Changeset 78e62dc in flexpart.git for src


Ignore:
Timestamp:
May 12, 2015, 12:28:19 PM (9 years ago)
Author:
flexpart <>
Branches:
master, 10.4.1_pesei, GFS_025, bugfixes+enhancements, dev, release-10, release-10.4.1, scaling-bug, univie
Children:
0f20c31
Parents:
2f8635b
Message:

New OH parameter in SPECIES files (now 3 instead of 2). New path to OH binariy files.

Location:
src
Files:
13 edited

Legend:

Unmodified
Added
Removed

  • src/FLEXPART.f90

    r8a65cb0 r78e62dc  
    6969
    7070  ! FLEXPART version string
    71   flexversion='Version 10.0pre  (2015-03-01)'
     71  flexversion='Version 10.0beta (2015-05-01)'
    7272  verbosity=0
    7373

  • src/FLEXPART_MPI.f90

    r2f8635b r78e62dc  
    7777
    7878  ! FLEXPART version string
    79   flexversion='Ver. 10.0pre MPI (2015-03-01)'
     79  flexversion='Ver. 10 Beta MPI (2015-05-01)'
    8080  verbosity=0
    8181
    … …  
    336336  !******************************************************************
    337337
     338  if (mp_measure_time) call mpif_mtime('iotime',0)
     339  if (lroot) then ! MPI: this part root process only
     340
    338341  if (lnetcdfout.eq.1) then
    339342    call writeheader_netcdf(lnest=.false.)
    … …  
    350353  endif
    351354
    352   if (lroot) then ! MPI: this part root process only
     355!
    353356    if (verbosity.gt.0) then
    354357      print*,'call writeheader'
    … …  
    364367  end if ! (mpif_pid == 0)
    365368
     369  if (mp_measure_time) call mpif_mtime('iotime',0)
     370
    366371  !open(unitdates,file=path(2)(1:length(2))//'dates')
    367 
    368 !open(unitdates,file=path(2)(1:length(2))//'dates')
    369372
    370373  if (verbosity.gt.0 .and. lroot) then

  • src/com_mod.f90

    r5f9d14a r78e62dc  
    2626  integer :: length(numpath+2*maxnests)
    2727  character(len=256) :: pathfile, flexversion, arg1, arg2
     28  character(len=256) :: ohfields_path
    2829 
    2930  ! path                    path names needed for trajectory model
    … …  
    3233  ! flexversion             version of flexpart
    3334  ! arg                     input arguments from launch at command line
     35  ! ohfields_path           path to binary files for OH fields
    3436
    3537  !********************************************************
    … …  
    163165  real :: rgs(maxspec,5,numclass),rlu(maxspec,5,numclass)
    164166  real :: rm(maxspec),dryvel(maxspec),kao(maxspec)
    165   real :: ohcconst(maxspec),ohdconst(maxspec)
     167  real :: ohcconst(maxspec),ohdconst(maxspec),ohnconst(maxspec)
    166168  ! se  it is possible to associate a species with a second one to make transfer from gas to aerosol
    167169  integer :: spec_ass(maxspec)

  • src/getfields_mpi.f90

    r5f9d14a r78e62dc  
    4343!
    4444!  eso 2014:
    45 !    MPI version. 3 fields instead of 2, to allow reading the newest in
    46 !    the background.
    47 !    Only one process (lmpreader=.true.) does the actual reading, while the
    48 !    rest call this routine only to update memind, memstat etc.
     45!    MPI version.
     46!    If running with number of processes >= mpi_mod::read_grp_min,
     47!    only one process (mpi_mod::lmpreader=.true.) does the actual reading, while
     48!    the rest call this routine only to update memind, memstat etc.
     49!
     50!    If mpi_mod::lmp_sync=.true., uses 3 fields instead of 2, to allow reading
     51!    the newest in the background.
    4952!
    5053!    Return memstat, which is the sum of
    … …  
    6164! indj                 indicates the number of the wind field to be read in  *
    6265! indmin               remembers the number of wind fields already treated   *
    63 ! memind(2)            pointer, on which place the wind fields are stored    *
    64 ! memtime(2) [s]       times of the wind fields, which are kept in memory    *
     66! memind(2[3])         pointer, on which place the wind fields are stored    *
     67! memtime(2[3]) [s]    times of the wind fields, which are kept in memory    *
    6568! itime [s]            current time since start date of trajectory calcu-    *
    6669!                      lation                                                *

  • src/gethourlyOH.f90

    r5f9d14a r78e62dc  
    120120    memOHtime(1)=0.
    121121
    122     jul2=bdate+real(1./24.,kind=dp)  ! date for next hour
     122    jul2=bdate+ldirect*real(1./24.,kind=dp)  ! date for next hour
    123123    call caldate(jul2,jjjjmmdd,hhmmss)
    124124    m2=(jjjjmmdd-(jjjjmmdd/10000)*10000)/100

  • src/mpi_mod.f90

    r5f9d14a r78e62dc  
    9090  integer :: tm1
    9191  integer, parameter :: nvar_async=27 !29 :DBG:
    92   !integer, dimension(:), allocatable :: tags
     92!integer, dimension(:), allocatable :: tags
    9393  integer, dimension(:), allocatable :: reqs
    9494
    … …  
    117117  logical, parameter :: mp_dbg_out = .false.
    118118  logical, parameter :: mp_time_barrier=.true.
    119   logical, parameter :: mp_measure_time=.true.
     119  logical, parameter :: mp_measure_time=.false.
    120120
    121121! for measuring CPU/Wall time
    … …  
    139139  real(dp) :: mp_conccalc_time_beg, mp_conccalc_time_end, mp_conccalc_time_total=0.
    140140  real(dp) :: mp_total_wtime_beg, mp_total_wtime_end, mp_total_wtime_total=0.
     141  real(dp) :: mp_vt_wtime_beg, mp_vt_wtime_end, mp_vt_wtime_total
     142  real(sp) :: mp_vt_time_beg, mp_vt_time_end, mp_vt_time_total
    141143
    142144! dat_lun           logical unit number for i/o
    … …  
    418420
    419421
    420 
    421422! redefine numpart as 'numpart per process' throughout the code
    422423!**************************************************************
    … …  
    438439
    439440    integer :: i
    440 
    441 
    442 !***********************************************************************
    443 
    444441
    445442! Time for MPI communications
    … …  
    12431240
    12441241    do dest=0,mp_np-1 ! mp_np-2 will also work if last proc reserved for reading
    1245                       ! TODO: use mp_partgroup_np here
     1242! TODO: use mp_partgroup_np here
    12461243      if (dest.eq.id_read) cycle
    12471244      i=dest*nvar_async
    … …  
    13391336             &MPI_COMM_WORLD,reqs(i),mp_ierr)
    13401337        if (mp_ierr /= 0) goto 600
    1341       ! else
    1342       !   i=i+2
     1338! else
     1339!   i=i+2
    13431340      end if
    13441341
    … …  
    13891386
    13901387! :TODO: don't need these
    1391     ! d3s1=d3_size1
    1392     ! d3s2=d3_size2
    1393     ! d2s1=d2_size1
    1394     ! d2s2=d2_size2
     1388! d3s1=d3_size1
     1389! d3s2=d3_size2
     1390! d2s1=d2_size1
     1391! d2s2=d2_size2
    13951392
    13961393! At the time this immediate receive is posted, memstat is the state of
    … …  
    15931590    call MPI_Waitall(n_req,reqs,MPI_STATUSES_IGNORE,mp_ierr)
    15941591!    endif
    1595     ! else
    1596     !   do i = 0, nvar_async*mp_np-1
    1597     !     if (mod(i,27).eq.0 .or. mod(i,28).eq.0) then
    1598     !       call MPI_Cancel(reqs(i),mp_ierr)
    1599     !       cycle
    1600     !     end if
    1601     !     call MPI_Wait(reqs(i),MPI_STATUS_IGNORE,mp_ierr)
    1602     !   end do
    1603     ! end if
     1592! else
     1593!   do i = 0, nvar_async*mp_np-1
     1594!     if (mod(i,27).eq.0 .or. mod(i,28).eq.0) then
     1595!       call MPI_Cancel(reqs(i),mp_ierr)
     1596!       cycle
     1597!     end if
     1598!     call MPI_Wait(reqs(i),MPI_STATUS_IGNORE,mp_ierr)
     1599!   end do
     1600! end if
    16041601
    16051602    if (mp_ierr /= 0) goto 600
    … …  
    17331730           & mp_comm_used, mp_ierr)
    17341731    end if
    1735 
    17361732
    17371733    if ((WETDEP).and.(ldirect.gt.0)) then
    … …  
    18541850      end if
    18551851
     1852    case ('verttransform')
     1853      if (imode.eq.0) then
     1854        mp_vt_wtime_beg = mpi_wtime()
     1855        call cpu_time(mp_vt_time_beg)
     1856      else
     1857        mp_vt_wtime_end = mpi_wtime()
     1858        call cpu_time(mp_vt_time_end)
     1859
     1860        mp_vt_wtime_total = mp_vt_wtime_total + (mp_vt_wtime_end - &
     1861             & mp_vt_wtime_beg)
     1862        mp_vt_time_total = mp_vt_time_total + (mp_vt_time_end - &
     1863             & mp_vt_time_beg)
     1864      end if
     1865
    18561866    case ('readwind')
    18571867      if (imode.eq.0) then
    … …  
    19091919!***********************************************************************
    19101920
    1911     if (mp_measure_time) then
     1921    IF (mp_measure_time) THEN
    19121922      do ip=0, mp_np-1
    19131923        call MPI_BARRIER(MPI_COMM_WORLD, mp_ierr)
    … …  
    19561966          write(*,FMT='(A60,TR1,F9.2)') 'TOTAL WALL TIME FOR CONCCALC:',&
    19571967               & mp_conccalc_time_total
     1968          ! write(*,FMT='(A60,TR1,F9.2)') 'TOTAL WALL TIME FOR VERTTRANSFORM:',&
     1969          !      & mp_vt_wtime_total
     1970          ! write(*,FMT='(A60,TR1,F9.2)') 'TOTAL CPU TIME FOR VERTTRANSFORM:',&
     1971          !      & mp_vt_time_total
    19581972! NB: the 'flush' function is possibly a gfortran-specific extension
    19591973          call flush()
    … …  
    19621976    end if
    19631977
     1978! This call to barrier is for correctly formatting output
     1979    call MPI_BARRIER(MPI_COMM_WORLD, mp_ierr)
     1980
     1981    if (lroot) then
     1982      write(*,FMT='(72("#"))')
     1983      WRITE(*,*) "To turn off output of time measurements, set "
     1984      WRITE(*,*) "    mp_measure_time=.false."
     1985      WRITE(*,*) "in file mpi_mod.f90"
     1986      write(*,FMT='(72("#"))')
     1987    end if
     1988
    19641989! j=mp_pid*nvar_async
    19651990! In the implementation with 3 fields, the processes may have posted
    19661991! MPI_Irecv requests that should be cancelled here
    19671992!! TODO:
    1968     ! if (.not.lmp_sync) then
    1969     !   r=mp_pid*nvar_async
    1970     !   do j=r,r+nvar_async-1
    1971     !     call MPI_Cancel(j,mp_ierr)
    1972     !     if (mp_ierr /= 0) write(*,*) '#### mpif_finalize::MPI_Cancel> ERROR ####'
    1973     !   end do
    1974     ! end if
     1993! if (.not.lmp_sync) then
     1994!   r=mp_pid*nvar_async
     1995!   do j=r,r+nvar_async-1
     1996!     call MPI_Cancel(j,mp_ierr)
     1997!     if (mp_ierr /= 0) write(*,*) '#### mpif_finalize::MPI_Cancel> ERROR ####'
     1998!   end do
     1999! end if
    19752000
    19762001    call MPI_FINALIZE(mp_ierr)
    … …  
    19812006
    19822007
    1983   end subroutine mpif_finalize
    1984 
    1985 
    1986   subroutine get_lun(my_lun)
     2008    end subroutine mpif_finalize
     2009
     2010
     2011    subroutine get_lun(my_lun)
    19872012!***********************************************************************
    19882013! get_lun:
    … …  
    19902015!***********************************************************************
    19912016
    1992     implicit none
    1993 
    1994     integer, intent(inout) :: my_lun
    1995     integer, save :: free_lun=100
    1996     logical :: exists, iopen
    1997 
    1998 !***********************************************************************
    1999 
    2000     loop1: do
    2001       inquire(UNIT=free_lun, EXIST=exists, OPENED=iopen)
    2002       if (exists .and. .not.iopen) exit loop1
    2003       free_lun = free_lun+1
    2004     end do loop1
    2005     my_lun = free_lun
    2006 
    2007   end subroutine get_lun
    2008 
    2009 
    2010   subroutine write_data_dbg(array_in, array_name, tstep, ident)
    2011 !***********************************************************************
    2012 ! Write one-dimensional arrays to disk (for debugging purposes)
    2013 !***********************************************************************
    2014     implicit none
    2015 
    2016     real, intent(in), dimension(:) :: array_in
    2017     integer, intent(in) :: tstep
    2018     integer :: lios
    2019     character(LEN=*), intent(in) :: ident, array_name
    2020 
    2021     character(LEN=8) :: c_ts
    2022     character(LEN=40) :: fn_1, fn_2
    2023 
    2024 !***********************************************************************
    2025 
    2026     write(c_ts, FMT='(I8.8,BZ)') tstep
    2027     fn_1='-'//trim(adjustl(c_ts))//'-'//trim(ident)
    2028     write(c_ts, FMT='(I2.2,BZ)') mp_np
    2029     fn_2= trim(adjustl(array_name))//trim(adjustl(fn_1))//'-np'//trim(adjustl(c_ts))//'.dat'
    2030 
    2031     call get_lun(dat_lun)
    2032     open(UNIT=dat_lun, FILE=fn_2, IOSTAT=lios, ACTION='WRITE', &
    2033          FORM='UNFORMATTED', STATUS='REPLACE')
    2034     write(UNIT=dat_lun, IOSTAT=lios) array_in
    2035     close(UNIT=dat_lun)
    2036 
    2037   end subroutine write_data_dbg
     2017      implicit none
     2018
     2019      integer, intent(inout) :: my_lun
     2020      integer, save :: free_lun=100
     2021      logical :: exists, iopen
     2022
     2023!***********************************************************************
     2024
     2025      loop1: do
     2026        inquire(UNIT=free_lun, EXIST=exists, OPENED=iopen)
     2027        if (exists .and. .not.iopen) exit loop1
     2028        free_lun = free_lun+1
     2029      end do loop1
     2030      my_lun = free_lun
     2031
     2032    end subroutine get_lun
     2033
     2034
     2035    subroutine write_data_dbg(array_in, array_name, tstep, ident)
     2036!***********************************************************************
     2037! Write one-dimensional arrays to file (for debugging purposes)
     2038!***********************************************************************
     2039      implicit none
     2040
     2041      real, intent(in), dimension(:) :: array_in
     2042      integer, intent(in) :: tstep
     2043      integer :: lios
     2044      character(LEN=*), intent(in) :: ident, array_name
     2045
     2046      character(LEN=8) :: c_ts
     2047      character(LEN=40) :: fn_1, fn_2
     2048
     2049!***********************************************************************
     2050
     2051      write(c_ts, FMT='(I8.8,BZ)') tstep
     2052      fn_1='-'//trim(adjustl(c_ts))//'-'//trim(ident)
     2053      write(c_ts, FMT='(I2.2,BZ)') mp_np
     2054      fn_2= trim(adjustl(array_name))//trim(adjustl(fn_1))//'-np'//trim(adjustl(c_ts))//'.dat'
     2055
     2056      call get_lun(dat_lun)
     2057      open(UNIT=dat_lun, FILE=fn_2, IOSTAT=lios, ACTION='WRITE', &
     2058           FORM='UNFORMATTED', STATUS='REPLACE')
     2059      write(UNIT=dat_lun, IOSTAT=lios) array_in
     2060      close(UNIT=dat_lun)
     2061
     2062    end subroutine write_data_dbg
    20382063
    20392064

  • src/ohreaction.f90

    r8a65cb0 r78e62dc  
    153153      do k=1,nspec                               
    154154        if (ohcconst(k).gt.0.) then
    155           ohrate=ohcconst(k)*temp**2*exp(-ohdconst(k)/temp)*oh_average
     155          ohrate=ohcconst(k)*temp**ohnconst(k)*exp(-ohdconst(k)/temp)*oh_average
    156156          ! new particle mass
    157157          restmass = xmass1(jpart,k)*exp(-1*ohrate*abs(ltsample))

  • src/readOHfield.f90

    r8a65cb0 r78e62dc  
    4646  use com_mod
    4747
    48 
    4948  implicit none
    5049
    … …  
    6968    ! open netcdf file
    7069    write(mm,fmt='(i2.2)') m
    71     thefile=trim(path(1))//'OH_FIELDS/'//'geos-chem.OH.2005'//mm//'01.nc'
     70!    thefile=trim(path(1))//'OH_FIELDS/'//'geos-chem.OH.2005'//mm//'01.nc'
     71    thefile=trim(ohfields_path)//'OH_FIELDS/'//'geos-chem.OH.2005'//mm//'01.nc'
    7272    ierr=nf_open(trim(thefile),NF_NOWRITE,nid)
    7373    if(ierr.ne.0) then
    … …  
    163163
    164164  ! open netcdf file
    165   thefile=trim(path(1))//'OH_FIELDS/jrate_average.nc'
     165!  thefile=trim(path(1))//'OH_FIELDS/jrate_average.nc'
     166  thefile=trim(ohfields_path)//'OH_FIELDS/jrate_average.nc'
    166167  ierr=nf_open(trim(thefile),NF_NOWRITE,nid)
    167168  if(ierr.ne.0) then

  • src/readcommand.f90

    r8a65cb0 r78e62dc  
    111111  lnetcdfout, &
    112112  surf_only, &
    113   cblflag
     113  cblflag, &
     114  ohfields_path
    114115
    115116  ! Presetting namelist command
    … …  
    143144  surf_only=0
    144145  cblflag=0
     146  ohfields_path="../../flexin/"
    145147
    146148  ! Open the command file and read user options
    … …  
    232234    if (old) call skplin(3,unitcommand)  !added by mc
    233235    read(unitcommand,*) cblflag          !added by mc
     236
    234237    close(unitcommand)
    235238

  • src/readreleases.f90

    r5f9d14a r78e62dc  
    385385    if (ohcconst(i).gt.0.) then
    386386      OHREA=.true.
    387       write (*,*) 'OHreaction switched on: ',ohcconst(i),i
     387      if (lroot) write (*,*) 'OHreaction switched on: ',ohcconst(i),i
    388388    endif
    389389

  • src/readspecies.f90

    r5f9d14a r78e62dc  
    4747  ! ohcconst             OH reaction rate constant C                           *
    4848  ! ohdconst             OH reaction rate constant D                           *
     49  ! ohnconst             OH reaction rate constant n                           *
    4950  ! id_spec              SPECIES number as referenced in RELEASE file          *
    5051  ! id_pos               position where SPECIES data shall be stored           *
    … …  
    6667  character(len=16) :: pspecies
    6768  real :: pdecay, pweta, pwetb, preldiff, phenry, pf0, pdensity, pdquer
    68   real :: pdsigma, pdryvel, pweightmolar, pohcconst, pohdconst, pspec_ass, pkao
     69  real :: pdsigma, pdryvel, pweightmolar, pohcconst, pohdconst, pohnconst, pspec_ass, pkao
    6970  real :: pweta_in, pwetb_in, pwetc_in, pwetd_in
    7071  integer :: readerror
    … …  
    7576       pweta_in, pwetb_in, pwetc_in, pwetd_in, &
    7677       preldiff, phenry, pf0, pdensity, pdquer, &
    77        pdsigma, pdryvel, pweightmolar, pohcconst, pohdconst, pspec_ass, pkao
     78       pdsigma, pdryvel, pweightmolar, pohcconst, pohdconst, pohnconst, pspec_ass, pkao
    7879
    7980  pspecies=" "
    … …  
    9495  pohcconst=-9.99
    9596  pohdconst=-9.9E-09
     97  pohnconst=2.0
    9698  pspec_ass=-9
    9799  pkao=-99.99
    … …  
    160162    read(unitspecies,'(f8.2)',end=22) ohdconst(pos_spec)
    161163!  write(*,*) ohdconst(pos_spec)
     164    read(unitspecies,'(f8.2)',end=22) ohnconst(pos_spec)
     165!  write(*,*) ohnconst(pos_spec)
    162166    read(unitspecies,'(i18)',end=22) spec_ass(pos_spec)
    163167!  write(*,*) spec_ass(pos_spec)
    … …  
    183187    pohcconst=ohcconst(pos_spec)
    184188    pohdconst=ohdconst(pos_spec)
     189    pohnconst=ohnconst(pos_spec)
    185190    pspec_ass=spec_ass(pos_spec)
    186191    pkao=kao(pos_spec)
    … …  
    206211    ohcconst(pos_spec)=pohcconst
    207212    ohdconst(pos_spec)=pohdconst
     213    ohnconst(pos_spec)=pohnconst
    208214    spec_ass(pos_spec)=pspec_ass
    209215    kao(pos_spec)=pkao

  • src/timemanager.f90

    r8a65cb0 r78e62dc  
    657657  if (linit_cond.ge.1) call initial_cond_output(itime)   ! dump initial cond. field
    658658
    659   close(104)
     659  !close(104)
    660660
    661661  ! De-allocate memory and end

  • src/timemanager_mpi.f90

    r5f9d14a r78e62dc  
    208208    endif
    209209
     210! This time measure includes reading/MPI communication (for the reader process),
     211! or MPI communication time only (for other processes)
    210212    if (mp_measure_time) call mpif_mtime('getfields',0)
    211213
    … …  
    213215
    214216    if (mp_measure_time) call mpif_mtime('getfields',1)
     217
     218
    215219
    216220! Broadcast fields to all MPI processes
    217221! Skip if all processes have called getfields or if no new fields
    218222!*****************************************************************
     223
     224    if (mp_measure_time.and..not.(lmpreader.and.lmp_use_reader)) call mpif_mtime('getfields',0)
    219225
    220226! Version 1 (lmp_sync=.true.) uses a read-ahead process where send/recv is done
    … …  
    258264
    259265    end if
     266
     267    if (mp_measure_time.and..not.(lmpreader.and.lmp_use_reader)) call mpif_mtime('getfields',1)
     268
    260269
    261270!*******************************************************************************
    … …  
    446455          call mpif_tm_reduce_grid
    447456
     457          if (mp_measure_time) call mpif_mtime('iotime',0)
    448458          if (surf_only.ne.1) then
    449459            if (lroot) then
    … …  
    470480            endif
    471481          endif
     482          if (mp_measure_time) call mpif_mtime('iotime',1)
    472483
    473484! :TODO: Correct calling of conc_surf above?
    … …  
    481492!*********************************************
    482493            call mpif_tm_reduce_grid_nest
     494 
     495           if (mp_measure_time) call mpif_mtime('iotime',0)
    483496
    484497            if (lnetcdfout.eq.0) then
    … …  
    515528            end if
    516529          end if
     530         
    517531
    518532          outnum=0.
    … …  
    520534        if ((iout.eq.4).or.(iout.eq.5)) call plumetraj(itime)
    521535        if (iflux.eq.1) call fluxoutput(itime)
     536        if (mp_measure_time) call mpif_mtime('iotime',1)
     537
    522538        if (lroot) write(*,45) itime,numpart*mp_partgroup_np,gridtotalunc,&
    523539             &wetgridtotalunc,drygridtotalunc
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