!> @file chem_modules.f90
!--------------------------------------------------------------------------------------------------!
! This file is part of the PALM model system.
!
! PALM is free software: you can redistribute it and/or modify it under the terms of the GNU General
! Public License as published by the Free Software Foundation, either version 3 of the License, or
! (at your option) any later version.
!
! PALM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
! implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
! Public License for more details.
!
! You should have received a copy of the GNU General Public License along with PALM. If not, see
! <http://www.gnu.org/licenses/>.
!
! Copyright 2018-2021 Leibniz Universitaet Hannover
! Copyright 2018-2021 Karlsruhe Institute of Technology
! Copyright 2018-2021 Freie Universitaet Berlin
!--------------------------------------------------------------------------------------------------!
!
! Authors:
! --------
! @author Farah Kanani-Suehring
! @author Basit Khan
! @author Sabine Banzhaf
! @author Emmanuele Russo
! @author Edward C. Chan
!
!--------------------------------------------------------------------------------------------------!
! Description:
! ------------
!> Definition of global PALM-4U chemistry variables
!--------------------------------------------------------------------------------------------------!
!
 MODULE chem_modules

    USE kinds

    IMPLICIT NONE

    REAL, PARAMETER ::  xm_air   =   28.964e-3             !< air      molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_C     =   12.01115e-3           !< C        molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_Ca    =   40.07800e-3           !< Ca       molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_Cd    =  112.41000e-3           !< Cd       molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_Cl    =   35.45300e-3           !< Cl       molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_dummy = 1000.0e-3               !< dummy    molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_F     =   18.99840e-3           !< F        molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_H     =    1.00790e-3           !< H        molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_K     =   39.09800e-3           !< K        molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_Mg    =   24.30500e-3           !< Mg       molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_N     =   14.00670e-3           !< N        molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_Na    =   22.98977e-3           !< Na       molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_O     =   15.99940e-3           !< O        molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_Pb    =  207.20000e-3           !< Pb       molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_Pb210 =  210.00000e-3           !< Pb (210) molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_Rn222 =  222.00000e-3           !< Rn (222) molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_S     =   32.06400e-3           !< S        molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_CO2   = xm_C + xm_O * 2         !< CO2      molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_h2o   = xm_H * 2 + xm_O         !< H2O      molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_HNO3  = xm_H + xm_N + xm_O * 3  !< HNO3     molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_o3    = xm_O * 3                !< O3       molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_N2O5  = xm_N * 2 + xm_O * 5     !< N2O5     molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_NH4   = xm_N + xm_H * 4         !< NH4      molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_NO3   = xm_N + xm_O * 3         !< NO3      molecular weight (kg/mol)
    REAL, PARAMETER ::  xm_SO4   = xm_S + xm_O * 4         !< SO4      molecular weight (kg/mol)

    CHARACTER (LEN=20) ::  bc_cs_b        = 'dirichlet'         !< namelist parameter: surface
                                                                !< boundary condition for concentration
    CHARACTER (LEN=20) ::  bc_cs_l        = 'undefined'         !< left boundary condition
    CHARACTER (LEN=20) ::  bc_cs_n        = 'undefined'         !< north boundary condition
    CHARACTER (LEN=20) ::  bc_cs_r        = 'undefined'         !< right boundary condition
    CHARACTER (LEN=20) ::  bc_cs_s        = 'undefined'         !< south boundary condition
    CHARACTER (LEN=20) ::  bc_cs_t        = 'initial_gradient'  !< namelist parameter: top boudary
                                                                !< condition for concentration
    CHARACTER (LEN=30) ::  chem_mechanism = 'phstatp'           !< namelist parameter: chemistry
                                                                !< mechanism
    CHARACTER (LEN=80) ::  daytype_mdh    = 'workday'           !< namelist parameter: type of day
                                                                !< - workday, weekend, holiday
    CHARACTER (LEN=80) ::  mode_emis      = 'PARAMETERIZED'     !< namelist parameter: mode of
                                                                !< chemistry emissions -
                                                                !< DEFAULT, EXPERT, PARAMETERIZED
    CHARACTER (LEN=10) ::  photolysis_scheme                    !< 'constant',
                                                                !< 'simple' (Simple parameterisation from MCM,
                                                                !< Saunders et al., 2003, Atmos. Chem. Phys., 3, 161-180
                                                                !< 'fastj'  (Wild et al., 2000, J. Atmos. Chem., 37, 245-282)
                                                                !< STILL NOT IMPLEMENTED
    CHARACTER (LEN=80) ::  time_fac_type  = 'MDH'               !< namelist parameter: type of time treatment in the mode_emis
                                                                !< DEFAULT - HOUR, MDH

    CHARACTER (LEN=11), DIMENSION(99) ::  cs_name             = 'novalue'  !< namelist parameter:
                                                                           !<names of species with given fluxes
                                                                           !< (see csflux)
    CHARACTER (LEN=11), DIMENSION(99) ::  cs_profile_name     = 'novalue'  !< namelist parameter:
                                                                           !< tbc...???
    CHARACTER (LEN=11), DIMENSION(99) ::  data_output_pr_cs   = 'novalue'  !< namelist parameter:
                                                                           !< tbc...???
    CHARACTER (LEN=11), DIMENSION(99) ::  surface_csflux_name = 'novalue'  !< namelist parameter:
                                                                           !< tbc...???

    INTEGER(iwp) ::  communicator_chem      !< stores the number of the MPI communicator to be used
                                            !< for ghost layer data exchange
                                            !< 1: cyclic, 2: cyclic along x, 3: cyclic along y,
                                            !< 4: non-cyclic

    INTEGER(iwp) ::  cs_pr_count_fl_res                    = 0      !< counter for vertical flux profiles of chemical species (resolved-scale)
    INTEGER(iwp) ::  cs_pr_count_fl_sgs                    = 0      !< counter for vertical flux profiles of chemical species (SGS)
    INTEGER(iwp) ::  cs_pr_count_sp                        = 0      !< counter for chemical species profiles
    INTEGER(iwp) ::  cs_vertical_gradient_level_ind(99,10) = -9999  !< grid index values of
                                                                    !< cs_vertical_gradient_level
    INTEGER(iwp) ::  emiss_lod                             = -1     !< namelist parameter: chem emission LOD (same as mode_emis)
                                                                    !< -1 = unassigned, 0 = parameterized, 1 = default,
                                                                    !< 2 = pre-processed
    INTEGER(iwp) ::  ibc_cs_b                                       !< integer flag for bc_cs_b
    INTEGER(iwp) ::  ibc_cs_t                                       !< integer flag for bc_cs_t
    INTEGER(iwp) ::  main_street_id                        = 0      !< namelist parameter: lower bound of main street IDs
                                                                    !< (OpenStreetMaps) for PARAMETERIZED mode
    INTEGER(iwp) ::  max_pr_cs                             = 0      !< number of chemistry profiles in output
    INTEGER(iwp) ::  max_street_id                         = 0      !< namelist parameter: upper bound of main street IDs
                                                                    !< (OpenStreetMaps) for PARAMETERIZED mode
    INTEGER(iwp) ::  n_matched_vars                                 !< number of matched emissions
                                                                    !< variables
    INTEGER(iwp) ::  side_street_id                        = 0      !< namelist parameter: lower bound of side street IDs
                                                                    !< (OpenStreetMaps) for PARAMETERIZED mode

    INTEGER(iwp), DIMENSION(99) ::  cs_pr_index_sp      = 0 !< index for chemical species mean profiles
    INTEGER(iwp), DIMENSION(99) ::  cs_pr_index_fl_res  = 0 !< index for chemical species sgs-flux profiles
    INTEGER(iwp), DIMENSION(99) ::  cs_pr_index_fl_sgs  = 0 !< index for chemical species resolved-scale flux profiles
    INTEGER(iwp), DIMENSION(99) ::  hom_index_fl_res    = 0 !< index of the resolved-scale flux profile with respect to the hom array
    INTEGER(iwp), DIMENSION(99) ::  hom_index_fl_sgs    = 0 !< index of the SGS flux profile with respect to the hom array
    INTEGER(iwp), DIMENSION(99) ::  hom_index_spec      = 0 !< index of the profile with respect to the hom array
    INTEGER(iwp), DIMENSION(:)  ::  match_spec_nox(1:2)     !< results of matching the input and model's NOx
    INTEGER(iwp), DIMENSION(:)  ::  match_spec_pm(1:3)      !< results of matching the input and model's PMs
    INTEGER(iwp), DIMENSION(:)  ::  match_spec_sox(1:2)     !< results of matching the input and model's SOx!

    INTEGER(iwp), DIMENSION(:), ALLOCATABLE ::  match_spec_input      !< index of input chem species
                                                                      !< for matching routine
    INTEGER(iwp), DIMENSION(:), ALLOCATABLE ::  match_spec_model      !< index of model chem species#
                                                                      !< for matching routine
    INTEGER(iwp), DIMENSION(:), ALLOCATABLE ::  match_spec_voc_input  !< index of VOC input
                                                                      !< components matching the model's VOCs
    INTEGER(iwp), DIMENSION(:), ALLOCATABLE ::  match_spec_voc_model  !< index of VOC model species
                                                                      !< matching the input VOCs comp.

    INTEGER(iwp), DIMENSION(:,:,:), ALLOCATABLE  ::  cs_advc_flags_s !< flags used to degrade order of advection scheme for
                                                                     !< chemical species near walls and lateral boundaries

    LOGICAL ::  bc_dirichlet_cs_l         = .FALSE.  !< flag for indicating a dirichlet condition at
                                                     !< the left boundary
    LOGICAL ::  bc_dirichlet_cs_n         = .FALSE.  !< flag for indicating a dirichlet condition at
                                                     !< the north boundary
    LOGICAL ::  bc_dirichlet_cs_r         = .FALSE.  !< flag for indicating a dirichlet condition at
                                                     !< the right boundary
    LOGICAL ::  bc_dirichlet_cs_s         = .FALSE.  !< flag for indicating a dirichlet condition at
                                                     !< the south boundary
    LOGICAL ::  bc_radiation_cs_l         = .FALSE.  !< flag for indicating a radiation/neumann
                                                     !< condition at the left boundary
    LOGICAL ::  bc_radiation_cs_n         = .FALSE.  !< flag for indicating a radiation/neumann
                                                     !< condition at the north boundary
    LOGICAL ::  bc_radiation_cs_r         = .FALSE.  !< flag for indicating a radiation/neumann
                                                     !< condition at the right boundary
    LOGICAL ::  bc_radiation_cs_s         = .FALSE.  !< flag for indicating a radiation/neumann
                                                     !< condition at the south boundary
    LOGICAL ::  constant_csflux(99)       = .TRUE.   !< internal flag, set to .FALSE. if no
                                                     !< surface_csflux is prescribed
    LOGICAL ::  call_chem_at_all_substeps = .FALSE.  !< namelist parameter: Never set true 
                                                     !< except for tests
    LOGICAL ::  chem_gasphase_on          = .TRUE.   !< namelist parameter: flag to switch off
                                                     !< chemical reactions
    LOGICAL ::  cs_pr_namelist_found      = .FALSE.  !< ...???
    LOGICAL ::  deposition_dry            = .FALSE.  !< namelist parameter: flag for activation of
                                                     !< deposition calculation
    LOGICAL ::  emissions_anthropogenic   = .FALSE.  !< namelist parameter: flag for turning on
                                                     !< anthropogenic emissions
    LOGICAL ::  emission_output_required  = .TRUE.   !< internal flag for requiring emission outputs
    LOGICAL ::  emiss_read_legacy_mode    = .TRUE.   !< namelist parameter: flag to read emission
                                                     !< data using legacy mode
    LOGICAL ::  nesting_chem              = .TRUE.   !< apply self-nesting for the chemistry model
    LOGICAL ::  nesting_offline_chem      = .TRUE.   !< apply offline nesting for the chemistry
                                                     !< model

    REAL(wp) ::  emiss_factor_main(99)             = -9999.0_wp  !< namelist parameter: weighting  factor
                                                                 !< for LOD 0 parameterized emissions
    REAL(wp) ::  emiss_factor_side(99)             = -9999.0_wp  !< namelist parameter: weighting  factor
                                                                 !< for LOD 0 parameterized emissions
    REAL(wp) ::  surface_csflux(99)                = 0.0_wp      !< namelist parameter: surface emission 
                                                                 !< flux or LOD 0 parameterized emissions
    REAL(wp) ::  wall_csflux(99,0:5)               = 0.0_wp      !< namelist parameter: ...???

    REAL(wp), DIMENSION(99)     ::  cs_surface = 0.0_wp        !< namelist parameter: chem species
                                                               !< concentration at surface
    REAL(wp), DIMENSION(99,100) ::  cs_heights = 9999999.9_wp  !< namelist parameter: height levels
                                                               !< for initial chem species concentrations
    REAL(wp), DIMENSION(99,100) ::  cs_profile = 9999999.9_wp  !< namelist parameter: chem species
                                                               !< concentration values at cs_heights levels

    REAL(wp), DIMENSION(:), ALLOCATABLE ::  bc_cs_t_val  !< vertical gradient of chemical species
                                                         !< near domain top
    REAL(wp), DIMENSION(:), ALLOCATABLE ::  css          !< scaling parameter for chem species

    REAL(wp), DIMENSION(:,:,:),   ALLOCATABLE, TARGET ::  sums_ws_l  !< subdomain sum of vertical chemistry flux w'ch'

    REAL(wp), DIMENSION(:,:,:,:), ALLOCATABLE ::  emis_distribution  !< emissions final values (main module output) ???

    REAL(wp), DIMENSION(:,:,:,:), ALLOCATABLE, TARGET ::  cs_1  !< pointer for swapping of
                                                                !< timelevels for respective quantity
    REAL(wp), DIMENSION(:,:,:,:), ALLOCATABLE, TARGET ::  cs_2  !< pointer for swapping of
                                                                !< timelevels for respective quantity
    REAL(wp), DIMENSION(:,:,:,:), ALLOCATABLE, TARGET ::  cs_3  !< pointer for swapping of
                                                                !< timelevels for respective quantity

    REAL(wp), DIMENSION(:,:,:), POINTER ::  cs     !< pointer: sgs chem spcs  ???
    REAL(wp), DIMENSION(:,:,:), POINTER ::  cs_p   !< pointer: prognostic value of sgs chem spcs ???
    REAL(wp), DIMENSION(:,:,:), POINTER ::  tcs_m  !< pointer: to tcs array (temp)

!
!-  Define chemical variables within chem_species
    TYPE species_def

       CHARACTER(LEN=15)                            ::  name         !< name of chemical species
       CHARACTER(LEN=15)                            ::  unit         !< unit (ppm for gases, kg m^-3
                                                                     !< for aerosol tracers)

       REAL(kind=wp), ALLOCATABLE, DIMENSION(:)     ::  conc_pr_init !< initial profile of chemical
                                                                     !< species

       REAL(kind=wp), ALLOCATABLE, DIMENSION(:,:)   ::  cssws_av     !< averaged fluxes of trace
                                                                     !< gases at surface
       REAL(kind=wp), ALLOCATABLE, DIMENSION(:,:)   ::  flux_s_cs    !< 6th-order advective flux at
                                                                     !< south face of grid box of chemical species (='cs')
       REAL(kind=wp), ALLOCATABLE, DIMENSION(:,:)   ::  diss_s_cs    !< artificial numerical dissipation
                                                                     !< flux at south face of grid box of chemical species

       REAL(kind=wp), ALLOCATABLE, DIMENSION(:,:,:) ::  conc_av      !< averaged concentrations
       REAL(kind=wp), ALLOCATABLE, DIMENSION(:,:,:) ::  flux_l_cs    !< 6th-order advective flux at
                                                                     !< left face of grid box of chemical species (='cs')
       REAL(kind=wp), ALLOCATABLE, DIMENSION(:,:,:) ::  diss_l_cs    !< artificial numerical dissipation
                                                                     !< flux at left face of grid box of chemical species

       REAL(kind=wp), POINTER, DIMENSION(:,:,:)     ::  conc         !< concentrations of trace
                                                                     !< gases
       REAL(kind=wp), POINTER, DIMENSION(:,:,:)     ::  conc_p       !< conc at prognostic time
                                                                     !< level
       REAL(kind=wp), POINTER, DIMENSION(:,:,:)     ::  tconc_m      !< weighted tendency of conc
                                                                     !< for previous sub-timestep (Runge-Kutta)

    END TYPE species_def
!
!-- Define photolysis frequencies in phot_frequen
    TYPE photols_def

       CHARACTER(LEN=15)                            :: name          !< name of pgotolysis frequency
       CHARACTER(LEN=15)                            :: unit          !< unit (1/s)

       REAL(kind=wp), POINTER, DIMENSION(:,:,:)     :: freq          !< photolysis frequency

    END TYPE photols_def


    TYPE(species_def), ALLOCATABLE, DIMENSION(:), TARGET ::  chem_species
    TYPE(photols_def), ALLOCATABLE, DIMENSION(:), TARGET ::  phot_frequen

    SAVE

 END MODULE chem_modules