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source: palm/trunk/SOURCE/chemistry_model_mod.f90 @ 2912

Last change on this file since 2912 was 2894, checked in by Giersch, 7 years ago
Reading/Writing? data in case of restart runs revised
Property svn:keywords set to `Id`
File size: 74.0 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	!
[2696]	25	!
[2657]	26	! Former revisions:
	27	! -----------------
[2696]	28	! $Id: chemistry_model_mod.f90 2894 2018-03-15 09:17:58Z knoop $
[2894]	29	! Calculations of the index range of the subdomain on file which overlaps with
	30	! the current subdomain are already done in read_restart_data_mod,
	31	! chem_last_actions was renamed to chem_wrd_local, chem_read_restart_data was
	32	! renamed to chem_rrd_local, chem_write_var_list was renamed to
	33	! chem_wrd_global, chem_read_var_list was renamed to chem_rrd_global,
	34	! chem_skip_var_list has been removed, variable named found has been
	35	! introduced for checking if restart data was found, reading of restart strings
	36	! has been moved completely to read_restart_data_mod, chem_rrd_local is already
	37	! inside the overlap loop programmed in read_restart_data_mod, todo list has
	38	! bees extended, redundant characters in chem_wrd_local have been removed,
	39	! the marker * end chemistry * is not necessary anymore, strings and their
	40	! respective lengths are written out and read now in case of restart runs to
	41	! get rid of prescribed character lengths
	42	!
	43	! 2815 2018-02-19 11:29:57Z suehring
[2815]	44	! Bugfix in restart mechanism,
	45	! rename chem_tendency to chem_prognostic_equations,
	46	! implement vector-optimized version of chem_prognostic_equations,
	47	! some clean up (incl. todo list)
	48	!
	49	! 2773 2018-01-30 14:12:54Z suehring
[2773]	50	! Declare variables required for nesting as public
	51	!
	52	! 2772 2018-01-29 13:10:35Z suehring
[2772]	53	! Bugfix in string handling
	54	!
	55	! 2768 2018-01-24 15:38:29Z kanani
[2768]	56	! Shorten lines to maximum length of 132 characters
	57	!
	58	! 2766 2018-01-22 17:17:47Z kanani
[2766]	59	! Removed preprocessor directive __chem
	60	!
	61	! 2756 2018-01-16 18:11:14Z suehring
[2756]	62	! Fill values in 3D output introduced.
	63	!
	64	! 2718 2018-01-02 08:49:38Z maronga
[2696]	65	! Initial revision
	66	!
[2657]	67	!
[2696]	68	!
	69	!
	70	! Authors:
	71	! --------
	72	! @author Renate Forkel
	73	! @author Farah Kanani-Suehring
	74	! @author Klaus Ketelsen
	75	! @author Basit Khan
	76	!
	77	!
[2657]	78	!------------------------------------------------------------------------------!
	79	! Description:
	80	! ------------
	81	!> Chemistry model for PALM-4U
[2894]	82	!> @todo Adjust chem_rrd_local to CASE structure of others modules. It is not
	83	!> allowed to use the chemistry model in a precursor run and additionally
	84	!> not using it in a main run
[2668]	85	!> @todo Update/clean-up todo list! (FK)
	86	!> @todo Set proper fill values (/= 0) for chem output arrays! (FK)
	87	!> @todo Add routine chem_check_parameters, add checks for inconsistent or
[2815]	88	!> unallowed parameter settings.
	89	!> CALL of chem_check_parameters from check_parameters. (FK)
[2668]	90	!> @todo Make routine chem_header available, CALL from header.f90
	91	!> (see e.g. how it is done in routine lsm_header in
	92	!> land_surface_model_mod.f90). chem_header should include all setup
	93	!> info about chemistry parameter settings. (FK)
[2657]	94	!> @todo Implement turbulent inflow of chem spcs in inflow_turbulence.
	95	!> @todo Separate boundary conditions for each chem spcs to be implemented
	96	!> @todo Currently only total concentration are calculated. Resolved, parameterized
	97	!> and chemistry fluxes although partially and some completely coded but
	98	!> are not operational/activated in this version. bK.
	99	!> @todo slight differences in passive scalar and chem spcs when chem reactions
	100	!> turned off. Need to be fixed. bK
[2815]	101	!> @todo test nesting for chem spcs, was implemented by suehring (kanani)
[2657]	102	!> @todo subroutine set_const_initial_values to be taken out from chemistry_model_mod !bK.
	103	!> @todo chemistry error messages
	104	!> @todo Format this module according to PALM coding standard (see e.g. module
	105	!> template under http://palm.muk.uni-hannover.de/mosaik/downloads/8 or
	106	!> D3_coding_standard.pdf under https://palm.muk.uni-hannover.de/trac/downloads/16)
	107	!
	108	!------------------------------------------------------------------------------!
	109
	110	MODULE chemistry_model_mod
[2766]	111
[2657]	112	USE kinds, ONLY: wp, iwp
	113	USE indices, ONLY: nz, nzb,nzt,nysg,nyng,nxlg,nxrg,nys,nyn
	114	USE pegrid, ONLY: myid, threads_per_task
	115	USE control_parameters, ONLY: dt_3d, ws_scheme_sca, initializing_actions, message_string, &
	116	omega, tsc, intermediate_timestep_count, &
	117	intermediate_timestep_count_max, &
	118	timestep_scheme, use_prescribed_profile_data
	119	USE arrays_3d, ONLY: hyp, pt, rdf_sc, tend, zu
	120	USE chem_gasphase_mod, ONLY: nspec, spc_names, nkppctrl, nmaxfixsteps, &
	121	t_steps, fill_temp, chem_gasphase_integrate, &
	122	nvar, atol, rtol, nphot, phot_names
	123	USE cpulog, ONLY: cpu_log, log_point
	124
	125	USE chem_modules
	126
	127
	128	IMPLICIT NONE
	129	PRIVATE
	130	SAVE
	131
	132	!- Define chemical variables
	133
	134	TYPE species_def
	135	CHARACTER(LEN=8) :: name
	136	CHARACTER(LEN=16) :: unit
	137	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc
	138	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_av
	139	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_p
	140	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: tconc_m
	141	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: cssws_av
	142	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: flux_s_cs
	143	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: diss_s_cs
	144	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: flux_l_cs
	145	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: diss_l_cs
	146	REAL(kind=wp),ALLOCATABLE,DIMENSION(:) :: conc_pr_init
	147	END TYPE species_def
	148
	149
	150	TYPE photols_def
	151	CHARACTER(LEN=8) :: name
	152	CHARACTER(LEN=16) :: unit
	153	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: freq
	154	END TYPE photols_def
	155
	156
	157	PUBLIC species_def
	158	PUBLIC photols_def
	159
	160
	161	TYPE(species_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: chem_species
	162	TYPE(photols_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: phot_frequen
	163
	164	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_1
	165	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_2
	166	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_3
	167	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_av
	168	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: freq_1
	169
	170	INTEGER,DIMENSION(nkppctrl) :: icntrl ! Fine tuning kpp
	171	REAL(kind=wp),DIMENSION(nkppctrl) :: rcntrl ! Fine tuning kpp
	172
	173	CHARACTER(10), PUBLIC :: photolysis_scheme
	174	! 'constant',
	175	! 'simple' (Simple parameterisation from MCM, Saunders et al., 2003, Atmos. Chem. Phys., 3, 161-180
	176	! 'fastj' (Wild et al., 2000, J. Atmos. Chem., 37, 245-282) STILL NOT IMPLEMENTED
	177
	178	PUBLIC nspec
	179	PUBLIC nvar
[2773]	180	PUBLIC spc_names
	181	PUBLIC spec_conc_2
[2657]	182
	183	!- Interface section
	184	INTERFACE chem_boundary_conds
	185	MODULE PROCEDURE chem_boundary_conds
	186	END INTERFACE chem_boundary_conds
	187
	188	INTERFACE chem_init
	189	MODULE PROCEDURE chem_init
	190	END INTERFACE chem_init
	191
	192	INTERFACE chem_init_profiles
	193	MODULE PROCEDURE chem_init_profiles
[2682]	194	END INTERFACE chem_init_profiles
[2657]	195
	196	INTERFACE chem_parin
	197	MODULE PROCEDURE chem_parin
	198	END INTERFACE chem_parin
	199
	200	INTERFACE chem_integrate
	201	MODULE PROCEDURE chem_integrate_ij
	202	END INTERFACE chem_integrate
	203
	204	INTERFACE chem_swap_timelevel
	205	MODULE PROCEDURE chem_swap_timelevel
	206	END INTERFACE chem_swap_timelevel
	207
	208	INTERFACE chem_define_netcdf_grid
	209	MODULE PROCEDURE chem_define_netcdf_grid
	210	END INTERFACE chem_define_netcdf_grid
	211
	212	INTERFACE chem_data_output_3d
	213	MODULE PROCEDURE chem_data_output_3d
	214	END INTERFACE chem_data_output_3d
	215
	216	INTERFACE chem_check_data_output
	217	MODULE PROCEDURE chem_check_data_output
	218	END INTERFACE chem_check_data_output
	219
	220	INTERFACE chem_check_data_output_pr
	221	MODULE PROCEDURE chem_check_data_output_pr
	222	END INTERFACE chem_check_data_output_pr
	223
	224	INTERFACE chem_3d_data_averaging
	225	MODULE PROCEDURE chem_3d_data_averaging
	226	END INTERFACE chem_3d_data_averaging
	227
[2894]	228	INTERFACE chem_wrd_local
	229	MODULE PROCEDURE chem_wrd_local
	230	END INTERFACE chem_wrd_local
[2657]	231
[2894]	232	INTERFACE chem_rrd_local
	233	MODULE PROCEDURE chem_rrd_local
	234	END INTERFACE chem_rrd_local
[2657]	235
[2815]	236	INTERFACE chem_prognostic_equations
	237	MODULE PROCEDURE chem_prognostic_equations
	238	MODULE PROCEDURE chem_prognostic_equations_ij
	239	END INTERFACE chem_prognostic_equations
[2657]	240
	241	INTERFACE chem_header
	242	MODULE PROCEDURE chem_header
	243	END INTERFACE chem_header
	244
[2668]	245	INTERFACE chem_emissions
	246	MODULE PROCEDURE chem_emissions
	247	END INTERFACE chem_emissions
[2657]	248
[2894]	249	! INTERFACE chem_wrd_global
	250	! MODULE PROCEDURE chem_wrd_global
	251	! END INTERFACE chem_wrd_global
[2668]	252	!
[2894]	253	! INTERFACE chem_rrd_global
	254	! MODULE PROCEDURE chem_rrd_global
	255	! END INTERFACE chem_rrd_global
[2657]	256
	257
[2815]	258	PUBLIC chem_3d_data_averaging, chem_boundary_conds, chem_check_data_output, &
[2657]	259	chem_check_data_output_pr, chem_data_output_3d, &
[2815]	260	chem_define_netcdf_grid, chem_emissions, chem_header, chem_init, &
[2894]	261	chem_init_profiles, chem_integrate, chem_wrd_local, &
[2815]	262	chem_parin, chem_prognostic_equations, &
[2894]	263	chem_rrd_local, chem_swap_timelevel
[2815]	264
[2657]	265
	266	CONTAINS
	267
	268	!------------------------------------------------------------------------------!
	269	!
	270	! Description:
	271	! ------------
	272	!> Subroutine to initialize and set all boundary conditions for chemical species
	273	!------------------------------------------------------------------------------!
	274
	275	SUBROUTINE chem_boundary_conds( mode )
	276
	277	USE control_parameters, &
	278	ONLY: air_chemistry, outflow_l, outflow_n, outflow_r, outflow_s
	279	USE indices, &
	280	ONLY: nxl, nxr, nxlg, nxrg, nyng, nysg, nzt
	281
	282	! USE prognostic_equations_mod, &
	283
	284	USE arrays_3d, &
	285	ONLY: dzu
	286	USE surface_mod, &
	287	ONLY: bc_h
	288
	289	CHARACTER (len=*), INTENT(IN) :: mode
	290	INTEGER(iwp) :: i !< grid index x direction.
	291	INTEGER(iwp) :: j !< grid index y direction.
	292	INTEGER(iwp) :: k !< grid index z direction.
	293	INTEGER(iwp) :: kb !< variable to set respective boundary value, depends on facing.
	294	INTEGER(iwp) :: l !< running index boundary type, for up- and downward-facing walls.
	295	INTEGER(iwp) :: m !< running index surface elements.
	296	INTEGER(iwp) :: lsp !< running index for chem spcs.
	297	INTEGER(iwp) :: lph !< running index for photolysis frequencies
	298
	299
	300	SELECT CASE ( TRIM( mode ) )
	301	CASE ( 'init' )
	302	DO lsp = 1, nspec
	303	IF ( surface_csflux(lsp) == 9999999.9_wp ) THEN
	304	constant_csflux(lsp) = .FALSE.
	305	ENDIF
	306	ENDDO
	307
	308	IF ( bc_cs_b == 'dirichlet' ) THEN
	309	ibc_cs_b = 0
	310	ELSEIF ( bc_cs_b == 'neumann' ) THEN
	311	ibc_cs_b = 1
	312	ELSE
	313	! message_string = 'unknown boundary condition: bc_cs_b ="' // TRIM( bc_cs_b ) // '"' ! bK commented
[2815]	314	CALL message( 'chem_boundary_conds', 'CM0010', 1, 2, 0, 6, 0 ) !< chemistry_model_mod should have special error numbers --> "CHEM###",
[2657]	315	ENDIF
	316	!
	317	!-- Set Integer flags and check for possible erroneous settings for top
	318	!-- boundary condition. bK added _cs_ here.
	319	IF ( bc_cs_t == 'dirichlet' ) THEN
	320	ibc_cs_t = 0
	321	ELSEIF ( bc_cs_t == 'neumann' ) THEN
	322	ibc_cs_t = 1
	323	ELSEIF ( bc_cs_t == 'initial_gradient' ) THEN
	324	ibc_cs_t = 2
	325	ELSEIF ( bc_cs_t == 'nested' ) THEN
	326	ibc_cs_t = 3
	327	ELSE
	328	! message_string = 'unknown boundary condition: bc_c_t ="' // TRIM( bc_cs_t ) // '"'
[2815]	329	CALL message( 'check_parameters', 'CM0011', 1, 2, 0, 6, 0 )
[2657]	330	ENDIF
	331
	332
	333	CASE ( 'set_bc_bottomtop' )
	334	!-- Bottom boundary condtions for chemical species
	335	DO lsp = 1, nspec
	336	IF ( ibc_cs_b == 0 ) THEN
	337	DO l = 0, 1
	338	!-- Set index kb: For upward-facing surfaces (l=0), kb=-1, i.e.
	339	!-- the chem_species(nsp)%conc_p value at the topography top (k-1)
	340	!-- is set; for downward-facing surfaces (l=1), kb=1, i.e. the
	341	!-- value at the topography bottom (k+1) is set.
	342
	343	kb = MERGE( -1, 1, l == 0 )
	344	!$OMP PARALLEL DO PRIVATE( i, j, k )
	345	DO m = 1, bc_h(l)%ns
	346	i = bc_h(l)%i(m)
	347	j = bc_h(l)%j(m)
	348	k = bc_h(l)%k(m)
	349	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc(k+kb,j,i)
	350	ENDDO
	351	ENDDO
	352
	353	ELSEIF ( ibc_cs_b == 1 ) THEN
	354	! in boundary_conds there is som extra loop over m here for passive tracer
	355	DO l = 0, 1
	356	kb = MERGE( -1, 1, l == 0 )
	357	!$OMP PARALLEL DO PRIVATE( i, j, k )
	358	DO m = 1, bc_h(l)%ns
	359	i = bc_h(l)%i(m)
	360	j = bc_h(l)%j(m)
	361	k = bc_h(l)%k(m)
	362	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc_p(k,j,i)
	363
	364	!< @todo: chem_species(nsp)%conc_p(k+kb,j,i) = chem_species(nsp)%conc(k+kb,j,i), &
	365	!< pls loop over nsp=1, NSPEC.
	366	!< @todo: We should also think about the possibility to have &
	367	!< individual boundary conditions for each species? This means, bc_cs_b, &
	368	!< bc_cs_t, ibc_cs_b, ibc_cs_t would need to be added to TYPE chem_species(nsp)%, &
	369	!< and the loop over nsp would have to be put outside of this IF-clause.
	370	!< i think its better we keep the same bonundary cond i.e. dirichlet or neumann
	371	!< for all chem spcs. ... !bK
	372
	373	ENDDO
	374	ENDDO
	375	ENDIF
	376	ENDDO ! end lsp loop
	377
	378	!-- Top boundary conditions for chemical species - Should this not be done for all species?
	379	IF ( ibc_cs_t == 0 ) THEN
	380	DO lsp = 1, nspec
	381	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc(nzt+1,:,:)
	382	ENDDO
	383	ELSEIF ( ibc_cs_t == 1 ) THEN
	384	DO lsp = 1, nspec
[2678]	385	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:)
[2657]	386	ENDDO
	387	ELSEIF ( ibc_cs_t == 2 ) THEN
	388	DO lsp = 1, nspec
[2678]	389	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:) + bc_cs_t_val(lsp) * dzu(nzt+1)
[2657]	390	ENDDO
	391	!@todo: bc_cs_t_val needs to be calculated,
	392	!see bc_pt_t_val = ( pt_init(nzt+1) - pt_init(nzt) ) / dzu(nzt+1)
	393	!(in time_integration). pt_init would be the counterpart to
	394	!chem_species(i)%conc_pr_init (see kchem_driver_FKa1408.f90 of my
	395	!"Hints: prescribing initial concentration.
	396	ENDIF
	397	!
	398	CASE ( 'set_bc_lateral' ) ! bK commented it
	399	!-- Lateral boundary conditions for chem species at inflow boundary
	400	!-- are automatically set when chem_species concentration is
	401	!-- initialized. The initially set value at the inflow boundary is not
	402	!-- touched during time integration, hence, this boundary value remains
	403	!-- at a constant value, which is the concentration that flows into the
	404	!-- domain.
	405	!-- Lateral boundary conditions for chem species at outflow boundary
	406
	407	IF ( outflow_s ) THEN
	408	DO lsp = 1, nspec
	409	chem_species(lsp)%conc_p(:,nys-1,:) = chem_species(lsp)%conc_p(:,nys,:)
	410	ENDDO
	411	ELSEIF ( outflow_n ) THEN
	412	DO lsp = 1, nspec
	413	chem_species(lsp)%conc_p(:,nyn+1,:) = chem_species(lsp)%conc_p(:,nyn,:)
	414	ENDDO
	415	ELSEIF ( outflow_l ) THEN
	416	DO lsp = 1, nspec
	417	chem_species(lsp)%conc_p(:,:,nxl-1) = chem_species(lsp)%conc_p(:,:,nxl)
	418	ENDDO
	419	ELSEIF ( outflow_r ) THEN
	420	DO lsp = 1, nspec
	421	chem_species(lsp)%conc_p(:,:,nxr+1) = chem_species(lsp)%conc_p(:,:,nxr)
	422	ENDDO
	423	ENDIF
	424
	425	END SELECT
	426
	427	END SUBROUTINE chem_boundary_conds
	428	!
	429	!------------------------------------------------------------------------------!
	430	!
	431	! Description:
	432	! ------------
	433	!> Subroutine defining initial vertical profiles of chemical species (given by
	434	!> namelist parameters chem_profiles and chem_heights) --> which should work
	435	!> analogue to parameters u_profile, v_profile and uv_heights)
	436	!------------------------------------------------------------------------------!
	437	SUBROUTINE chem_init_profiles !< SUBROUTINE is called from chem_init in case of
	438	!< TRIM( initializing_actions ) /= 'read_restart_data'
	439	!< We still need to see what has to be done in case of restart run
	440	USE chem_modules
	441
	442	IMPLICIT NONE
	443
	444	!-- Local variables
	445	INTEGER :: lsp !< running index for number of species in derived data type species_def
	446	INTEGER :: lsp_pr !< running index for number of species in cs_names, cs_profiles etc
	447	INTEGER :: lpr_lev !< running index for profile level for each chem spcs.
	448	INTEGER :: npr_lev !< the next available profile lev
	449
	450	!-----------------
	451	!-- To prescribe/initialize a vertically constant 'cs_profile', another parameter
	452	!-- "cs_surface" is introduced. If "cs_profile" and "cs_heights" are prescribed,
	453	!-- their values will override the constant profile given by "cs_surface".
	454
[2668]	455	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
[2657]	456	lsp_pr = 1
	457	DO WHILE ( TRIM( cs_name( lsp_pr ) ) /= 'novalue' ) !'novalue' is the default
	458	DO lsp = 1, nspec !
	459	!-- Create initial profile (conc_pr_init) for each chemical species
	460	IF ( TRIM( chem_species(lsp)%name ) == TRIM( cs_name(lsp_pr) ) ) THEN !
[2682]	461	! IF ( cs_profile(1,1) == 9999999.9_wp ) THEN
[2657]	462	!-- Set a vertically constant profile based on the surface conc (cs_surface(lsp_pr)) of each species
	463	DO lpr_lev = 0, nzt+1
	464	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_surface(lsp_pr)
	465	ENDDO
	466
[2682]	467	! ELSE
	468	! IF ( cs_heights(lsp,1) /= 0.0_wp ) THEN
	469	! message_string = 'cs_heights(1,1) must be 0.0'
[2815]	470	! CALL message( 'chem_check_parameters', 'CM0012', 1, 2, 0, 6, 0 )
[2682]	471	! ENDIF
	472	!
	473	! IF ( omega /= 0.0_wp ) THEN
	474	! message_string = 'Coriolis force must be switched off (by setting omega=0.0)' // &
	475	! ' when prescribing the forcing by u_profile and v_profile'
	476	! CALL message( 'check_parameters', 'PA0347', 1, 2, 0, 6, 0 )
	477	! ENDIF
	478	!
	479	! use_prescribed_profile_data = .TRUE.
	480	!
	481	! npr_lev = 1
	482	! ! chem_sddpecies(lsp)%conc_pr_init(0) = 0.0_wp
	483	! DO lpr_lev = 1, nz+1
	484	! IF ( npr_lev < 100 ) THEN
	485	! DO WHILE ( cs_heights(lsp, npr_lev+1) <= zu(lpr_lev) )
	486	! npr_lev = npr_lev + 1
	487	! IF ( npr_lev == 100 ) EXIT
	488	! ENDDO
	489	! ENDIF
	490	!
	491	! IF ( npr_lev < 100 .AND. cs_heights(lsp, npr_lev + 1) /= 9999999.9_wp ) THEN
	492	! chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp, npr_lev) + &
	493	! ( zu(lpr_lev) - cs_heights(lsp, npr_lev) ) / &
	494	! ( cs_heights(lsp, npr_lev + 1) - cs_heights(lsp, npr_lev ) ) * &
	495	! ( cs_profile(lsp, npr_lev + 1) - cs_profile(lsp, npr_lev ) )
	496	! ELSE
	497	! chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp, npr_lev)
	498	! ENDIF
	499	! ENDDO
	500	! ENDIF
[2657]	501	!-- If a profile is prescribed explicity using cs_profiles and cs_heights, we then have to fill the
	502	!-- chem_species(lsp)%conc_pr_init for the specific "lsp" based on the cs_profiles(lsp_pr,:)
	503	!-- and cs_heights(lsp_pr,:).
	504	ENDIF
	505	ENDDO
	506	lsp_pr = lsp_pr + 1
	507	ENDDO
[2668]	508	! ELSE
[2657]	509	! IF (chem_debug1 ) print*,'code to be added for initializing_actions == read_restart_data' !bK
[2668]	510	! ENDIF
[2657]	511
	512	!-- Now, go back to chem_init and use the contents of chem_species(lsp)%conc_pr_init to
	513	!-- initialize the 3D conc arrays, as it is currently taken care of in chem_set_constant_values.
	514	!-- After initializing the 3D arrays, these can be used to set the boundary conditions in the
	515	!-- subroutine kchem_boundary_conds, which should be called from boundary_conds.f90.
	516
	517
	518	END SUBROUTINE chem_init_profiles
	519	!
	520	!------------------------------------------------------------------------------!
	521	!
	522	! Description:
	523	! ------------
	524	!> Subroutine initializating chemistry_model_mod
	525	!------------------------------------------------------------------------------!
	526	SUBROUTINE chem_init
	527
	528
	529	USE control_parameters, &
	530	ONLY: message_string, io_blocks, io_group, turbulent_inflow
	531
	532	USE arrays_3d, &
	533	ONLY: mean_inflow_profiles
	534
	535	USE pegrid
	536
	537	IMPLICIT none
	538	!-- local variables
	539	INTEGER :: i,j !< running index for for horiz numerical grid points
	540	INTEGER :: lsp !< running index for chem spcs
	541	INTEGER :: lpr_lev !< running index for chem spcs profile level
	542	!
	543	!-- NOPOINTER version not implemented yet
[2682]	544	! #if defined( __nopointer )
	545	! message_string = 'The chemistry module only runs with POINTER version'
	546	! CALL message( 'chemistry_model_mod', 'CM0001', 1, 2, 0, 6, 0 )
	547	! #endif
	548	!
	549	!-- Allocate memory for chemical species
	550	ALLOCATE( chem_species(nspec) )
	551	ALLOCATE( spec_conc_1 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	552	ALLOCATE( spec_conc_2 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	553	ALLOCATE( spec_conc_3 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	554	ALLOCATE( spec_conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	555	ALLOCATE( phot_frequen(nphot) )
	556	ALLOCATE( freq_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nphot) )
	557	ALLOCATE( bc_cs_t_val(nspec) )
	558	!
	559	!-- Initialize arrays
	560	spec_conc_1 (:,:,:,:) = 0.0_wp
	561	spec_conc_2 (:,:,:,:) = 0.0_wp
	562	spec_conc_3 (:,:,:,:) = 0.0_wp
	563	spec_conc_av(:,:,:,:) = 0.0_wp
[2657]	564
[2682]	565
[2657]	566	DO lsp = 1, nspec
	567	chem_species(lsp)%name = spc_names(lsp)
	568
	569	chem_species(lsp)%conc (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1 (:,:,:,lsp)
	570	chem_species(lsp)%conc_p (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2 (:,:,:,lsp)
	571	chem_species(lsp)%tconc_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_3 (:,:,:,lsp)
	572	chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_av(:,:,:,lsp)
	573
	574	ALLOCATE (chem_species(lsp)%cssws_av(nysg:nyng,nxlg:nxrg))
[2682]	575	chem_species(lsp)%cssws_av = 0.0_wp
	576	!
	577	!-- (todo (FK): This needs to be revised. This block must go somewhere else)
[2657]	578	! IF ( ws_scheme_sca ) THEN
	579	ALLOCATE (chem_species(lsp)%flux_s_cs(nzb+1:nzt,0:threads_per_task-1))
	580	ALLOCATE (chem_species(lsp)%diss_s_cs(nzb+1:nzt,0:threads_per_task-1))
	581	ALLOCATE (chem_species(lsp)%flux_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
	582	ALLOCATE (chem_species(lsp)%diss_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
	583	chem_species(lsp)%flux_s_cs = 0.0_wp
	584	chem_species(lsp)%flux_l_cs = 0.0_wp
	585	chem_species(lsp)%diss_s_cs = 0.0_wp
	586	chem_species(lsp)%diss_l_cs = 0.0_wp
	587	! ENDIF
[2682]	588	!
	589	!-- Allocate memory for initial concentration profiles
	590	!-- (concentration values come from namelist)
	591	!-- (todo (FK): Because of this, chem_init is called in palm before
	592	!-- check_parameters, since conc_pr_init is used there.
	593	!-- We have to find another solution since chem_init should
	594	!-- eventually be called from init_3d_model!!)
	595	ALLOCATE ( chem_species(lsp)%conc_pr_init(0:nz+1) )
	596	chem_species(lsp)%conc_pr_init(:) = 0.0_wp
[2657]	597
	598	ENDDO
	599
	600	!
	601	!-- Set initial concentration of profiles prescribed by parameters cs_profile
	602	!-- and cs_heights in the namelist &chemistry_par
[2682]	603	!-- (todo (FK): chem_init_profiles not ready yet, has some bugs)
	604	! CALL chem_init_profiles
[2657]	605	!
	606	!-- Initialize model variables
	607
	608
	609	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
	610	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
	611
	612
	613	!-- First model run of a possible job queue.
	614	!-- Initial profiles of the variables must be computes.
	615	IF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
[2668]	616	! CALL location_message( 'initializing with 1D model profiles', .FALSE. )
[2657]	617	!
	618	! CALL init_1d_model ...... decide to call or not later !bK
	619
	620	!-- Transfer initial profiles to the arrays of the 3D model
	621	DO lsp = 1, nspec
	622	DO i = nxlg, nxrg
	623	DO j = nysg, nyng
	624	DO lpr_lev = 1, nz + 1
	625	chem_species(lsp)%conc(lpr_lev,j,i) = chem_species(lsp)%conc_pr_init(lpr_lev)
	626	ENDDO
	627	ENDDO
	628	ENDDO
	629	ENDDO
	630
	631	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
	632	THEN
[2668]	633	! CALL location_message( 'initializing with constant profiles', .FALSE. )
[2657]	634
	635
	636
	637	!-- Set initial horizontal velocities at the lowest computational grid
	638	!-- levels to zero in order to avoid too small time steps caused by the
	639	!-- diffusion limit in the initial phase of a run (at k=1, dz/2 occurs
	640	!-- in the limiting formula!).
	641
	642	DO lsp = 1, nspec
	643	DO i = nxlg, nxrg
	644	DO j = nysg, nyng
	645	chem_species(lsp)%conc(:,j,i) = chem_species(lsp)%conc_pr_init !ITS THERE bK
	646	ENDDO
	647	ENDDO
	648	ENDDO
	649
[2668]	650	! ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) &
	651	! THEN
	652	! CALL location_message( 'initializing by user', .FALSE. )
[2657]	653	!
	654	!-- Initialization will completely be done by the user
[2668]	655	!-- (FK: This should be called only once, in init_3d_model, i.e. remove it here)
	656	! CALL user_init_3d_model
	657	! CALL location_message( 'finished', .TRUE. )
[2657]	658
	659	ENDIF
	660
	661	!-- Store initial chem spcs profile
	662	! DO lsp = 1, nvar
	663	! hom_cs(:,1,115,:) = SPREAD( chem_species(lsp)%conc(:,nys,nxl), 2, statistic_regions+1 )
	664	! ENDDO
	665	!
	666	!-- If required, change the surface chem spcs at the start of the 3D run
	667	IF ( cs_surface_initial_change(1) /= 0.0_wp ) THEN
	668	DO lsp = 1, nspec
	669	chem_species(lsp)%conc(nzb,:,:) = chem_species(lsp)%conc(nzb,:,:) + &
	670	cs_surface_initial_change(lsp)
	671	ENDDO
	672	ENDIF
	673	!
	674	!-- Initiale old and new time levels.
	675	DO lsp = 1, nvar
	676	chem_species(lsp)%tconc_m = 0.0_wp
[2682]	677	chem_species(lsp)%conc_p = chem_species(lsp)%conc
[2657]	678	ENDDO
	679
	680	ENDIF
	681
[2682]	682
	683
[2657]	684	!--- new code add above this line
	685	DO lsp = 1, nphot
	686	phot_frequen(lsp)%name = phot_names(lsp)
	687	! IF( myid == 0 ) THEN
	688	! WRITE(6,'(a,i4,3x,a)') 'Photolysis: ',lsp,trim(phot_names(lsp))
	689	! ENDIF
	690	phot_frequen(lsp)%freq(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => freq_1(:,:,:,lsp)
	691	ENDDO
	692
	693	!-- Set initial values
	694	! Not required any more, this can now be done with the namelist by setting cs_surface
	695	! and cs_name without specifying cs_profile (Nevertheless, we still want to keep it for a while)
	696	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
	697	! CALL set_const_initial_values
	698	! ENDIF
[2682]	699
[2657]	700	RETURN
	701
	702	CONTAINS
	703	!------------------------------------------------------------------------------!
	704	!
	705	! Description:
	706	! ------------
	707	!> Subroutine setting constant initial values of chemical species
	708	!------------------------------------------------------------------------------!
	709	SUBROUTINE set_const_initial_values
	710	! Not required any more, this can now be done with the namelist by setting cs_surface
	711	! and cs_name without specifying cs_profile (Nevertheless, we still want to keep it for a while)
	712	IMPLICIT none
	713
	714	!-- local variables
	715	INTEGER :: lsp
	716
	717	IF(myid == 0) THEN
	718	write(6,'(/,a,/)') ' chemics >>>> Set constant Initial Values: '
	719	ENDIF
	720
	721	! Default values are taken from smog.def from supplied kpp example
	722	DO lsp = 1, nspec
	723	IF(trim(chem_species(lsp)%name) == 'NO') THEN
	724	! chem_species(lsp)%conc = 8.725*1.0E+08
	725	! chem_species(lsp)%conc = 0.05_wp !added by bK
	726	chem_species(lsp)%conc = 0.01_wp !added by RFo
	727	ELSEIF (trim(chem_species(lsp)%name) == 'NO2') THEN
	728	! chem_species(lsp)%conc = 2.240*1.0E+08
	729	! chem_species(lsp)%conc = 0.01_wp !added by bK
	730	chem_species(lsp)%conc = 0.05_wp !added by RFo
	731	ELSEIF( trim( chem_species(lsp)%name ) == 'O3' ) THEN
	732	chem_species(lsp)%conc = 0.05_wp !added by bK
	733	ELSEIF(trim(chem_species(lsp)%name) == 'H2O') THEN
	734	! chem_species(lsp)%conc = 5.326*1.0E+11
	735	chem_species(lsp)%conc = 1.30*1.0E+4_wp !added by bK
	736	ELSEIF(trim(chem_species(lsp)%name) == 'O2') THEN
	737	chem_species(lsp)%conc = 2.0*1.0E+5_wp !added by bK
	738	ELSEIF(trim(chem_species(lsp)%name) == 'RH') THEN
	739	chem_species(lsp)%conc = 0.001_wp !added by RFo
	740	ELSEIF(trim(chem_species(lsp)%name) == 'CO') THEN
	741	chem_species(lsp)%conc = 0.5_wp !added by RFo
	742	ELSEIF(trim(chem_species(lsp)%name) == 'RCHO') THEN
	743	! chem_species(lsp)%conc = 2.0_wp !added by bK
	744	chem_species(lsp)%conc = 0.01_wp !added by RFo
	745	! ELSEIF(trim(chem_species(lsp)%name) == 'OH') THEN
	746	! chem_species(lsp)%conc = 1.0*1.0E-07_wp !added by bK
	747	! ELSEIF(trim(chem_species(lsp)%name) == 'HO2') THEN
	748	! chem_species(lsp)%conc = 1*1.0E-7_wp !added by bK
	749	! ELSEIF(trim(chem_species(lsp)%name) == 'RCOO2') THEN ! corrected RFo
	750	! chem_species(lsp)%conc = 1.0*1.0E-7_wp !added by bK
	751	! ELSEIF(trim(chem_species(lsp)%name) == 'RCOO2NO2') THEN
	752	! chem_species(lsp)%conc = 1.0*1.0E-7_wp !added by bK
	753	ELSE
	754	! H2O = 2.0e+04;
	755	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) = 0.0_wp
	756	ENDIF
	757
	758	IF(myid == 0) THEN
[2772]	759	WRITE(6,'(a,3x,a,3x,a,e12.4)') ' Species: ',chem_species(lsp)%name(1:7), &
	760	'Initial Value = ',chem_species(lsp)%conc(nzb,nysg,nxlg)
[2657]	761	ENDIF
	762	ENDDO
	763
	764	! #if defined( __nopointer )
	765	! !kk Hier mit message abbrechen
	766	! if(myid == 0) then
	767	! write(6,*) ' KPP does only run with POINTER Version'
	768	! end if
	769	! stop 'error'
	770	! #endif
	771
	772	RETURN
	773	END SUBROUTINE set_const_initial_values
	774
	775
	776	END SUBROUTINE chem_init
	777	!
	778	!------------------------------------------------------------------------------!
	779	!
	780	! Description:
	781	! ------------
	782	!> Subroutine defining parin for &chemistry_par for chemistry model
	783	!------------------------------------------------------------------------------!
	784	SUBROUTINE chem_parin
[2682]	785
[2657]	786	USE control_parameters, &
	787	ONLY: air_chemistry
[2682]	788
[2657]	789	USE chem_modules
[2682]	790
	791	USE kinds
[2657]	792
	793	IMPLICIT none
	794
[2682]	795	CHARACTER (LEN=80) :: line !< dummy string that contains the current line of the parameter file
	796
	797	REAL(wp), DIMENSION(nmaxfixsteps) :: my_steps !< List of fixed timesteps my_step(1) = 0.0 automatic stepping
[2657]	798
[2668]	799	NAMELIST /chemistry_par/ bc_cs_b, &
	800	bc_cs_t, &
	801	call_chem_at_all_substeps, &
	802	chem_debug0, &
	803	chem_debug1, &
	804	chem_debug2, &
	805	chem_gasphase_on, &
	806	cs_heights, &
	807	cs_name, &
	808	cs_profile, &
	809	cs_profile_name, &
	810	cs_surface, &
	811	emiss_factor_main, &
	812	emiss_factor_side, &
	813	icntrl, &
	814	main_street_id, &
[2678]	815	max_street_id, &
[2668]	816	my_steps, &
	817	rcntrl, &
	818	side_street_id, &
	819	photolysis_scheme, &
	820	wall_csflux, &
	821	cs_vertical_gradient, &
	822	top_csflux, &
	823	surface_csflux, &
[2678]	824	surface_csflux_name, &
[2668]	825	cs_surface_initial_change, &
	826	cs_vertical_gradient_level
[2657]	827
	828	!-- analogue to chem_names(nspj) we could invent chem_surfaceflux(nspj) and chem_topflux(nspj)
	829	!-- so this way we could prescribe a specific flux value for each species
	830	!> chemistry_par for initial profiles
	831	!> cs_names = 'O3', 'NO2', 'NO', ... to set initial profiles)
	832	!> cs_heights(1,:) = 0.0, 100.0, 500.0, 2000.0, .... (height levels where concs will be prescribed for O3)
	833	!> cs_heights(2,:) = 0.0, 200.0, 400.0, 1000.0, .... (same for NO2 etc.)
	834	!> cs_profiles(1,:) = 10.0, 20.0, 20.0, 30.0, ..... (chem spcs conc at height lvls chem_heights(1,:)) etc.
	835	!> If the respective concentration profile should be constant with height, then use "cs_surface( number of spcs)"
	836	!> then write these cs_surface values to chem_species(lsp)%conc_pr_init(:)
	837
[2668]	838	!
	839	!-- Read chem namelist
	840	!-- (todo: initialize these parameters in declaration part, do this for
	841	!-- all chemistry_par namelist parameters)
[2657]	842	icntrl = 0
	843	rcntrl = 0.0_wp
	844	my_steps = 0.0_wp
	845	icntrl(2) = 1
	846	photolysis_scheme = 'simple'
	847	atol = 1.0_wp
	848	rtol = 0.01_wp
	849	!
	850	!-- Try to find chemistry package
	851	REWIND ( 11 )
	852	line = ' '
	853	DO WHILE ( INDEX( line, '&chemistry_par' ) == 0 )
[2668]	854	READ ( 11, '(A)', END=10 ) line
[2657]	855	ENDDO
	856	BACKSPACE ( 11 )
	857	!
[2668]	858	!-- Read chemistry namelist
[2657]	859	READ ( 11, chemistry_par )
[2668]	860	!
	861	!-- Enable chemistry model
	862	air_chemistry = .TRUE.
[2657]	863
[2668]	864
[2657]	865	10 CONTINUE
	866
[2668]	867	t_steps = my_steps !(todo: Why not directly make t_steps a
	868	! namelist parameter?)
[2657]	869
	870	END SUBROUTINE chem_parin
	871
	872	!
	873	!------------------------------------------------------------------------------!
	874	!
	875	! Description:
	876	! ------------
	877	!> Subroutine to integrate chemical species in the given chemical mechanism
	878	!------------------------------------------------------------------------------!
	879
	880	SUBROUTINE chem_integrate_ij (i, j)
	881
	882	USE cpulog, &
	883	ONLY: cpu_log, log_point
	884	USE statistics, & ! ## RFo
	885	ONLY: weight_pres
	886	USE control_parameters, & ! ## RFo
	887	ONLY: dt_3d, intermediate_timestep_count
	888
	889	IMPLICIT none
	890	INTEGER,INTENT(IN) :: i,j
	891
	892	!-- local variables
	893	INTEGER(iwp) :: lsp !< running index for chem spcs.
	894	INTEGER(iwp) :: lph !< running index for photolysis frequencies
	895	INTEGER :: k,m,istatf
	896	INTEGER,dimension(20) :: istatus
	897	REAL(kind=wp),dimension(nzb+1:nzt,nspec) :: tmp_conc
	898	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_temp
	899	REAL(kind=wp),dimension(nzb+1:nzt,nphot) :: tmp_phot
	900	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_fact
	901	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_fact_i !< conversion factor between molecules cm^{-3} and ppm
	902	REAL(wp) :: conv !< conversion factor
	903	REAL(wp), PARAMETER :: ppm2fr = 1.0e-6_wp !< Conversion factor ppm to fraction
	904	REAL(wp), PARAMETER :: pref_i = 1._wp / 100000.0_wp !< inverse reference pressure (1/Pa)
	905	REAL(wp), PARAMETER :: t_std = 273.15_wp !< standard pressure (Pa)
	906	REAL(wp), PARAMETER :: p_std = 101325.0_wp !< standard pressure (Pa)
	907	REAL(wp), PARAMETER :: r_cp = 0.286_wp !< R / cp (exponent for potential temperature)
	908	REAL(wp), PARAMETER :: vmolcm = 22.414e3_wp !< Mole volume (22.414 l) in cm^{-3}
	909	REAL(wp), PARAMETER :: xna = 6.022e23_wp !< Avogadro number (molecules/mol)
	910
	911
	912	REAL(kind=wp) :: dt_chem
	913
	914	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'start' )
	915	!< Set chem_gasphase_on to .FALSE. if you want to skip computation of gas phase chemistry
	916	IF (chem_gasphase_on) THEN
	917
	918	tmp_temp(:) = pt(:,j,i) * ( hyp(nzb+1:nzt) / 100000.0_wp )**0.286_wp
	919	! ppm to molecules/cm**3
	920	! tmp_fact = 1.e-6_wp6.022e23_wp/(22.414_wp1000._wp) * 273.15_wp * hyp(nzb+1:nzt)/( 101300.0_wp * tmp_temp )
	921	conv = ppm2fr * xna / vmolcm
	922	tmp_fact(:) = conv * t_std * hyp(nzb+1:nzt) / (tmp_temp(:) * p_std)
	923	tmp_fact_i = 1.0_wp/tmp_fact
	924
	925	CALL fill_temp (istatf, tmp_temp) !< Load constant temperature into kpp context
	926	! CALL fill_temp (istatf, pt(nzb+1:nzt,j,i)) !< Load temperature into kpp context
	927
	928	DO lsp = 1,nspec
	929	tmp_conc(:,lsp) = chem_species(lsp)%conc(nzb+1:nzt,j,i) * tmp_fact(:)
	930	ENDDO
	931
	932	DO lph = 1,nphot
	933	tmp_phot(:,lph) = phot_frequen(lph)%freq(nzb+1:nzt,j,i)
	934	ENDDO
	935
	936	IF(myid == 0 .AND. chem_debug0 ) THEN
	937	IF (i == 10 .and. j == 10) WRITE(0,*) 'begin chemics step ',dt_3d
	938	ENDIF
	939
	940	!-- Compute length of time step # RFo
	941	IF ( call_chem_at_all_substeps ) THEN
	942	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
	943	ELSE
	944	dt_chem = dt_3d
	945	ENDIF
	946
	947	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'start' )
	948
	949
	950	CALL chem_gasphase_integrate (dt_chem, tmp_conc, tmp_temp, tmp_phot, istatus=istatus)
	951
	952
	953	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'stop' )
	954
	955	DO lsp = 1,nspec
	956	chem_species(lsp)%conc (nzb+1:nzt,j,i) = tmp_conc(:,lsp) * tmp_fact_i(:) ! RFo
	957	ENDDO
	958
	959	! IF (myid == 0 .AND. chem_debug2 ) THEN
	960	! IF (i == 10 .and. j == 10) WRITE(6,'(a,8i7)') ' KPP Status ',istatus(1:8)
	961	! write(6,'(a,8i7)') ' KPP Status ',istatus(1:8)
	962	! ENDIF
	963
	964	ENDIF
	965	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'stop' )
	966
	967	RETURN
	968	END SUBROUTINE chem_integrate_ij
	969	!
	970	!------------------------------------------------------------------------------!
	971	!
	972	! Description:
	973	! ------------
	974	!> Subroutine for swapping of timelevels for chemical species
	975	!> called out from subroutine swap_timelevel
	976	!------------------------------------------------------------------------------!
	977
	978	SUBROUTINE chem_swap_timelevel (level)
	979	IMPLICIT none
	980
	981	INTEGER,INTENT(IN) :: level
	982
	983	!-- local variables
	984
	985	INTEGER :: lsp
	986
	987	! print,' entering chem_swap_timelevel *) '
	988	if(level == 0) then
	989	do lsp=1, nvar
	990	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
	991	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
	992	end do
	993	else
	994	do lsp=1, nvar
	995	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
	996	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
	997	end do
	998	end if
	999
	1000	RETURN
	1001	END SUBROUTINE chem_swap_timelevel
	1002
	1003	!------------------------------------------------------------------------------!
	1004	!
	1005	! Description:
	1006	! ------------
	1007	!> Subroutine defining appropriate grid for netcdf variables.
	1008	!> It is called out from subroutine netcdf.
	1009	!------------------------------------------------------------------------------!
	1010	SUBROUTINE chem_define_netcdf_grid( var, found, grid_x, grid_y, grid_z )
	1011
	1012	IMPLICIT NONE
	1013
	1014	CHARACTER (LEN=*), INTENT(IN) :: var !<
	1015	LOGICAL, INTENT(OUT) :: found !<
	1016	CHARACTER (LEN=*), INTENT(OUT) :: grid_x !<
	1017	CHARACTER (LEN=*), INTENT(OUT) :: grid_y !<
	1018	CHARACTER (LEN=*), INTENT(OUT) :: grid_z !<
	1019
	1020	found = .TRUE.
	1021
	1022	if(var(1:3) == 'kc_') then !< always the same grid for chemistry variables
	1023	grid_x = 'x'
	1024	grid_y = 'y'
	1025	grid_z = 'zu' !< kk Use same z axis as u variables. Has to be checked if OK
	1026	else
	1027	found = .FALSE.
	1028	grid_x = 'none'
	1029	grid_y = 'none'
	1030	grid_z = 'none'
	1031	end if
	1032
	1033	! write(6,*) 'chem_define_netcdf_grid ',TRIM(var),' ',trim(grid_x),' ',found
	1034
	1035	END SUBROUTINE chem_define_netcdf_grid
	1036	!
	1037	!------------------------------------------------------------------------------!
	1038	!
	1039	! Description:
	1040	! ------------
	1041	!> Subroutine for checking data output for chemical species
	1042	!------------------------------------------------------------------------------!
	1043
	1044	SUBROUTINE chem_check_data_output( var, unit, i, ilen, k )
	1045
	1046
	1047	USE control_parameters, &
	1048	ONLY: data_output, message_string
	1049
	1050	IMPLICIT NONE
	1051
	1052	CHARACTER (LEN=*) :: unit !<
	1053	CHARACTER (LEN=*) :: var !<
	1054
	1055	INTEGER(iwp) :: i, lsp
	1056	INTEGER(iwp) :: ilen
	1057	INTEGER(iwp) :: k
	1058
	1059	CHARACTER(len=16) :: spec_name
	1060
	1061	unit = 'illegal'
	1062
	1063	spec_name = TRIM(var(4:)) !< var 1:3 is 'kc_'.
	1064
	1065	DO lsp=1,nspec
	1066	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
	1067	unit = 'ppm'
	1068	ENDIF
	1069	! It is possible to plant PM10 and PM25 into the gasphase chemistry code
	1070	! ! as passive species (e.g. 'passive' in GASPHASE_PREPROC/mechanisms):
	1071	! ! set unit to micrograms per m**3 for PM10 and PM25 (PM2.5)
	1072	IF (spec_name(1:2) == 'PM') THEN
	1073	unit = 'ug m-3'
	1074	ENDIF
	1075	ENDDO
	1076
	1077	DO lsp=1,nphot
	1078	IF (TRIM(spec_name) == TRIM(phot_frequen(lsp)%name)) THEN
	1079	unit = 'sec-1'
	1080	ENDIF
	1081	ENDDO
	1082
	1083
	1084	RETURN
	1085	END SUBROUTINE chem_check_data_output
	1086	!
	1087	!------------------------------------------------------------------------------!
	1088	!
	1089	! Description:
	1090	! ------------
	1091	!> Subroutine for checking data output of profiles for chemistry model
	1092	!------------------------------------------------------------------------------!
	1093
	1094	SUBROUTINE chem_check_data_output_pr( variable, var_count, unit, dopr_unit )
	1095
	1096
	1097	USE arrays_3d, &
	1098	ONLY: zu
	1099
	1100	USE control_parameters, &
	1101	ONLY: data_output_pr, message_string, air_chemistry
	1102
	1103	USE indices
	1104
	1105	USE profil_parameter
	1106
	1107	USE statistics
	1108
	1109
	1110	IMPLICIT NONE
	1111
	1112	CHARACTER (LEN=*) :: unit !<
	1113	CHARACTER (LEN=*) :: variable !<
	1114	CHARACTER (LEN=*) :: dopr_unit
	1115	CHARACTER(len=16) :: spec_name
	1116
	1117	INTEGER(iwp) :: var_count, lsp !<
	1118
	1119
	1120	spec_name = TRIM(variable(4:))
	1121	! write(9,*) 'fm #32 .. air_chemistry ', air_chemistry
	1122
	1123	IF ( .NOT. air_chemistry ) THEN
	1124	message_string = 'data_output_pr = ' // &
	1125	TRIM( data_output_pr(var_count) ) // ' is not imp' // &
	1126	'lemented for air_chemistry = .FALSE.'
	1127	! CALL message( 'check_parameters', 'PA0185', 1, 2, 0, 6, 0 )
	1128	ELSE
	1129	DO lsp = 1, nspec
	1130	IF (TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
	1131	dopr_index(var_count) = 900
	1132	dopr_unit = 'ppm'
	1133	hom(:,2,900,:) = SPREAD( zu, 2, statistic_regions+1 )
	1134	ENDIF
	1135	ENDDO
	1136	ENDIF
	1137
	1138	END SUBROUTINE chem_check_data_output_pr
	1139	!
	1140	!------------------------------------------------------------------------------!
	1141	!
	1142	! Description:
	1143	! ------------
	1144	!> Subroutine defining 3D output variables for chemical species
	1145	!------------------------------------------------------------------------------!
	1146
	1147
[2756]	1148	SUBROUTINE chem_data_output_3d( av, variable, found, local_pf, fill_value )
[2657]	1149
	1150
	1151	USE indices
	1152
	1153	USE kinds
	1154
	1155
	1156	IMPLICIT NONE
	1157
	1158	CHARACTER (LEN=*) :: variable !<
	1159	LOGICAL :: found !<
	1160	INTEGER(iwp) :: av !<
	1161
[2756]	1162	REAL(wp) :: fill_value !<
	1163	REAL(sp), DIMENSION(nxl:nxr,nys:nyn,nzb:nzt+1) :: local_pf
	1164
	1165
[2657]	1166	!-- local variables
	1167
	1168	INTEGER :: i, j, k, lsp
	1169	CHARACTER(len=16) :: spec_name
	1170
	1171
	1172	found = .FALSE.
	1173
	1174	spec_name = TRIM(variable(4:))
	1175	!av == 0
	1176
	1177	DO lsp=1,nspec
	1178	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
[2772]	1179	IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ' // TRIM(variable) // &
	1180	TRIM(chem_species(lsp)%name)
[2657]	1181
	1182	IF (av == 0) THEN
	1183	DO i = nxl, nxr
	1184	DO j = nys, nyn
	1185	DO k = nzb, nzt+1
[2756]	1186	local_pf(i,j,k) = MERGE( &
	1187	chem_species(lsp)%conc(k,j,i), &
	1188	REAL( fill_value, KIND = wp ), &
	1189	BTEST( wall_flags_0(k,j,i), 0 ) )
[2657]	1190	ENDDO
	1191	ENDDO
	1192	ENDDO
	1193
	1194	ELSE
	1195	DO i = nxl, nxr
	1196	DO j = nys, nyn
	1197	DO k = nzb, nzt+1
[2756]	1198	local_pf(i,j,k) = MERGE( &
	1199	chem_species(lsp)%conc_av(k,j,i),&
	1200	REAL( fill_value, KIND = wp ), &
	1201	BTEST( wall_flags_0(k,j,i), 0 ) )
[2657]	1202	ENDDO
	1203	ENDDO
	1204	ENDDO
	1205	ENDIF
	1206
	1207	found = .TRUE.
	1208	ENDIF
	1209	ENDDO
	1210
	1211	RETURN
	1212	END SUBROUTINE chem_data_output_3d
	1213	!
	1214	!------------------------------------------------------------------------------!
	1215	!
	1216	! Description:
	1217	! ------------
	1218	!> Subroutine for averaging 3D data of chemical species
	1219	!------------------------------------------------------------------------------!
	1220
	1221	SUBROUTINE chem_3d_data_averaging ( mode, variable )
	1222
	1223	USE control_parameters
	1224
	1225	USE indices
	1226
	1227	USE kinds
	1228
	1229	USE surface_mod, &
	1230	ONLY: surf_def_h, surf_lsm_h, surf_usm_h
	1231
	1232	IMPLICIT NONE
	1233
	1234	CHARACTER (LEN=*) :: mode !<
	1235	CHARACTER (LEN=*) :: variable !<
	1236
	1237
	1238	INTEGER(iwp) :: i !< grid index x direction
	1239	INTEGER(iwp) :: j !< grid index y direction
	1240	INTEGER(iwp) :: k !< grid index z direction
	1241	INTEGER(iwp) :: m !< running index surface type
	1242	INTEGER(iwp) :: lsp !< running index for chem spcs
	1243	INTEGER(iwp) :: lsp_2 !< it looks like redundent .. will be delted ..bK
	1244
	1245	IF ( mode == 'allocate' ) THEN
	1246	DO lsp = 1, nspec
	1247	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	1248	! lsp_2 = lsp
	1249	chem_species(lsp)%conc_av = 0.0_wp
	1250
	1251	ENDIF
	1252	ENDDO
	1253
	1254	ELSEIF ( mode == 'sum' ) THEN
	1255
	1256	DO lsp = 1, nspec
	1257	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	1258	! lsp_2 = lsp
	1259	DO i = nxlg, nxrg
	1260	DO j = nysg, nyng
	1261	DO k = nzb, nzt+1
	1262	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) + &
	1263	chem_species(lsp)%conc(k,j,i)
	1264	ENDDO
	1265	ENDDO
	1266	ENDDO
	1267	ELSEIF ( TRIM(variable(4:)) == TRIM('cssws*') ) THEN
	1268	DO m = 1, surf_def_h(0)%ns
	1269	i = surf_def_h(0)%i(m)
	1270	j = surf_def_h(0)%j(m)
	1271	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) + surf_def_h(0)%cssws(lsp,m)
	1272	ENDDO
	1273	DO m = 1, surf_lsm_h%ns
	1274	i = surf_lsm_h%i(m)
	1275	j = surf_lsm_h%j(m)
	1276	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) + surf_lsm_h%cssws(lsp,m)
	1277	ENDDO
	1278	DO m = 1, surf_usm_h%ns
	1279	i = surf_usm_h%i(m)
	1280	j = surf_usm_h%j(m)
	1281	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) + surf_usm_h%cssws(lsp,m)
	1282	ENDDO
	1283
	1284	ENDIF
	1285	ENDDO
	1286
	1287	ELSEIF ( mode == 'average' ) THEN
	1288	DO lsp = 1, nspec
	1289	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	1290	! lsp_2 = lsp
	1291	DO i = nxlg, nxrg
	1292	DO j = nysg, nyng
	1293	DO k = nzb, nzt+1
	1294	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) / REAL( average_count_3d, KIND=wp )
	1295	ENDDO
	1296	ENDDO
	1297	ENDDO
	1298
	1299	ELSEIF (TRIM(variable(4:)) == TRIM('cssws*') ) THEN
	1300	DO i = nxlg, nxrg
	1301	DO j = nysg, nyng
	1302	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) / REAL( average_count_3d, KIND=wp )
	1303	ENDDO
	1304	ENDDO
	1305	CALL exchange_horiz_2d( chem_species(lsp)%cssws_av, nbgp )
	1306	ENDIF
	1307	ENDDO
	1308
	1309	ENDIF
	1310
	1311	END SUBROUTINE chem_3d_data_averaging
	1312
	1313	!------------------------------------------------------------------------------!
	1314	!
	1315	! Description:
	1316	! ------------
	1317	!> Subroutine to write restart data for chemistry model
	1318	!------------------------------------------------------------------------------!
[2894]	1319	SUBROUTINE chem_wrd_local
[2657]	1320
	1321
	1322	IMPLICIT NONE
	1323
[2815]	1324	INTEGER(iwp) :: lsp !<
[2894]	1325
[2657]	1326	! REAL(kind=wp), DIMENSION(nzb:nzt+1,nysg:nyng,nxlg:nxrg) :: chems_conc
[2815]	1327
	1328
[2894]	1329	DO lsp = 1, nspec
[2668]	1330
[2894]	1331	CALL wrd_write_string( TRIM( chem_species(lsp)%name ))
	1332	WRITE ( 14 ) chem_species(lsp)%conc
[2657]	1333
[2894]	1334	CALL wrd_write_string( TRIM( chem_species(lsp)%name )//'_av' )
	1335	WRITE ( 14 ) chem_species(lsp)%conc_av
[2657]	1336
[2894]	1337	ENDDO
[2657]	1338
[2894]	1339
	1340	END SUBROUTINE chem_wrd_local
	1341
[2657]	1342	!------------------------------------------------------------------------------!
	1343	!
	1344	! Description:
	1345	! ------------
	1346	!> Subroutine to read restart data of chemical species
	1347	!------------------------------------------------------------------------------!
	1348
[2894]	1349	SUBROUTINE chem_rrd_local( i, k, nxlf, nxlc, nxl_on_file, nxrf, nxrc, &
	1350	nxr_on_file, nynf, nync, nyn_on_file, nysf, nysc, &
	1351	nys_on_file, tmp_3d, found )
[2657]	1352
	1353	USE control_parameters
	1354
	1355	USE indices
	1356
	1357	USE pegrid
	1358
	1359	IMPLICIT NONE
	1360
	1361	CHARACTER (LEN=20) :: spc_name_av !<
	1362
	1363	INTEGER(iwp) :: i, lsp !<
	1364	INTEGER(iwp) :: k !<
	1365	INTEGER(iwp) :: nxlc !<
	1366	INTEGER(iwp) :: nxlf !<
	1367	INTEGER(iwp) :: nxl_on_file !<
	1368	INTEGER(iwp) :: nxrc !<
	1369	INTEGER(iwp) :: nxrf !<
	1370	INTEGER(iwp) :: nxr_on_file !<
	1371	INTEGER(iwp) :: nync !<
	1372	INTEGER(iwp) :: nynf !<
	1373	INTEGER(iwp) :: nyn_on_file !<
	1374	INTEGER(iwp) :: nysc !<
	1375	INTEGER(iwp) :: nysf !<
	1376	INTEGER(iwp) :: nys_on_file !<
[2815]	1377
[2894]	1378	LOGICAL, INTENT(OUT) :: found
[2657]	1379
[2894]	1380	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]	1381
[2815]	1382
[2894]	1383	found = .FALSE.
[2657]	1384
[2815]	1385
[2894]	1386	IF ( ALLOCATED(chem_species) ) THEN
[2657]	1387
[2894]	1388	DO lsp = 1, nspec
[2815]	1389
[2894]	1390	!< for time-averaged chemical conc.
	1391	spc_name_av = TRIM(chem_species(lsp)%name)//'_av'
[2657]	1392
[2894]	1393	IF (restart_string(1:length) == TRIM(chem_species(lsp)%name) ) &
	1394	THEN
	1395	!< read data into tmp_3d
	1396	IF ( k == 1 ) READ ( 13 ) tmp_3d
	1397	!< fill ..%conc in the restart run
	1398	chem_species(lsp)%conc(:,nysc-nbgp:nync+nbgp, &
	1399	nxlc-nbgp:nxrc+nbgp) = &
	1400	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
	1401	found = .TRUE.
	1402	ELSEIF (restart_string(1:length) == spc_name_av ) THEN
	1403	IF ( k == 1 ) READ ( 13 ) tmp_3d
	1404	chem_species(lsp)%conc_av(:,nysc-nbgp:nync+nbgp, &
	1405	nxlc-nbgp:nxrc+nbgp) = &
	1406	tmp_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)
	1407	found = .TRUE.
[2815]	1408	ENDIF
[2894]	1409
[2657]	1410	ENDDO
	1411
[2894]	1412	ENDIF
[2657]	1413
	1414
[2894]	1415	END SUBROUTINE chem_rrd_local
[2657]	1416
	1417
	1418	!------------------------------------------------------------------------------!
	1419	!
	1420	! Description:
	1421	! ------------
[2815]	1422	!> Subroutine calculating prognostic equations for chemical species
	1423	!> (cache-optimized).
	1424	!> Routine is called separately for each chemical species over a loop from
	1425	!> prognostic_equations.
[2657]	1426	!------------------------------------------------------------------------------!
[2815]	1427	SUBROUTINE chem_prognostic_equations_ij ( cs_scalar_p, cs_scalar, tcs_scalar_m, pr_init_cs, &
[2768]	1428	i, j, i_omp_start, tn, ilsp, flux_s_cs, diss_s_cs, &
	1429	flux_l_cs, diss_l_cs )
[2657]	1430	USE pegrid
	1431	USE advec_ws, ONLY: advec_s_ws
	1432	USE advec_s_pw_mod, ONLY: advec_s_pw
	1433	USE advec_s_up_mod, ONLY: advec_s_up
	1434	USE diffusion_s_mod, ONLY: diffusion_s
	1435	USE indices, ONLY: wall_flags_0
[2768]	1436	USE surface_mod, ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
	1437	surf_usm_v
[2657]	1438
[2815]	1439
[2657]	1440	IMPLICIT NONE
	1441
[2768]	1442	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p, cs_scalar, tcs_scalar_m
[2657]	1443
	1444	INTEGER(iwp),INTENT(IN) :: i, j, i_omp_start, tn, ilsp
	1445	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: flux_s_cs !<
	1446	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: diss_s_cs !<
	1447	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: flux_l_cs !<
	1448	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: diss_l_cs !<
	1449	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
	1450
	1451	!-- local variables
	1452
	1453	INTEGER :: k
	1454	!
	1455	!-- Tendency-terms for chem spcs.
	1456	tend(:,j,i) = 0.0_wp
	1457	!
	1458	!-- Advection terms
	1459	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	1460	IF ( ws_scheme_sca ) THEN
	1461	CALL advec_s_ws( i, j, cs_scalar, 'kc', flux_s_cs, diss_s_cs, &
	1462	flux_l_cs, diss_l_cs, i_omp_start, tn )
	1463	ELSE
	1464	CALL advec_s_pw( i, j, cs_scalar )
	1465	ENDIF
	1466	ELSE
	1467	CALL advec_s_up( i, j, cs_scalar )
	1468	ENDIF
	1469
	1470	!
	1471
[2815]	1472	!-- Diffusion terms (the last three arguments are zero)
[2657]	1473
	1474	CALL diffusion_s( i, j, cs_scalar, &
	1475	surf_def_h(0)%cssws(ilsp,:), surf_def_h(1)%cssws(ilsp,:), &
	1476	surf_def_h(2)%cssws(ilsp,:), &
	1477	surf_lsm_h%cssws(ilsp,:), surf_usm_h%cssws(ilsp,:), &
	1478	surf_def_v(0)%cssws(ilsp,:), surf_def_v(1)%cssws(ilsp,:), &
	1479	surf_def_v(2)%cssws(ilsp,:), surf_def_v(3)%cssws(ilsp,:), &
	1480	surf_lsm_v(0)%cssws(ilsp,:), surf_lsm_v(1)%cssws(ilsp,:), &
	1481	surf_lsm_v(2)%cssws(ilsp,:), surf_lsm_v(3)%cssws(ilsp,:), &
	1482	surf_usm_v(0)%cssws(ilsp,:), surf_usm_v(1)%cssws(ilsp,:), &
	1483	surf_usm_v(2)%cssws(ilsp,:), surf_usm_v(3)%cssws(ilsp,:) )
	1484
	1485	!
	1486	!-- Prognostic equation for chem spcs
	1487	DO k = nzb+1, nzt
	1488	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) + ( dt_3d * &
	1489	( tsc(2) * tend(k,j,i) + &
	1490	tsc(3) * tcs_scalar_m(k,j,i) ) &
	1491	- tsc(5) * rdf_sc(k) &
	1492	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
	1493	) &
	1494	* MERGE( 1.0_wp, 0.0_wp, &
	1495	BTEST( wall_flags_0(k,j,i), 0 ) &
	1496	)
	1497
	1498	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
	1499	ENDDO
	1500
	1501	!
	1502	!-- Calculate tendencies for the next Runge-Kutta step
	1503	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	1504	IF ( intermediate_timestep_count == 1 ) THEN
	1505	DO k = nzb+1, nzt
	1506	tcs_scalar_m(k,j,i) = tend(k,j,i)
	1507	ENDDO
	1508	ELSEIF ( intermediate_timestep_count < &
	1509	intermediate_timestep_count_max ) THEN
	1510	DO k = nzb+1, nzt
	1511	tcs_scalar_m(k,j,i) = -9.5625_wp * tend(k,j,i) + &
	1512	5.3125_wp * tcs_scalar_m(k,j,i)
	1513	ENDDO
	1514	ENDIF
	1515	ENDIF
[2815]	1516
	1517	END SUBROUTINE chem_prognostic_equations_ij
	1518
	1519
	1520	!------------------------------------------------------------------------------!
[2657]	1521	!
[2815]	1522	! Description:
	1523	! ------------
	1524	!> Subroutine calculating prognostic equations for chemical species
	1525	!> (vector-optimized).
	1526	!> Routine is called separately for each chemical species over a loop from
	1527	!> prognostic_equations.
	1528	!------------------------------------------------------------------------------!
	1529	SUBROUTINE chem_prognostic_equations ( cs_scalar_p, cs_scalar, tcs_scalar_m, &
	1530	pr_init_cs, ilsp )
[2657]	1531
[2815]	1532	USE advec_s_pw_mod, &
	1533	ONLY: advec_s_pw
	1534
	1535	USE advec_s_up_mod, &
	1536	ONLY: advec_s_up
	1537
	1538	USE advec_ws, &
	1539	ONLY: advec_s_ws
	1540
	1541	USE diffusion_s_mod, &
	1542	ONLY: diffusion_s
	1543
	1544	USE indices, &
	1545	ONLY: nxl, nxr, nyn, nys, wall_flags_0
	1546
	1547	USE pegrid
	1548
	1549	USE surface_mod, &
	1550	ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
	1551	surf_usm_v
	1552
	1553	IMPLICIT NONE
	1554
	1555	INTEGER :: i !< running index
	1556	INTEGER :: j !< running index
	1557	INTEGER :: k !< running index
	1558
	1559	INTEGER(iwp),INTENT(IN) :: ilsp !<
	1560
	1561	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
	1562
	1563	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar !<
	1564	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p !<
	1565	REAL(wp), DIMENSION(:,:,:), POINTER :: tcs_scalar_m !<
	1566
	1567
	1568	!
	1569	!-- Tendency terms for chemical species
	1570	tend = 0.0_wp
	1571	!
	1572	!-- Advection terms
	1573	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	1574	IF ( ws_scheme_sca ) THEN
	1575	CALL advec_s_ws( cs_scalar, 'kc' )
	1576	ELSE
	1577	CALL advec_s_pw( cs_scalar )
	1578	ENDIF
	1579	ELSE
	1580	CALL advec_s_up( cs_scalar )
	1581	ENDIF
	1582	!
	1583	!-- Diffusion terms (the last three arguments are zero)
	1584	CALL diffusion_s( cs_scalar, &
	1585	surf_def_h(0)%cssws(ilsp,:), &
	1586	surf_def_h(1)%cssws(ilsp,:), &
	1587	surf_def_h(2)%cssws(ilsp,:), &
	1588	surf_lsm_h%cssws(ilsp,:), &
	1589	surf_usm_h%cssws(ilsp,:), &
	1590	surf_def_v(0)%cssws(ilsp,:), &
	1591	surf_def_v(1)%cssws(ilsp,:), &
	1592	surf_def_v(2)%cssws(ilsp,:), &
	1593	surf_def_v(3)%cssws(ilsp,:), &
	1594	surf_lsm_v(0)%cssws(ilsp,:), &
	1595	surf_lsm_v(1)%cssws(ilsp,:), &
	1596	surf_lsm_v(2)%cssws(ilsp,:), &
	1597	surf_lsm_v(3)%cssws(ilsp,:), &
	1598	surf_usm_v(0)%cssws(ilsp,:), &
	1599	surf_usm_v(1)%cssws(ilsp,:), &
	1600	surf_usm_v(2)%cssws(ilsp,:), &
	1601	surf_usm_v(3)%cssws(ilsp,:) )
	1602	!
	1603	!-- Prognostic equation for chemical species
	1604	DO i = nxl, nxr
	1605	DO j = nys, nyn
	1606	DO k = nzb+1, nzt
	1607	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) &
	1608	+ ( dt_3d * &
	1609	( tsc(2) * tend(k,j,i) &
	1610	+ tsc(3) * tcs_scalar_m(k,j,i) &
	1611	) &
	1612	- tsc(5) * rdf_sc(k) &
	1613	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
	1614	) &
	1615	* MERGE( 1.0_wp, 0.0_wp, BTEST( wall_flags_0(k,j,i), 0 ) )
	1616
	1617	IF ( cs_scalar_p(k,j,i) < 0.0_wp ) cs_scalar_p(k,j,i) = 0.1_wp * cs_scalar(k,j,i)
	1618	ENDDO
	1619	ENDDO
	1620	ENDDO
	1621	!
	1622	!-- Calculate tendencies for the next Runge-Kutta step
	1623	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	1624	IF ( intermediate_timestep_count == 1 ) THEN
	1625	DO i = nxl, nxr
	1626	DO j = nys, nyn
	1627	DO k = nzb+1, nzt
	1628	tcs_scalar_m(k,j,i) = tend(k,j,i)
	1629	ENDDO
	1630	ENDDO
	1631	ENDDO
	1632	ELSEIF ( intermediate_timestep_count < &
	1633	intermediate_timestep_count_max ) THEN
	1634	DO i = nxl, nxr
	1635	DO j = nys, nyn
	1636	DO k = nzb+1, nzt
	1637	tcs_scalar_m(k,j,i) = - 9.5625_wp * tend(k,j,i) &
	1638	+ 5.3125_wp * tcs_scalar_m(k,j,i)
	1639	ENDDO
	1640	ENDDO
	1641	ENDDO
	1642	ENDIF
	1643	ENDIF
	1644
	1645	END SUBROUTINE chem_prognostic_equations
	1646
	1647
[2657]	1648	!------------------------------------------------------------------------------!
	1649	!
	1650	! Description:
	1651	! ------------
	1652	!> Subroutine defining header output for chemistry model
	1653	!------------------------------------------------------------------------------!
	1654	SUBROUTINE chem_header ( io )
	1655
	1656	IMPLICIT NONE
	1657
	1658	INTEGER(iwp), INTENT(IN) :: io !< Unit of the output file
	1659
	1660	! print*,'the header subroutine is still not operational'
	1661	!!
	1662	!!-- Write chemistry model header
	1663	! WRITE( io, 3 )
	1664	!
	1665	! IF ( radiation_scheme == "constant" ) THEN
	1666	! WRITE( io, 4 ) net_radiation
	1667	! ELSEIF ( radiation_scheme == "clear-sky" ) THEN
	1668	! WRITE( io, 5 )
	1669	! ELSEIF ( radiation_scheme == "rrtmg" ) THEN
	1670	! WRITE( io, 6 )
	1671	! IF ( .NOT. lw_radiation ) WRITE( io, 10 )
	1672	! IF ( .NOT. sw_radiation ) WRITE( io, 11 )
	1673	! ENDIF
	1674	!
	1675	! IF ( albedo_type == 0 ) THEN
	1676	! WRITE( io, 7 ) albedo
	1677	! ELSE
	1678	! WRITE( io, 8 ) TRIM( albedo_type_name(albedo_type) )
	1679	! ENDIF
	1680	! IF ( constant_albedo ) THEN
	1681	! WRITE( io, 9 )
	1682	! ENDIF
	1683	!
	1684	! IF ( radiation .AND. radiation_scheme /= 'constant' ) THEN
	1685	! WRITE ( io, 1 ) lambda
	1686	! WRITE ( io, 2 ) day_init, time_utc_init
	1687	! ENDIF
	1688	!
	1689	! WRITE( io, 12 ) dt_radiation
	1690	!
	1691	! 1 FORMAT (' Geograph. longitude : lambda = ',F4.1,' degr')
	1692	! 2 FORMAT (' Day of the year at model start : day_init = ',I3 &
	1693	! /' UTC time at model start : time_utc_init = ',F7.1' s')
	1694	! 3 FORMAT (//' Radiation model information:'/ &
	1695	! ' ----------------------------'/)
	1696	! 4 FORMAT (' --> Using constant net radiation: net_radiation = ', F6.2, &
	1697	! // 'W/m**2')
	1698	! 5 FORMAT (' --> Simple radiation scheme for clear sky is used (no clouds,', &
	1699	! ' default)')
	1700	! 6 FORMAT (' --> RRTMG scheme is used')
	1701	! 7 FORMAT (/' User-specific surface albedo: albedo =', F6.3)
	1702	! 8 FORMAT (/' Albedo is set for land surface type: ', A)
	1703	! 9 FORMAT (/' --> Albedo is fixed during the run')
	1704	!10 FORMAT (/' --> Longwave radiation is disabled')
	1705	!11 FORMAT (/' --> Shortwave radiation is disabled.')
	1706	!12 FORMAT (' Timestep: dt_radiation = ', F6.2, ' s')
	1707	!
	1708	!
	1709	END SUBROUTINE chem_header
[2668]	1710
	1711	!------------------------------------------------------------------------------
	1712	! Description:
	1713	! ------------
	1714	!> Subroutine reading restart data for chemistry model input parameters
	1715	! (FK: To make restarts work, I had to comment this routine. We actually
	1716	! don't need it, since the namelist parameters are always read in,
	1717	! also in case of a restart run)
	1718	!------------------------------------------------------------------------------
[2894]	1719	! SUBROUTINE chem_rrd_global
	1720	!
	1721	! USE chem_modules
	1722	!
	1723	! USE control_parameters, &
	1724	! ONLY: length, message_string, restart_string
[2668]	1725	!
	1726	!
	1727	! IMPLICIT NONE
	1728	!
	1729	!
	1730	!
[2894]	1731	! DO
[2668]	1732	!
[2894]	1733	! SELECT CASE ( restart_string(1:length) )
[2668]	1734	!
	1735	! CASE ( 'bc_cs_b' )
	1736	! READ ( 13 ) bc_cs_b
[2894]	1737	!
	1738	! CASE DEFAULT
	1739	!
	1740	! EXIT
	1741	!
[2668]	1742	! END SELECT
	1743	!
[2894]	1744	!!
	1745	!!-- Read next string and its length
	1746	! READ ( 13 ) length
	1747	! READ ( 13 ) restart_string(1:length)
[2668]	1748	!
	1749	! ENDDO
	1750	!
[2894]	1751	! END SUBROUTINE chem_rrd_global
[2668]	1752
	1753
	1754	!------------------------------------------------------------------------------!
[2657]	1755	!
[2668]	1756	! Description:
	1757	! ------------
	1758	!> Subroutine writing restart data for chemistry model input parameters
	1759	! (FK: To make restarts work, I had to comment this routine. We actually
	1760	! don't need it, since the namelist parameters are always read in,
	1761	! also in case of a restart run)
[2657]	1762	!------------------------------------------------------------------------------!
[2894]	1763	! SUBROUTINE chem_wrd_global
[2668]	1764	!
	1765	! USE chem_modules
	1766	!
	1767	! USE kinds
	1768	!
	1769	!
	1770	! IMPLICIT NONE
	1771	!
	1772	! INTEGER(iwp) :: lsp !< running index for chem spcs
	1773	!
	1774	! !
	1775	! !-- Writing out input parameters that are not part of chemistry_par namelist
	1776	! !-- (namelist parameters are anyway read in again in case of restart)
	1777	! DO lsp = 1, nvar
[2894]	1778	! CALL wrd_write_string( 'conc_pr_init_'//chem_species(lsp)%name )
[2668]	1779	! WRITE ( 14 ) chem_species(lsp)%conc_pr_init
	1780	! ENDDO
	1781	!
	1782	!
[2894]	1783	! END SUBROUTINE chem_wrd_global
[2668]	1784
	1785
	1786	!------------------------------------------------------------------------------!
[2657]	1787	!
	1788	! Description:
	1789	! ------------
[2668]	1790	!> Subroutine for emission
[2657]	1791	!------------------------------------------------------------------------------!
[2668]	1792	SUBROUTINE chem_emissions
[2657]	1793
[2668]	1794	USE chem_modules
	1795
	1796	USE netcdf_data_input_mod, &
	1797	ONLY: street_type_f
	1798
	1799	USE surface_mod, &
	1800	ONLY: surf_lsm_h
[2657]	1801
	1802
[2668]	1803	IMPLICIT NONE
[2657]	1804
[2678]	1805	INTEGER(iwp) :: i !< running index for grid in x-direction
	1806	INTEGER(iwp) :: j !< running index for grid in y-direction
	1807	INTEGER(iwp) :: m !< running index for horizontal surfaces
[2668]	1808	INTEGER(iwp) :: lsp !< running index for chem spcs
[2657]	1809
[2668]	1810	!
	1811	!-- Comment??? (todo)
[2678]	1812	IF ( street_type_f%from_file ) THEN
	1813	!
	1814	!-- Streets are lsm surfaces, hence, no usm surface treatment required
	1815	DO m = 1, surf_lsm_h%ns
	1816	i = surf_lsm_h%i(m)
	1817	j = surf_lsm_h%j(m)
	1818
	1819	IF ( street_type_f%var(j,i) >= main_street_id .AND. &
	1820	street_type_f%var(j,i) < max_street_id ) THEN
	1821	DO lsp = 1, nvar
	1822	surf_lsm_h%cssws(lsp,m) = emiss_factor_main * surface_csflux(lsp)
	1823	ENDDO
	1824	ELSEIF ( street_type_f%var(j,i) >= side_street_id .AND. &
	1825	street_type_f%var(j,i) < main_street_id ) THEN
	1826	DO lsp = 1, nvar
	1827	surf_lsm_h%cssws(lsp,m) = emiss_factor_side * surface_csflux(lsp)
	1828	ENDDO
[2682]	1829	ELSE
	1830	surf_lsm_h%cssws(:,m) = 0.0_wp
[2678]	1831	ENDIF
	1832	ENDDO
	1833
	1834	ENDIF
[2657]	1835
[2668]	1836	END SUBROUTINE chem_emissions
[2657]	1837
	1838
	1839	END MODULE chemistry_model_mod
	1840

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