PROGRAM testphys1d
! to use  'getin'
      USE ioipsl_getincom, only: getin
      use dimphy, only : init_dimphy
      use mod_grid_phy_lmdz, only : regular_lonlat
      use infotrac, only: nqtot, tname, nqperes,nqfils
      use comsoil_h, only: volcapa, layer, mlayer, inertiedat, 
     &                     inertiesoil,nsoilmx,flux_geo
      use comgeomfi_h, only: sinlat, ini_fillgeom
      use surfdat_h, only: albedodat, z0_default, emissiv, emisice,
     &                     albedice, iceradius, dtemisice, z0,
     &                     zmea, zstd, zsig, zgam, zthe, phisfi,
     &                     watercaptag, watercap, hmons, summit, base
      use slope_mod, only: theta_sl, psi_sl
      use comslope_mod, only: def_slope,subslope_dist,def_slope_mean
      use phyredem, only: physdem0,physdem1
      use geometry_mod, only: init_geometry
      use watersat_mod, only: watersat
      use tracer_mod, only: igcm_h2o_vap,igcm_h2o_ice,igcm_co2,noms
      use planete_h, only: year_day, periheli, aphelie, peri_day,
     &                     obliquit, emin_turb, lmixmin
      use comcstfi_h, only: pi, rad, omeg, g, mugaz, rcp, r, cpp
      use time_phylmdz_mod, only: daysec, dtphys, day_step,
     &                            ecritphy, iphysiq
      use dimradmars_mod, only: tauvis,totcloudfrac
      use dust_param_mod, only: tauscaling
      USE comvert_mod, ONLY: ap,bp,aps,bps,pa,preff,sig,
     &                       presnivs,pseudoalt,scaleheight
      USE vertical_layers_mod, ONLY: init_vertical_layers
      USE logic_mod, ONLY: hybrid
      use physics_distribution_mod, only: init_physics_distribution
      use regular_lonlat_mod, only: init_regular_lonlat
      use mod_interface_dyn_phys, only: init_interface_dyn_phys
      USE phys_state_var_init_mod, ONLY: phys_state_var_init
      USE physiq_mod, ONLY: physiq
      USE read_profile_mod, ONLY: read_profile
      use inichim_newstart_mod, only: inichim_newstart
      use phyetat0_mod, only: phyetat0
      USE netcdf, only: NF90_OPEN, NF90_NOERR, NF90_NOWRITE,
     &                  nf90_strerror
      use iostart, only: open_startphy,get_var, close_startphy
      use write_output_mod, only: write_output
      IMPLICIT NONE

c=======================================================================
c   subject:
c   --------
c   PROGRAM useful to run physical part of the martian GCM in a 1D column
c       
c Can be compiled with a command like (e.g. for 25 layers)
c  "makegcm -p mars -d 25 testphys1d"
c It requires the files "testphys1d.def" "callphys.def"
c   and a 'run.def' file (containing a "INCLUDEDEF=callphys.def" line)
c      and a file describing the sigma layers (e.g. "z2sig.def")
c
c   author: Frederic Hourdin, R.Fournier,F.Forget
c   -------
c   
c   update: 12/06/2003 including chemistry (S. Lebonnois) 
c                            and water ice (F. Montmessin)
c 
c=======================================================================

      include "dimensions.h"
      integer, parameter :: ngrid = 1 !(2+(jjm-1)*iim - 1/jjm)
      integer, parameter :: nlayer = llm
!#include "dimradmars.h"
!#include "comgeomfi.h"
!#include "surfdat.h"
!#include "slope.h"
!#include "comsoil.h"
!#include "comdiurn.h"
      include "callkeys.h"
!#include "comsaison.h"
!#include "control.h"
      include "netcdf.inc"
      include "comg1d.h"
!#include "advtrac.h"

c --------------------------------------------------------------
c  Declarations
c --------------------------------------------------------------
c
      INTEGER unitstart      ! unite d'ecriture de "startfi"
      INTEGER nlevel,nsoil,ndt
      INTEGER ilayer,ilevel,isoil,idt,iq
      LOGICAl firstcall,lastcall
      LOGICAL write_prof
c
      real,parameter :: odpref=610. ! DOD reference pressure (Pa)
c
      INTEGER day0,dayn          ! date initial (sol ; =0 a Ls=0) and final
      REAL day           ! date durant le run
      REAL time             ! time (0<time<1 ; time=0.5 a midi)
      REAL play(nlayer)   ! Pressure at the middle of the layers (Pa)
      REAL plev(nlayer+1) ! intermediate pressure levels (pa)
      REAL psurf,tsurf(1)      
      REAL u(nlayer),v(nlayer)  ! zonal, meridional wind
      REAL gru,grv   ! prescribed "geostrophic" background wind
      REAL temp(nlayer)   ! temperature at the middle of the layers
      REAL,ALLOCATABLE :: q(:,:) ! tracer mixing ratio (e.g. kg/kg)
      REAL,ALLOCATABLE :: qsurf(:) ! tracer surface budget (e.g. kg.m-2)
      REAL tsoil(nsoilmx)   ! subsurface soik temperature (K)
      REAL emis(1)          ! surface layer
      REAL albedo(1,1)      ! surface albedo
      REAL :: wstar(1)=0.    ! Thermals vertical velocity
      REAL q2(nlayer+1)   ! Turbulent Kinetic Energy
      REAL zlay(nlayer)   ! altitude estimee dans les couches (km)

c    Physical and dynamical tandencies (e.g.  m.s-2, K/s, Pa/s)
      REAL du(nlayer),dv(nlayer),dtemp(nlayer)
      REAL dudyn(nlayer),dvdyn(nlayer),dtempdyn(nlayer)
      REAL dpsurf(1)    
      REAL,ALLOCATABLE :: dq(:,:)
      REAL,ALLOCATABLE :: dqdyn(:,:)

c   Various intermediate variables
      INTEGER flagthermo,flagh2o
      REAL zls
      REAL phi(nlayer),h(nlayer),s(nlayer)
      REAL pks, ptif, w(nlayer)
      REAL qtotinit,qtot
      real,allocatable :: mqtot(:)
      INTEGER ierr, aslun
      REAL tmp1(0:nlayer),tmp2(0:nlayer)
      integer :: nq=1 ! number of tracers
      real :: latitude(1), longitude(1), cell_area(1)
      ! dummy variables along "dynamics scalar grid"
      real,allocatable :: qdyn(:,:,:,:),psdyn(:,:)

      character*2 str2
      character (len=7) :: str7
      character(len=44) :: txt

c   New flag to compute paleo orbital configurations + few variables JN
      REAL halfaxe, excentric, Lsperi
      Logical paleomars
c   JN : Force atmospheric water profiles
      REAL atm_wat_profile
      REAL,ALLOCATABLE :: zqsat(:) ! useful for (atm_wat_profile=2)


c   MVals: isotopes as in the dynamics (CRisi)
      INTEGER :: ifils,ipere,generation
      CHARACTER(len=30), ALLOCATABLE, DIMENSION(:) :: tnom_transp ! transporting fluid short name
      CHARACTER(len=80) :: line ! to store a line of text     
      INTEGER ierr0
      LOGICAL :: continu

      logical :: present

c   LL: Subsurface geothermal flux
      real :: flux_geo_tmp

c   RV: Start from a startfi and not run.def
      logical :: startfile_1D
      REAL tab_cntrl(100)
      LOGICAL :: found
      REAL albedo_read(1,2,1)      ! surface albedo

c   LL: Possibility to add subsurface ice
      REAL :: ice_depth            ! depth of the ice table, ice_depth < 0. means no ice
      REAL :: inertieice = 2100.   ! ice thermal inertia
      integer :: iref
 
c=======================================================================

c=======================================================================
c INITIALISATION
c=======================================================================
! initialize "serial/parallel" related stuff
!      CALL init_phys_lmdz(iim,jjp1,llm,1,(/(jjm-1)*iim+2/))
!      CALL init_phys_lmdz(1,1,llm,1,(/1/))
!      call initcomgeomphy


c ------------------------------------------------------
c  Loading run parameters from "run.def" file
c ------------------------------------------------------


! check if 'run.def' file is around (otherwise reading parameters
! from callphys.def via getin() routine won't work.
      open(99,file='run.def',status='old',form='formatted',
     &     iostat=ierr)
      if (ierr.ne.0) then
        write(*,*) 'Cannot find required file "run.def"'
        write(*,*) '  (which should contain some input parameters'
        write(*,*) '   along with the following line:'
        write(*,*) '   INCLUDEDEF=callphys.def'
        write(*,*) '   )'
        write(*,*) ' ... might as well stop here ...'
        stop
      else
        close(99)
      endif

      write(*,*)'Do you want to start with a startfi and write 
     &           a restartfi?'
      startfile_1D=.false.
      call getin("startfile_1D",startfile_1D)
      write(*,*)" startfile_1D = ", startfile_1D

c ------------------------------------------------------
c  Prescribed constants to be set here
c ------------------------------------------------------

c      if(.not. startfile_1D ) then

      pi=2.E+0*asin(1.E+0)

c     Mars planetary constants
c     ----------------------------
      rad=3397200.               ! mars radius (m)  ~3397200 m
      daysec=88775.              ! length of a sol (s)  ~88775 s
      omeg=4.*asin(1.)/(daysec)  ! rotation rate (rad.s-1)
      g=3.72                     ! gravity (m.s-2) ~3.72  
      mugaz=43.49                ! atmosphere mola mass (g.mol-1) ~43.49
      rcp=.256793                ! = r/cp  ~0.256793
      r= 8.314511E+0 *1000.E+0/mugaz
      cpp= r/rcp
      year_day = 669             ! lenght of year (sols) ~668.6
      periheli = 206.66          ! minimum sun-mars distance (Mkm) ~206.66
      aphelie = 249.22           ! maximum sun-mars distance (Mkm) ~249.22
      halfaxe = 227.94           ! demi-grand axe de l'ellipse
      peri_day =  485.           ! perihelion date (sols since N. Spring)
      obliquit = 25.2            ! Obliquity (deg) ~25.2         
      excentric = 0.0934         ! Eccentricity (0.0934)         
 
c     Planetary Boundary Layer and Turbulence parameters 
c     --------------------------------------------------
      z0_default =  1.e-2        ! surface roughness (m) ~0.01 
      emin_turb = 1.e-6          ! minimal turbulent energy ~1.e-8
      lmixmin = 30               ! mixing length ~100
 
c     cap properties and surface emissivities
c     ----------------------------------------------------
      emissiv= 0.95              ! Bare ground emissivity ~.95
      emisice(1)=0.95            ! Northern cap emissivity
      emisice(2)=0.95            ! Southern cap emisssivity
      albedice(1)=0.5            ! Northern cap albedo
      albedice(2)=0.5            ! Southern cap albedo
      iceradius(1) = 100.e-6     ! mean scat radius of CO2 snow (north)
      iceradius(2) = 100.e-6     ! mean scat radius of CO2 snow (south)
      dtemisice(1) = 2.          ! time scale for snow metamorphism (north)
      dtemisice(2) = 2.          ! time scale for snow metamorphism (south)

c      endif ! .not. startfile_1D

c     mesh surface (not a very usefull quantity in 1D)
c     ----------------------------------------------------
      cell_area(1)=1.E+0


! check if there is a 'traceur.def' file
! and process it.
      ! load tracer names from file 'traceur.def'
        open(90,file='traceur.def',status='old',form='formatted',
     &       iostat=ierr)
        if (ierr.ne.0) then
          write(*,*) 'Cannot find required file "traceur.def"'
          write(*,*) ' If you want to run with tracers, I need it'
          write(*,*) ' ... might as well stop here ...'
          stop
        else
          write(*,*) "testphys1d: Reading file traceur.def"
          ! read number of tracers:
          read(90,*,iostat=ierr) nq
          nqtot=nq ! set value of nqtot (in infotrac module) as nq
          if (ierr.ne.0) then
            write(*,*) "testphys1d: error reading number of tracers"
            write(*,*) "   (first line of traceur.def) "
            stop
          endif
          if (nq<1) then
            write(*,*) "testphys1d: error number of tracers"
            write(*,*) "is nq=",nq," but must be >=1!"
            stop
          endif
        endif
        ! allocate arrays:
        allocate(tname(nq))
        allocate(q(nlayer,nq))
        allocate(zqsat(nlayer))
        allocate(qsurf(nq))
        allocate(dq(nlayer,nq))
        allocate(dqdyn(nlayer,nq))
        allocate(mqtot(nq))
        allocate(tnom_transp(nq))
        
        ! read tracer names from file traceur.def
        do iq=1,nq
          read(90,'(80a)',iostat=ierr) line ! store the line from traceur.def
          if (ierr.ne.0) then
            write(*,*) 'testphys1d: error reading tracer names...'
            stop
          endif
          ! if format is tnom_0, tnom_transp (isotopes)
          read(line,*,iostat=ierr0) tname(iq),tnom_transp(iq)
          if (ierr0.ne.0) then
            read(line,*) tname(iq)
            tnom_transp(iq)='air'
          endif

        enddo
        close(90)

       ! Isotopes: as in the 3D case we have to determine father/son relations for isotopes and carrying fluid
       ALLOCATE(nqfils(nqtot))
       nqperes=0
       nqfils(:)=0  
       DO iq=1,nqtot
       if (tnom_transp(iq) == 'air') then
         ! ceci est un traceur père
         WRITE(*,*) 'Le traceur',iq,', appele ',
     &          trim(tname(iq)),', est un pere'
         nqperes=nqperes+1
       else !if (tnom_transp(iq) == 'air') then
         ! ceci est un fils. Qui est son père?
         WRITE(*,*) 'Le traceur',iq,', appele ',
     &                trim(tname(iq)),', est un fils'
         continu=.true.
         ipere=1
         do while (continu)           
           if (tnom_transp(iq) .eq. tname(ipere)) then
             ! Son père est ipere
             WRITE(*,*) 'Le traceur',iq,'appele ',
     &   trim(tname(iq)),' est le fils de ',
     &   ipere,'appele ',trim(tname(ipere))
             nqfils(ipere)=nqfils(ipere)+1         
             continu=.false.
           else !if (tnom_transp(iq) == tnom_0(ipere)) then
             ipere=ipere+1 
             if (ipere.gt.nqtot) then
                 WRITE(*,*) 'Le traceur',iq,'appele ',
     &           trim(tname(iq)),', est orpelin.'
                 CALL abort_gcm('infotrac_init',
     &                  'Un traceur est orphelin',1)
             endif !if (ipere.gt.nqtot) then
           endif !if (tnom_transp(iq) == tnom_0(ipere)) then
         enddo !do while (continu)
       endif !if (tnom_transp(iq) == 'air') then
       enddo !DO iq=1,nqtot
       WRITE(*,*) 'nqperes=',nqperes    
       WRITE(*,*) 'nqfils=',nqfils

        ! initialize tracers here:
        write(*,*) "testphys1d: initializing tracers"
        call read_profile(nq, nlayer, qsurf, q)

      call init_physics_distribution(regular_lonlat,4,
     &                               1,1,1,nlayer,1)

      if(.not. startfile_1D ) then

c  Date and local time at beginning of run
c  ---------------------------------------
c    Date (in sols since spring solstice) at beginning of run
      day0 = 0 ! default value for day0
      write(*,*) 'Initial date (in martian sols ; =0 at Ls=0)?'
      call getin("day0",day0)
      day=float(day0)
      write(*,*) " day0 = ",day0
c  Local time at beginning of run 
      time=0 ! default value for time
      write(*,*)'Initial local time (in hours, between 0 and 24)?'
      call getin("time",time)
      write(*,*)" time = ",time
      time=time/24.E+0 ! convert time (hours) to fraction of sol

      else
      call open_startphy("startfi.nc")
      call get_var("controle",tab_cntrl,found)
       if (.not.found) then
         call abort_physic("open_startphy", 
     &        "tabfi: Failed reading <controle> array",1)
       else
         write(*,*)'tabfi: tab_cntrl',tab_cntrl
       endif
       day0 = tab_cntrl(3)
       day=float(day0)

       call get_var("Time",time,found)

       call close_startphy

      endif !startfile_1D

c  Discretization (Definition of grid and time steps)
c  --------------
c
      nlevel=nlayer+1
      nsoil=nsoilmx

      day_step=48 ! default value for day_step
      PRINT *,'Number of time steps per sol ?'
      call getin("day_step",day_step)
      write(*,*) " day_step = ",day_step

      ecritphy=day_step ! default value for ecritphy, output every time step

      ndt=10 ! default value for ndt
      PRINT *,'Number of sols to run ?'
      call getin("ndt",ndt)
      write(*,*) " ndt = ",ndt

      dayn=day0+ndt
      ndt=ndt*day_step     
      dtphys=daysec/day_step  

c Imposed surface pressure
c ------------------------------------
c

      psurf=610. ! default value for psurf
      PRINT *,'Surface pressure (Pa) ?'
      call getin("psurf",psurf)
      write(*,*) " psurf = ",psurf

c Reference pressures
      pa=20.   ! transition pressure (for hybrid coord.)
      preff=610.      ! reference surface pressure
 
c Aerosol properties
c --------------------------------
      tauvis=0.2 ! default value for tauvis (dust opacity)
      write(*,'("Reference dust opacity at ",f4.0," Pa ?")')odpref
      call getin("tauvis",tauvis)
      write(*,*) " tauvis = ",tauvis

c Orbital parameters
c ------------------

      if(.not. startfile_1D ) then

      paleomars=.false. ! Default: no water ice reservoir
      call getin("paleomars",paleomars)
      if (paleomars.eqv..true.) then
        write(*,*) "paleomars=", paleomars
        write(*,*) "Orbital parameters from callphys.def"
        write(*,*) "Enter eccentricity & Lsperi"
        print *, 'Martian eccentricity (0<e<1) ?'
        call getin('excentric ',excentric)
        write(*,*)"excentric =",excentric 
        print *, 'Solar longitude of perihelion (0<Ls<360) ?'
        call getin('Lsperi',Lsperi )
        write(*,*)"Lsperi=",Lsperi 
        Lsperi = Lsperi*pi/180.0 ! Put it in rad for peri_day
        periheli = halfaxe*(1-excentric)
        aphelie = halfaxe*(1+excentric)
        call call_dayperi(Lsperi,excentric,peri_day,year_day)
        write(*,*) "Corresponding orbital params for GCM"
        write(*,*) " periheli = ",periheli
        write(*,*) " aphelie = ",aphelie
        write(*,*) "date of perihelion (sol)",peri_day
      else
        write(*,*) "paleomars=", paleomars
        write(*,*) "Default present-day orbital parameters"
        write(*,*) "Unless specified otherwise"
        print *,'Min. distance Sun-Mars (Mkm)?'
        call getin("periheli",periheli)
        write(*,*) " periheli = ",periheli

        print *,'Max. distance Sun-Mars (Mkm)?'
        call getin("aphelie",aphelie)
        write(*,*) " aphelie = ",aphelie

        print *,'Day of perihelion?'
        call getin("periday",peri_day)
        write(*,*) " periday = ",peri_day

        print *,'Obliquity?'
        call getin("obliquit",obliquit)
        write(*,*) " obliquit = ",obliquit
      end if

      endif !(.not. startfile_1D )
 
c  latitude/longitude
c  ------------------
      latitude(1)=0 ! default value for latitude
      PRINT *,'latitude (in degrees) ?'
      call getin("latitude",latitude(1))
      write(*,*) " latitude = ",latitude
      latitude=latitude*pi/180.E+0
      longitude=0.E+0
      longitude=longitude*pi/180.E+0

!  some initializations (some of which have already been
!  done above!) and loads parameters set in callphys.def
!  and allocates some arrays 
!Mars possible matter with dtphys in input and include!!!
! Initializations below should mimick what is done in iniphysiq for 3D GCM
      call init_interface_dyn_phys
      call init_regular_lonlat(1,1,longitude,latitude,
     &                   (/0.,0./),(/0.,0./))
      call init_geometry(1,longitude,latitude,
     &                   (/0.,0.,0.,0./),(/0.,0.,0.,0./),
     &                   cell_area)
! Ehouarn: init_vertial_layers called later (because disvert not called yet)
!      call init_vertical_layers(nlayer,preff,scaleheight,
!     &                      ap,bp,aps,bps,presnivs,pseudoalt)
      call init_dimphy(1,nlayer) ! Initialize dimphy module
      call phys_state_var_init(1,llm,nq,tname,
     .          day0,dayn,time,
     .          daysec,dtphys,
     .          rad,g,r,cpp,
     .          nqperes,nqfils)! MVals: variables isotopes
      call ini_fillgeom(1,latitude,longitude,(/1.0/))
      call conf_phys(1,llm,nq)

      ! in 1D model physics are called every time step
      ! ovverride iphysiq value that has been set by conf_phys
      if (iphysiq/=1) then
        write(*,*) "testphys1d: setting iphysiq=1"
        iphysiq=1
      endif 

c  Initialize albedo / soil thermal inertia
c  ----------------------------------------
c

      if(.not. startfile_1D ) then

      albedodat(1)=0.2 ! default value for albedodat
      PRINT *,'Albedo of bare ground ?'
      call getin("albedo",albedodat(1))
      write(*,*) " albedo = ",albedodat(1)
      albedo(1,1)=albedodat(1)

      inertiedat(1,1)=400 ! default value for inertiedat
      PRINT *,'Soil thermal inertia (SI) ?'
      call getin("inertia",inertiedat(1,1))
      write(*,*) " inertia = ",inertiedat(1,1)

      ice_depth = -1 ! default value: no ice
      CALL getin("subsurface_ice_depth",ice_depth)

      z0(1)=z0_default ! default value for roughness
      write(*,*) 'Surface roughness length z0 (m)?'
      call getin("z0",z0(1))
      write(*,*) " z0 = ",z0(1)

      endif !(.not. startfile_1D ) 

! Initialize local slope parameters (only matters if "callslope"
! is .true. in callphys.def)
      ! slope inclination angle (deg) 0: horizontal, 90: vertical
      theta_sl(1)=0.0 ! default: no inclination
      call getin("slope_inclination",theta_sl(1))
      ! slope orientation (deg)
      ! 0 == Northward, 90 == Eastward, 180 == Southward, 270 == Westward
      psi_sl(1)=0.0 ! default value
      call getin("slope_orientation",psi_sl(1))
      
      ! sub-slopes parameters (assuming no sub-slopes distribution for now). 
      def_slope(1)=-90 ! minimum slope angle
      def_slope(2)=90 ! maximum slope angle
      subslope_dist(1,1)=1 ! fraction of subslopes in mesh 
c
c  for the gravity wave scheme
c  ---------------------------------
c
      zmea(1)=0.E+0
      zstd(1)=0.E+0
      zsig(1)=0.E+0
      zgam(1)=0.E+0
      zthe(1)=0.E+0
c
c  for the slope wind scheme
c  ---------------------------------
c  
      hmons(1)=0.E+0
      PRINT *,'hmons is initialized to ',hmons(1)
      summit(1)=0.E+0
      PRINT *,'summit is initialized to ',summit(1)
      base(1)=0.E+0
c
c  Default values initializing the coefficients calculated later
c  ---------------------------------
c  
      tauscaling(1)=1. ! calculated in aeropacity_mod.F
      totcloudfrac(1)=1. ! calculated in watercloud_mod.F      

c   Specific initializations for "physiq"
c   -------------------------------------
c   surface geopotential is not used (or useful) since in 1D
c   everything is controled by surface pressure
      phisfi(1)=0.E+0

c   Initialization to take into account prescribed winds
c   ------------------------------------------------------
      ptif=2.E+0*omeg*sinlat(1)
 
c    geostrophic wind
      gru=10. ! default value for gru
      PRINT *,'zonal eastward component of the geostrophic wind (m/s) ?'
      call getin("u",gru)
      write(*,*) " u = ",gru
      grv=0. !default value for grv
      PRINT *,'meridional northward component of the geostrophic',
     &' wind (m/s) ?'
      call getin("v",grv)
      write(*,*) " v = ",grv

c     Initialize winds  for first time step
      DO ilayer=1,nlayer
         u(ilayer)=gru
         v(ilayer)=grv
         w(ilayer)=0 ! default: no vertical wind
      ENDDO

c     Initialize turbulente kinetic energy
      DO ilevel=1,nlevel
         q2(ilevel)=0.E+0
      ENDDO

c  CO2 ice on the surface
c  -------------------
      ! get the index of co2 tracer (not known at this stage)
      igcm_co2=0
      do iq=1,nq
        if (trim(tname(iq))=="co2") then
          igcm_co2=iq
        endif
      enddo
      if (igcm_co2==0) then
        write(*,*) "testphys1d error, missing co2 tracer!"
        stop
      endif

      if(.not. startfile_1D ) then
      qsurf(igcm_co2)=0.E+0 ! default value for co2ice
      PRINT *,'Initial CO2 ice on the surface (kg.m-2)'
      call getin("co2ice",qsurf(igcm_co2))
      write(*,*) " co2ice = ",qsurf(igcm_co2)
      endif !(.not. startfile_1D )

c
c  emissivity
c  ----------
      if(.not. startfile_1D ) then
      emis=emissiv
      IF (qsurf(igcm_co2).eq.1.E+0) THEN
         emis=emisice(1) ! northern hemisphere
         IF(latitude(1).LT.0) emis=emisice(2) ! southern hemisphere
      ENDIF
      endif !(.not. startfile_1D ) 
 

c  Compute pressures and altitudes of atmospheric levels 
c  ----------------------------------------------------------------

c    Vertical Coordinates
c    """"""""""""""""""""
      hybrid=.true.
      PRINT *,'Hybrid coordinates ?'
      call getin("hybrid",hybrid)
      write(*,*) " hybrid = ", hybrid

      CALL  disvert_noterre
      ! now that disvert has been called, initialize module vertical_layers_mod
      call init_vertical_layers(nlayer,preff,scaleheight,
     &                      ap,bp,aps,bps,presnivs,pseudoalt)

      DO ilevel=1,nlevel
        plev(ilevel)=ap(ilevel)+psurf*bp(ilevel)
      ENDDO

      DO ilayer=1,nlayer
        play(ilayer)=aps(ilayer)+psurf*bps(ilayer)
      ENDDO

      DO ilayer=1,nlayer
        zlay(ilayer)=-200.E+0 *r*log(play(ilayer)/plev(1))
     &   /g
      ENDDO


c  Initialize temperature profile
c  --------------------------------------
      pks=psurf**rcp

c altitude in km in profile: divide zlay by 1000
      tmp1(0)=0.E+0
      DO ilayer=1,nlayer
        tmp1(ilayer)=zlay(ilayer)/1000.E+0
      ENDDO

      call profile(nlayer+1,tmp1,tmp2)

      tsurf=tmp2(0)
      DO ilayer=1,nlayer
        temp(ilayer)=tmp2(ilayer)
      ENDDO
      

! Initialize soil properties and temperature
! ------------------------------------------
      volcapa=1.e6 ! volumetric heat capacity

      if(.not. startfile_1D ) then

! Initialize depths
! -----------------
       do isoil=1,nsoil
         layer(isoil)=2.e-4*(2.**(isoil-1)) ! layer depth
       enddo

! Creating the new soil inertia table if there is subsurface ice :
       IF (ice_depth.gt.0) THEN 
         iref = 1 ! ice/regolith boundary index
           IF (ice_depth.lt.layer(1)) THEN
             inertiedat(1,1) = sqrt( layer(1) /
     &        ( (ice_depth/inertiedat(1,1)**2) +
     &        ((layer(1)-ice_depth)/inertieice**2) ) )
             DO isoil=1,nsoil 
              inertiedat(1,isoil) = inertieice
             ENDDO    
           ELSE ! searching for the ice/regolith boundary :
           DO isoil=1,nsoil 
            IF ((ice_depth.ge.layer(isoil)).and.
     &         (ice_depth.lt.layer(isoil+1))) THEN
                  iref=isoil+1
                  EXIT
            ENDIF
           ENDDO
!         We then change the soil inertia table :
           DO isoil=1,iref-1 
            inertiedat(1,isoil) = inertiedat(1,1)
           ENDDO
!         We compute the transition in layer(iref)
           inertiedat(1,iref) = sqrt( (layer(iref)-layer(iref-1)) /
     &          ( ((ice_depth-layer(iref-1))/inertiedat(1,1)**2) +
     &          ((layer(iref)-ice_depth)/inertieice**2) ) ) 
!         Finally, we compute the underlying ice :
           DO isoil=iref+1,nsoil
            inertiedat(1,isoil) = inertieice
           ENDDO
         ENDIF ! (ice_depth.lt.layer(1))      
       ELSE ! ice_depth <0 all is set to surface thermal inertia
         DO isoil=1,nsoil
           inertiedat(1,isoil)=inertiedat(1,1) ! soil thermal inertia
         ENDDO
       ENDIF ! ice_depth.gt.0

       inertiesoil(1,:,1) = inertiedat(1,:)

       DO isoil = 1,nsoil
         tsoil(isoil)=tsurf(1)  ! soil temperature
       ENDDO

      endif !(.not. startfile_1D )

      flux_geo_tmp=0.
      call getin("flux_geo",flux_geo_tmp)
      flux_geo(:,:) = flux_geo_tmp

! Initialize depths
! -----------------
      do isoil=0,nsoil-1
        mlayer(isoil)=2.e-4*(2.**(isoil-0.5)) ! mid-layer depth
      enddo
      do isoil=1,nsoil
        layer(isoil)=2.e-4*(2.**(isoil-1)) ! layer depth
      enddo

c    Initialize traceurs
c    ---------------------------

      if (photochem.or.callthermos) then
         write(*,*) 'Initializing chemical species'
         ! flagthermo=0: initialize over all atmospheric layers
         flagthermo=0
         ! check if "h2o_vap" has already been initialized
         ! (it has been if there is a "profile_h2o_vap" file around)
         inquire(file="profile_h2o_vap",exist=present)
         if (present) then
           flagh2o=0 ! 0: do not initialize h2o_vap
         else
           flagh2o=1 ! 1: initialize h2o_vap in inichim_newstart
         endif
         
         ! hack to accomodate that inichim_newstart assumes that
         ! q & psurf arrays are on the dynamics scalar grid
         allocate(qdyn(2,1,llm,nq),psdyn(2,1))
         qdyn(1,1,1:llm,1:nq)=q(1:llm,1:nq)
         psdyn(1:2,1)=psurf
         call inichim_newstart(ngrid,nq,qdyn,qsurf,psdyn,
     $                         flagh2o,flagthermo)
         q(1:llm,1:nq)=qdyn(1,1,1:llm,1:nq)
      endif

c Check if the surface is a water ice reservoir 
c --------------------------------------------------
      if(.not. startfile_1D ) then
      watercap(1,:)=0 ! Initialize watercap
      endif !(.not. startfile_1D )
      watercaptag(1)=.false. ! Default: no water ice reservoir
      print *,'Water ice cap on ground ?'
      call getin("watercaptag",watercaptag)
      write(*,*) " watercaptag = ",watercaptag
      
c Check if the atmospheric water profile is specified
c ---------------------------------------------------
      ! Adding an option to force atmospheric water values JN
      atm_wat_profile=-1 ! Default: free atm wat profile
      print *,'Force atmospheric water vapor profile ?'
      call getin("atm_wat_profile",atm_wat_profile)
      write(*,*) "atm_wat_profile = ", atm_wat_profile
      if (atm_wat_profile.EQ.-1) then
        write(*,*) "Free atmospheric water vapor profile"
        write(*,*) "Total water is conserved on the column"
      else if (atm_wat_profile.EQ.0) then
        write(*,*) "Dry atmospheric water vapor profile"
      else if ((atm_wat_profile.GT.0).and.(atm_wat_profile.LE.1)) then
        write(*,*) "Prescribed atmospheric water vapor MMR profile"
        write(*,*) "Unless it reaches saturation (maximal value)"
        write(*,*) "MMR chosen : ", atm_wat_profile
      endif 


c    Initialization for GRADS outputs in "g1d.dat" and "g1d.ctl"
c    ----------------------------------------------------------------
c    (output done in "writeg1d", typically called by "physiq.F")

        g1d_nlayer=nlayer
        g1d_nomfich='g1d.dat'
        g1d_unitfich=40
        g1d_nomctl='g1d.ctl'
        g1d_unitctl=41
        g1d_premier=.true.
        g2d_premier=.true.

c  Write a "startfi" file
c  --------------------
c  This file will be read during the first call to "physiq".
c  It is needed to transfert physics variables to "physiq"...

      if(.not. startfile_1D ) then

      call physdem0("startfi.nc",longitude,latitude,nsoilmx,ngrid,
     &              llm,nq,dtphys,float(day0),0.,cell_area,
     &              albedodat,inertiedat,def_slope,subslope_dist)
      call physdem1("startfi.nc",nsoilmx,ngrid,llm,nq,
     &              dtphys,time,
     &              tsurf,tsoil,inertiesoil,albedo,emis,
     &              q2,qsurf,tauscaling,
     &              totcloudfrac,wstar,watercap)
      endif !(.not. startfile_1D )

c=======================================================================
c  1D MODEL TIME STEPPING LOOP
c=======================================================================
c
      firstcall=.true.
      lastcall=.false.
      DO idt=1,ndt
        IF (idt.eq.ndt) lastcall=.true.
c        IF (idt.eq.ndt-day_step-1) then       !test
c         lastcall=.true.
c         call solarlong(day*1.0,zls)
c         write(103,*) 'Ls=',zls*180./pi
c         write(103,*) 'Lat=', latitude(1)*180./pi
c         write(103,*) 'Tau=', tauvis/odpref*psurf
c         write(103,*) 'RunEnd - Atmos. Temp. File'
c         write(103,*) 'RunEnd - Atmos. Temp. File'
c         write(104,*) 'Ls=',zls*180./pi
c         write(104,*) 'Lat=', latitude(1)
c         write(104,*) 'Tau=', tauvis/odpref*psurf
c         write(104,*) 'RunEnd - Atmos. Temp. File'
c        ENDIF

c     compute geopotential
c     ~~~~~~~~~~~~~~~~~~~~~
      DO ilayer=1,nlayer
        s(ilayer)=(aps(ilayer)/psurf+bps(ilayer))**rcp
        h(ilayer)=cpp*temp(ilayer)/(pks*s(ilayer))
      ENDDO
      phi(1)=pks*h(1)*(1.E+0-s(1))
      DO ilayer=2,nlayer
         phi(ilayer)=phi(ilayer-1)+
     &               pks*(h(ilayer-1)+h(ilayer))*.5E+0
     &                  *(s(ilayer-1)-s(ilayer))

      ENDDO

c       Force atmospheric water if asked
c       Added "atm_wat_profile" flag (JN)
c       -------------------------------------
        call watersat(nlayer,temp,play,zqsat)
        DO iq = 1, nq
          IF ((iq.eq.igcm_h2o_vap).and.(atm_wat_profile.eq.0)) THEN
            DO ilayer=1,nlayer
             q(ilayer,igcm_h2o_vap)=0.
c             write(*,*) "atm_wat_profile dry"
            ENDDO! ilayer=1,nlayer
          ELSE IF((iq.eq.igcm_h2o_vap).and.(atm_wat_profile.gt.0)
     &             .and.(atm_wat_profile.le.1)) THEN
            DO ilayer=1,nlayer
             q(ilayer,igcm_h2o_vap)=min(zqsat(ilayer),atm_wat_profile)
c             write(*,*) "atm_wat_profile wet"
            ENDDO! ilayer=1,nlayer
          ELSE IF ((iq.eq.igcm_h2o_ice).and.
     &                  (atm_wat_profile.ne.-1)) THEN
            DO ilayer=1,nlayer
             q(ilayer,igcm_h2o_ice)=0.
c             write(*,*) "atm_wat_profile : reset ice"
            ENDDO! ilayer=1,nlayer
          ENDIF  !((iq.eq.igcm_h2o_vap).and.(atm_wat_profile.eq.2)) THEN
        ENDDO
        CALL write_output('qsat',
     &                         'qsat',
     &                         'kg/kg',zqsat(:))



!      write(*,*) "testphys1d avant q", q(1,:)
c       call physics
c       --------------------
      CALL physiq (1,llm,nq,
     ,     firstcall,lastcall,
     ,     day,time,dtphys,
     ,     plev,play,phi,
     ,     u, v,temp, q,  
     ,     w,
C - outputs
     s     du, dv, dtemp, dq,dpsurf)
!      write(*,*) "testphys1d apres q", q(1,:)


c       wind increment : specific for 1D
c       --------------------------------
 
c       The physics compute the tendencies on u and v,
c       here we just add Coriolos effect
c
c       DO ilayer=1,nlayer
c          du(ilayer)=du(ilayer)+ptif*(v(ilayer)-grv)
c          dv(ilayer)=dv(ilayer)+ptif*(-u(ilayer)+gru)
c       ENDDO

c       For some tests : No coriolis force at equator
c       if(latitude(1).eq.0.) then
          DO ilayer=1,nlayer
             du(ilayer)=du(ilayer)+ (gru-u(ilayer))/1.e4
             dv(ilayer)=dv(ilayer)+ (grv-v(ilayer))/1.e4
          ENDDO
c       end if
c      
c
c       Compute time for next time step
c       ---------------------------------------
        firstcall=.false.
        time=time+dtphys/daysec
        IF (time.gt.1.E+0) then
            time=time-1.E+0
            day=day+1
        ENDIF

c       compute winds and temperature for next time step
c       ----------------------------------------------------------

        DO ilayer=1,nlayer
           u(ilayer)=u(ilayer)+dtphys*du(ilayer)
           v(ilayer)=v(ilayer)+dtphys*dv(ilayer)
           temp(ilayer)=temp(ilayer)+dtphys*dtemp(ilayer)
        ENDDO

c       compute pressure for next time step 
c       ----------------------------------------------------------

           psurf=psurf+dtphys*dpsurf(1)   ! surface pressure change
           DO ilevel=1,nlevel
             plev(ilevel)=ap(ilevel)+psurf*bp(ilevel)
           ENDDO
           DO ilayer=1,nlayer
             play(ilayer)=aps(ilayer)+psurf*bps(ilayer)
           ENDDO

!       increment tracers
        DO iq = 1, nq
          DO ilayer=1,nlayer
             q(ilayer,iq)=q(ilayer,iq)+dtphys*dq(ilayer,iq)
          ENDDO
        ENDDO

      ENDDO   ! of idt=1,ndt ! end of time stepping loop
      
      ! update the profiles files at the end of the run
      write_prof=.false.
      call getin("write_prof",write_prof)
      IF (write_prof) then
              DO iq = 1, nq
        	call writeprofile(nlayer,q(:,iq),noms(iq),iq)
              ENDDO
      ENDIF


c    ========================================================
c    OUTPUTS
c    ========================================================

c    finalize and close grads files "g1d.dat" and "g1d.ctl"

c        CALL endg1d(1,nlayer,zphi/(g*1000.),ndt)
        CALL endg1d(1,nlayer,zlay/1000.,ndt)

      write(*,*) "testphys1d: Everything is cool."

      END
 
c***********************************************************************
c***********************************************************************
c     Dummy subroutines used only in 3D, but required to
c     compile testphys1d (to cleanly use writediagfi)

      subroutine gr_fi_dyn(nfield,ngrid,im,jm,pfi,pdyn)

      IMPLICIT NONE

      INTEGER im,jm,ngrid,nfield
      REAL pdyn(im,jm,nfield)
      REAL pfi(ngrid,nfield)
      
      if (ngrid.ne.1) then
        write(*,*) "gr_fi_dyn error: in 1D ngrid should be 1!!!"
        stop
      endif
      
      pdyn(1,1,1:nfield)=pfi(1,1:nfield)
      
      end
 
c***********************************************************************
c***********************************************************************