#define c_str(s) ('s\0')
      subroutine init_all
      implicit real(a-h,o-z),integer(i-n)
c************************************************************************
      include 'comm_para.h'
      include 'comm_main.h'
      include 'comm_new.h'
      include 'comm_data.h'
      include 'diffiso.h'
      include 'comm_tracer.h'
      include 'comm_nao.h'
      include 'comm_bio.h'
      include 'comm_tios.h'
      real inp_flt

      npten = MPTEN

c...............getting input & output filenames from the command line
      call inout (ioin)
 
c...............input model parameters.
      call model_input(npt,mbox)
      call model_memory (nxp, nyp, nz, npt) 
      call make_iox (nxp, nyp, mask, iox, nlok, lok, nsponge, lsponge,
     *               nrelax, lrelax, iglob, inx, iny)
      if (nrelax.gt.MAXSP) then
         print*,'increase MAXSP'
         stop
      endif
      call scaset (iox,xm,ym,xp,yp,f,emx,emy,cosl,cosli,emx2,emy2,tp,dx2i,dy2i,ycos)
      call ylat_degrees(npt,nxp,iox,ym,y_deg)
      call depth_init (npt, zin)

      call new_topo (nxp, nyp, nz, npt, zin, dzin, hin, nsig, sigma, dept, 
     *               h, nptk, nzi)

      call bndrys(npt,iox,tp,isxk,isyk,mask,h,nzi,
     *            isk,iyk,lxxk,lyyk,lxyk,lyxk,snxk,snyk,lok,
     *            lpbcwk,lpbcek,ifxk,ifpxk,ifyk,dept)

      call bndrys_new(npt,nzi,lxxk,lyyk,nzibx,nziby)

c..............compute some geometry stuff
      call aarea_new(npt,nxp,nyp,nz,lxxk,lyyk,snxk,snyk,mask,iox,emx,emy,
     *   area,basin,isk,nzi,h,isyk,lpbcwk,lpbcek,saxmk,saxpk,saymk,saypk,
     *   tp,sxp,syp,sxm,sym,mbox)

      if (irest .eq. 0) then
         NEWRUN = .true. 
         call init_rstrt (nxp, nyp, nz, npt, zin, tp)
      else
         NEWRUN = irest .ge. 3 .or. irest .lt. 0
         if (irest.eq.1 .or. irest.eq.2) CALL TIOS_CNTRL (3, 1)
         call read_rstrt (nxp, nyp, nz, npt)
      endif
c..............initialize Temperature/Salinity Climatology (for sponges):

      call clim_init(npt,nstart,hin,sigma,dzin,h,
     *                 hclim,tclim,sclim,dclim,pclim,tp,nsponge,lsponge)


      if (irest .eq. 0) then
         call h_init (npt, nz, nzi, nstart, h, hclim)
         call temp_init (npt,nz,nstart,t_in,t,tclim)
         call salt_init (npt,nz,nstart,s_in,sal,sclim)
      endif

      call situ_dens (npt, nz, nzi, t, sal, dens, h)
      call potn_dens (npt, nz, nzi, t, sal, pdens) 
      if (diffiso_alpha.gt.0.or.initkmap.eq.5) then
          call slope(npt,pdens,dens,nz,nzi,h,lxxk,lyyk,lxyk,lyxk,snxk,
     *    snyk,isyk,isk,lok,tp,lpbcwk,lpbcek,saxmk,saxpk,saymk,saypk,xmld)
      endif

      if (use_diffiso.or.itank.eq.1) call Kmap_init (npt, nz, nxp, nyp)

c..............initialize Heat/EP forcing:
      if (use_ice) then
         call amlice_data_init(nstart,npt,nxp,nyp, 
     *        t, sst, cld, solr, sal, sss, prcp, nrelax, lrelax, nstep_pbl)
         if (use_dyice) then
          call init_dyice (nxp,nyp,ntrac_sur,npt,iox,xm,ym,delt)
         endif
         
      else
         call hflx_init (nstart,npt,nxp,nyp,t,sst,cld,solr,nrelax,lrelax)
         call ep_init (nstart, npt, sal, sss, prcp)
      endif

      call diff_init(npt,nz,iglob,mgrid)

c..............initialize Wind forcing:
      tenso = enso_start + enso_scale * nstart
      tmonth = mod(tenso,12.)   ! month of the year, [0,12)
      if (tmonth.lt.0) tmonth = tmonth + 12.
      if (inao.eq.1) tscl_anom = cos ( freq_nao*(tenso-1.5) )

      call tau_init (nstart, npt, tscl_anom, dtx,dty, taux_anom,tauy_anom,tmonth) 
      if (use_river) call river_init (npt,nxp,nyp,nz,nzi,xm,ym,iox,h)

c..............initialize grad(H)/H:
      call gradH_init (nxp,nyp,npt, zin, gradH, dept,
     *     saxpk,saypk,isk,tp,dx2i,dy2i,ycos,inx,iny,lxxk,lyyk)

      dt_sub  = delt * D2SEC
      dnt     = dt_sub * real(ncyc)
      dtmix   = dt_sub * real(limp)
      dtbio   = delt * 24.  ! biology time step, in hours
      dtshap  = dt_sub * real(nshapu)
      DLT_MIX = 2.0 * dtmix 

      if (use_trac ) call tracer_input(npt,nz,ntimes,nstart,nstep)
      if (use_trac .or. use_bio) then
         call tracer_init(npt,nz,nzi,nstart,nxp,nyp,iox,tr,t,h,xm,ym,trclim)
      endif
      if (use_bio) then
         ibio = ntrac*npt*nz + 1
         ibio1 = ntrac*npt*(nz+1) + 1
         if (use_bio_old) then
         call BIOINI_old(TR(ibio),FTR(ibio1),ntrac_bio,NFLBIO,NZ,NZI,NPT,
     *        KBIO,XZM,XZE,XPAR,XPARZE,XPARZM,FLXBIO,XLE,XLM,XLT,XLN)
         else
 
         call BIOINI(TR(ibio),FTR(ibio1),ntrac_bio,NFLBIO,NZ,NZI,NPT,KBIO,XPAR,
     *        FPAR,FLXBIO,XLE,XLT,XLN,XZE,XZM)
         endif
      endif
         
c..............initialize TIOS io-system
      call init_data_out (ftios, fbt, nxp, nyp, npt, nz, xm, ym, en)

      CALL TIOS_CNTRL (4, delt)
c
      iday_new  = int(nstart*delt)
      iday_curr = iday_new

      if (ibaro .ne. 0) then
         eps = bt_fac/dt_sub
         call init_baro (iglob,eps,nxp,nyp,nxyc,ncsk,iox,nbxk,lxxk,
     *        nbyk,lyxk,alon,blon,alat,blat,xm,ym,dept,dep_max,gradH,adelt)
         if (irest .ne. 0) then
            call make_big (nxp,nyp,npt,psi,psin,inx,iny,isk,mask)
            call curlH (nxp,nyp,npt,psin,dept,dx2i,dy2i,ycos,inx,iny,ubar,vbar)
         endif
      endif

      istep           = 0
      i_baro_step     = 0
      i_slope_step    = 0
      i_mix_step      = 0
      largestep_count = 0
      mix_count       = 0
      i_propag_step   = 0

      anom_fac_temp = inp_flt(c_str(Anom_fac_temp), 2.)
      anom_fac_trac = inp_flt(c_str(Anom_fac_trac), 2.)
      if (irest .le. 0) then
         call add_anom(npt,nxp,nyp,nz,nzi,xm,ym,iox,h,t,anom_fac_temp)
         if (ntrac.eq.1) then
            call add_anom(npt,nxp,nyp,nz,nzi,xm,ym,iox,h,tr,anom_fac_trac)
         endif
      endif

      call kmixinit
         
      return
      end