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source: palm/trunk/SOURCE/chemistry_model_mod.f90 @ 2769

Last change on this file since 2769 was 2768, checked in by kanani, 7 years ago
Added parameter check, reduced line length, some formatting
Property svn:keywords set to `Id`
File size: 72.9 KB

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[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 2768 2018-01-24 15:38:29Z raasch $
[2768]	29	! Shorten lines to maximum length of 132 characters
	30	!
	31	! 2766 2018-01-22 17:17:47Z kanani
[2766]	32	! Removed preprocessor directive __chem
	33	!
	34	! 2756 2018-01-16 18:11:14Z suehring
[2756]	35	! Fill values in 3D output introduced.
	36	!
	37	! 2718 2018-01-02 08:49:38Z maronga
[2696]	38	! Initial revision
	39	!
[2657]	40	!
[2696]	41	!
	42	!
	43	! Authors:
	44	! --------
	45	! @author Renate Forkel
	46	! @author Farah Kanani-Suehring
	47	! @author Klaus Ketelsen
	48	! @author Basit Khan
	49	!
	50	!
[2657]	51	!------------------------------------------------------------------------------!
	52	! Description:
	53	! ------------
	54	!> Chemistry model for PALM-4U
[2668]	55	!> @todo Update/clean-up todo list! (FK)
	56	!> @todo Chemistry for prognostic_equations_vector! (FK)
	57	!> @todo Set proper fill values (/= 0) for chem output arrays! (FK)
	58	!> @todo Add routine chem_check_parameters, add checks for inconsistent or
	59	!> unallowed parameter settings (e.g. "only cache optimized version
	60	!> available"). CALL of chem_check_parameters from check_parameters. (FK)
	61	!> @todo Make routine chem_header available, CALL from header.f90
	62	!> (see e.g. how it is done in routine lsm_header in
	63	!> land_surface_model_mod.f90). chem_header should include all setup
	64	!> info about chemistry parameter settings. (FK)
[2657]	65	!> @todo Implement turbulent inflow of chem spcs in inflow_turbulence.
	66	!> @todo Separate boundary conditions for each chem spcs to be implemented
	67	!> @todo Currently only total concentration are calculated. Resolved, parameterized
	68	!> and chemistry fluxes although partially and some completely coded but
	69	!> are not operational/activated in this version. bK.
	70	!> @todo slight differences in passive scalar and chem spcs when chem reactions
	71	!> turned off. Need to be fixed. bK
	72	!> @todo introduce nesting for chem spcs. bK
	73	!> @todo subroutine set_const_initial_values to be taken out from chemistry_model_mod !bK.
	74	!> @todo chemistry error messages
	75	!> @todo Format this module according to PALM coding standard (see e.g. module
	76	!> template under http://palm.muk.uni-hannover.de/mosaik/downloads/8 or
	77	!> D3_coding_standard.pdf under https://palm.muk.uni-hannover.de/trac/downloads/16)
	78	!
	79	!------------------------------------------------------------------------------!
	80
	81	MODULE chemistry_model_mod
[2766]	82
[2657]	83	USE kinds, ONLY: wp, iwp
	84	USE indices, ONLY: nz, nzb,nzt,nysg,nyng,nxlg,nxrg,nys,nyn
	85	USE pegrid, ONLY: myid, threads_per_task
	86	USE control_parameters, ONLY: dt_3d, ws_scheme_sca, initializing_actions, message_string, &
	87	omega, tsc, intermediate_timestep_count, &
	88	intermediate_timestep_count_max, &
	89	timestep_scheme, use_prescribed_profile_data
	90	USE arrays_3d, ONLY: hyp, pt, rdf_sc, tend, zu
	91	USE chem_gasphase_mod, ONLY: nspec, spc_names, nkppctrl, nmaxfixsteps, &
	92	t_steps, fill_temp, chem_gasphase_integrate, &
	93	nvar, atol, rtol, nphot, phot_names
	94	USE cpulog, ONLY: cpu_log, log_point
	95
	96	USE chem_modules
	97
	98
	99	IMPLICIT NONE
	100	PRIVATE
	101	SAVE
	102
	103	!- Define chemical variables
	104
	105	TYPE species_def
	106	CHARACTER(LEN=8) :: name
	107	CHARACTER(LEN=16) :: unit
	108	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc
	109	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_av
	110	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: conc_p
	111	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: tconc_m
	112	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: cssws_av
	113	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: flux_s_cs
	114	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:) :: diss_s_cs
	115	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: flux_l_cs
	116	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:) :: diss_l_cs
	117	REAL(kind=wp),ALLOCATABLE,DIMENSION(:) :: conc_pr_init
	118	END TYPE species_def
	119
	120
	121	TYPE photols_def
	122	CHARACTER(LEN=8) :: name
	123	CHARACTER(LEN=16) :: unit
	124	REAL(kind=wp),POINTER,DIMENSION(:,:,:) :: freq
	125	END TYPE photols_def
	126
	127
	128	PUBLIC species_def
	129	PUBLIC photols_def
	130
	131
	132	TYPE(species_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: chem_species
	133	TYPE(photols_def),ALLOCATABLE,DIMENSION(:),TARGET, PUBLIC :: phot_frequen
	134
	135	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_1
	136	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_2
	137	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_3
	138	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: spec_conc_av
	139	REAL(kind=wp),ALLOCATABLE,DIMENSION(:,:,:,:),TARGET :: freq_1
	140
	141	INTEGER,DIMENSION(nkppctrl) :: icntrl ! Fine tuning kpp
	142	REAL(kind=wp),DIMENSION(nkppctrl) :: rcntrl ! Fine tuning kpp
	143
	144	CHARACTER(10), PUBLIC :: photolysis_scheme
	145	! 'constant',
	146	! 'simple' (Simple parameterisation from MCM, Saunders et al., 2003, Atmos. Chem. Phys., 3, 161-180
	147	! 'fastj' (Wild et al., 2000, J. Atmos. Chem., 37, 245-282) STILL NOT IMPLEMENTED
	148
	149	PUBLIC nspec
	150	PUBLIC nvar
	151	PUBLIC spc_names
	152
	153	!- Interface section
	154	INTERFACE chem_boundary_conds
	155	MODULE PROCEDURE chem_boundary_conds
	156	END INTERFACE chem_boundary_conds
	157
	158	INTERFACE chem_init
	159	MODULE PROCEDURE chem_init
	160	END INTERFACE chem_init
	161
	162	INTERFACE chem_init_profiles
	163	MODULE PROCEDURE chem_init_profiles
[2682]	164	END INTERFACE chem_init_profiles
[2657]	165
	166	INTERFACE chem_parin
	167	MODULE PROCEDURE chem_parin
	168	END INTERFACE chem_parin
	169
	170	INTERFACE chem_integrate
	171	MODULE PROCEDURE chem_integrate_ij
	172	END INTERFACE chem_integrate
	173
	174	INTERFACE chem_swap_timelevel
	175	MODULE PROCEDURE chem_swap_timelevel
	176	END INTERFACE chem_swap_timelevel
	177
	178	INTERFACE chem_define_netcdf_grid
	179	MODULE PROCEDURE chem_define_netcdf_grid
	180	END INTERFACE chem_define_netcdf_grid
	181
	182	INTERFACE chem_data_output_3d
	183	MODULE PROCEDURE chem_data_output_3d
	184	END INTERFACE chem_data_output_3d
	185
	186	INTERFACE chem_check_data_output
	187	MODULE PROCEDURE chem_check_data_output
	188	END INTERFACE chem_check_data_output
	189
	190	INTERFACE chem_check_data_output_pr
	191	MODULE PROCEDURE chem_check_data_output_pr
	192	END INTERFACE chem_check_data_output_pr
	193
	194	INTERFACE chem_3d_data_averaging
	195	MODULE PROCEDURE chem_3d_data_averaging
	196	END INTERFACE chem_3d_data_averaging
	197
	198	INTERFACE chem_last_actions
	199	MODULE PROCEDURE chem_last_actions
	200	END INTERFACE chem_last_actions
	201
	202	INTERFACE chem_read_restart_data
	203	MODULE PROCEDURE chem_read_restart_data
	204	END INTERFACE chem_read_restart_data
	205
	206	INTERFACE chem_tendency
	207	MODULE PROCEDURE chem_tendency
	208	END INTERFACE chem_tendency
	209
	210	INTERFACE chem_header
	211	MODULE PROCEDURE chem_header
	212	END INTERFACE chem_header
	213
[2668]	214	INTERFACE chem_emissions
	215	MODULE PROCEDURE chem_emissions
	216	END INTERFACE chem_emissions
[2657]	217
[2668]	218	! INTERFACE chem_write_var_list
	219	! MODULE PROCEDURE chem_write_var_list
	220	! END INTERFACE chem_write_var_list
	221	!
	222	! INTERFACE chem_read_var_list
	223	! MODULE PROCEDURE chem_read_var_list
	224	! END INTERFACE chem_read_var_list
	225	!
	226	! INTERFACE chem_skip_var_list
	227	! MODULE PROCEDURE chem_skip_var_list
	228	! END INTERFACE chem_skip_var_list
[2657]	229
	230
	231	PUBLIC chem_boundary_conds, chem_check_data_output, &
	232	chem_check_data_output_pr, chem_data_output_3d, &
	233	chem_define_netcdf_grid, chem_header, chem_init, &
	234	chem_init_profiles, chem_integrate, chem_parin, &
	235	chem_swap_timelevel, chem_last_actions, chem_read_restart_data, &
[2668]	236	chem_tendency, chem_3d_data_averaging, chem_emissions!, chem_write_var_list, &
	237	!chem_read_var_list, chem_skip_var_list
[2657]	238
	239
	240	CONTAINS
	241
	242	!------------------------------------------------------------------------------!
	243	!
	244	! Description:
	245	! ------------
	246	!> Subroutine to initialize and set all boundary conditions for chemical species
	247	!------------------------------------------------------------------------------!
	248
	249	SUBROUTINE chem_boundary_conds( mode )
	250
	251	USE control_parameters, &
	252	ONLY: air_chemistry, outflow_l, outflow_n, outflow_r, outflow_s
	253	USE indices, &
	254	ONLY: nxl, nxr, nxlg, nxrg, nyng, nysg, nzt
	255
	256	! USE prognostic_equations_mod, &
	257
	258	USE arrays_3d, &
	259	ONLY: dzu
	260	USE surface_mod, &
	261	ONLY: bc_h
	262
	263	CHARACTER (len=*), INTENT(IN) :: mode
	264	INTEGER(iwp) :: i !< grid index x direction.
	265	INTEGER(iwp) :: j !< grid index y direction.
	266	INTEGER(iwp) :: k !< grid index z direction.
	267	INTEGER(iwp) :: kb !< variable to set respective boundary value, depends on facing.
	268	INTEGER(iwp) :: l !< running index boundary type, for up- and downward-facing walls.
	269	INTEGER(iwp) :: m !< running index surface elements.
	270	INTEGER(iwp) :: lsp !< running index for chem spcs.
	271	INTEGER(iwp) :: lph !< running index for photolysis frequencies
	272
	273
	274	SELECT CASE ( TRIM( mode ) )
	275	CASE ( 'init' )
	276	DO lsp = 1, nspec
	277	IF ( surface_csflux(lsp) == 9999999.9_wp ) THEN
	278	constant_csflux(lsp) = .FALSE.
	279	ENDIF
	280	ENDDO
	281
	282	IF ( bc_cs_b == 'dirichlet' ) THEN
	283	ibc_cs_b = 0
	284	ELSEIF ( bc_cs_b == 'neumann' ) THEN
	285	ibc_cs_b = 1
	286	ELSE
	287	! message_string = 'unknown boundary condition: bc_cs_b ="' // TRIM( bc_cs_b ) // '"' ! bK commented
	288	CALL message( 'chem_boundary_conds', 'CHEM001', 1, 2, 0, 6, 0 ) !< chemistry_model_mod should have special error numbers --> "CHEM###",
	289	ENDIF
	290	!
	291	!-- Set Integer flags and check for possible erroneous settings for top
	292	!-- boundary condition. bK added _cs_ here.
	293	IF ( bc_cs_t == 'dirichlet' ) THEN
	294	ibc_cs_t = 0
	295	ELSEIF ( bc_cs_t == 'neumann' ) THEN
	296	ibc_cs_t = 1
	297	ELSEIF ( bc_cs_t == 'initial_gradient' ) THEN
	298	ibc_cs_t = 2
	299	ELSEIF ( bc_cs_t == 'nested' ) THEN
	300	ibc_cs_t = 3
	301	ELSE
	302	! message_string = 'unknown boundary condition: bc_c_t ="' // TRIM( bc_cs_t ) // '"'
	303	CALL message( 'check_parameters', 'CHEM002', 1, 2, 0, 6, 0 )
	304	ENDIF
	305
	306
	307	CASE ( 'set_bc_bottomtop' )
	308	!-- Bottom boundary condtions for chemical species
	309	DO lsp = 1, nspec
	310	IF ( ibc_cs_b == 0 ) THEN
	311	DO l = 0, 1
	312	!-- Set index kb: For upward-facing surfaces (l=0), kb=-1, i.e.
	313	!-- the chem_species(nsp)%conc_p value at the topography top (k-1)
	314	!-- is set; for downward-facing surfaces (l=1), kb=1, i.e. the
	315	!-- value at the topography bottom (k+1) is set.
	316
	317	kb = MERGE( -1, 1, l == 0 )
	318	!$OMP PARALLEL DO PRIVATE( i, j, k )
	319	DO m = 1, bc_h(l)%ns
	320	i = bc_h(l)%i(m)
	321	j = bc_h(l)%j(m)
	322	k = bc_h(l)%k(m)
	323	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc(k+kb,j,i)
	324	ENDDO
	325	ENDDO
	326
	327	ELSEIF ( ibc_cs_b == 1 ) THEN
	328	! in boundary_conds there is som extra loop over m here for passive tracer
	329	DO l = 0, 1
	330	kb = MERGE( -1, 1, l == 0 )
	331	!$OMP PARALLEL DO PRIVATE( i, j, k )
	332	DO m = 1, bc_h(l)%ns
	333	i = bc_h(l)%i(m)
	334	j = bc_h(l)%j(m)
	335	k = bc_h(l)%k(m)
	336	chem_species(lsp)%conc_p(k+kb,j,i) = chem_species(lsp)%conc_p(k,j,i)
	337
	338	!< @todo: chem_species(nsp)%conc_p(k+kb,j,i) = chem_species(nsp)%conc(k+kb,j,i), &
	339	!< pls loop over nsp=1, NSPEC.
	340	!< @todo: We should also think about the possibility to have &
	341	!< individual boundary conditions for each species? This means, bc_cs_b, &
	342	!< bc_cs_t, ibc_cs_b, ibc_cs_t would need to be added to TYPE chem_species(nsp)%, &
	343	!< and the loop over nsp would have to be put outside of this IF-clause.
	344	!< i think its better we keep the same bonundary cond i.e. dirichlet or neumann
	345	!< for all chem spcs. ... !bK
	346
	347	ENDDO
	348	ENDDO
	349	ENDIF
	350	ENDDO ! end lsp loop
	351
	352	!-- Top boundary conditions for chemical species - Should this not be done for all species?
	353	IF ( ibc_cs_t == 0 ) THEN
	354	DO lsp = 1, nspec
	355	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc(nzt+1,:,:)
	356	ENDDO
	357	ELSEIF ( ibc_cs_t == 1 ) THEN
	358	DO lsp = 1, nspec
[2678]	359	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:)
[2657]	360	ENDDO
	361	ELSEIF ( ibc_cs_t == 2 ) THEN
	362	DO lsp = 1, nspec
[2678]	363	chem_species(lsp)%conc_p(nzt+1,:,:) = chem_species(lsp)%conc_p(nzt,:,:) + bc_cs_t_val(lsp) * dzu(nzt+1)
[2657]	364	ENDDO
	365	!@todo: bc_cs_t_val needs to be calculated,
	366	!see bc_pt_t_val = ( pt_init(nzt+1) - pt_init(nzt) ) / dzu(nzt+1)
	367	!(in time_integration). pt_init would be the counterpart to
	368	!chem_species(i)%conc_pr_init (see kchem_driver_FKa1408.f90 of my
	369	!"Hints: prescribing initial concentration.
	370	ENDIF
	371	!
	372	CASE ( 'set_bc_lateral' ) ! bK commented it
	373	!-- Lateral boundary conditions for chem species at inflow boundary
	374	!-- are automatically set when chem_species concentration is
	375	!-- initialized. The initially set value at the inflow boundary is not
	376	!-- touched during time integration, hence, this boundary value remains
	377	!-- at a constant value, which is the concentration that flows into the
	378	!-- domain.
	379	!-- Lateral boundary conditions for chem species at outflow boundary
	380
	381	IF ( outflow_s ) THEN
	382	DO lsp = 1, nspec
	383	chem_species(lsp)%conc_p(:,nys-1,:) = chem_species(lsp)%conc_p(:,nys,:)
	384	ENDDO
	385	ELSEIF ( outflow_n ) THEN
	386	DO lsp = 1, nspec
	387	chem_species(lsp)%conc_p(:,nyn+1,:) = chem_species(lsp)%conc_p(:,nyn,:)
	388	ENDDO
	389	ELSEIF ( outflow_l ) THEN
	390	DO lsp = 1, nspec
	391	chem_species(lsp)%conc_p(:,:,nxl-1) = chem_species(lsp)%conc_p(:,:,nxl)
	392	ENDDO
	393	ELSEIF ( outflow_r ) THEN
	394	DO lsp = 1, nspec
	395	chem_species(lsp)%conc_p(:,:,nxr+1) = chem_species(lsp)%conc_p(:,:,nxr)
	396	ENDDO
	397	ENDIF
	398
	399	END SELECT
	400
	401	END SUBROUTINE chem_boundary_conds
	402	!
	403	!------------------------------------------------------------------------------!
	404	!
	405	! Description:
	406	! ------------
	407	!> Subroutine defining initial vertical profiles of chemical species (given by
	408	!> namelist parameters chem_profiles and chem_heights) --> which should work
	409	!> analogue to parameters u_profile, v_profile and uv_heights)
	410	!------------------------------------------------------------------------------!
	411	SUBROUTINE chem_init_profiles !< SUBROUTINE is called from chem_init in case of
	412	!< TRIM( initializing_actions ) /= 'read_restart_data'
	413	!< We still need to see what has to be done in case of restart run
	414	USE chem_modules
	415
	416	IMPLICIT NONE
	417
	418	!-- Local variables
	419	INTEGER :: lsp !< running index for number of species in derived data type species_def
	420	INTEGER :: lsp_pr !< running index for number of species in cs_names, cs_profiles etc
	421	INTEGER :: lpr_lev !< running index for profile level for each chem spcs.
	422	INTEGER :: npr_lev !< the next available profile lev
	423
	424	!-----------------
	425	!-- To prescribe/initialize a vertically constant 'cs_profile', another parameter
	426	!-- "cs_surface" is introduced. If "cs_profile" and "cs_heights" are prescribed,
	427	!-- their values will override the constant profile given by "cs_surface".
	428
[2668]	429	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
[2657]	430	lsp_pr = 1
	431	DO WHILE ( TRIM( cs_name( lsp_pr ) ) /= 'novalue' ) !'novalue' is the default
	432	DO lsp = 1, nspec !
	433	!-- Create initial profile (conc_pr_init) for each chemical species
	434	IF ( TRIM( chem_species(lsp)%name ) == TRIM( cs_name(lsp_pr) ) ) THEN !
[2682]	435	! IF ( cs_profile(1,1) == 9999999.9_wp ) THEN
[2657]	436	!-- Set a vertically constant profile based on the surface conc (cs_surface(lsp_pr)) of each species
	437	DO lpr_lev = 0, nzt+1
	438	chem_species(lsp)%conc_pr_init(lpr_lev) = cs_surface(lsp_pr)
	439	ENDDO
	440
[2682]	441	! ELSE
	442	! IF ( cs_heights(lsp,1) /= 0.0_wp ) THEN
	443	! message_string = 'cs_heights(1,1) must be 0.0'
	444	! CALL message( 'chem_check_parameters', 'CHEM0004', 1, 2, 0, 6, 0 )
	445	! ENDIF
	446	!
	447	! IF ( omega /= 0.0_wp ) THEN
	448	! message_string = 'Coriolis force must be switched off (by setting omega=0.0)' // &
	449	! ' when prescribing the forcing by u_profile and v_profile'
	450	! CALL message( 'check_parameters', 'PA0347', 1, 2, 0, 6, 0 )
	451	! ENDIF
	452	!
	453	! use_prescribed_profile_data = .TRUE.
	454	!
	455	! npr_lev = 1
	456	! ! chem_sddpecies(lsp)%conc_pr_init(0) = 0.0_wp
	457	! DO lpr_lev = 1, nz+1
	458	! IF ( npr_lev < 100 ) THEN
	459	! DO WHILE ( cs_heights(lsp, npr_lev+1) <= zu(lpr_lev) )
	460	! npr_lev = npr_lev + 1
	461	! IF ( npr_lev == 100 ) EXIT
	462	! ENDDO
	463	! ENDIF
	464	!
	465	! IF ( npr_lev < 100 .AND. cs_heights(lsp, npr_lev + 1) /= 9999999.9_wp ) THEN
	466	! chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp, npr_lev) + &
	467	! ( zu(lpr_lev) - cs_heights(lsp, npr_lev) ) / &
	468	! ( cs_heights(lsp, npr_lev + 1) - cs_heights(lsp, npr_lev ) ) * &
	469	! ( cs_profile(lsp, npr_lev + 1) - cs_profile(lsp, npr_lev ) )
	470	! ELSE
	471	! chem_species(lsp)%conc_pr_init(lpr_lev) = cs_profile(lsp, npr_lev)
	472	! ENDIF
	473	! ENDDO
	474	! ENDIF
[2657]	475	!-- If a profile is prescribed explicity using cs_profiles and cs_heights, we then have to fill the
	476	!-- chem_species(lsp)%conc_pr_init for the specific "lsp" based on the cs_profiles(lsp_pr,:)
	477	!-- and cs_heights(lsp_pr,:).
	478	ENDIF
	479	ENDDO
	480	lsp_pr = lsp_pr + 1
	481	ENDDO
[2668]	482	! ELSE
[2657]	483	! IF (chem_debug1 ) print*,'code to be added for initializing_actions == read_restart_data' !bK
[2668]	484	! ENDIF
[2657]	485
	486	!-- Now, go back to chem_init and use the contents of chem_species(lsp)%conc_pr_init to
	487	!-- initialize the 3D conc arrays, as it is currently taken care of in chem_set_constant_values.
	488	!-- After initializing the 3D arrays, these can be used to set the boundary conditions in the
	489	!-- subroutine kchem_boundary_conds, which should be called from boundary_conds.f90.
	490
	491
	492	END SUBROUTINE chem_init_profiles
	493	!
	494	!------------------------------------------------------------------------------!
	495	!
	496	! Description:
	497	! ------------
	498	!> Subroutine initializating chemistry_model_mod
	499	!------------------------------------------------------------------------------!
	500	SUBROUTINE chem_init
	501
	502
	503	USE control_parameters, &
	504	ONLY: message_string, io_blocks, io_group, turbulent_inflow
	505
	506	USE arrays_3d, &
	507	ONLY: mean_inflow_profiles
	508
	509	USE pegrid
	510
	511	IMPLICIT none
	512	!-- local variables
	513	INTEGER :: i,j !< running index for for horiz numerical grid points
	514	INTEGER :: lsp !< running index for chem spcs
	515	INTEGER :: lpr_lev !< running index for chem spcs profile level
	516	!
	517	!-- NOPOINTER version not implemented yet
[2682]	518	! #if defined( __nopointer )
	519	! message_string = 'The chemistry module only runs with POINTER version'
	520	! CALL message( 'chemistry_model_mod', 'CM0001', 1, 2, 0, 6, 0 )
	521	! #endif
	522	!
	523	!-- Allocate memory for chemical species
	524	ALLOCATE( chem_species(nspec) )
	525	ALLOCATE( spec_conc_1 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	526	ALLOCATE( spec_conc_2 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	527	ALLOCATE( spec_conc_3 (nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	528	ALLOCATE( spec_conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nspec) )
	529	ALLOCATE( phot_frequen(nphot) )
	530	ALLOCATE( freq_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg,nphot) )
	531	ALLOCATE( bc_cs_t_val(nspec) )
	532	!
	533	!-- Initialize arrays
	534	spec_conc_1 (:,:,:,:) = 0.0_wp
	535	spec_conc_2 (:,:,:,:) = 0.0_wp
	536	spec_conc_3 (:,:,:,:) = 0.0_wp
	537	spec_conc_av(:,:,:,:) = 0.0_wp
[2657]	538
[2682]	539
[2657]	540	DO lsp = 1, nspec
	541	chem_species(lsp)%name = spc_names(lsp)
	542
	543	chem_species(lsp)%conc (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1 (:,:,:,lsp)
	544	chem_species(lsp)%conc_p (nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2 (:,:,:,lsp)
	545	chem_species(lsp)%tconc_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_3 (:,:,:,lsp)
	546	chem_species(lsp)%conc_av(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_av(:,:,:,lsp)
	547
	548	ALLOCATE (chem_species(lsp)%cssws_av(nysg:nyng,nxlg:nxrg))
[2682]	549	chem_species(lsp)%cssws_av = 0.0_wp
	550	!
	551	!-- (todo (FK): This needs to be revised. This block must go somewhere else)
[2657]	552	! IF ( ws_scheme_sca ) THEN
	553	ALLOCATE (chem_species(lsp)%flux_s_cs(nzb+1:nzt,0:threads_per_task-1))
	554	ALLOCATE (chem_species(lsp)%diss_s_cs(nzb+1:nzt,0:threads_per_task-1))
	555	ALLOCATE (chem_species(lsp)%flux_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
	556	ALLOCATE (chem_species(lsp)%diss_l_cs(nzb+1:nzt,nys:nyn,0:threads_per_task-1))
	557	chem_species(lsp)%flux_s_cs = 0.0_wp
	558	chem_species(lsp)%flux_l_cs = 0.0_wp
	559	chem_species(lsp)%diss_s_cs = 0.0_wp
	560	chem_species(lsp)%diss_l_cs = 0.0_wp
	561	! ENDIF
[2682]	562	!
	563	!-- Allocate memory for initial concentration profiles
	564	!-- (concentration values come from namelist)
	565	!-- (todo (FK): Because of this, chem_init is called in palm before
	566	!-- check_parameters, since conc_pr_init is used there.
	567	!-- We have to find another solution since chem_init should
	568	!-- eventually be called from init_3d_model!!)
	569	ALLOCATE ( chem_species(lsp)%conc_pr_init(0:nz+1) )
	570	chem_species(lsp)%conc_pr_init(:) = 0.0_wp
[2657]	571
	572	ENDDO
	573
	574	!
	575	!-- Set initial concentration of profiles prescribed by parameters cs_profile
	576	!-- and cs_heights in the namelist &chemistry_par
[2682]	577	!-- (todo (FK): chem_init_profiles not ready yet, has some bugs)
	578	! CALL chem_init_profiles
[2657]	579	!
	580	!-- Initialize model variables
	581
	582
	583	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
	584	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
	585
	586
	587	!-- First model run of a possible job queue.
	588	!-- Initial profiles of the variables must be computes.
	589	IF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
[2668]	590	! CALL location_message( 'initializing with 1D model profiles', .FALSE. )
[2657]	591	!
	592	! CALL init_1d_model ...... decide to call or not later !bK
	593
	594	!-- Transfer initial profiles to the arrays of the 3D model
	595	DO lsp = 1, nspec
	596	DO i = nxlg, nxrg
	597	DO j = nysg, nyng
	598	DO lpr_lev = 1, nz + 1
	599	chem_species(lsp)%conc(lpr_lev,j,i) = chem_species(lsp)%conc_pr_init(lpr_lev)
	600	ENDDO
	601	ENDDO
	602	ENDDO
	603	ENDDO
	604
	605	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
	606	THEN
[2668]	607	! CALL location_message( 'initializing with constant profiles', .FALSE. )
[2657]	608
	609
	610
	611	!-- Set initial horizontal velocities at the lowest computational grid
	612	!-- levels to zero in order to avoid too small time steps caused by the
	613	!-- diffusion limit in the initial phase of a run (at k=1, dz/2 occurs
	614	!-- in the limiting formula!).
	615
	616	DO lsp = 1, nspec
	617	DO i = nxlg, nxrg
	618	DO j = nysg, nyng
	619	chem_species(lsp)%conc(:,j,i) = chem_species(lsp)%conc_pr_init !ITS THERE bK
	620	ENDDO
	621	ENDDO
	622	ENDDO
	623
[2668]	624	! ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) &
	625	! THEN
	626	! CALL location_message( 'initializing by user', .FALSE. )
[2657]	627	!
	628	!-- Initialization will completely be done by the user
[2668]	629	!-- (FK: This should be called only once, in init_3d_model, i.e. remove it here)
	630	! CALL user_init_3d_model
	631	! CALL location_message( 'finished', .TRUE. )
[2657]	632
	633	ENDIF
	634
	635	!-- Store initial chem spcs profile
	636	! DO lsp = 1, nvar
	637	! hom_cs(:,1,115,:) = SPREAD( chem_species(lsp)%conc(:,nys,nxl), 2, statistic_regions+1 )
	638	! ENDDO
	639	!
	640	!-- If required, change the surface chem spcs at the start of the 3D run
	641	IF ( cs_surface_initial_change(1) /= 0.0_wp ) THEN
	642	DO lsp = 1, nspec
	643	chem_species(lsp)%conc(nzb,:,:) = chem_species(lsp)%conc(nzb,:,:) + &
	644	cs_surface_initial_change(lsp)
	645	ENDDO
	646	ENDIF
	647	!
	648	!-- Initiale old and new time levels.
	649	DO lsp = 1, nvar
	650	chem_species(lsp)%tconc_m = 0.0_wp
[2682]	651	chem_species(lsp)%conc_p = chem_species(lsp)%conc
[2657]	652	ENDDO
[2682]	653	! CALL location_message( 'finished', .TRUE. )
[2657]	654
[2682]	655	!
	656	!-- (todo (FK): Restarts not available yet. It is not correct to call
	657	!-- read_3d_binary here)
[2657]	658	ELSEIF ( TRIM( initializing_actions ) == 'read_restart_data' .OR. &
	659	TRIM( initializing_actions ) == 'cyclic_fill' ) &
	660	THEN
	661
[2682]	662	message_string = 'so far, restarts are not possible with chemistry'
	663	CALL message( 'chem_init', 'CM0002', 1, 2, 0, 6, 0 )
	664	! CALL location_message( 'initializing in case of restart / cyclic_fill', &
	665	! .FALSE. )
	666	! !
	667	! !-- When reading data for cyclic fill of 3D prerun data files, read
	668	! !-- some of the global variables from the restart file which are required
	669	! !-- for initializing the inflow
	670	! IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
	671	! DO i = 0, io_blocks-1
	672	! IF ( i == io_group ) THEN
	673	! CALL read_parts_of_var_list
	674	! CALL close_file( 13 )
	675	! ENDIF
	676	! #if defined( __parallel )
	677	! CALL MPI_BARRIER( comm2d, ierr )
	678	! #endif
	679	! ENDDO
	680	! ENDIF
	681	! !
	682	! !-- Read binary data from restart file
	683	! DO i = 0, io_blocks-1
	684	! IF ( i == io_group ) THEN
	685	! CALL read_3d_binary
	686	! ENDIF
	687	! #if defined( __parallel )
	688	! CALL MPI_BARRIER( comm2d, ierr )
	689	! #endif
	690	! ENDDO
	691	! !
	692	! !-- Initialization of the turbulence recycling method
	693	! IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. &
	694	! turbulent_inflow ) THEN
	695	! !
	696	! !-- First store the profiles to be used at the inflow.
	697	! !-- These profiles are the (temporally) and horizontally averaged vertical
	698	! !-- profiles from the prerun. Alternatively, prescribed profiles
	699	! !-- for u,v-components can be used.
	700	! ALLOCATE( mean_inflow_profiles(nzb:nzt+1,8) )
	701	! ! mean_inflow_profiles(:,8) = hom_sum(:,115,0) !cs
	702	!
	703	! ! IF ( inflow_l) THEN
	704	! ! DO j = nysg, nyng
	705	! ! DO k = nzb, nzt+1
	706	! ! DO lsp = 1, nvar
	707	! ! chem_species(lsp)%conc(k,j,nxlg:-1) = mean_inflow_profiles(k,8) ???
	708	! ! ENDDO
	709	! ! ENDDO
	710	! ! ENDDO
	711	! ! ENDIF
	712	! ENDIF
	713	!
	714	! !-- Inside buildings set velocities and TKE back to zero
	715	! ! IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. &
	716	! ! topography /= 'flat' ) THEN
	717	! ! ......
	718	! ! ENDIF
	719	! !
	720	! !-- Initialize new time levels (only done in order to set boundary values
	721	! !-- including ghost points)
	722	! DO lsp = 1, nvar
	723	! chem_species(lsp)%conc_p = chem_species(lsp)%conc
	724	! ENDDO
	725	! !
	726	! !-- Allthough tendency arrays are set in prognostic_equations, they have
	727	! !-- have to be predefined here because they are used (but multiplied with 0)
	728	! !-- there before they are set.
	729	!
	730	! DO lsp = 1, nvar
	731	! chem_species(lsp)%tconc_m = 0.0_wp
	732	! ENDDO
[2657]	733
	734	ELSE
	735	!
	736	!-- Actually this part of the programm should not be reached
	737	message_string = 'unknown initializing problem'
[2682]	738	CALL message( 'chem_init', 'CM0003', 1, 2, 0, 6, 0 )
[2657]	739	ENDIF
	740
[2682]	741
	742
[2657]	743	!--- new code add above this line
	744	DO lsp = 1, nphot
	745	phot_frequen(lsp)%name = phot_names(lsp)
	746	! IF( myid == 0 ) THEN
	747	! WRITE(6,'(a,i4,3x,a)') 'Photolysis: ',lsp,trim(phot_names(lsp))
	748	! ENDIF
	749	phot_frequen(lsp)%freq(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => freq_1(:,:,:,lsp)
	750	ENDDO
	751
	752	!-- Set initial values
	753	! Not required any more, this can now be done with the namelist by setting cs_surface
	754	! and cs_name without specifying cs_profile (Nevertheless, we still want to keep it for a while)
	755	! IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
	756	! CALL set_const_initial_values
	757	! ENDIF
[2682]	758
[2657]	759	RETURN
	760
	761	CONTAINS
	762	!------------------------------------------------------------------------------!
	763	!
	764	! Description:
	765	! ------------
	766	!> Subroutine setting constant initial values of chemical species
	767	!------------------------------------------------------------------------------!
	768	SUBROUTINE set_const_initial_values
	769	! Not required any more, this can now be done with the namelist by setting cs_surface
	770	! and cs_name without specifying cs_profile (Nevertheless, we still want to keep it for a while)
	771	IMPLICIT none
	772
	773	!-- local variables
	774	INTEGER :: lsp
	775
	776	IF(myid == 0) THEN
	777	write(6,'(/,a,/)') ' chemics >>>> Set constant Initial Values: '
	778	ENDIF
	779
	780	! Default values are taken from smog.def from supplied kpp example
	781	DO lsp = 1, nspec
	782	IF(trim(chem_species(lsp)%name) == 'NO') THEN
	783	! chem_species(lsp)%conc = 8.725*1.0E+08
	784	! chem_species(lsp)%conc = 0.05_wp !added by bK
	785	chem_species(lsp)%conc = 0.01_wp !added by RFo
	786	ELSEIF (trim(chem_species(lsp)%name) == 'NO2') THEN
	787	! chem_species(lsp)%conc = 2.240*1.0E+08
	788	! chem_species(lsp)%conc = 0.01_wp !added by bK
	789	chem_species(lsp)%conc = 0.05_wp !added by RFo
	790	ELSEIF( trim( chem_species(lsp)%name ) == 'O3' ) THEN
	791	chem_species(lsp)%conc = 0.05_wp !added by bK
	792	ELSEIF(trim(chem_species(lsp)%name) == 'H2O') THEN
	793	! chem_species(lsp)%conc = 5.326*1.0E+11
	794	chem_species(lsp)%conc = 1.30*1.0E+4_wp !added by bK
	795	ELSEIF(trim(chem_species(lsp)%name) == 'O2') THEN
	796	chem_species(lsp)%conc = 2.0*1.0E+5_wp !added by bK
	797	ELSEIF(trim(chem_species(lsp)%name) == 'RH') THEN
	798	chem_species(lsp)%conc = 0.001_wp !added by RFo
	799	ELSEIF(trim(chem_species(lsp)%name) == 'CO') THEN
	800	chem_species(lsp)%conc = 0.5_wp !added by RFo
	801	ELSEIF(trim(chem_species(lsp)%name) == 'RCHO') THEN
	802	! chem_species(lsp)%conc = 2.0_wp !added by bK
	803	chem_species(lsp)%conc = 0.01_wp !added by RFo
	804	! ELSEIF(trim(chem_species(lsp)%name) == 'OH') THEN
	805	! chem_species(lsp)%conc = 1.0*1.0E-07_wp !added by bK
	806	! ELSEIF(trim(chem_species(lsp)%name) == 'HO2') THEN
	807	! chem_species(lsp)%conc = 1*1.0E-7_wp !added by bK
	808	! ELSEIF(trim(chem_species(lsp)%name) == 'RCOO2') THEN ! corrected RFo
	809	! chem_species(lsp)%conc = 1.0*1.0E-7_wp !added by bK
	810	! ELSEIF(trim(chem_species(lsp)%name) == 'RCOO2NO2') THEN
	811	! chem_species(lsp)%conc = 1.0*1.0E-7_wp !added by bK
	812	ELSE
	813	! H2O = 2.0e+04;
	814	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) = 0.0_wp
	815	ENDIF
	816
	817	IF(myid == 0) THEN
[2768]	818	WRITE(6,'(a,3x,a,3x,a,e12.4)') ' Species: ',chem_species(lsp)%name(1:7),' &
	819	Initial Value = ',chem_species(lsp)%conc(nzb,nysg,nxlg)
[2657]	820	ENDIF
	821	ENDDO
	822
	823	! #if defined( __nopointer )
	824	! !kk Hier mit message abbrechen
	825	! if(myid == 0) then
	826	! write(6,*) ' KPP does only run with POINTER Version'
	827	! end if
	828	! stop 'error'
	829	! #endif
	830
	831	RETURN
	832	END SUBROUTINE set_const_initial_values
	833
	834
	835	END SUBROUTINE chem_init
	836	!
	837	!------------------------------------------------------------------------------!
	838	!
	839	! Description:
	840	! ------------
	841	!> Subroutine defining parin for &chemistry_par for chemistry model
	842	!------------------------------------------------------------------------------!
	843	SUBROUTINE chem_parin
[2682]	844
[2657]	845	USE control_parameters, &
	846	ONLY: air_chemistry
[2682]	847
[2657]	848	USE chem_modules
[2682]	849
	850	USE kinds
[2657]	851
	852	IMPLICIT none
	853
[2682]	854	CHARACTER (LEN=80) :: line !< dummy string that contains the current line of the parameter file
	855
	856	REAL(wp), DIMENSION(nmaxfixsteps) :: my_steps !< List of fixed timesteps my_step(1) = 0.0 automatic stepping
[2657]	857
[2668]	858	NAMELIST /chemistry_par/ bc_cs_b, &
	859	bc_cs_t, &
	860	call_chem_at_all_substeps, &
	861	chem_debug0, &
	862	chem_debug1, &
	863	chem_debug2, &
	864	chem_gasphase_on, &
	865	cs_heights, &
	866	cs_name, &
	867	cs_profile, &
	868	cs_profile_name, &
	869	cs_surface, &
	870	emiss_factor_main, &
	871	emiss_factor_side, &
	872	icntrl, &
	873	main_street_id, &
[2678]	874	max_street_id, &
[2668]	875	my_steps, &
	876	rcntrl, &
	877	side_street_id, &
	878	photolysis_scheme, &
	879	wall_csflux, &
	880	cs_vertical_gradient, &
	881	top_csflux, &
	882	surface_csflux, &
[2678]	883	surface_csflux_name, &
[2668]	884	cs_surface_initial_change, &
	885	cs_vertical_gradient_level
[2657]	886
	887	!-- analogue to chem_names(nspj) we could invent chem_surfaceflux(nspj) and chem_topflux(nspj)
	888	!-- so this way we could prescribe a specific flux value for each species
	889	!> chemistry_par for initial profiles
	890	!> cs_names = 'O3', 'NO2', 'NO', ... to set initial profiles)
	891	!> cs_heights(1,:) = 0.0, 100.0, 500.0, 2000.0, .... (height levels where concs will be prescribed for O3)
	892	!> cs_heights(2,:) = 0.0, 200.0, 400.0, 1000.0, .... (same for NO2 etc.)
	893	!> cs_profiles(1,:) = 10.0, 20.0, 20.0, 30.0, ..... (chem spcs conc at height lvls chem_heights(1,:)) etc.
	894	!> If the respective concentration profile should be constant with height, then use "cs_surface( number of spcs)"
	895	!> then write these cs_surface values to chem_species(lsp)%conc_pr_init(:)
	896
[2668]	897	!
	898	!-- Read chem namelist
	899	!-- (todo: initialize these parameters in declaration part, do this for
	900	!-- all chemistry_par namelist parameters)
[2657]	901	icntrl = 0
	902	rcntrl = 0.0_wp
	903	my_steps = 0.0_wp
	904	icntrl(2) = 1
	905	photolysis_scheme = 'simple'
	906	atol = 1.0_wp
	907	rtol = 0.01_wp
	908	!
	909	!-- Try to find chemistry package
	910	REWIND ( 11 )
	911	line = ' '
	912	DO WHILE ( INDEX( line, '&chemistry_par' ) == 0 )
[2668]	913	READ ( 11, '(A)', END=10 ) line
[2657]	914	ENDDO
	915	BACKSPACE ( 11 )
	916	!
[2668]	917	!-- Read chemistry namelist
[2657]	918	READ ( 11, chemistry_par )
[2668]	919	!
	920	!-- Enable chemistry model
	921	air_chemistry = .TRUE.
[2657]	922
[2668]	923	!
	924	!-- FK: Not in use/needed (yet), since chemistry_par namelist is always read in
	925	! IF ( TRIM( initializing_actions ) == 'read_restart_data' ) THEN
	926	! CALL chem_read_var_list
	927	! ENDIF
	928
[2657]	929	10 CONTINUE
	930
[2668]	931	t_steps = my_steps !(todo: Why not directly make t_steps a
	932	! namelist parameter?)
[2657]	933
	934	END SUBROUTINE chem_parin
	935
	936	!
	937	!------------------------------------------------------------------------------!
	938	!
	939	! Description:
	940	! ------------
	941	!> Subroutine to integrate chemical species in the given chemical mechanism
	942	!------------------------------------------------------------------------------!
	943
	944	SUBROUTINE chem_integrate_ij (i, j)
	945
	946	USE cpulog, &
	947	ONLY: cpu_log, log_point
	948	USE statistics, & ! ## RFo
	949	ONLY: weight_pres
	950	USE control_parameters, & ! ## RFo
	951	ONLY: dt_3d, intermediate_timestep_count
	952
	953	IMPLICIT none
	954	INTEGER,INTENT(IN) :: i,j
	955
	956	!-- local variables
	957	INTEGER(iwp) :: lsp !< running index for chem spcs.
	958	INTEGER(iwp) :: lph !< running index for photolysis frequencies
	959	INTEGER :: k,m,istatf
	960	INTEGER,dimension(20) :: istatus
	961	REAL(kind=wp),dimension(nzb+1:nzt,nspec) :: tmp_conc
	962	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_temp
	963	REAL(kind=wp),dimension(nzb+1:nzt,nphot) :: tmp_phot
	964	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_fact
	965	REAL(kind=wp),dimension(nzb+1:nzt) :: tmp_fact_i !< conversion factor between molecules cm^{-3} and ppm
	966	REAL(wp) :: conv !< conversion factor
	967	REAL(wp), PARAMETER :: ppm2fr = 1.0e-6_wp !< Conversion factor ppm to fraction
	968	REAL(wp), PARAMETER :: pref_i = 1._wp / 100000.0_wp !< inverse reference pressure (1/Pa)
	969	REAL(wp), PARAMETER :: t_std = 273.15_wp !< standard pressure (Pa)
	970	REAL(wp), PARAMETER :: p_std = 101325.0_wp !< standard pressure (Pa)
	971	REAL(wp), PARAMETER :: r_cp = 0.286_wp !< R / cp (exponent for potential temperature)
	972	REAL(wp), PARAMETER :: vmolcm = 22.414e3_wp !< Mole volume (22.414 l) in cm^{-3}
	973	REAL(wp), PARAMETER :: xna = 6.022e23_wp !< Avogadro number (molecules/mol)
	974
	975
	976	REAL(kind=wp) :: dt_chem
	977
	978	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'start' )
	979	!< Set chem_gasphase_on to .FALSE. if you want to skip computation of gas phase chemistry
	980	IF (chem_gasphase_on) THEN
	981
	982	tmp_temp(:) = pt(:,j,i) * ( hyp(nzb+1:nzt) / 100000.0_wp )**0.286_wp
	983	! ppm to molecules/cm**3
	984	! tmp_fact = 1.e-6_wp6.022e23_wp/(22.414_wp1000._wp) * 273.15_wp * hyp(nzb+1:nzt)/( 101300.0_wp * tmp_temp )
	985	conv = ppm2fr * xna / vmolcm
	986	tmp_fact(:) = conv * t_std * hyp(nzb+1:nzt) / (tmp_temp(:) * p_std)
	987	tmp_fact_i = 1.0_wp/tmp_fact
	988
	989	CALL fill_temp (istatf, tmp_temp) !< Load constant temperature into kpp context
	990	! CALL fill_temp (istatf, pt(nzb+1:nzt,j,i)) !< Load temperature into kpp context
	991
	992	DO lsp = 1,nspec
	993	tmp_conc(:,lsp) = chem_species(lsp)%conc(nzb+1:nzt,j,i) * tmp_fact(:)
	994	ENDDO
	995
	996	DO lph = 1,nphot
	997	tmp_phot(:,lph) = phot_frequen(lph)%freq(nzb+1:nzt,j,i)
	998	ENDDO
	999
	1000	IF(myid == 0 .AND. chem_debug0 ) THEN
	1001	IF (i == 10 .and. j == 10) WRITE(0,*) 'begin chemics step ',dt_3d
	1002	ENDIF
	1003
	1004	!-- Compute length of time step # RFo
	1005	IF ( call_chem_at_all_substeps ) THEN
	1006	dt_chem = dt_3d * weight_pres(intermediate_timestep_count)
	1007	ELSE
	1008	dt_chem = dt_3d
	1009	ENDIF
	1010
	1011	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'start' )
	1012
	1013
	1014	CALL chem_gasphase_integrate (dt_chem, tmp_conc, tmp_temp, tmp_phot, istatus=istatus)
	1015
	1016
	1017	CALL cpu_log( log_point(81), '{chem_gasphase_integrate}', 'stop' )
	1018
	1019	DO lsp = 1,nspec
	1020	chem_species(lsp)%conc (nzb+1:nzt,j,i) = tmp_conc(:,lsp) * tmp_fact_i(:) ! RFo
	1021	ENDDO
	1022
	1023	! IF (myid == 0 .AND. chem_debug2 ) THEN
	1024	! IF (i == 10 .and. j == 10) WRITE(6,'(a,8i7)') ' KPP Status ',istatus(1:8)
	1025	! write(6,'(a,8i7)') ' KPP Status ',istatus(1:8)
	1026	! ENDIF
	1027
	1028	ENDIF
	1029	CALL cpu_log( log_point(80), '[chem_integrate_ij]', 'stop' )
	1030
	1031	RETURN
	1032	END SUBROUTINE chem_integrate_ij
	1033	!
	1034	!------------------------------------------------------------------------------!
	1035	!
	1036	! Description:
	1037	! ------------
	1038	!> Subroutine for swapping of timelevels for chemical species
	1039	!> called out from subroutine swap_timelevel
	1040	!------------------------------------------------------------------------------!
	1041
	1042	SUBROUTINE chem_swap_timelevel (level)
	1043	IMPLICIT none
	1044
	1045	INTEGER,INTENT(IN) :: level
	1046
	1047	!-- local variables
	1048
	1049	INTEGER :: lsp
	1050
	1051	! print,' entering chem_swap_timelevel *) '
	1052	if(level == 0) then
	1053	do lsp=1, nvar
	1054	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
	1055	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
	1056	end do
	1057	else
	1058	do lsp=1, nvar
	1059	chem_species(lsp)%conc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_2(:,:,:,lsp)
	1060	chem_species(lsp)%conc_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg) => spec_conc_1(:,:,:,lsp)
	1061	end do
	1062	end if
	1063
	1064	RETURN
	1065	END SUBROUTINE chem_swap_timelevel
	1066
	1067	!------------------------------------------------------------------------------!
	1068	!
	1069	! Description:
	1070	! ------------
	1071	!> Subroutine defining appropriate grid for netcdf variables.
	1072	!> It is called out from subroutine netcdf.
	1073	!------------------------------------------------------------------------------!
	1074	SUBROUTINE chem_define_netcdf_grid( var, found, grid_x, grid_y, grid_z )
	1075
	1076	IMPLICIT NONE
	1077
	1078	CHARACTER (LEN=*), INTENT(IN) :: var !<
	1079	LOGICAL, INTENT(OUT) :: found !<
	1080	CHARACTER (LEN=*), INTENT(OUT) :: grid_x !<
	1081	CHARACTER (LEN=*), INTENT(OUT) :: grid_y !<
	1082	CHARACTER (LEN=*), INTENT(OUT) :: grid_z !<
	1083
	1084	found = .TRUE.
	1085
	1086	if(var(1:3) == 'kc_') then !< always the same grid for chemistry variables
	1087	grid_x = 'x'
	1088	grid_y = 'y'
	1089	grid_z = 'zu' !< kk Use same z axis as u variables. Has to be checked if OK
	1090	else
	1091	found = .FALSE.
	1092	grid_x = 'none'
	1093	grid_y = 'none'
	1094	grid_z = 'none'
	1095	end if
	1096
	1097	! write(6,*) 'chem_define_netcdf_grid ',TRIM(var),' ',trim(grid_x),' ',found
	1098
	1099	END SUBROUTINE chem_define_netcdf_grid
	1100	!
	1101	!------------------------------------------------------------------------------!
	1102	!
	1103	! Description:
	1104	! ------------
	1105	!> Subroutine for checking data output for chemical species
	1106	!------------------------------------------------------------------------------!
	1107
	1108	SUBROUTINE chem_check_data_output( var, unit, i, ilen, k )
	1109
	1110
	1111	USE control_parameters, &
	1112	ONLY: data_output, message_string
	1113
	1114	IMPLICIT NONE
	1115
	1116	CHARACTER (LEN=*) :: unit !<
	1117	CHARACTER (LEN=*) :: var !<
	1118
	1119	INTEGER(iwp) :: i, lsp
	1120	INTEGER(iwp) :: ilen
	1121	INTEGER(iwp) :: k
	1122
	1123	CHARACTER(len=16) :: spec_name
	1124
	1125	unit = 'illegal'
	1126
	1127	spec_name = TRIM(var(4:)) !< var 1:3 is 'kc_'.
	1128
	1129	DO lsp=1,nspec
	1130	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
	1131	unit = 'ppm'
	1132	ENDIF
	1133	! It is possible to plant PM10 and PM25 into the gasphase chemistry code
	1134	! ! as passive species (e.g. 'passive' in GASPHASE_PREPROC/mechanisms):
	1135	! ! set unit to micrograms per m**3 for PM10 and PM25 (PM2.5)
	1136	IF (spec_name(1:2) == 'PM') THEN
	1137	unit = 'ug m-3'
	1138	ENDIF
	1139	ENDDO
	1140
	1141	DO lsp=1,nphot
	1142	IF (TRIM(spec_name) == TRIM(phot_frequen(lsp)%name)) THEN
	1143	unit = 'sec-1'
	1144	ENDIF
	1145	ENDDO
	1146
	1147
	1148	RETURN
	1149	END SUBROUTINE chem_check_data_output
	1150	!
	1151	!------------------------------------------------------------------------------!
	1152	!
	1153	! Description:
	1154	! ------------
	1155	!> Subroutine for checking data output of profiles for chemistry model
	1156	!------------------------------------------------------------------------------!
	1157
	1158	SUBROUTINE chem_check_data_output_pr( variable, var_count, unit, dopr_unit )
	1159
	1160
	1161	USE arrays_3d, &
	1162	ONLY: zu
	1163
	1164	USE control_parameters, &
	1165	ONLY: data_output_pr, message_string, air_chemistry
	1166
	1167	USE indices
	1168
	1169	USE profil_parameter
	1170
	1171	USE statistics
	1172
	1173
	1174	IMPLICIT NONE
	1175
	1176	CHARACTER (LEN=*) :: unit !<
	1177	CHARACTER (LEN=*) :: variable !<
	1178	CHARACTER (LEN=*) :: dopr_unit
	1179	CHARACTER(len=16) :: spec_name
	1180
	1181	INTEGER(iwp) :: var_count, lsp !<
	1182
	1183
	1184	spec_name = TRIM(variable(4:))
	1185	! write(9,*) 'fm #32 .. air_chemistry ', air_chemistry
	1186
	1187	IF ( .NOT. air_chemistry ) THEN
	1188	message_string = 'data_output_pr = ' // &
	1189	TRIM( data_output_pr(var_count) ) // ' is not imp' // &
	1190	'lemented for air_chemistry = .FALSE.'
	1191	! CALL message( 'check_parameters', 'PA0185', 1, 2, 0, 6, 0 )
	1192	ELSE
	1193	DO lsp = 1, nspec
	1194	IF (TRIM( spec_name ) == TRIM( chem_species(lsp)%name ) ) THEN
	1195	dopr_index(var_count) = 900
	1196	dopr_unit = 'ppm'
	1197	hom(:,2,900,:) = SPREAD( zu, 2, statistic_regions+1 )
	1198	ENDIF
	1199	ENDDO
	1200	ENDIF
	1201
	1202	END SUBROUTINE chem_check_data_output_pr
	1203	!
	1204	!------------------------------------------------------------------------------!
	1205	!
	1206	! Description:
	1207	! ------------
	1208	!> Subroutine defining 3D output variables for chemical species
	1209	!------------------------------------------------------------------------------!
	1210
	1211
[2756]	1212	SUBROUTINE chem_data_output_3d( av, variable, found, local_pf, fill_value )
[2657]	1213
	1214
	1215	USE indices
	1216
	1217	USE kinds
	1218
	1219
	1220	IMPLICIT NONE
	1221
	1222	CHARACTER (LEN=*) :: variable !<
	1223	LOGICAL :: found !<
	1224	INTEGER(iwp) :: av !<
	1225
[2756]	1226	REAL(wp) :: fill_value !<
	1227	REAL(sp), DIMENSION(nxl:nxr,nys:nyn,nzb:nzt+1) :: local_pf
	1228
	1229
[2657]	1230	!-- local variables
	1231
	1232	INTEGER :: i, j, k, lsp
	1233	CHARACTER(len=16) :: spec_name
	1234
	1235
	1236	found = .FALSE.
	1237
	1238	spec_name = TRIM(variable(4:))
	1239	!av == 0
	1240
	1241	DO lsp=1,nspec
	1242	IF (TRIM(spec_name) == TRIM(chem_species(lsp)%name)) THEN
[2768]	1243	IF(myid == 0 .AND. chem_debug0 ) WRITE(6,*) 'Output of species ',TRIM(variable),' &
	1244	',TRIM(chem_species(lsp)%name)
[2657]	1245
	1246	IF (av == 0) THEN
	1247	DO i = nxl, nxr
	1248	DO j = nys, nyn
	1249	DO k = nzb, nzt+1
[2756]	1250	local_pf(i,j,k) = MERGE( &
	1251	chem_species(lsp)%conc(k,j,i), &
	1252	REAL( fill_value, KIND = wp ), &
	1253	BTEST( wall_flags_0(k,j,i), 0 ) )
[2657]	1254	ENDDO
	1255	ENDDO
	1256	ENDDO
	1257
	1258	ELSE
	1259	DO i = nxl, nxr
	1260	DO j = nys, nyn
	1261	DO k = nzb, nzt+1
[2756]	1262	local_pf(i,j,k) = MERGE( &
	1263	chem_species(lsp)%conc_av(k,j,i),&
	1264	REAL( fill_value, KIND = wp ), &
	1265	BTEST( wall_flags_0(k,j,i), 0 ) )
[2657]	1266	ENDDO
	1267	ENDDO
	1268	ENDDO
	1269	ENDIF
	1270
	1271	found = .TRUE.
	1272	ENDIF
	1273	ENDDO
	1274
	1275	RETURN
	1276	END SUBROUTINE chem_data_output_3d
	1277	!
	1278	!------------------------------------------------------------------------------!
	1279	!
	1280	! Description:
	1281	! ------------
	1282	!> Subroutine for averaging 3D data of chemical species
	1283	!------------------------------------------------------------------------------!
	1284
	1285	SUBROUTINE chem_3d_data_averaging ( mode, variable )
	1286
	1287	USE control_parameters
	1288
	1289	USE indices
	1290
	1291	USE kinds
	1292
	1293	USE surface_mod, &
	1294	ONLY: surf_def_h, surf_lsm_h, surf_usm_h
	1295
	1296	IMPLICIT NONE
	1297
	1298	CHARACTER (LEN=*) :: mode !<
	1299	CHARACTER (LEN=*) :: variable !<
	1300
	1301
	1302	INTEGER(iwp) :: i !< grid index x direction
	1303	INTEGER(iwp) :: j !< grid index y direction
	1304	INTEGER(iwp) :: k !< grid index z direction
	1305	INTEGER(iwp) :: m !< running index surface type
	1306	INTEGER(iwp) :: lsp !< running index for chem spcs
	1307	INTEGER(iwp) :: lsp_2 !< it looks like redundent .. will be delted ..bK
	1308
	1309	IF ( mode == 'allocate' ) THEN
	1310	DO lsp = 1, nspec
	1311	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	1312	! lsp_2 = lsp
	1313	chem_species(lsp)%conc_av = 0.0_wp
	1314
	1315	ENDIF
	1316	ENDDO
	1317
	1318	ELSEIF ( mode == 'sum' ) THEN
	1319
	1320	DO lsp = 1, nspec
	1321	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	1322	! lsp_2 = lsp
	1323	DO i = nxlg, nxrg
	1324	DO j = nysg, nyng
	1325	DO k = nzb, nzt+1
	1326	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) + &
	1327	chem_species(lsp)%conc(k,j,i)
	1328	ENDDO
	1329	ENDDO
	1330	ENDDO
	1331	ELSEIF ( TRIM(variable(4:)) == TRIM('cssws*') ) THEN
	1332	DO m = 1, surf_def_h(0)%ns
	1333	i = surf_def_h(0)%i(m)
	1334	j = surf_def_h(0)%j(m)
	1335	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) + surf_def_h(0)%cssws(lsp,m)
	1336	ENDDO
	1337	DO m = 1, surf_lsm_h%ns
	1338	i = surf_lsm_h%i(m)
	1339	j = surf_lsm_h%j(m)
	1340	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) + surf_lsm_h%cssws(lsp,m)
	1341	ENDDO
	1342	DO m = 1, surf_usm_h%ns
	1343	i = surf_usm_h%i(m)
	1344	j = surf_usm_h%j(m)
	1345	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) + surf_usm_h%cssws(lsp,m)
	1346	ENDDO
	1347
	1348	ENDIF
	1349	ENDDO
	1350
	1351	ELSEIF ( mode == 'average' ) THEN
	1352	DO lsp = 1, nspec
	1353	IF (TRIM(variable(4:)) == TRIM(chem_species(lsp)%name)) THEN
	1354	! lsp_2 = lsp
	1355	DO i = nxlg, nxrg
	1356	DO j = nysg, nyng
	1357	DO k = nzb, nzt+1
	1358	chem_species(lsp)%conc_av(k,j,i) = chem_species(lsp)%conc_av(k,j,i) / REAL( average_count_3d, KIND=wp )
	1359	ENDDO
	1360	ENDDO
	1361	ENDDO
	1362
	1363	ELSEIF (TRIM(variable(4:)) == TRIM('cssws*') ) THEN
	1364	DO i = nxlg, nxrg
	1365	DO j = nysg, nyng
	1366	chem_species(lsp)%cssws_av(j,i) = chem_species(lsp)%cssws_av(j,i) / REAL( average_count_3d, KIND=wp )
	1367	ENDDO
	1368	ENDDO
	1369	CALL exchange_horiz_2d( chem_species(lsp)%cssws_av, nbgp )
	1370	ENDIF
	1371	ENDDO
	1372
	1373	ENDIF
	1374
	1375	END SUBROUTINE chem_3d_data_averaging
	1376
	1377	!------------------------------------------------------------------------------!
	1378	!
	1379	! Description:
	1380	! ------------
	1381	!> Subroutine to write restart data for chemistry model
	1382	!------------------------------------------------------------------------------!
[2668]	1383	SUBROUTINE chem_last_actions
[2657]	1384
	1385
	1386	USE control_parameters
	1387
	1388	USE kinds
	1389
	1390	IMPLICIT NONE
	1391
	1392	INTEGER(iwp) :: lsp !<
[2668]	1393	CHARACTER(LEN=20) :: cspcs_name
	1394	CHARACTER(LEN=20) :: cspcs_name_av
[2657]	1395	! REAL(kind=wp), DIMENSION(nzb:nzt+1,nysg:nyng,nxlg:nxrg) :: chems_conc
	1396
	1397	IF ( write_binary ) THEN
[2668]	1398	DO lsp = 1, nspec
	1399	cspcs_name = ' '
	1400	cspcs_name_av = ' '
	1401	cspcs_name = TRIM(chem_species(lsp)%name)
	1402	cspcs_name_av = TRIM(chem_species(lsp)%name)//'_av'
	1403
[2657]	1404	WRITE(14) cspcs_name ; WRITE(14) chem_species(lsp)%conc
	1405	WRITE(14) cspcs_name_av; WRITE(14) chem_species(lsp)%conc_av
	1406	ENDDO
	1407
[2668]	1408	WRITE ( 14 ) '* end chem * '
[2657]	1409
	1410	ENDIF
	1411
[2668]	1412	END SUBROUTINE chem_last_actions
[2657]	1413
	1414	!------------------------------------------------------------------------------!
	1415	!
	1416	! Description:
	1417	! ------------
	1418	!> Subroutine to read restart data of chemical species
	1419	!------------------------------------------------------------------------------!
	1420
[2668]	1421	SUBROUTINE chem_read_restart_data( i, nxlfa, nxl_on_file, nxrfa, nxr_on_file, &
	1422	nynfa, nyn_on_file, nysfa, nys_on_file, &
	1423	offset_xa, offset_ya, overlap_count, tmp_2d, tmp_3d)
[2657]	1424
	1425	USE control_parameters
	1426
	1427	USE indices
	1428
	1429	USE kinds
	1430
	1431	USE pegrid
	1432
	1433	IMPLICIT NONE
	1434
	1435	CHARACTER (LEN=20) :: field_char !<
	1436	CHARACTER (LEN=20) :: spc_name_av !<
	1437
	1438	INTEGER(iwp) :: i, lsp !<
	1439	INTEGER(iwp) :: k !<
	1440	INTEGER(iwp) :: nxlc !<
	1441	INTEGER(iwp) :: nxlf !<
	1442	INTEGER(iwp) :: nxl_on_file !<
	1443	INTEGER(iwp) :: nxrc !<
	1444	INTEGER(iwp) :: nxrf !<
	1445	INTEGER(iwp) :: nxr_on_file !<
	1446	INTEGER(iwp) :: nync !<
	1447	INTEGER(iwp) :: nynf !<
	1448	INTEGER(iwp) :: nyn_on_file !<
	1449	INTEGER(iwp) :: nysc !<
	1450	INTEGER(iwp) :: nysf !<
	1451	INTEGER(iwp) :: nys_on_file !<
	1452	INTEGER(iwp) :: overlap_count !<
	1453
	1454	INTEGER(iwp), DIMENSION(numprocs_previous_run,1000) :: nxlfa !<
	1455	INTEGER(iwp), DIMENSION(numprocs_previous_run,1000) :: nxrfa !<
	1456	INTEGER(iwp), DIMENSION(numprocs_previous_run,1000) :: nynfa !<
	1457	INTEGER(iwp), DIMENSION(numprocs_previous_run,1000) :: nysfa !<
	1458	INTEGER(iwp), DIMENSION(numprocs_previous_run,1000) :: offset_xa !<
	1459	INTEGER(iwp), DIMENSION(numprocs_previous_run,1000) :: offset_ya !<
	1460	!!
	1461	REAL(wp), DIMENSION(nys_on_file-nbgp:nyn_on_file+nbgp, & !< 2D array to temp store data
	1462	nxl_on_file-nbgp:nxr_on_file+nbgp) :: tmp_2d !<
	1463	REAL(wp), DIMENSION(nzb:nzt+1,nys_on_file-nbgp:nyn_on_file+nbgp, & !<
	1464	nxl_on_file-nbgp:nxr_on_file+nbgp) :: tmp_3d !< 3D array to temp store data
	1465
	1466
	1467	IF ( initializing_actions == 'read_restart_data' ) THEN
	1468	READ ( 13 ) field_char
	1469
	1470	DO WHILE ( TRIM( field_char ) /= '* end chem *')
	1471	DO k = 1, overlap_count
	1472	nxlf = nxlfa(i,k)
	1473	nxlc = nxlfa(i,k) + offset_xa(i,k)
	1474	nxrf = nxrfa(i,k)
	1475	nxrc = nxrfa(i,k) + offset_xa(i,k)
	1476	nysf = nysfa(i,k)
	1477	nysc = nysfa(i,k) + offset_ya(i,k)
	1478	nynf = nynfa(i,k)
	1479	nync = nynfa(i,k) + offset_ya(i,k)
	1480
[2668]	1481	DO lsp = 1, nspec
[2657]	1482	spc_name_av = TRIM(chem_species(lsp)%name)//'_av'
[2668]	1483	IF (TRIM( field_char ) == TRIM(chem_species(lsp)%name) ) THEN
[2657]	1484	IF ( k == 1 ) READ ( 13 ) tmp_3d !< read data into tmp_3d
	1485	chem_species(lsp)%conc = tmp_3d !< fill ..%conc in the restart run
	1486	ELSEIF (TRIM( field_char ) == spc_name_av ) THEN
	1487	IF( k == 1 ) READ ( 13 ) tmp_3d
	1488	chem_species(lsp)%conc_av = tmp_3d
	1489	ENDIF
	1490
	1491	ENDDO
	1492
	1493	ENDDO
	1494
	1495	READ ( 13 ) field_char
	1496
	1497	ENDDO
	1498
[2668]	1499	! IF (TRIM( field_char ) == TRIM('surface_csflux') ) THEN
	1500	! READ ( 13 ) surface_csflux
	1501	! ENDIF
[2657]	1502
	1503	ENDIF
	1504
[2668]	1505	END SUBROUTINE chem_read_restart_data
[2657]	1506	!
	1507	!------------------------------------------------------------------------------!
	1508	!
	1509	! Description:
	1510	! ------------
	1511	!> Subroutine calculating tendencies for chemical species
	1512	!------------------------------------------------------------------------------!
	1513
[2768]	1514	SUBROUTINE chem_tendency ( cs_scalar_p, cs_scalar, tcs_scalar_m, pr_init_cs, &
	1515	i, j, i_omp_start, tn, ilsp, flux_s_cs, diss_s_cs, &
	1516	flux_l_cs, diss_l_cs )
[2657]	1517	USE pegrid
	1518	USE advec_ws, ONLY: advec_s_ws
	1519	USE advec_s_pw_mod, ONLY: advec_s_pw
	1520	USE advec_s_up_mod, ONLY: advec_s_up
	1521	USE diffusion_s_mod, ONLY: diffusion_s
	1522	USE indices, ONLY: wall_flags_0
[2768]	1523	USE surface_mod, ONLY: surf_def_h, surf_def_v, surf_lsm_h, surf_lsm_v, surf_usm_h, &
	1524	surf_usm_v
[2657]	1525	!> Only one chem_spcs recieved prog_eqns at time.
	1526	!> cem_tendency is called in prog_eqns over loop => nvar
	1527
	1528	IMPLICIT NONE
	1529
[2768]	1530	REAL(wp), DIMENSION(:,:,:), POINTER :: cs_scalar_p, cs_scalar, tcs_scalar_m
[2657]	1531
	1532	INTEGER(iwp),INTENT(IN) :: i, j, i_omp_start, tn, ilsp
	1533	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: flux_s_cs !<
	1534	REAL(wp), DIMENSION(nzb+1:nzt,0:threads_per_task-1) :: diss_s_cs !<
	1535	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: flux_l_cs !<
	1536	REAL(wp), DIMENSION(nzb+1:nzt,nys:nyn,0:threads_per_task-1) :: diss_l_cs !<
	1537	REAL(wp), DIMENSION(0:nz+1) :: pr_init_cs !<
	1538
	1539	!-- local variables
	1540
	1541	INTEGER :: k
	1542	!
	1543	!-- Tendency-terms for chem spcs.
	1544	tend(:,j,i) = 0.0_wp
	1545	!
	1546	!-- Advection terms
	1547	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	1548	IF ( ws_scheme_sca ) THEN
	1549	CALL advec_s_ws( i, j, cs_scalar, 'kc', flux_s_cs, diss_s_cs, &
	1550	flux_l_cs, diss_l_cs, i_omp_start, tn )
	1551	ELSE
	1552	CALL advec_s_pw( i, j, cs_scalar )
	1553	ENDIF
	1554	ELSE
	1555	CALL advec_s_up( i, j, cs_scalar )
	1556	ENDIF
	1557
	1558	!
	1559
	1560	!-- Diffusion terms ( ie hinteren 3 sind 0 )
	1561
	1562	CALL diffusion_s( i, j, cs_scalar, &
	1563	surf_def_h(0)%cssws(ilsp,:), surf_def_h(1)%cssws(ilsp,:), &
	1564	surf_def_h(2)%cssws(ilsp,:), &
	1565	surf_lsm_h%cssws(ilsp,:), surf_usm_h%cssws(ilsp,:), &
	1566	surf_def_v(0)%cssws(ilsp,:), surf_def_v(1)%cssws(ilsp,:), &
	1567	surf_def_v(2)%cssws(ilsp,:), surf_def_v(3)%cssws(ilsp,:), &
	1568	surf_lsm_v(0)%cssws(ilsp,:), surf_lsm_v(1)%cssws(ilsp,:), &
	1569	surf_lsm_v(2)%cssws(ilsp,:), surf_lsm_v(3)%cssws(ilsp,:), &
	1570	surf_usm_v(0)%cssws(ilsp,:), surf_usm_v(1)%cssws(ilsp,:), &
	1571	surf_usm_v(2)%cssws(ilsp,:), surf_usm_v(3)%cssws(ilsp,:) )
	1572
	1573	!
	1574	!-- Prognostic equation for chem spcs
	1575	DO k = nzb+1, nzt
	1576	cs_scalar_p(k,j,i) = cs_scalar(k,j,i) + ( dt_3d * &
	1577	( tsc(2) * tend(k,j,i) + &
	1578	tsc(3) * tcs_scalar_m(k,j,i) ) &
	1579	- tsc(5) * rdf_sc(k) &
	1580	* ( cs_scalar(k,j,i) - pr_init_cs(k) ) &
	1581	) &
	1582	* MERGE( 1.0_wp, 0.0_wp, &
	1583	BTEST( wall_flags_0(k,j,i), 0 ) &
	1584	)
	1585
	1586	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
	1587	ENDDO
	1588
	1589	!
	1590	!-- Calculate tendencies for the next Runge-Kutta step
	1591	IF ( timestep_scheme(1:5) == 'runge' ) THEN
	1592	IF ( intermediate_timestep_count == 1 ) THEN
	1593	DO k = nzb+1, nzt
	1594	tcs_scalar_m(k,j,i) = tend(k,j,i)
	1595	ENDDO
	1596	ELSEIF ( intermediate_timestep_count < &
	1597	intermediate_timestep_count_max ) THEN
	1598	DO k = nzb+1, nzt
	1599	tcs_scalar_m(k,j,i) = -9.5625_wp * tend(k,j,i) + &
	1600	5.3125_wp * tcs_scalar_m(k,j,i)
	1601	ENDDO
	1602	ENDIF
	1603	ENDIF
	1604	!
	1605	END SUBROUTINE chem_tendency
	1606
	1607	!------------------------------------------------------------------------------!
	1608	!
	1609	! Description:
	1610	! ------------
	1611	!> Subroutine defining header output for chemistry model
	1612	!------------------------------------------------------------------------------!
	1613	SUBROUTINE chem_header ( io )
	1614
	1615	IMPLICIT NONE
	1616
	1617	INTEGER(iwp), INTENT(IN) :: io !< Unit of the output file
	1618
	1619	! print*,'the header subroutine is still not operational'
	1620	!!
	1621	!!-- Write chemistry model header
	1622	! WRITE( io, 3 )
	1623	!
	1624	! IF ( radiation_scheme == "constant" ) THEN
	1625	! WRITE( io, 4 ) net_radiation
	1626	! ELSEIF ( radiation_scheme == "clear-sky" ) THEN
	1627	! WRITE( io, 5 )
	1628	! ELSEIF ( radiation_scheme == "rrtmg" ) THEN
	1629	! WRITE( io, 6 )
	1630	! IF ( .NOT. lw_radiation ) WRITE( io, 10 )
	1631	! IF ( .NOT. sw_radiation ) WRITE( io, 11 )
	1632	! ENDIF
	1633	!
	1634	! IF ( albedo_type == 0 ) THEN
	1635	! WRITE( io, 7 ) albedo
	1636	! ELSE
	1637	! WRITE( io, 8 ) TRIM( albedo_type_name(albedo_type) )
	1638	! ENDIF
	1639	! IF ( constant_albedo ) THEN
	1640	! WRITE( io, 9 )
	1641	! ENDIF
	1642	!
	1643	! IF ( radiation .AND. radiation_scheme /= 'constant' ) THEN
	1644	! WRITE ( io, 1 ) lambda
	1645	! WRITE ( io, 2 ) day_init, time_utc_init
	1646	! ENDIF
	1647	!
	1648	! WRITE( io, 12 ) dt_radiation
	1649	!
	1650	! 1 FORMAT (' Geograph. longitude : lambda = ',F4.1,' degr')
	1651	! 2 FORMAT (' Day of the year at model start : day_init = ',I3 &
	1652	! /' UTC time at model start : time_utc_init = ',F7.1' s')
	1653	! 3 FORMAT (//' Radiation model information:'/ &
	1654	! ' ----------------------------'/)
	1655	! 4 FORMAT (' --> Using constant net radiation: net_radiation = ', F6.2, &
	1656	! // 'W/m**2')
	1657	! 5 FORMAT (' --> Simple radiation scheme for clear sky is used (no clouds,', &
	1658	! ' default)')
	1659	! 6 FORMAT (' --> RRTMG scheme is used')
	1660	! 7 FORMAT (/' User-specific surface albedo: albedo =', F6.3)
	1661	! 8 FORMAT (/' Albedo is set for land surface type: ', A)
	1662	! 9 FORMAT (/' --> Albedo is fixed during the run')
	1663	!10 FORMAT (/' --> Longwave radiation is disabled')
	1664	!11 FORMAT (/' --> Shortwave radiation is disabled.')
	1665	!12 FORMAT (' Timestep: dt_radiation = ', F6.2, ' s')
	1666	!
	1667	!
	1668	END SUBROUTINE chem_header
[2668]	1669
	1670	!------------------------------------------------------------------------------
	1671	! Description:
	1672	! ------------
	1673	!> Subroutine reading restart data for chemistry model input parameters
	1674	! (FK: To make restarts work, I had to comment this routine. We actually
	1675	! don't need it, since the namelist parameters are always read in,
	1676	! also in case of a restart run)
	1677	!------------------------------------------------------------------------------
	1678	! SUBROUTINE chem_read_var_list
	1679	!
	1680	! ! USE kinds
	1681	! ! USE chem_modules
	1682	!
	1683	!
	1684	! IMPLICIT NONE
	1685	!
	1686	! CHARACTER (LEN=30) :: variable_chr !< dummy variable to read string
	1687	!
	1688	!
	1689	! READ ( 13 ) variable_chr
	1690	! DO WHILE ( TRIM( variable_chr ) /= '* end chemistry *' )
	1691	!
	1692	! SELECT CASE ( TRIM( variable_chr ) )
	1693	!
	1694	! CASE ( 'bc_cs_b' )
	1695	! READ ( 13 ) bc_cs_b
	1696	!
	1697	!
	1698	! END SELECT
	1699	!
	1700	! READ ( 13 ) variable_chr
	1701	!
	1702	! ENDDO
	1703	!
	1704	! END SUBROUTINE chem_read_var_list
	1705
	1706	!------------------------------------------------------------------------------
	1707	! Description:
	1708	! ------------
	1709	!> Skipping the chemistry-module parameters from restart-file (binary format).
	1710	! (FK: To make restarts work, I had to comment this routine. We actually
	1711	! don't need it, since the namelist parameters are always read in,
	1712	! also in case of a restart run)
	1713	!------------------------------------------------------------------------------
	1714	! SUBROUTINE chem_skip_var_list
	1715	!
	1716	! IMPLICIT NONE
	1717	!
	1718	! CHARACTER (LEN=1) :: cdum
	1719	! CHARACTER (LEN=30) :: variable_chr
	1720	!
	1721	! READ ( 13 ) variable_chr
	1722	!
	1723	! DO WHILE ( TRIM( variable_chr ) /= '* end chemistry *' )
	1724	!
	1725	! READ ( 13 ) cdum
	1726	! READ ( 13 ) variable_chr
	1727	!
	1728	! ENDDO
	1729	!
	1730	! END SUBROUTINE chem_skip_var_list
	1731
	1732
	1733	!------------------------------------------------------------------------------!
[2657]	1734	!
[2668]	1735	! Description:
	1736	! ------------
	1737	!> Subroutine writing restart data for chemistry model input parameters
	1738	! (FK: To make restarts work, I had to comment this routine. We actually
	1739	! don't need it, since the namelist parameters are always read in,
	1740	! also in case of a restart run)
[2657]	1741	!------------------------------------------------------------------------------!
[2668]	1742	! SUBROUTINE chem_write_var_list
	1743	!
	1744	! USE chem_modules
	1745	!
	1746	! USE kinds
	1747	!
	1748	!
	1749	! IMPLICIT NONE
	1750	!
	1751	! INTEGER(iwp) :: lsp !< running index for chem spcs
	1752	!
	1753	! !
	1754	! !-- Writing out input parameters that are not part of chemistry_par namelist
	1755	! !-- (namelist parameters are anyway read in again in case of restart)
	1756	! DO lsp = 1, nvar
	1757	! WRITE ( 14 ) 'conc_pr_init_'//chem_species(lsp)%name
	1758	! WRITE ( 14 ) chem_species(lsp)%conc_pr_init
	1759	! ENDDO
	1760	!
	1761	! WRITE ( 14 ) '* end chemistry * '
	1762	!
	1763	! END SUBROUTINE chem_write_var_list
	1764
	1765
	1766	!------------------------------------------------------------------------------!
[2657]	1767	!
	1768	! Description:
	1769	! ------------
[2668]	1770	!> Subroutine for emission
[2657]	1771	!------------------------------------------------------------------------------!
[2668]	1772	SUBROUTINE chem_emissions
[2657]	1773
[2668]	1774	USE chem_modules
	1775
	1776	USE netcdf_data_input_mod, &
	1777	ONLY: street_type_f
	1778
	1779	USE surface_mod, &
	1780	ONLY: surf_lsm_h
[2657]	1781
	1782
[2668]	1783	IMPLICIT NONE
[2657]	1784
[2678]	1785	INTEGER(iwp) :: i !< running index for grid in x-direction
	1786	INTEGER(iwp) :: j !< running index for grid in y-direction
	1787	INTEGER(iwp) :: m !< running index for horizontal surfaces
[2668]	1788	INTEGER(iwp) :: lsp !< running index for chem spcs
[2657]	1789
[2668]	1790	!
	1791	!-- Comment??? (todo)
[2678]	1792	IF ( street_type_f%from_file ) THEN
	1793	!
	1794	!-- Streets are lsm surfaces, hence, no usm surface treatment required
	1795	DO m = 1, surf_lsm_h%ns
	1796	i = surf_lsm_h%i(m)
	1797	j = surf_lsm_h%j(m)
	1798
	1799	IF ( street_type_f%var(j,i) >= main_street_id .AND. &
	1800	street_type_f%var(j,i) < max_street_id ) THEN
	1801	DO lsp = 1, nvar
	1802	surf_lsm_h%cssws(lsp,m) = emiss_factor_main * surface_csflux(lsp)
	1803	ENDDO
	1804	ELSEIF ( street_type_f%var(j,i) >= side_street_id .AND. &
	1805	street_type_f%var(j,i) < main_street_id ) THEN
	1806	DO lsp = 1, nvar
	1807	surf_lsm_h%cssws(lsp,m) = emiss_factor_side * surface_csflux(lsp)
	1808	ENDDO
[2682]	1809	ELSE
	1810	surf_lsm_h%cssws(:,m) = 0.0_wp
[2678]	1811	ENDIF
	1812	ENDDO
	1813
	1814	ENDIF
[2657]	1815
[2668]	1816	END SUBROUTINE chem_emissions
[2657]	1817
	1818
	1819	END MODULE chemistry_model_mod
	1820

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