Merge branch 'dev' into GFS_025

.gitignore

+log*
+noh*
+diff*
 FP_ecmwf_gfortran*
 *.o
 *_mod.mod
@@ -6,3 +9,4 @@ class_gribfile.mod
 output
 FLEXPART
 FLEXPART_MPI
+FLEX*

src/calcfluxes.f90

@@ -63,11 +63,13 @@ subroutine calcfluxes(nage,jpart,xold,yold,zold)
   if ((ixave.ge.0).and.(jyave.ge.0).and.(ixave.le.numxgrid-1).and. &
        (jyave.le.numygrid-1)) then
     do kz=1,numzgrid                ! determine height of cell
-      if (outheighthalf(kz).gt.zold) goto 11
+!      if (outheighthalf(kz).gt.zold) goto 11
+      if (outheight(kz).gt.zold) goto 11 !sec, use upper layer instead of mid layer
     end do
 11   k1=min(numzgrid,kz)
     do kz=1,numzgrid                ! determine height of cell
-      if (outheighthalf(kz).gt.ztra1(jpart)) goto 21
+!      if (outheighthalf(kz).gt.ztra1(jpart)) goto 21
+      if (outheight(kz).gt.ztra1(jpart)) goto 21
     end do
 21   k2=min(numzgrid,kz)
 
@@ -95,8 +97,10 @@ subroutine calcfluxes(nage,jpart,xold,yold,zold)
   ! 1) Particle does not cross domain boundary
 
     if (abs(xold-xtra1(jpart)).lt.real(nx)/2.) then
-      ix1=int((xold*dx+xoutshift)/dxout+0.5)
-      ix2=int((xtra1(jpart)*dx+xoutshift)/dxout+0.5)
+      ix1=int((xold*dx+xoutshift)/dxout)              ! flux throught the western boundary (sec)
+      ix2=int((xtra1(jpart)*dx+xoutshift)/dxout)      ! flux throught the western boundary (sec)
+!      ix1=int((xold*dx+xoutshift)/dxout+0.5) 
+!      ix2=int((xtra1(jpart)*dx+xoutshift)/dxout+0.5)
       do k=1,nspec
         do ix=ix1,ix2-1
           if ((ix.ge.0).and.(ix.le.numxgrid-1)) then
@@ -144,8 +148,10 @@ subroutine calcfluxes(nage,jpart,xold,yold,zold)
 
   if ((kzave.le.numzgrid).and.(ixave.ge.0).and. &
        (ixave.le.numxgrid-1)) then
-    jy1=int((yold*dy+youtshift)/dyout+0.5)
-    jy2=int((ytra1(jpart)*dy+youtshift)/dyout+0.5)
+    jy1=int((yold*dy+youtshift)/dyout)         ! flux throught the southern boundary (sec)
+    jy2=int((ytra1(jpart)*dy+youtshift)/dyout) ! flux throught the southern boundary (sec)
+!    jy1=int((yold*dy+youtshift)/dyout+0.5)
+!    jy2=int((ytra1(jpart)*dy+youtshift)/dyout+0.5)
 
     do k=1,nspec
       do jy=jy1,jy2-1

src/init_domainfill.f90

@@ -208,13 +208,16 @@ subroutine init_domainfill
               if (ztra1(numpart+jj).gt.height(nz)-0.5) &
                    ztra1(numpart+jj)=height(nz)-0.5
 
-
 ! Interpolate PV to the particle position
 !****************************************
               ixm=int(xtra1(numpart+jj))
               jym=int(ytra1(numpart+jj))
               ixp=ixm+1
               jyp=jym+1
+              if (jyp.gt.180) then
+                 write (*,*) 'init_domainfill, over: ',jyp,jym,ytra1(numpart+jj),jy,ran1(idummy),ny
+                 jyp=jym
+              endif
               ddx=xtra1(numpart+jj)-real(ixm)
               ddy=ytra1(numpart+jj)-real(jym)
               rddx=1.-ddx

src/netcdf_output_mod.f90

@@ -35,11 +35,11 @@ module netcdf_output_mod
                        xpoint1,ypoint1,xpoint2,ypoint2,zpoint1,zpoint2,npart,xmass
   use outg_mod,  only: outheight,oroout,densityoutgrid,factor3d,volume,&
                        wetgrid,wetgridsigma,drygrid,drygridsigma,grid,gridsigma,&
-                       area,arean,volumen, orooutn, p0out, t0out
+                       area,arean,volumen, orooutn, areaeast, areanorth, p0out, t0out
   use par_mod,   only: dep_prec, sp, dp, maxspec, maxreceptor, nclassunc,&
                        unitoutrecept,unitoutreceptppt, nxmax,unittmp, &
                        write_p0t0
-  use com_mod,   only: path,length,ldirect,ibdate,ibtime,iedate,ietime, &
+  use com_mod,   only: path,length,ldirect,bdate,ibdate,ibtime,iedate,ietime, &
                        loutstep,loutaver,loutsample,outlon0,outlat0,&
                        numxgrid,numygrid,dxout,dyout,numzgrid, height, &
                        outlon0n,outlat0n,dxoutn,dyoutn,numxgridn,numygridn, &
@@ -66,7 +66,7 @@ module netcdf_output_mod
   private
 
   public :: writeheader_netcdf,concoutput_surf_nest_netcdf,concoutput_netcdf,&
-       &concoutput_nest_netcdf,concoutput_surf_netcdf
+       &concoutput_nest_netcdf,concoutput_surf_netcdf,fluxoutput_netcdf
 
 !  include 'netcdf.inc'
 
@@ -1519,6 +1519,259 @@ subroutine concoutput_surf_nest_netcdf(itime,outnum)
 
 end subroutine concoutput_surf_nest_netcdf
 
+subroutine fluxoutput_netcdf(itime)
+     
+  !                            i
+  !*****************************************************************************
+  !                                                                            *
+  !     Output of the gridded fluxes.                                          *
+  !     Eastward, westward, northward, southward, upward and downward gross    *
+  !     fluxes are written to output file in either sparse matrix or grid dump *
+  !     format, whichever is more efficient.                                   *
+  !                                                                            *
+  !     Author: A. Stohl                                                       *
+  !                                                                            *
+  !     04 April 2000                                                          *
+  !     netcdfoutput S. Eckhardt, 2020                                         *
+  !                                                                            *
+  !*****************************************************************************
+
+   use flux_mod
+
+  implicit none
+
+  real(kind=dp) :: jul
+  integer :: itime,ix,jy,kz,ks,nage,jjjjmmdd,ihmmss,kp,i
+  
+  character(len=255) :: ncfname
+  character :: adate*8,atime*6,timeunit*32,anspec*3
+
+  integer :: ncid 
+  integer :: timeDimID, latDimID, lonDimID, levDimID
+  integer :: nspecDimID, npointDimID, nageclassDimID, ncharDimID, pointspecDimID
+  integer :: tID, lonID, latID, levID, lageID, fluxID
+  integer, dimension(6)       :: dIDs
+  integer :: cache_size
+  real, allocatable, dimension(:) :: coord
+
+
+  ! Determine current calendar date, needed for the file name
+  !**********************************************************
+
+  jul=bdate+real(itime,kind=dp)/86400._dp
+  call caldate(jul,jjjjmmdd,ihmmss)
+  write(adate,'(i8.8)') jjjjmmdd
+  write(atime,'(i6.6)') ihmmss
+
+  ncfname=path(2)(1:length(2))//'grid_flux_'//adate// &
+       atime//'.nc'
+
+  ! setting cache size in bytes. It is set to 4 times the largest data block that is written
+  !   size_type x nx x ny x nz
+  ! create file
+
+  cache_size = 16 * numxgrid * numygrid * numzgrid
+  call nf90_err(nf90_create(trim(ncfname), cmode = nf90_hdf5, ncid = ncid, &
+    cache_size = cache_size))  
+
+  ! create dimensions:
+  !*************************
+  ! time
+  call nf90_err(nf90_def_dim(ncid, 'time', nf90_unlimited, timeDimID))
+  timeunit = 'seconds since '//adate(1:4)//'-'//adate(5:6)// &
+     '-'//adate(7:8)//' '//atime(1:2)//':'//atime(3:4)
+
+  call nf90_err(nf90_def_dim(ncid, 'longitude', numxgrid, lonDimID))
+  call nf90_err(nf90_def_dim(ncid, 'latitude', numygrid, latDimID))
+  call nf90_err(nf90_def_dim(ncid, 'height', numzgrid, levDimID))
+  call nf90_err(nf90_def_dim(ncid, 'numspec', nspec, nspecDimID))
+  call nf90_err(nf90_def_dim(ncid, 'pointspec', maxpointspec_act, pointspecDimID))
+  call nf90_err(nf90_def_dim(ncid, 'nageclass', nageclass, nageclassDimID))
+  call nf90_err(nf90_def_dim(ncid, 'nchar', 45, ncharDimID))
+  call nf90_err(nf90_def_dim(ncid, 'numpoint', numpoint, npointDimID))
+
+
+  ! create variables
+  !*************************
+
+  ! time
+  call nf90_err(nf90_def_var(ncid, 'time', nf90_int, (/ timeDimID /), tID))
+  call nf90_err(nf90_put_att(ncid, tID, 'units', timeunit))
+  call nf90_err(nf90_put_att(ncid, tID, 'calendar', 'proleptic_gregorian'))
+  timeID = tID
+
+  ! lon
+  call nf90_err(nf90_def_var(ncid, 'longitude', nf90_float, (/ lonDimID /), lonID))
+  call nf90_err(nf90_put_att(ncid, lonID, 'long_name', 'longitude in degree east'))
+  call nf90_err(nf90_put_att(ncid, lonID, 'axis', 'Lon'))
+  call nf90_err(nf90_put_att(ncid, lonID, 'units', 'degrees_east'))
+  call nf90_err(nf90_put_att(ncid, lonID, 'standard_name', 'grid_longitude'))
+  call nf90_err(nf90_put_att(ncid, lonID, 'description', 'grid cell centers'))
+
+  ! lat
+  call nf90_err(nf90_def_var(ncid, 'latitude', nf90_float, (/ latDimID /), latID))
+  call nf90_err(nf90_put_att(ncid, latID, 'long_name', 'latitude in degree north'))
+  call nf90_err(nf90_put_att(ncid, latID, 'axis', 'Lat'))
+  call nf90_err(nf90_put_att(ncid, latID, 'units', 'degrees_north'))
+  call nf90_err(nf90_put_att(ncid, latID, 'standard_name', 'grid_latitude'))
+  call nf90_err(nf90_put_att(ncid, latID, 'description', 'grid cell centers'))
+
+  ! height
+  call nf90_err(nf90_def_var(ncid, 'height', nf90_float, (/ levDimID /), levID))
+  call nf90_err(nf90_put_att(ncid, levID, 'units', 'meters'))
+  call nf90_err(nf90_put_att(ncid, levID, 'positive', 'up'))
+  call nf90_err(nf90_put_att(ncid, levID, 'standard_name', 'height'))
+
+  if (.not.allocated(coord)) allocate(coord(numxgrid)) 
+  do i = 1,numxgrid
+     coord(i) = outlon0 + (i-0.5)*dxout
+  enddo
+  call nf90_err(nf90_put_var(ncid, lonID, coord(1:numxgrid)))
+  deallocate(coord)
+  if (.not.allocated(coord)) allocate(coord(numygrid))
+  do i = 1,numygrid
+     coord(i) = outlat0 + (i-0.5)*dyout
+  enddo
+  call nf90_err(nf90_put_var(ncid, latID, coord(1:numygrid)))
+  deallocate(coord)
+  call nf90_err(nf90_put_var(ncid, levID, outheight(1:numzgrid)))
+
+  ! write time, one field per time - different to the others!
+  call nf90_err(nf90_put_var( ncid, timeID, itime, (/ 1 /)))
+  
+  dIDs = (/ londimid, latdimid, levdimid, timedimid, pointspecdimid, nageclassdimid /)
+
+  do ks=1,nspec
+    do kp=1,maxpointspec_act
+      do nage=1,nageclass
+ 
+         write(anspec,'(i3.3)') ks
+
+ ! East Flux
+        call nf90_err(nf90_def_var(ncid,'flux_east_'//anspec, nf90_float, dIDs, &
+             fluxID))
+
+        do jy=0,numygrid-1
+          do ix=0,numxgrid-1
+            do kz=1, numzgrid
+               grid(ix,jy,kz)=flux(1,ix,jy,kz,ks,kp,nage) 
+            end do
+          end do
+        end do
+
+        call nf90_err(nf90_put_var(ncid,fluxid,1.e12*grid(0:numxgrid-1,0:numygrid-1,1:numzgrid)&
+            /areaeast(0:numxgrid-1,0:numygrid-1,1:numzgrid)/loutstep,&
+           (/ 1,1,1,1,kp,nage /), (/ numxgrid,numygrid,numzgrid,1,1,1 /) ))
+
+ ! West Flux
+        call nf90_err(nf90_def_var(ncid,'flux_west_'//anspec, nf90_float, dIDs, &
+             fluxID))
+
+        do jy=0,numygrid-1
+          do ix=0,numxgrid-1
+            do kz=1, numzgrid
+               grid(ix,jy,kz)=flux(2,ix,jy,kz,ks,kp,nage) 
+            end do
+          end do
+        end do
+
+        call nf90_err(nf90_put_var(ncid,fluxid,1.e12*grid(0:numxgrid-1,0:numygrid-1,1:numzgrid)&
+            /areaeast(0:numxgrid-1,0:numygrid-1,1:numzgrid)/loutstep,&
+           (/ 1,1,1,1,kp,nage /), (/ numxgrid,numygrid,numzgrid,1,1,1 /) ))
+
+ ! North Flux
+        call nf90_err(nf90_def_var(ncid,'flux_north_'//anspec, nf90_float, dIDs, &
+             fluxID))
+
+        do jy=0,numygrid-1
+          do ix=0,numxgrid-1
+            do kz=1, numzgrid
+               grid(ix,jy,kz)=flux(4,ix,jy,kz,ks,kp,nage) 
+            end do
+          end do
+        end do
+
+        call nf90_err(nf90_put_var(ncid,fluxid,1.e12*grid(0:numxgrid-1,0:numygrid-1,1:numzgrid)&
+            /areanorth(0:numxgrid-1,0:numygrid-1,1:numzgrid)/loutstep,&
+           (/ 1,1,1,1,kp,nage /), (/ numxgrid,numygrid,numzgrid,1,1,1 /) ))
+
+ ! South Flux
+        call nf90_err(nf90_def_var(ncid,'flux_south_'//anspec, nf90_float, dIDs, &
+             fluxID))
+
+        do jy=0,numygrid-1
+          do ix=0,numxgrid-1
+            do kz=1, numzgrid
+               grid(ix,jy,kz)=flux(3,ix,jy,kz,ks,kp,nage) 
+            end do
+          end do
+        end do
+
+        call nf90_err(nf90_put_var(ncid,fluxid,1.e12*grid(0:numxgrid-1,0:numygrid-1,1:numzgrid)&
+            /areanorth(0:numxgrid-1,0:numygrid-1,1:numzgrid)/loutstep,&
+           (/ 1,1,1,1,kp,nage /), (/ numxgrid,numygrid,numzgrid,1,1,1 /) ))
+
+ ! Up Flux
+        call nf90_err(nf90_def_var(ncid,'flux_up_'//anspec, nf90_float, dIDs, &
+             fluxID))
+
+        do jy=0,numygrid-1
+          do ix=0,numxgrid-1
+            do kz=1, numzgrid
+               grid(ix,jy,kz)=flux(5,ix,jy,kz,ks,kp,nage)/area(ix,jy)
+            end do
+          end do
+        end do
+
+        call nf90_err(nf90_put_var(ncid,fluxid,1.e12*grid(0:numxgrid-1,0:numygrid-1,1:numzgrid)&
+            /loutstep,&
+           (/ 1,1,1,1,kp,nage /), (/ numxgrid,numygrid,numzgrid,1,1,1 /) ))
+
+ ! Down Flux
+        call nf90_err(nf90_def_var(ncid,'flux_down_'//anspec, nf90_float, dIDs, &
+             fluxID))
+
+        do jy=0,numygrid-1
+          do ix=0,numxgrid-1
+            do kz=1, numzgrid
+               grid(ix,jy,kz)=flux(6,ix,jy,kz,ks,kp,nage)/area(ix,jy)
+            end do
+          end do
+        end do
+
+        call nf90_err(nf90_put_var(ncid,fluxid,1.e12*grid(0:numxgrid-1,0:numygrid-1,1:numzgrid)&
+            /loutstep,&
+           (/ 1,1,1,1,kp,nage /), (/ numxgrid,numygrid,numzgrid,1,1,1 /) ))
+
+      end do
+    end do
+  end do
+
+  ! Close netCDF file
+  call nf90_err(nf90_close(ncid))
+
+  ! Reinitialization of grid
+  !*************************
+
+  do ks=1,nspec
+    do kp=1,maxpointspec_act
+      do jy=0,numygrid-1
+        do ix=0,numxgrid-1
+          do kz=1,numzgrid
+            do nage=1,nageclass
+              do i=1,6
+                flux(i,ix,jy,kz,ks,kp,nage)=0.
+              end do
+            end do
+          end do
+        end do
+      end do
+    end do
+  end do
+
+
+end subroutine fluxoutput_netcdf
+
 end module netcdf_output_mod
 
 

src/readspecies.f90

@@ -41,7 +41,7 @@ subroutine readspecies(id_spec,pos_spec)
 
   implicit none
 
-  integer :: i, pos_spec,j
+  integer :: i, pos_spec,j,icheck_dow_hour
   integer :: idow,ihour,id_spec
   character(len=3) :: aspecnumb
   logical :: spec_found
@@ -228,13 +228,17 @@ subroutine readspecies(id_spec,pos_spec)
     ohdconst(pos_spec)=pohdconst
     ohnconst(pos_spec)=pohnconst
 
+
+    icheck_dow_hour=0
     do j=1,24     ! 24 hours, starting with 0-1 local time
       area_hour(pos_spec,j)=parea_hour(j)
       point_hour(pos_spec,j)=ppoint_hour(j)
+      if (parea_hour(j).ne.1 .or. ppoint_hour(j).ne.1) icheck_dow_hour=1
     end do
     do j=1,7      ! 7 days of the week, starting with Monday
       area_dow(pos_spec,j)=parea_dow(j)
       point_dow(pos_spec,j)=ppoint_dow(j)
+      if (parea_dow(j).ne.1 .or. ppoint_dow(j).ne.1) icheck_dow_hour=1
     end do
 
   endif
@@ -356,6 +360,11 @@ subroutine readspecies(id_spec,pos_spec)
   endif
 20 continue
 
+  if ((icheck_dow_hour.eq.1).and.(ldirect.lt.0)) then
+    write(*,*) '#### FLEXPART MODEL WARNING                     ####'
+    write(*,*) '#### The variation for an emission release      ####'
+    write(*,*) '#### will have no effect in backward mode       ####'  
+  endif
 
 22 close(unitspecies)
 

src/timemanager.f90

@@ -84,7 +84,7 @@ subroutine timemanager(metdata_format)
   use com_mod
 #ifdef USE_NCF
   use netcdf_output_mod, only: concoutput_netcdf,concoutput_nest_netcdf,&
-       &concoutput_surf_netcdf,concoutput_surf_nest_netcdf
+       &concoutput_surf_netcdf,concoutput_surf_nest_netcdf,fluxoutput_netcdf
 #endif
 
   implicit none
@@ -432,7 +432,10 @@ subroutine timemanager(metdata_format)
           outnum=0.
         endif
         if ((iout.eq.4).or.(iout.eq.5)) call plumetraj(itime)
-        if (iflux.eq.1) call fluxoutput(itime)
+        if ((iflux.eq.1).and.(lnetcdfout.eq.0)) call fluxoutput(itime)
+#ifdef USE_NCF
+        if ((iflux.eq.1).and.(lnetcdfout.eq.1)) call fluxoutput_netcdf(itime)
+#endif
         write(*,45) itime,numpart,gridtotalunc,wetgridtotalunc,drygridtotalunc
  
         !CGZ-lifetime: output species lifetime

src/timemanager_mpi.f90

@@ -555,7 +555,8 @@ subroutine timemanager(metdata_format)
           outnum=0.
         endif
         if ((iout.eq.4).or.(iout.eq.5)) call plumetraj(itime)
-        if (iflux.eq.1) call fluxoutput(itime)
+        if ((iflux.eq.1).and.(lnetcdfout.eq.0)) call fluxoutput(itime)
+        if ((iflux.eq.1).and.(lnetcdfout.eq.1)) call fluxoutput_netcdf(itime)
         if (mp_measure_time) call mpif_mtime('iotime',1)