timemanager_mpi.f90 33.6 KB
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!**********************************************************************
! Copyright 1998,1999,2000,2001,2002,2005,2007,2008,2009,2010         *
! Andreas Stohl, Petra Seibert, A. Frank, Gerhard Wotawa,             *
! Caroline Forster, Sabine Eckhardt, John Burkhart, Harald Sodemann   *
!                                                                     *
! This file is part of FLEXPART.                                      *
!                                                                     *
! FLEXPART 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.                                 *
!                                                                     *
! FLEXPART 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 FLEXPART.  If not, see <http://www.gnu.org/licenses/>.   *
!**********************************************************************

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subroutine timemanager(metdata_format)
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!*****************************************************************************
!                                                                            *
! Handles the computation of trajectories, i.e. determines which             *
! trajectories have to be computed at what time.                             *
! Manages dry+wet deposition routines, radioactive decay and the computation *
! of concentrations.                                                         *
!                                                                            *
!     Author: A. Stohl                                                       *
!                                                                            *
!     20 May 1996                                                            *
!                                                                            *
!*****************************************************************************
!  Changes, Bernd C. Krueger, Feb. 2001:                                     *
!        Call of convmix when new windfield is read                          *
!------------------------------------                                        *
!  Changes Petra Seibert, Sept 2002                                          *
!     fix wet scavenging problem                                             *
!     Code may not be correct for decay of deposition!                       *
!  Changes Petra Seibert, Nov 2002                                           *
!     call convection BEFORE new fields are read in BWD mode                 *
!  Changes Caroline Forster, Feb 2005                                        *
!   new interface between flexpart and convection scheme                     *
!   Emanuel's latest subroutine convect43c.f is used                         *
!  Changes Stefan Henne, Harald Sodemann, 2013-2014                          *
!   added netcdf output code                                                 *
!  Changes Espen Sollum 2014                                                 *
!   MPI version                                                              *
!   Variables uap,ucp,uzp,us,vs,ws,cbt now in module com_mod                 *
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!  Unified ECMWF and GFS builds                                              *
!   Marian Harustak, 12.5.2017                                               *
!   - Added passing of metdata_format as it was needed by called routines    *
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!*****************************************************************************
!                                                                            *
! Variables:                                                                 *
! dep                .true. if either wet or dry deposition is switched on   *
! decay(maxspec) [1/s] decay constant for radioactive decay                  *
! drydep             .true. if dry deposition is switched on                 *
! ideltas [s]        modelling period                                        *
! itime [s]          actual temporal position of calculation                 *
! ldeltat [s]        time since computation of radioact. decay of depositions*
! loutaver [s]       averaging period for concentration calculations         *
! loutend [s]        end of averaging for concentration calculations         *
! loutnext [s]       next time at which output fields shall be centered      *
! loutsample [s]     sampling interval for averaging of concentrations       *
! loutstart [s]      start of averaging for concentration calculations       *
! loutstep [s]       time interval for which concentrations shall be         *
!                    calculated                                              *
! npoint(maxpart)    index, which starting point the trajectory has          *
!                    starting positions of trajectories                      *
! nstop              serves as indicator for fate of particles               *
!                    in the particle loop                                    *
! nstop1             serves as indicator for wind fields (see getfields)     *
! memstat            additional indicator for wind fields (see getfields)    *
! outnum             number of samples for each concentration calculation    *
! prob               probability of absorption at ground due to dry          *
!                    deposition                                              *
! wetdep             .true. if wet deposition is switched on                 *
! weight             weight for each concentration sample (1/2 or 1)         *
! uap(maxpart),ucp(maxpart),uzp(maxpart) = random velocities due to          *
!                    turbulence                                              *
! us(maxpart),vs(maxpart),ws(maxpart) = random velocities due to inter-      *
!                    polation                                                *
! xtra1(maxpart), ytra1(maxpart), ztra1(maxpart) =                           *
!                    spatial positions of trajectories                       *
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! metdata_format     format of metdata (ecmwf/gfs)                           *
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!                                                                            *
! Constants:                                                                 *
! maxpart            maximum number of trajectories                          *
!                                                                            *
!*****************************************************************************

  use unc_mod
  use point_mod
  use xmass_mod
  use flux_mod
  use outg_mod
  use oh_mod
  use par_mod
  use com_mod
  use mpi_mod
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#ifdef USE_NCF
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  use netcdf_output_mod, only: concoutput_netcdf,concoutput_nest_netcdf,&
       &concoutput_surf_netcdf,concoutput_surf_nest_netcdf
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#endif
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  implicit none

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  integer :: metdata_format
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  logical :: reqv_state=.false. ! .true. if waiting for a MPI_Irecv to complete
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  integer :: j,ks,kp,l,n,itime=0,nstop,nstop1,memstat=0
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! integer :: ksp
  integer :: ip
  integer :: loutnext,loutstart,loutend
  integer :: ix,jy,ldeltat,itage,nage
  integer :: i_nan=0,ii_nan,total_nan_intl=0  !added by mc to check instability in CBL scheme 
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  integer :: numpart_tot_mpi ! for summing particles on all processes
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  real :: outnum,weight,prob(maxspec)
  real :: decfact

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  real(sp) :: gridtotalunc
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  real(dep_prec) :: drygridtotalunc=0_dep_prec,wetgridtotalunc=0_dep_prec,&
       & drydeposit(maxspec)=0_dep_prec
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  real :: xold,yold,zold,xmassfract
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  real, parameter :: e_inv = 1.0/exp(1.0)
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! Measure time spent in timemanager
  if (mp_measure_time) call mpif_mtime('timemanager',0)

! First output for time 0
!************************

  loutnext=loutstep/2
  outnum=0.
  loutstart=loutnext-loutaver/2
  loutend=loutnext+loutaver/2


!**********************************************************************
! Loop over the whole modelling period in time steps of mintime seconds
!**********************************************************************

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  if (lroot.or.mp_dev_mode) then
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  !  write(*,45) itime,numpart*mp_partgroup_np,gridtotalunc,wetgridtotalunc,drygridtotalunc
    write(*,46) float(itime)/3600,itime,numpart*mp_partgroup_np
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    if (verbosity.gt.0) then
      write (*,*) 'timemanager> starting simulation'
    end if
  end if ! (lroot)

!CGZ-lifetime: set lifetime to 0
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  ! checklifetime(:,:)=0
  ! species_lifetime(:,:)=0
  ! print*, 'Initialized lifetime'
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!CGZ-lifetime: set lifetime to 0



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  do itime=0,ideltas,lsynctime
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! Computation of wet deposition, OH reaction and mass transfer
! between two species every lsynctime seconds
! maybe wet depo frequency can be relaxed later but better be on safe side
! wetdepo must be called BEFORE new fields are read in but should not
! be called in the very beginning before any fields are loaded, or
! before particles are in the system
! Code may not be correct for decay of deposition
! changed by Petra Seibert 9/02
!********************************************************************

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    if (mp_dbg_mode) write(*,*) 'myid, itime: ',mp_pid,itime
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    if (WETDEP .and. itime .ne. 0 .and. numpart .gt. 0) then
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      if (verbosity.gt.0) then
        write (*,*) 'timemanager> call wetdepo'
      endif

      if (mp_measure_time) call mpif_mtime('wetdepo',0)
        
! readwind process skips this step
      if (.not.(lmpreader.and.lmp_use_reader)) then
        call wetdepo(itime,lsynctime,loutnext)
      end if

      if (mp_measure_time) call mpif_mtime('wetdepo',1)
    end if

    if (OHREA .and. itime .ne. 0 .and. numpart .gt. 0) then
! readwind process skips this step
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      if (.not.(lmpreader.and.lmp_use_reader)) then
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        call ohreaction(itime,lsynctime,loutnext)
      endif
    end if

    if (assspec .and. itime .ne. 0 .and. numpart .gt. 0) then
      stop 'associated species not yet implemented!'
!     call transferspec(itime,lsynctime,loutnext)
    endif


! compute convection for backward runs
!*************************************

    if ((ldirect.eq.-1).and.(lconvection.eq.1).and.(itime.lt.0)) then
      if (verbosity.gt.0) then
        write (*,*) 'timemanager> call convmix -- backward'
      endif
! readwind process skips this step
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      if (.not.(lmpreader.and.lmp_use_reader)) call convmix(itime,metdata_format)
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    endif

! Get necessary wind fields if not available
!*******************************************
    if (verbosity.gt.0 .and. lmpreader) then
      write (*,*) 'timemanager> call getfields'
    endif

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! This time measure includes reading/MPI communication (for the reader process),
! or MPI communication time only (for other processes)
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    if (mp_measure_time) call mpif_mtime('getfields',0)

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    call getfields(itime,nstop1,memstat,metdata_format)
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    if (mp_measure_time) call mpif_mtime('getfields',1)

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! Broadcast fields to all MPI processes 
! Skip if all processes have called getfields or if no new fields
!*****************************************************************

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    if (mp_measure_time.and..not.(lmpreader.and.lmp_use_reader)) call mpif_mtime('getfields',0)

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! Two approaches to MPI getfields is implemented:
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! Version 1 (lmp_sync=.true.) uses a read-ahead process where send/recv is done
! in sync at start of each new field time interval
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!
! Version 2 (lmp_sync=.false.) is for holding three fields in memory. Uses a
! read-ahead process where sending/receiving of the 3rd fields is done in
! the background in parallel with performing computations with fields 1&2
!********************************************************************************

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    if (lmp_sync.and.lmp_use_reader.and.memstat.gt.0) then
      call mpif_gf_send_vars(memstat)
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      if (numbnests>0) call mpif_gf_send_vars_nest(memstat)
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! Version 2  (lmp_sync=.false.) is also used whenever 2 new fields are
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! read (as at first time step), in which case async send/recv is impossible.
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    else if (.not.lmp_sync.and.lmp_use_reader.and.memstat.ge.32) then
      call mpif_gf_send_vars(memstat)
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      if (numbnests>0) call mpif_gf_send_vars_nest(memstat)
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    end if

    if (.not.lmp_sync) then
    
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! Reader process:
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      if (memstat.gt.0..and.memstat.lt.32.and.lmp_use_reader.and.lmpreader) then
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        if (mp_dev_mode) write(*,*) 'Reader process: calling mpif_gf_send_vars_async' 
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        call mpif_gf_send_vars_async(memstat)
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        if (numbnests>0) call mpif_gf_send_vars_nest_async(memstat)
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      end if

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! Completion check:
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! Issued at start of each new field period. 
      if (memstat.ne.0.and.memstat.lt.32.and.lmp_use_reader) then
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        call mpif_gf_request
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      end if

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! Recveiving process(es):
! eso TODO: at this point we do not know if clwc/ciwc will be available
! at next time step. Issue receive request anyway, cancel at mpif_gf_request
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      if (memstat.gt.0.and.lmp_use_reader.and..not.lmpreader) then
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        if (mp_dev_mode) write(*,*) 'Receiving process: calling mpif_gf_send_vars_async. PID: ', mp_pid
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        call mpif_gf_recv_vars_async(memstat)
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        if (numbnests>0) call mpif_gf_recv_vars_nest_async(memstat)
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      end if

    end if

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    if (mp_measure_time.and..not.(lmpreader.and.lmp_use_reader)) call mpif_mtime('getfields',1)

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! For validation and tests: call the function below to set all fields to simple
! homogeneous values
!    if (mp_dev_mode) call set_fields_synthetic

!*******************************************************************************

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    if (lmpreader.and.nstop1.gt.1) stop 'NO METEO FIELDS AVAILABLE'

! Reader process goes back to top of time loop (unless simulation end)
!*********************************************************************

    if (lmpreader.and.lmp_use_reader) then
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      if (itime.lt.ideltas*ldirect) then
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        cycle
      else
        goto 999
      end if
    end if


! Get hourly OH fields if not available 
!****************************************************
    if (OHREA) then
      if (verbosity.gt.0) then
        write (*,*) 'timemanager> call gethourlyOH'
      endif
      call gethourlyOH(itime)
    endif


! Release particles
!******************

    if (verbosity.gt.0.and.lroot) then
      write (*,*) 'timemanager>  Release particles'
    endif

    if (mdomainfill.ge.1) then
      if (itime.eq.0) then
        if (verbosity.gt.0) then
          write (*,*) 'timemanager>  call init_domainfill'
        endif
        call init_domainfill
      else
        if (verbosity.gt.0.and.lroot) then
          write (*,*) 'timemanager>  call boundcond_domainfill'
        endif
        call boundcond_domainfill(itime,loutend)
      endif
    else
      if (verbosity.gt.0.and.lroot) then
        print*,'call releaseparticles'  
      endif
      call releaseparticles(itime)
    endif


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! Check if particles should be redistributed among processes
!***********************************************************
    call mpif_calculate_part_redist(itime)


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! Compute convective mixing for forward runs
! for backward runs it is done before next windfield is read in
!**************************************************************

    if ((ldirect.eq.1).and.(lconvection.eq.1)) then
      if (verbosity.gt.0) then
        write (*,*) 'timemanager> call convmix -- forward'
      endif
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      call convmix(itime,metdata_format)
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    endif

! If middle of averaging period of output fields is reached, accumulated
! deposited mass radioactively decays
!***********************************************************************

    if (DEP.and.(itime.eq.loutnext).and.(ldirect.gt.0)) then
      do ks=1,nspec
        do kp=1,maxpointspec_act
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          if (decay(ks).gt.0.) then ! TODO move this statement up 2 levels
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            do nage=1,nageclass
              do l=1,nclassunc
! Mother output grid
                do jy=0,numygrid-1
                  do ix=0,numxgrid-1
                    wetgridunc(ix,jy,ks,kp,l,nage)= &
                         wetgridunc(ix,jy,ks,kp,l,nage)* &
                         exp(-1.*outstep*decay(ks))
                    drygridunc(ix,jy,ks,kp,l,nage)= &
                         drygridunc(ix,jy,ks,kp,l,nage)* &
                         exp(-1.*outstep*decay(ks))
                  end do
                end do
! Nested output grid
                if (nested_output.eq.1) then
                  do jy=0,numygridn-1
                    do ix=0,numxgridn-1
                      wetgriduncn(ix,jy,ks,kp,l,nage)= &
                           wetgriduncn(ix,jy,ks,kp,l,nage)* &
                           exp(-1.*outstep*decay(ks))
                      drygriduncn(ix,jy,ks,kp,l,nage)= &
                           drygriduncn(ix,jy,ks,kp,l,nage)* &
                           exp(-1.*outstep*decay(ks))
                    end do
                  end do
                endif
              end do
            end do
          endif
        end do
      end do
    endif


!!! CHANGE: These lines may be switched on to check the conservation
!!! of mass within FLEXPART
!   if (itime.eq.loutnext) then
!   do 247 ksp=1, nspec
!   do 247 kp=1, maxpointspec_act
!47         xm(ksp,kp)=0.

!   do 249 ksp=1, nspec
!     do 249 j=1,numpart
!          if (ioutputforeachrelease.eq.1) then
!            kp=npoint(j)
!          else
!            kp=1
!          endif
!       if (itra1(j).eq.itime) then
!          xm(ksp,kp)=xm(ksp,kp)+xmass1(j,ksp)
!         write(*,*) 'xmass: ',xmass1(j,ksp),j,ksp,nspec
!       endif
!49     continue
!  do 248 ksp=1,nspec
!  do 248 kp=1,maxpointspec_act
!  xm_depw(ksp,kp)=0.
!  xm_depd(ksp,kp)=0.
!     do 248 nage=1,nageclass
!       do 248 ix=0,numxgrid-1
!         do 248 jy=0,numygrid-1
!           do 248 l=1,nclassunc
!              xm_depw(ksp,kp)=xm_depw(ksp,kp)
!    +                  +wetgridunc(ix,jy,ksp,kp,l,nage)
!48                 xm_depd(ksp,kp)=xm_depd(ksp,kp)
!    +                  +drygridunc(ix,jy,ksp,kp,l,nage)
!             do 246 ksp=1,nspec
!46                    write(88,'(2i10,3e12.3)')
!    +              itime,ksp,(xm(ksp,kp),kp=1,maxpointspec_act),
!    +                (xm_depw(ksp,kp),kp=1,maxpointspec_act),
!    +                (xm_depd(ksp,kp),kp=1,maxpointspec_act)
!  endif
!!! CHANGE




! Check whether concentrations are to be calculated
!**************************************************

    if ((ldirect*itime.ge.ldirect*loutstart).and. &
         (ldirect*itime.le.ldirect*loutend)) then ! add to grid
      if (mod(itime-loutstart,loutsample).eq.0) then

! If we are exactly at the start or end of the concentration averaging interval,
! give only half the weight to this sample
!*****************************************************************************

        if ((itime.eq.loutstart).or.(itime.eq.loutend)) then
          weight=0.5
        else
          weight=1.0
        endif
        outnum=outnum+weight

        call conccalc(itime,weight)

      endif

! :TODO: MPI output of particle positions;  each process sequentially
!   access the same file
      if ((mquasilag.eq.1).and.(itime.eq.(loutstart+loutend)/2)) &
           call partoutput_short(itime)    ! dump particle positions in extremely compressed format


! Output and reinitialization of grid
! If necessary, first sample of new grid is also taken
!*****************************************************

      if ((itime.eq.loutend).and.(outnum.gt.0.)) then
        if ((iout.le.3.).or.(iout.eq.5)) then

! MPI: Root process collects/sums grids
!**************************************
          call mpif_tm_reduce_grid

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          if (mp_measure_time) call mpif_mtime('iotime',0)
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          if (surf_only.ne.1) then
            if (lroot) then
              if (lnetcdfout.eq.1) then 
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#ifdef USE_NCF
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                call concoutput_netcdf(itime,outnum,gridtotalunc,wetgridtotalunc,&
                     &drygridtotalunc)
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#endif
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              else 
                call concoutput(itime,outnum,gridtotalunc,wetgridtotalunc,drygridtotalunc)
              endif
            else
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! zero arrays on non-root processes
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              gridunc(:,:,:,:,:,:,:)=0.
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              creceptor(:,:)=0.
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            end if
          else 
            if (lroot) then
              if (lnetcdfout.eq.1) then
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#ifdef USE_NCF
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                call concoutput_surf_netcdf(itime,outnum,gridtotalunc,wetgridtotalunc,&
                     &drygridtotalunc)
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#endif
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              else
                call concoutput_surf(itime,outnum,gridtotalunc,wetgridtotalunc,drygridtotalunc)
              end if
            else
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! zero arrays on non-root processes
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              gridunc(:,:,:,:,:,:,:)=0.
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              creceptor(:,:)=0.
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            endif
          endif
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          if (mp_measure_time) call mpif_mtime('iotime',1)
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          if (nested_output.eq.1) then

! MPI: Root process collects/sums nested grids
!*********************************************
            call mpif_tm_reduce_grid_nest
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            if (mp_measure_time) call mpif_mtime('iotime',0)
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            if (lnetcdfout.eq.0) then
              if (surf_only.ne.1) then

                if (lroot) then
                  call concoutput_nest(itime,outnum)
                else
                  griduncn(:,:,:,:,:,:,:)=0.
                end if

              else  ! :TODO: check for zeroing in the netcdf module
                call concoutput_surf_nest(itime,outnum)
              end if
            else
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#ifdef USE_NCF
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              if (surf_only.ne.1) then
                if (lroot) then              
                  call concoutput_nest_netcdf(itime,outnum)
                else
                  griduncn(:,:,:,:,:,:,:)=0.
                end if
              else 
                if (lroot) then
                  call concoutput_surf_nest_netcdf(itime,outnum)
                else
                  griduncn(:,:,:,:,:,:,:)=0.
                end if
              endif
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#endif
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            end if
          end if
          outnum=0.
        endif
        if ((iout.eq.4).or.(iout.eq.5)) call plumetraj(itime)
        if (iflux.eq.1) call fluxoutput(itime)
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        if (mp_measure_time) call mpif_mtime('iotime',1)

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! Decide whether to write an estimate of the number of particles released, 
! or exact number (require MPI reduce operation)
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        if (mp_dbg_mode) then
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          numpart_tot_mpi = numpart
        else
          numpart_tot_mpi = numpart*mp_partgroup_np
        end if
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        if (mp_exact_numpart.and..not.(lmpreader.and.lmp_use_reader).and.&
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             &.not.mp_dbg_mode) then
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          call MPI_Reduce(numpart, numpart_tot_mpi, 1, MPI_INTEGER, MPI_SUM, id_root, &
               & mp_comm_used, mp_ierr)
        endif
        
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        !CGZ-lifetime: output species lifetime
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        if (lroot.or.mp_dbg_mode) then
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        !   write(*,*) 'Overview species lifetime in days', &
        !        real((species_lifetime(:,1)/species_lifetime(:,2))/real(3600.0*24.0))
        !   write(*,*) 'all info:',species_lifetime
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          write(*,45) itime,numpart_tot_mpi,gridtotalunc,&
               &wetgridtotalunc,drygridtotalunc
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        !   if (verbosity.gt.0) then
        !     write (*,*) 'timemanager> starting simulation'
        !   end if
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        end if
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        ! Write number of particles for all processes
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        if (mp_dev_mode) write(*,*) "PID, itime, numpart", mp_pid,itime,numpart


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45      format(i13,' SECONDS SIMULATED: ',i13, ' PARTICLES:    Uncertainty: ',3f7.3)
46      format(' Simulated ',f7.1,' hours (',i13,' s), ',i13, ' particles')
        if (ipout.ge.1) then
          do ip=0, mp_partgroup_np-1
            if (ip.eq.mp_partid) call partoutput(itime) ! dump particle positions
            call mpif_mpi_barrier
          end do
        end if

        loutnext=loutnext+loutstep
        loutstart=loutnext-loutaver/2
        loutend=loutnext+loutaver/2
        if (itime.eq.loutstart) then
          weight=0.5
          outnum=outnum+weight
          call conccalc(itime,weight)
        endif


! Check, whether particles are to be split:
! If so, create new particles and attribute all information from the old
! particles also to the new ones; old and new particles both get half the
! mass of the old ones
!************************************************************************
        
        if (ldirect*itime.ge.ldirect*itsplit) then
          n=numpart
          do j=1,numpart
            if (ldirect*itime.ge.ldirect*itrasplit(j)) then
!                if (n.lt.maxpart) then
              if (n.lt.maxpart_mpi) then
                n=n+1
                itrasplit(j)=2*(itrasplit(j)-itramem(j))+itramem(j)
                itrasplit(n)=itrasplit(j)
                itramem(n)=itramem(j)
                itra1(n)=itra1(j)
                idt(n)=idt(j)
                npoint(n)=npoint(j)
                nclass(n)=nclass(j)
                xtra1(n)=xtra1(j)
                ytra1(n)=ytra1(j)
                ztra1(n)=ztra1(j)
                uap(n)=uap(j)
                ucp(n)=ucp(j)
                uzp(n)=uzp(j)
                us(n)=us(j)
                vs(n)=vs(j)
                ws(n)=ws(j)
                cbt(n)=cbt(j)
                do ks=1,nspec
                  xmass1(j,ks)=xmass1(j,ks)/2.
                  xmass1(n,ks)=xmass1(j,ks)
                end do
              endif
            endif
          end do
          numpart=n
        endif
      endif
    endif
    

    if (itime.eq.ideltas) exit         ! almost finished

! Compute interval since radioactive decay of deposited mass was computed
!************************************************************************

    if (itime.lt.loutnext) then
      ldeltat=itime-(loutnext-loutstep)
    else                                  ! first half of next interval
      ldeltat=itime-loutnext
    endif


! Loop over all particles
!************************
    if (mp_measure_time) call mpif_mtime('partloop1',0)

!--------------------------------------------------------------------------------
! various variables for testing reason of CBL scheme, by mc
    well_mixed_vector=0. !erase vector to test well mixed condition: modified by mc
    well_mixed_norm=0.   !erase normalization to test well mixed condition: modified by mc
    avg_ol=0.
    avg_wst=0.
    avg_h=0.
    avg_air_dens=0.  !erase vector to obtain air density at particle positions: modified by mc
!--------------------------------------------------------------------------------

    do j=1,numpart

! If integration step is due, do it
!**********************************

      if (itra1(j).eq.itime) then

        if (ioutputforeachrelease.eq.1) then
          kp=npoint(j)
        else
          kp=1
        endif
! Determine age class of the particle
        itage=abs(itra1(j)-itramem(j))
        do nage=1,nageclass
          if (itage.lt.lage(nage)) exit
        end do

! Initialize newly released particle
!***********************************

        if ((itramem(j).eq.itime).or.(itime.eq.0)) &
             call initialize(itime,idt(j),uap(j),ucp(j),uzp(j), &
             us(j),vs(j),ws(j),xtra1(j),ytra1(j),ztra1(j),cbt(j))

! Memorize particle positions
!****************************

        xold=xtra1(j)
        yold=ytra1(j)
        zold=ztra1(j)

! Integrate Lagevin equation for lsynctime seconds
!*************************************************

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        if (mp_measure_time) call mpif_mtime('advance',0)
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        call advance(itime,npoint(j),idt(j),uap(j),ucp(j),uzp(j), &
             us(j),vs(j),ws(j),nstop,xtra1(j),ytra1(j),ztra1(j),prob, &
             cbt(j))

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        if (mp_measure_time) call mpif_mtime('advance',1)

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! Calculate the gross fluxes across layer interfaces
!***************************************************

        if (iflux.eq.1) call calcfluxes(nage,j,xold,yold,zold)


! Determine, when next time step is due
! If trajectory is terminated, mark it
!**************************************

        if (nstop.gt.1) then
          if (linit_cond.ge.1) call initial_cond_calc(itime,j)
          itra1(j)=-999999999
        else
          itra1(j)=itime+lsynctime


! Dry deposition and radioactive decay for each species
! Also check maximum (of all species) of initial mass remaining on the particle;
! if it is below a threshold value, terminate particle
!*****************************************************************************

          xmassfract=0.
          do ks=1,nspec
            if (decay(ks).gt.0.) then             ! radioactive decay
              decfact=exp(-real(abs(lsynctime))*decay(ks))
            else
              decfact=1.
            endif

            if (DRYDEPSPEC(ks)) then        ! dry deposition
              drydeposit(ks)=xmass1(j,ks)*prob(ks)*decfact
              xmass1(j,ks)=xmass1(j,ks)*(1.-prob(ks))*decfact
              if (decay(ks).gt.0.) then   ! correct for decay (see wetdepo)
                drydeposit(ks)=drydeposit(ks)* &
                     exp(real(abs(ldeltat))*decay(ks))
              endif
            else                           ! no dry deposition
              xmass1(j,ks)=xmass1(j,ks)*decfact
            endif

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! Skip check on mass fraction when npoint represents particle number
            if (mdomainfill.eq.0.and.mquasilag.eq.0) then
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              if (xmass(npoint(j),ks).gt.0.)then 
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                   xmassfract=max(xmassfract,real(npart(npoint(j)))* &
                   xmass1(j,ks)/xmass(npoint(j),ks))
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                   !CGZ-lifetime: Check mass fraction left/save lifetime
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                   ! if(lroot.and.real(npart(npoint(j)))*xmass1(j,ks)/xmass(npoint(j),ks).lt.e_inv.and.checklifetime(j,ks).eq.0.)then
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                       !Mass below 1% of initial >register lifetime
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                   !     checklifetime(j,ks)=abs(itra1(j)-itramem(j))
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                   !     species_lifetime(ks,1)=species_lifetime(ks,1)+abs(itra1(j)-itramem(j))
                   !     species_lifetime(ks,2)= species_lifetime(ks,2)+1
                   ! endif
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                   !CGZ-lifetime: Check mass fraction left/save lifetime
                   
              endif
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            else
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              xmassfract=1.0
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            endif
          end do

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          if (xmassfract.lt.minmass) then ! .and. sum(real(npart(npoint(j)))*xmass1(j,:)).lt.1.0) then   ! terminate all particles carrying less mass
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          !            print*,'terminated particle ',j,' for small mass (', sum(real(npart(npoint(j)))* &
          !         xmass1(j,:)), ' of ', sum(xmass(npoint(j),:)),')'
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            itra1(j)=-999999999
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            if (verbosity.gt.0) then
              print*,'terminated particle ',j,' for small mass'
            endif
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          endif

!        Sabine Eckhardt, June 2008
!        don't create depofield for backward runs
          if (DRYDEP.AND.(ldirect.eq.1)) then
            call drydepokernel(nclass(j),drydeposit,real(xtra1(j)), &
                 real(ytra1(j)),nage,kp)
            if (nested_output.eq.1) call drydepokernel_nest( &
                 nclass(j),drydeposit,real(xtra1(j)),real(ytra1(j)), &
                 nage,kp)
          endif

! Terminate trajectories that are older than maximum allowed age
!***************************************************************

          if (abs(itra1(j)-itramem(j)).ge.lage(nageclass)) then
            if (linit_cond.ge.1) &
                 call initial_cond_calc(itime+lsynctime,j)
            itra1(j)=-999999999
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            if (verbosity.gt.0) then
              print*, 'terminated particle ',j,'for age'
            endif
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          endif
        endif

      endif

    end do ! j=1, numpart

    if(mp_measure_time) call mpif_mtime('partloop1',1)


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! Counter of "unstable" particle velocity during a time scale
! of maximumtl=20 minutes (defined in com_mod)
!************************************************************
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    total_nan_intl=0
    i_nan=i_nan+1 ! added by mc to count nan during a time of maxtl (i.e. maximum tl fixed here to 20 minutes, see com_mod)
    sum_nan_count(i_nan)=nan_count
    if (i_nan > maxtl/lsynctime) i_nan=1 !lsynctime must be <= maxtl
    do ii_nan=1, (maxtl/lsynctime) 
      total_nan_intl=total_nan_intl+sum_nan_count(ii_nan)
    end do

! Output to keep track of the numerical instabilities in CBL simulation
! and if they are compromising the final result (or not):
    if (cblflag.eq.1) print *,j,itime,'nan_synctime',nan_count,'nan_tl',total_nan_intl  


  end do ! itime=0,ideltas,lsynctime


! Complete the calculation of initial conditions for particles not yet terminated
!*****************************************************************************

! eso :TODO: this not implemented yet (transfer particles to PID 0 or rewrite)
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! the tools to do this are already in mpi_mod.f90
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  if (lroot) then 
    do j=1,numpart
      if (linit_cond.ge.1) call initial_cond_calc(itime,j)
    end do
  end if


  if (ipout.eq.2) then
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! MPI process 0 creates the file, the other processes append to it
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    do ip=0, mp_partgroup_np-1
      if (ip.eq.mp_partid) then 
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        !if (mp_dbg_mode) write(*,*) 'call partoutput(itime), proc, mp_partid',ip,mp_partid
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        call partoutput(itime)    ! dump particle positions
      end if
      call mpif_mpi_barrier
    end do
  end if

! eso :TODO: MPI
  if (linit_cond.ge.1.and.lroot) call initial_cond_output(itime)   ! dump initial cond. field


! De-allocate memory and end
!***************************

999 if (iflux.eq.1) then
    deallocate(flux)
  endif
  if (OHREA) then
    deallocate(OH_field,OH_hourly,lonOH,latOH,altOH)
  endif
  if (ldirect.gt.0) then
    deallocate(drygridunc,wetgridunc)
  endif
  deallocate(gridunc)
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  deallocate(xpoint1,xpoint2,ypoint1,ypoint2,zpoint1,zpoint2,xmass)
  if (allocated(checklifetime)) deallocate(checklifetime)
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  deallocate(ireleasestart,ireleaseend,npart,kindz)
  deallocate(xmasssave)
  if (nested_output.eq.1) then
    deallocate(orooutn, arean, volumen)
    if (ldirect.gt.0) then
      deallocate(griduncn,drygriduncn,wetgriduncn)
    endif
  endif
  deallocate(outheight,outheighthalf)
  deallocate(oroout, area, volume)

  if (mp_measure_time) call mpif_mtime('timemanager',1)

end subroutine timemanager