTINE chem_header ( io )
[3085]	1377
[3281]	1378	IMPLICIT NONE
[3085]	1379
	1380	INTEGER(iwp), INTENT(IN) :: io !< Unit of the output file
[3281]	1381	INTEGER(iwp) :: lsp !< running index for chem spcs
[3282]	1382	INTEGER(iwp) :: cs_fixed
	1383	CHARACTER (LEN=80) :: docsflux_chr
	1384	CHARACTER (LEN=80) :: docsinit_chr
	1385
[3281]	1386	!
	1387	!-- Write chemistry model header
	1388	WRITE( io, 1 )
[3085]	1389
[3281]	1390	!-- Gasphase reaction status
	1391	IF ( chem_gasphase_on ) THEN
	1392	WRITE( io, 2 )
	1393	ELSE
	1394	WRITE( io, 3 )
	1395	ENDIF
	1396
	1397	! Chemistry time-step
	1398	WRITE ( io, 4 ) cs_time_step
	1399
	1400	!-- Emission mode info
	1401	IF ( mode_emis == "DEFAULT" ) THEN
	1402	WRITE( io, 5 )
	1403	ELSEIF ( mode_emis == "PARAMETERIZED" ) THEN
	1404	WRITE( io, 6 )
	1405	ELSEIF ( mode_emis == "PRE-PROCESSED" ) THEN
	1406	WRITE( io, 7 )
	1407	ENDIF
	1408
	1409	!-- Photolysis scheme info
	1410	IF ( photolysis_scheme == "simple" ) THEN
	1411	WRITE( io, 8 )
	1412	ELSEIF (photolysis_scheme == "conastant" ) THEN
	1413	WRITE( io, 9 )
	1414	ENDIF
	1415
	1416	!-- Emission flux info
	1417	lsp = 1
	1418	docsflux_chr ='Chemical species for surface emission flux: '
	1419	DO WHILE ( surface_csflux_name(lsp) /= 'novalue' )
	1420	docsflux_chr = TRIM( docsflux_chr ) // ' ' // TRIM( surface_csflux_name(lsp) ) // ','
	1421	IF ( LEN_TRIM( docsflux_chr ) >= 75 ) THEN
	1422	WRITE ( io, 10 ) docsflux_chr
	1423	docsflux_chr = ' '
	1424	ENDIF
	1425	lsp = lsp + 1
	1426	ENDDO
	1427
	1428	IF ( docsflux_chr /= '' ) THEN
	1429	WRITE ( io, 10 ) docsflux_chr
	1430	ENDIF
	1431
	1432
	1433	!-- initializatoin of Surface and profile chemical species
	1434
	1435	lsp = 1
	1436	docsinit_chr ='Chemical species for initial surface and profile emissions: '
	1437	DO WHILE ( cs_name(lsp) /= 'novalue' )
	1438	docsinit_chr = TRIM( docsinit_chr ) // ' ' // TRIM( cs_name(lsp) ) // ','
	1439	IF ( LEN_TRIM( docsinit_chr ) >= 75 ) THEN
	1440	WRITE ( io, 11 ) docsinit_chr
	1441	docsinit_chr = ' '
	1442	ENDIF
	1443	lsp = lsp + 1
	1444	ENDDO
	1445
	1446	IF ( docsinit_chr /= '' ) THEN
	1447	WRITE ( io, 11 ) docsinit_chr
	1448	ENDIF
	1449
	1450	!-- number of variable and fix chemical species and number of reactions
[3282]	1451	cs_fixed = nspec - nvar
	1452	WRITE ( io, * ) ' --> Chemical species, variable: ', nvar
	1453	WRITE ( io, * ) ' --> Chemical species, fixed : ', cs_fixed
	1454	WRITE ( io, * ) ' --> Total number of reactions : ', nreact
[3281]	1455
	1456
	1457	1 FORMAT (//' Chemistry model information:'/ &
	1458	' ----------------------------'/)
	1459	2 FORMAT (' --> Chemical reactions are turned on')
	1460	3 FORMAT (' --> Chemical reactions are turned off')
	1461	4 FORMAT (' --> Time-step for chemical species: ',F6.2, ' s')
	1462	5 FORMAT (' --> Emission mode = DEFAULT ')
	1463	6 FORMAT (' --> Emission mode = PARAMETERIZED ')
	1464	7 FORMAT (' --> Emission mode = PRE-PROCESSED ')
	1465	8 FORMAT (' --> Photolysis scheme used = simple ')
	1466	9 FORMAT (' --> Photolysis scheme used = constant ')
[3282]	1467	10 FORMAT (/' ',A)
	1468	11 FORMAT (/' ',A)
[3085]	1469	!
	1470	!
[3281]	1471	END SUBROUTINE chem_header
[3085]	1472
	1473	!
	1474	!------------------------------------------------------------------------------!
	1475	!
	1476	! Description:
	1477	! ------------
[2535]	1478	!> Subroutine initializating chemistry_model_mod
[2425]	1479	!------------------------------------------------------------------------------!
[3281]	1480	SUBROUTINE chem_init
[2535]	1481
[3281]	1482	USE control_parameters, &
	1483	ONLY: message_string, io_blocks, io_group, turbulent_inflow
	1484	USE arrays_3d, &
	1485	ONLY: mean_inflow_profiles
	1486	USE pegrid
[3085]	1487
[3281]	1488	IMPLICIT none
	1489	!-- local variables
	1490	INTEGER :: i,j !< running index for for horiz numerical grid points
	1491	INTEGER :: lsp !< running index for chem spcs
	1492	INTEGER :: lpr_lev !< running index for chem spcs profile level
[2535]	1493	!
	1494	!-- NOPOINTER version not implemented yet
[2828]	1495	! #if defined( __nopointer )
	1496	! message_string = 'The chemistry module only runs with POINTER version'
	1497	! CALL message( 'chemistry_model_mod', 'CM0001', 1, 2, 0, 6, 0 )
	1498	! #endif
	1499	!
	1500	!-- Allocate memory for chemical species
[3281]	1501	ALLOCATE( chem_species(nspec) )
	1502	ALLOCATE( spec_conc_1 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	1503	ALLOCATE( spec_conc_2 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	1504	ALLOCATE( spec_conc_3 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	1505	ALLOCATE( spec_conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	1506	ALLOCATE( phot_frequen(nphot) )
	1507	ALLOCATE( freq_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nphot) )
	1508	ALLOCATE( bc_cs_t_val(nspec) )
[2828]	1509	!
	1510	!-- Initialize arrays
[3281]	1511	spec_conc_1 (:,:,:,:) = 0.0_wp
	1512	spec_conc_2 (:,:,:,:) = 0.0_wp
	1513	spec_conc_3 (:,:,:,:) = 0.0_wp
	1514	spec_conc_av(:,:,:,:) = 0.0_wp
[2535]	1515
[2828]	1516
[3281]	1517	DO lsp = 1, nspec
	1518	chem_species(lsp)%name = spc_names(lsp)
[2535]	1519
[3281]	1520	chem_species(lsp)%conc (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1 (:,:,:,lsp)
	1521	chem_species(lsp)%conc_p (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2 (:,:,:,lsp)
	1522	chem_species(lsp)%tconc_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_3 (:,:,:,lsp)
	1523	chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_av(:,:,:,lsp)
[2425]	1524
[3281]	1525	ALLOCATE (chem_species(lsp)%cssws_av(nysg:nyng,nxlg:nxrg))
	1526	chem_species(lsp)%cssws_av = 0.0_wp
[2828]	1527	!
[3282]	1528	!-- The following block can be useful when emission module is not applied. &
	1529	!-- if emission module is applied the following block will be overwritten.
	1530	ALLOCATE (chem_species(lsp)%flux_s_cs(nzb+1:nzt,0:threads_per_task-1))
	1531	ALLOCATE (chem_species(lsp)%diss_s_cs(nzb+1:nzt,0:threads_per_task-1))
	1532	ALLOCATE (chem_species(lsp)%flux_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
	1533	ALLOCATE (chem_species(lsp)%diss_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
	1534	chem_species(lsp)%flux_s_cs = 0.0_wp
	1535	chem_species(lsp)%flux_l_cs = 0.0_wp
	1536	chem_species(lsp)%diss_s_cs = 0.0_wp
	1537	chem_species(lsp)%diss_l_cs = 0.0_wp
[2828]	1538	!
	1539	!-- Allocate memory for initial concentration profiles
	1540	!-- (concentration values come from namelist)
[3282]	1541	!-- (@todo (FK): Because of this, chem_init is called in palm before
[2828]	1542	!-- check_parameters, since conc_pr_init is used there.
	1543	!-- We have to find another solution since chem_init should
	1544	!-- eventually be called from init_3d_model!!)
[3281]	1545	ALLOCATE ( chem_species(lsp)%conc_pr_init(0:nz+1) )
	1546	chem_species(lsp)%conc_pr_init(:) = 0.0_wp
[2425]	1547
[3281]	1548	ENDDO
[2425]	1549
[2615]	1550	!
[3281]	1551	!-- Initial concentration of profiles is prescribed by parameters cs_profile
	1552	!-- and cs_heights in the namelist &chemistry_parameters
	1553	CALL chem_init_profiles
	1554
	1555
[2615]	1556	!
	1557	!-- Initialize model variables
[2425]	1558
[3114]	1559
[3281]	1560	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
	1561	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
[2425]	1562
[3228]	1563
[2615]	1564	!-- First model run of a possible job queue.
[3282]	1565	!-- Initial profiles of the variables must be computed.
[3281]	1566	IF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
[3282]	1567	CALL location_message( 'initializing with 1D chemistry model profiles', .FALSE. )
[2615]	1568	!
	1569	!-- Transfer initial profiles to the arrays of the 3D model
[3281]	1570	DO lsp = 1, nspec
	1571	DO i = nxlg, nxrg
	1572	DO j = nysg, nyng
	1573	DO lpr_lev = 1, nz + 1
	1574	chem_species(lsp)%conc(lpr_lev,j,i) = chem_species(lsp)%conc_pr_init(lpr_lev)
	1575	ENDDO
[2615]	1576	ENDDO
[3281]	1577	ENDDO
	1578	ENDDO
	1579
	1580	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
	1581	THEN
[3282]	1582	CALL location_message( 'initializing with constant chemistry profiles', .FALSE. )
[2425]	1583
[3281]	1584	DO lsp = 1, nspec
	1585	DO i = nxlg, nxrg
	1586	DO j = nysg, nyng
	1587	chem_species(lsp)%conc(:,j,i) = chem_species(lsp)%conc_pr_init
	1588	ENDDO
[2615]	1589	ENDDO
	1590	ENDDO
	1591
[3281]	1592	ENDIF
[2615]	1593
[2535]	1594	!
[3281]	1595	!-- If required, change the surface chem spcs at the start of the 3D run
	1596	IF ( cs_surface_initial_change(1) /= 0.0_wp ) THEN
	1597	DO lsp = 1, nspec
	1598	chem_species(lsp)%conc(nzb,:,:) = chem_species(lsp)%conc(nzb,:,:) + &
	1599	cs_surface_initial_change(lsp)
	1600	ENDDO
	1601	ENDIF
	1602	!
	1603	!-- Initiale old and new time levels.
	1604	DO lsp = 1, nvar
	1605	chem_species(lsp)%tconc_m = 0.0_wp
	1606	chem_species(lsp)%conc_p = chem_species(lsp)%conc
[2615]	1607	ENDDO
[2592]	1608
[3281]	1609	ENDIF
[2535]	1610
[3114]	1611
	1612
[3281]	1613	!--- new code add above this line
	1614	DO lsp = 1, nphot
	1615	phot_frequen(lsp)%name = phot_names(lsp)
[3373]	1616	!
	1617	!-- todo: remove or replace by "CALL message" mechanism (kanani)
[3281]	1618	! IF( myid == 0 ) THEN
	1619	! WRITE(6,'(a,i4,3x,a)') 'Photolysis: ',lsp,trim(phot_names(lsp))
	1620	! ENDIF
	1621	phot_frequen(lsp)%freq(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => freq_1(:,:,:,lsp)
	1622	ENDDO
[2425]	1623
[3281]	1624	RETURN
[2425]	1625
[3085]	1626	END SUBROUTINE chem_init
[2425]	1627
[2535]	1628	!
	1629	!------------------------------------------------------------------------------!
	1630	!
	1631	! Description:
	1632	! ------------
[3085]	1633	!> Subroutine defining initial vertical profiles of chemical species (given by
	1634	!> namelist parameters chem_profiles and chem_heights) --> which should work
	1635	!> analogue to parameters u_profile, v_profile and uv_heights)
[2535]	1636	!------------------------------------------------------------------------------!
[3281]	1637	SUBROUTINE chem_init_profiles !< SUBROUTINE is called from chem_init in case of
	1638	!< TRIM( initializing_actions ) /= 'read_restart_data'
	1639	!< We still need to see what has to be done in case of restart run
	1640	USE chem_modules
[2615]	1641
[3281]	1642	IMPLICIT NONE
[2425]	1643
[3281]	1644	!-- Local variables
	1645	INTEGER :: lsp !< running index for number of species in derived data type species_def
	1646	INTEGER :: lsp_usr !< running index for number of species (user defined) in cs_names, cs_profiles etc
	1647	INTEGER :: lpr_lev !< running index for profile level for each chem spcs.
	1648	INTEGER :: npr_lev !< the next available profile lev
[2425]	1649
[3085]	1650	!-----------------
	1651	!-- Parameter "cs_profile" and "cs_heights" are used to prescribe user defined initial profiles
	1652	!-- and heights. If parameter "cs_profile" is not prescribed then initial surface values
	1653	!-- "cs_surface" are used as constant initial profiles for each species. If "cs_profile" and
	1654	!-- "cs_heights" are prescribed, their values will!override the constant profile given by
	1655	!-- "cs_surface".
[3114]	1656	!
[3281]	1657	IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
	1658	lsp_usr = 1
	1659	DO WHILE ( TRIM( cs_name( lsp_usr ) ) /= 'novalue' ) !'novalue' is the default
	1660	DO lsp = 1, nspec !
[3282]	1661	!-- create initial profile (conc_pr_init) for each chemical species
[3281]	1662	IF ( TRIM( chem_species(lsp)%name ) == TRIM( cs_name(lsp_usr) ) ) THEN !
	1663	IF ( cs_profile(lsp_usr,1) == 9999999.9_wp ) THEN
[3282]	1664	!-- set a vertically constant profile based on the surface conc (cs_surface(lsp_usr)) of each species
	1665	DO lpr_lev = 0, nzt+1
	1666	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_surface(lsp_usr)
	1667	ENDDO
[3281]	1668	ELSE
	1669	IF ( cs_heights(1,1) /= 0.0_wp ) THEN
	1670	message_string = 'The surface value of cs_heights must be 0.0'
	1671	CALL message( 'chem_check_parameters', 'CM0434', 1, 2, 0, 6, 0 )
	1672	ENDIF
	1673
	1674	use_prescribed_profile_data = .TRUE.
	1675
	1676	npr_lev = 1
	1677	! chem_species(lsp)%conc_pr_init(0) = 0.0_wp
	1678	DO lpr_lev = 1, nz+1
	1679	IF ( npr_lev < 100 ) THEN
	1680	DO WHILE ( cs_heights(lsp_usr, npr_lev+1) <= zu(lpr_lev) )
	1681	npr_lev = npr_lev + 1
	1682	IF ( npr_lev == 100 ) THEN
	1683	message_string = 'number of chem spcs exceeding the limit'
	1684	CALL message( 'chem_check_parameters', 'CM0435', 1, 2, 0, 6, 0 )
	1685	EXIT
	1686	ENDIF
	1687	ENDDO
	1688	ENDIF
	1689	IF ( npr_lev < 100 .AND. cs_heights(lsp_usr, npr_lev + 1) /= 9999999.9_wp ) THEN
	1690	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp_usr, npr_lev) + &
	1691	( zu(lpr_lev) - cs_heights(lsp_usr, npr_lev) ) / &
	1692	( cs_heights(lsp_usr, (npr_lev + 1)) - cs_heights(lsp_usr, npr_lev ) ) * &
	1693	( cs_profile(lsp_usr, (npr_lev + 1)) - cs_profile(lsp_usr, npr_lev ) )
	1694	ELSE
	1695	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp_usr, npr_lev)
	1696	ENDIF
	1697	ENDDO
[3085]	1698	ENDIF
[3282]	1699	!-- If a profile is prescribed explicity using cs_profiles and cs_heights, then
	1700	!-- chem_species(lsp)%conc_pr_init is populated with the specific "lsp" based
	1701	!-- on the cs_profiles(lsp_usr,:) and cs_heights(lsp_usr,:).
[3281]	1702	ENDIF
	1703	ENDDO
	1704	lsp_usr = lsp_usr + 1
[3085]	1705	ENDDO
[3281]	1706	ENDIF
[2425]	1707
[3281]	1708	END SUBROUTINE chem_init_profiles
[2828]	1709	!
[2535]	1710	!------------------------------------------------------------------------------!
	1711	!
	1712	! Description:
	1713	! ------------
	1714	!> Subroutine to integrate chemical species in the given chemical mechanism
	1715	!------------------------------------------------------------------------------!
	1716
[3281]	1717	SUBROUTINE chem_integrate_ij (i, j)
[2425]	1718
[3281]	1719	USE cpulog, &
	1720	ONLY: cpu_log, log_point
[3287]	1721	USE statistics, &
[3281]	1722	ONLY: weight_pres
[3287]	1723	USE control_parameters, &
[3281]	1724	ONLY: dt_3d, intermediate_timestep_count,simulated_time
[2425]	1725
[3281]	1726	IMPLICIT none
	1727	INTEGER,INTENT(IN) :: i,j
[2425]	1728
[3281]	1729	!-- local variables
[3282]	1730	INTEGER(iwp) :: lsp !< running index for chem spcs.
	1731	INTEGER(iwp) :: lph !< running index for photolysis frequencies
[3281]	1732	INTEGER :: k,m,istatf
	1733	INTEGER,DIMENSION(20) :: istatus
	1734	REAL(kind=wp),DIMENSION(nzb+1:nzt,nspec) :: tmp_conc
	1735	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_temp
	1736	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_qvap
	1737	REAL(kind=wp),DIMENSION(nzb+1:nzt,nphot) :: tmp_phot
	1738	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_fact
	1739	REAL(kind=wp),DIMENSION(nzb+1:nzt) :: tmp_fact_i !< conversion factor between
	1740	!< molecules cm^{-3} and ppm
[3185]	1741
[3281]	1742	INTEGER,DIMENSION(nzb+1:nzt) :: nacc !< Number of accepted steps
	1743	INTEGER,DIMENSION(nzb+1:nzt) :: nrej !< Number of rejected steps
[3185]	1744
[3281]	1745	REAL(wp) :: conv !< conversion factor
	1746	REAL(wp), PARAMETER :: ppm2fr = 1.0e-6_wp !< Conversion factor ppm to fraction
	1747	REAL(wp), PARAMETER :: xm_air = 28.96_wp !< Mole mass of dry air
	1748	REAL(wp), PARAMETER :: xm_h2o = 18.01528_wp !< Mole mass of water vapor
	1749	REAL(wp), PARAMETER :: pref_i = 1._wp / 100000.0_wp !< inverse reference pressure (1/Pa)
	1750	REAL(wp), PARAMETER :: t_std = 273.15_wp !< standard pressure (Pa)
	1751	REAL(wp), PARAMETER :: p_std = 101325.0_wp !< standard pressure (Pa)
	1752	REAL(wp), PARAMETER :: vmolcm = 22.414e3_wp !< Mole volume (22.414 l) in cm^{-3}
	1753	REAL(wp), PARAMETER :: xna = 6.022e23_wp !< Avogadro number (molecules/mol)
[2425]	1754
[3281]	1755	REAL(wp),DIMENSION(size(rcntrl)) :: rcntrl_local
[2615]	1756
[3185]	1757
[3281]	1758	REAL(kind=wp) :: dt_chem
[2425]	1759
[2535]	1760	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'start' )
[3282]	1761	!< set chem_gasphase_on to .FALSE. if you want to skip computation of gas phase chemistry
[3281]	1762	IF (chem_gasphase_on) THEN
	1763	nacc = 0
	1764	nrej = 0
[2635]	1765
[3287]	1766	tmp_temp(:) = pt(nzb+1:nzt,j,i) * exner(nzb+1:nzt)
[3282]	1767	! ppm to molecules/cm**3
[3287]	1768	! 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]	1769	conv = ppm2fr * xna / vmolcm
	1770	tmp_fact(:) = conv * t_std * hyp(nzb+1:nzt) / (tmp_temp(:) * p_std)
	1771	tmp_fact_i = 1.0_wp/tmp_fact
[2615]	1772
[3281]	1773	IF ( humidity ) THEN
[3292]	1774	IF ( bulk_cloud_model ) THEN
[3281]	1775	tmp_qvap(:) = ( q(nzb+1:nzt,j,i) - ql(nzb+1:nzt,j,i) ) * xm_air/xm_h2o * tmp_fact(:)
	1776	ELSE
	1777	tmp_qvap(:) = q(nzb+1:nzt,j,i) * xm_air/xm_h2o * tmp_fact(:)
	1778	ENDIF
[3114]	1779	ELSE
[3281]	1780	tmp_qvap(:) = 0.01 * tmp_fact(:) !< Constant value for q if water vapor is not computed
[3114]	1781	ENDIF
	1782
[3281]	1783	DO lsp = 1,nspec
	1784	tmp_conc(:,lsp) = chem_species(lsp)%conc(nzb+1:nzt,j,i) * tmp_fact(:)
	1785	ENDDO
[2425]	1786
[3281]	1787	DO lph = 1,nphot
	1788	tmp_phot(:,lph) = phot_frequen(lph)%freq(nzb+1:nzt,j,i)
	1789	ENDDO
[3373]	1790	!
	1791	!-- todo: remove (kanani)
	1792	! IF(myid == 0 .AND. chem_debug0 ) THEN
	1793	! IF (i == 10 .and. j == 10) WRITE(0,*) 'begin chemics step ',dt_3d
	1794	! ENDIF
[2425]	1795
[3281]	1796	!-- Compute length of time step
	1797	IF ( call_chem_at_all_substeps ) THEN
	1798	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
	1799	ELSE
	1800	dt_chem = dt_3d
	1801	ENDIF
[2425]	1802
[3281]	1803	cs_time_step = dt_chem
[2425]	1804
[3281]	1805	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'start' )
[2425]	1806
[3281]	1807	IF(maxval(rcntrl) > 0.0) THEN ! Only if rcntrl is set
	1808	IF( simulated_time <= 2*dt_3d) THEN
	1809	rcntrl_local = 0
[3373]	1810	!
	1811	!-- todo: remove (kanani)
	1812	! WRITE(9,'(a,2f10.3)') 'USE Default rcntrl in the first steps ',simulated_time,dt_3d
[3281]	1813	ELSE
	1814	rcntrl_local = rcntrl
	1815	ENDIF
	1816	ELSE
	1817	rcntrl_local = 0
	1818	END IF
[2425]	1819
[3281]	1820	CALL chem_gasphase_integrate (dt_chem, tmp_conc, tmp_temp, tmp_qvap, tmp_fact, tmp_phot, &
	1821	icntrl_i = icntrl, rcntrl_i = rcntrl_local, xnacc = nacc, xnrej = nrej, istatus=istatus)
[2425]	1822
[3281]	1823	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'stop' )
[2425]	1824
[3281]	1825	DO lsp = 1,nspec
	1826	chem_species(lsp)%conc (nzb+1:nzt,j,i) = tmp_conc(:,lsp) * tmp_fact_i(:)
	1827	ENDDO
[3185]	1828
[2535]	1829
[3281]	1830	ENDIF
	1831	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'stop' )
	1832
[2615]	1833	RETURN
[3281]	1834	END SUBROUTINE chem_integrate_ij
[2535]	1835	!
	1836	!------------------------------------------------------------------------------!
	1837	!
	1838	! Description:
	1839	! ------------
[3085]	1840	!> Subroutine defining parin for &chemistry_parameters for chemistry model
[2535]	1841	!------------------------------------------------------------------------------!
[3281]	1842	SUBROUTINE chem_parin
[3085]	1843
[3281]	1844	USE chem_modules
	1845	USE control_parameters
[3287]	1846
[3281]	1847	USE kinds
	1848	USE pegrid
	1849	USE statistics
	1850
	1851	IMPLICIT NONE
[2425]	1852
[3282]	1853	CHARACTER (LEN=80) :: line !< dummy string that contains the current line of the parameter file
[3281]	1854	CHARACTER (LEN=3) :: cs_prefix
[2425]	1855
[3282]	1856	REAL(wp), DIMENSION(nmaxfixsteps) :: my_steps !< List of fixed timesteps my_step(1) = 0.0 automatic stepping
	1857	INTEGER(iwp) :: i !<
	1858	INTEGER(iwp) :: j !<
	1859	INTEGER(iwp) :: max_pr_cs_tmp !<
[2425]	1860
	1861
[3281]	1862	NAMELIST /chemistry_parameters/ bc_cs_b, &
[3085]	1863	bc_cs_t, &
	1864	call_chem_at_all_substeps, &
	1865	chem_debug0, &
	1866	chem_debug1, &
	1867	chem_debug2, &
	1868	chem_gasphase_on, &
	1869	cs_heights, &
	1870	cs_name, &
	1871	cs_profile, &
	1872	cs_profile_name, &
	1873	cs_surface, &
	1874	decycle_chem_lr, &
	1875	decycle_chem_ns, &
	1876	decycle_method, &
	1877	emiss_factor_main, &
	1878	emiss_factor_side, &
	1879	icntrl, &
	1880	main_street_id, &
	1881	max_street_id, &
	1882	my_steps, &
[3228]	1883	nest_chemistry, &
[3085]	1884	rcntrl, &
	1885	side_street_id, &
	1886	photolysis_scheme, &
	1887	wall_csflux, &
	1888	cs_vertical_gradient, &
	1889	top_csflux, &
	1890	surface_csflux, &
	1891	surface_csflux_name, &
	1892	cs_surface_initial_change, &
[3190]	1893	cs_vertical_gradient_level, &
[3282]	1894	! namelist parameters for emissions
[3190]	1895	mode_emis, &
	1896	time_fac_type, &
	1897	daytype_mdh, &
	1898	do_emis
[3085]	1899
	1900	!-- analogue to chem_names(nspj) we could invent chem_surfaceflux(nspj) and chem_topflux(nspj)
	1901	!-- so this way we could prescribe a specific flux value for each species
	1902	!> chemistry_parameters for initial profiles
	1903	!> cs_names = 'O3', 'NO2', 'NO', ... to set initial profiles)
	1904	!> cs_heights(1,:) = 0.0, 100.0, 500.0, 2000.0, .... (height levels where concs will be prescribed for O3)
	1905	!> cs_heights(2,:) = 0.0, 200.0, 400.0, 1000.0, .... (same for NO2 etc.)
	1906	!> cs_profiles(1,:) = 10.0, 20.0, 20.0, 30.0, ..... (chem spcs conc at height lvls chem_heights(1,:)) etc.
	1907	!> If the respective concentration profile should be constant with height, then use "cs_surface( number of spcs)"
	1908	!> then write these cs_surface values to chem_species(lsp)%conc_pr_init(:)
[2425]	1909
	1910	!
[3085]	1911	!-- Read chem namelist
[3185]	1912
[3281]	1913	INTEGER :: ier
	1914	CHARACTER(LEN=64) :: text
	1915	CHARACTER(LEN=8) :: solver_type
[3185]	1916
[3281]	1917	icntrl = 0
	1918	rcntrl = 0.0_wp
	1919	my_steps = 0.0_wp
	1920	photolysis_scheme = 'simple'
	1921	atol = 1.0_wp
	1922	rtol = 0.01_wp
	1923	!
	1924	!-- Try to find chemistry package
	1925	REWIND ( 11 )
	1926	line = ' '
	1927	DO WHILE ( INDEX( line, '&chemistry_parameters' ) == 0 )
[3287]	1928	READ ( 11, '(A)', END=20 ) line
[3281]	1929	ENDDO
	1930	BACKSPACE ( 11 )
	1931	!
	1932	!-- Read chemistry namelist
[3287]	1933	READ ( 11, chemistry_parameters, ERR = 10, END = 20 )
[3281]	1934	!
	1935	!-- Enable chemistry model
	1936	air_chemistry = .TRUE.
[3449]	1937	GOTO 20
[3287]	1938
[3449]	1939	10 BACKSPACE( 11 )
	1940	READ( 11 , '(A)') line
	1941	CALL parin_fail_message( 'chemistry_parameters', line )
[3287]	1942
[3449]	1943	20 CONTINUE
[3287]	1944
	1945	!
	1946	!-- check for emission mode for chem species
[3281]	1947	IF ( (mode_emis /= 'PARAMETERIZED') .AND. ( mode_emis /= 'DEFAULT') .AND. (mode_emis /= 'PRE-PROCESSED' ) ) THEN
	1948	message_string = 'Incorrect mode_emiss option select. Please check spelling'
	1949	CALL message( 'chem_check_parameters', 'CM0436', 1, 2, 0, 6, 0 )
	1950	ENDIF
[2425]	1951
[3282]	1952	t_steps = my_steps
	1953
	1954	!-- Determine the number of user-defined profiles and append them to the
	1955	!-- standard data output (data_output_pr)
[3085]	1956	max_pr_cs_tmp = 0
	1957	i = 1
[2425]	1958
[3085]	1959	DO WHILE ( data_output_pr(i) /= ' ' .AND. i <= 100 )
	1960	IF ( TRIM( data_output_pr(i)(1:3)) == 'kc_' ) THEN
	1961	max_pr_cs_tmp = max_pr_cs_tmp+1
[2615]	1962	ENDIF
[3085]	1963	i = i +1
[2615]	1964	ENDDO
[2425]	1965
[3085]	1966	IF ( max_pr_cs_tmp > 0 ) THEN
	1967	cs_pr_namelist_found = .TRUE.
	1968	max_pr_cs = max_pr_cs_tmp
[2914]	1969	ENDIF
[3185]	1970
	1971	! Set Solver Type
[3260]	1972	IF(icntrl(3) == 0) THEN
[3185]	1973	solver_type = 'rodas3' !Default
[3260]	1974	ELSE IF(icntrl(3) == 1) THEN
[3185]	1975	solver_type = 'ros2'
[3260]	1976	ELSE IF(icntrl(3) == 2) THEN
[3185]	1977	solver_type = 'ros3'
[3260]	1978	ELSE IF(icntrl(3) == 3) THEN
[3185]	1979	solver_type = 'ro4'
[3260]	1980	ELSE IF(icntrl(3) == 4) THEN
[3185]	1981	solver_type = 'rodas3'
[3260]	1982	ELSE IF(icntrl(3) == 5) THEN
[3185]	1983	solver_type = 'rodas4'
[3260]	1984	ELSE IF(icntrl(3) == 6) THEN
[3185]	1985	solver_type = 'Rang3'
[3260]	1986	ELSE
[3373]	1987	message_string = 'illegal solver type'
	1988	CALL message( 'chem_parin', 'PA0506', 1, 2, 0, 6, 0 )
[3260]	1989	END IF
[3185]	1990
[3373]	1991	!
	1992	!-- todo: remove or replace by "CALL message" mechanism (kanani)
	1993	! write(text,*) 'gas_phase chemistry: solver_type = ',trim(solver_type)
[3185]	1994	!kk Has to be changed to right calling sequence
	1995	!kk CALL location_message( trim(text), .FALSE. )
[3373]	1996	! IF(myid == 0) THEN
	1997	! write(9,*) ' '
	1998	! write(9,*) 'kpp setup '
	1999	! write(9,*) ' '
	2000	! write(9,*) ' gas_phase chemistry: solver_type = ',trim(solver_type)
	2001	! write(9,*) ' '
	2002	! write(9,*) ' Hstart = ',rcntrl(3)
	2003	! write(9,*) ' FacMin = ',rcntrl(4)
	2004	! write(9,*) ' FacMax = ',rcntrl(5)
	2005	! write(9,*) ' '
	2006	! IF(vl_dim > 1) THEN
	2007	! write(9,*) ' Vector mode vektor length = ',vl_dim
	2008	! ELSE
	2009	! write(9,*) ' Scalar mode'
	2010	! ENDIF
	2011	! write(9,*) ' '
	2012	! END IF
[3185]	2013
[3281]	2014	RETURN
[2491]	2015
[3281]	2016	END SUBROUTINE chem_parin
[2467]	2017
	2018	!
[2828]	2019	!------------------------------------------------------------------------------!
[2467]	2020	!
[2828]	2021	! Description:
	2022	! ------------
	2023	!> Subroutine calculating prognostic equations for chemical species
	2024	!> (vector-optimized).
	2025	!> Routine is called separately for each chemical species over a loop from
	2026	!> prognostic_equations.
	2027	!------------------------------------------------------------------------------!
[3281]	2028	SUBROUTINE chem_prognostic_equations ( cs_scalar_p, cs_scalar, tcs_scalar_m, &
	2029	pr_init_cs, ilsp )
[2467]	2030
[3281]	2031	USE advec_s_pw_mod, &
	2032	ONLY: advec_s_pw
	2033	USE advec_s_up_mod, &
	2034	ONLY: advec_s_up
	2035	USE advec_ws, &
	2036	ONLY: advec_s_ws
	2037	USE diffusion_s_mod, &
	2038	ONLY: diffusion_s
	2039	USE indices, &
	2040	ONLY: nxl, nxr, nyn, nys, wall_flags_0
	2041	USE pegrid
	2042	USE surface_mod, &
	2043	ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
	2044	surf_usm_v
[2828]	2045
[3281]	2046	IMPLICIT NONE
[2828]	2047
[3281]	2048	INTEGER :: i !< running index
	2049	INTEGER :: j !< running index
	2050	INTEGER :: k !< running index
[2828]	2051
[3281]	2052	INTEGER(iwp),INTENT(IN) :: ilsp !<
[2828]	2053
[3281]	2054	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
[2828]	2055
[3281]	2056	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar !<
	2057	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p !<
	2058	REAL(wp), DIMENSION(:,:,:), POINTER :: tcs_scalar_m !<
[2828]	2059
	2060
[3281]	2061	!
	2062	!-- Tendency terms for chemical species
	2063	tend = 0.0_wp
	2064	!
	2065	!-- Advection terms
	2066	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	2067	IF ( ws_scheme_sca ) THEN
	2068	CALL advec_s_ws( cs_scalar, 'kc' )
	2069	ELSE
	2070	CALL advec_s_pw( cs_scalar )
	2071	ENDIF
[2828]	2072	ELSE
[3281]	2073	CALL advec_s_up( cs_scalar )
[2828]	2074	ENDIF
[3281]	2075	!
	2076	!-- Diffusion terms (the last three arguments are zero)
	2077	CALL diffusion_s( cs_scalar, &
	2078	surf_def_h(0)%cssws(ilsp,:), &
	2079	surf_def_h(1)%cssws(ilsp,:), &
	2080	surf_def_h(2)%cssws(ilsp,:), &
	2081	surf_lsm_h%cssws(ilsp,:), &
	2082	surf_usm_h%cssws(ilsp,:), &
	2083	surf_def_v(0)%cssws(ilsp,:), &
	2084	surf_def_v(1)%cssws(ilsp,:), &
	2085	surf_def_v(2)%cssws(ilsp,:), &
	2086	surf_def_v(3)%cssws(ilsp,:), &
	2087	surf_lsm_v(0)%cssws(ilsp,:), &
	2088	surf_lsm_v(1)%cssws(ilsp,:), &
	2089	surf_lsm_v(2)%cssws(ilsp,:), &
	2090	surf_lsm_v(3)%cssws(ilsp,:), &
	2091	surf_usm_v(0)%cssws(ilsp,:), &
	2092	surf_usm_v(1)%cssws(ilsp,:), &
	2093	surf_usm_v(2)%cssws(ilsp,:), &
	2094	surf_usm_v(3)%cssws(ilsp,:) )
	2095	!
	2096	!-- Prognostic equation for chemical species
	2097	DO i = nxl, nxr
	2098	DO j = nys, nyn
	2099	DO k = nzb+1, nzt
	2100	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) &
	2101	+ ( dt_3d * &
	2102	( tsc(2) * tend(k,j,i) &
	2103	+ tsc(3) * tcs_scalar_m(k,j,i) &
	2104	) &
	2105	- tsc(5) * rdf_sc(k) &
	2106	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
	2107	) &
	2108	* MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_0(k,j,i), 0 ) )
[2828]	2109
[3281]	2110	IF ( cs_scalar_p(k,j,i) < 0.0_wp ) cs_scalar_p(k,j,i) = 0.1_wp * cs_scalar(k,j,i)
	2111	ENDDO
[2828]	2112	ENDDO
	2113	ENDDO
[3281]	2114	!
	2115	!-- Calculate tendencies for the next Runge-Kutta step
	2116	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	2117	IF ( intermediate_timestep_count == 1 ) THEN
	2118	DO i = nxl, nxr
	2119	DO j = nys, nyn
	2120	DO k = nzb+1, nzt
	2121	tcs_scalar_m(k,j,i) = tend(k,j,i)
	2122	ENDDO
[2828]	2123	ENDDO
	2124	ENDDO
[3281]	2125	ELSEIF ( intermediate_timestep_count < &
	2126	intermediate_timestep_count_max ) THEN
	2127	DO i = nxl, nxr
	2128	DO j = nys, nyn
	2129	DO k = nzb+1, nzt
	2130	tcs_scalar_m(k,j,i) = - 9.5625_wp * tend(k,j,i) &
	2131	+ 5.3125_wp * tcs_scalar_m(k,j,i)
	2132	ENDDO
[2828]	2133	ENDDO
	2134	ENDDO
[3281]	2135	ENDIF
[2828]	2136	ENDIF
	2137
[3281]	2138	END SUBROUTINE chem_prognostic_equations
[3228]	2139
[2482]	2140	!------------------------------------------------------------------------------!
[2535]	2141	!
[2482]	2142	! Description:
	2143	! ------------
[3085]	2144	!> Subroutine calculating prognostic equations for chemical species
	2145	!> (cache-optimized).
	2146	!> Routine is called separately for each chemical species over a loop from
	2147	!> prognostic_equations.
[2482]	2148	!------------------------------------------------------------------------------!
[3281]	2149	SUBROUTINE chem_prognostic_equations_ij ( cs_scalar_p, cs_scalar, tcs_scalar_m, pr_init_cs, &
	2150	i, j, i_omp_start, tn, ilsp, flux_s_cs, diss_s_cs, &
	2151	flux_l_cs, diss_l_cs )
	2152	USE pegrid
	2153	USE advec_ws, ONLY: advec_s_ws
	2154	USE advec_s_pw_mod, ONLY: advec_s_pw
	2155	USE advec_s_up_mod, ONLY: advec_s_up
	2156	USE diffusion_s_mod, ONLY: diffusion_s
	2157	USE indices, ONLY: wall_flags_0
	2158	USE surface_mod, ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
	2159	surf_usm_v
[3085]	2160
	2161
[3281]	2162	IMPLICIT NONE
[3085]	2163
[3281]	2164	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p, cs_scalar, tcs_scalar_m
[3085]	2165
[3281]	2166	INTEGER(iwp),INTENT(IN) :: i, j, i_omp_start, tn, ilsp
	2167	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: flux_s_cs !<
	2168	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: diss_s_cs !<
	2169	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: flux_l_cs !<
	2170	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: diss_l_cs !<
	2171	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
[3085]	2172
	2173	!-- local variables
	2174
[3281]	2175	INTEGER :: k
	2176	!
	2177	!-- Tendency-terms for chem spcs.
	2178	tend(:,j,i) = 0.0_wp
[3085]	2179	!
	2180	!-- Advection terms
[3281]	2181	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	2182	IF ( ws_scheme_sca ) THEN
	2183	CALL advec_s_ws( i, j, cs_scalar, 'kc', flux_s_cs, diss_s_cs, &
	2184	flux_l_cs, diss_l_cs, i_omp_start, tn )
	2185	ELSE
	2186	CALL advec_s_pw( i, j, cs_scalar )
	2187	ENDIF
[3085]	2188	ELSE
[3281]	2189	CALL advec_s_up( i, j, cs_scalar )
[3085]	2190	ENDIF
	2191
	2192	!
	2193
	2194	!-- Diffusion terms (the last three arguments are zero)
	2195
[3281]	2196	CALL diffusion_s( i, j, cs_scalar, &
	2197	surf_def_h(0)%cssws(ilsp,:), surf_def_h(1)%cssws(ilsp,:), &
	2198	surf_def_h(2)%cssws(ilsp,:), &
	2199	surf_lsm_h%cssws(ilsp,:), surf_usm_h%cssws(ilsp,:), &
	2200	surf_def_v(0)%cssws(ilsp,:), surf_def_v(1)%cssws(ilsp,:), &
	2201	surf_def_v(2)%cssws(ilsp,:), surf_def_v(3)%cssws(ilsp,:), &
	2202	surf_lsm_v(0)%cssws(ilsp,:), surf_lsm_v(1)%cssws(ilsp,:), &
	2203	surf_lsm_v(2)%cssws(ilsp,:), surf_lsm_v(3)%cssws(ilsp,:), &
	2204	surf_usm_v(0)%cssws(ilsp,:), surf_usm_v(1)%cssws(ilsp,:), &
	2205	surf_usm_v(2)%cssws(ilsp,:), surf_usm_v(3)%cssws(ilsp,:) )
	2206
[3085]	2207	!
	2208	!-- Prognostic equation for chem spcs
[3281]	2209	DO k = nzb+1, nzt
	2210	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) + ( dt_3d * &
	2211	( tsc(2) * tend(k,j,i) + &
	2212	tsc(3) * tcs_scalar_m(k,j,i) ) &
	2213	- tsc(5) * rdf_sc(k) &
	2214	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
	2215	) &
	2216	* MERGE( 1.0_wp, 0.0_wp, &
	2217	BTEST( wall_flags_0(k,j,i), 0 ) &
	2218	)
[2467]	2219
[3281]	2220	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
	2221	ENDDO
[3085]	2222
[2482]	2223	!
[3085]	2224	!-- Calculate tendencies for the next Runge-Kutta step
[3281]	2225	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	2226	IF ( intermediate_timestep_count == 1 ) THEN
	2227	DO k = nzb+1, nzt
	2228	tcs_scalar_m(k,j,i) = tend(k,j,i)
	2229	ENDDO
	2230	ELSEIF ( intermediate_timestep_count < &
	2231	intermediate_timestep_count_max ) THEN
	2232	DO k = nzb+1, nzt
	2233	tcs_scalar_m(k,j,i) = -9.5625_wp * tend(k,j,i) + &
	2234	5.3125_wp * tcs_scalar_m(k,j,i)
	2235	ENDDO
	2236	ENDIF
[3085]	2237	ENDIF
	2238
[3281]	2239	END SUBROUTINE chem_prognostic_equations_ij
[3085]	2240
[2482]	2241	!
[3085]	2242	!------------------------------------------------------------------------------!
	2243	!
	2244	! Description:
	2245	! ------------
	2246	!> Subroutine to read restart data of chemical species
	2247	!------------------------------------------------------------------------------!
[2828]	2248
[3281]	2249	SUBROUTINE chem_rrd_local( i, k, nxlf, nxlc, nxl_on_file, nxrf, nxrc, &
	2250	nxr_on_file, nynf, nync, nyn_on_file, nysf, nysc, &
	2251	nys_on_file, tmp_3d, found )
	2252
	2253	USE control_parameters
	2254
	2255	USE indices
	2256
	2257	USE pegrid
[3085]	2258
[3281]	2259	IMPLICIT NONE
[3085]	2260
[3281]	2261	CHARACTER (LEN=20) :: spc_name_av !<
	2262
	2263	INTEGER(iwp) :: i, lsp !<
	2264	INTEGER(iwp) :: k !<
	2265	INTEGER(iwp) :: nxlc !<
	2266	INTEGER(iwp) :: nxlf !<
	2267	INTEGER(iwp) :: nxl_on_file !<
	2268	INTEGER(iwp) :: nxrc !<
	2269	INTEGER(iwp) :: nxrf !<
	2270	INTEGER(iwp) :: nxr_on_file !<
	2271	INTEGER(iwp) :: nync !<
	2272	INTEGER(iwp) :: nynf !<
	2273	INTEGER(iwp) :: nyn_on_file !<
	2274	INTEGER(iwp) :: nysc !<
	2275	INTEGER(iwp) :: nysf !<
	2276	INTEGER(iwp) :: nys_on_file !<
[3085]	2277
[3281]	2278	LOGICAL, INTENT(OUT) :: found
[3085]	2279
[3281]	2280	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]	2281
	2282
[3281]	2283	found = .FALSE.
[3085]	2284
	2285
[3281]	2286	IF ( ALLOCATED(chem_species) ) THEN
[3085]	2287
[3281]	2288	DO lsp = 1, nspec
[3085]	2289
[3281]	2290	!< for time-averaged chemical conc.
	2291	spc_name_av = TRIM(chem_species(lsp)%name)//'_av'
[3085]	2292
[3281]	2293	IF (restart_string(1:length) == TRIM(chem_species(lsp)%name) ) &
	2294	THEN
	2295	!< read data into tmp_3d
	2296	IF ( k == 1 ) READ ( 13 ) tmp_3d
	2297	!< fill ..%conc in the restart run
	2298	chem_species(lsp)%conc(:,nysc-nbgp:nync+nbgp, &
	2299	nxlc-nbgp:nxrc+nbgp) = &
	2300	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
	2301	found = .TRUE.
	2302	ELSEIF (restart_string(1:length) == spc_name_av ) THEN
	2303	IF ( k == 1 ) READ ( 13 ) tmp_3d
	2304	chem_species(lsp)%conc_av(:,nysc-nbgp:nync+nbgp, &
	2305	nxlc-nbgp:nxrc+nbgp) = &
	2306	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
	2307	found = .TRUE.
	2308	ENDIF
[3085]	2309
[3281]	2310	ENDDO
[3085]	2311
[3281]	2312	ENDIF
[3085]	2313
	2314
[3281]	2315	END SUBROUTINE chem_rrd_local
[3085]	2316	!
	2317	!-------------------------------------------------------------------------------!
	2318	!> Description:
	2319	!> Calculation of horizontally averaged profiles
	2320	!> This routine is called for every statistic region (sr) defined by the user,
	2321	!> but at least for the region "total domain" (sr=0).
	2322	!> quantities.
[2828]	2323	!------------------------------------------------------------------------------!
[3281]	2324	SUBROUTINE chem_statistics( mode, sr, tn )
[3085]	2325
	2326
[3281]	2327	USE arrays_3d
	2328	USE indices
	2329	USE kinds
	2330	USE pegrid
	2331	USE statistics
[3085]	2332
	2333	USE user
	2334
	2335	IMPLICIT NONE
	2336
	2337	CHARACTER (LEN=*) :: mode !<
	2338
	2339	INTEGER(iwp) :: i !< running index on x-axis
	2340	INTEGER(iwp) :: j !< running index on y-axis
	2341	INTEGER(iwp) :: k !< vertical index counter
	2342	INTEGER(iwp) :: sr !< statistical region
	2343	INTEGER(iwp) :: tn !< thread number
	2344	INTEGER(iwp) :: n !<
	2345	INTEGER(iwp) :: m !<
	2346	INTEGER(iwp) :: lpr !< running index chem spcs
	2347	! REAL(wp), &
	2348	! DIMENSION(dots_num_palm+1:dots_max) :: &
	2349	! ts_value_l !<
	2350
	2351	IF ( mode == 'profiles' ) THEN
[2615]	2352	!
[3085]	2353	!-- Sample on how to calculate horizontally averaged profiles of user-
	2354	!-- defined quantities. Each quantity is identified by the index
	2355	!-- "pr_palm+#" where "#" is an integer starting from 1. These
	2356	!-- user-profile-numbers must also be assigned to the respective strings
	2357	!-- given by data_output_pr_cs in routine user_check_data_output_pr.
	2358	!-- hom(:,:,:,:) = dim-1 = vertical level, dim-2= 1: met-species,2:zu/zw, dim-3 = quantity( e.g.
	2359	! wpt), dim-4 = statistical region.
	2360
	2361	!$OMP DO
	2362	DO i = nxl, nxr
	2363	DO j = nys, nyn
	2364	DO k = nzb, nzt+1
	2365	DO lpr = 1, cs_pr_count
	2366
	2367	sums_l(k,pr_palm+lpr,tn) = sums_l(k,pr_palm+lpr,tn) + &
	2368	chem_species(cs_pr_index(lpr))%conc(k,j,i) * &
	2369	rmask(j,i,sr) * &
	2370	MERGE( 1.0_wp, 0.0_wp, &
	2371	BTEST( wall_flags_0(k,j,i), 22 ) )
	2372	ENDDO
	2373	ENDDO
	2374	ENDDO
	2375	ENDDO
	2376	ELSEIF ( mode == 'time_series' ) THEN
[3282]	2377	CALL location_message( 'Time series not calculated for chemistry', .TRUE. )
	2378	ENDIF
[3085]	2379
[3281]	2380	END SUBROUTINE chem_statistics
[3085]	2381	!
	2382	!------------------------------------------------------------------------------!
	2383	!
[2828]	2384	! Description:
	2385	! ------------
[3085]	2386	!> Subroutine for swapping of timelevels for chemical species
	2387	!> called out from subroutine swap_timelevel
	2388	!------------------------------------------------------------------------------!
	2389
[3281]	2390	SUBROUTINE chem_swap_timelevel (level)
[3085]	2391
[3281]	2392	IMPLICIT none
[3085]	2393
[3281]	2394	INTEGER,INTENT(IN) :: level
	2395	!-- local variables
	2396	INTEGER :: lsp
[3085]	2397
[3298]	2398
[3281]	2399	IF ( level == 0 ) THEN
	2400	DO lsp=1, nvar
	2401	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
	2402	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
	2403	ENDDO
	2404	ELSE
	2405	DO lsp=1, nvar
	2406	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
	2407	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
	2408	ENDDO
	2409	ENDIF
[3085]	2410
[3281]	2411	RETURN
	2412	END SUBROUTINE chem_swap_timelevel
[3085]	2413	!
[2615]	2414	!------------------------------------------------------------------------------!
[3085]	2415	!
[2615]	2416	! Description:
	2417	! ------------
[3085]	2418	!> Subroutine to write restart data for chemistry model
[2615]	2419	!------------------------------------------------------------------------------!
[3281]	2420	SUBROUTINE chem_wrd_local
[2482]	2421
[3281]	2422	IMPLICIT NONE
[2615]	2423
[3281]	2424	INTEGER(iwp) :: lsp !<
[2615]	2425
[3281]	2426	DO lsp = 1, nspec
	2427	CALL wrd_write_string( TRIM( chem_species(lsp)%name ))
	2428	WRITE ( 14 ) chem_species(lsp)%conc
	2429	CALL wrd_write_string( TRIM( chem_species(lsp)%name )//'_av' )
	2430	WRITE ( 14 ) chem_species(lsp)%conc_av
	2431	ENDDO
[2615]	2432
[3281]	2433	END SUBROUTINE chem_wrd_local
[2615]	2434	END MODULE chemistry_model_mod
	2435

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