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source: palm/trunk/SOURCE/chemistry_model_mod.f90 @ 3241

Last change on this file since 3241 was 3241, checked in by raasch, 6 years ago
various changes to avoid compiler warnings (mainly removal of unused variables)
Property svn:keywords set to `Id`
File size: 75.4 KB

Rev	Line
[2657]	1	!> @file chemistry_model_mod.f90
	2	!------------------------------------------------------------------------------!
[2696]	3	! This file is part of the PALM model system.
[2657]	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	!
[2718]	17	! Copyright 1997-2018 Leibniz Universitaet Hannover
	18	! Copyright 2017-2018 Karlsruhe Institute of Technology
	19	! Copyright 2017-2018 Freie Universitaet Berlin
[2657]	20	!------------------------------------------------------------------------------!
	21	!
	22	! Current revisions:
	23	! -----------------
	24	!
[3215]	25	!
[2657]	26	! Former revisions:
	27	! -----------------
[2696]	28	! $Id: chemistry_model_mod.f90 3241 2018-09-12 15:02:00Z raasch $
[3215]	29	! +nest_chemistry
	30	!
	31	! 3209 2018-08-27 16:58:37Z suehring
[3183]	32	! Rename flags indicating outflow boundary conditions
	33	!
	34	! 3182 2018-07-27 13:36:03Z suehring
[3173]	35	! Revise output of surface quantities in case of overhanging structures
	36	!
	37	! 3045 2018-05-28 07:55:41Z Giersch
[3045]	38	! error messages revised
	39	!
	40	! 3014 2018-05-09 08:42:38Z maronga
[3014]	41	! Bugfix: nzb_do and nzt_do were not used for 3d data output
	42	!
	43	! 3004 2018-04-27 12:33:25Z Giersch
[3004]	44	! Comment concerning averaged data output added
	45	!
	46	! 2932 2018-03-26 09:39:22Z maronga
[2932]	47	! renamed chemistry_par to chemistry_parameters
	48	!
	49	! 2894 2018-03-15 09:17:58Z Giersch
[2894]	50	! Calculations of the index range of the subdomain on file which overlaps with
	51	! the current subdomain are already done in read_restart_data_mod,
	52	! chem_last_actions was renamed to chem_wrd_local, chem_read_restart_data was
	53	! renamed to chem_rrd_local, chem_write_var_list was renamed to
	54	! chem_wrd_global, chem_read_var_list was renamed to chem_rrd_global,
	55	! chem_skip_var_list has been removed, variable named found has been
	56	! introduced for checking if restart data was found, reading of restart strings
	57	! has been moved completely to read_restart_data_mod, chem_rrd_local is already
	58	! inside the overlap loop programmed in read_restart_data_mod, todo list has
	59	! bees extended, redundant characters in chem_wrd_local have been removed,
	60	! the marker * end chemistry * is not necessary anymore, strings and their
	61	! respective lengths are written out and read now in case of restart runs to
	62	! get rid of prescribed character lengths
	63	!
	64	! 2815 2018-02-19 11:29:57Z suehring
[2815]	65	! Bugfix in restart mechanism,
	66	! rename chem_tendency to chem_prognostic_equations,
	67	! implement vector-optimized version of chem_prognostic_equations,
	68	! some clean up (incl. todo list)
	69	!
	70	! 2773 2018-01-30 14:12:54Z suehring
[2773]	71	! Declare variables required for nesting as public
	72	!
	73	! 2772 2018-01-29 13:10:35Z suehring
[2772]	74	! Bugfix in string handling
	75	!
	76	! 2768 2018-01-24 15:38:29Z kanani
[2768]	77	! Shorten lines to maximum length of 132 characters
	78	!
	79	! 2766 2018-01-22 17:17:47Z kanani
[2766]	80	! Removed preprocessor directive __chem
	81	!
	82	! 2756 2018-01-16 18:11:14Z suehring
[2756]	83	! Fill values in 3D output introduced.
	84	!
	85	! 2718 2018-01-02 08:49:38Z maronga
[2696]	86	! Initial revision
	87	!
[2657]	88	!
[2696]	89	!
	90	!
	91	! Authors:
	92	! --------
	93	! @author Renate Forkel
	94	! @author Farah Kanani-Suehring
	95	! @author Klaus Ketelsen
	96	! @author Basit Khan
	97	!
	98	!
[2657]	99	!------------------------------------------------------------------------------!
	100	! Description:
	101	! ------------
	102	!> Chemistry model for PALM-4U
[2894]	103	!> @todo Adjust chem_rrd_local to CASE structure of others modules. It is not
	104	!> allowed to use the chemistry model in a precursor run and additionally
	105	!> not using it in a main run
[2668]	106	!> @todo Update/clean-up todo list! (FK)
	107	!> @todo Set proper fill values (/= 0) for chem output arrays! (FK)
	108	!> @todo Add routine chem_check_parameters, add checks for inconsistent or
[2815]	109	!> unallowed parameter settings.
	110	!> CALL of chem_check_parameters from check_parameters. (FK)
[2668]	111	!> @todo Make routine chem_header available, CALL from header.f90
	112	!> (see e.g. how it is done in routine lsm_header in
	113	!> land_surface_model_mod.f90). chem_header should include all setup
	114	!> info about chemistry parameter settings. (FK)
[2657]	115	!> @todo Implement turbulent inflow of chem spcs in inflow_turbulence.
	116	!> @todo Separate boundary conditions for each chem spcs to be implemented
	117	!> @todo Currently only total concentration are calculated. Resolved, parameterized
	118	!> and chemistry fluxes although partially and some completely coded but
	119	!> are not operational/activated in this version. bK.
	120	!> @todo slight differences in passive scalar and chem spcs when chem reactions
	121	!> turned off. Need to be fixed. bK
[2815]	122	!> @todo test nesting for chem spcs, was implemented by suehring (kanani)
[2657]	123	!> @todo subroutine set_const_initial_values to be taken out from chemistry_model_mod !bK.
	124	!> @todo chemistry error messages
	125	!> @todo Format this module according to PALM coding standard (see e.g. module
	126	!> template under http://palm.muk.uni-hannover.de/mosaik/downloads/8 or
	127	!> D3_coding_standard.pdf under https://palm.muk.uni-hannover.de/trac/downloads/16)
	128	!
	129	!------------------------------------------------------------------------------!
	130
	131	MODULE chemistry_model_mod
[2766]	132
[2657]	133	USE kinds, ONLY: wp, iwp
	134	USE indices, ONLY: nz, nzb,nzt,nysg,nyng,nxlg,nxrg,nys,nyn
	135	USE pegrid, ONLY: myid, threads_per_task
	136	USE control_parameters, ONLY: dt_3d, ws_scheme_sca, initializing_actions, message_string, &
	137	omega, tsc, intermediate_timestep_count, &
	138	intermediate_timestep_count_max, &
	139	timestep_scheme, use_prescribed_profile_data
	140	USE arrays_3d, ONLY: hyp, pt, rdf_sc, tend, zu
	141	USE chem_gasphase_mod, ONLY: nspec, spc_names, nkppctrl, nmaxfixsteps, &
	142	t_steps, fill_temp, chem_gasphase_integrate, &
	143	nvar, atol, rtol, nphot, phot_names
	144	USE cpulog, ONLY: cpu_log, log_point
	145
	146	USE chem_modules
	147
	148
	149	IMPLICIT NONE
	150	PRIVATE
	151	SAVE
	152
[3209]	153	LOGICAL :: nest_chemistry = .TRUE. !< flag for nesting mode of chemical species, independent on parent or not
	154	!
[2657]	155	!- Define chemical variables
	156	TYPE species_def
	157	CHARACTER(LEN=8) :: name
	158	CHARACTER(LEN=16) :: unit
	159	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc
	160	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_av
	161	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_p
	162	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: tconc_m
	163	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: cssws_av
	164	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: flux_s_cs
	165	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: diss_s_cs
	166	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: flux_l_cs
	167	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: diss_l_cs
	168	REAL(kind=wp),ALLOCATABLE,DIMENSION(:) :: conc_pr_init
	169	END TYPE species_def
	170
	171
	172	TYPE photols_def
	173	CHARACTER(LEN=8) :: name
	174	CHARACTER(LEN=16) :: unit
	175	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: freq
	176	END TYPE photols_def
	177
	178
	179	PUBLIC species_def
	180	PUBLIC photols_def
	181
	182
	183	TYPE(species_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: chem_species
	184	TYPE(photols_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: phot_frequen
	185
	186	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_1
	187	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_2
	188	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_3
	189	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_av
	190	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: freq_1
	191
	192	INTEGER,DIMENSION(nkppctrl) :: icntrl ! Fine tuning kpp
	193	REAL(kind=wp),DIMENSION(nkppctrl) :: rcntrl ! Fine tuning kpp
	194
	195	CHARACTER(10), PUBLIC :: photolysis_scheme
	196	! 'constant',
	197	! 'simple' (Simple parameterisation from MCM, Saunders et al., 2003, Atmos. Chem. Phys., 3, 161-180
	198	! 'fastj' (Wild et al., 2000, J. Atmos. Chem., 37, 245-282) STILL NOT IMPLEMENTED
	199
[3209]	200	PUBLIC nest_chemistry, nspec
[2657]	201	PUBLIC nvar
[2773]	202	PUBLIC spc_names
	203	PUBLIC spec_conc_2
[2657]	204
	205	!- Interface section
	206	INTERFACE chem_boundary_conds
	207	MODULE PROCEDURE chem_boundary_conds
	208	END INTERFACE chem_boundary_conds
	209
	210	INTERFACE chem_init
	211	MODULE PROCEDURE chem_init
	212	END INTERFACE chem_init
	213
	214	INTERFACE chem_init_profiles
	215	MODULE PROCEDURE chem_init_profiles
[2682]	216	END INTERFACE chem_init_profiles
[2657]	217
	218	INTERFACE chem_parin
	219	MODULE PROCEDURE chem_parin
	220	END INTERFACE chem_parin
	221
	222	INTERFACE chem_integrate
	223	MODULE PROCEDURE chem_integrate_ij
	224	END INTERFACE chem_integrate
	225
	226	INTERFACE chem_swap_timelevel
	227	MODULE PROCEDURE chem_swap_timelevel
	228	END INTERFACE chem_swap_timelevel
	229
	230	INTERFACE chem_define_netcdf_grid
	231	MODULE PROCEDURE chem_define_netcdf_grid
	232	END INTERFACE chem_define_netcdf_grid
	233
	234	INTERFACE chem_data_output_3d
	235	MODULE PROCEDURE chem_data_output_3d
	236	END INTERFACE chem_data_output_3d
	237
	238	INTERFACE chem_check_data_output
	239	MODULE PROCEDURE chem_check_data_output
	240	END INTERFACE chem_check_data_output
	241
	242	INTERFACE chem_check_data_output_pr
	243	MODULE PROCEDURE chem_check_data_output_pr
	244	END INTERFACE chem_check_data_output_pr
	245
	246	INTERFACE chem_3d_data_averaging
	247	MODULE PROCEDURE chem_3d_data_averaging
	248	END INTERFACE chem_3d_data_averaging
	249
[2894]	250	INTERFACE chem_wrd_local
	251	MODULE PROCEDURE chem_wrd_local
	252	END INTERFACE chem_wrd_local
[2657]	253
[2894]	254	INTERFACE chem_rrd_local
	255	MODULE PROCEDURE chem_rrd_local
	256	END INTERFACE chem_rrd_local
[2657]	257
[2815]	258	INTERFACE chem_prognostic_equations
	259	MODULE PROCEDURE chem_prognostic_equations
	260	MODULE PROCEDURE chem_prognostic_equations_ij
	261	END INTERFACE chem_prognostic_equations
[2657]	262
	263	INTERFACE chem_header
	264	MODULE PROCEDURE chem_header
	265	END INTERFACE chem_header
	266
[2668]	267	INTERFACE chem_emissions
	268	MODULE PROCEDURE chem_emissions
	269	END INTERFACE chem_emissions
[2657]	270
[2894]	271	! INTERFACE chem_wrd_global
	272	! MODULE PROCEDURE chem_wrd_global
	273	! END INTERFACE chem_wrd_global
[2668]	274	!
[2894]	275	! INTERFACE chem_rrd_global
	276	! MODULE PROCEDURE chem_rrd_global
	277	! END INTERFACE chem_rrd_global
[2657]	278
	279
[2815]	280	PUBLIC chem_3d_data_averaging, chem_boundary_conds, chem_check_data_output, &
[2657]	281	chem_check_data_output_pr, chem_data_output_3d, &
[2815]	282	chem_define_netcdf_grid, chem_emissions, chem_header, chem_init, &
[2894]	283	chem_init_profiles, chem_integrate, chem_wrd_local, &
[2815]	284	chem_parin, chem_prognostic_equations, &
[2894]	285	chem_rrd_local, chem_swap_timelevel
[2815]	286
[2657]	287
	288	CONTAINS
	289
	290	!------------------------------------------------------------------------------!
	291	!
	292	! Description:
	293	! ------------
	294	!> Subroutine to initialize and set all boundary conditions for chemical species
	295	!------------------------------------------------------------------------------!
	296
	297	SUBROUTINE chem_boundary_conds( mode )
	298
	299	USE control_parameters, &
[3241]	300	ONLY: bc_radiation_l, bc_radiation_n, bc_radiation_r, bc_radiation_s
	301
[2657]	302	USE indices, &
[3241]	303	ONLY: nxl, nxr, nzt
[2657]	304
	305	USE arrays_3d, &
[3182]	306	ONLY: dzu
[3241]	307
[2657]	308	USE surface_mod, &
[3182]	309	ONLY: bc_h
[2657]	310
	311	CHARACTER (len=*), INTENT(IN) :: mode
	312	INTEGER(iwp) :: i !< grid index x direction.
	313	INTEGER(iwp) :: j !< grid index y direction.
	314	INTEGER(iwp) :: k !< grid index z direction.
	315	INTEGER(iwp) :: kb !< variable to set respective boundary value, depends on facing.
	316	INTEGER(iwp) :: l !< running index boundary type, for up- and downward-facing walls.
	317	INTEGER(iwp) :: m !< running index surface elements.
	318	INTEGER(iwp) :: lsp !< running index for chem spcs.
	319
	320
	321	SELECT CASE ( TRIM( mode ) )
	322	CASE ( 'init' )
	323	DO lsp = 1, nspec
	324	IF ( surface_csflux(lsp) == 9999999.9_wp ) THEN
	325	constant_csflux(lsp) = .FALSE.
	326	ENDIF
	327	ENDDO
	328
	329	IF ( bc_cs_b == 'dirichlet' ) THEN
	330	ibc_cs_b = 0
	331	ELSEIF ( bc_cs_b == 'neumann' ) THEN
	332	ibc_cs_b = 1
	333	ELSE
	334	! message_string = 'unknown boundary condition: bc_cs_b ="' // TRIM( bc_cs_b ) // '"' ! bK commented
[2815]	335	CALL message( 'chem_boundary_conds', 'CM0010', 1, 2, 0, 6, 0 ) !< chemistry_model_mod should have special error numbers --> "CHEM###",
[2657]	336	ENDIF
	337	!
	338	!-- Set Integer flags and check for possible erroneous settings for top
	339	!-- boundary condition. bK added _cs_ here.
	340	IF ( bc_cs_t == 'dirichlet' ) THEN
	341	ibc_cs_t = 0
	342	ELSEIF ( bc_cs_t == 'neumann' ) THEN
	343	ibc_cs_t = 1
	344	ELSEIF ( bc_cs_t == 'initial_gradient' ) THEN
	345	ibc_cs_t = 2
	346	ELSEIF ( bc_cs_t == 'nested' ) THEN
	347	ibc_cs_t = 3
	348	ELSE
	349	! message_string = 'unknown boundary condition: bc_c_t ="' // TRIM( bc_cs_t ) // '"'
[2815]	350	CALL message( 'check_parameters', 'CM0011', 1, 2, 0, 6, 0 )
[2657]	351	ENDIF
	352
	353
	354	CASE ( 'set_bc_bottomtop' )
	355	!-- Bottom boundary condtions for chemical species
	356	DO lsp = 1, nspec
	357	IF ( ibc_cs_b == 0 ) THEN
	358	DO l = 0, 1
	359	!-- Set index kb: For upward-facing surfaces (l=0), kb=-1, i.e.
	360	!-- the chem_species(nsp)%conc_p value at the topography top (k-1)
	361	!-- is set; for downward-facing surfaces (l=1), kb=1, i.e. the
	362	!-- value at the topography bottom (k+1) is set.
	363
	364	kb = MERGE( -1, 1, l == 0 )
	365	!$OMP PARALLEL DO PRIVATE( i, j, k )
	366	DO m = 1, bc_h(l)%ns
	367	i = bc_h(l)%i(m)
	368	j = bc_h(l)%j(m)
	369	k = bc_h(l)%k(m)
	370	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc(k+kb,j,i)
	371	ENDDO
	372	ENDDO
	373
	374	ELSEIF ( ibc_cs_b == 1 ) THEN
	375	! in boundary_conds there is som extra loop over m here for passive tracer
	376	DO l = 0, 1
	377	kb = MERGE( -1, 1, l == 0 )
	378	!$OMP PARALLEL DO PRIVATE( i, j, k )
	379	DO m = 1, bc_h(l)%ns
	380	i = bc_h(l)%i(m)
	381	j = bc_h(l)%j(m)
	382	k = bc_h(l)%k(m)
	383	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc_p(k,j,i)
	384
	385	!< @todo: chem_species(nsp)%conc_p(k+kb,j,i) = chem_species(nsp)%conc(k+kb,j,i), &
	386	!< pls loop over nsp=1, NSPEC.
	387	!< @todo: We should also think about the possibility to have &
	388	!< individual boundary conditions for each species? This means, bc_cs_b, &
	389	!< bc_cs_t, ibc_cs_b, ibc_cs_t would need to be added to TYPE chem_species(nsp)%, &
	390	!< and the loop over nsp would have to be put outside of this IF-clause.
	391	!< i think its better we keep the same bonundary cond i.e. dirichlet or neumann
	392	!< for all chem spcs. ... !bK
	393
	394	ENDDO
	395	ENDDO
	396	ENDIF
	397	ENDDO ! end lsp loop
	398
	399	!-- Top boundary conditions for chemical species - Should this not be done for all species?
	400	IF ( ibc_cs_t == 0 ) THEN
	401	DO lsp = 1, nspec
	402	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc(nzt+1,:,:)
	403	ENDDO
	404	ELSEIF ( ibc_cs_t == 1 ) THEN
	405	DO lsp = 1, nspec
[2678]	406	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:)
[2657]	407	ENDDO
	408	ELSEIF ( ibc_cs_t == 2 ) THEN
	409	DO lsp = 1, nspec
[2678]	410	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:) + bc_cs_t_val(lsp) * dzu(nzt+1)
[2657]	411	ENDDO
	412	!@todo: bc_cs_t_val needs to be calculated,
	413	!see bc_pt_t_val = ( pt_init(nzt+1) - pt_init(nzt) ) / dzu(nzt+1)
	414	!(in time_integration). pt_init would be the counterpart to
	415	!chem_species(i)%conc_pr_init (see kchem_driver_FKa1408.f90 of my
	416	!"Hints: prescribing initial concentration.
	417	ENDIF
	418	!
	419	CASE ( 'set_bc_lateral' ) ! bK commented it
	420	!-- Lateral boundary conditions for chem species at inflow boundary
	421	!-- are automatically set when chem_species concentration is
	422	!-- initialized. The initially set value at the inflow boundary is not
	423	!-- touched during time integration, hence, this boundary value remains
	424	!-- at a constant value, which is the concentration that flows into the
	425	!-- domain.
	426	!-- Lateral boundary conditions for chem species at outflow boundary
	427
[3182]	428	IF ( bc_radiation_s ) THEN
[2657]	429	DO lsp = 1, nspec
	430	chem_species(lsp)%conc_p(:,nys-1,:) = chem_species(lsp)%conc_p(:,nys,:)
	431	ENDDO
[3182]	432	ELSEIF ( bc_radiation_n ) THEN
[2657]	433	DO lsp = 1, nspec
	434	chem_species(lsp)%conc_p(:,nyn+1,:) = chem_species(lsp)%conc_p(:,nyn,:)
	435	ENDDO
[3182]	436	ELSEIF ( bc_radiation_l ) THEN
[2657]	437	DO lsp = 1, nspec
	438	chem_species(lsp)%conc_p(:,:,nxl-1) = chem_species(lsp)%conc_p(:,:,nxl)
	439	ENDDO
[3182]	440	ELSEIF ( bc_radiation_r ) THEN
[2657]	441	DO lsp = 1, nspec
	442	chem_species(lsp)%conc_p(:,:,nxr+1) = chem_species(lsp)%conc_p(:,:,nxr)
	443	ENDDO
	444	ENDIF
	445
	446	END SELECT
	447
	448	END SUBROUTINE chem_boundary_conds
	449	!
	450	!------------------------------------------------------------------------------!
	451	!
	452	! Description:
	453	! ------------
	454	!> Subroutine defining initial vertical profiles of chemical species (given by
	455	!> namelist parameters chem_profiles and chem_heights) --> which should work
	456	!> analogue to parameters u_profile, v_profile and uv_heights)
	457	!------------------------------------------------------------------------------!
	458	SUBROUTINE chem_init_profiles !< SUBROUTINE is called from chem_init in case of
	459	!< TRIM( initializing_actions ) /= 'read_restart_data'
	460	!< We still need to see what has to be done in case of restart run
	461	USE chem_modules
	462
	463	IMPLICIT NONE
	464
	465	!-- Local variables
	466	INTEGER :: lsp !< running index for number of species in derived data type species_def
	467	INTEGER :: lsp_pr !< running index for number of species in cs_names, cs_profiles etc
	468	INTEGER :: lpr_lev !< running index for profile level for each chem spcs.
[3241]	469	! INTEGER :: npr_lev !< the next available profile lev
[2657]	470
	471	!-----------------
	472	!-- To prescribe/initialize a vertically constant 'cs_profile', another parameter
	473	!-- "cs_surface" is introduced. If "cs_profile" and "cs_heights" are prescribed,
	474	!-- their values will override the constant profile given by "cs_surface".
	475
[2668]	476	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
[2657]	477	lsp_pr = 1
	478	DO WHILE ( TRIM( cs_name( lsp_pr ) ) /= 'novalue' ) !'novalue' is the default
	479	DO lsp = 1, nspec !
	480	!-- Create initial profile (conc_pr_init) for each chemical species
	481	IF ( TRIM( chem_species(lsp)%name ) == TRIM( cs_name(lsp_pr) ) ) THEN !
[2682]	482	! IF ( cs_profile(1,1) == 9999999.9_wp ) THEN
[2657]	483	!-- Set a vertically constant profile based on the surface conc (cs_surface(lsp_pr)) of each species
	484	DO lpr_lev = 0, nzt+1
	485	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_surface(lsp_pr)
	486	ENDDO
	487
[2682]	488	! ELSE
	489	! IF ( cs_heights(lsp,1) /= 0.0_wp ) THEN
	490	! message_string = 'cs_heights(1,1) must be 0.0'
[2815]	491	! CALL message( 'chem_check_parameters', 'CM0012', 1, 2, 0, 6, 0 )
[2682]	492	! ENDIF
	493	!
	494	! IF ( omega /= 0.0_wp ) THEN
	495	! message_string = 'Coriolis force must be switched off (by setting omega=0.0)' // &
	496	! ' when prescribing the forcing by u_profile and v_profile'
	497	! CALL message( 'check_parameters', 'PA0347', 1, 2, 0, 6, 0 )
	498	! ENDIF
	499	!
	500	! use_prescribed_profile_data = .TRUE.
	501	!
	502	! npr_lev = 1
	503	! ! chem_sddpecies(lsp)%conc_pr_init(0) = 0.0_wp
	504	! DO lpr_lev = 1, nz+1
	505	! IF ( npr_lev < 100 ) THEN
	506	! DO WHILE ( cs_heights(lsp, npr_lev+1) <= zu(lpr_lev) )
	507	! npr_lev = npr_lev + 1
	508	! IF ( npr_lev == 100 ) EXIT
	509	! ENDDO
	510	! ENDIF
	511	!
	512	! IF ( npr_lev < 100 .AND. cs_heights(lsp, npr_lev + 1) /= 9999999.9_wp ) THEN
	513	! chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp, npr_lev) + &
	514	! ( zu(lpr_lev) - cs_heights(lsp, npr_lev) ) / &
	515	! ( cs_heights(lsp, npr_lev + 1) - cs_heights(lsp, npr_lev ) ) * &
	516	! ( cs_profile(lsp, npr_lev + 1) - cs_profile(lsp, npr_lev ) )
	517	! ELSE
	518	! chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp, npr_lev)
	519	! ENDIF
	520	! ENDDO
	521	! ENDIF
[2657]	522	!-- If a profile is prescribed explicity using cs_profiles and cs_heights, we then have to fill the
	523	!-- chem_species(lsp)%conc_pr_init for the specific "lsp" based on the cs_profiles(lsp_pr,:)
	524	!-- and cs_heights(lsp_pr,:).
	525	ENDIF
	526	ENDDO
	527	lsp_pr = lsp_pr + 1
	528	ENDDO
[2668]	529	! ELSE
[2657]	530	! IF (chem_debug1 ) print*,'code to be added for initializing_actions == read_restart_data' !bK
[2668]	531	! ENDIF
[2657]	532
	533	!-- Now, go back to chem_init and use the contents of chem_species(lsp)%conc_pr_init to
	534	!-- initialize the 3D conc arrays, as it is currently taken care of in chem_set_constant_values.
	535	!-- After initializing the 3D arrays, these can be used to set the boundary conditions in the
	536	!-- subroutine kchem_boundary_conds, which should be called from boundary_conds.f90.
	537
	538
	539	END SUBROUTINE chem_init_profiles
	540	!
	541	!------------------------------------------------------------------------------!
	542	!
	543	! Description:
	544	! ------------
	545	!> Subroutine initializating chemistry_model_mod
	546	!------------------------------------------------------------------------------!
	547	SUBROUTINE chem_init
	548
	549	USE pegrid
	550
	551	IMPLICIT none
	552	!-- local variables
	553	INTEGER :: i,j !< running index for for horiz numerical grid points
	554	INTEGER :: lsp !< running index for chem spcs
	555	INTEGER :: lpr_lev !< running index for chem spcs profile level
	556	!
	557	!-- NOPOINTER version not implemented yet
[2682]	558	! #if defined( __nopointer )
	559	! message_string = 'The chemistry module only runs with POINTER version'
	560	! CALL message( 'chemistry_model_mod', 'CM0001', 1, 2, 0, 6, 0 )
	561	! #endif
	562	!
	563	!-- Allocate memory for chemical species
	564	ALLOCATE( chem_species(nspec) )
	565	ALLOCATE( spec_conc_1 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	566	ALLOCATE( spec_conc_2 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	567	ALLOCATE( spec_conc_3 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	568	ALLOCATE( spec_conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	569	ALLOCATE( phot_frequen(nphot) )
	570	ALLOCATE( freq_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nphot) )
	571	ALLOCATE( bc_cs_t_val(nspec) )
	572	!
	573	!-- Initialize arrays
	574	spec_conc_1 (:,:,:,:) = 0.0_wp
	575	spec_conc_2 (:,:,:,:) = 0.0_wp
	576	spec_conc_3 (:,:,:,:) = 0.0_wp
	577	spec_conc_av(:,:,:,:) = 0.0_wp
[2657]	578
[2682]	579
[2657]	580	DO lsp = 1, nspec
	581	chem_species(lsp)%name = spc_names(lsp)
	582
	583	chem_species(lsp)%conc (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1 (:,:,:,lsp)
	584	chem_species(lsp)%conc_p (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2 (:,:,:,lsp)
	585	chem_species(lsp)%tconc_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_3 (:,:,:,lsp)
	586	chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_av(:,:,:,lsp)
	587
	588	ALLOCATE (chem_species(lsp)%cssws_av(nysg:nyng,nxlg:nxrg))
[2682]	589	chem_species(lsp)%cssws_av = 0.0_wp
	590	!
	591	!-- (todo (FK): This needs to be revised. This block must go somewhere else)
[2657]	592	! IF ( ws_scheme_sca ) THEN
	593	ALLOCATE (chem_species(lsp)%flux_s_cs(nzb+1:nzt,0:threads_per_task-1))
	594	ALLOCATE (chem_species(lsp)%diss_s_cs(nzb+1:nzt,0:threads_per_task-1))
	595	ALLOCATE (chem_species(lsp)%flux_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
	596	ALLOCATE (chem_species(lsp)%diss_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
	597	chem_species(lsp)%flux_s_cs = 0.0_wp
	598	chem_species(lsp)%flux_l_cs = 0.0_wp
	599	chem_species(lsp)%diss_s_cs = 0.0_wp
	600	chem_species(lsp)%diss_l_cs = 0.0_wp
	601	! ENDIF
[2682]	602	!
	603	!-- Allocate memory for initial concentration profiles
	604	!-- (concentration values come from namelist)
	605	!-- (todo (FK): Because of this, chem_init is called in palm before
	606	!-- check_parameters, since conc_pr_init is used there.
	607	!-- We have to find another solution since chem_init should
	608	!-- eventually be called from init_3d_model!!)
	609	ALLOCATE ( chem_species(lsp)%conc_pr_init(0:nz+1) )
	610	chem_species(lsp)%conc_pr_init(:) = 0.0_wp
[2657]	611
	612	ENDDO
	613
	614	!
	615	!-- Set initial concentration of profiles prescribed by parameters cs_profile
[2932]	616	!-- and cs_heights in the namelist &chemistry_parameters
[2682]	617	!-- (todo (FK): chem_init_profiles not ready yet, has some bugs)
	618	! CALL chem_init_profiles
[2657]	619	!
	620	!-- Initialize model variables
	621
	622
	623	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
	624	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
	625
	626
	627	!-- First model run of a possible job queue.
	628	!-- Initial profiles of the variables must be computes.
	629	IF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
[2668]	630	! CALL location_message( 'initializing with 1D model profiles', .FALSE. )
[2657]	631	!
	632	! CALL init_1d_model ...... decide to call or not later !bK
	633
	634	!-- Transfer initial profiles to the arrays of the 3D model
	635	DO lsp = 1, nspec
	636	DO i = nxlg, nxrg
	637	DO j = nysg, nyng
	638	DO lpr_lev = 1, nz + 1
	639	chem_species(lsp)%conc(lpr_lev,j,i) = chem_species(lsp)%conc_pr_init(lpr_lev)
	640	ENDDO
	641	ENDDO
	642	ENDDO
	643	ENDDO
	644
	645	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
	646	THEN
[2668]	647	! CALL location_message( 'initializing with constant profiles', .FALSE. )
[2657]	648
	649
	650
	651	!-- Set initial horizontal velocities at the lowest computational grid
	652	!-- levels to zero in order to avoid too small time steps caused by the
	653	!-- diffusion limit in the initial phase of a run (at k=1, dz/2 occurs
	654	!-- in the limiting formula!).
	655
	656	DO lsp = 1, nspec
	657	DO i = nxlg, nxrg
	658	DO j = nysg, nyng
	659	chem_species(lsp)%conc(:,j,i) = chem_species(lsp)%conc_pr_init !ITS THERE bK
	660	ENDDO
	661	ENDDO
	662	ENDDO
	663
[2668]	664	! ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) &
	665	! THEN
	666	! CALL location_message( 'initializing by user', .FALSE. )
[2657]	667	!
	668	!-- Initialization will completely be done by the user
[2668]	669	!-- (FK: This should be called only once, in init_3d_model, i.e. remove it here)
	670	! CALL user_init_3d_model
	671	! CALL location_message( 'finished', .TRUE. )
[2657]	672
	673	ENDIF
	674
	675	!-- Store initial chem spcs profile
	676	! DO lsp = 1, nvar
	677	! hom_cs(:,1,115,:) = SPREAD( chem_species(lsp)%conc(:,nys,nxl), 2, statistic_regions+1 )
	678	! ENDDO
	679	!
	680	!-- If required, change the surface chem spcs at the start of the 3D run
	681	IF ( cs_surface_initial_change(1) /= 0.0_wp ) THEN
	682	DO lsp = 1, nspec
	683	chem_species(lsp)%conc(nzb,:,:) = chem_species(lsp)%conc(nzb,:,:) + &
	684	cs_surface_initial_change(lsp)
	685	ENDDO
	686	ENDIF
	687	!
	688	!-- Initiale old and new time levels.
	689	DO lsp = 1, nvar
	690	chem_species(lsp)%tconc_m = 0.0_wp
[2682]	691	chem_species(lsp)%conc_p = chem_species(lsp)%conc
[2657]	692	ENDDO
	693
	694	ENDIF
	695
[2682]	696
	697
[2657]	698	!--- new code add above this line
	699	DO lsp = 1, nphot
	700	phot_frequen(lsp)%name = phot_names(lsp)
	701	! IF( myid == 0 ) THEN
	702	! WRITE(6,'(a,i4,3x,a)') 'Photolysis: ',lsp,trim(phot_names(lsp))
	703	! ENDIF
	704	phot_frequen(lsp)%freq(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => freq_1(:,:,:,lsp)
	705	ENDDO
	706
	707	!-- Set initial values
	708	! Not required any more, this can now be done with the namelist by setting cs_surface
	709	! and cs_name without specifying cs_profile (Nevertheless, we still want to keep it for a while)
	710	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
	711	! CALL set_const_initial_values
	712	! ENDIF
[2682]	713
[2657]	714	RETURN
	715
	716	CONTAINS
	717	!------------------------------------------------------------------------------!
	718	!
	719	! Description:
	720	! ------------
	721	!> Subroutine setting constant initial values of chemical species
	722	!------------------------------------------------------------------------------!
	723	SUBROUTINE set_const_initial_values
	724	! Not required any more, this can now be done with the namelist by setting cs_surface
	725	! and cs_name without specifying cs_profile (Nevertheless, we still want to keep it for a while)
	726	IMPLICIT none
	727
	728	!-- local variables
	729	INTEGER :: lsp
	730
	731	IF(myid == 0) THEN
	732	write(6,'(/,a,/)') ' chemics >>>> Set constant Initial Values: '
	733	ENDIF
	734
	735	! Default values are taken from smog.def from supplied kpp example
	736	DO lsp = 1, nspec
	737	IF(trim(chem_species(lsp)%name) == 'NO') THEN
	738	! chem_species(lsp)%conc = 8.725*1.0E+08
	739	! chem_species(lsp)%conc = 0.05_wp !added by bK
	740	chem_species(lsp)%conc = 0.01_wp !added by RFo
	741	ELSEIF (trim(chem_species(lsp)%name) == 'NO2') THEN
	742	! chem_species(lsp)%conc = 2.240*1.0E+08
	743	! chem_species(lsp)%conc = 0.01_wp !added by bK
	744	chem_species(lsp)%conc = 0.05_wp !added by RFo
	745	ELSEIF( trim( chem_species(lsp)%name ) == 'O3' ) THEN
	746	chem_species(lsp)%conc = 0.05_wp !added by bK
	747	ELSEIF(trim(chem_species(lsp)%name) == 'H2O') THEN
	748	! chem_species(lsp)%conc = 5.326*1.0E+11
	749	chem_species(lsp)%conc = 1.30*1.0E+4_wp !added by bK
	750	ELSEIF(trim(chem_species(lsp)%name) == 'O2') THEN
	751	chem_species(lsp)%conc = 2.0*1.0E+5_wp !added by bK
	752	ELSEIF(trim(chem_species(lsp)%name) == 'RH') THEN
	753	chem_species(lsp)%conc = 0.001_wp !added by RFo
	754	ELSEIF(trim(chem_species(lsp)%name) == 'CO') THEN
	755	chem_species(lsp)%conc = 0.5_wp !added by RFo
	756	ELSEIF(trim(chem_species(lsp)%name) == 'RCHO') THEN
	757	! chem_species(lsp)%conc = 2.0_wp !added by bK
	758	chem_species(lsp)%conc = 0.01_wp !added by RFo
	759	! ELSEIF(trim(chem_species(lsp)%name) == 'OH') THEN
	760	! chem_species(lsp)%conc = 1.0*1.0E-07_wp !added by bK
	761	! ELSEIF(trim(chem_species(lsp)%name) == 'HO2') THEN
	762	! chem_species(lsp)%conc = 1*1.0E-7_wp !added by bK
	763	! ELSEIF(trim(chem_species(lsp)%name) == 'RCOO2') THEN ! corrected RFo
	764	! chem_species(lsp)%conc = 1.0*1.0E-7_wp !added by bK
	765	! ELSEIF(trim(chem_species(lsp)%name) == 'RCOO2NO2') THEN
	766	! chem_species(lsp)%conc = 1.0*1.0E-7_wp !added by bK
	767	ELSE
	768	! H2O = 2.0e+04;
	769	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) = 0.0_wp
	770	ENDIF
	771
	772	IF(myid == 0) THEN
[2772]	773	WRITE(6,'(a,3x,a,3x,a,e12.4)') ' Species: ',chem_species(lsp)%name(1:7), &
	774	'Initial Value = ',chem_species(lsp)%conc(nzb,nysg,nxlg)
[2657]	775	ENDIF
	776	ENDDO
	777
	778	! #if defined( __nopointer )
	779	! !kk Hier mit message abbrechen
	780	! if(myid == 0) then
	781	! write(6,*) ' KPP does only run with POINTER Version'
	782	! end if
	783	! stop 'error'
	784	! #endif
	785
	786	RETURN
	787	END SUBROUTINE set_const_initial_values
	788
	789
	790	END SUBROUTINE chem_init
	791	!
	792	!------------------------------------------------------------------------------!
	793	!
	794	! Description:
	795	! ------------
[2932]	796	!> Subroutine defining parin for &chemistry_parameters for chemistry model
[2657]	797	!------------------------------------------------------------------------------!
	798	SUBROUTINE chem_parin
[2682]	799
[2657]	800	USE control_parameters, &
	801	ONLY: air_chemistry
[2682]	802
[2657]	803	USE chem_modules
[2682]	804
	805	USE kinds
[2657]	806
	807	IMPLICIT none
	808
[2682]	809	CHARACTER (LEN=80) :: line !< dummy string that contains the current line of the parameter file
	810
	811	REAL(wp), DIMENSION(nmaxfixsteps) :: my_steps !< List of fixed timesteps my_step(1) = 0.0 automatic stepping
[2657]	812
[2932]	813	NAMELIST /chemistry_parameters/ bc_cs_b, &
	814	bc_cs_t, &
	815	call_chem_at_all_substeps, &
	816	chem_debug0, &
	817	chem_debug1, &
	818	chem_debug2, &
	819	chem_gasphase_on, &
	820	cs_heights, &
	821	cs_name, &
	822	cs_profile, &
	823	cs_profile_name, &
	824	cs_surface, &
	825	emiss_factor_main, &
	826	emiss_factor_side, &
	827	icntrl, &
	828	main_street_id, &
	829	max_street_id, &
	830	my_steps, &
[3209]	831	nest_chemistry, &
[2932]	832	rcntrl, &
	833	side_street_id, &
	834	photolysis_scheme, &
	835	wall_csflux, &
	836	cs_vertical_gradient, &
	837	top_csflux, &
	838	surface_csflux, &
	839	surface_csflux_name, &
	840	cs_surface_initial_change, &
	841	cs_vertical_gradient_level
[2657]	842
	843	!-- analogue to chem_names(nspj) we could invent chem_surfaceflux(nspj) and chem_topflux(nspj)
	844	!-- so this way we could prescribe a specific flux value for each species
[2932]	845	!> chemistry_parameters for initial profiles
[2657]	846	!> cs_names = 'O3', 'NO2', 'NO', ... to set initial profiles)
	847	!> cs_heights(1,:) = 0.0, 100.0, 500.0, 2000.0, .... (height levels where concs will be prescribed for O3)
	848	!> cs_heights(2,:) = 0.0, 200.0, 400.0, 1000.0, .... (same for NO2 etc.)
	849	!> cs_profiles(1,:) = 10.0, 20.0, 20.0, 30.0, ..... (chem spcs conc at height lvls chem_heights(1,:)) etc.
	850	!> If the respective concentration profile should be constant with height, then use "cs_surface( number of spcs)"
	851	!> then write these cs_surface values to chem_species(lsp)%conc_pr_init(:)
	852
[2668]	853	!
	854	!-- Read chem namelist
	855	!-- (todo: initialize these parameters in declaration part, do this for
[2932]	856	!-- all chemistry_parameters namelist parameters)
[2657]	857	icntrl = 0
	858	rcntrl = 0.0_wp
	859	my_steps = 0.0_wp
	860	icntrl(2) = 1
	861	photolysis_scheme = 'simple'
	862	atol = 1.0_wp
	863	rtol = 0.01_wp
	864	!
	865	!-- Try to find chemistry package
	866	REWIND ( 11 )
	867	line = ' '
[2932]	868	DO WHILE ( INDEX( line, '&chemistry_parameters' ) == 0 )
[2668]	869	READ ( 11, '(A)', END=10 ) line
[2657]	870	ENDDO
	871	BACKSPACE ( 11 )
	872	!
[2668]	873	!-- Read chemistry namelist
[2932]	874	READ ( 11, chemistry_parameters )
[2668]	875	!
	876	!-- Enable chemistry model
	877	air_chemistry = .TRUE.
[2657]	878
[2668]	879
[2657]	880	10 CONTINUE
	881
[2668]	882	t_steps = my_steps !(todo: Why not directly make t_steps a
	883	! namelist parameter?)
[2657]	884
	885	END SUBROUTINE chem_parin
	886
	887	!
	888	!------------------------------------------------------------------------------!
	889	!
	890	! Description:
	891	! ------------
	892	!> Subroutine to integrate chemical species in the given chemical mechanism
	893	!------------------------------------------------------------------------------!
	894
	895	SUBROUTINE chem_integrate_ij (i, j)
	896
	897	USE cpulog, &
	898	ONLY: cpu_log, log_point
	899	USE statistics, & ! ## RFo
	900	ONLY: weight_pres
	901	USE control_parameters, & ! ## RFo
	902	ONLY: dt_3d, intermediate_timestep_count
	903
	904	IMPLICIT none
	905	INTEGER,INTENT(IN) :: i,j
	906
	907	!-- local variables
	908	INTEGER(iwp) :: lsp !< running index for chem spcs.
	909	INTEGER(iwp) :: lph !< running index for photolysis frequencies
[3241]	910	INTEGER :: istatf
[2657]	911	INTEGER,dimension(20) :: istatus
	912	REAL(kind=wp),dimension(nzb+1:nzt,nspec) :: tmp_conc
	913	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_temp
	914	REAL(kind=wp),dimension(nzb+1:nzt,nphot) :: tmp_phot
	915	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_fact
	916	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_fact_i !< conversion factor between molecules cm^{-3} and ppm
	917	REAL(wp) :: conv !< conversion factor
	918	REAL(wp), PARAMETER :: ppm2fr = 1.0e-6_wp !< Conversion factor ppm to fraction
	919	REAL(wp), PARAMETER :: t_std = 273.15_wp !< standard pressure (Pa)
	920	REAL(wp), PARAMETER :: p_std = 101325.0_wp !< standard pressure (Pa)
	921	REAL(wp), PARAMETER :: vmolcm = 22.414e3_wp !< Mole volume (22.414 l) in cm^{-3}
	922	REAL(wp), PARAMETER :: xna = 6.022e23_wp !< Avogadro number (molecules/mol)
	923
	924
	925	REAL(kind=wp) :: dt_chem
	926
	927	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'start' )
	928	!< Set chem_gasphase_on to .FALSE. if you want to skip computation of gas phase chemistry
	929	IF (chem_gasphase_on) THEN
	930
	931	tmp_temp(:) = pt(:,j,i) * ( hyp(nzb+1:nzt) / 100000.0_wp )**0.286_wp
	932	! ppm to molecules/cm**3
	933	! tmp_fact = 1.e-6_wp6.022e23_wp/(22.414_wp1000._wp) * 273.15_wp * hyp(nzb+1:nzt)/( 101300.0_wp * tmp_temp )
	934	conv = ppm2fr * xna / vmolcm
	935	tmp_fact(:) = conv * t_std * hyp(nzb+1:nzt) / (tmp_temp(:) * p_std)
	936	tmp_fact_i = 1.0_wp/tmp_fact
	937
	938	CALL fill_temp (istatf, tmp_temp) !< Load constant temperature into kpp context
	939	! CALL fill_temp (istatf, pt(nzb+1:nzt,j,i)) !< Load temperature into kpp context
	940
	941	DO lsp = 1,nspec
	942	tmp_conc(:,lsp) = chem_species(lsp)%conc(nzb+1:nzt,j,i) * tmp_fact(:)
	943	ENDDO
	944
	945	DO lph = 1,nphot
	946	tmp_phot(:,lph) = phot_frequen(lph)%freq(nzb+1:nzt,j,i)
	947	ENDDO
	948
	949	IF(myid == 0 .AND. chem_debug0 ) THEN
	950	IF (i == 10 .and. j == 10) WRITE(0,*) 'begin chemics step ',dt_3d
	951	ENDIF
	952
	953	!-- Compute length of time step # RFo
	954	IF ( call_chem_at_all_substeps ) THEN
	955	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
	956	ELSE
	957	dt_chem = dt_3d
	958	ENDIF
	959
	960	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'start' )
	961
	962
	963	CALL chem_gasphase_integrate (dt_chem, tmp_conc, tmp_temp, tmp_phot, istatus=istatus)
	964
	965
	966	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'stop' )
	967
	968	DO lsp = 1,nspec
	969	chem_species(lsp)%conc (nzb+1:nzt,j,i) = tmp_conc(:,lsp) * tmp_fact_i(:) ! RFo
	970	ENDDO
	971
	972	! IF (myid == 0 .AND. chem_debug2 ) THEN
	973	! IF (i == 10 .and. j == 10) WRITE(6,'(a,8i7)') ' KPP Status ',istatus(1:8)
	974	! write(6,'(a,8i7)') ' KPP Status ',istatus(1:8)
	975	! ENDIF
	976
	977	ENDIF
	978	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'stop' )
	979
	980	RETURN
	981	END SUBROUTINE chem_integrate_ij
	982	!
	983	!------------------------------------------------------------------------------!
	984	!
	985	! Description:
	986	! ------------
	987	!> Subroutine for swapping of timelevels for chemical species
	988	!> called out from subroutine swap_timelevel
	989	!------------------------------------------------------------------------------!
	990
	991	SUBROUTINE chem_swap_timelevel (level)
	992	IMPLICIT none
	993
	994	INTEGER,INTENT(IN) :: level
	995
	996	!-- local variables
	997
	998	INTEGER :: lsp
	999
	1000	! print,' entering chem_swap_timelevel *) '
	1001	if(level == 0) then
	1002	do lsp=1, nvar
	1003	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
	1004	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
	1005	end do
	1006	else
	1007	do lsp=1, nvar
	1008	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
	1009	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
	1010	end do
	1011	end if
	1012
	1013	RETURN
	1014	END SUBROUTINE chem_swap_timelevel
	1015
	1016	!------------------------------------------------------------------------------!
	1017	!
	1018	! Description:
	1019	! ------------
	1020	!> Subroutine defining appropriate grid for netcdf variables.
	1021	!> It is called out from subroutine netcdf.
	1022	!------------------------------------------------------------------------------!
	1023	SUBROUTINE chem_define_netcdf_grid( var, found, grid_x, grid_y, grid_z )
	1024
	1025	IMPLICIT NONE
	1026
	1027	CHARACTER (LEN=*), INTENT(IN) :: var !<
	1028	LOGICAL, INTENT(OUT) :: found !<
	1029	CHARACTER (LEN=*), INTENT(OUT) :: grid_x !<
	1030	CHARACTER (LEN=*), INTENT(OUT) :: grid_y !<
	1031	CHARACTER (LEN=*), INTENT(OUT) :: grid_z !<
	1032
	1033	found = .TRUE.
	1034
	1035	if(var(1:3) == 'kc_') then !< always the same grid for chemistry variables
	1036	grid_x = 'x'
	1037	grid_y = 'y'
	1038	grid_z = 'zu' !< kk Use same z axis as u variables. Has to be checked if OK
	1039	else
	1040	found = .FALSE.
	1041	grid_x = 'none'
	1042	grid_y = 'none'
	1043	grid_z = 'none'
	1044	end if
	1045
	1046	! write(6,*) 'chem_define_netcdf_grid ',TRIM(var),' ',trim(grid_x),' ',found
	1047
	1048	END SUBROUTINE chem_define_netcdf_grid
	1049	!
	1050	!------------------------------------------------------------------------------!
	1051	!
	1052	! Description:
	1053	! ------------
	1054	!> Subroutine for checking data output for chemical species
	1055	!------------------------------------------------------------------------------!
	1056
	1057	SUBROUTINE chem_check_data_output( var, unit, i, ilen, k )
	1058
	1059	IMPLICIT NONE
	1060
	1061	CHARACTER (LEN=*) :: unit !<
	1062	CHARACTER (LEN=*) :: var !<
	1063
[3241]	1064	INTEGER(iwp) :: i, ilen, k, lsp
[2657]	1065
	1066	CHARACTER(len=16) :: spec_name
	1067
	1068	unit = 'illegal'
	1069
	1070	spec_name = TRIM(var(4:)) !< var 1:3 is 'kc_'.
	1071
	1072	DO lsp=1,nspec
	1073	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
	1074	unit = 'ppm'
	1075	ENDIF
	1076	! It is possible to plant PM10 and PM25 into the gasphase chemistry code
	1077	! ! as passive species (e.g. 'passive' in GASPHASE_PREPROC/mechanisms):
	1078	! ! set unit to micrograms per m**3 for PM10 and PM25 (PM2.5)
	1079	IF (spec_name(1:2) == 'PM') THEN
	1080	unit = 'ug m-3'
	1081	ENDIF
	1082	ENDDO
	1083
	1084	DO lsp=1,nphot
	1085	IF (TRIM(spec_name) == TRIM(phot_frequen(lsp)%name)) THEN
	1086	unit = 'sec-1'
	1087	ENDIF
	1088	ENDDO
	1089
	1090
	1091	RETURN
	1092	END SUBROUTINE chem_check_data_output
	1093	!
	1094	!------------------------------------------------------------------------------!
	1095	!
	1096	! Description:
	1097	! ------------
	1098	!> Subroutine for checking data output of profiles for chemistry model
	1099	!------------------------------------------------------------------------------!
	1100
	1101	SUBROUTINE chem_check_data_output_pr( variable, var_count, unit, dopr_unit )
	1102
	1103
	1104	USE arrays_3d, &
	1105	ONLY: zu
	1106
	1107	USE control_parameters, &
	1108	ONLY: data_output_pr, message_string, air_chemistry
	1109
	1110	USE indices
	1111
	1112	USE profil_parameter
	1113
	1114	USE statistics
	1115
	1116
	1117	IMPLICIT NONE
	1118
	1119	CHARACTER (LEN=*) :: unit !<
	1120	CHARACTER (LEN=*) :: variable !<
	1121	CHARACTER (LEN=*) :: dopr_unit
	1122	CHARACTER(len=16) :: spec_name
	1123
	1124	INTEGER(iwp) :: var_count, lsp !<
	1125
	1126
	1127	spec_name = TRIM(variable(4:))
	1128	! write(9,*) 'fm #32 .. air_chemistry ', air_chemistry
	1129
	1130	IF ( .NOT. air_chemistry ) THEN
	1131	message_string = 'data_output_pr = ' // &
	1132	TRIM( data_output_pr(var_count) ) // ' is not imp' // &
	1133	'lemented for air_chemistry = .FALSE.'
[3045]	1134	! CALL message( 'check_parameters', 'PA0XXX', 1, 2, 0, 6, 0 )
[2657]	1135	ELSE
	1136	DO lsp = 1, nspec
	1137	IF (TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
	1138	dopr_index(var_count) = 900
	1139	dopr_unit = 'ppm'
	1140	hom(:,2,900,:) = SPREAD( zu, 2, statistic_regions+1 )
	1141	ENDIF
	1142	ENDDO
	1143	ENDIF
	1144
	1145	END SUBROUTINE chem_check_data_output_pr
	1146	!
	1147	!------------------------------------------------------------------------------!
	1148	!
	1149	! Description:
	1150	! ------------
	1151	!> Subroutine defining 3D output variables for chemical species
	1152	!------------------------------------------------------------------------------!
	1153
	1154
[3014]	1155	SUBROUTINE chem_data_output_3d( av, variable, found, local_pf, fill_value, nzb_do, nzt_do )
[2657]	1156
	1157
	1158	USE indices
	1159
	1160	USE kinds
	1161
	1162
	1163	IMPLICIT NONE
	1164
	1165	CHARACTER (LEN=*) :: variable !<
[3014]	1166
[2657]	1167	INTEGER(iwp) :: av !<
[3014]	1168	INTEGER(iwp) :: nzb_do !< lower limit of the data output (usually 0)
	1169	INTEGER(iwp) :: nzt_do !< vertical upper limit of the data output (usually nz_do3d)
[2657]	1170
[3014]	1171	LOGICAL :: found !<
	1172
[2756]	1173	REAL(wp) :: fill_value !<
[3014]	1174	REAL(sp), DIMENSION(nxl:nxr,nys:nyn,nzb_do:nzt_do) :: local_pf
[2756]	1175
	1176
[2657]	1177	!-- local variables
	1178
	1179	INTEGER :: i, j, k, lsp
	1180	CHARACTER(len=16) :: spec_name
	1181
	1182
	1183	found = .FALSE.
	1184
	1185	spec_name = TRIM(variable(4:))
	1186	!av == 0
	1187
	1188	DO lsp=1,nspec
	1189	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
[2772]	1190	IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
	1191	TRIM(chem_species(lsp)%name)
[2657]	1192
	1193	IF (av == 0) THEN
	1194	DO i = nxl, nxr
	1195	DO j = nys, nyn
[3014]	1196	DO k = nzb_do, nzt_do
[2756]	1197	local_pf(i,j,k) = MERGE( &
	1198	chem_species(lsp)%conc(k,j,i), &
	1199	REAL( fill_value, KIND = wp ), &
	1200	BTEST( wall_flags_0(k,j,i), 0 ) )
[2657]	1201	ENDDO
	1202	ENDDO
	1203	ENDDO
	1204
	1205	ELSE
	1206	DO i = nxl, nxr
	1207	DO j = nys, nyn
[3014]	1208	DO k = nzb_do, nzt_do
[2756]	1209	local_pf(i,j,k) = MERGE( &
	1210	chem_species(lsp)%conc_av(k,j,i),&
	1211	REAL( fill_value, KIND = wp ), &
	1212	BTEST( wall_flags_0(k,j,i), 0 ) )
[2657]	1213	ENDDO
	1214	ENDDO
	1215	ENDDO
	1216	ENDIF
	1217
	1218	found = .TRUE.
	1219	ENDIF
	1220	ENDDO
	1221
	1222	RETURN
	1223	END SUBROUTINE chem_data_output_3d
	1224	!
	1225	!------------------------------------------------------------------------------!
	1226	!
	1227	! Description:
	1228	! ------------
[3004]	1229	!> Subroutine for averaging 3D data of chemical species. Due to the fact that
	1230	!> the averaged chem arrays are allocated in chem_init, no if-query concerning
	1231	!> the allocation is required (in any mode). Attention: If you just specify an
	1232	!> averaged output quantity in the _p3dr file during restarts the first output
	1233	!> includes the time between the beginning of the restart run and the first
	1234	!> output time (not necessarily the whole averaging_interval you have
	1235	!> specified in your _p3d/_p3dr file )
[2657]	1236	!------------------------------------------------------------------------------!
	1237
	1238	SUBROUTINE chem_3d_data_averaging ( mode, variable )
	1239
	1240	USE control_parameters
	1241
	1242	USE indices
	1243
	1244	USE kinds
	1245
	1246	USE surface_mod, &
	1247	ONLY: surf_def_h, surf_lsm_h, surf_usm_h
	1248
	1249	IMPLICIT NONE
	1250
	1251	CHARACTER (LEN=*) :: mode !<
	1252	CHARACTER (LEN=*) :: variable !<
	1253
[3173]	1254	LOGICAL :: match_def !< flag indicating natural-type surface
	1255	LOGICAL :: match_lsm !< flag indicating natural-type surface
	1256	LOGICAL :: match_usm !< flag indicating urban-type surface
[2657]	1257
	1258	INTEGER(iwp) :: i !< grid index x direction
	1259	INTEGER(iwp) :: j !< grid index y direction
	1260	INTEGER(iwp) :: k !< grid index z direction
	1261	INTEGER(iwp) :: m !< running index surface type
	1262	INTEGER(iwp) :: lsp !< running index for chem spcs
	1263
	1264	IF ( mode == 'allocate' ) THEN
	1265	DO lsp = 1, nspec
	1266	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	1267	chem_species(lsp)%conc_av = 0.0_wp
	1268	ENDIF
	1269	ENDDO
	1270
	1271	ELSEIF ( mode == 'sum' ) THEN
	1272
	1273	DO lsp = 1, nspec
	1274	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	1275	DO i = nxlg, nxrg
	1276	DO j = nysg, nyng
	1277	DO k = nzb, nzt+1
	1278	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) + &
	1279	chem_species(lsp)%conc(k,j,i)
	1280	ENDDO
	1281	ENDDO
	1282	ENDDO
	1283	ELSEIF ( TRIM(variable(4:)) == TRIM('cssws*') ) THEN
[3173]	1284	DO i = nxl, nxr
	1285	DO j = nys, nyn
	1286	match_def = surf_def_h(0)%start_index(j,i) <= &
	1287	surf_def_h(0)%end_index(j,i)
	1288	match_lsm = surf_lsm_h%start_index(j,i) <= &
	1289	surf_lsm_h%end_index(j,i)
	1290	match_usm = surf_usm_h%start_index(j,i) <= &
	1291	surf_usm_h%end_index(j,i)
	1292
	1293	IF ( match_def ) THEN
	1294	m = surf_def_h(0)%end_index(j,i)
	1295	chem_species(lsp)%cssws_av(j,i) = &
	1296	chem_species(lsp)%cssws_av(j,i) + &
	1297	surf_def_h(0)%cssws(lsp,m)
	1298	ELSEIF ( match_lsm .AND. .NOT. match_usm ) THEN
	1299	m = surf_lsm_h%end_index(j,i)
	1300	chem_species(lsp)%cssws_av(j,i) = &
	1301	chem_species(lsp)%cssws_av(j,i) + &
	1302	surf_lsm_h%cssws(lsp,m)
	1303	ELSEIF ( match_usm ) THEN
	1304	m = surf_usm_h%end_index(j,i)
	1305	chem_species(lsp)%cssws_av(j,i) = &
	1306	chem_species(lsp)%cssws_av(j,i) + &
	1307	surf_usm_h%cssws(lsp,m)
	1308	ENDIF
	1309	ENDDO
[2657]	1310	ENDDO
	1311	ENDIF
	1312	ENDDO
	1313
	1314	ELSEIF ( mode == 'average' ) THEN
	1315	DO lsp = 1, nspec
	1316	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	1317	DO i = nxlg, nxrg
	1318	DO j = nysg, nyng
	1319	DO k = nzb, nzt+1
	1320	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) / REAL( average_count_3d, KIND=wp )
	1321	ENDDO
	1322	ENDDO
	1323	ENDDO
	1324
	1325	ELSEIF (TRIM(variable(4:)) == TRIM('cssws*') ) THEN
	1326	DO i = nxlg, nxrg
	1327	DO j = nysg, nyng
	1328	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) / REAL( average_count_3d, KIND=wp )
	1329	ENDDO
	1330	ENDDO
	1331	CALL exchange_horiz_2d( chem_species(lsp)%cssws_av, nbgp )
	1332	ENDIF
	1333	ENDDO
	1334
	1335	ENDIF
	1336
	1337	END SUBROUTINE chem_3d_data_averaging
	1338
	1339	!------------------------------------------------------------------------------!
	1340	!
	1341	! Description:
	1342	! ------------
	1343	!> Subroutine to write restart data for chemistry model
	1344	!------------------------------------------------------------------------------!
[2894]	1345	SUBROUTINE chem_wrd_local
[2657]	1346
	1347
	1348	IMPLICIT NONE
	1349
[2815]	1350	INTEGER(iwp) :: lsp !<
[2894]	1351
[2657]	1352	! REAL(kind=wp), DIMENSION(nzb:nzt+1,nysg:nyng,nxlg:nxrg) :: chems_conc
[2815]	1353
	1354
[2894]	1355	DO lsp = 1, nspec
[2668]	1356
[2894]	1357	CALL wrd_write_string( TRIM( chem_species(lsp)%name ))
	1358	WRITE ( 14 ) chem_species(lsp)%conc
[2657]	1359
[2894]	1360	CALL wrd_write_string( TRIM( chem_species(lsp)%name )//'_av' )
	1361	WRITE ( 14 ) chem_species(lsp)%conc_av
[2657]	1362
[2894]	1363	ENDDO
[2657]	1364
[2894]	1365
	1366	END SUBROUTINE chem_wrd_local
	1367
[2657]	1368	!------------------------------------------------------------------------------!
	1369	!
	1370	! Description:
	1371	! ------------
	1372	!> Subroutine to read restart data of chemical species
	1373	!------------------------------------------------------------------------------!
	1374
[2894]	1375	SUBROUTINE chem_rrd_local( i, k, nxlf, nxlc, nxl_on_file, nxrf, nxrc, &
	1376	nxr_on_file, nynf, nync, nyn_on_file, nysf, nysc, &
	1377	nys_on_file, tmp_3d, found )
[2657]	1378
	1379	USE control_parameters
	1380
	1381	USE indices
	1382
	1383	USE pegrid
	1384
	1385	IMPLICIT NONE
	1386
	1387	CHARACTER (LEN=20) :: spc_name_av !<
	1388
	1389	INTEGER(iwp) :: i, lsp !<
	1390	INTEGER(iwp) :: k !<
	1391	INTEGER(iwp) :: nxlc !<
	1392	INTEGER(iwp) :: nxlf !<
	1393	INTEGER(iwp) :: nxl_on_file !<
	1394	INTEGER(iwp) :: nxrc !<
	1395	INTEGER(iwp) :: nxrf !<
	1396	INTEGER(iwp) :: nxr_on_file !<
	1397	INTEGER(iwp) :: nync !<
	1398	INTEGER(iwp) :: nynf !<
	1399	INTEGER(iwp) :: nyn_on_file !<
	1400	INTEGER(iwp) :: nysc !<
	1401	INTEGER(iwp) :: nysf !<
	1402	INTEGER(iwp) :: nys_on_file !<
[2815]	1403
[2894]	1404	LOGICAL, INTENT(OUT) :: found
[2657]	1405
[2894]	1406	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
[2657]	1407
[2815]	1408
[2894]	1409	found = .FALSE.
[2657]	1410
[2815]	1411
[2894]	1412	IF ( ALLOCATED(chem_species) ) THEN
[2657]	1413
[2894]	1414	DO lsp = 1, nspec
[2815]	1415
[2894]	1416	!< for time-averaged chemical conc.
	1417	spc_name_av = TRIM(chem_species(lsp)%name)//'_av'
[2657]	1418
[2894]	1419	IF (restart_string(1:length) == TRIM(chem_species(lsp)%name) ) &
	1420	THEN
	1421	!< read data into tmp_3d
	1422	IF ( k == 1 ) READ ( 13 ) tmp_3d
	1423	!< fill ..%conc in the restart run
	1424	chem_species(lsp)%conc(:,nysc-nbgp:nync+nbgp, &
	1425	nxlc-nbgp:nxrc+nbgp) = &
	1426	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
	1427	found = .TRUE.
	1428	ELSEIF (restart_string(1:length) == spc_name_av ) THEN
	1429	IF ( k == 1 ) READ ( 13 ) tmp_3d
	1430	chem_species(lsp)%conc_av(:,nysc-nbgp:nync+nbgp, &
	1431	nxlc-nbgp:nxrc+nbgp) = &
	1432	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
	1433	found = .TRUE.
[2815]	1434	ENDIF
[2894]	1435
[2657]	1436	ENDDO
	1437
[2894]	1438	ENDIF
[2657]	1439
	1440
[2894]	1441	END SUBROUTINE chem_rrd_local
[2657]	1442
	1443
	1444	!------------------------------------------------------------------------------!
	1445	!
	1446	! Description:
	1447	! ------------
[2815]	1448	!> Subroutine calculating prognostic equations for chemical species
	1449	!> (cache-optimized).
	1450	!> Routine is called separately for each chemical species over a loop from
	1451	!> prognostic_equations.
[2657]	1452	!------------------------------------------------------------------------------!
[2815]	1453	SUBROUTINE chem_prognostic_equations_ij ( cs_scalar_p, cs_scalar, tcs_scalar_m, pr_init_cs, &
[2768]	1454	i, j, i_omp_start, tn, ilsp, flux_s_cs, diss_s_cs, &
	1455	flux_l_cs, diss_l_cs )
[2657]	1456	USE pegrid
	1457	USE advec_ws, ONLY: advec_s_ws
	1458	USE advec_s_pw_mod, ONLY: advec_s_pw
	1459	USE advec_s_up_mod, ONLY: advec_s_up
	1460	USE diffusion_s_mod, ONLY: diffusion_s
	1461	USE indices, ONLY: wall_flags_0
[2768]	1462	USE surface_mod, ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
	1463	surf_usm_v
[2657]	1464
[2815]	1465
[2657]	1466	IMPLICIT NONE
	1467
[2768]	1468	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p, cs_scalar, tcs_scalar_m
[2657]	1469
	1470	INTEGER(iwp),INTENT(IN) :: i, j, i_omp_start, tn, ilsp
	1471	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: flux_s_cs !<
	1472	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: diss_s_cs !<
	1473	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: flux_l_cs !<
	1474	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: diss_l_cs !<
	1475	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
	1476
	1477	!-- local variables
	1478
	1479	INTEGER :: k
	1480	!
	1481	!-- Tendency-terms for chem spcs.
	1482	tend(:,j,i) = 0.0_wp
	1483	!
	1484	!-- Advection terms
	1485	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	1486	IF ( ws_scheme_sca ) THEN
	1487	CALL advec_s_ws( i, j, cs_scalar, 'kc', flux_s_cs, diss_s_cs, &
	1488	flux_l_cs, diss_l_cs, i_omp_start, tn )
	1489	ELSE
	1490	CALL advec_s_pw( i, j, cs_scalar )
	1491	ENDIF
	1492	ELSE
	1493	CALL advec_s_up( i, j, cs_scalar )
	1494	ENDIF
	1495
	1496	!
	1497
[2815]	1498	!-- Diffusion terms (the last three arguments are zero)
[2657]	1499
	1500	CALL diffusion_s( i, j, cs_scalar, &
	1501	surf_def_h(0)%cssws(ilsp,:), surf_def_h(1)%cssws(ilsp,:), &
	1502	surf_def_h(2)%cssws(ilsp,:), &
	1503	surf_lsm_h%cssws(ilsp,:), surf_usm_h%cssws(ilsp,:), &
	1504	surf_def_v(0)%cssws(ilsp,:), surf_def_v(1)%cssws(ilsp,:), &
	1505	surf_def_v(2)%cssws(ilsp,:), surf_def_v(3)%cssws(ilsp,:), &
	1506	surf_lsm_v(0)%cssws(ilsp,:), surf_lsm_v(1)%cssws(ilsp,:), &
	1507	surf_lsm_v(2)%cssws(ilsp,:), surf_lsm_v(3)%cssws(ilsp,:), &
	1508	surf_usm_v(0)%cssws(ilsp,:), surf_usm_v(1)%cssws(ilsp,:), &
	1509	surf_usm_v(2)%cssws(ilsp,:), surf_usm_v(3)%cssws(ilsp,:) )
	1510
	1511	!
	1512	!-- Prognostic equation for chem spcs
	1513	DO k = nzb+1, nzt
	1514	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) + ( dt_3d * &
	1515	( tsc(2) * tend(k,j,i) + &
	1516	tsc(3) * tcs_scalar_m(k,j,i) ) &
	1517	- tsc(5) * rdf_sc(k) &
	1518	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
	1519	) &
	1520	* MERGE( 1.0_wp, 0.0_wp, &
	1521	BTEST( wall_flags_0(k,j,i), 0 ) &
	1522	)
	1523
	1524	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
	1525	ENDDO
	1526
	1527	!
	1528	!-- Calculate tendencies for the next Runge-Kutta step
	1529	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	1530	IF ( intermediate_timestep_count == 1 ) THEN
	1531	DO k = nzb+1, nzt
	1532	tcs_scalar_m(k,j,i) = tend(k,j,i)
	1533	ENDDO
	1534	ELSEIF ( intermediate_timestep_count < &
	1535	intermediate_timestep_count_max ) THEN
	1536	DO k = nzb+1, nzt
	1537	tcs_scalar_m(k,j,i) = -9.5625_wp * tend(k,j,i) + &
	1538	5.3125_wp * tcs_scalar_m(k,j,i)
	1539	ENDDO
	1540	ENDIF
	1541	ENDIF
[2815]	1542
	1543	END SUBROUTINE chem_prognostic_equations_ij
	1544
	1545
	1546	!------------------------------------------------------------------------------!
[2657]	1547	!
[2815]	1548	! Description:
	1549	! ------------
	1550	!> Subroutine calculating prognostic equations for chemical species
	1551	!> (vector-optimized).
	1552	!> Routine is called separately for each chemical species over a loop from
	1553	!> prognostic_equations.
	1554	!------------------------------------------------------------------------------!
	1555	SUBROUTINE chem_prognostic_equations ( cs_scalar_p, cs_scalar, tcs_scalar_m, &
	1556	pr_init_cs, ilsp )
[2657]	1557
[2815]	1558	USE advec_s_pw_mod, &
	1559	ONLY: advec_s_pw
	1560
	1561	USE advec_s_up_mod, &
	1562	ONLY: advec_s_up
	1563
	1564	USE advec_ws, &
	1565	ONLY: advec_s_ws
	1566
	1567	USE diffusion_s_mod, &
	1568	ONLY: diffusion_s
	1569
	1570	USE indices, &
	1571	ONLY: nxl, nxr, nyn, nys, wall_flags_0
	1572
	1573	USE pegrid
	1574
	1575	USE surface_mod, &
	1576	ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
	1577	surf_usm_v
	1578
	1579	IMPLICIT NONE
	1580
	1581	INTEGER :: i !< running index
	1582	INTEGER :: j !< running index
	1583	INTEGER :: k !< running index
	1584
	1585	INTEGER(iwp),INTENT(IN) :: ilsp !<
	1586
	1587	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
	1588
	1589	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar !<
	1590	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p !<
	1591	REAL(wp), DIMENSION(:,:,:), POINTER :: tcs_scalar_m !<
	1592
	1593
	1594	!
	1595	!-- Tendency terms for chemical species
	1596	tend = 0.0_wp
	1597	!
	1598	!-- Advection terms
	1599	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	1600	IF ( ws_scheme_sca ) THEN
	1601	CALL advec_s_ws( cs_scalar, 'kc' )
	1602	ELSE
	1603	CALL advec_s_pw( cs_scalar )
	1604	ENDIF
	1605	ELSE
	1606	CALL advec_s_up( cs_scalar )
	1607	ENDIF
	1608	!
	1609	!-- Diffusion terms (the last three arguments are zero)
	1610	CALL diffusion_s( cs_scalar, &
	1611	surf_def_h(0)%cssws(ilsp,:), &
	1612	surf_def_h(1)%cssws(ilsp,:), &
	1613	surf_def_h(2)%cssws(ilsp,:), &
	1614	surf_lsm_h%cssws(ilsp,:), &
	1615	surf_usm_h%cssws(ilsp,:), &
	1616	surf_def_v(0)%cssws(ilsp,:), &
	1617	surf_def_v(1)%cssws(ilsp,:), &
	1618	surf_def_v(2)%cssws(ilsp,:), &
	1619	surf_def_v(3)%cssws(ilsp,:), &
	1620	surf_lsm_v(0)%cssws(ilsp,:), &
	1621	surf_lsm_v(1)%cssws(ilsp,:), &
	1622	surf_lsm_v(2)%cssws(ilsp,:), &
	1623	surf_lsm_v(3)%cssws(ilsp,:), &
	1624	surf_usm_v(0)%cssws(ilsp,:), &
	1625	surf_usm_v(1)%cssws(ilsp,:), &
	1626	surf_usm_v(2)%cssws(ilsp,:), &
	1627	surf_usm_v(3)%cssws(ilsp,:) )
	1628	!
	1629	!-- Prognostic equation for chemical species
	1630	DO i = nxl, nxr
	1631	DO j = nys, nyn
	1632	DO k = nzb+1, nzt
	1633	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) &
	1634	+ ( dt_3d * &
	1635	( tsc(2) * tend(k,j,i) &
	1636	+ tsc(3) * tcs_scalar_m(k,j,i) &
	1637	) &
	1638	- tsc(5) * rdf_sc(k) &
	1639	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
	1640	) &
	1641	* MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_0(k,j,i), 0 ) )
	1642
	1643	IF ( cs_scalar_p(k,j,i) < 0.0_wp ) cs_scalar_p(k,j,i) = 0.1_wp * cs_scalar(k,j,i)
	1644	ENDDO
	1645	ENDDO
	1646	ENDDO
	1647	!
	1648	!-- Calculate tendencies for the next Runge-Kutta step
	1649	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	1650	IF ( intermediate_timestep_count == 1 ) THEN
	1651	DO i = nxl, nxr
	1652	DO j = nys, nyn
	1653	DO k = nzb+1, nzt
	1654	tcs_scalar_m(k,j,i) = tend(k,j,i)
	1655	ENDDO
	1656	ENDDO
	1657	ENDDO
	1658	ELSEIF ( intermediate_timestep_count < &
	1659	intermediate_timestep_count_max ) THEN
	1660	DO i = nxl, nxr
	1661	DO j = nys, nyn
	1662	DO k = nzb+1, nzt
	1663	tcs_scalar_m(k,j,i) = - 9.5625_wp * tend(k,j,i) &
	1664	+ 5.3125_wp * tcs_scalar_m(k,j,i)
	1665	ENDDO
	1666	ENDDO
	1667	ENDDO
	1668	ENDIF
	1669	ENDIF
	1670
	1671	END SUBROUTINE chem_prognostic_equations
	1672
	1673
[2657]	1674	!------------------------------------------------------------------------------!
	1675	!
	1676	! Description:
	1677	! ------------
	1678	!> Subroutine defining header output for chemistry model
	1679	!------------------------------------------------------------------------------!
	1680	SUBROUTINE chem_header ( io )
	1681
	1682	IMPLICIT NONE
	1683
	1684	INTEGER(iwp), INTENT(IN) :: io !< Unit of the output file
	1685
	1686	! print*,'the header subroutine is still not operational'
	1687	!!
	1688	!!-- Write chemistry model header
	1689	! WRITE( io, 3 )
	1690	!
	1691	! IF ( radiation_scheme == "constant" ) THEN
	1692	! WRITE( io, 4 ) net_radiation
	1693	! ELSEIF ( radiation_scheme == "clear-sky" ) THEN
	1694	! WRITE( io, 5 )
	1695	! ELSEIF ( radiation_scheme == "rrtmg" ) THEN
	1696	! WRITE( io, 6 )
	1697	! IF ( .NOT. lw_radiation ) WRITE( io, 10 )
	1698	! IF ( .NOT. sw_radiation ) WRITE( io, 11 )
	1699	! ENDIF
	1700	!
	1701	! IF ( albedo_type == 0 ) THEN
	1702	! WRITE( io, 7 ) albedo
	1703	! ELSE
	1704	! WRITE( io, 8 ) TRIM( albedo_type_name(albedo_type) )
	1705	! ENDIF
	1706	! IF ( constant_albedo ) THEN
	1707	! WRITE( io, 9 )
	1708	! ENDIF
	1709	!
	1710	! IF ( radiation .AND. radiation_scheme /= 'constant' ) THEN
	1711	! WRITE ( io, 1 ) lambda
	1712	! WRITE ( io, 2 ) day_init, time_utc_init
	1713	! ENDIF
	1714	!
	1715	! WRITE( io, 12 ) dt_radiation
	1716	!
	1717	! 1 FORMAT (' Geograph. longitude : lambda = ',F4.1,' degr')
	1718	! 2 FORMAT (' Day of the year at model start : day_init = ',I3 &
	1719	! /' UTC time at model start : time_utc_init = ',F7.1' s')
	1720	! 3 FORMAT (//' Radiation model information:'/ &
	1721	! ' ----------------------------'/)
	1722	! 4 FORMAT (' --> Using constant net radiation: net_radiation = ', F6.2, &
	1723	! // 'W/m**2')
	1724	! 5 FORMAT (' --> Simple radiation scheme for clear sky is used (no clouds,', &
	1725	! ' default)')
	1726	! 6 FORMAT (' --> RRTMG scheme is used')
	1727	! 7 FORMAT (/' User-specific surface albedo: albedo =', F6.3)
	1728	! 8 FORMAT (/' Albedo is set for land surface type: ', A)
	1729	! 9 FORMAT (/' --> Albedo is fixed during the run')
	1730	!10 FORMAT (/' --> Longwave radiation is disabled')
	1731	!11 FORMAT (/' --> Shortwave radiation is disabled.')
	1732	!12 FORMAT (' Timestep: dt_radiation = ', F6.2, ' s')
	1733	!
	1734	!
	1735	END SUBROUTINE chem_header
[2668]	1736
	1737	!------------------------------------------------------------------------------
	1738	! Description:
	1739	! ------------
	1740	!> Subroutine reading restart data for chemistry model input parameters
	1741	! (FK: To make restarts work, I had to comment this routine. We actually
	1742	! don't need it, since the namelist parameters are always read in,
	1743	! also in case of a restart run)
	1744	!------------------------------------------------------------------------------
[2894]	1745	! SUBROUTINE chem_rrd_global
	1746	!
	1747	! USE chem_modules
	1748	!
	1749	! USE control_parameters, &
	1750	! ONLY: length, message_string, restart_string
[2668]	1751	!
	1752	!
	1753	! IMPLICIT NONE
	1754	!
	1755	!
	1756	!
[2894]	1757	! DO
[2668]	1758	!
[2894]	1759	! SELECT CASE ( restart_string(1:length) )
[2668]	1760	!
	1761	! CASE ( 'bc_cs_b' )
	1762	! READ ( 13 ) bc_cs_b
[2894]	1763	!
	1764	! CASE DEFAULT
	1765	!
	1766	! EXIT
	1767	!
[2668]	1768	! END SELECT
	1769	!
[2894]	1770	!!
	1771	!!-- Read next string and its length
	1772	! READ ( 13 ) length
	1773	! READ ( 13 ) restart_string(1:length)
[2668]	1774	!
	1775	! ENDDO
	1776	!
[2894]	1777	! END SUBROUTINE chem_rrd_global
[2668]	1778
	1779
	1780	!------------------------------------------------------------------------------!
[2657]	1781	!
[2668]	1782	! Description:
	1783	! ------------
	1784	!> Subroutine writing restart data for chemistry model input parameters
	1785	! (FK: To make restarts work, I had to comment this routine. We actually
	1786	! don't need it, since the namelist parameters are always read in,
	1787	! also in case of a restart run)
[2657]	1788	!------------------------------------------------------------------------------!
[2894]	1789	! SUBROUTINE chem_wrd_global
[2668]	1790	!
	1791	! USE chem_modules
	1792	!
	1793	! USE kinds
	1794	!
	1795	!
	1796	! IMPLICIT NONE
	1797	!
	1798	! INTEGER(iwp) :: lsp !< running index for chem spcs
	1799	!
	1800	! !
[2932]	1801	! !-- Writing out input parameters that are not part of chemistry_parameters
	1802	! !-- namelist (namelist parameters are anyway read in again in case of restart)
[2668]	1803	! DO lsp = 1, nvar
[2894]	1804	! CALL wrd_write_string( 'conc_pr_init_'//chem_species(lsp)%name )
[2668]	1805	! WRITE ( 14 ) chem_species(lsp)%conc_pr_init
	1806	! ENDDO
	1807	!
	1808	!
[2894]	1809	! END SUBROUTINE chem_wrd_global
[2668]	1810
	1811
	1812	!------------------------------------------------------------------------------!
[2657]	1813	!
	1814	! Description:
	1815	! ------------
[2668]	1816	!> Subroutine for emission
[2657]	1817	!------------------------------------------------------------------------------!
[2668]	1818	SUBROUTINE chem_emissions
[2657]	1819
[2668]	1820	USE chem_modules
	1821
	1822	USE netcdf_data_input_mod, &
	1823	ONLY: street_type_f
	1824
	1825	USE surface_mod, &
	1826	ONLY: surf_lsm_h
[2657]	1827
	1828
[2668]	1829	IMPLICIT NONE
[2657]	1830
[2678]	1831	INTEGER(iwp) :: i !< running index for grid in x-direction
	1832	INTEGER(iwp) :: j !< running index for grid in y-direction
	1833	INTEGER(iwp) :: m !< running index for horizontal surfaces
[2668]	1834	INTEGER(iwp) :: lsp !< running index for chem spcs
[2657]	1835
[2668]	1836	!
	1837	!-- Comment??? (todo)
[2678]	1838	IF ( street_type_f%from_file ) THEN
	1839	!
	1840	!-- Streets are lsm surfaces, hence, no usm surface treatment required
	1841	DO m = 1, surf_lsm_h%ns
	1842	i = surf_lsm_h%i(m)
	1843	j = surf_lsm_h%j(m)
	1844
	1845	IF ( street_type_f%var(j,i) >= main_street_id .AND. &
	1846	street_type_f%var(j,i) < max_street_id ) THEN
	1847	DO lsp = 1, nvar
	1848	surf_lsm_h%cssws(lsp,m) = emiss_factor_main * surface_csflux(lsp)
	1849	ENDDO
	1850	ELSEIF ( street_type_f%var(j,i) >= side_street_id .AND. &
	1851	street_type_f%var(j,i) < main_street_id ) THEN
	1852	DO lsp = 1, nvar
	1853	surf_lsm_h%cssws(lsp,m) = emiss_factor_side * surface_csflux(lsp)
	1854	ENDDO
[2682]	1855	ELSE
	1856	surf_lsm_h%cssws(:,m) = 0.0_wp
[2678]	1857	ENDIF
	1858	ENDDO
	1859
	1860	ENDIF
[2657]	1861
[2668]	1862	END SUBROUTINE chem_emissions
[2657]	1863
	1864
	1865	END MODULE chemistry_model_mod
	1866

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