From 65dfe7e277b0f4a88b3ad8da0dabb6d019bcd0be Mon Sep 17 00:00:00 2001
From: ronesy <rlt@nilu.no>
Date: Fri, 10 May 2024 11:37:04 +0200
Subject: [PATCH] Included changes for using satellite observations and
satellite data preprocessor: prep_satellite
---
README.txt | 46 +-
grid_to_ncdf/README_gridncdf.txt | 13 +-
grid_to_ncdf/SETTINGS | 8 +
grid_to_ncdf/factor_convert.f90 | 97 +++
grid_to_ncdf/grid_convert.f90 | 51 +-
grid_to_ncdf/grid_to_ncdf.f90 | 25 +-
grid_to_ncdf/init_convert.f90 | 146 +++++
grid_to_ncdf/initialize.f90 | 30 +-
grid_to_ncdf/makefile | 2 +
grid_to_ncdf/mod_flexpart.f90 | 96 ++-
grid_to_ncdf/mod_settings.f90 | 8 +
grid_to_ncdf/write_ncdf.f90 | 20 +-
prep_flexpart/README_prepflex.txt | 2 +-
prep_flexpart/{SETTINGS_co2 => SETTINGS} | 18 +-
prep_flexpart/SETTINGS_co2_nest | 113 ----
prep_flexpart/SETTINGS_ghg | 113 ----
prep_flexpart/SETTINGS_ghg_nest | 113 ----
prep_flexpart/job_prep_flexpart.sh | 2 +-
prep_flexpart/list_obsfiles.f90 | 8 -
prep_flexpart/mod_settings.f90 | 4 +
prep_flexpart/mod_var.f90 | 3 +-
prep_flexpart/prep_outgrid.f90 | 11 +
prep_flexpart/process_obs.f90 | 4 +-
prep_flexpart/read_basic.f90 | 9 +-
prep_flexpart/read_icos.f90 | 11 +-
prep_flexpart/read_noaa.f90 | 9 +-
prep_flexpart/read_obspack.f90 | 9 +-
prep_flexpart/read_reclist.f90 | 5 +-
prep_flexpart/read_wdcgg.f90 | 9 +-
prep_flexpart/run_flexpart.sh | 15 +-
prep_flexpart/sbatch_prep_flexpart.sh | 4 +-
prep_fluxes/FLUXES_co2_bbg | 68 ---
prep_fluxes/FLUXES_co2_ff | 68 ---
prep_fluxes/FLUXES_co2_nee | 68 ---
prep_fluxes/FLUXES_co2_ocn | 68 ---
prep_fluxes/README_prepflux.txt | 3 +-
prep_fluxes/{FLUXES_ghg => SETTINGS_FLUX} | 4 +-
prep_fluxes/job_prep_flux.sh | 2 +-
prep_fluxes/sbatch_prep_flux.sh | 2 +-
prep_regions/initialize.f90 | 41 +-
prep_regions/mod_settings.f90 | 28 +
prep_regions/mod_strings.f90 | 92 ++-
prep_regions/mod_var.f90 | 2 +-
prep_regions/prep_regions.f90 | 13 +-
prep_regions/read_obs.f90 | 237 +++++---
prep_regions/read_reclist.f90 | 5 +-
prep_satellite/SETTINGS_bremen | 155 +++++
prep_satellite/SETTINGS_oco2 | 157 +++++
prep_satellite/SETTINGS_tropomi | 159 +++++
prep_satellite/average.f90 | 468 +++++++++++++++
prep_satellite/geodarea.f90 | 61 ++
prep_satellite/get_bremen.f90 | 431 +++++++++++++
prep_satellite/get_oco2.f90 | 465 ++++++++++++++
prep_satellite/get_tropomi.f90 | 552 +++++++++++++++++
prep_satellite/gridarea.f90 | 64 ++
prep_satellite/main.f90 | 86 +++
prep_satellite/makefile | 40 ++
prep_satellite/mod_dates.f90 | 176 ++++++
prep_satellite/mod_save.f90 | 225 +++++++
prep_satellite/mod_settings.f90 | 567 ++++++++++++++++++
prep_satellite/mod_var.f90 | 39 ++
prep_satellite/prep_ageclass.f90 | 69 +++
prep_satellite/prep_command.f90 | 171 ++++++
prep_satellite/prep_outgrid.f90 | 131 ++++
prep_satellite/prep_pathnames.f90 | 75 +++
prep_satellite/run_flexpart.sh | 97 +++
prep_satellite/sbatch_satellite.sh | 15 +
prep_syndata/get_obs.f90 | 18 +-
prep_syndata/initialize.f90 | 36 +-
prep_syndata/job_prep_syndata.sh | 4 +-
prep_syndata/mod_save.f90 | 123 +++-
prep_syndata/mod_settings.f90 | 26 +-
prep_syndata/mod_strings.f90 | 19 +-
prep_syndata/sbatch.sh | 4 +-
...ghg_nest_config => SETTINGS_ch4sat_config} | 62 +-
...S_ghg_nest_files => SETTINGS_ch4sat_files} | 63 +-
settings/SETTINGS_co2_config | 6 +
settings/SETTINGS_co2_files | 24 +-
settings/SETTINGS_co2_nest_config | 161 -----
settings/SETTINGS_co2_nest_files | 133 ----
settings/SETTINGS_ghg_config | 10 +-
settings/SETTINGS_ghg_files | 20 +-
source/README_source.txt | 4 +-
source/average_fp.f90 | 12 +-
source/calc_conc.f90 | 8 +-
source/congrad.f90 | 10 +-
source/get_initconc.f90 | 8 +-
source/init_cini.f90 | 48 +-
source/init_cini_month.f90 | 64 +-
source/init_co2.f90 | 21 +-
source/init_ghg.f90 | 26 +-
source/initialize.f90 | 73 ++-
source/m1qn3_interface.f90 | 4 +
source/mod_flexpart.f90 | 12 +-
source/mod_obs.f90 | 52 +-
source/mod_save.f90 | 62 +-
source/mod_settings.f90 | 34 +-
source/mod_strings.f90 | 15 +-
source/read_obs.f90 | 285 ++++++---
source/read_reclist.f90 | 21 +-
source/sbatch_flexinvert.sh | 6 +-
source/simulate.f90 | 153 +++--
102 files changed, 6034 insertions(+), 1501 deletions(-)
create mode 100644 grid_to_ncdf/factor_convert.f90
create mode 100644 grid_to_ncdf/init_convert.f90
rename prep_flexpart/{SETTINGS_co2 => SETTINGS} (89%)
delete mode 100644 prep_flexpart/SETTINGS_co2_nest
delete mode 100644 prep_flexpart/SETTINGS_ghg
delete mode 100644 prep_flexpart/SETTINGS_ghg_nest
delete mode 100644 prep_fluxes/FLUXES_co2_bbg
delete mode 100644 prep_fluxes/FLUXES_co2_ff
delete mode 100644 prep_fluxes/FLUXES_co2_nee
delete mode 100644 prep_fluxes/FLUXES_co2_ocn
rename prep_fluxes/{FLUXES_ghg => SETTINGS_FLUX} (92%)
create mode 100644 prep_satellite/SETTINGS_bremen
create mode 100644 prep_satellite/SETTINGS_oco2
create mode 100644 prep_satellite/SETTINGS_tropomi
create mode 100644 prep_satellite/average.f90
create mode 100644 prep_satellite/geodarea.f90
create mode 100644 prep_satellite/get_bremen.f90
create mode 100644 prep_satellite/get_oco2.f90
create mode 100644 prep_satellite/get_tropomi.f90
create mode 100644 prep_satellite/gridarea.f90
create mode 100644 prep_satellite/main.f90
create mode 100644 prep_satellite/makefile
create mode 100644 prep_satellite/mod_dates.f90
create mode 100644 prep_satellite/mod_save.f90
create mode 100644 prep_satellite/mod_settings.f90
create mode 100644 prep_satellite/mod_var.f90
create mode 100644 prep_satellite/prep_ageclass.f90
create mode 100644 prep_satellite/prep_command.f90
create mode 100644 prep_satellite/prep_outgrid.f90
create mode 100644 prep_satellite/prep_pathnames.f90
create mode 100755 prep_satellite/run_flexpart.sh
create mode 100755 prep_satellite/sbatch_satellite.sh
rename settings/{SETTINGS_ghg_nest_config => SETTINGS_ch4sat_config} (78%)
rename settings/{SETTINGS_ghg_nest_files => SETTINGS_ch4sat_files} (71%)
delete mode 100644 settings/SETTINGS_co2_nest_config
delete mode 100644 settings/SETTINGS_co2_nest_files
diff --git a/README.txt b/README.txt
index fe9fe0a..83cfac9 100644
--- a/README.txt
+++ b/README.txt
@@ -1,40 +1,56 @@
================================================================
- FLEXINVERT-Plus
+ FLEXINVERT
================================================================
Description:
- FLEXINVERT-Plus is a Bayesian inversion framework
+
+ FLEXINVERT is a Bayesian inversion framework
for optimizing fluxes of different atmospheric
species (e.g. CO2, CH4, BC).
Contents:
- 1) prep_flexpart:
+
+ prep_flexpart:
- selects (and optionally averages) observations and prepares
flexpart runs with releases for each observation
- - flexpart grid_time output files written per release
+ - flexpart grid_time output files are written per release
- note need at least FLEXPART-v10.2
- 2) prep_fluxes:
+
+ prep_satellite:
+ - selects (and optionally averages) satellite retrievals and
+ prepares flexpart releases for each retrieval and the
+ flexpart options files
+ - flexpart grid_time output files are written per retrieval
+ and represent the total column source receptor relationship
+ - note need at least FLEXPART-v10.4beta
+
+ prep_fluxes:
- regrids fluxes (fluxes need to be at the same spatial
resolution as the flexpart grid_time files)
- writes fluxes in a standard ncdf format required by
- FLEXINVERT-Plus
- 3) prep_regions (optional):
+ FLEXINVERT
+
+ prep_regions (optional):
- prepares variable resolution grid for the inversion based
on flexpart flux sensitivities (output from prep_flexpart)
(alternatively can provide own regions definition file)
- 4) settings:
+
+ settings:
- contains example SETTINGS_config and SETTINGS_files files
- for FLEXINVERT-Plus
- 5) source:
- - source code for FLEXINVERT-Plus
- 6) prep_syndata:
- - prepares synthetic data for testing and OSEs
+ for FLEXINVERT
+
+ source:
+ - source code for FLEXINVERT (for the actual inversion)
+
+ prep_syndata:
+ - prepares synthetic data for testing and OSSEs
- uses output from a forward run and adds random
perturbations to the prior fluxes and observations
according to the error covariance matrices
- 7) grid_to_ncdf:
- - extra tool (not needed for FLEXINVERT-Plus) to convert
+
+ grid_to_ncdf:
+ - extra tool (not needed for FLEXINVERT) to convert
the binary grid_time files to NetCDF
diff --git a/grid_to_ncdf/README_gridncdf.txt b/grid_to_ncdf/README_gridncdf.txt
index 58691c1..2328418 100644
--- a/grid_to_ncdf/README_gridncdf.txt
+++ b/grid_to_ncdf/README_gridncdf.txt
@@ -1,14 +1,17 @@
================================================================
- FLEXINVERT-Plus BINARY TO NETCDF CONVERTOR
+ FLEXINVERT binary to netcdf converter
================================================================
Description:
- Converts FLEXPART grid_time files from sparse binary format
- to netcdf. Note this is not needed to run FLEXINVERT-Plus but
- is an extra tool that users may find helpful, e.g. for viewing
- the footprints.
+ Converts one of the following flexpart output file types:
+ - grid_time
+ - grid_initial
+ - factor_drygrid
+ from sparse binary format to netcdf. Note this is not needed to
+ run FLEXINVERT but is an extra tool that users may find helpful,
+ e.g. for viewing the footprints.
Usage:
1) compile with gfortran using: make
diff --git a/grid_to_ncdf/SETTINGS b/grid_to_ncdf/SETTINGS
index 0020b77..732a96f 100644
--- a/grid_to_ncdf/SETTINGS
+++ b/grid_to_ncdf/SETTINGS
@@ -22,9 +22,17 @@ file_recept: /myfile.txt
datei: 20140701
datef: 20140831
+# Directory frequency: 'month' or 'day'
+# note: use 'day' for satellite retrievals (otherwise use 'month')
+filefreq: month
+
# Nested output (true/false)
lnested: .true.
# Inversion formatted flexpart output (true/false)
linversionout: .true.
+# Type of input (0 = grid_time, 1 = grid_initial, 2 = factor for dryair)
+intype: 0
+
+
diff --git a/grid_to_ncdf/factor_convert.f90 b/grid_to_ncdf/factor_convert.f90
new file mode 100644
index 0000000..0c0d687
--- /dev/null
+++ b/grid_to_ncdf/factor_convert.f90
@@ -0,0 +1,97 @@
+!---------------------------------------------------------------------------------------
+! GRID_TO_NCDF: factor_convert
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2017, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> factor_convert
+!!
+!! Purpose:
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine factor_convert(files, config, nr, timestamp)
+
+ use mod_var
+ use mod_settings
+ use mod_flexpart
+ use mod_dates
+
+ implicit none
+
+ type (files_t), intent(in out) :: files
+ type (config_t), intent(in) :: config
+ integer, intent(in) :: nr
+ integer, intent(in) :: timestamp
+
+ character(max_path_len) :: filename, filedates, path_flexpart, path_output
+ character(len=8) :: adate
+ character(len=6) :: atime
+ logical :: lexist
+ integer :: nfiles, nread, i, ierr, n
+ integer :: jjjjmmdd, hhmiss
+ real, dimension(:,:,:), allocatable :: grid
+ real(kind=8), dimension(:), allocatable :: ftime, dates
+ real(kind=8) :: jdate
+
+ ! path names
+ if ( trim(config%filefreq).eq.'month' ) then
+ write(adate,'(I6.6)') timestamp/100
+ print*, adate
+ else if ( trim(config%filefreq).eq.'day' ) then
+ write(adate,'(I8.8)') timestamp
+ endif
+ path_flexpart = trim(files%path_flexpart)//trim(recname(nr))//'/'//trim(adate)//'/'
+ path_output = trim(files%path_output)//trim(recname(nr))//'/'
+ filedates = trim(path_flexpart)//'dates'
+
+ ! read binary file
+ call get_nread(filedates, nread)
+ allocate ( dates(nread) )
+ allocate ( ftime(nread) )
+ allocate ( grid(nxgrid,nygrid,nread) )
+ call read_dates(filedates, nread, dates)
+ do n = 1, nread
+ ftime(n) = juldate(int(dates(n)/1d6),int(dates(n)-floor(dates(n)/1d6)*1d6))
+ end do
+ grid(:,:,:) = 1.
+ if ( config%lnested ) then
+ filename = trim(path_flexpart)//'factor_drygrid_nest'
+ else
+ filename = trim(path_flexpart)//'factor_drygrid'
+ endif
+ inquire ( file=trim(filename),exist=lexist )
+ if ( lexist ) then
+ write(*,*) 'Reading correction factor :'//trim(filename)
+ call read_factor(filename, nread, nxgrid, nygrid, nxshift, grid)
+ endif
+
+ ! output file name
+ if ( config%lnested ) then
+ filename = trim(path_output)//'factor_drygrid_nest.nc'
+ else
+ filename = trim(path_output)//'factor_drygrid.nc'
+ endif
+
+ ! write as ncdf
+ call write_ncdf(config, filename, ftime, grid)
+
+ deallocate( grid )
+ deallocate( ftime )
+ deallocate( dates )
+
+end subroutine factor_convert
+
diff --git a/grid_to_ncdf/grid_convert.f90 b/grid_to_ncdf/grid_convert.f90
index efaba9e..4c3adfd 100644
--- a/grid_to_ncdf/grid_convert.f90
+++ b/grid_to_ncdf/grid_convert.f90
@@ -23,7 +23,7 @@
!!
!---------------------------------------------------------------------------------------
-subroutine grid_convert(files, config, nr, amonth)
+subroutine grid_convert(files, config, nr, timestamp)
use mod_var
use mod_settings
@@ -33,8 +33,9 @@ subroutine grid_convert(files, config, nr, amonth)
implicit none
type (files_t), intent(in out) :: files
- type (config_t), intent(in) :: config
+ type (config_t), intent(in out) :: config
integer, intent(in) :: nr
+ integer, intent(in) :: timestamp
character(max_path_len) :: filename, filedates, path_flexpart, path_output
character(len=max_path_len), dimension(:), allocatable :: filelist
@@ -53,7 +54,13 @@ subroutine grid_convert(files, config, nr, amonth)
integer :: numx, numy
! list all grid files in directory
- path_flexpart = trim(files%path_flexpart)//trim(recname(nr))//'/'//trim(amonth)//'/'
+ if ( trim(config%filefreq).eq.'month' ) then
+ write(adate,'(I6.6)') timestamp/100
+ print*, adate
+ else if ( trim(config%filefreq).eq.'day' ) then
+ write(adate,'(I8.8)') timestamp
+ endif
+ path_flexpart = trim(files%path_flexpart)//trim(recname(nr))//'/'//trim(adate)//'/'
path_output = trim(files%path_output)//trim(recname(nr))//'/'
print*, path_flexpart
print*, path_output
@@ -110,42 +117,56 @@ subroutine grid_convert(files, config, nr, amonth)
! read binary grid files
if ( config%lnested ) then
adate = filelist(i)(16:23)
- atime = filelist(i)(24:29)
+ if ( trim(config%filefreq).eq.'month' ) then
+ atime = filelist(i)(24:29)
+ else if ( trim(config%filefreq).eq.'day' ) then
+ ! assume satellite -> get number of retrieval
+ atime = filelist(i)(25:30)
+ endif
else
adate = filelist(i)(11:18)
- atime = filelist(i)(19:24)
+ if ( trim(config%filefreq).eq.'month' ) then
+ atime = filelist(i)(19:24)
+ else if ( trim(config%filefreq).eq.'day' ) then
+ ! assume satellite -> get number of retrieval
+ atime = filelist(i)(20:25)
+ endif
endif
-! print*, 'adate = ',adate
-! print*, 'atime = ',atime
read(adate,*) jjjjmmdd
read(atime,*) hhmiss
-! print*, 'jjjjmmdd = ',jjjjmmdd
-! print*, 'hhmiss = ',hhmiss
+ print*, 'jjjjmmdd = ',jjjjmmdd
+ print*, 'hhmiss = ',hhmiss
if ( config%linversionout ) then
jdate = juldate(jjjjmmdd, hhmiss)
else
jdate = juldate(datei,timei)
endif
-! print*, 'jdate = ',jdate
filename = trim(path_flexpart)//trim(filelist(i))
if ( config%linversionout ) then
call read_grid(config, filename, filedates, jdate, nxgrid, nygrid, grid, gtime)
else
call read_grid_std(config, filename, jdate, nxgrid, nygrid, grid, gtime)
endif
-! print*, 'gtime = ',gtime
! write to ncdf
do n = 1, ngrid
call caldate(gtime(n), jjjjmmdd, hhmiss)
time(n) = real(jjjjmmdd,kind=8)*100d0+real(hhmiss/10000,kind=8)
end do
- print*, 'time = ',time
if ( config%lnested ) then
- filename = trim(path_output)//'grid_time_nest_'//adate//atime//'_001.nc'
+ if ( trim(config%filefreq).eq.'month' ) then
+ filename = trim(path_output)//'grid_time_nest_'//adate//atime//'_001.nc'
+ else if ( trim(config%filefreq).eq.'day' ) then
+ ! assume satellite
+ filename = trim(path_output)//'grid_time_nest_'//adate//'_'//atime//'.nc'
+ endif
else
- filename = trim(path_output)//'grid_time_'//adate//atime//'_001.nc'
+ if ( trim(config%filefreq).eq.'month' ) then
+ filename = trim(path_output)//'grid_time_'//adate//atime//'_001.nc'
+ else if ( trim(config%filefreq).eq.'day' ) then
+ filename = trim(path_output)//'grid_time_'//adate//'_'//atime//'.nc'
+ endif
endif
- call write_ncdf(filename, time, grid)
+ call write_ncdf(config, filename, time, grid)
end do
deallocate( grid )
diff --git a/grid_to_ncdf/grid_to_ncdf.f90 b/grid_to_ncdf/grid_to_ncdf.f90
index 1de5465..dd7f9a8 100644
--- a/grid_to_ncdf/grid_to_ncdf.f90
+++ b/grid_to_ncdf/grid_to_ncdf.f90
@@ -40,7 +40,7 @@ program grid_to_ncdf
character(len=6) :: adate
integer :: nr
integer :: yyyymmdd, hhmiss, eomday
- real(kind=8) :: juldatei, juldatef, jd
+ real(kind=8) :: juldatei, juldatef, jd, dt
call getarg(1,settings_files)
if (settings_files == '') then
@@ -60,14 +60,27 @@ program grid_to_ncdf
jd = juldatei
do while ( jd.le.juldatef )
call caldate(jd, yyyymmdd, hhmiss)
- write(adate,'(I6.6)') yyyymmdd/100
- call grid_convert(files, config, nr, adate)
- eomday = calceomday(yyyymmdd/100)
- jd = jd + dble(eomday)
+ select case ( config%intype )
+ case (0)
+ ! grid_time
+ call grid_convert(files, config, nr, yyyymmdd)
+ case (1)
+ ! grid_initial
+ call init_convert(files, config, nr, yyyymmdd)
+ case (2)
+ ! factor
+ call factor_convert(files, config, nr, yyyymmdd)
+ endselect
+ if ( trim(config%filefreq).eq.'month' ) then
+ eomday = calceomday(yyyymmdd/100)
+ dt = dble(eomday)
+ else if ( trim(config%filefreq).eq.'day' ) then
+ dt = 1d0
+ endif
+ jd = jd + dt
end do
end do
-
end program
diff --git a/grid_to_ncdf/init_convert.f90 b/grid_to_ncdf/init_convert.f90
new file mode 100644
index 0000000..a57bfeb
--- /dev/null
+++ b/grid_to_ncdf/init_convert.f90
@@ -0,0 +1,146 @@
+!---------------------------------------------------------------------------------------
+! GRID_TO_NCDF: init_convert
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2017, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> init_convert
+!!
+!! Purpose:
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine init_convert(files, config, nr, timestamp)
+
+ use mod_var
+ use mod_settings
+ use mod_flexpart
+ use mod_dates
+
+ implicit none
+
+ type (files_t), intent(in out) :: files
+ type (config_t), intent(in) :: config
+ integer, intent(in) :: nr
+ integer, intent(in) :: timestamp
+
+ character(max_path_len) :: filename, filedates, path_flexpart, path_output
+ character(len=max_path_len), dimension(:), allocatable :: filelist
+ character(len=8) :: adate
+ character(len=6) :: atime
+ character(len=3) :: anspec
+ logical :: lexist
+ integer :: nfiles, i, ierr, n
+ integer :: jjjjmmdd, hhmiss
+ real, dimension(:,:,:), allocatable :: grid
+ real(kind=8), dimension(:), allocatable :: levels
+ real(kind=8) :: jdate
+ integer :: numpoint
+ integer :: ibdate, ibtime
+ integer, dimension(maxpoint) :: releases
+ real :: bndx, bndy, delx, dely
+ integer :: numx, numy
+
+ ! list all grid files in directory
+ if ( trim(config%filefreq).eq.'month' ) then
+ write(adate,'(I6.6)') timestamp/100
+ print*, adate
+ else if ( trim(config%filefreq).eq.'day' ) then
+ write(adate,'(I8.8)') timestamp
+ endif
+ path_flexpart = trim(files%path_flexpart)//trim(recname(nr))//'/'//trim(adate)//'/'
+ path_output = trim(files%path_output)//trim(recname(nr))//'/'
+ print*, path_flexpart
+ print*, path_output
+ call system('mkdir '//trim(path_output))
+ call system('ls '//trim(path_flexpart)//' | grep grid_initial_ | wc -l > '//trim(path_output)//'files.txt')
+ call system('ls '//trim(path_flexpart)//' | grep grid_initial_ >> '//trim(path_output)//'files.txt')
+
+ ! read file list
+ open(100,file=trim(path_output)//'files.txt',status="old",action="read",iostat=ierr)
+ if ( ierr.ne.0 ) then
+ print*, 'ERROR: problem read files.txt'
+ stop
+ endif
+ read(100,*) nfiles
+ allocate( filelist(nfiles) )
+ do i = 1, nfiles
+ read(100,fmt='(A)',iostat=ierr) filelist(i)
+ if (ierr.ne.0) exit
+ end do
+ close(100)
+
+ ! read header for this month to get ngrid
+ filename = trim(path_flexpart)//'header'
+ inquire(file=trim(filename),exist=lexist)
+ if ( .not.lexist ) then
+ print*, 'ERROR: cannot find flexpart header'
+ stop
+ endif
+ print*, 'Reading flexpart header: '//trim(filename)
+ call read_header(filename, numpoint, ibdate, ibtime, releases, &
+ numx, numy, bndx, bndy, delx, dely)
+ print*, 'numx, numy, bndx, bndy, delx, dely = ',numx,numy,bndx,bndy,delx,dely
+ allocate( grid(nxgrid,nygrid,nzgrid) )
+ allocate( levels(nzgrid) )
+ ! trick to use write_ncdf also for grid_initial
+ ngrid = nzgrid
+ levels(:) = dble(outheight(1:nzgrid))
+
+ ! loop over files
+ filedates = trim(path_flexpart)//'dates'
+ do i = 1, nfiles
+ ! read binary grid files
+ adate = filelist(i)(14:21)
+ if ( trim(config%filefreq).eq.'month' ) then
+ atime = filelist(i)(22:27)
+ else if ( trim(config%filefreq).eq.'day' ) then
+ ! assume satellite -> get number of retrieval
+ atime = filelist(i)(23:28)
+ endif
+ print*, 'adate = ',adate
+ print*, 'atime = ',atime
+ read(adate,*) jjjjmmdd
+ read(atime,*) hhmiss
+ print*, 'jjjjmmdd = ',jjjjmmdd
+ print*, 'hhmiss = ',hhmiss
+ if ( config%linversionout ) then
+ jdate = juldate(jjjjmmdd, hhmiss)
+ else
+ jdate = juldate(datei,timei)
+ endif
+! print*, 'jdate = ',jdate
+ filename = trim(path_flexpart)//trim(filelist(i))
+ if ( config%linversionout ) then
+ call read_init(filename, grid)
+ else
+ call read_init_std(filename, grid)
+ endif
+ ! write to ncdf
+ if ( trim(config%filefreq).eq.'month' ) then
+ filename = trim(path_output)//'grid_initial_'//adate//atime//'_001.nc'
+ else if ( trim(config%filefreq).eq.'day' ) then
+ ! assume satellite
+ filename = trim(path_output)//'grid_initial_'//adate//'_'//atime//'.nc'
+ endif
+ call write_ncdf(config, filename, levels, grid)
+ end do
+
+ deallocate( grid )
+ deallocate( levels )
+
+end subroutine init_convert
+
diff --git a/grid_to_ncdf/initialize.f90 b/grid_to_ncdf/initialize.f90
index d71b8e3..ab0df23 100644
--- a/grid_to_ncdf/initialize.f90
+++ b/grid_to_ncdf/initialize.f90
@@ -38,6 +38,7 @@ subroutine initialize(files, config)
logical :: lexist
integer :: yyyymm
character(len=6) :: adate
+ character(len=8) :: areldate
integer :: numpoint
integer :: ibdate, ibtime
integer, dimension(maxpoint) :: releases
@@ -48,19 +49,39 @@ subroutine initialize(files, config)
! read list of receptors
! ----------------------
- filename = trim(files%file_recept)
- call read_reclist(filename)
+ if ( trim(config%filefreq).eq.'month' ) then
+ filename = trim(files%file_recept)
+ call read_reclist(filename)
+ else
+ ! assume satellite retrievals -> no reclist
+ nrec = 1
+ allocate ( recname(nrec) )
+ recname(1) = ''
+ endif
! initialize flexpart variables
! -----------------------------
yyyymm=config%datei/100
write(adate,'(i6)') yyyymm
+ write(areldate,'(i8)') config%datei
lexist = .false.
i = 1
do while ( (.not.lexist).and.(i.le.nrec) )
- if ( .not.config%lnested ) filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header'
- if ( config%lnested ) filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header_nest'
+ if ( (.not.config%lnested).or.config%intype.eq.1 ) then
+ if ( trim(config%filefreq).eq.'month' ) then
+ filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header'
+ else
+ filename = trim(files%path_flexpart)//trim(areldate)//'/header'
+ endif
+ else if ( config%lnested ) then
+ if ( trim(config%filefreq).eq.'month' ) then
+ filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header_nest'
+ else
+ filename = trim(files%path_flexpart)//trim(areldate)//'/header_nest'
+ endif
+ endif
+ print*, filename
inquire(file=trim(filename),exist=lexist)
i = i + 1
end do
@@ -91,6 +112,7 @@ subroutine initialize(files, config)
print*, 'trajdays = ',trajdays
print*, 'ngrid = ',ngrid
print*, 'nxshift = ',nxshift
+ print*, 'nxgrid, nygrid, nzgrid = ',nxgrid,nygrid,nzgrid
! initialize lon and lat dimensions
if ( .not.allocated(glon) ) allocate( glon(nxgrid) )
diff --git a/grid_to_ncdf/makefile b/grid_to_ncdf/makefile
index b47ea6a..75feccc 100644
--- a/grid_to_ncdf/makefile
+++ b/grid_to_ncdf/makefile
@@ -17,6 +17,8 @@ SRCS = mod_var.f90 \
mod_flexpart.f90 \
initialize.f90 \
grid_convert.f90 \
+ init_convert.f90 \
+ factor_convert.f90 \
write_ncdf.f90 \
read_reclist.f90 \
grid_to_ncdf.f90
diff --git a/grid_to_ncdf/mod_flexpart.f90 b/grid_to_ncdf/mod_flexpart.f90
index bd5acb8..0480e61 100644
--- a/grid_to_ncdf/mod_flexpart.f90
+++ b/grid_to_ncdf/mod_flexpart.f90
@@ -33,7 +33,7 @@ module mod_flexpart
implicit none
private
- public :: read_header, read_grid, read_init, &
+ public :: read_header, read_grid, read_init, read_factor, &
read_grid_std, read_init_std, get_nread, read_dates
contains
@@ -179,7 +179,7 @@ module mod_flexpart
real(kind=8), dimension(ngrid), intent(in out) :: gtime
real, parameter :: scaleconc=1.e12
- real, parameter :: smallnum=1.e-38
+ real, parameter :: smallnum=tiny(0.)
logical :: lexist
integer :: ierr
integer :: nread
@@ -190,7 +190,7 @@ module mod_flexpart
real, dimension(numx*numy) :: sparse_dump_r
real, dimension(:,:,:), allocatable :: work
integer(kind=4), dimension(:), allocatable :: times
- real(kind=4), dimension(:), allocatable :: dates
+ real(kind=8), dimension(:), allocatable :: dates
real(kind=8) :: jdrel
real(kind=8), dimension(:), allocatable :: jdtime
@@ -215,6 +215,7 @@ module mod_flexpart
! open grid_time file
inquire ( file=trim(filename),exist=lexist )
+ print*, filename
if ( .not.lexist ) then
write(*,*) 'WARNING: cannot find '//trim(filename)
go to 10
@@ -226,6 +227,7 @@ module mod_flexpart
endif
! read footprints
+ n = 0
do nt = 1, ngrid
read(100,iostat=ierr,end=20) jjjjmmdd
read(100,iostat=ierr,end=20) hhmiss
@@ -311,7 +313,7 @@ module mod_flexpart
real(kind=8), dimension(ngrid), intent(in out) :: gtime
real, parameter :: scaleconc=1.e12
- real, parameter :: smallnum=1.e-38
+ real, parameter :: smallnum=tiny(0.)
logical :: lexist
integer :: ierr
integer :: sp_count_i, sp_count_r
@@ -414,12 +416,13 @@ module mod_flexpart
real, dimension(nxgrid,nygrid,nzgrid), intent(in out) :: gridinit
real, parameter :: scaleconc=1.e12
- real, parameter :: smallnum=1.e-38
+ real, parameter :: smallnum=tiny(0.)
logical :: lexist
integer :: ierr
integer :: sp_count_i, sp_count_r
integer :: jjjjmmdd, hhmiss
- integer :: ii, ir, fact, n, nt, jy, ix, kz
+ integer :: ii, ir, n, nt, jy, ix, kz
+ real :: fact
integer, dimension(nxgrid*nygrid*nzgrid) :: sparse_dump_i
real, dimension(nxgrid*nygrid*nzgrid) :: sparse_dump_r
@@ -439,7 +442,7 @@ module mod_flexpart
read(100) jjjjmmdd
read(100) hhmiss
- fact = 1
+ fact = 1.
read(100) sp_count_i
read(100) (sparse_dump_i(ix), ix=1, sp_count_i)
read(100) sp_count_r
@@ -459,6 +462,9 @@ module mod_flexpart
gridinit(ix+1,jy+1,kz) = abs(sparse_dump_r(ir))*scaleconc
end do
+ ! shift grid by xshift along longitudinal dimension
+ gridinit = cshift(gridinit, shift=-1*nxshift, dim=1)
+
close(100)
10 continue
@@ -552,7 +558,7 @@ module mod_flexpart
character(len=max_path_len), intent(in) :: filename
integer, intent(in) :: nread
- real(kind=4), dimension(nread), intent(in out) :: dates
+ real(kind=8), dimension(nread), intent(in out) :: dates
character(len=14) :: tmp
integer :: ierr, n
@@ -574,6 +580,80 @@ module mod_flexpart
end subroutine read_dates
! --------------------------------------------------
+ ! read_factor
+ ! --------------------------------------------------
+ !> read_factor
+ !!
+ !! Purpose: Reads the correction factor (i.e. ratio
+ !! of the wet to dry air density for
+ !! correcting mixing ratios for dry air).
+ !!
+ ! --------------------------------------------------
+
+ subroutine read_factor(filename, nread, numx, numy, xshift, factor)
+
+ use mod_var
+
+ implicit none
+
+ character(len=max_path_len), intent(in) :: filename
+ integer, intent(in) :: nread
+ integer, intent(in) :: numx, numy, xshift
+ real, dimension(numx,numy,nread), intent(in out) :: factor
+
+ real, parameter :: smallnum=tiny(0.)
+ logical :: lexist
+ integer :: ierr
+ integer :: sp_count_i, sp_count_r
+ integer :: ii, ir, n, nt, jy, ix
+ real :: fact
+ integer, dimension(numx*numy) :: sparse_dump_i
+ real, dimension(numx*numy) :: sparse_dump_r
+
+ ! open factor file
+ inquire ( file=trim(filename),exist=lexist )
+ if ( .not.lexist ) then
+ write(*,*) 'WARNING: cannot find '//trim(filename)
+ go to 10
+ endif
+ open(100,file=trim(filename),form='unformatted',action='read',status='old',iostat=ierr)
+ if( ierr.ne.0 ) then
+ write(*,*) 'WARNING: cannot read '//trim(filename)
+ go to 10
+ endif
+
+ ! read footprints
+ do nt = 1, nread
+ fact = 1.
+ read(100) sp_count_i
+ read(100) (sparse_dump_i(ix), ix=1,sp_count_i)
+ read(100) sp_count_r
+ read(100) (sparse_dump_r(ix), ix=1,sp_count_r)
+ ii = 0
+ do ir = 1, sp_count_r
+ if ((sparse_dump_r(ir)*fact).gt.smallnum) then
+ ii = ii + 1
+ n = sparse_dump_i(ii)
+ fact = fact*(-1.)
+ else
+ n = n + 1
+ endif
+ jy = (n - numx * numy)/numx
+ ix = n - numx * numy - numx * jy
+ factor(ix+1,jy+1,nt) = abs(sparse_dump_r(ir))
+ end do
+ end do
+
+ close(100)
+
+ ! shift grid by xshift along longitudinal dimension
+ factor = cshift(factor, shift=-1*xshift, dim=1)
+
+ 10 continue
+
+ end subroutine read_factor
+
+ ! --------------------------------------------------
end module mod_flexpart
diff --git a/grid_to_ncdf/mod_settings.f90 b/grid_to_ncdf/mod_settings.f90
index 6a897d2..ef6bf34 100644
--- a/grid_to_ncdf/mod_settings.f90
+++ b/grid_to_ncdf/mod_settings.f90
@@ -48,6 +48,8 @@ module mod_settings
integer :: datef ! end date (yyyymmdd)
logical :: lnested ! use nested flexpart output (true or false)
logical :: linversionout ! inversion formatted flexpart output (true or false)
+ integer :: intype ! 0 = grid_time, 1 = grid_initial, 2 = factor for dryair
+ character(len=6) :: filefreq ! frequency of file directories
end type config_t
@@ -288,12 +290,18 @@ module mod_settings
identifier = "datef:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) config%datef = cn
+ identifier = "filefreq:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) config%filefreq = cc
identifier = "lnested:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) config%lnested = cl
identifier = "linversionout:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) config%linversionout = cl
+ identifier = "intype:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) config%intype = cn
endif
diff --git a/grid_to_ncdf/write_ncdf.f90 b/grid_to_ncdf/write_ncdf.f90
index 4bf72ca..8e4c72e 100644
--- a/grid_to_ncdf/write_ncdf.f90
+++ b/grid_to_ncdf/write_ncdf.f90
@@ -32,13 +32,15 @@
!!
!---------------------------------------------------------------------------------------
-subroutine write_ncdf(filename, time, grid)
+subroutine write_ncdf(config, filename, time, grid)
use mod_var
+ use mod_settings
use netcdf
implicit none
+ type (config_t), intent(in) :: config
character(len=max_path_len), intent(in) :: filename
real(kind=8), dimension(ngrid), intent(in) :: time
real, dimension(nxgrid,nygrid,ngrid), intent(in) :: grid
@@ -51,9 +53,21 @@ subroutine write_ncdf(filename, time, grid)
! variable and dimension names
lonname = 'longitude'
latname = 'latitude'
- timename = 'time'
+ select case ( config%intype )
+ case(0)
+ ! grid time
+ timename = 'time'
+ varunit = 'sm3/kg'
+ case (1)
+ ! grid initial
+ timename = 'height'
+ varunit = 'kg/kg'
+ case (2)
+ ! factor
+ timename = 'time'
+ varunit = 'kg/kg'
+ endselect
varname = 'grid'
- varunit = 'sm3/kg'
! open netcdf file
print*, 'Writing file: ',trim(filename)
diff --git a/prep_flexpart/README_prepflex.txt b/prep_flexpart/README_prepflex.txt
index 0292831..aa71b4c 100644
--- a/prep_flexpart/README_prepflex.txt
+++ b/prep_flexpart/README_prepflex.txt
@@ -1,6 +1,6 @@
================================================================
- FLEXPART PRE-PROCESSOR
+ FLEXPART pre-processor
================================================================
diff --git a/prep_flexpart/SETTINGS_co2 b/prep_flexpart/SETTINGS
similarity index 89%
rename from prep_flexpart/SETTINGS_co2
rename to prep_flexpart/SETTINGS
index 66f1501..ad393e6 100644
--- a/prep_flexpart/SETTINGS_co2
+++ b/prep_flexpart/SETTINGS
@@ -9,26 +9,26 @@
# Path and file settings
# flexpart source path
-path_flexpart: /mypath/FLEXPART/
+path_flexpart: /mypath/flexpart/
# path where to write options folder (root only, recname and month are appended)
-path_options: /mypath/TEST_INPUT/FLEXPART/CO2/NO_NEST/
+path_options: /mypath/flexpart_options/
# path where to write flexpart output (root only, recname and month are appended)
-path_output: /mypath/TEST_OUTPUT/FLEXOUT/CO2/NO_NEST/
+path_output: /mypath/flexpart_output/
# path to OH fields (if use OH chemistry)
-path_ohfield: /mypath_to_ohfields/
+path_ohfield: /mypath/ohfields/
# path to observations
-path_obs: /mypath/TEST_INPUT/OBS/CO2/
+path_obs: /mypath/obs/
# path where to write observation output
-path_obsout: /mypath/TEST_OUTPUT/OBS/CO2/
+path_obsout: /mypath/obs_out/
# observation file format (one of obspack, wdcgg, noaa, basic, icos)
obsformat: obspack
# observation file suffix
suffix: .txt
# receptor list file
-file_recept: /mypath/TEST_INPUT/reclist_co2.txt
+file_recept: /mypath/input/reclist.txt
# AVAILABLE files
-file_avail: /mypath_to_available_file/AVAILABLE
-file_availnest: /mypath_to_available_file/AVAILABLE
+file_avail: /mypath/available_files/AVAILABLE
+file_availnest: /mypath/available_files/AVAILABLE
# General settings
# make flexpart releases only when there are observations (1) or at regular intervals (0)
diff --git a/prep_flexpart/SETTINGS_co2_nest b/prep_flexpart/SETTINGS_co2_nest
deleted file mode 100644
index 66b4251..0000000
--- a/prep_flexpart/SETTINGS_co2_nest
+++ /dev/null
@@ -1,113 +0,0 @@
-# ==================================================
-#
-# FLEXPART RUN SETTINGS
-#
-# comment lines start with '#'
-# each parameter line starts with 'parameter name:'
-#
-# ==================================================
-
-# Path and file settings
-# flexpart source path
-path_flexpart: /mypath/FLEXPART/
-# path where to write options folder (root only, recname and month are appended)
-path_options: /mypath/TEST_INPUT/FLEXPART/CO2/NEST/
-# path where to write flexpart output (root only, recname and month are appended)
-path_output: /mypath/TEST_OUTPUT/FLEXOUT/CO2/NEST/
-# path to OH fields (if use OH chemistry)
-path_ohfield: /mypath_to_ohfields/
-# path to observations
-path_obs: /mypath/TEST_INPUT/OBS/CO2/
-# path where to write observation output
-path_obsout: /mypath/TEST_OUTPUT/OBS/CO2/
-# observation file format (one of obspack, wdcgg, noaa, basic, icos)
-obsformat: obspack
-# observation file suffix
-suffix: .txt
-# receptor list file
-file_recept: /mypath/TEST_INPUT/reclist_co2.txt
-# AVAILABLE files
-file_avail: /mypath_to_available_file/AVAILABLE
-file_availnest: /mypath_to_available_file/AVAILABLE
-
-# General settings
-# make flexpart releases only when there are observations (1) or at regular intervals (0)
-# important: if set lrelease = 0 observations have to be from fixed locations (not aircraft, ship, satellite)
-lrelease: 0
-# if regular flexpart releases (lrelease = 0) set frequency (hours)
-relfreq: 1
-# select afternoon observations (night for mountains) (select = 1, no selection = 0)
-lselect: 1
-# average observations (average = 1, no average = 0)
-laverage: 0
-# averaging interval if laverage = 1 (hours)
-intaverage: 0
-# flexpart file format (namelist = 1, ascii = 0)
-lnamelist: 1
-
-# COMMAND settings
-# start date of simulation (yyyymmdd)
-datei: 20120101
-# end date of simulation (yyyymmdd)
-datef: 20120201
-# output rate (secs)
-outrate: 10800
-# time average of output (secs)
-outaverage: 10800
-# sampling rate of output (secs)
-outsample: 1800
-# (mass unit = 1, mixing ratio unit = 2)
-ind_source: 1
-# (mass unit = 1, mixing ratio unit = 2)
-ind_receptor: 2
-# use nested output (0 = no, 1 = yes)
-lnested: 1
-# output sensitivity to initial conditions (for backward runs, 0 = none, 1 = mass unit, 2 = mass mixing ratio)
-linit_cond: 2
-
-# OUTGRID settings
-# longitude of lower left corner of output grid
-outlonleft: -179.00
-# latitude of lower left corner of output grid
-outlatlower: -90.00
-# number of longitudinal grid cells in output grid
-numxgrid: 180
-# number of latitudinal grid cells in output grid
-numygrid: 90
-# longitudinal resolution in output grid
-dxout: 2.0
-# latitudinal resolution in outout grid
-dyout: 2.0
-# longitude of lower left corner of nested grid (used if nested_output = 1)
-outlonnest: -15.0
-# latitude of lower left corner of nested grid (used if nested_output = 1)
-outlatnest: 30.0
-# number of longitudinal grid cells in nested grid (used if nested_output = 1)
-numxnest: 100.0
-# number of latitudinal grid cells in nested grid (used if nested_output = 1)
-numynest: 90.0
-# longitudinal resolution in nested grid (used if nested_output = 1)
-dxoutnest: 0.5
-# latitudinal resolution in nested grid (used if nested_output = 1)
-dyoutnest: 0.5
-# comma-separated list of vertical levels in output grid (meters)
-zlevel: 100,500,1000,2000,3000,5000,7000,9000,12000,15000,20000,50000
-
-# RELEASES settings
-# species (see: /options/SPECIES/spec_overview)
-species: CO2
-# start date of releases (yyyymmdd)
-reldatei: 20120101
-#end date of releases (yyyymmdd)
-reldatef: 20120201
-# number of particles per grid cell
-npart: 10000
-# release heights relative to (1 = ground, 2 = sea level)
-zref: 2
-# orography inputfile (if zref = 1)
-file_orog: none
-
-# AGECLASS settings
-# ageclass (sec)
-ageclass: 259200
-
diff --git a/prep_flexpart/SETTINGS_ghg b/prep_flexpart/SETTINGS_ghg
deleted file mode 100644
index 42d8263..0000000
--- a/prep_flexpart/SETTINGS_ghg
+++ /dev/null
@@ -1,113 +0,0 @@
-# ==================================================
-#
-# FLEXPART RUN SETTINGS
-#
-# comment lines start with '#'
-# each parameter line starts with 'parameter name:'
-#
-# ==================================================
-
-# Path and file settings
-# flexpart source path
-path_flexpart: /mypath/FLEXPART/
-# path where to write options folder (root only, recname and month are appended)
-path_options: /mypath/TEST_INPUT/FLEXPART/GHG/NO_NEST/
-# path where to write flexpart output (root only, recname and month are appended)
-path_output: /mypath/TEST_OUTPUT/FLEXOUT/GHG/NO_NEST/
-# path to OH fields (if use OH chemistry)
-path_ohfield: /mypath_to_ohfields/
-# path to observations
-path_obs: /mypath/TEST_INPUT/OBS/GHG/
-# path where to write observation output
-path_obsout: /mypath/TEST_OUTPUT/OBS/GHG/
-# observation file format (one of obspack, wdcgg, noaa, basic, icos)
-obsformat: wdcgg
-# observation file suffix
-suffix: .dat
-# receptor list file
-file_recept: /mypath/TEST_INPUT/reclist_ghg.txt
-# AVAILABLE files
-file_avail: /mypath_to_available_file/AVAILABLE
-file_availnest: /mypath_to_available_file/AVAILABLE
-
-# General settings
-# make flexpart releases only when there are observations (1) or at regular intervals (0)
-# important: if set lrelease = 0 observations have to be from fixed locations (not aircraft, ship, satellite)
-lrelease: 0
-# if regular flexpart releases (lrelease = 0) set frequency (hours)
-relfreq: 1
-# select afternoon observations (night for mountains) (select = 1, no selection = 0)
-lselect: 0
-# average observations (average = 1, no average = 0)
-laverage: 0
-# averaging interval if laverage = 1 (hours)
-intaverage: 1
-# flexpart file format (namelist = 1, ascii = 0)
-lnamelist: 1
-
-# COMMAND settings
-# start date of simulation (yyyymmdd)
-datei: 20120101
-# end date of simulation (yyyymmdd)
-datef: 20120201
-# output rate (secs)
-outrate: 86400
-# time average of output (secs)
-outaverage: 86400
-# sampling rate of output (secs)
-outsample: 1800
-# (mass unit = 1, mixing ratio unit = 2)
-ind_source: 1
-# (mass unit = 1, mixing ratio unit = 2)
-ind_receptor: 2
-# use nested output (0 = no, 1 = yes)
-lnested: 0
-# output sensitivity to initial conditions (for backward runs, 0 = none, 1 = mass unit, 2 = mass mixing ratio)
-linit_cond: 2
-
-# OUTGRID settings
-# longitude of lower left corner of output grid
-outlonleft: -179.00
-# latitude of lower left corner of output grid
-outlatlower: -90.00
-# number of longitudinal grid cells in output grid
-numxgrid: 360
-# number of latitudinal grid cells in output grid
-numygrid: 180
-# longitudinal resolution in output grid
-dxout: 1.0
-# latitudinal resolution in outout grid
-dyout: 1.0
-# longitude of lower left corner of nested grid (used if nested_output = 1)
-outlonnest: -15.0
-# latitude of lower left corner of nested grid (used if nested_output = 1)
-outlatnest: 30.0
-# number of longitudinal grid cells in nested grid (used if nested_output = 1)
-numxnest: 100.0
-# number of latitudinal grid cells in nested grid (used if nested_output = 1)
-numynest: 90.0
-# longitudinal resolution in nested grid (used if nested_output = 1)
-dxoutnest: 0.5
-# latitudinal resolution in nested grid (used if nested_output = 1)
-dyoutnest: 0.5
-# comma-separated list of vertical levels in output grid (meters)
-zlevel: 100,500,1000,2000,3000,5000,7000,9000,12000,15000,20000,50000
-
-# RELEASES settings
-# species (see: /options/SPECIES/spec_overview)
-species: CH4
-# start date of releases (yyyymmdd)
-reldatei: 20120101
-#end date of releases (yyyymmdd)
-reldatef: 20120201
-# number of particles per grid cell
-npart: 10000
-# release heights relative to (1 = ground, 2 = sea level)
-zref: 2
-# orography inputfile (if zref = 1)
-file_orog: none
-
-# AGECLASS settings
-# ageclass (sec)
-ageclass: 432000
-
diff --git a/prep_flexpart/SETTINGS_ghg_nest b/prep_flexpart/SETTINGS_ghg_nest
deleted file mode 100644
index ae52bc0..0000000
--- a/prep_flexpart/SETTINGS_ghg_nest
+++ /dev/null
@@ -1,113 +0,0 @@
-# ==================================================
-#
-# FLEXPART RUN SETTINGS
-#
-# comment lines start with '#'
-# each parameter line starts with 'parameter name:'
-#
-# ==================================================
-
-# Path and file settings
-# flexpart source path
-path_flexpart: /mypath/FLEXPART/
-# path where to write options folder (root only, recname and month are appended)
-path_options: /mypath/TEST_INPUT/FLEXPART/GHG/NEST/
-# path where to write flexpart output (root only, recname and month are appended)
-path_output: /mypath/TEST_OUTPUT/FLEXOUT/GHG/NEST/
-# path to OH fields (if use OH chemistry)
-path_ohfield: /mypath_to_ohfields/
-# path to observations
-path_obs: /mypath/TEST_INPUT/OBS/GHG/
-# path where to write observation output
-path_obsout: /mypath/TEST_OUTPUT/OBS/GHG/
-# observation file format (one of obspack, wdcgg, noaa, icos)
-obsformat: noaa
-# observation file suffix
-suffix: event.txt
-# receptor list file
-file_recept: /mypath/TEST_INPUT/reclist_ghg.txt
-# AVAILABLE files
-file_avail: /mypath_to_available_file/AVAILABLE
-file_availnest: /mypath_to_available_file/AVAILABLE
-
-# General settings
-# make flexpart releases only when there are observations (1) or at regular intervals (0)
-# important: if set lrelease = 0 observations have to be from fixed locations (not aircraft, ship, satellite)
-lrelease: 0
-# if regular flexpart releases (lrelease = 0) set frequency (hours)
-relfreq: 1
-# select afternoon observations (night for mountains) (select = 1, no selection = 0)
-lselect: 0
-# average observations (average = 1, no average = 0)
-laverage: 0
-# averaging interval if laverage = 1 (hours)
-intaverage: 1
-# flexpart file format (namelist = 1, ascii = 0)
-lnamelist: 1
-
-# COMMAND settings
-# start date of simulation (yyyymmdd)
-datei: 20120101
-# end date of simulation (yyyymmdd)
-datef: 20120201
-# output rate (secs)
-outrate: 86400
-# time average of output (secs)
-outaverage: 86400
-# sampling rate of output (secs)
-outsample: 1800
-# (mass unit = 1, mixing ratio unit = 2)
-ind_source: 1
-# (mass unit = 1, mixing ratio unit = 2)
-ind_receptor: 2
-# use nested output (0 = no, 1 = yes)
-lnested: 1
-# output sensitivity to initial conditions (for backward runs, 0 = none, 1 = mass unit, 2 = mass mixing ratio)
-linit_cond: 2
-
-# OUTGRID settings
-# longitude of lower left corner of output grid
-outlonleft: -179.00
-# latitude of lower left corner of output grid
-outlatlower: -90.00
-# number of longitudinal grid cells in output grid
-numxgrid: 180
-# number of latitudinal grid cells in output grid
-numygrid: 90
-# longitudinal resolution in output grid
-dxout: 2.0
-# latitudinal resolution in outout grid
-dyout: 2.0
-# longitude of lower left corner of nested grid (used if nested_output = 1)
-outlonnest: -15.0
-# latitude of lower left corner of nested grid (used if nested_output = 1)
-outlatnest: 30.0
-# number of longitudinal grid cells in nested grid (used if nested_output = 1)
-numxnest: 100.0
-# number of latitudinal grid cells in nested grid (used if nested_output = 1)
-numynest: 90.0
-# longitudinal resolution in nested grid (used if nested_output = 1)
-dxoutnest: 0.5
-# latitudinal resolution in nested grid (used if nested_output = 1)
-dyoutnest: 0.5
-# comma-separated list of vertical levels in output grid (meters)
-zlevel: 100,500,1000,2000,3000,5000,7000,9000,12000,15000,20000,50000
-
-# RELEASES settings
-# species (see: /options/SPECIES/spec_overview)
-species: CH4
-# start date of releases (yyyymmdd)
-reldatei: 20120101
-#end date of releases (yyyymmdd)
-reldatef: 20120201
-# number of particles per grid cell
-npart: 10000
-# release heights relative to (1 = ground, 2 = sea level)
-zref: 2
-# orography inputfile (if zref = 1)
-file_orog: none
-
-# AGECLASS settings
-# ageclass (sec)
-ageclass: 432000
-
diff --git a/prep_flexpart/job_prep_flexpart.sh b/prep_flexpart/job_prep_flexpart.sh
index a8c6d91..cd3a6bd 100755
--- a/prep_flexpart/job_prep_flexpart.sh
+++ b/prep_flexpart/job_prep_flexpart.sh
@@ -1,6 +1,6 @@
#!/bin/bash
#---------------------------------------------------
-file='./SETTINGS_ghg_nest'
+file='./SETTINGS'
./prep_flexpart ${file}
diff --git a/prep_flexpart/list_obsfiles.f90 b/prep_flexpart/list_obsfiles.f90
index fa48a1b..ce62464 100644
--- a/prep_flexpart/list_obsfiles.f90
+++ b/prep_flexpart/list_obsfiles.f90
@@ -36,14 +36,6 @@ subroutine list_obsfiles(settings)
! list observation files
! ----------------------
- call system('rm -f '//trim(settings%path_obsout)//'obsfiles.txt')
-
- ! use find to descend into subdirectories (filelist then contains file path and requires editting read_xxx.f90)
-! call system ('find ' //trim(settings%path_obs)// ' -not -path "*/\.*" -type f \( -iname "' //'*'//trim(settings%suffix)// &
-! '" \) | wc -l > '//trim(settings%path_obsout)//'obsfiles.txt')
-! call system ('find ' //trim(settings%path_obs)// ' -not -path "*/\.*" -type f \( -iname "' //'*'//trim(settings%suffix)// &
-! '" \) >> '//trim(settings%path_obsout)//'obsfiles.txt')
-
call system('rm -f '//trim(settings%path_obsout)//'obsfiles.txt')
call system('ls '//trim(settings%path_obs)//'*'//trim(settings%suffix)//' | wc -l > '//trim(settings%path_obsout)//'obsfiles.txt')
call system('ls '//trim(settings%path_obs)//' | grep '//trim(settings%suffix)//' >> '//trim(settings%path_obsout)//'obsfiles.txt')
diff --git a/prep_flexpart/mod_settings.f90 b/prep_flexpart/mod_settings.f90
index f6ea9a6..5b740c5 100644
--- a/prep_flexpart/mod_settings.f90
+++ b/prep_flexpart/mod_settings.f90
@@ -45,6 +45,7 @@ module mod_settings
character(len=max_path_len) :: file_recept
character(len=max_path_len) :: file_avail
character(len=max_path_len) :: file_availnest
+ character(len=max_name_len) :: windfield
character(len=max_name_len) :: obsformat
character(len=max_name_len) :: suffix
@@ -344,6 +345,9 @@ module mod_settings
identifier = "file_availnest:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) settings%file_availnest = cc
+ identifier = "windfield:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%windfield = cc
! General settings
identifier = "lselect:"
diff --git a/prep_flexpart/mod_var.f90 b/prep_flexpart/mod_var.f90
index 8cd4fa0..05fbe5d 100644
--- a/prep_flexpart/mod_var.f90
+++ b/prep_flexpart/mod_var.f90
@@ -31,11 +31,12 @@ module mod_var
integer, parameter :: max_path_len=200
integer, parameter :: max_name_len=100
integer, parameter :: maxobs=5000
+ integer, parameter :: recname_len=3
real(kind=8) :: jdatei, jdatef
real(kind=8) :: jreldatei, jreldatef
integer :: nrec
integer :: nfiles
- character(len=3), dimension(:), allocatable :: recname
+ character(len=recname_len), dimension(:), allocatable :: recname
character(len=256), dimension(:), allocatable :: filelist
real, dimension(:), allocatable :: reclon, reclat, recalt
diff --git a/prep_flexpart/prep_outgrid.f90 b/prep_flexpart/prep_outgrid.f90
index 4a54ef1..4be6291 100644
--- a/prep_flexpart/prep_outgrid.f90
+++ b/prep_flexpart/prep_outgrid.f90
@@ -79,6 +79,17 @@ subroutine prep_outgrid(settings, jd, nr)
! preset namelist variables
outlon0 = settings%outlonleft
+ ! correction for FLEXPART windfields
+ if ( settings%outlonleft.le.-180. ) then
+ if ( settings%windfield.eq.'oper' ) then
+ outlon0 = -179.
+ else if ( settings%windfield.eq.'era5' ) then
+ outlon0 = -179.5
+ else
+ write(*,*) 'ERROR: prep_outgrid: unknown windfield type'
+ stop
+ endif
+ endif
outlat0 = settings%outlatlower
numxgrid = settings%numxgrid
numygrid = settings%numygrid
diff --git a/prep_flexpart/process_obs.f90 b/prep_flexpart/process_obs.f90
index 81fe389..b09f559 100644
--- a/prep_flexpart/process_obs.f90
+++ b/prep_flexpart/process_obs.f90
@@ -112,7 +112,7 @@ subroutine process_obs(settings, nobs, freq, jdobs, latobs, lonobs, altobs, conc
do while( jdate.le.jdobs(nobs) )
jdt = dnint(jdate*1.e6)/1.e6
if ( n.ne.nprev ) then
- if ( settings%intaverage.ge.6. ) then
+ if ( settings%intaverage.ge.2. ) then
if ( n.eq.1 ) then
! if long averaging interval start at 00:00
jdatestart = dint(jdate)
@@ -125,7 +125,7 @@ subroutine process_obs(settings, nobs, freq, jdobs, latobs, lonobs, altobs, conc
jdatestart = jdt
endif
endif
- if( n.eq.nprev .and. settings%intaverage.ge.6. ) then
+ if( n.eq.nprev .and. settings%intaverage.ge.2. ) then
! if no observation in last averaging interval (i.e. did not enter while loop below)
! increment start date
print*, 'incrementing start date'
diff --git a/prep_flexpart/read_basic.f90 b/prep_flexpart/read_basic.f90
index efbf336..fc0c5a2 100644
--- a/prep_flexpart/read_basic.f90
+++ b/prep_flexpart/read_basic.f90
@@ -60,6 +60,7 @@ subroutine read_basic(settings, jd, nr, nobs, obs)
character(len=max_path_len) :: file_out
character(len=max_path_len) :: file_obs
+ character(len=max_path_len) :: rowfmt
character(len=200) :: line
character(len=200), dimension(50) :: args
character(len=3) :: flag
@@ -202,9 +203,10 @@ subroutine read_basic(settings, jd, nr, nobs, obs)
endif
! write observations to file
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)'
do i = 1, nobs
call caldate(obs%jdi(i), jjjjmmdd, hhmiss)
- write(100,fmt='(A3,1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)') &
+ write(100,fmt=rowfmt) &
trim(recname(nr)), jjjjmmdd, hhmiss, obs%jdi(i), out_repr_time, obs%con(i), obs%err(i), obs%num(i)
end do
close(100)
@@ -213,15 +215,16 @@ subroutine read_basic(settings, jd, nr, nobs, obs)
print*, 'lat, lon , alt: ',obs%lat(1), obs%lon(1), obs%alt(1)
file_out = trim(settings%path_obsout)//'stnlist_detail.txt'
inquire(file=trim(file_out),exist=lexist)
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,F7.2,1X,F7.2,1X,F7.1)'
if( lexist ) then
! append to existing
open(100,file=trim(file_out),status='old',action='write',access='append',iostat=ierr)
- write(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F6.1)') trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
+ write(100,fmt=rowfmt) trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
close(100)
else
! create new file
open(100,file=trim(file_out),status='new',action='write',iostat=ierr)
- write(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F6.1)') trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
+ write(100,fmt=rowfmt) trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
close(100)
endif
diff --git a/prep_flexpart/read_icos.f90 b/prep_flexpart/read_icos.f90
index afd049c..1368edd 100644
--- a/prep_flexpart/read_icos.f90
+++ b/prep_flexpart/read_icos.f90
@@ -60,6 +60,7 @@ subroutine read_icos(settings, jd, nr, nobs, obs)
character(len=max_path_len) :: file_out
character(len=max_path_len) :: file_obs
+ character(len=max_path_len) :: rowfmt
character(len=200) :: line
character(len=200), dimension(20) :: args
character(len=1) :: flag
@@ -137,6 +138,8 @@ subroutine read_icos(settings, jd, nr, nobs, obs)
else if ( settings%zref.eq.2 ) then
! metres above sea level
alt = alt + hgt
+ ! use adjusted altitude for model orography
+ alt = recalt(nr)
endif
print*, 'lat, lon, alt: ',lat, lon, alt
@@ -225,9 +228,10 @@ subroutine read_icos(settings, jd, nr, nobs, obs)
endif
! write observations to file
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)'
do i = 1, nobs
call caldate(obs%jdi(i), jjjjmmdd, hhmiss)
- write(100,fmt='(A3,1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)') &
+ write(100,fmt=rowfmt) &
trim(recname(nr)), jjjjmmdd, hhmiss, obs%jdi(i), out_repr_time, obs%con(i), obs%err(i), obs%num(i)
end do
close(100)
@@ -235,15 +239,16 @@ subroutine read_icos(settings, jd, nr, nobs, obs)
! write detailed station list file
file_out = trim(settings%path_obsout)//'stnlist_detail.txt'
inquire(file=trim(file_out),exist=lexist)
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,F7.2,1X,F7.2,1X,F7.1)'
if( lexist ) then
! append to existing
open(100,file=trim(file_out),status='old',action='write',access='append',iostat=ierr)
- write(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F6.1)') trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
+ write(100,fmt=rowfmt) trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
close(100)
else
! create new file
open(100,file=trim(file_out),status='new',action='write',iostat=ierr)
- write(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F6.1)') trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
+ write(100,fmt=rowfmt) trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
close(100)
endif
diff --git a/prep_flexpart/read_noaa.f90 b/prep_flexpart/read_noaa.f90
index a375085..06f5943 100644
--- a/prep_flexpart/read_noaa.f90
+++ b/prep_flexpart/read_noaa.f90
@@ -60,6 +60,7 @@ subroutine read_noaa(settings, jd, nr, nobs, obs)
character(len=max_path_len) :: file_out
character(len=max_path_len) :: file_obs
+ character(len=max_path_len) :: rowfmt
character(len=200) :: line
character(len=200), dimension(50) :: args
character(len=3) :: flag
@@ -264,9 +265,10 @@ subroutine read_noaa(settings, jd, nr, nobs, obs)
endif
! write observations to file
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)'
do i = 1, nobs
call caldate(obs%jdi(i), jjjjmmdd, hhmiss)
- write(100,fmt='(A3,1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)') &
+ write(100,fmt=rowfmt) &
trim(recname(nr)), jjjjmmdd, hhmiss, obs%jdi(i), out_repr_time, obs%con(i), obs%err(i), obs%num(i)
end do
close(100)
@@ -275,15 +277,16 @@ subroutine read_noaa(settings, jd, nr, nobs, obs)
print*, 'lat, lon , alt: ',obs%lat(1), obs%lon(1), obs%alt(1)
file_out = trim(settings%path_obsout)//'stnlist_detail.txt'
inquire(file=trim(file_out),exist=lexist)
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,F7.2,1X,F7.2,1X,F7.1)'
if( lexist ) then
! append to existing
open(100,file=trim(file_out),status='old',action='write',access='append',iostat=ierr)
- write(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F6.1)') trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
+ write(100,fmt=rowfmt) trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
close(100)
else
! create new file
open(100,file=trim(file_out),status='new',action='write',iostat=ierr)
- write(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F6.1)') trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
+ write(100,fmt=rowfmt) trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
close(100)
endif
diff --git a/prep_flexpart/read_obspack.f90 b/prep_flexpart/read_obspack.f90
index 3eee360..dc11b94 100644
--- a/prep_flexpart/read_obspack.f90
+++ b/prep_flexpart/read_obspack.f90
@@ -60,6 +60,7 @@ subroutine read_obspack(settings, jd, nr, nobs, obs)
character(len=max_path_len) :: file_out
character(len=max_path_len) :: file_obs
+ character(len=max_path_len) :: rowfmt
character(len=200) :: line
character(len=200), dimension(20) :: args
character(len=4) :: version
@@ -229,9 +230,10 @@ subroutine read_obspack(settings, jd, nr, nobs, obs)
endif
! write observations to file
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)'
do i = 1, nobs
call caldate(obs%jdi(i), jjjjmmdd, hhmiss)
- write(100,fmt='(A3,1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)') &
+ write(100,fmt=rowfmt) &
trim(recname(nr)), jjjjmmdd, hhmiss, obs%jdi(i), out_repr_time, obs%con(i), obs%err(i), obs%num(i)
end do
close(100)
@@ -239,15 +241,16 @@ subroutine read_obspack(settings, jd, nr, nobs, obs)
! write detailed station list file
file_out = trim(settings%path_obsout)//'stnlist_detail.txt'
inquire(file=trim(file_out),exist=lexist)
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,F7.2,1X,F7.2,1X,F7.1)'
if( lexist ) then
! append to existing
open(100,file=trim(file_out),status='old',action='write',access='append',iostat=ierr)
- write(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F6.1)') trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
+ write(100,fmt=rowfmt) trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
close(100)
else
! create new file
open(100,file=trim(file_out),status='new',action='write',iostat=ierr)
- write(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F6.1)') trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
+ write(100,fmt=rowfmt) trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
close(100)
endif
diff --git a/prep_flexpart/read_reclist.f90 b/prep_flexpart/read_reclist.f90
index 6494c33..e87a494 100644
--- a/prep_flexpart/read_reclist.f90
+++ b/prep_flexpart/read_reclist.f90
@@ -36,6 +36,7 @@ subroutine read_reclist(filename)
character(len=max_path_len), intent(in) :: filename
character(len=200) :: line
+ character(len=max_path_len) :: rowfmt
integer :: ierr
integer :: cnt
@@ -69,8 +70,10 @@ subroutine read_reclist(filename)
open(100,file=trim(filename),action='read',status='old',iostat=ierr)
write(*,*) 'Receptors: '
+! write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,F7.2,1X,F7.2,1X,F7.2)'
+ write(rowfmt,fmt='(A,I1,A)') '(A',3,',1X,F7.2,1X,F7.2,1X,F7.2)'
do cnt = 1, nrec
- read(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F7.2)') recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
+ read(100,fmt=rowfmt) recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
print*, recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
end do
diff --git a/prep_flexpart/read_wdcgg.f90 b/prep_flexpart/read_wdcgg.f90
index 47be546..48499d1 100644
--- a/prep_flexpart/read_wdcgg.f90
+++ b/prep_flexpart/read_wdcgg.f90
@@ -60,6 +60,7 @@ subroutine read_wdcgg(settings, jd, nr, nobs, obs)
character(len=max_path_len) :: file_out
character(len=max_path_len) :: file_obs
+ character(len=max_path_len) :: rowfmt
character(len=200) :: line
character(len=200), dimension(30) :: args
character(len=10) :: adate
@@ -214,9 +215,10 @@ subroutine read_wdcgg(settings, jd, nr, nobs, obs)
endif
! write observations to file
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)'
do i = 1, nobs
call caldate(obs%jdi(i), jjjjmmdd, hhmiss)
- write(100,fmt='(A3,1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)') &
+ write(100,fmt=rowfmt) &
trim(recname(nr)), jjjjmmdd, hhmiss, obs%jdi(i), out_repr_time, obs%con(i), obs%err(i), obs%num(i)
end do
close(100)
@@ -224,15 +226,16 @@ subroutine read_wdcgg(settings, jd, nr, nobs, obs)
! write detailed station list file
file_out = trim(settings%path_obsout)//'stnlist_detail.txt'
inquire(file=trim(file_out),exist=lexist)
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,F7.2,1X,F7.2,1X,F7.1)'
if( lexist ) then
! append to existing
open(100,file=trim(file_out),status='old',action='write',access='append',iostat=ierr)
- write(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F6.1)') trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
+ write(100,fmt=rowfmt) trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
close(100)
else
! create new file
open(100,file=trim(file_out),status='new',action='write',iostat=ierr)
- write(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F6.1)') trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
+ write(100,fmt=rowfmt) trim(recname(nr)), obs%lat(1), obs%lon(1), obs%alt(1)
close(100)
endif
diff --git a/prep_flexpart/run_flexpart.sh b/prep_flexpart/run_flexpart.sh
index ad6f390..1d03b1b 100755
--- a/prep_flexpart/run_flexpart.sh
+++ b/prep_flexpart/run_flexpart.sh
@@ -6,8 +6,8 @@
# 1. edit the directories, exename, list of stations
# months and year below
# 2. for slurm set SLURM = 1 otherwise uses nohup
-# 3. the meteorology used for flexpart can be
-# specified by METEO
+# 3. specific options for compiling flexpart given
+# in variable COMMAND
# 4. run the script:
# ./run_flexpart.sh
#---------------------------------------------------
@@ -21,13 +21,12 @@ ROOTDIR=${DIR:0:$LEN}
# User settings
SLURM=1
-#TIMELIM=2-00:00:00
TIMELIM=12:00:00
PARTITION="nilu"
-EXENAME=FP_ecmwf_gfortran
-METEO=ecmwf
-DIRFLEX=/home/rthompson/REPOS/GITHUB/FLEXPART/
-DIROPTIONS=${ROOTDIR}TEST_INPUT/FLEXPART/GHG/NEST/
+EXENAME=FLEXPART
+COMMAND="-j serial 'ncf=yes'"
+DIRFLEX=/mypath/flexpart/
+DIROPTIONS=/mypath/flexpart_options/
STNLIST=(SSL)
MONLIST=(01)
YEAR=2012
@@ -46,7 +45,7 @@ ARRAYMON=`seq 1 ${NMON}`
cd ${DIRFLEX}src/
if [ ! `ls ${DIRFLEX}src/${EXENAME}` ]; then
- make ${METEO}
+ make ${COMMAND}
if [ ! `ls ${DIRFLEX}src/${EXENAME}` ]; then
echo "cannot create exec: "${DIRFLEX}src/${EXENAME}
exit -1
diff --git a/prep_flexpart/sbatch_prep_flexpart.sh b/prep_flexpart/sbatch_prep_flexpart.sh
index 403d640..6fc859b 100755
--- a/prep_flexpart/sbatch_prep_flexpart.sh
+++ b/prep_flexpart/sbatch_prep_flexpart.sh
@@ -1,7 +1,7 @@
#!/bin/bash
#---------------------------------------------------
-partition=debug
-settings_files='./SETTINGS_ghg'
+partition=nilu
+settings_files='./SETTINGS'
#---------------------------------------------------
cat <<EOF > run_job.sh
diff --git a/prep_fluxes/FLUXES_co2_bbg b/prep_fluxes/FLUXES_co2_bbg
deleted file mode 100644
index 212a9f3..0000000
--- a/prep_fluxes/FLUXES_co2_bbg
+++ /dev/null
@@ -1,68 +0,0 @@
-# ==================================================
-#
-# FILE SETTINGS
-#
-# comment lines start with '#'
-# each parameter line starts with 'parameter name:'
-#
-# ==================================================
-
-# Input flux:
-# midpoints (logical) lon/lat coordinates are grid cell midpoints?
-# coeff = factor to convert from input to output units
-# nx_in = number of longitudinal grid cells
-# ny_in = number of latitudinal grid cells
-# ntime = number of time steps
-# timeref = ref date if timestamp is julian days (yyyymmdd) otherwise 0
-# timestamp = sec or month (if julian days and timeref is not 0 this is ignored)
-file_in: /mypath/TEST_INPUT/FLUXES/CO2/CO2_BBG_2012_05x05.nc
-varname_in: emisco2
-lonname_in: longitude
-latname_in: latitude
-timename_in: time
-midpoints: .true.
-coeff: 1.
-nx_in: 720
-ny_in: 360
-ntime: 12
-indextime: 1
-timeref: 19000101
-timestamp:
-
-# Output flux:
-# year = year for timestamp
-# nx_out = number of longitudinal grid cells
-# ny_out = number of latitudinal grid cells
-# dx_out = longitudinal resolution
-# dy_out = latitudinal resolution
-# ntime_out = number of time steps
-# llx_out = left longitude of domain
-# lly_out = lower latitude of domain
-file_out: /mypath/TEST_OUTPUT/FLUXES/CO2/CO2_BBG_2012_10x10.nc
-varname_out: emisco2
-varunit: kgC/m2/h
-lonname_out: longitude
-latname_out: latitude
-timename_out: time
-year: 2012
-nx_out: 360
-ny_out: 180
-dx_out: 1.0
-dy_out: 1.0
-ntime_out: 12
-llx_out: -180
-lly_out: -90
-
-# Monthly scalars:
-# one file with monthly temporal resolution containing
-# scalars for the annual fluxes in each grid cell
-# spatial resolution must be the same as file_in
-file_scalar:
-varname_scalar:
-lonname_scalar:
-latname_scalar:
-timename_scalar:
-
-
-
-
diff --git a/prep_fluxes/FLUXES_co2_ff b/prep_fluxes/FLUXES_co2_ff
deleted file mode 100644
index 1e95dcd..0000000
--- a/prep_fluxes/FLUXES_co2_ff
+++ /dev/null
@@ -1,68 +0,0 @@
-# ==================================================
-#
-# FILE SETTINGS
-#
-# comment lines start with '#'
-# each parameter line starts with 'parameter name:'
-#
-# ==================================================
-
-# Input flux:
-# midpoints (logical) lon/lat coordinates are grid cell midpoints?
-# coeff = factor to convert from input to output units
-# nx_in = number of longitudinal grid cells
-# ny_in = number of latitudinal grid cells
-# ntime = number of time steps
-# timeref = ref date if timestamp is julian days (yyyymmdd) otherwise 0
-# timestamp = sec, hour, or month (if julian days and timeref is not 0 this is ignored)
-file_in: /mypath/TEST_INPUT/FLUXES/CO2/EDGARv4.3_BP2016_emissions.co2.global.0.5x0.5.1hr.201201.nc
-varname_in: emission
-lonname_in: lon
-latname_in: lat
-timename_in: time
-midpoints: .true.
-coeff: 1.
-nx_in: 720
-ny_in: 360
-ntime: 744
-indextime: 1
-timeref: 0
-timestamp: hour
-
-# Output flux:
-# year = year for timestamp
-# nx_out = number of longitudinal grid cells
-# ny_out = number of latitudinal grid cells
-# dx_out = longitudinal resolution
-# dy_out = latitudinal resolution
-# ntime_out = number of time steps
-# llx_out = left longitude of domain
-# lly_out = lower latitude of domain
-file_out: /mypath/TEST_OUTPUT/FLUXES/CO2/CO2_FF_201201_10x10.nc
-varname_out: emisco2
-varunit: micromol/m2/s
-lonname_out: longitude
-latname_out: latitude
-timename_out: time
-year: 2012
-nx_out: 360
-ny_out: 180
-dx_out: 1.0
-dy_out: 1.0
-ntime_out: 744
-llx_out: -180
-lly_out: -90
-
-# Monthly scalars:
-# one file with monthly temporal resolution containing
-# scalars for the annual fluxes in each grid cell
-# spatial resolution must be the same as file_in
-file_scalar:
-varname_scalar:
-lonname_scalar:
-latname_scalar:
-timename_scalar:
-
-
-
-
diff --git a/prep_fluxes/FLUXES_co2_nee b/prep_fluxes/FLUXES_co2_nee
deleted file mode 100644
index 05d0e94..0000000
--- a/prep_fluxes/FLUXES_co2_nee
+++ /dev/null
@@ -1,68 +0,0 @@
-# ==================================================
-#
-# FILE SETTINGS
-#
-# comment lines start with '#'
-# each parameter line starts with 'parameter name:'
-#
-# ==================================================
-
-# Input flux:
-# midpoints (logical) lon/lat coordinates are grid cell midpoints?
-# coeff = factor to convert from input to output units
-# nx_in = number of longitudinal grid cells
-# ny_in = number of latitudinal grid cells
-# ntime = number of time steps
-# timeref = ref date if timestamp is julian days (yyyymmdd) otherwise 0
-# timestamp = sec or month (if julian days and timeref is not 0 this is ignored)
-file_in: /mypath/TEST_INPUT/FLUXES/CO2/CO2_NEE_2012_05x05.nc
-varname_in: nee
-lonname_in: longitude
-latname_in: latitude
-timename_in: time
-midpoints: .true.
-coeff: 1.
-nx_in: 720
-ny_in: 360
-ntime: 2920
-indextime: 1
-timeref: 19000101
-timestamp:
-
-# Output flux:
-# year = year for timestamp
-# nx_out = number of longitudinal grid cells
-# ny_out = number of latitudinal grid cells
-# dx_out = longitudinal resolution
-# dy_out = latitudinal resolution
-# ntime_out = number of time steps
-# llx_out = left longitude of domain
-# lly_out = lower latitude of domain
-file_out: /mypath/TEST_OUTPUT/FLUXES/CO2/CO2_NEE_2012_10x10.nc
-varname_out: nee
-varunit: kgC/m2/h
-lonname_out: longitude
-latname_out: latitude
-timename_out: time
-year: 2012
-nx_out: 360
-ny_out: 180
-dx_out: 1.0
-dy_out: 1.0
-ntime_out: 2920
-llx_out: -180
-lly_out: -90
-
-# Monthly scalars:
-# one file with monthly temporal resolution containing
-# scalars for the annual fluxes in each grid cell
-# spatial resolution must be the same as file_in
-file_scalar:
-varname_scalar:
-lonname_scalar:
-latname_scalar:
-timename_scalar:
-
-
-
-
diff --git a/prep_fluxes/FLUXES_co2_ocn b/prep_fluxes/FLUXES_co2_ocn
deleted file mode 100644
index c55337e..0000000
--- a/prep_fluxes/FLUXES_co2_ocn
+++ /dev/null
@@ -1,68 +0,0 @@
-# ==================================================
-#
-# FILE SETTINGS
-#
-# comment lines start with '#'
-# each parameter line starts with 'parameter name:'
-#
-# ==================================================
-
-# Input flux:
-# midpoints (logical) lon/lat coordinates are grid cell midpoints?
-# coeff = factor to convert from input to output units
-# nx_in = number of longitudinal grid cells
-# ny_in = number of latitudinal grid cells
-# ntime = number of time steps
-# timeref = ref date if timestamp is julian days (yyyymmdd) otherwise 0
-# timestamp = sec or month (if julian days and timeref is not 0 this is ignored)
-file_in: /mypath/TEST_INPUT/FLUXES/CO2/CO2_OCEAN_2012_05x05.nc
-varname_in: emisco2
-lonname_in: longitude
-latname_in: latitude
-timename_in: time
-midpoints: .true.
-coeff: 1.
-nx_in: 720
-ny_in: 360
-ntime: 12
-indextime: 1
-timeref: 19000101
-timestamp:
-
-# Output flux:
-# year = year for timestamp
-# nx_out = number of longitudinal grid cells
-# ny_out = number of latitudinal grid cells
-# dx_out = longitudinal resolution
-# dy_out = latitudinal resolution
-# ntime_out = number of time steps
-# llx_out = left longitude of domain
-# lly_out = lower latitude of domain
-file_out: /mypath/TEST_OUTPUT/FLUXES/CO2/CO2_OCEAN_2012_10x10.nc
-varname_out: emisco2
-varunit: kgC/m2/h
-lonname_out: longitude
-latname_out: latitude
-timename_out: time
-year: 2012
-nx_out: 360
-ny_out: 180
-dx_out: 1.0
-dy_out: 1.0
-ntime_out: 12
-llx_out: -180
-lly_out: -90
-
-# Monthly scalars:
-# one file with monthly temporal resolution containing
-# scalars for the annual fluxes in each grid cell
-# spatial resolution must be the same as file_in
-file_scalar:
-varname_scalar:
-lonname_scalar:
-latname_scalar:
-timename_scalar:
-
-
-
-
diff --git a/prep_fluxes/README_prepflux.txt b/prep_fluxes/README_prepflux.txt
index a7bb335..a19d6be 100644
--- a/prep_fluxes/README_prepflux.txt
+++ b/prep_fluxes/README_prepflux.txt
@@ -13,11 +13,10 @@ Note:
same resolution as the FLEXPART output files (grid_time)
For annual mean fluxes (e.g. CO2 fossil fuel) can apply a
monthly scaling factor to give monthly resolved fluxes
- (see e.g. FLUXES_FF)
Usage:
1) compile with gfortran using: make
- 2) create/edit a settings file: e.g. FLUXES_test
+ 2) create/edit a settings file: e.g. SETTINGS_FLUX
3) edit the bash script: job_prep_flux.sh
(or alternatively for slurm sbatch_prep_flux.sh)
4) run the bash script: ./job_prep_flux.sh
diff --git a/prep_fluxes/FLUXES_ghg b/prep_fluxes/SETTINGS_FLUX
similarity index 92%
rename from prep_fluxes/FLUXES_ghg
rename to prep_fluxes/SETTINGS_FLUX
index f85dbb9..d902882 100644
--- a/prep_fluxes/FLUXES_ghg
+++ b/prep_fluxes/SETTINGS_FLUX
@@ -15,7 +15,7 @@
# ntime = number of time steps
# timeref = ref date if timestamp is julian days (yyyymmdd) otherwise 0
# timestamp = sec or month (if julian days and timeref is not 0 this is ignored)
-file_in: /mypath/TEST_INPUT/FLUXES/GHG/CH4_TOTAL_2012_05x05.nc
+file_in: /mypath/flux/flux_input.nc
varname_in: emisch4
lonname_in: longitude
latname_in: latitude
@@ -38,7 +38,7 @@ timestamp:
# ntime_out = number of time steps
# llx_out = left longitude of domain
# lly_out = lower latitude of domain
-file_out: /mypath/TEST_OUTPUT/FLUXES/GHG/CH4_TOTAL_2012_10x10.nc
+file_out: /mypath/flux/flux_output.nc
varname_out: emisch4
varunit: kgC/m2/h
lonname_out: longitude
diff --git a/prep_fluxes/job_prep_flux.sh b/prep_fluxes/job_prep_flux.sh
index 4a2f798..369b9e2 100755
--- a/prep_fluxes/job_prep_flux.sh
+++ b/prep_fluxes/job_prep_flux.sh
@@ -1,6 +1,6 @@
#!/bin/bash
#---------------------------------------------------
-file='./FLUXES_ghg'
+file='./SETTINGS_FLUX'
./prep_flux ${file}
diff --git a/prep_fluxes/sbatch_prep_flux.sh b/prep_fluxes/sbatch_prep_flux.sh
index 45739b8..7d43b64 100755
--- a/prep_fluxes/sbatch_prep_flux.sh
+++ b/prep_fluxes/sbatch_prep_flux.sh
@@ -1,6 +1,6 @@
#!/bin/bash
#---------------------------------------------------
-file='./FLUXES_ghg'
+file='./SETTINGS_FLUX'
#---------------------------------------------------
cat <<EOF > run_job.sh
diff --git a/prep_regions/initialize.f90 b/prep_regions/initialize.f90
index 0cfb8ab..1f11671 100644
--- a/prep_regions/initialize.f90
+++ b/prep_regions/initialize.f90
@@ -49,6 +49,7 @@ subroutine initialize(files, config)
character(max_path_len) :: filename
logical :: lexist
integer :: yyyymm
+ character(len=8) :: areldate
character(6) :: adate
character(4) :: ayear
integer :: numpoint
@@ -63,28 +64,38 @@ subroutine initialize(files, config)
filename = trim(files%file_recept)
inquire(file=trim(filename),exist=lexist)
- if (.not.lexist) then
+ if ( .not.lexist.and.config%ground ) then
write(*,*) 'ERROR: cannot find '//trim(filename)
stop
+ else if ( lexist.and.config%ground ) then
+ write(*,*) 'Reading receptor list: '//trim(filename)
+ call read_reclist(filename)
endif
- write(*,*) 'Reading receptor list: '//trim(filename)
- call read_reclist(filename)
! initialize flexpart variables
! -----------------------------
- yyyymm=config%datei/100
- write(adate,'(i6)') yyyymm
- lexist = .false.
- i = 1
- print*, 'nrec:',nrec
- do while ( (.not.lexist).and.(i.le.nrec) )
- if ( .not.config%nested ) filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header'
- if ( config%nested ) filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header_nest'
- print*, filename
+ ! read header for global output
+ if ( config%satellite.and.nrec.eq.0 ) then
+ ! satellite only
+ write(areldate,'(I8)') config%datei
+ if ( .not.config%nested ) filename = trim(files%path_flexsat)//areldate//'/header'
+ if ( config%nested ) filename = trim(files%path_flexsat)//areldate//'/header_nest'
inquire(file=trim(filename),exist=lexist)
- i = i + 1
- end do
+ else
+ ! ground-based output
+ yyyymm=config%datei/100
+ write(adate,'(i6)') yyyymm
+ lexist = .false.
+ i = 1
+ do while ( (.not.lexist).and.(i.le.nrec) )
+ if ( .not.config%nested ) filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header'
+ if ( config%nested ) filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header_nest'
+ print*, filename
+ inquire(file=trim(filename),exist=lexist)
+ i = i + 1
+ end do
+ endif
if ( .not.lexist ) then
print*, 'ERROR initialize: cannot find flexpart header'
stop
@@ -129,6 +140,8 @@ subroutine initialize(files, config)
if ( config%spec.eq.'co2' ) then
if ( config%nested ) then
files%filename_flx = str_replace( files%filenest_nee, 'YYYY', ayear)
+ print*, 'filenest_nee = ',files%filenest_nee
+ print*, 'filename_flx = ',files%filename_flx
files%varname_flx = files%varnest_nee
files%lonname_flx = files%lonnest_nee
files%latname_flx = files%latnest_nee
diff --git a/prep_regions/mod_settings.f90 b/prep_regions/mod_settings.f90
index f928a29..ddbdb4a 100644
--- a/prep_regions/mod_settings.f90
+++ b/prep_regions/mod_settings.f90
@@ -36,9 +36,11 @@ module mod_settings
character(len=max_path_len) :: path_prior ! path to prior fluxes
character(len=max_path_len) :: path_obs ! path to observations
+ character(len=max_path_len) :: path_satobs ! path to satellite observations
character(len=max_path_len) :: path_output ! path to output
character(len=max_name_len) :: suffix ! observation file name suffix
character(len=max_path_len) :: path_flexpart ! path to flexpart output
+ character(len=max_path_len) :: path_flexsat ! path to flexpart output for satellites
character(len=max_name_len) :: file_log ! log file name
character(len=max_path_len) :: file_regions ! region definitions file
character(len=max_name_len) :: varname_regs ! regions variable name
@@ -84,6 +86,8 @@ module mod_settings
integer :: datei ! start date (yyyymmdd)
integer :: datef ! end date (yyyymmdd)
logical :: nested ! use nested flexpart output (true or false)
+ logical :: satellite ! use satellite observations (true or false)
+ logical :: ground ! use ground-based observations (true or false)
real :: w_edge_lon ! lon of western edge of inversion grid
real :: s_edge_lat ! lat of southern edge of inversion grid
real :: e_edge_lon ! lon of eastern edge of inversion grid
@@ -319,12 +323,18 @@ module mod_settings
identifier = "path_obs:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_obs = cc
+ identifier = "path_satobs:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) files%path_satobs = cc
identifier = "suffix:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%suffix = cc
identifier = "path_flexpart:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_flexpart = cc
+ identifier = "path_flexsat:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) files%path_flexsat = cc
identifier = "path_output:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_output = cc
@@ -448,6 +458,10 @@ module mod_settings
logical :: match, cl
character(len=20), dimension(3) :: temp
+ ! default logical settings
+ config%satellite = .false.
+ config%ground = .false.
+
! open file
open (100, file = trim (filename), status = 'old', iostat=ierr)
if(ierr.gt.0) then
@@ -484,6 +498,14 @@ module mod_settings
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) config%datef = int(cn)
+ ! read observation settings
+ identifier = "satellite:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) config%satellite = cl
+ identifier = "ground:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) config%ground = cl
+
! read inversion domain settings
identifier = "nested:"
call read_content (line, identifier, cc, cn, cl, match)
@@ -514,6 +536,12 @@ module mod_settings
end do read_loop
+ ! some initial checks
+ if ( .not.config%ground.and..not.config%satellite ) then
+ print*, 'ERROR: at least one of ground and satellite must be true'
+ stop
+ endif
+
end subroutine read_config_settings
! --------------------------------------------------
diff --git a/prep_regions/mod_strings.f90 b/prep_regions/mod_strings.f90
index bb42549..486199a 100644
--- a/prep_regions/mod_strings.f90
+++ b/prep_regions/mod_strings.f90
@@ -32,7 +32,7 @@ module mod_strings
character(*), private, parameter :: lower_case = 'abcdefghijklmnopqrstuvwxyz'
character(*), private, parameter :: upper_case = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
- public :: to_upper, to_lower, str_replace
+ public :: to_upper, to_lower, str_replace, split
contains
@@ -111,20 +111,100 @@ module mod_strings
character(*), intent(in) :: repstr
character(max_path_len) :: string_out
character(max_path_len) :: strtmp1, strtmp2
- integer :: strlen, replen, n
+ integer :: strlen, substrlen, replen, n
strlen = len_trim(string_in)
replen = len_trim(repstr)
+ substrlen = len_trim(substr)
! find first position of substr in string_in
n = index( string_in, substr, back=.false. )
- strtmp1 = string_in(1:n-1)
+ if ((n-1).gt.0) then
+ strtmp1 = string_in(1:n-1)
+ else
+ ! empty string
+ strtmp1 = ''
+ n = 1
+ endif
+! print*, 'str_replace first pos n, strtmp1 = ',n, strtmp1
! find last position of substr in string_in
- n = index( string_in, substr, back=.true. )
- strtmp2 = string_in(n+replen:strlen)
- string_out = trim(strtmp1)//trim(repstr)//trim(strtmp2)
+ n = index( string_in, substr, back=.true. )
+ strtmp2 = string_in(n+substrlen:strlen)
+! print*, 'str_replace last pos n, strtmp2 = ',n, strtmp2
+ string_out = trim(strtmp1)//trim(repstr)//trim(strtmp2)
end function str_replace
+ ! --------------------------------------------------
+ ! split string
+ ! --------------------------------------------------
+
+ subroutine split(str,delims,before,sep)
+
+ ! Routine finds the first instance of a character from 'delims' in the
+ ! the string 'str'. The characters before the found delimiter are
+ ! output in 'before'. The characters after the found delimiter are
+ ! output in 'str'. The optional output character 'sep' contains the
+ ! found delimiter. A delimiter in 'str' is treated like an ordinary
+ ! character if it is preceded by a backslash (\). If the backslash
+ ! character is desired in 'str', then precede it with another backslash.
+
+ character(len=*) :: str, delims, before
+ character,optional :: sep
+ logical :: pres
+ character :: ch,cha
+ integer :: i, k, ibsl, ipos, iposa, lenstr
+
+ pres=present(sep)
+ str=adjustl(str)
+ lenstr=len_trim(str)
+ if(lenstr == 0) return ! string str is empty
+ k=0
+ ibsl=0 ! backslash initially inactive
+ before=' '
+ do i=1,lenstr
+ ch=str(i:i)
+ if(ibsl == 1) then ! backslash active
+ k=k+1
+ before(k:k)=ch
+ ibsl=0
+ cycle
+ end if
+ if(ch == '\') then ! backslash with backslash inactive
+ k=k+1
+ before(k:k)=ch
+ ibsl=1
+ cycle
+ end if
+ ipos=index(delims,ch)
+ if(ipos == 0) then ! character is not a delimiter
+ k=k+1
+ before(k:k)=ch
+ cycle
+ end if
+ if(ch /= ' ') then ! character is a delimiter that is not a space
+ str=str(i+1:)
+ if(pres) sep=ch
+ exit
+ end if
+ cha=str(i+1:i+1) ! character is a space delimiter
+ iposa=index(delims,cha)
+ if(iposa > 0) then ! next character is a delimiter
+ str=str(i+2:)
+ if(pres) sep=cha
+ exit
+ else
+ str=str(i+1:)
+ if(pres) sep=ch
+ exit
+ end if
+ end do
+ if(i >= lenstr) str=''
+ str=trim(str)
+ before=trim(before)
+ return
+
+ end subroutine split
+
! --------------------------------------------------
end module mod_strings
diff --git a/prep_regions/mod_var.f90 b/prep_regions/mod_var.f90
index 14a5a58..6393249 100644
--- a/prep_regions/mod_var.f90
+++ b/prep_regions/mod_var.f90
@@ -32,7 +32,7 @@ module mod_var
integer, parameter :: max_name_len=50 ! max character length of variable names
integer, parameter :: recname_len=7 ! length of receptor names
real, parameter :: numscale=1.e12 ! numeric scaling factor
- integer, parameter :: maxpoint=1000 ! max number of releases per receptor per month
+ integer, parameter :: maxpoint=50000 ! max number of releases per receptor per month
integer, parameter :: maxspec=10 ! max number of species in a flexpart run
integer, parameter :: maxlev=50 ! max number of vertical levels in flexpart output
integer, parameter :: maxobs=100000 ! max number of observations
diff --git a/prep_regions/prep_regions.f90 b/prep_regions/prep_regions.f90
index 0c25d37..ad66a6d 100644
--- a/prep_regions/prep_regions.f90
+++ b/prep_regions/prep_regions.f90
@@ -45,7 +45,8 @@ program prep_regions
real, dimension(:,:), allocatable :: surfinf
real, dimension(:,:), allocatable :: flux, mask
real(kind=8), dimension(:), allocatable :: obstimes, avetimes
- character(4), dimension(:), allocatable :: recs
+ real, dimension(:), allocatable :: cdryair
+ character(recname_len), dimension(:), allocatable :: recs
real, dimension(:,:), allocatable :: nbox_xy
integer :: ierr,ix,jy
logical :: lexist
@@ -95,12 +96,16 @@ program prep_regions
! read observations
allocate( obstimes(maxobs), stat=ierr )
+ if ( ierr.ne.0 ) stop 'ERROR: not enough memory'
allocate( avetimes(maxobs), stat=ierr )
+ if ( ierr.ne.0 ) stop 'ERROR: not enough memory'
allocate( recs(maxobs), stat=ierr )
if ( ierr.ne.0 ) stop 'ERROR: not enough memory'
+ allocate( cdryair(maxobs), stat=ierr )
+ if ( ierr.ne.0 ) stop 'ERROR: not enough memory'
obstimes(:) = 0d0
avetimes(:) = 0d0
- call read_obs(files, recs, obstimes, avetimes)
+ call read_obs(files, config, recs, cdryair, obstimes, avetimes)
! mean surface influence (i.e. flux sensitivity)
allocate( surfinf(nxregrid,nyregrid), stat=ierr )
@@ -113,7 +118,7 @@ program prep_regions
varname = 'surfinf'
call read_ncdf(files, config, filename, varname, surfinf)
else
- call get_surfinf(files, config, recs, obstimes, avetimes, surfinf)
+ call get_surfinf(files, config, recs, cdryair, obstimes, avetimes, surfinf)
endif
! calculate regions
@@ -128,7 +133,7 @@ program prep_regions
! write lsm
allocate( mask(nxregrid,nyregrid), stat=ierr)
mask=lsm
- open(100,file=trim(files%path_output)//'lsm.txt',action='write',status='new')
+ open(100,file=trim(files%path_output)//'lsm.txt',action='write',status='replace')
write(rowfmt,'(A,I6,A)') '(',nxregrid,'(F5.2,1X))'
do jy = 1,nyregrid
write(100,rowfmt) lsm(:,jy)
diff --git a/prep_regions/read_obs.f90 b/prep_regions/read_obs.f90
index 33a87bb..d6a5cdb 100644
--- a/prep_regions/read_obs.f90
+++ b/prep_regions/read_obs.f90
@@ -26,48 +26,63 @@
!! Inputs
!! files - file data structure
!! reclist - list of receptor IDs
+!! cdryair - total column dry air concentration (mol/m2)
!! obstimes - list of observation time stamps as julian days
!! avetimes - list of observation averaging times as julian days
!!
!---------------------------------------------------------------------------------------
-subroutine read_obs(files, reclist, obstimes, avetimes)
+subroutine read_obs(files, config, reclist, cdryair, obstimes, avetimes)
+ use netcdf
use mod_settings
use mod_strings
use mod_var
use mod_dates
+ use mod_ncdf, only : check
implicit none
type (files_t), intent(in) :: files
+ type (config_t), intent(in) :: config
real(kind=8), dimension(maxobs), intent(in out) :: obstimes
real(kind=8), dimension(maxobs), intent(in out) :: avetimes
- character(4), dimension(maxobs), intent(in out) :: reclist
+ real, dimension(maxobs), intent(in out) :: cdryair
+ character(recname_len), dimension(maxobs), intent(in out) :: reclist
character(len=max_path_len), dimension(:), allocatable :: filelist
- character(len=7) :: recs
- character(len=200) :: header
+ character(len=max_path_len) :: numfmt, rowfmt
+ character(len=recname_len) :: recs
+ character(len=200) :: header, species, string, before, sep
character(len=200), dimension(18) :: args
real, dimension(16) :: temp
integer :: ierr
integer :: cnt
integer :: narg, n, reclen
- integer :: nf, nfiles, nr
+ integer :: nf, nfiles
integer :: yyyymmdd, hhmiss, yyyy, mm, dd, hh, mi, ss, hl
real(kind=8) :: jdate, avetime
real :: conc, err, lon, alt
- integer :: num
+ integer :: num, nr, nretr
+ integer :: ncid, dimid, varid
+ integer, dimension(:), allocatable :: idate, itime
+ real, dimension(:), allocatable :: cdryair_loc
! list observation files
! ----------------------
- print*, trim(files%path_obs)
- print*, trim(files%suffix)
- print*, trim(files%path_output)
-
- call system('ls '//trim(files%path_obs)//'*'//trim(files%suffix)//' | wc -l > '//trim(files%path_output)//'obsfiles.txt')
- call system('ls '//trim(files%path_obs)//' | grep '//trim(files%suffix)//' >> '//trim(files%path_output)//'obsfiles.txt')
+ if ( config%ground.and.config%satellite ) then
+ call system('ls '//trim(files%path_obs)//'*'//trim(files%suffix)//&
+ ' '//trim(files%path_satobs)//'*.nc'//' | wc -l > '//trim(files%path_output)//'obsfiles.txt')
+ call system('ls '//trim(files%path_obs)//' | grep '//trim(files%suffix)//' >> '//trim(files%path_output)//'obsfiles.txt')
+ call system('ls '//trim(files%path_satobs)//' | grep .nc >> '//trim(files%path_output)//'obsfiles.txt')
+ else if ( config%ground ) then
+ call system('ls '//trim(files%path_obs)//'*'//trim(files%suffix)//' | wc -l > '//trim(files%path_output)//'obsfiles.txt')
+ call system('ls '//trim(files%path_obs)//' | grep '//trim(files%suffix)//' >> '//trim(files%path_output)//'obsfiles.txt')
+ else if ( config%satellite ) then
+ call system('ls '//trim(files%path_satobs)//'*.nc'//' | wc -l > '//trim(files%path_output)//'obsfiles.txt')
+ call system('ls '//trim(files%path_satobs)//' | grep .nc >> '//trim(files%path_output)//'obsfiles.txt')
+ endif
open(100,file=trim(files%path_output)//'obsfiles.txt',action='read',status='old',iostat=ierr)
if ( ierr.ne. 0 ) then
@@ -88,89 +103,131 @@ subroutine read_obs(files, reclist, obstimes, avetimes)
cnt = 0
do nf = 1, nfiles
- ! check this file belongs to receptor in reclist
- ! added option for 4 character length names
- if (filelist(nf)(4:4).eq.'_' )then
- recs = filelist(nf)(1:3)
- reclen=3
- else
- recs = filelist(nf)(1:4)
- reclen=4
- endif
- print*, 'read_obs: rec = ',recs
- if ( .not.( any(recname(:)(1:4).eq.to_upper(recs)) ) .and. .not.( any(recname(:)(1:3).eq.to_upper(recs)) )) go to 10
-
- ! open input file
- open(100,file=trim(files%path_obs)//trim(filelist(nf)),action='read',status='old',iostat=ierr)
- if ( ierr.ne.0 ) then
- write(*,*) 'WARNING: cannot open: '//trim(files%path_obs)//trim(filelist(nf))
- go to 10
- endif
- write(*,*) 'Reading file: '//trim(files%path_obs)//trim(filelist(nf))
-
- ! station coordinates for data selection
- do nr = 1, nrec
- if ( to_upper(recs).eq.recname(nr) ) then
- lon = reclon(nr)
- alt = recalt(nr)
- go to 20
- endif
- end do
+ ! check if ground-based or satellite observation
+ string = filelist(nf)
+ call split(string,".",before,sep)
+
+ print*, 'string = ',string
+ print*, 'before = ',before
+
+ if ( trim(string).eq.'nc' ) then
+
+ ! satellite
+ ! ---------
+
+ ! check if data is in inversion time interval
+ read(before(19:26),*) yyyymmdd
+ print*, 'read_obs: before = ',before(19:26)
+ jdate = juldate(yyyymmdd, 0)
+ if ( jdate.lt.juldatei.or.jdate.gt.juldatef ) cycle
+
+ ! read ncdf file
+ call check( nf90_open(trim(files%path_satobs)//trim(filelist(nf)),nf90_NOWRITE,ncid) )
+ call check( nf90_inq_dimid(ncid,'retrieval',dimid) )
+ call check( nf90_inquire_dimension(ncid,dimid,len=nretr) )
+ allocate( idate(nretr), stat=ierr )
+ allocate( itime(nretr), stat=ierr )
+ allocate( cdryair_loc(nretr), stat=ierr )
+ call check( nf90_inq_varid(ncid,'idate',varid) )
+ call check( nf90_get_var(ncid,varid,idate) )
+ call check( nf90_inq_varid(ncid,'itime',varid) )
+ call check( nf90_get_var(ncid,varid,itime) )
+ call check( nf90_inq_varid(ncid,'cdryair',varid) )
+ call check( nf90_get_var(ncid,varid,cdryair_loc) )
+ call check( nf90_close(ncid) )
+
+ write(numfmt,fmt='(A,I1,A,I1,A)') '(I',recname_len,'.',recname_len,')'
+ do nr = 1, nretr
+ cnt = cnt + 1
+ write(recs,fmt=numfmt) nr
+ jdate = juldate(idate(nr), itime(nr))
+ obstimes(cnt) = jdate
+ avetimes(cnt) = 0d0
+ cdryair(cnt) = cdryair_loc(nr)
+ reclist(cnt) = trim(recs)
+ end do
+
+ deallocate( idate )
+ deallocate( itime )
+ deallocate( cdryair_loc )
+
+ else if ( string.eq.trim(files%suffix) ) then
+
+ ! ground-based
+ ! ------------
+
+ ! check this file belongs to receptor in reclist
+ call split(before,"_",recs,sep)
+ species = trim(before)
+ reclen = len_trim(recs)
+
+ print*, 'species = ',species
+ print*, 'recs = ',recs
+
+ if ( .not.( any(recname(:)(1:reclen).eq.to_upper(recs)) ) ) go to 10
+
+ ! open input file
+ open(100,file=trim(files%path_obs)//trim(filelist(nf)),action='read',status='old',iostat=ierr)
+ if ( ierr.ne.0 ) then
+ write(*,*) 'WARNING: cannot open: '//trim(files%path_obs)//trim(filelist(nf))
+ go to 10
+ endif
+ write(*,*) 'Reading file: '//trim(files%path_obs)//trim(filelist(nf))
+
+ ! station coordinates for data selection
+ do nr = 1, nrec
+ if ( to_upper(recs).eq.recname(nr) ) then
+ lon = reclon(nr)
+ alt = recalt(nr)
+ go to 20
+ endif
+ end do
20 continue
- ! read header
- read (100, fmt='(A)', iostat=ierr) header
- print*, 'read_obs: header = ',header
-
- ! read data
- read_loop: do
- ! if obs file contains avetime
- if ( reclen.eq.4 ) then
- read(100,fmt='(A4,1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)',iostat=ierr) &
- recs, yyyymmdd, hhmiss, jdate, avetime, conc, err, num
- else
- read(100,fmt='(A3,1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)',iostat=ierr) &
- recs, yyyymmdd, hhmiss, jdate, avetime, conc, err, num
- endif
- ! if obs file doesn't contain avetime (backwards compatability)
-! avetime = 0d0
-! if ( reclen.eq.4 ) then
-! read(100,fmt='(A4,1X,I8,1X,I6,1X,F14.6,1X,F10.4,1X,F10.4,1X,I4)',iostat=ierr) &
-! recs, yyyymmdd, hhmiss, jdate, conc, err, num
-! else
-! read(100,fmt='(A3,1X,I8,1X,I6,1X,F14.6,1X,F10.4,1X,F10.4,1X,I4)',iostat=ierr) &
-! recs, yyyymmdd, hhmiss, jdate, conc, err, num
-! endif
- if ( ierr.gt.0 ) exit read_loop
- if ( jdate.ge.(juldatef+1d0) ) exit read_loop
- if ( jdate.lt.juldatei ) cycle read_loop
- if ( conc.le.-999. ) cycle read_loop
- ! select day/night for low/high alt sites
- hh = hhmiss/10000
- hl = hh + int(lon*24./360.)
- if ( hl.lt.0 ) then
- hl = hl + 24
- else if ( hl.ge.24 ) then
- hl = hl - 24
- endif
- if ( alt.le.1000. ) then
- if ( (hl.lt.11).or.(hl.gt.15) ) cycle read_loop
- else
- if ( (hl.gt.3).and.(hl.lt.23) ) cycle read_loop
- endif
- if ( conc.le.-999. ) cycle read_loop
-
- cnt = cnt + 1
- obstimes(cnt) = jdate
- avetimes(cnt) = avetime
- reclist(cnt) = recs
- end do read_loop
-
- ! close input file
- close(100)
+ ! read header
+ read (100, fmt='(A)', iostat=ierr) header
+ print*, 'read_obs: header = ',header
+
+ ! read data
+ read_loop: do
+ ! if obs file contains avetime
+ write(rowfmt,'(A,I1,A)') '(A',reclen,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)'
+ read(100,fmt=rowfmt,iostat=ierr) recs, yyyymmdd, hhmiss, jdate, avetime, conc, err, num
+ ! if obs file doesn't contain avetime (backwards compatability)
+! avetime = 0d0
+! write(rowfmt,'(A,I1,A)') '(A',reclen,',1X,I8,1X,I6,1X,F14.6,1X,F10.4,1X,F10.4,1X,I4)'
+! read(100,fmt=rowfmt,iostat=ierr) recs, yyyymmdd, hhmiss, jdate, conc, err, num
+ if ( ierr.gt.0 ) exit read_loop
+ if ( jdate.ge.(juldatef+1d0) ) exit read_loop
+ if ( jdate.lt.juldatei ) cycle read_loop
+ if ( conc.le.-999. ) cycle read_loop
+ ! select day/night for low/high alt sites
+ hh = hhmiss/10000
+ hl = hh + int(lon*24./360.)
+ if ( hl.lt.0 ) then
+ hl = hl + 24
+ else if ( hl.ge.24 ) then
+ hl = hl - 24
+ endif
+ if ( alt.le.1000. ) then
+ if ( (hl.lt.11).or.(hl.gt.15) ) cycle read_loop
+ else
+ if ( (hl.gt.3).and.(hl.lt.23) ) cycle read_loop
+ endif
+ if ( conc.le.-999. ) cycle read_loop
+ cnt = cnt + 1
+ obstimes(cnt) = jdate
+ avetimes(cnt) = avetime
+ reclist(cnt) = trim(recs)
+ end do read_loop
+
+ ! close input file
+ close(100)
10 continue
+ endif ! satellite or ground-based
+
end do
print*, 'read_obs: cnt = ',cnt
diff --git a/prep_regions/read_reclist.f90 b/prep_regions/read_reclist.f90
index 82bb1f4..253c273 100644
--- a/prep_regions/read_reclist.f90
+++ b/prep_regions/read_reclist.f90
@@ -30,6 +30,7 @@ subroutine read_reclist(filename)
implicit none
character(len=max_path_len), intent(in) :: filename
+ character(len=max_path_len) :: rowfmt
character(len=200) :: line
integer :: ierr
integer :: cnt
@@ -64,8 +65,10 @@ subroutine read_reclist(filename)
open(100,file=trim(filename),action='read',status='old',iostat=ierr)
write(*,*) 'Receptors: '
+! write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,F6.2,1X,F6.2,1X,F7.2)'
+ write(rowfmt,fmt='(A,I1,A)') '(A',3,',1X,F7.2,1X,F7.2,1X,F7.2)'
do cnt = 1, nrec
- read(100,fmt='(A4,1X,F6.2,1X,F6.2,1X,F7.2)') recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
+ read(100,fmt=rowfmt) recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
write(*,*) recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
! read(100,*) recname(cnt)
! write(*,*) recname(cnt)
diff --git a/prep_satellite/SETTINGS_bremen b/prep_satellite/SETTINGS_bremen
new file mode 100644
index 0000000..4788ef4
--- /dev/null
+++ b/prep_satellite/SETTINGS_bremen
@@ -0,0 +1,155 @@
+# ==================================================
+#
+# SATELLITE DATA SETTINGS
+#
+# comment lines start with '#'
+# each parameter line starts with 'parameter name:'
+#
+# ==================================================
+
+# PATHS AND FILES
+
+# satellite instrument/retrieval
+satellite: bremen
+# name to include in output files
+satname: esa_ch4
+# flexpart source path
+path_flexpart: /mypath/FLEXPART_v104/
+# path where to write options folders (folders are created daily)
+path_options: /mypath/flexpart_input/
+# path where to write flexpart output
+path_output: /mypath/flexpart_output/
+# path to OH fields (if use OH chemistry)
+path_ohfield: /mypath/OH_fields/
+# path to satellite data
+path_obs: /mypath/satellite_data/
+# suffix satellite files
+suffix: ESACCI
+# path where to write observation output
+path_obsout: /mypath/satellite_obs_out/
+# AVAILABLE files
+file_avail: /mypath/AVAILABLE
+file_availnest: /mypath/AVAILABLE
+# windfields to use (determines lon of domain for flexpart run) (oper, era5)
+windfield: oper
+
+# SATELLITE VARIABLES
+
+# select only retrievals only land (no sunglint)
+landonly: .true.
+# number measurements along flight direction
+nmeas_name: sounding_dim
+# number of pixels across swath
+npixel_name: ground_pixel
+# number of lat/lon coordinates for each pixel
+ncoord_name: corners_dim
+# number of retrieval levels
+nlevel_name: level_dim
+# time variable
+time_name: time
+# quality flag
+qa_name: xch4_quality_flag
+# quality cutoff value (0 = good, 1 = bad, values > qa_cutoff discarded)
+qa_cutoff: 0.1
+# mixing ratio (ppbv)
+vmr_name: xch4
+# mixing ratio precision (ppb)
+verr_name: xch4_uncertainty
+# latitude bounds
+lat_name: latitude_corners
+# longitude bounds
+lon_name: longitude_corners
+# column averaging kernel
+ak_name: xch4_averaging_kernel
+# mixing ratio apriori (mol/m2)
+apri_name: ch4_profile_apriori
+# pressure levels (hPa)
+pdel_name: pressure_levels
+# pressure weighting
+dryair_name: pressure_weight
+# land fraction
+landfrac_name: land_fraction
+
+# COMMAND
+
+# start date of simulation (yyyymmdd)
+datei: 20200702
+# end date of simulation (yyyymmdd)
+datef: 20200801
+# output rate (secs)
+outrate: 86400
+# time average of output (secs)
+outaverage: 86400
+# sampling rate of output (secs)
+outsample: 1800
+# (mass unit = 1, mixing ratio unit = 2)
+ind_source: 1
+# (mass unit = 1, mixing ratio unit = 2)
+ind_receptor: 2
+# use nested output (0 = no, 1 = yes)
+lnested: 0
+# output sensitivity to initial conditions (for backward runs, 0 = none, 1 = mass unit, 2 = mass mixing ratio)
+linit_cond: 2
+
+# OUTGRID
+
+# NOTE: domain specified will determine where retrievals are selected
+
+# longitude of lower left corner of output grid
+# for global use -180 (adjusts automatically for windfield)
+outlonleft: -180.00
+# latitude of lower left corner of output grid
+outlatlower: -90.00
+# number of longitudinal grid cells in output grid
+numxgrid: 180
+# number of latitudinal grid cells in output grid
+numygrid: 90
+# longitudinal resolution in output grid
+dxout: 2.0
+# latitudinal resolution in outout grid
+dyout: 2.0
+# longitude of lower left corner of nested grid (used if nested_output = 1)
+outlonnest: 50.0
+# latitude of lower left corner of nested grid (used if nested_output = 1)
+outlatnest: 47.0
+# number of longitudinal grid cells in nested grid (used if nested_output = 1)
+numxnest: 140
+# number of latitudinal grid cells in nested grid (used if nested_output = 1)
+numynest: 60
+# longitudinal resolution in nested grid (used if nested_output = 1)
+dxoutnest: 0.5
+# latitudinal resolution in nested grid (used if nested_output = 1)
+dyoutnest: 0.5
+# comma-separated list of vertical levels in output grid (meters)
+zlevel: 250, 750, 1500, 2500, 3500, 4500, 5500, 6500, 7500, 8500, 9500, 11000, 13000, 15000, 17000, 19000, 21250, 23750, 26250, 28750, 32500, 37500, 42500, 47500
+
+# RELEASES
+
+# species (see: /options/SPECIES/spec_overview)
+species: CH4
+# ageclass (sec)
+ageclass: 1728000
+# number of particles per column
+npart: 40000
+# mass of particles (arbitrary)
+mass: 1000
+
+# AVERAGING
+
+# average retrievals etc. (true/false)
+avg_pixels: .true.
+# If averaging need to set following (else ignored):
+# use predefined grid from file (true/false)
+usegridfile: .false.
+# if usegridfile is true specify file:
+filegrid:
+# min grid resolution (degrees)
+dmin: 1.0
+# number of resolution steps
+nsteps: 2
+# cutoff standard deviation
+cutoff: 15.
+# min number of retrievals in grid box in order to keep it
+nmin: 10
+
+
diff --git a/prep_satellite/SETTINGS_oco2 b/prep_satellite/SETTINGS_oco2
new file mode 100644
index 0000000..d0bf61f
--- /dev/null
+++ b/prep_satellite/SETTINGS_oco2
@@ -0,0 +1,157 @@
+# ==================================================
+#
+# SATELLITE DATA SETTINGS
+#
+# comment lines start with '#'
+# each parameter line starts with 'parameter name:'
+#
+# ==================================================
+
+# PATHS AND FILES
+
+# satellite instrument/retrieval
+satellite: oco2
+# name to include in output files
+satname: oco2_co2
+# flexpart source path
+path_flexpart: /mypath/FLEXPART_v104/
+# path where to write options folders (folders are created daily)
+path_options: /mypath/flexpart_input/
+# path where to write flexpart output
+path_output: /mypath/flexpart_output/
+# path to OH fields (if use OH chemistry)
+path_ohfield: /mypath/OH_fields/
+# path to satellite data
+path_obs: /mypath/satellite_data/
+# suffix satellite files
+suffix: oco2_LtCO2
+# path where to write observation output
+path_obsout: /mypath/satellite_obs_out/
+# AVAILABLE files
+file_avail: /mypath/AVAILABLE
+file_availnest: /mypath/AVAILABLE
+# windfields to use (determines lon of domain for flexpart run) (oper, era5)
+windfield: era5
+
+# SATELLITE VARIABLES
+
+# select only retrievals only land
+landonly: .false.
+# select operation mode (-1 = Both, 0 = Nadir, 1 = Glint)
+opmode_sel: -1
+# number measurements along flight direction
+nmeas_name: sounding_id
+# number of lat/lon coordinates for each pixel
+ncoord_name: vertices
+# number of retrieval levels
+nlevel_name: levels
+# operation mode
+oper_name: Sounding/operation_mode
+# quality flag
+qa_name: xco2_quality_flag
+# quality cutoff value (0 = good, 1 = bad, values > qa_cutoff discarded)
+qa_cutoff: 0.1
+# times of soundings
+time_name: time
+# mixing ratio (ppm)
+vmr_name: xco2
+# mixing ratio precision (ppm)
+verr_name: xco2_uncertainty
+# latitude bounds
+lat_name: vertex_latitude
+# longitude bounds
+lon_name: vertex_longitude
+# column averaging kernel
+ak_name: xco2_averaging_kernel
+# mixing ratio apriori (ppm)
+apri_name: co2_profile_apriori
+# pressure levels (hPa)
+pdel_name: pressure_levels
+# pressure weighting
+dryair_name: pressure_weight
+# land fraction
+landfrac_name: Sounding/land_fraction
+
+# COMMAND
+
+# start date of simulation (yyyymmdd)
+datei: 20200101
+# end date of simulation (yyyymmdd)
+datef: 20200102
+# output rate (secs)
+outrate: 10800
+# time average of output (secs)
+outaverage: 10800
+# sampling rate of output (secs)
+outsample: 1800
+# (mass unit = 1, mixing ratio unit = 2)
+ind_source: 1
+# (mass unit = 1, mixing ratio unit = 2)
+ind_receptor: 2
+# use nested output (0 = no, 1 = yes)
+lnested: 0
+# output sensitivity to initial conditions (for backward runs, 0 = none, 1 = mass unit, 2 = mass mixing ratio)
+linit_cond: 2
+
+# OUTGRID
+
+# NOTE: domain specified will determine where retrievals are selected
+
+# longitude of lower left corner of output grid
+# for global use -180 (adjusts automatically for windfield)
+outlonleft: -180.00
+# latitude of lower left corner of output grid
+outlatlower: -90.00
+# number of longitudinal grid cells in output grid
+numxgrid: 180
+# number of latitudinal grid cells in output grid
+numygrid: 90
+# longitudinal resolution in output grid
+dxout: 2.0
+# latitudinal resolution in outout grid
+dyout: 2.0
+# longitude of lower left corner of nested grid (used if nested_output = 1)
+outlonnest: -15.0
+# latitude of lower left corner of nested grid (used if nested_output = 1)
+outlatnest: 33.0
+# number of longitudinal grid cells in nested grid (used if nested_output = 1)
+numxnest: 100
+# number of latitudinal grid cells in nested grid (used if nested_output = 1)
+numynest: 80
+# longitudinal resolution in nested grid (used if nested_output = 1)
+dxoutnest: 0.5
+# latitudinal resolution in nested grid (used if nested_output = 1)
+dyoutnest: 0.5
+# comma-separated list of vertical levels in output grid (meters)
+zlevel: 250, 750, 1500, 2500, 3500, 4500, 5500, 6500, 7500, 8500, 9500, 11000, 13000, 15000, 17000, 19000, 21250, 23750, 26250, 28750, 32500, 37500, 42500, 47500
+
+# RELEASES
+
+# species (see: /options/SPECIES/spec_overview)
+species: CO2
+# ageclass (sec)
+ageclass: 864000
+# number of particles per column
+npart: 40000
+# mass of particles (arbitrary)
+mass: 1000
+
+# AVERAGING
+
+# average retrievals etc. (true/false)
+avg_pixels: .true.
+# If averaging need to set following (else ignored):
+# use predefined grid from file (true/false)
+usegridfile: .false.
+# if usegridfile is true specify file:
+filegrid:
+# min grid resolution (degrees)
+dmin: 0.5
+# number of resolution steps
+nsteps: 2
+# cutoff standard deviation
+cutoff: 1.
+# min number of retrievals in grid box in order to keep it
+nmin: 1
+
+
diff --git a/prep_satellite/SETTINGS_tropomi b/prep_satellite/SETTINGS_tropomi
new file mode 100644
index 0000000..d1142ff
--- /dev/null
+++ b/prep_satellite/SETTINGS_tropomi
@@ -0,0 +1,159 @@
+# ==================================================
+#
+# SATELLITE DATA SETTINGS
+#
+# comment lines start with '#'
+# each parameter line starts with 'parameter name:'
+#
+# ==================================================
+
+# PATHS AND FILES
+
+# satellite instrument/retrieval (tropomi, bremen)
+satellite: tropomi
+# name to include in output files
+satname: s5p_ch4
+# flexpart source path
+path_flexpart: /mypath/FLEXPART_v104/
+# path where to write options folders (folders are created daily)
+path_options: /mypath/flexpart_input/
+# path where to write flexpart output
+path_output: /mypath/flexpart_output/
+# path to OH fields (if use OH chemistry)
+path_ohfield: /mypath/OH_fields/
+# path to satellite data
+path_obs: /mypath/satellite_data/
+# suffix satellite files
+suffix: S5P_RPRO_L2__CH4
+# path where to write observation output
+path_obsout: /mypath/satellite_obs_out/
+# AVAILABLE files
+file_avail: /mypath/AVAILABLE
+file_availnest: /mypath/AVAILABLE
+# windfields to use (determines lon of domain for flexpart run) (oper, era5)
+windfield: oper
+
+# SATELLITE VARIABLES
+
+# select only retrievals only land (no sunglint)
+landonly: .true.
+# number measurements along flight direction
+nmeas_name: PRODUCT/scanline
+# number of pixels across swath
+npixel_name: PRODUCT/ground_pixel
+# number of lat/lon coordinates for each pixel
+ncoord_name: PRODUCT/corner
+# number of retrieval levels
+nlevel_name: PRODUCT/level
+# reference time variable (seconds since 2010-01-01 00:00 UTC)
+time_name: PRODUCT/time
+# time start of scan (string)
+tdel_name: PRODUCT/delta_time
+# quality flag
+qa_name: PRODUCT/qa_value
+# quality cutoff value (values < qa_cutoff discarded)
+#qa_cutoff: 1.0
+qa_cutoff: 0.9999
+# mixing ratio (ppb)
+vmr_name: PRODUCT/methane_mixing_ratio_bias_corrected
+# mixing ratio precision (ppb)
+verr_name: PRODUCT/methane_mixing_ratio_precision
+# latitude bounds
+lat_name: PRODUCT/SUPPORT_DATA/GEOLOCATIONS/latitude_bounds
+# longitude bounds
+lon_name: PRODUCT/SUPPORT_DATA/GEOLOCATIONS/longitude_bounds
+# column averaging kernel
+ak_name: PRODUCT/SUPPORT_DATA/DETAILED_RESULTS/column_averaging_kernel
+# mixing ratio apriori (mol/m2)
+apri_name: PRODUCT/SUPPORT_DATA/INPUT_DATA/methane_profile_apriori
+# dry air subcolumns (mol/m2)
+dryair_name: PRODUCT/SUPPORT_DATA/INPUT_DATA/dry_air_subcolumns
+# surface pressure (Pa)
+psurf_name: PRODUCT/SUPPORT_DATA/INPUT_DATA/surface_pressure
+# pressure intervals (Pa)
+pdel_name: PRODUCT/SUPPORT_DATA/INPUT_DATA/pressure_interval
+# surface classification
+surfclass_name: PRODUCT/SUPPORT_DATA/INPUT_DATA/surface_classification
+
+# COMMAND
+
+# start date of simulation (yyyymmdd)
+datei: 20200701
+# end date of simulation (yyyymmdd)
+datef: 20200702
+# output rate (secs)
+outrate: 86400
+# time average of output (secs)
+outaverage: 86400
+# sampling rate of output (secs)
+outsample: 1800
+# (mass unit = 1, mixing ratio unit = 2)
+ind_source: 1
+# (mass unit = 1, mixing ratio unit = 2)
+ind_receptor: 2
+# use nested output (0 = no, 1 = yes)
+lnested: 0
+# output sensitivity to initial conditions (for backward runs, 0 = none, 1 = mass unit, 2 = mass mixing ratio)
+linit_cond: 2
+
+# OUTGRID
+
+# NOTE: domain specified will determine where retrievals are selected
+
+# longitude of lower left corner of output grid
+# for global use -180 (adjusts automatically for windfield)
+outlonleft: -180.00
+# latitude of lower left corner of output grid
+outlatlower: -90.00
+# number of longitudinal grid cells in output grid
+numxgrid: 180
+# number of latitudinal grid cells in output grid
+numygrid: 90
+# longitudinal resolution in output grid
+dxout: 2.0
+# latitudinal resolution in outout grid
+dyout: 2.0
+# longitude of lower left corner of nested grid (used if nested_output = 1)
+outlonnest: 50.0
+# latitude of lower left corner of nested grid (used if nested_output = 1)
+outlatnest: 47.0
+# number of longitudinal grid cells in nested grid (used if nested_output = 1)
+numxnest: 140
+# number of latitudinal grid cells in nested grid (used if nested_output = 1)
+numynest: 60
+# longitudinal resolution in nested grid (used if nested_output = 1)
+dxoutnest: 0.5
+# latitudinal resolution in nested grid (used if nested_output = 1)
+dyoutnest: 0.5
+# comma-separated list of vertical levels in output grid (meters)
+zlevel: 250, 750, 1500, 2500, 3500, 4500, 5500, 6500, 7500, 8500, 9500, 11000, 13000, 15000, 17000, 19000, 21250, 23750, 26250, 28750, 32500, 37500, 42500, 47500
+
+# RELEASES
+
+# species (see: /options/SPECIES/spec_overview)
+species: CH4
+# ageclass (sec)
+ageclass: 1728000
+# number of particles per column
+npart: 40000
+# mass of particles (arbitrary)
+mass: 1000
+
+# AVERAGING
+
+# average retrievals etc (true/false)
+avg_pixels: .true.
+# If averaing need to specify following (else ignored):
+# use predefined grid from file (true/false)
+usegridfile: .false.
+# if usegridfile is true specify file:
+filegrid:
+# min grid resolution (degrees)
+dmin: 0.5
+# number of resolution steps
+nsteps: 3
+# cutoff standard deviation
+cutoff: 20.
+# min number of retrievals in gridbox in order to keep
+nmin: 10.
+
diff --git a/prep_satellite/average.f90 b/prep_satellite/average.f90
new file mode 100644
index 0000000..5ba267b
--- /dev/null
+++ b/prep_satellite/average.f90
@@ -0,0 +1,468 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: average
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2022, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> average
+!!
+!! Purpose: Averages individual retrievals to a grid of variable resolution
+!! where the grid resolution is adapted based on the degree of variability
+!! in the column mixing ratios
+!!
+!! column average concentration over N retrievals
+!! c_av = cpri_av + sum(cak_av_i*v_av_i) + (1/N)*sum(sum(cak_ij*vpri_ij))
+!! where v_av_i is average modelled concentration each layer
+!! v_av_i = H_av_i*x*vdryair_av_i
+!!
+!! Interface:
+!!
+!! Inputs
+!! settings - settings data structure
+!!
+!! Outputs
+!!
+!! Externals
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine average(settings, idate, itime, xpoints, ypoints, zpoint1, zpoint2, vmr_out, verr_out,&
+ vapri_out, cpri, cakpri, cak_out, cdryair, vdryair_out, nretr, ncoord, nlayer)
+
+ use mod_settings
+ use mod_var
+ use mod_dates
+
+ implicit none
+
+ type (settings_t), intent(in) :: settings
+ integer, dimension(maxretr), intent(in out) :: idate, itime
+ real, dimension(maxretr,ncoord), intent(in out) :: xpoints, ypoints
+ real, dimension(maxretr,nlayer), intent(in out) :: zpoint1, zpoint2
+ real, dimension(maxretr,nlayer), intent(in out) :: vapri_out, vdryair_out, cak_out
+ real, dimension(maxretr), intent(in out) :: vmr_out, verr_out
+ real, dimension(maxretr), intent(in out) :: cdryair, cpri, cakpri
+ integer, intent(in out) :: nretr
+ integer, intent(in) :: ncoord, nlayer
+
+ character(max_name_len) :: line
+ real :: llx, lly, urx, ury, xav, yav
+ real, dimension(settings%nsteps) :: stepres
+ real :: res, box_mean, box_sd, box_err, rwork, area
+ integer :: nbox, nbox_new, num, numbox, numx, numy
+ integer :: ix, jy, ixy, n, nn, nr, ns, nb, nl, ierr
+ integer :: jjjjmmdd, hhmiss
+ integer, dimension(:), allocatable :: retr_nbox, iretr, iretr_keep, mark_box, idate_mean, itime_mean
+ real, dimension(:), allocatable :: llx_box, lly_box, res_box, warea
+ real, dimension(:), allocatable :: vmr_mean, vmr_sd, cpri_mean, cdryair_mean, cakpri_mean
+ real, dimension(:,:), allocatable :: cak_mean, vdryair_mean, xpts_box, ypts_box, zpt1_box, zpt2_box
+ integer, dimension(4) :: num_subbox
+ real(kind=8) :: jdmean
+
+ ! if use predefined grid skip following
+ ! note: predefined grid overrides domain bounds given in SETTINGS
+ if ( settings%usegridfile ) then
+ go to 10
+ endif
+
+ ! domain bounds
+ if ( settings%lnested.eq.1 ) then
+ llx = settings%outlonnest
+ lly = settings%outlatnest
+ urx = llx + settings%numxnest*settings%dxoutnest
+ ury = lly + settings%numynest*settings%dyoutnest
+ else
+ llx = settings%outlonleft
+ lly = settings%outlatlower
+ urx = llx + settings%numxgrid*settings%dxout
+ ury = lly + settings%numygrid*settings%dyout
+ endif
+ print*, 'llx, lly, urx, ury = ',llx,lly,urx,ury
+
+ ! resolution steps
+ stepres(1) = settings%dmin
+ do ns = 2, settings%nsteps
+ stepres(ns) = stepres(ns-1)*2
+ end do
+ print*, 'stepres = ',stepres
+
+ ! initialize at coarsest resolution
+ ! ---------------------------------
+
+ allocate( retr_nbox(nretr) )
+ allocate( iretr(nretr) )
+ allocate( iretr_keep(nretr) )
+ res = stepres(settings%nsteps)
+! numx = (urx - llx)/res
+ numx = (urx - llx)/res + 1 ! to cover whole domain
+! numy = (ury - lly)/res
+ numy = (ury - lly)/res + 1
+ nbox = numx*numy
+ if ( nbox.gt.maxbox ) then
+ write(logid,*) 'ERROR: maxbox too small'
+ stop
+ endif
+ print*, 'numx, numy, nbox = ',numx, numy, nbox
+ allocate( llx_box(maxbox) )
+ allocate( lly_box(maxbox) )
+ allocate( res_box(maxbox) )
+ allocate( mark_box(maxbox) )
+ allocate( warea(maxbox) )
+ mark_box(:) = 0
+ mark_box(1:nbox) = 1
+ ! allocate retrievals to corresponding box
+ do nr = 1, nretr
+ ix = floor((sum(xpoints(nr,:)/4.) - llx)/res) + 1
+ jy = floor((sum(ypoints(nr,:)/4.) - lly)/res) + 1
+ ixy = (jy - 1)*numx + ix
+ retr_nbox(nr) = ixy
+ if ( nr.lt.50 ) then
+ print*, 'xpoint, ypoint = ',sum(xpoints(nr,:))/4., sum(ypoints(nr,:))/4.
+ print*, 'ix, jy, ixy = ',ix,jy,ixy
+ endif
+ end do
+ ! calculate box coordinates
+ do nb = 1, nbox
+ jy = (nb - 1)/numx + 1
+ ix = nb - (jy - 1)*numx
+ llx_box(nb) = llx + (ix - 1)*res
+ lly_box(nb) = lly + (jy - 1)*res
+ end do
+ !** test
+ print*, 'box coords:'
+ do nb = 1, 20
+ print*, llx_box(nb), lly_box(nb)
+ end do
+ !**
+ res_box(:) = res
+ print*, 'retr_nbox(1:20) = ',retr_nbox(1:20)
+
+ ! loop over resolution steps
+ ! --------------------------
+
+ do ns = settings%nsteps-1, 1, -1
+ print*, 'STEP = ',ns
+ print*, '-----------'
+ res = stepres(ns)
+ print*, 'res = ',res
+ !--- loop over marked boxes
+ do nb = 1, nbox
+ if ( mark_box(nb).eq.0 ) cycle
+ print*, 'nb = ',nb
+ ! calculate sd of retrievals in each box
+ iretr(:) = 0
+ num = 0
+ do nr = 1, nretr
+ if ( retr_nbox(nr).eq.nb ) then
+ num = num + 1
+ iretr(num) = nr
+ endif
+ end do
+ print*, 'num of retrievals in current box = ',num
+ if ( num.gt.1 ) then
+ box_mean = sum(vmr_out(iretr(1:num)))/real(num)
+ box_sd = sqrt(sum((vmr_out(iretr(1:num))-box_mean)**2)/real(num - 1))
+ else if ( num.eq.1 ) then
+ box_mean = vmr_out(iretr(num))
+ box_sd = 1.
+ else
+ box_mean = -999.
+ box_sd = -999.
+ endif
+ print*, 'box mean, sd = ',box_mean,box_sd
+ ! check if this box should be divided further
+ if ( (box_sd.lt.settings%cutoff) ) then
+ ! only keep if retrievals spread over all sub-boxes otherwise divide
+ num_subbox(:) = 0
+ do nn = 1, num
+ nr = iretr(nn)
+ do n = 1, 4
+ jy = (n - 1)/2 + 1
+ ix = n - (jy - 1)*2
+ if ( sum(ypoints(nr,:)/4.).gt.(lly_box(nb)+(jy-1)*res).and.sum(ypoints(nr,:)/4.).lt.(lly_box(nb)+jy*res).and.&
+ sum(xpoints(nr,:)/4.).gt.(llx_box(nb)+(ix-1)*res).and.sum(xpoints(nr,:)/4.).lt.(llx_box(nb)+ix*res) ) then
+ num_subbox(n) = num_subbox(n) + 1
+ endif
+ end do ! n
+! endif ! nb
+ end do ! nn
+ print*, 'num_subbox = ',num_subbox(:)
+ if ( all(num_subbox.gt.0) ) then
+ mark_box(nb) = 0 ! do not divide box
+ else if ( box_sd.eq.-999. ) then
+ mark_box(nb) = 0 ! no retrievals in box
+ endif
+ endif
+ end do ! nbox
+ !--- divide boxes
+ print*, 'DIVIDE'
+ print*, '------'
+ nbox_new = nbox
+ ! loop over boxes and divide
+ do nb = 1, nbox
+ if ( mark_box(nb).eq.0 ) cycle ! do not divide box
+ print*, 'nb = ',nb
+ ! divide box into 4 so add 3 new ones
+ ! first box keeps old nb, llx and lly bounds, but update res
+ res_box(nb) = res
+ ! new boxes get numbers nbox_nb + n
+ do n = 1, 3
+ ! coordinates of new boxes
+ jy = n/2
+ ix = n - jy*2
+ llx_box(nbox_new+n) = llx_box(nb) + ix*res
+ lly_box(nbox_new+n) = lly_box(nb) + jy*res
+ res_box(nbox_new+n) = res
+ mark_box(nbox_new+n) = 1
+ print*, 'nbox_new + n = ',nbox_new + n
+ print*, 'llx_box(nb) = ',llx_box(nb)
+ print*, 'llx_box(nbox_new+n) = ',llx_box(nbox_new+n)
+ print*, 'lly_box(nb) = ',lly_box(nb)
+ print*, 'lly_box(nbox_new+n) = ',lly_box(nbox_new+n)
+ end do
+ ! update retrieval box numbers
+ do nr = 1, nretr
+ if ( retr_nbox(nr).ne.nb ) cycle
+ ix = floor((sum(xpoints(nr,:)/4.) - llx_box(nb))/res) ! not +1 because resuse nbox number for first grid in divided box
+ jy = floor((sum(ypoints(nr,:)/4.) - lly_box(nb))/res)
+ print*, 'update retrieval box no.s: ix, jy = ',ix,jy
+ print*, 'retr_nbox(nr): old = ',retr_nbox(nr)
+ if ( .not.((ix.eq.0).and.(jy.eq.0)) ) retr_nbox(nr) = nbox_new + jy*2 + ix
+ print*, 'retr_nbox(nr): new = ',retr_nbox(nr)
+ end do
+ nbox_new = nbox_new + 3
+ if ( nbox_new.gt.maxbox ) then
+ write(logid,*) 'ERROR: maxbox too small'
+ stop
+ endif
+ end do ! nb
+ ! update nbox
+ nbox = nbox_new
+ print*, 'nbox_new = ',nbox_new
+ end do ! ns
+
+ ! TESTING
+! open(100,file=trim(settings%filegrid),action='write',status='replace',iostat=ierr)
+! write(100,*) 'llx_box lly_box res_box'
+! print*, 'llx_box(1) = ',llx_box(1)
+! do nb = 1, nbox
+! write(100,fmt='(F7.2,1X,F7.2,1X,F7.2)') llx_box(nb), lly_box(nb), res_box(nb)
+! end do
+! close(100)
+! open(100,file=trim(settings%path_obsout)//'retr_nbox_orig.txt',action='write',status='replace',iostat=ierr)
+! do nr = 1, nretr
+! write(100,fmt='(I8)') retr_nbox(nr)
+! end do
+! close(100)
+
+10 continue
+ if ( settings%usegridfile ) then
+ allocate( llx_box(maxbox) )
+ allocate( lly_box(maxbox) )
+ allocate( res_box(maxbox) )
+ allocate( retr_nbox(nretr) )
+ allocate( iretr(nretr) )
+ ! read llx_box, lly_box, res_box from file
+ write(logid,*) 'Reading averaging grid from file'
+ open(100,file=trim(settings%filegrid),status='old',action='read',iostat=ierr)
+ if ( ierr.eq.0 ) then
+ read(100,*) line
+ do n = 1, maxbox
+ read(100,fmt='(F7.2,1X,F7.2,1X,F7.2)',iostat=ierr) llx_box(n), lly_box(n), res_box(n)
+ if ( ierr.ne.0 ) exit
+ end do
+ nbox = n - 1
+ print*, 'nbox = ',nbox
+ close(100)
+ else
+ write(logid,*) 'ERROR: file not found ',settings%filegrid
+ stop
+ endif
+ ! allocate retrievals to corresponding box
+ print*, 'nretr = ',nretr
+ do nb = 1, nbox
+ do nr = 1, nretr
+ xav = sum(xpoints(nr,:))/4.
+ yav = sum(ypoints(nr,:))/4.
+ if ( (xav.gt.llx_box(nb)).and.(xav.lt.(llx_box(nb)+res_box(nb))).and. &
+ (yav.gt.lly_box(nb)).and.(yav.lt.(lly_box(nb)+res_box(nb))) ) then
+ retr_nbox(nr) = nb
+ endif
+ end do
+ end do
+ ! TESTING
+! open(100,file=trim(settings%path_obsout)//'retr_nbox_file.txt',action='write',status='replace',iostat=ierr)
+! do nr = 1, nretr
+! write(100,fmt='(I8)') retr_nbox(nr)
+! end do
+! close(100)
+ endif ! usegridfile
+
+ ! prepare output
+ ! --------------
+
+ allocate( vmr_mean(nbox) )
+ allocate( vmr_sd(nbox) )
+ allocate( cpri_mean(nbox) )
+ allocate( cdryair_mean(nbox) )
+ allocate( cakpri_mean(nbox) )
+ allocate( cak_mean(nbox,nlayer) )
+ allocate( vdryair_mean(nbox,nlayer) )
+ allocate( xpts_box(nbox,ncoord) )
+ allocate( ypts_box(nbox,ncoord) )
+ allocate( zpt1_box(nbox,nlayer) )
+ allocate( zpt2_box(nbox,nlayer) )
+ allocate( idate_mean(nbox) )
+ allocate( itime_mean(nbox) )
+
+ ! loop over boxes
+ numbox = 0
+ do nb = 1, nbox
+ ! mean and sd of retrievals in each box
+ num = 0
+ iretr(:) = 0
+ do nr = 1, nretr
+ if ( retr_nbox(nr).eq.nb ) then
+ num = num + 1
+ iretr(num) = nr
+ endif
+ end do
+ if ( num.ge.settings%nmin ) then
+ ! only use boxes with > nmin retrievals
+ ! area weighting
+ warea(:) = 0.
+ do n = 1, num
+ call geodarea(xpoints(iretr(n),:), ypoints(iretr(n),:), warea(n))
+ end do
+ warea(1:num) = warea(1:num)/sum(warea(1:num))
+ print*, 'sum(warea) = ',sum(warea(1:num))
+ print*, 'range(warea) = ',minval(warea(1:num)),maxval(warea(1:num))
+ box_mean = dot_product(warea(1:num), vmr_out(iretr(1:num)))
+ if ( num.eq.1 ) then
+ box_sd = verr_out(iretr(num))
+ else
+ box_sd = sqrt(sum((vmr_out(iretr(1:num))-box_mean)**2)/real(num - 1))
+ endif
+ box_err = sqrt(dot_product(warea(1:num), verr_out(iretr(1:num))**2))
+ ! only keep retrievals within +/- 2 sd of mean
+ nn = 0
+ iretr_keep(:) = 0
+ do n = 1, num
+ if ( vmr_out(iretr(n)).gt.(box_mean-2.*box_sd).and.vmr_out(iretr(n)).lt.(box_mean+2.*box_sd) ) then
+ nn = nn + 1
+ iretr_keep(nn) = iretr(n)
+ endif
+ end do
+ ! calculate mean of kept retrievals
+ warea(:) = 0.
+ do n = 1, nn
+ call geodarea(xpoints(iretr_keep(n),:), ypoints(iretr_keep(n),:), warea(n))
+ end do
+ warea(1:nn) = warea(1:nn)/sum(warea(1:nn))
+ print*, 'sum(warea) = ',sum(warea(1:nn))
+ print*, 'range(warea) = ',minval(warea(1:nn)),maxval(warea(1:nn))
+ box_mean = dot_product(warea(1:nn), vmr_out(iretr_keep(1:nn)))
+ if ( nn.eq.1 ) then
+ box_sd = vmr_out(iretr_keep(nn))
+ else
+ box_sd = sqrt(sum((vmr_out(iretr_keep(1:nn))-box_mean)**2)/real(nn - 1))
+ endif
+ box_err = sqrt(dot_product(warea(1:nn), verr_out(iretr_keep(1:nn))**2))
+ ! for below use num and iretr
+ iretr(:) = 0
+ iretr(:) = iretr_keep(:)
+ ! reset and update for this box
+ num = nn
+ numbox = numbox + 1
+ else
+ ! reject this box -> too few retrievals
+ cycle
+ endif
+ ! mean column mixing ratio
+ vmr_mean(numbox) = box_mean
+ ! mean column uncertainty
+ vmr_sd(numbox) = box_err
+ ! mean column prior convolved with averaging kernel
+ rwork = 0.
+ do n = 1, num
+ if ( settings%satellite.eq.'tropomi' ) then
+ rwork = rwork + warea(n)*dot_product(cak_out(iretr(n),:),vapri_out(iretr(n),:))
+ else if (settings%satellite.eq.'bremen' ) then
+ do nl = 1, nlayer
+ rwork = rwork + warea(n)*vdryair_out(iretr(n),nl)*vapri_out(iretr(n),nl)*cak_out(iretr(n),nl)
+ end do
+ endif
+ end do
+ cakpri_mean(numbox) = rwork
+ ! mean column prior
+ cpri_mean(numbox) = dot_product(warea(1:num),cpri(iretr(1:num)))
+ ! mean averaging kernel
+ cak_mean(numbox,:) = matmul(warea(1:num),cak_out(iretr(1:num),:))
+ ! mean column dry air concentration
+ cdryair_mean(numbox) = dot_product(warea(1:num),cdryair(iretr(1:num)))
+ ! mean dry air concentration
+ vdryair_mean(numbox,:) = matmul(warea(1:num),vdryair_out(iretr(1:num),:))
+ ! box coordinates
+ xpts_box(numbox,(/1,4/)) = llx_box(nb)
+ xpts_box(numbox,(/2,3/)) = llx_box(nb) + res_box(nb)
+ ypts_box(numbox,(/1,2/)) = lly_box(nb)
+ ypts_box(numbox,(/3,4/)) = lly_box(nb) + res_box(nb)
+ zpt1_box(numbox,:) = matmul(warea(1:num),zpoint1(iretr(1:num),:))
+ zpt2_box(numbox,:) = matmul(warea(1:num),zpoint2(iretr(1:num),:))
+ ! date and time
+ jdmean = 0d0
+ do n = 1, num
+ jdmean = jdmean + juldate(idate(iretr(n)),itime(iretr(n)))
+ end do
+ jdmean = jdmean/dble(num)
+ call caldate(jdmean, jjjjmmdd, hhmiss)
+ idate_mean(numbox) = jjjjmmdd
+ itime_mean(numbox) = hhmiss
+ end do
+ print*, 'zpt1_box(1:10,:) = ',zpt1_box(1:10,:)
+ nretr = numbox
+ write(logid,*) 'Number of averaged retrievals = ',nretr
+ print*, 'nretr = ',nretr
+ vmr_out(1:nretr) = vmr_mean(1:nretr)
+ verr_out(1:nretr) = vmr_sd(1:nretr)
+ cdryair(1:nretr) = cdryair_mean(1:nretr)
+ vdryair_out(1:nretr,:) = vdryair_mean(1:nretr,:)
+ cak_out(1:nretr,:) = cak_mean(1:nretr,:)
+ cpri(1:nretr) = cpri_mean(1:nretr)
+ cakpri(1:nretr) = cakpri_mean(1:nretr)
+ xpoints(1:nretr,:) = xpts_box(1:nretr,:)
+ ypoints(1:nretr,:) = ypts_box(1:nretr,:)
+ zpoint1(1:nretr,:) = zpt1_box(1:nretr,:)
+ zpoint2(1:nretr,:) = zpt2_box(1:nretr,:)
+ idate(1:nretr) = idate_mean(1:nretr)
+ itime(1:nretr) = itime_mean(1:nretr)
+ deallocate( vmr_mean )
+ deallocate( vmr_sd )
+ deallocate( cdryair_mean )
+ deallocate( vdryair_mean )
+ deallocate( cak_mean )
+ deallocate( cpri_mean )
+ deallocate( cakpri_mean )
+ deallocate( xpts_box )
+ deallocate( ypts_box )
+ deallocate( zpt1_box )
+ deallocate( zpt2_box )
+ deallocate( warea )
+ deallocate( idate_mean )
+ deallocate( itime_mean )
+
+end subroutine average
+
diff --git a/prep_satellite/geodarea.f90 b/prep_satellite/geodarea.f90
new file mode 100644
index 0000000..34ce0bd
--- /dev/null
+++ b/prep_satellite/geodarea.f90
@@ -0,0 +1,61 @@
+!---------------------------------------------------------------------------------------
+! PREP_FLUXES: geodarea
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2017, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> geodarea
+!!
+!! Purpose: Calculates the area of a rectangle assuming spherical earth.
+!!
+!! Interface:
+!!
+!! Inputs
+!! ypoints - latitudinal coordinates (length 4)
+!! xpoints - longitudinal coordinates (length 4)
+!!
+!! Outputs
+!! area - area of grid cell
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine geodarea(xpoints,ypoints,area)
+
+ implicit none
+
+ real, dimension(4), intent(in) :: xpoints, ypoints
+ real, intent(out) :: area
+
+ real, parameter :: pi=3.14159265, rearth=6.371e6, pih=pi/180.
+ real :: work, distx, disty
+ real, dimension(4) :: rlons, rlats
+
+ ! distance between two points using Haversine formula
+ rlons = xpoints*pih
+ rlats = ypoints*pih
+ ! longitude distance
+ work = cos(rlats(1))*cos(rlats(2))*(sin(rlons(2) - rlons(1))/2.)**2
+ work = sin((rlats(2) - rlats(1))/2.)**2 + work
+ distx = 2.*rearth*asin(sqrt(work))
+ ! latitude distance
+ work = cos(rlats(2))*cos(rlats(3))*(sin(rlons(3) - rlons(2))/2.)**2
+ work = sin((rlats(3) - rlats(2))/2.)**2 + work
+ disty = 2.*rearth*asin(sqrt(work))
+ work = tan(distx/(2.*rearth))*tan(disty/(2.*rearth))
+ area = 4.*rearth**2*asin(work)
+
+end subroutine geodarea
+
diff --git a/prep_satellite/get_bremen.f90 b/prep_satellite/get_bremen.f90
new file mode 100644
index 0000000..e428896
--- /dev/null
+++ b/prep_satellite/get_bremen.f90
@@ -0,0 +1,431 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: get_bremen
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2022, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> get_bremen
+!!
+!! Purpose: Reads observations and auxilliary data from the specified satellite and
+!! and writes the output into files that can be directly used by FLEXPART
+!! and, for inversions, by FLEXINVERT
+!!
+!! Interface:
+!!
+!! Inputs
+!! settings - settings data structure
+!!
+!! Outputs
+!!
+!! Externals
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine get_bremen(settings)
+
+ use mod_settings
+ use mod_var
+ use mod_dates
+ use mod_save
+ use netcdf
+
+ implicit none
+
+ type (settings_t), intent(in) :: settings
+
+ character(max_name_len), dimension(:), allocatable :: filelist, filereadlist
+ character(max_name_len) :: line, filename
+ character(len=8) :: adate
+ character(len=6) :: atime
+ character(len=3) :: aspec
+ character(len=6), dimension(4) :: units
+ integer :: i, ierr, n, nf, nl, nm, np, nt, nbits, iswater
+ integer :: nfiles, nread, nretr, npx_in_scan
+ real(kind=8) :: jdatei, jdatef, jd, days_since_ref, jdateref, jdmeas
+ real :: sec_since_midnight
+ integer :: jjjjmmdd, hhmiss, hh, mi, ss
+ integer, parameter :: refdate = 19700101
+ integer, parameter :: lsynctime = 600
+ integer :: ntime, nmeas, npixel, nlevel, ncoord, nlayer
+ real, dimension(:,:), allocatable :: lat_bnds, lon_bnds
+ real, dimension(:), allocatable :: vmr, verr, time, landfrac, qa
+ real, dimension(:,:), allocatable :: pres, vapri, vdryair, cak
+ real, dimension(:,:), allocatable :: xpoints, ypoints
+ real, dimension(:,:), allocatable :: zpoint1, zpoint2
+ real, dimension(:,:), allocatable :: cak_out, vapri_out, vdryair_out
+ real, dimension(:), allocatable :: vmr_out, verr_out
+ real, dimension(:), allocatable :: cpri, cakpri, cdryair
+ integer, dimension(:), allocatable :: idate, itime
+ integer :: specnum, nchar
+ integer :: ncid, dimid, varid
+ real :: nest_llx, nest_lly, nest_urx, nest_ury
+ real :: llx, lly, urx, ury
+
+ ! get species number
+ ! ------------------
+
+ open(100,file=trim(settings%path_flexpart)//'options/SPECIES/spec_overview',status='old',action='read',iostat=ierr)
+ nchar = len_trim(settings%species)
+ do while ( ierr.eq.0 )
+ read (100, fmt='(A)', iostat=ierr) line
+ if ( line(len_trim(line)-nchar+1:len_trim(line)) == trim(settings%species) ) ierr = 1
+ end do
+ read(line(9:11),*) specnum
+ write(logid,*) 'species: ',settings%species
+ write(logid,*) 'specnum: ',specnum
+ write(logid,*) 'qa cutoff: ',settings%qa_cutoff
+ close(100)
+
+ ! define domains
+ ! --------------------
+
+ llx = settings%outlonleft
+ lly = settings%outlatlower
+ urx = llx + settings%numxgrid*settings%dxout
+ ury = lly + settings%numygrid*settings%dyout
+
+ if ( settings%lnested.eq.1 ) then
+ nest_llx = settings%outlonnest
+ nest_lly = settings%outlatnest
+ nest_urx = nest_llx + settings%numxnest*settings%dxoutnest
+ nest_ury = nest_lly + settings%numynest*settings%dyoutnest
+ endif
+ print*, 'llx,lly,urx,ury = ',llx,lly,urx,ury
+ if (settings%lnested.eq.1) print*, 'nest_llx,nest_lly,nest_urx,nest_ury = ',nest_llx,nest_lly,nest_urx,nest_ury
+
+ ! list satellite files
+ ! ----------------------
+
+ call system('find '//trim(settings%path_obs)//' -type f | grep '//trim(settings%suffix)//&
+ ' | wc -l > '//trim(settings%path_obsout)//'obsfiles.txt')
+ call system('find '//trim(settings%path_obs)//' -type f | grep '//trim(settings%suffix)//&
+ ' >> '//trim(settings%path_obsout)//'obsfiles.txt')
+
+ open(100,file=trim(settings%path_obsout)//'obsfiles.txt',action='read',status='old',iostat=ierr)
+ if ( ierr.ne. 0 ) then
+ write(logid,*) 'ERROR: cannot open obsfiles.txt'
+ stop
+ endif
+ read(100,*,iostat=ierr) nfiles
+ allocate ( filelist(nfiles), stat = ierr )
+ allocate ( filereadlist(nfiles), stat = ierr )
+ do nf = 1, nfiles
+ read(100,fmt='(A)',iostat=ierr) filelist(nf)
+ if (ierr.ne.0) exit
+ end do
+ close(100)
+
+ ! loop over days
+ ! --------------
+
+ jdatei = juldate(settings%datei, 0)
+ jdatef = juldate(settings%datef, 0)
+ jd = jdatei
+
+ read_loop: do
+
+ if ( jd.gt.jdatef ) exit read_loop
+
+ ! search files for current date
+ call caldate(jd, jjjjmmdd, hhmiss)
+ write(adate,fmt='(I8.8)') jjjjmmdd
+ write(logid,*) 'current day: ',adate
+ nread = 0
+ do n = 1, nfiles
+ do i = 1, len_trim(filelist(n))
+ if ( filelist(n)(i:(i+7)).eq.adate ) then
+ nread = nread + 1
+ filereadlist(nread) = filelist(n)
+ exit
+ endif
+ end do
+ end do
+ write(logid,*) 'number of files for current day: ',nread
+ if ( nread.eq.0 ) then
+ jd = jd + 1d0
+ cycle read_loop
+ endif
+
+ ! loop over files
+ ! ---------------
+
+ do n = 1, nread
+
+ ! open file
+ write(logid,*) 'reading file: ',filereadlist(n)
+ call check( nf90_open(trim(filereadlist(n)),nf90_NOWRITE,ncid) )
+
+ ! dimension variables
+ call check( nf90_inq_dimid(ncid,trim(settings%nmeas_name),dimid) )
+ call check( nf90_inquire_dimension(ncid,dimid,len=nmeas) )
+ write(logid,*) 'number of retrievals: ',nmeas
+ call check( nf90_inq_dimid(ncid,trim(settings%ncoord_name),dimid) )
+ call check( nf90_inquire_dimension(ncid,dimid,len=ncoord) )
+ write(logid,*) 'number of geocoordinates: ',ncoord
+ call check( nf90_inq_dimid(ncid,trim(settings%nlevel_name),dimid) )
+ call check( nf90_inquire_dimension(ncid,dimid,len=nlevel) )
+ nlayer = nlevel - 1
+ write(logid,*) 'number of vertical layers: ',nlayer
+
+ ! geolocation variables
+ allocate( lat_bnds(ncoord,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate lat_bnds'
+ call check( nf90_inq_varid(ncid,trim(settings%lat_name),varid) )
+ call check( nf90_get_var(ncid,varid,lat_bnds) )
+ allocate( lon_bnds(ncoord,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate lon_bnds'
+ call check( nf90_inq_varid(ncid,trim(settings%lon_name),varid) )
+ call check( nf90_get_var(ncid,varid,lon_bnds) )
+
+ ! product variables
+ allocate( time(nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate time'
+ call check( nf90_inq_varid(ncid,trim(settings%time_name),varid) )
+ call check( nf90_get_var(ncid,varid,time) )
+ allocate( pres(nlevel,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate pres'
+ call check( nf90_inq_varid(ncid,trim(settings%pdel_name),varid) )
+ call check( nf90_get_var(ncid,varid,pres) )
+ allocate( qa(nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate qa'
+ call check( nf90_inq_varid(ncid,trim(settings%qa_name),varid) )
+ call check( nf90_get_var(ncid,varid,qa) )
+ allocate( vmr(nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vmr'
+ call check( nf90_inq_varid(ncid,trim(settings%vmr_name),varid) )
+ call check( nf90_get_var(ncid,varid,vmr) )
+ allocate( verr(nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate verr'
+ call check( nf90_inq_varid(ncid,trim(settings%verr_name),varid) )
+ call check( nf90_get_var(ncid,varid,verr) )
+ ! convert hPa -> Pa for consistency with flexpart
+ pres = pres*100.
+
+ ! detailed results variables
+ allocate( cak(nlayer,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate cak'
+ call check( nf90_inq_varid(ncid,trim(settings%ak_name),varid) )
+ call check( nf90_get_var(ncid,varid,cak) )
+ allocate( vapri(nlayer,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vapri'
+ call check( nf90_inq_varid(ncid,trim(settings%apri_name),varid) )
+ call check( nf90_get_var(ncid,varid,vapri) )
+ allocate( vdryair(nlayer,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vdryair'
+ call check( nf90_inq_varid(ncid,trim(settings%dryair_name),varid) )
+ call check( nf90_get_var(ncid,varid,vdryair) )
+ allocate( landfrac(nmeas), stat=ierr )
+ call check( nf90_inq_varid(ncid,trim(settings%landfrac_name),varid) )
+ call check( nf90_get_var(ncid,varid,landfrac) )
+
+ call check( nf90_close(ncid))
+
+ ! select retrievals and extract needed info
+ if( n.eq.1 ) then
+ allocate( xpoints(maxretr,ncoord) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate xpoints'
+ allocate( ypoints(maxretr,ncoord) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate ypoints'
+ allocate( zpoint1(maxretr,nlayer) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate zpoint1'
+ allocate( zpoint2(maxretr,nlayer) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate zpoint2'
+ allocate( idate(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate idate'
+ allocate( itime(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate itime'
+ allocate( cak_out(maxretr,nlayer) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate cak_out'
+ allocate( vapri_out(maxretr,nlayer) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vapri_out'
+ allocate( vdryair_out(maxretr,nlayer) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vdryair_out'
+ allocate( vmr_out(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vmr_out'
+ allocate( verr_out(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate verr_out'
+ nretr = 0
+ endif
+ do nm = 1, nmeas
+ ! exclude retrievals above quality cutoff
+ if ( qa(nm).gt.settings%qa_cutoff ) cycle
+ ! if landonly exclude pixels with less than 50% land
+ if ( settings%landonly.and.landfrac(nm).lt.50. ) cycle
+ if ( settings%lnested.eq.1 ) then
+ ! if nested domain exclude pixels outside
+ if ( any(lon_bnds(:,nm).lt.nest_llx).or. &
+ any(lon_bnds(:,nm).gt.nest_urx).or. &
+ any(lat_bnds(:,nm).lt.nest_lly).or. &
+ any(lat_bnds(:,nm).gt.nest_ury) ) cycle
+ else
+ ! if not nested exclude pixels outside global domain
+ if ( any(lon_bnds(:,nm).lt.llx).or. &
+ any(lon_bnds(:,nm).gt.urx).or. &
+ any(lat_bnds(:,nm).lt.lly).or. &
+ any(lat_bnds(:,nm).gt.ury) ) cycle
+ endif
+ jdateref = juldate(refdate, 0)
+ days_since_ref = jd - jdateref
+ sec_since_midnight = time(nm) - sngl(days_since_ref)*24.*3600.
+ jdmeas = jd + dble(sec_since_midnight/24./3600.)
+ ! exclude retrievals if not for current day
+ if ( floor(jdmeas).ne.jd ) cycle
+ call caldate(jdmeas, jjjjmmdd, hhmiss)
+ nretr = nretr + 1
+ idate(nretr) = jjjjmmdd
+ itime(nretr) = hhmiss
+ ! corners ordered anticlockwise from lower left
+ xpoints(nretr,:) = lon_bnds(:,nm)
+ ypoints(nretr,:) = lat_bnds(:,nm)
+ ! pressure levels
+ do nl = 1, nlevel
+ if ( nl.lt.nlevel ) zpoint1(nretr,nl) = pres(nl,nm)
+ if ( nl.gt.1 ) zpoint2(nretr,nl-1) = pres(nl,nm)
+ end do
+ cak_out(nretr,:) = cak(:,nm)
+ vapri_out(nretr,:) = vapri(:,nm)
+ vdryair_out(nretr,:) = vdryair(:,nm)
+ vmr_out(nretr) = vmr(nm)
+ ! unlike official retrieval no factor of 2 necessary for error
+ verr_out(nretr) = verr(nm)
+ end do
+ print*, 'range(pres) = ',minval(pres),maxval(pres)
+ print*, 'range(zpoint1) = ',minval(zpoint1),maxval(zpoint1)
+
+ write(logid,*) 'number of retrievals: ',nretr
+
+ if ( allocated(lat_bnds) ) deallocate(lat_bnds)
+ if ( allocated(lon_bnds) ) deallocate(lon_bnds)
+ if ( allocated(vapri) ) deallocate(vapri)
+ if ( allocated(vdryair) ) deallocate(vdryair)
+ if ( allocated(cak) ) deallocate(cak)
+ if ( allocated(time) ) deallocate(time)
+ if ( allocated(pres) ) deallocate(pres)
+ if ( allocated(qa) ) deallocate(qa)
+ if ( allocated(vmr) ) deallocate(vmr)
+ if ( allocated(verr) ) deallocate(verr)
+ if ( allocated(landfrac) ) deallocate(landfrac)
+
+ end do ! nread
+
+ if ( nretr.eq.0 ) go to 10
+
+ ! calculate column prior (units ppbv)
+ allocate( cpri(nretr), stat=ierr )
+ do nm = 1, nretr
+ cpri(nm) = dot_product(vapri_out(nm,:), vdryair_out(nm,:))
+ end do
+
+ !! test
+ print*, 'vdryair_out(1:10,:) = ',vdryair_out(1:10,:)
+
+ ! calculate column prior convolved with averaging kernel (units ppbv)
+ allocate( cakpri(nretr), stat=ierr )
+ do nm = 1, nretr
+ do nl = 1, nlayer
+ cakpri(nm) = cakpri(nm) + vdryair_out(nm,nl)*vapri_out(nm,nl)*cak_out(nm,nl)
+ end do
+ end do
+
+ ! column dry-air not needed but only as dummy variable
+ allocate( cdryair(nretr) )
+ cdryair(:) = 1.
+
+ ! average pixels
+ ! --------------
+
+ if ( settings%avg_pixels ) then
+ call average(settings, idate, itime, xpoints, ypoints, zpoint1, zpoint2, vmr_out, verr_out,&
+ vapri_out, cpri, cakpri, cak_out, cdryair, vdryair_out, nretr, ncoord, nlayer)
+ endif
+
+ ! write output data
+ ! -----------------
+
+ ! adjust itime
+ ! needed so that with flexpart rounding to lsynctime all retrievals are still for current day
+ do nm = 1, nretr
+ if ( itime(nm).gt.(235959-lsynctime*100/60) ) then
+ itime(nm) = 235950-lsynctime*100/60
+ endif
+ end do
+
+ ! write command file
+ call prep_command(settings,jd)
+
+ ! write outgrid file
+ call prep_outgrid(settings,jd)
+
+ ! write ageclasses file
+ call prep_ageclass(settings,jd)
+
+ ! write pathnames file
+ call prep_pathnames(settings,jd)
+
+ ! units of output data: dryair, cdryair, cpri, vmr
+ units(1) = 'none'
+ units(2) = 'none'
+ units(3) = 'ppbv'
+ units(4) = 'ppbv'
+
+ ! write releases data for flexpart
+ call write_releases(settings,nretr,nlayer,ncoord,xpoints,ypoints,zpoint1,zpoint2,&
+ idate,itime,cak_out,vdryair_out,specnum,units)
+
+ ! write retrieval data for flexinvert
+ call write_retrieval(settings,nretr,ncoord,xpoints,ypoints,idate,itime,&
+ cpri,cakpri,vmr_out,verr_out,cdryair,units)
+
+ ! copy standard input files to options folder
+ write(aspec,fmt='(I3.3)') specnum
+ call system('mkdir -p '//trim(settings%path_options)//adate//'/options/SPECIES/')
+ filename = trim(settings%path_flexpart)//'options/SPECIES/SPECIES_'//aspec
+ call system('cp '//trim(filename)//' '//trim(settings%path_options)//adate//'/options/SPECIES/')
+ call system('cp '//trim(settings%path_flexpart)//'options/*.dat'//' '//trim(settings%path_options)//adate//'/options/')
+ call system('cp '//trim(settings%path_flexpart)//'options/*.t'//' '//trim(settings%path_options)//adate//'/options/')
+
+ ! no retrievals on this day
+10 continue
+
+ ! prepare for next day
+ ! --------------------
+
+ if ( allocated(xpoints) ) deallocate(xpoints)
+ if ( allocated(ypoints) ) deallocate(ypoints)
+ if ( allocated(zpoint1) ) deallocate(zpoint1)
+ if ( allocated(zpoint2) ) deallocate(zpoint2)
+ if ( allocated(idate) ) deallocate(idate)
+ if ( allocated(itime) ) deallocate(itime)
+ if ( allocated(cak_out) ) deallocate(cak_out)
+ if ( allocated(vapri_out) ) deallocate(vapri_out)
+ if ( allocated(vdryair_out) ) deallocate(vdryair_out)
+ if ( allocated(vmr_out) ) deallocate(vmr_out)
+ if ( allocated(verr_out) ) deallocate(verr_out)
+ if ( allocated(cpri) ) deallocate(cpri)
+ if ( allocated(cakpri) ) deallocate(cakpri)
+ if ( allocated(cdryair) ) deallocate(cdryair)
+
+ ! iterate over days
+ jd = jd + 1d0
+
+ end do read_loop
+
+ if ( allocated(filelist) ) deallocate(filelist)
+ if ( allocated(filereadlist) ) deallocate(filereadlist)
+
+
+end subroutine get_bremen
+
diff --git a/prep_satellite/get_oco2.f90 b/prep_satellite/get_oco2.f90
new file mode 100644
index 0000000..e206ef5
--- /dev/null
+++ b/prep_satellite/get_oco2.f90
@@ -0,0 +1,465 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: get_oco2
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2022, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> get_oco2
+!!
+!! Purpose: Reads observations and auxilliary data from the specified satellite and
+!! and writes the output into files that can be directly used by FLEXPART
+!! and, for inversions, by FLEXINVERT
+!!
+!! Note: Variables with vertical dimension are ordered from TOA to the surface
+!! Retrieval made at pressure levels (interface of layers)
+!!
+!! Interface:
+!!
+!! Inputs
+!! settings - settings data structure
+!!
+!! Outputs
+!!
+!! Externals
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine get_oco2(settings)
+
+ use mod_settings
+ use mod_var
+ use mod_dates
+ use mod_save
+ use netcdf
+
+ implicit none
+
+ type (settings_t), intent(in) :: settings
+
+ character(max_name_len), dimension(:), allocatable :: filelist, filereadlist
+ character(max_name_len) :: line, filename, string, grpname
+ character(len=8) :: adate, strtmp
+ character(len=6) :: atime
+ character(len=3) :: aspec
+ character(len=6), dimension(4) :: units
+ integer :: i, ierr, n, nf, nl, ln, nm, np, nt
+ integer :: nfiles, nread, nretr
+ real(kind=8) :: jdatei, jdatef, jd, jdateref, jdmeas
+ integer :: jjjjmmdd, jjmmdd, hhmiss
+ integer :: hh, mi, ss
+ integer, parameter :: refdate = 19700101
+ integer, parameter :: lsynctime = 600
+ integer :: ntime, nmeas, nlevel, ncoord
+ real(kind=8), dimension(:), allocatable :: time
+ real, dimension(:,:), allocatable :: lat_bnds, lon_bnds
+ real, dimension(:), allocatable :: vmr, verr, landfrac, qa
+ real, dimension(:,:), allocatable :: pres, vapri, vdryair, cak
+ real, dimension(:,:), allocatable :: xpoints, ypoints
+ real, dimension(:,:), allocatable :: zpoint1, zpoint2
+ real, dimension(:,:), allocatable :: cak_out, vapri_out, vdryair_out
+ real, dimension(:), allocatable :: vmr_out, verr_out
+ real, dimension(:), allocatable :: cpri, cakpri, cdryair
+ integer, dimension(:), allocatable :: idate, itime, oper_mode
+ integer :: specnum, nchar
+ integer :: ncid, grpid, dimid, varid
+ real :: nest_llx, nest_lly, nest_urx, nest_ury
+ real :: llx, lly, urx, ury
+
+ ! get species number
+ ! ------------------
+
+ open(100,file=trim(settings%path_flexpart)//'options/SPECIES/spec_overview',status='old',action='read',iostat=ierr)
+ nchar = len_trim(settings%species)
+ do while ( ierr.eq.0 )
+ read (100, fmt='(A)', iostat=ierr) line
+ if ( line(len_trim(line)-nchar+1:len_trim(line)) == trim(settings%species) ) ierr = 1
+ end do
+ read(line(9:11),*) specnum
+ write(logid,*) 'species: ',settings%species
+ write(logid,*) 'specnum: ',specnum
+ write(logid,*) 'qa cutoff: ',settings%qa_cutoff
+ close(100)
+
+ ! define domains
+ ! --------------------
+
+ llx = settings%outlonleft
+ lly = settings%outlatlower
+ urx = llx + settings%numxgrid*settings%dxout
+ ury = lly + settings%numygrid*settings%dyout
+
+ if ( settings%lnested.eq.1 ) then
+ nest_llx = settings%outlonnest
+ nest_lly = settings%outlatnest
+ nest_urx = nest_llx + settings%numxnest*settings%dxoutnest
+ nest_ury = nest_lly + settings%numynest*settings%dyoutnest
+ endif
+ print*, 'llx,lly,urx,ury = ',llx,lly,urx,ury
+ if (settings%lnested.eq.1) print*, 'nest_llx,nest_lly,nest_urx,nest_ury = ',nest_llx,nest_lly,nest_urx,nest_ury
+
+ ! list satellite files
+ ! ----------------------
+
+ call system('find '//trim(settings%path_obs)//' -type f | grep '//trim(settings%suffix)//&
+ ' | wc -l > '//trim(settings%path_obsout)//'obsfiles.txt')
+ call system('find '//trim(settings%path_obs)//' -type f | grep '//trim(settings%suffix)//&
+ ' >> '//trim(settings%path_obsout)//'obsfiles.txt')
+
+ open(100,file=trim(settings%path_obsout)//'obsfiles.txt',action='read',status='old',iostat=ierr)
+ if ( ierr.ne. 0 ) then
+ write(logid,*) 'ERROR: cannot open obsfiles.txt'
+ stop
+ endif
+ read(100,*,iostat=ierr) nfiles
+ allocate ( filelist(nfiles), stat = ierr )
+ allocate ( filereadlist(nfiles), stat = ierr )
+ do nf = 1, nfiles
+ read(100,fmt='(A)',iostat=ierr) filelist(nf)
+ if (ierr.ne.0) exit
+ end do
+ close(100)
+
+ ! loop over days
+ ! --------------
+
+ jdateref = juldate(refdate, 0)
+ jdatei = juldate(settings%datei, 0)
+ jdatef = juldate(settings%datef, 0)
+ jd = jdatei
+
+ print*, settings%datei, settings%datef
+
+ read_loop: do
+
+ if ( jd.gt.jdatef ) exit read_loop
+
+ ! search files for current date
+ call caldate(jd, jjjjmmdd, hhmiss)
+ write(strtmp,fmt='(I8)') jjjjmmdd
+ adate = strtmp(3:8)
+ write(logid,*) 'current day: ',trim(adate)
+ nread = 0
+ do n = 1, nfiles
+ do i = 1, len_trim(filelist(n))
+ if ( filelist(n)(i:(i+5)).eq.trim(adate) ) then
+ nread = nread + 1
+ filereadlist(nread) = filelist(n)
+ exit
+ endif
+ end do
+ end do
+ write(logid,*) 'number of files for current day: ',nread
+ if ( nread.eq.0 ) then
+ jd = jd + 1d0
+ cycle read_loop
+ endif
+ adate = strtmp
+
+ ! loop over files
+ ! ---------------
+
+ do n = 1, nread
+
+ ! open file
+ write(logid,*) 'reading file: ',filereadlist(n)
+ call check( nf90_open(trim(filereadlist(n)),nf90_NOWRITE,ncid) )
+
+ ! dimension variables
+ call check( nf90_inq_dimid(ncid,trim(settings%nmeas_name),dimid) )
+ call check( nf90_inquire_dimension(ncid,dimid,len=nmeas) )
+ write(logid,*) 'number of soundings: ',nmeas
+ call check( nf90_inq_dimid(ncid,trim(settings%ncoord_name),dimid) )
+ call check( nf90_inquire_dimension(ncid,dimid,len=ncoord) )
+ write(logid,*) 'number of geocoordinates: ',ncoord
+ call check( nf90_inq_dimid(ncid,trim(settings%nlevel_name),dimid) )
+ call check( nf90_inquire_dimension(ncid,dimid,len=nlevel) )
+ write(logid,*) 'number of vertical levels: ',nlevel
+
+ ! geolocation variables
+ allocate( lat_bnds(ncoord,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate lat_bnds'
+ call check( nf90_inq_varid(ncid,trim(settings%lat_name),varid) )
+ call check( nf90_get_var(ncid,varid,lat_bnds) )
+ allocate( lon_bnds(ncoord,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate lon_bnds'
+ call check( nf90_inq_varid(ncid,trim(settings%lon_name),varid) )
+ call check( nf90_get_var(ncid,varid,lon_bnds) )
+
+ ! sounding variables
+ allocate(oper_mode(nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate oper_mode'
+ string = settings%oper_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_ncid(ncid,trim(grpname),grpid) )
+ call check( nf90_inq_varid(grpid,trim(string),varid) )
+ call check( nf90_get_var(grpid,varid,oper_mode) )
+ print*, 'read oper mode'
+ allocate( landfrac(nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate landfrac'
+ string = settings%landfrac_name
+ call split(string,'/',grpname)
+ print*, 'grpname = ',grpname
+ print*, 'string = ',string
+ call check( nf90_inq_ncid(ncid,trim(grpname),grpid) )
+ print*, 'grpid = ',grpid
+ call check( nf90_inq_varid(grpid,trim(string),varid) )
+ print*, 'varid = ',varid
+ call check( nf90_get_var(grpid,varid,landfrac) )
+ print*, 'read land fraction'
+
+ ! product variables
+ allocate( time(nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate time'
+ call check( nf90_inq_varid(ncid,trim(settings%time_name),varid) )
+ call check( nf90_get_var(ncid,varid,time) )
+ allocate( pres(nlevel,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate pres'
+ call check( nf90_inq_varid(ncid,trim(settings%pdel_name),varid) )
+ call check( nf90_get_var(ncid,varid,pres) )
+ ! convert hPa -> Pa for consistency with flexpart
+ pres = pres*100.
+ allocate( qa(nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate qa'
+ call check( nf90_inq_varid(ncid,trim(settings%qa_name),varid) )
+ call check( nf90_get_var(ncid,varid,qa) )
+ allocate( vmr(nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vmr'
+ call check( nf90_inq_varid(ncid,trim(settings%vmr_name),varid) )
+ call check( nf90_get_var(ncid,varid,vmr) )
+ allocate( verr(nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate verr'
+ call check( nf90_inq_varid(ncid,trim(settings%verr_name),varid) )
+ call check( nf90_get_var(ncid,varid,verr) )
+ ! multiply uncertainty by factor of 2 according to documentation
+ verr = verr*2.
+ allocate( cak(nlevel,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate cak'
+ call check( nf90_inq_varid(ncid,trim(settings%ak_name),varid) )
+ call check( nf90_get_var(ncid,varid,cak) )
+ allocate( vapri(nlevel,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vapri'
+ call check( nf90_inq_varid(ncid,trim(settings%apri_name),varid) )
+ call check( nf90_get_var(ncid,varid,vapri) )
+ allocate( vdryair(nlevel,nmeas), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vdryair'
+ call check( nf90_inq_varid(ncid,trim(settings%dryair_name),varid) )
+ call check( nf90_get_var(ncid,varid,vdryair) )
+
+ call check( nf90_close(ncid))
+
+ ! select retrievals and extract needed info
+ if( n.eq.1 ) then
+ allocate( xpoints(maxretr,ncoord) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate xpoints'
+ allocate( ypoints(maxretr,ncoord) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate ypoints'
+ allocate( zpoint1(maxretr,nlevel) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate zpoint1'
+ allocate( zpoint2(maxretr,nlevel) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate zpoint2'
+ allocate( idate(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate idate'
+ allocate( itime(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate itime'
+ allocate( cak_out(maxretr,nlevel) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate cak_out'
+ allocate( vapri_out(maxretr,nlevel) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vapri_out'
+ allocate( vdryair_out(maxretr,nlevel) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vdryair_out'
+ allocate( vmr_out(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vmr_out'
+ allocate( verr_out(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate verr_out'
+ nretr = 0
+
+ ! checking
+ print*, 'range(landfrac) = ',minval(landfrac),maxval(landfrac)
+ print*, 'range(qa) = ',minval(qa),maxval(qa)
+ print*, 'range(vmr) = ',minval(vmr),maxval(vmr)
+ print*, 'range(verr) = ',minval(verr),maxval(verr)
+
+ endif
+ do nm = 1, nmeas
+ ! exclude retrievals from certain operation mode
+ if ( (oper_mode(nm).ne.settings%opmode_sel).and.(settings%opmode_sel.ge.0) ) cycle
+ ! exclude retrievals above quality cutoff
+ if ( qa(nm).gt.settings%qa_cutoff ) cycle
+ ! if landonly exclude pixels with less than 50% land
+ if ( settings%landonly.and.landfrac(nm).lt.50. ) cycle
+ if ( settings%lnested.eq.1 ) then
+ ! if nested domain exclude pixels outside
+ if ( any(lon_bnds(:,nm).lt.nest_llx).or. &
+ any(lon_bnds(:,nm).gt.nest_urx).or. &
+ any(lat_bnds(:,nm).lt.nest_lly).or. &
+ any(lat_bnds(:,nm).gt.nest_ury) ) cycle
+ else
+ ! if not nested exclude pixels outside global domain
+ if ( any(lon_bnds(:,nm).lt.llx).or. &
+ any(lon_bnds(:,nm).gt.urx).or. &
+ any(lat_bnds(:,nm).lt.lly).or. &
+ any(lat_bnds(:,nm).gt.ury) ) cycle
+ endif
+ ! timestamp is seconds since ref date
+ jdmeas = time(nm)/3600d0/24d0 + jdateref
+ ! exclude retrievals if not for current day
+ if ( floor(jdmeas).ne.jd ) cycle
+ call caldate(jdmeas, jjjjmmdd, hhmiss)
+ nretr = nretr + 1
+ idate(nretr) = jjjjmmdd
+ itime(nretr) = hhmiss
+ ! corners ordered anticlockwise from lower left
+ xpoints(nretr,:) = lon_bnds(:,nm)
+ ypoints(nretr,:) = lat_bnds(:,nm)
+ ! pressure levels
+ ! ordered from TOA to surface so reverse order for flexpart
+ do nl = 1, nlevel
+ ln = nlevel - nl + 1
+ zpoint1(nretr,ln) = pres(nl,nm)
+ zpoint2(nretr,ln) = pres(nl,nm)
+ cak_out(nretr,ln) = cak(nl,nm)
+ vapri_out(nretr,ln) = vapri(nl,nm)
+ vdryair_out(nretr,ln) = vdryair(nl,nm)
+ end do
+ vmr_out(nretr) = vmr(nm)
+ verr_out(nretr) = verr(nm)
+ end do
+
+ write(logid,*) 'number of retrievals: ',nretr
+
+ if ( allocated(lat_bnds) ) deallocate(lat_bnds)
+ if ( allocated(lon_bnds) ) deallocate(lon_bnds)
+ if ( allocated(vapri) ) deallocate(vapri)
+ if ( allocated(vdryair) ) deallocate(vdryair)
+ if ( allocated(cak) ) deallocate(cak)
+ if ( allocated(time) ) deallocate(time)
+ if ( allocated(pres) ) deallocate(pres)
+ if ( allocated(qa) ) deallocate(qa)
+ if ( allocated(vmr) ) deallocate(vmr)
+ if ( allocated(verr) ) deallocate(verr)
+ if ( allocated(landfrac) ) deallocate(landfrac)
+ if ( allocated(oper_mode) ) deallocate(oper_mode)
+
+ end do ! nread
+
+ if ( nretr.eq.0 ) go to 10
+
+ ! calculate column prior (units ppbv)
+ allocate( cpri(nretr), stat=ierr )
+ do nm = 1, nretr
+ cpri(nm) = dot_product(vapri_out(nm,:), vdryair_out(nm,:))
+ end do
+
+ !! test
+ print*, 'vdryair_out(1:10,:) = ',vdryair_out(1:10,:)
+
+ ! calculate column prior convolved with averaging kernel (units ppbv)
+ allocate( cakpri(nretr), stat=ierr )
+ do nm = 1, nretr
+ do nl = 1, nlevel
+ cakpri(nm) = cakpri(nm) + vdryair_out(nm,nl)*vapri_out(nm,nl)*cak_out(nm,nl)
+ end do
+ end do
+
+ ! column dry-air not needed but only as dummy variable
+ allocate( cdryair(nretr) )
+ cdryair(:) = 1.
+
+ ! average pixels
+ ! --------------
+
+ if ( settings%avg_pixels ) then
+ call average(settings, idate, itime, xpoints, ypoints, zpoint1, zpoint2, vmr_out, verr_out,&
+ vapri_out, cpri, cakpri, cak_out, cdryair, vdryair_out, nretr, ncoord, nlevel)
+ endif
+
+ ! write output data
+ ! -----------------
+
+ ! adjust itime
+ ! needed so that with flexpart rounding to lsynctime all retrievals are still for current day
+ do nm = 1, nretr
+ if ( itime(nm).gt.(235959-lsynctime*100/60) ) then
+ itime(nm) = 235950-lsynctime*100/60
+ endif
+ end do
+
+ ! write command file
+ call prep_command(settings,jd)
+
+ ! write outgrid file
+ call prep_outgrid(settings,jd)
+
+ ! write ageclasses file
+ call prep_ageclass(settings,jd)
+
+ ! write pathnames file
+ call prep_pathnames(settings,jd)
+
+ ! units of output data: dryair, cdryair, cpri, vmr
+ units(1) = 'none'
+ units(2) = 'none'
+ units(3) = 'ppmv'
+ units(4) = 'ppmv'
+
+ ! write releases data for flexpart
+ call write_releases(settings,nretr,nlevel,ncoord,xpoints,ypoints,zpoint1,zpoint2,&
+ idate,itime,cak_out,vdryair_out,specnum,units)
+
+ ! write retrieval data for flexinvert
+ call write_retrieval(settings,nretr,ncoord,xpoints,ypoints,idate,itime,&
+ cpri,cakpri,vmr_out,verr_out,cdryair,units)
+
+ ! copy standard input files to options folder
+ write(aspec,fmt='(I3.3)') specnum
+ call system('mkdir -p '//trim(settings%path_options)//adate//'/options/SPECIES/')
+ filename = trim(settings%path_flexpart)//'options/SPECIES/SPECIES_'//aspec
+ call system('cp '//trim(filename)//' '//trim(settings%path_options)//adate//'/options/SPECIES/')
+ call system('cp '//trim(settings%path_flexpart)//'options/*.dat'//' '//trim(settings%path_options)//adate//'/options/')
+ call system('cp '//trim(settings%path_flexpart)//'options/*.t'//' '//trim(settings%path_options)//adate//'/options/')
+
+ ! no retrievals on this day
+10 continue
+
+ ! prepare for next day
+ ! --------------------
+
+ if ( allocated(xpoints) ) deallocate(xpoints)
+ if ( allocated(ypoints) ) deallocate(ypoints)
+ if ( allocated(zpoint1) ) deallocate(zpoint1)
+ if ( allocated(zpoint2) ) deallocate(zpoint2)
+ if ( allocated(idate) ) deallocate(idate)
+ if ( allocated(itime) ) deallocate(itime)
+ if ( allocated(cak_out) ) deallocate(cak_out)
+ if ( allocated(vapri_out) ) deallocate(vapri_out)
+ if ( allocated(vdryair_out) ) deallocate(vdryair_out)
+ if ( allocated(vmr_out) ) deallocate(vmr_out)
+ if ( allocated(verr_out) ) deallocate(verr_out)
+ if ( allocated(cpri) ) deallocate(cpri)
+ if ( allocated(cakpri) ) deallocate(cakpri)
+ if ( allocated(cdryair) ) deallocate(cdryair)
+
+ ! iterate over days
+ jd = jd + 1d0
+
+ end do read_loop
+
+ if ( allocated(filelist) ) deallocate(filelist)
+ if ( allocated(filereadlist) ) deallocate(filereadlist)
+
+
+end subroutine get_oco2
+
diff --git a/prep_satellite/get_tropomi.f90 b/prep_satellite/get_tropomi.f90
new file mode 100644
index 0000000..bf8477d
--- /dev/null
+++ b/prep_satellite/get_tropomi.f90
@@ -0,0 +1,552 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: get_tropomi
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2022, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> get_tropomi
+!!
+!! Purpose: Reads observations and auxilliary data from the specified satellite and
+!! and writes the output into files that can be directly used by FLEXPART
+!! and, for inversions, by FLEXINVERT
+!!
+!! Interface:
+!!
+!! Inputs
+!! settings - settings data structure
+!!
+!! Outputs
+!!
+!! Externals
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine get_tropomi(settings)
+
+ use mod_settings
+ use mod_var
+ use mod_dates
+ use mod_save
+ use netcdf
+
+ implicit none
+
+ type (settings_t), intent(in) :: settings
+
+ character(max_name_len), dimension(:), allocatable :: filelist, filereadlist
+ character(max_name_len) :: line, string, grpname, filename
+ character(max_name_len) :: suppdata_grpname, geodata_grpname, indata_grpname, details_grpname
+ character(len=8) :: adate
+ character(len=8) :: surfclass_bin
+ character(len=6) :: atime
+ character(len=3) :: aspec
+ character(len=2) :: amon, aday
+ character(len=6), dimension(4) :: units
+ integer :: i, ierr, n, nf, nl, nm, np, nt, nbits, iswater
+ integer :: nfiles, nread, nretr
+ real(kind=8) :: jdatei, jdatef, jd, ndays, jref, jdmeas
+ integer :: jjjjmmdd, hhmiss, mm, dd, hh, mi, ss
+ integer, parameter :: refdate = 20100101
+ integer, parameter :: reftime = 0
+ integer, parameter :: lsynctime = 600
+ integer :: ntime, nmeas, npixel, nlevel, ncoord, nlayer
+ real, dimension(:,:,:,:), allocatable :: lat_bnds, lon_bnds
+ real, dimension(:,:,:), allocatable :: psurf, pdel, vmr, verr, qa
+ real, dimension(:,:,:,:), allocatable :: vapri, vdryair, cak
+ real, dimension(:,:), allocatable :: xpoints, ypoints
+ real, dimension(:,:), allocatable :: zpoint1, zpoint2
+ real, dimension(:,:), allocatable :: cak_out, vapri_out, vdryair_out
+ real, dimension(:), allocatable :: vmr_out, verr_out
+ real, dimension(:), allocatable :: cpri, cakpri, cdryair
+ integer, dimension(:), allocatable :: idate, itime, time
+ integer, dimension(:,:), allocatable :: timedel
+ integer, dimension(:,:,:), allocatable :: surfclass
+ integer :: specnum, nchar
+ integer :: ncid, grpid, supp_grpid, geo_grpid, in_grpid, det_grpid
+ integer :: dimid, varid
+ real :: nest_llx, nest_lly, nest_urx, nest_ury
+ real :: llx, lly, urx, ury
+ real :: sclfact, offset
+ real, parameter :: bignum=huge(0.)
+
+ write(logid,*) 'largest number that can be handled (used to define NA) = ',bignum
+
+ ! get species number
+ ! ------------------
+
+ open(100,file=trim(settings%path_flexpart)//'options/SPECIES/spec_overview',status='old',action='read',iostat=ierr)
+ nchar = len_trim(settings%species)
+ do while ( ierr.eq.0 )
+ read (100, fmt='(A)', iostat=ierr) line
+ if ( line(len_trim(line)-nchar+1:len_trim(line)) == trim(settings%species) ) ierr = 1
+ end do
+ read(line(9:11),*) specnum
+ write(logid,*) 'species: ',settings%species
+ write(logid,*) 'specnum: ',specnum
+ close(100)
+
+ ! define domains
+ ! --------------
+
+ llx = settings%outlonleft
+ lly = settings%outlatlower
+ urx = llx + settings%numxgrid*settings%dxout
+ ury = lly + settings%numygrid*settings%dyout
+
+ if ( settings%lnested.eq.1 ) then
+ nest_llx = settings%outlonnest
+ nest_lly = settings%outlatnest
+ nest_urx = nest_llx + settings%numxnest*settings%dxoutnest
+ nest_ury = nest_lly + settings%numynest*settings%dyoutnest
+ endif
+
+ ! list satellite files
+ ! ----------------------
+
+ call system('find '//trim(settings%path_obs)//' -type f | grep '//trim(settings%suffix) &
+ //' | wc -l > '//trim(settings%path_obsout)//'obsfiles.txt',ierr)
+ if ( ierr.eq.0 ) then
+ call system('find '//trim(settings%path_obs)//' -type f | grep '//trim(settings%suffix) &
+ //' >> '//trim(settings%path_obsout)//'obsfiles.txt')
+ else
+ write(logid,*) 'ERROR: cannot find observation files'
+ stop
+ endif
+
+ open(100,file=trim(settings%path_obsout)//'obsfiles.txt',action='read',status='old',iostat=ierr)
+ if ( ierr.ne. 0 ) then
+ write(logid,*) 'ERROR: cannot open obsfiles.txt'
+ stop
+ endif
+ read(100,*,iostat=ierr) nfiles
+ allocate ( filelist(nfiles), stat = ierr )
+ allocate ( filereadlist(nfiles), stat = ierr )
+ do nf = 1, nfiles
+ read(100,fmt='(A)',iostat=ierr) filelist(nf)
+ if (ierr.ne.0) exit
+ end do
+ close(100)
+
+ ! loop over days
+ ! --------------
+
+ jdatei = juldate(settings%datei, 0)
+ jdatef = juldate(settings%datef, 0)
+ jd = jdatei
+
+ read_loop: do
+
+ if ( jd.gt.jdatef ) exit read_loop
+
+ ! search files for current date
+ call caldate(jd, jjjjmmdd, hhmiss)
+ write(adate,fmt='(I8.8)') jjjjmmdd
+ write(logid,*) 'current day: ',adate
+ mm = jjjjmmdd/100 - (jjjjmmdd/10000)*100
+ dd = jjjjmmdd - (jjjjmmdd/100)*100
+ write(amon,fmt='(I2.2)') mm
+ write(aday,fmt='(I2.2)') dd
+ nread = 0
+ do n = 1, nfiles
+ do i = 1, len_trim(filelist(n))-18
+ if ( filelist(n)(i:(i+7)).eq.adate ) then
+ nread = nread + 1
+ filereadlist(nread) = filelist(n)
+ exit
+ endif
+ end do
+ end do
+ write(logid,*) 'number of files for current day: ',nread
+ if ( nread.eq.0 ) then
+ jd = jd + 1d0
+ cycle read_loop
+ endif
+
+ ! loop over files
+ ! ---------------
+
+ do n = 1, nread
+
+ ! open file
+ write(logid,*) 'reading file: ',filereadlist(n)
+ call check( nf90_open(trim(filereadlist(n)),nf90_NOWRITE,ncid) )
+
+ ! dimension variables
+ string = settings%time_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_ncid(ncid,trim(grpname),grpid) )
+ call check( nf90_inq_dimid(grpid,trim(string),dimid) )
+ call check( nf90_inquire_dimension(grpid,dimid,len=ntime) )
+ write(logid,*) 'number reference times: ',ntime
+ string = settings%nmeas_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_ncid(ncid,trim(grpname),grpid) )
+ call check( nf90_inq_dimid(grpid,trim(string),dimid) )
+ call check( nf90_inquire_dimension(grpid,dimid,len=nmeas) )
+ write(logid,*) 'number of scanlines: ',nmeas
+ string = settings%npixel_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_ncid(ncid,trim(grpname),grpid) )
+ call check( nf90_inq_dimid(grpid,trim(string),dimid) )
+ call check( nf90_inquire_dimension(grpid,dimid,len=npixel) )
+ write(logid,*) 'number of pixels: ',npixel
+ string = settings%ncoord_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_ncid(ncid,trim(grpname),grpid) )
+ call check( nf90_inq_dimid(grpid,trim(string),dimid) )
+ call check( nf90_inquire_dimension(grpid,dimid,len=ncoord) )
+ write(logid,*) 'number of geocoordinates: ',ncoord
+ string = settings%nlevel_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_ncid(ncid,trim(grpname),grpid) )
+ call check( nf90_inq_dimid(grpid,trim(string),dimid) )
+ call check( nf90_inquire_dimension(grpid,dimid,len=nlevel) )
+ nlayer = nlevel - 1
+ write(logid,*) 'number of vertical layers: ',nlayer
+
+ ! geolocation variables
+ allocate( lat_bnds(ncoord,npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate lat_bnds'
+ allocate( lon_bnds(ncoord,npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate lon_bnds'
+ string = settings%lon_name
+ call split(string,'/',grpname)
+ call split(string,'/',suppdata_grpname)
+ call split(string,'/',geodata_grpname)
+ call check( nf90_inq_ncid(ncid,trim(grpname),grpid) )
+ call check( nf90_inq_ncid(grpid,trim(suppdata_grpname),supp_grpid) )
+ call check( nf90_inq_ncid(supp_grpid,trim(geodata_grpname),geo_grpid) )
+ call check( nf90_inq_varid(geo_grpid,trim(string),varid) )
+ call check( nf90_get_var(geo_grpid,varid,lon_bnds) )
+ write(logid,*) 'read longitude'
+ string = settings%lat_name
+ call split(string,'/',grpname)
+ call split(string,'/',suppdata_grpname)
+ call split(string,'/',geodata_grpname)
+ call check( nf90_inq_varid(geo_grpid,trim(string),varid) )
+ call check( nf90_get_var(geo_grpid,varid,lat_bnds) )
+ write(logid,*) 'read latitude'
+
+ ! input data variables
+ allocate( psurf(npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate psurf'
+ allocate( pdel(npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate pdel'
+ allocate( surfclass(npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate surfclass'
+ allocate( vapri(nlayer,npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vapri'
+ allocate( vdryair(nlayer,npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vdryair'
+ string = settings%psurf_name
+ call split(string,'/',grpname)
+ call split(string,'/',suppdata_grpname)
+ call split(string,'/',indata_grpname)
+ call check( nf90_inq_ncid(ncid,trim(grpname),grpid) )
+ call check( nf90_inq_ncid(grpid,trim(suppdata_grpname),supp_grpid) )
+ call check( nf90_inq_ncid(supp_grpid,trim(indata_grpname),in_grpid) )
+ call check( nf90_inq_varid(in_grpid,trim(string),varid) )
+ call check( nf90_get_var(in_grpid,varid,psurf) )
+ write(logid,*) 'read surface pressure'
+ string = settings%pdel_name
+ call split(string,'/',grpname)
+ call split(string,'/',suppdata_grpname)
+ call split(string,'/',indata_grpname)
+ call check( nf90_inq_varid(in_grpid,trim(string),varid) )
+ call check( nf90_get_var(in_grpid,varid,pdel) )
+ write(logid,*) 'read pressure coordinates'
+ string = settings%apri_name
+ call split(string,'/',grpname)
+ call split(string,'/',suppdata_grpname)
+ call split(string,'/',indata_grpname)
+ call check( nf90_inq_varid(in_grpid,trim(string),varid) )
+ call check( nf90_get_var(in_grpid,varid,vapri) )
+ write(logid,*) 'read prior vertical profile'
+ string = settings%dryair_name
+ call split(string,'/',grpname)
+ call split(string,'/',suppdata_grpname)
+ call split(string,'/',indata_grpname)
+ call check( nf90_inq_varid(in_grpid,trim(string),varid) )
+ call check( nf90_get_var(in_grpid,varid,vdryair) )
+ write(logid,*) 'read dry air profile'
+ string = settings%surfclass_name
+ call split(string,'/',grpname)
+ call split(string,'/',suppdata_grpname)
+ call split(string,'/',indata_grpname)
+ call check( nf90_inq_varid(in_grpid,trim(string),varid) )
+ call check( nf90_get_var(in_grpid,varid,surfclass) )
+ write(logid,*) 'read surface class'
+
+ ! detailed results variables
+ allocate( cak(nlayer,npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate cak'
+ string = settings%ak_name
+ call split(string,'/',grpname)
+ call split(string,'/',suppdata_grpname)
+ call split(string,'/',details_grpname)
+ call check( nf90_inq_ncid(supp_grpid,trim(details_grpname),det_grpid) )
+ call check( nf90_inq_varid(det_grpid,trim(string),varid) )
+ call check( nf90_get_var(det_grpid,varid,cak) )
+ write(logid,*) 'read column averaging kernel'
+
+ ! product variables
+ allocate( qa(npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate qa'
+ allocate( vmr(npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vmr'
+ allocate( verr(npixel,nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate verr'
+ allocate( timedel(nmeas,ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate timedel'
+ allocate( time(ntime), stat=ierr )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate time'
+ string = settings%qa_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_ncid(ncid,trim(grpname),grpid) )
+ call check( nf90_inq_varid(grpid,trim(string),varid) )
+ call check( nf90_get_var(grpid,varid,qa) )
+ call check( nf90_get_att(grpid,varid,'scale_factor',sclfact) )
+ call check( nf90_get_att(grpid,varid,'add_offset',offset) )
+ qa = qa*sclfact + offset
+
+ write(logid,*) 'read quality value'
+ string = settings%vmr_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_varid(grpid,trim(string),varid) )
+ call check( nf90_get_var(grpid,varid,vmr) )
+ write(logid,*) 'read total column mixing ratio'
+ string = settings%verr_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_varid(grpid,trim(string),varid) )
+ call check( nf90_get_var(grpid,varid,verr) )
+ write(logid,*) 'read total column error'
+ string = settings%tdel_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_varid(grpid,trim(string),varid) )
+ call check( nf90_get_var(grpid,varid,timedel) )
+ write(logid,*) 'read delta time'
+ string = settings%time_name
+ call split(string,'/',grpname)
+ call check( nf90_inq_varid(grpid,trim(string),varid) )
+ call check( nf90_get_var(grpid,varid,time) )
+ write(logid,*) 'reference time = ', time
+
+ call check( nf90_close(ncid))
+
+! print*, 'range(qa) = ',minval(qa),maxval(qa)
+
+ ! select retrievals and extract needed info
+ if( n.eq.1 ) then
+ allocate( xpoints(maxretr,ncoord) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate xpoints'
+ allocate( ypoints(maxretr,ncoord) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate ypoints'
+ allocate( zpoint1(maxretr,nlayer) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate zpoint1'
+ allocate( zpoint2(maxretr,nlayer) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate zpoint2'
+ allocate( idate(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate idate'
+ allocate( itime(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate itime'
+ allocate( cak_out(maxretr,nlayer) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate cak_out'
+ allocate( vapri_out(maxretr,nlayer) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vapri_out'
+ allocate( vdryair_out(maxretr,nlayer) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vdryair_out'
+ allocate( vmr_out(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate vmr_out'
+ allocate( verr_out(maxretr) )
+ if ( ierr.ne.0 ) write(logid,*) 'ERROR: cannot allocate verr_out'
+ cak_out(:,:)=0.
+ vapri_out(:,:)=0.
+ vmr_out(:)=0.
+ verr_out(:)=0.
+ nretr = 0
+ endif
+ do nt = 1, ntime
+ ndays = dble(time(nt))/3600d0/24d0
+ jref = juldate(refdate, reftime)
+ do nm = 1, nmeas
+ do np = 1, npixel
+ ! exclude retrievals below quality cutoff
+ if ( qa(np,nm,nt).lt.settings%qa_cutoff ) cycle
+ ! exclude retrievals with few degrees of freedom
+ if ( sum(cak(:,np,nm,nt)).lt.10. ) cycle
+ write(surfclass_bin, fmt='(B0)') surfclass(np,nm,nt)
+ nbits = len_trim(surfclass_bin)
+ read(surfclass_bin(nbits:nbits),*) iswater
+ ! if landonly exclude pixels over water
+ if ( settings%landonly.and.iswater.eq.1 ) cycle
+ if ( settings%lnested.eq.1 ) then
+ ! if nested domain exclude pixels outside
+ if ( any(lon_bnds(:,np,nm,nt).lt.nest_llx).or. &
+ any(lon_bnds(:,np,nm,nt).gt.nest_urx).or. &
+ any(lat_bnds(:,np,nm,nt).lt.nest_lly).or. &
+ any(lat_bnds(:,np,nm,nt).gt.nest_ury) ) cycle
+ else
+ ! if not nested exclude pixels outside global domain
+ if ( any(lon_bnds(:,np,nm,nt).lt.llx).or. &
+ any(lon_bnds(:,np,nm,nt).gt.urx).or. &
+ any(lat_bnds(:,np,nm,nt).lt.lly).or. &
+ any(lat_bnds(:,np,nm,nt).gt.ury) ) cycle
+ endif
+ jdmeas = jref+ndays+dble(timedel(nm,nt))/1000d0/3600d0/24d0
+ ! exclude retrievals if not for current day
+ if ( floor(jdmeas).ne.jd ) cycle
+ if ( vmr(np,nm,nt).ge.bignum ) cycle
+ call caldate(jdmeas, jjjjmmdd, hhmiss)
+ nretr = nretr + 1
+ idate(nretr) = jjjjmmdd
+ itime(nretr) = hhmiss
+ ! corners ordered anticlockwise from lower left
+ xpoints(nretr,:) = lon_bnds(:,np,nm,nt)
+ ypoints(nretr,:) = lat_bnds(:,np,nm,nt)
+ ! pressure levels are equipressure apart
+ zpoint1(nretr,1) = psurf(np,nm,nt)
+ zpoint2(nretr,1) = psurf(np,nm,nt) - pdel(np,nm,nt)
+ do nl = 2, nlayer
+ zpoint1(nretr,nl) = zpoint1(nretr,nl-1) - pdel(np,nm,nt)
+ zpoint2(nretr,nl) = zpoint2(nretr,nl-1) - pdel(np,nm,nt)
+ end do
+ cak_out(nretr,:) = cak(:,np,nm,nt)
+ vapri_out(nretr,:) = vapri(:,np,nm,nt)
+ vdryair_out(nretr,:) = vdryair(:,np,nm,nt)
+ vmr_out(nretr) = vmr(np,nm,nt)
+ ! uncertainties for XCH4 based on single sounding precision due to measurement noise ->
+ ! for overall uncertainty estimate multiply by factor 2 to reflect scatter of single sounding errors
+ verr_out(nretr) = 2.*verr(np,nm,nt)
+ end do ! npixel
+ end do ! nmeas
+ end do ! ntime
+
+ write(logid,*) 'number of retrievals: ',nretr
+
+ if ( allocated(lat_bnds) ) deallocate(lat_bnds)
+ if ( allocated(lon_bnds) ) deallocate(lon_bnds)
+ if ( allocated(psurf) ) deallocate(psurf)
+ if ( allocated(pdel) ) deallocate(pdel)
+ if ( allocated(vapri) ) deallocate(vapri)
+ if ( allocated(vdryair) ) deallocate(vdryair)
+ if ( allocated(cak) ) deallocate(cak)
+ if ( allocated(timedel) ) deallocate(timedel)
+ if ( allocated(time) ) deallocate(time)
+ if ( allocated(qa) ) deallocate(qa)
+ if ( allocated(vmr) ) deallocate(vmr)
+ if ( allocated(verr) ) deallocate(verr)
+ if ( allocated(surfclass) ) deallocate(surfclass)
+
+ end do ! nread
+
+ print*, 'itime(1), itime(nretr) = ',itime(1),itime(nretr)
+
+ ! calculate column prior (units mol/m2)
+ allocate( cpri(nretr), stat=ierr )
+ cpri = sum(vapri_out(1:nretr,:), dim=2)
+
+ ! calculate column prior convolved with averaging kernel (units mol/m2)
+ allocate( cakpri(nretr), stat=ierr )
+ do nm = 1, nretr
+ cakpri(nm) = dot_product(vapri_out(nm,:), cak_out(nm,:))
+ end do
+
+ ! calculate column dry air (units mol/m2)
+ allocate( cdryair(nretr), stat=ierr )
+ cdryair = sum(vdryair_out(1:nretr,:), dim=2)
+
+ ! average pixels
+ ! --------------
+
+ if ( settings%avg_pixels ) then
+ call average(settings, idate, itime, xpoints, ypoints, zpoint1, zpoint2, vmr_out, verr_out,&
+ vapri_out, cpri, cakpri, cak_out, cdryair, vdryair_out, nretr, ncoord, nlayer)
+ endif
+
+ ! write output data
+ ! -----------------
+
+ ! adjust itime
+ ! needed so that with flexpart rounding to lsynctime all retrievals are still for current day
+ do nm = 1, nretr
+ if ( itime(nm).gt.(235959-lsynctime*100/60) ) then
+ itime(nm) = 235950-lsynctime*100/60
+ endif
+ end do
+
+ ! write command file
+ call prep_command(settings,jd)
+
+ ! write outgrid file
+ call prep_outgrid(settings,jd)
+
+ ! write ageclasses file
+ call prep_ageclass(settings,jd)
+
+ ! write pathnames file
+ call prep_pathnames(settings,jd)
+
+ ! units of output data: dryair, cdryair, cpri, vmr
+ units(1) = 'mol/m2'
+ units(2) = 'mol/m2'
+ units(3) = 'mol/m2'
+ units(4) = 'ppbv'
+
+ ! write releases data for flexpart
+ call write_releases(settings,nretr,nlayer,ncoord,xpoints,ypoints,zpoint1,zpoint2,&
+ idate,itime,cak_out,vdryair_out,specnum,units)
+
+ ! write retrieval data for flexinvert
+ call write_retrieval(settings,nretr,ncoord,xpoints,ypoints,idate,itime,&
+ cpri,cakpri,vmr_out,verr_out,cdryair,units)
+
+ ! copy standard input files to options folder
+ write(aspec,fmt='(I3.3)') specnum
+ call system('mkdir -p '//trim(settings%path_options)//adate//'/options/SPECIES/')
+ filename = trim(settings%path_flexpart)//'options/SPECIES/SPECIES_'//aspec
+ call system('cp '//trim(filename)//' '//trim(settings%path_options)//adate//'/options/SPECIES/')
+ call system('cp '//trim(settings%path_flexpart)//'options/*.dat'//' '//trim(settings%path_options)//adate//'/options/')
+ call system('cp '//trim(settings%path_flexpart)//'options/*.t'//' '//trim(settings%path_options)//adate//'/options/')
+
+ ! prepare for next day
+ ! --------------------
+
+ if ( allocated(xpoints) ) deallocate(xpoints)
+ if ( allocated(ypoints) ) deallocate(ypoints)
+ if ( allocated(zpoint1) ) deallocate(zpoint1)
+ if ( allocated(zpoint2) ) deallocate(zpoint2)
+ if ( allocated(idate) ) deallocate(idate)
+ if ( allocated(itime) ) deallocate(itime)
+ if ( allocated(cak_out) ) deallocate(cak_out)
+ if ( allocated(vapri_out) ) deallocate(vapri_out)
+ if ( allocated(vdryair_out) ) deallocate(vdryair_out)
+ if ( allocated(vmr_out) ) deallocate(vmr_out)
+ if ( allocated(verr_out) ) deallocate(verr_out)
+ if ( allocated(cpri) ) deallocate(cpri)
+ if ( allocated(cakpri) ) deallocate(cakpri)
+ if ( allocated(cdryair) ) deallocate(cdryair)
+
+ ! iterate over days
+ jd = jd + 1d0
+
+ end do read_loop
+
+ if ( allocated(filelist) ) deallocate(filelist)
+ if ( allocated(filereadlist) ) deallocate(filereadlist)
+
+
+end subroutine get_tropomi
+
diff --git a/prep_satellite/gridarea.f90 b/prep_satellite/gridarea.f90
new file mode 100644
index 0000000..25714df
--- /dev/null
+++ b/prep_satellite/gridarea.f90
@@ -0,0 +1,64 @@
+!---------------------------------------------------------------------------------------
+! PREP_FLUXES: gridarea
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2017, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> gridarea
+!!
+!! Purpose: Calculates the area of a grid cell.
+!!
+!! Interface:
+!!
+!! Inputs
+!! ylat - latitude of grid centre
+!! dy - resolution in latitudinal direction
+!! dx - resolution in longitudinal direction
+!!
+!! Outputs
+!! area - area of grid cell
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine gridarea(ylat,dy,dx,area)
+
+ implicit none
+
+ real, intent(in) :: ylat,dy,dx
+ real, intent(out) :: area
+
+ real, parameter :: pi=3.14159265, rearth=6.371e6, pih=pi/180.
+ real :: ylata, ylatp, ylatm
+ real :: cosfact, cosfactp, cosfactm, hzone
+
+ ylata=ylat
+ ylatp=ylat+0.5*dy
+ ylatm=ylat-0.5*dy
+ if (ylatm.lt.0.and.ylatp.gt.0) then
+ hzone = rearth*pih
+ else
+ cosfact=COS(ylata*pih)*rearth
+ cosfactp=COS(ylatp*pih)*rearth
+ cosfactm=COS(ylatm*pih)*rearth
+ if(cosfactp.lt.cosfactm) then
+ hzone=SQRT(rearth**2-cosfactp**2)-SQRT(rearth**2-cosfactm**2)
+ else
+ hzone=SQRT(rearth**2-cosfactm**2)-SQRT(rearth**2-cosfactp**2)
+ endif
+ endif
+ area=2.*pi*rearth*hzone*dx/360.
+
+end subroutine gridarea
diff --git a/prep_satellite/main.f90 b/prep_satellite/main.f90
new file mode 100644
index 0000000..60685ff
--- /dev/null
+++ b/prep_satellite/main.f90
@@ -0,0 +1,86 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: main
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2022, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> main
+!!
+!! Purpose: Prepares the input files needed to run FLEXPART for satellite or other
+!! column measurements to give a total column source-receptor-relationship
+!!
+!! Prepares the following:
+!!
+!! COMMAND - flexpart settings
+!! OUTGRID - definition of flexpart output grid
+!! AGECLASS - definition of age of particles
+!! releases.nc - definition of all releases for all retrievals
+!! auxilliary.nc - supporting info (averageing kernel)
+!!
+!!
+!---------------------------------------------------------------------------------------
+
+program main
+
+ use mod_var
+ use mod_dates
+ use mod_settings
+
+ implicit none
+
+ ! set types
+ type (settings_t) :: settings
+
+ character(max_path_len) :: settings_file, logfile
+ integer :: ierr
+
+ ! initialization
+ ! --------------
+
+ call getarg(1,settings_file)
+ if (settings_file == '') then
+ stop 'ERROR: need to specify SETTINGS file'
+ endif
+
+ call getarg(2,logfile)
+ if (logfile == '') then
+ stop 'ERROR: need to specify logfile'
+ endif
+ open(logid,file=trim(logfile),status='replace',action='write',iostat=ierr)
+
+ ! read settings
+ call read_settings(settings_file, settings)
+
+ ! get satellite data
+ ! ------------------
+
+ if ( settings%satellite.eq.'tropomi' ) then
+ ! tropomi
+ call get_tropomi(settings)
+ else if ( settings%satellite.eq.'bremen' ) then
+ ! bremen retrieval for tropomi
+ call get_bremen(settings)
+ else if ( settings%satellite.eq.'oco2' ) then
+ call get_oco2(settings)
+ else
+ ! add other satellites here
+ write(logid,*) 'ERROR: unknown satellite type'
+ stop
+ endif
+
+
+end program
+
diff --git a/prep_satellite/makefile b/prep_satellite/makefile
new file mode 100644
index 0000000..9b0516c
--- /dev/null
+++ b/prep_satellite/makefile
@@ -0,0 +1,40 @@
+F90 = gfortran
+LIBPATH = /usr/lib/
+INCPATH = /usr/include/
+LNK = -o
+CMPL = -c
+LIBS = -lnetcdf -lnetcdff
+#FFLAGS = -O2 -m64 -mcmodel=medium -fconvert=little-endian -frecord-marker=4 -ffree-form
+FFLAGS = -O0 -g -m64 -fbounds-check -mcmodel=medium -fconvert=little-endian -frecord-marker=4 -ffree-form \
+ -fbacktrace
+LDFLAGS = $(FFLAGS) -L$(LIBPATH) -I$(INCPATH) $(LIBS)
+
+MAIN = prep_satellite
+
+SRCS = mod_var.f90 \
+ mod_dates.f90 \
+ mod_settings.f90 \
+ mod_save.f90 \
+ gridarea.f90 \
+ geodarea.f90 \
+ prep_command.f90 \
+ prep_outgrid.f90 \
+ prep_ageclass.f90 \
+ prep_pathnames.f90 \
+ average.f90 \
+ get_tropomi.f90 \
+ get_bremen.f90 \
+ get_oco2.f90 \
+ main.f90
+
+
+OBJECTS = $(SRCS:.f90=.o)
+$(MAIN): $(OBJECTS) $(MODULES)
+ $(F90) $(LNK) $(MAIN) $(OBJECTS) $(LIBS)
+%.o : %.f90
+ $(F90) $(LDFLAGS) $(CMPL) $< -o $@
+
+clean:
+ rm -f $(OBJECTS) $(MODULES)
+
+
diff --git a/prep_satellite/mod_dates.f90 b/prep_satellite/mod_dates.f90
new file mode 100644
index 0000000..dfe3afc
--- /dev/null
+++ b/prep_satellite/mod_dates.f90
@@ -0,0 +1,176 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: mod_dates
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2022, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> mod_dates
+!!
+!! Purpose: Module of date functions.
+!!
+!---------------------------------------------------------------------------------------
+
+module mod_dates
+
+ implicit none
+
+ contains
+
+ ! --------------------------------------------------
+ ! caldate
+ ! --------------------------------------------------
+ !> caldate
+ !!
+ !! Purpose: Converts a julian date number to date
+ !! and time format YYYYMMDD, HHMISS
+ !! according to the gregorian calender
+ !!
+ ! --------------------------------------------------
+
+ subroutine caldate(jdate, yyyymmdd, hhmiss)
+
+ real(kind=8), intent(in) :: jdate
+ integer, intent(out) :: yyyymmdd, hhmiss
+ integer :: yyyy, mm, dd, hh, mi, ss
+ integer :: julday, ja, jb, jc, jd, je, jalpha
+ integer, parameter :: igreg = 2299161
+
+ julday=int(jdate)
+ if(julday.ge.igreg) then
+ jalpha=int(((julday-1867216)-0.25)/36524.25)
+ ja=julday+1+jalpha-int(0.25*jalpha)
+ else
+ ja=julday
+ endif
+ jb=ja+1524
+ jc=int(6680.+((jb-2439870)-122.1)/365.25)
+ jd=365*jc+int(0.25*jc)
+ je=int((jb-jd)/30.6001)
+ dd=jb-jd-int(30.6001*je)
+ mm=je-1
+ if(mm.gt.12) mm=mm-12
+ yyyy=jc-4715
+ if(mm.gt.2) yyyy=yyyy-1
+ if(yyyy.le.0) yyyy=yyyy-1
+
+ yyyymmdd=10000*yyyy+100*mm+dd
+ hh=int(24.*(jdate-float(julday)))
+ mi=int(1440.*(jdate-float(julday))-60.*float(hh))
+ ss=nint(86400.*(jdate-float(julday))-3600.*float(hh))-60.*float(mi)
+ if(ss.eq.60) then ! 60 seconds = 1 minute
+ ss=0
+ mi=mi+1
+ endif
+ if(mi.eq.60) then
+ mi=0
+ hh=hh+1
+ endif
+ hhmiss=10000*hh+100*mi+ss
+
+ end subroutine caldate
+
+ ! --------------------------------------------------
+ ! julday
+ ! --------------------------------------------------
+ !> julday
+ !!
+ !! Purpose: Converts the date and time format
+ !! YYYYMMDD and HHMMSS to a julian date
+ !! number.
+ !!
+ ! --------------------------------------------------
+
+ real(kind=8) function juldate(yyyymmdd,hhmiss)
+
+ integer, intent(in) :: yyyymmdd,hhmiss
+ integer :: yyyy,mm,hh,dd,mi,ss
+ integer :: julday,jy,jm,ja
+ integer, parameter :: igreg=15+31*(10+12*1582)
+
+ yyyy=yyyymmdd/10000
+ mm=(yyyymmdd-10000*yyyy)/100
+ dd=yyyymmdd-10000*yyyy-100*mm
+ hh=hhmiss/10000
+ mi=(hhmiss-10000*hh)/100
+ ss=hhmiss-10000*hh-100*mi
+
+ if(yyyy.eq.0) print*, 'ERROR: there is no year zero'
+ if(yyyy.lt.0) yyyy=yyyy+1
+ if(mm.gt.2) then
+ jy=yyyy
+ jm=mm+1
+ else
+ jy=yyyy-1
+ jm=mm+13
+ endif
+ julday=int(365.25*jy)+int(30.6001*jm)+dd+1720995
+ if (dd+31*(mm+12*yyyy).ge.igreg) then
+ ja=int(0.01*jy)
+ julday=julday+2-ja+int(0.25*ja)
+ endif
+
+ juldate=dble(float(julday))+dble(float(hh)/24.)&
+ &+dble(float(mi)/1440.)+dble(float(ss)/86400.)
+
+ end function juldate
+
+ ! --------------------------------------------------
+ ! calceomday
+ ! --------------------------------------------------
+ !> calceomday
+ !!
+ !! Purpose: Calculates number of days in a given
+ !! year, month currently only considers
+ !! years after 1900.
+ !!
+ ! --------------------------------------------------
+
+ integer function calceomday(yyyymm)
+
+ integer, intent(in) :: yyyymm
+ integer :: yyyy,mm
+ integer, dimension(12) :: leapdays,days
+ integer :: eomday
+
+ leapdays=(/31,29,31,30,31,30,31,31,30,31,30,31/)
+ days=(/31,28,31,30,31,30,31,31,30,31,30,31/)
+
+ yyyy=floor(yyyymm/100.)
+ mm=yyyymm-yyyy*100
+
+ if((float(yyyy)/100.).eq.float(yyyy/100)) then
+ if((float(yyyy)/400.).eq.float(yyyy/400)) then
+ eomday=leapdays(mm)
+ else
+ eomday=days(mm)
+ endif
+ else
+ if((float(yyyy)/4.).eq.float(yyyy/4)) then
+ eomday=leapdays(mm)
+ else
+ eomday=days(mm)
+ endif
+ endif
+
+ calceomday=eomday
+
+ end function calceomday
+
+ ! --------------------------------------------------
+
+end module mod_dates
+
+
diff --git a/prep_satellite/mod_save.f90 b/prep_satellite/mod_save.f90
new file mode 100644
index 0000000..f3cfaf5
--- /dev/null
+++ b/prep_satellite/mod_save.f90
@@ -0,0 +1,225 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: mod_save
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2022, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> mod_save
+!!
+!! Purpose: Writes retrieval and releases data to netcdf files
+!!
+!---------------------------------------------------------------------------------------
+
+module mod_save
+
+ use mod_settings
+ use mod_var
+ use netcdf
+
+ implicit none
+ private
+
+ public :: check, write_releases, write_retrieval
+
+ contains
+
+ ! --------------------------------------------------
+ ! check
+ ! --------------------------------------------------
+
+ subroutine check(status)
+
+ integer, intent(in) :: status
+
+ if ( status.ne.nf90_noerr ) then
+ write(logid,*) trim(nf90_strerror(status))
+ stop
+ end if
+
+ end subroutine check
+
+ ! --------------------------------------------------
+ ! write_releases
+ !
+ ! total column SRR calculated as
+ !
+ ! SRR_col = sum(a_i * SRR_i * vdryair_i)
+ !
+ ! where
+ ! a_i ith layer of column averaging kernel
+ ! vdryair_i dry air weighting in ith layer
+ ! SRR_col column SRR in units of s.mol/kg
+ ! (after dividing by height of surface
+ ! layer)
+ !
+ ! --------------------------------------------------
+
+ subroutine write_releases(settings,nretr,nlayer,ncoord,xpoints,ypoints,zpoint1,zpoint2,&
+ idate,itime,cak_out,vdryair_out,specnum,units)
+
+ type (settings_t), intent(in) :: settings
+ integer, intent(in) :: nretr, nlayer, ncoord
+ real, dimension(maxretr,ncoord), intent(in) :: xpoints, ypoints
+ real, dimension(maxretr,nlayer), intent(in) :: zpoint1, zpoint2
+ integer, dimension(maxretr), intent(in) :: idate, itime
+ real, dimension(maxretr,nlayer), intent(in) :: cak_out, vdryair_out
+ integer, intent(in) :: specnum
+ character(len=6), dimension(4), intent(in) :: units
+
+ character(len=8) :: adate
+ character(max_name_len) :: filename, pathout
+ integer :: ncid, nrid, nlid, ncoid
+ integer :: xptid, yptid, zpt1id, zpt2id
+ integer :: dateid, timeid, cakid, dairid, npartid
+
+ write(adate,fmt='(I8.8)') idate(1)
+ filename = 'releases_'//trim(settings%satname)//'_'//adate//'.nc'
+ pathout = trim(settings%path_options)//adate//'/options/'
+ call system('mkdir '//trim(pathout))
+ write(logid,*) 'writing file: ',trim(pathout)//trim(filename)
+
+ ! create file
+ call check( nf90_create(trim(pathout)//trim(filename), nf90_clobber, ncid) )
+
+ ! define dimensions and variables
+ call check( nf90_def_dim(ncid, 'retrieval', nretr, nrid) )
+ call check( nf90_def_dim(ncid, 'nlayer', nlayer, nlid) )
+ call check( nf90_def_dim(ncid, 'ncoord', ncoord, ncoid) )
+ call check( nf90_def_var(ncid, 'xpoints', nf90_real, (/nrid, ncoid/), xptid) )
+ call check( nf90_put_att(ncid, xptid, 'units', 'degrees_east') )
+ call check( nf90_def_var(ncid, 'ypoints', nf90_real, (/nrid, ncoid/), yptid) )
+ call check( nf90_put_att(ncid, yptid, 'units', 'degrees_north') )
+ call check( nf90_def_var(ncid, 'zpoint1', nf90_real, (/nrid, nlid/), zpt1id) )
+ call check( nf90_put_att(ncid, zpt1id, 'units', 'Pa') )
+ call check( nf90_def_var(ncid, 'zpoint2', nf90_real, (/nrid, nlid/), zpt2id) )
+ call check( nf90_put_att(ncid, zpt2id, 'units', 'Pa') )
+ call check( nf90_def_var(ncid, 'idate', nf90_int, nrid, dateid) )
+ call check( nf90_put_att(ncid, dateid, 'units', 'none') )
+ call check( nf90_def_var(ncid, 'itime', nf90_int, nrid, timeid) )
+ call check( nf90_put_att(ncid, timeid, 'units', 'none') )
+ call check( nf90_def_var(ncid, 'cak', nf90_real, (/nrid, nlid/), cakid) )
+ call check( nf90_put_att(ncid, cakid, 'units', 'none') )
+ call check( nf90_def_var(ncid, 'dryair', nf90_real, (/nrid, nlid/), dairid) )
+ call check( nf90_put_att(ncid, dairid, 'units', trim(units(1))) )
+ call check( nf90_put_att(ncid, nf90_global, 'specnum', specnum) )
+ call check( nf90_put_att(ncid, nf90_global, 'mass', settings%mass) )
+ call check( nf90_put_att(ncid, nf90_global, 'npart', settings%npart) )
+
+ ! exit define mode
+ call check( nf90_enddef(ncid) )
+
+ ! insert variables
+ call check( nf90_put_var(ncid, xptid, xpoints(1:nretr,:)) )
+ call check( nf90_put_var(ncid, yptid, ypoints(1:nretr,:)) )
+ call check( nf90_put_var(ncid, zpt1id, zpoint1(1:nretr,:)) )
+ call check( nf90_put_var(ncid, zpt2id, zpoint2(1:nretr,:)) )
+ call check( nf90_put_var(ncid, dateid, idate(1:nretr)) )
+ call check( nf90_put_var(ncid, timeid, itime(1:nretr)) )
+ call check( nf90_put_var(ncid, cakid, cak_out(1:nretr,:)) )
+ call check( nf90_put_var(ncid, dairid, vdryair_out(1:nretr,:)) )
+
+ ! close file
+ call check( nf90_close(ncid) )
+
+ end subroutine write_releases
+
+ ! --------------------------------------------------
+ ! write_retrieval
+ !
+ ! model total column is:
+ !
+ ! vmod = cpri - cakpri + SRR_col * flux
+ !
+ ! and total column mixing ratio (ppbv) is
+ !
+ ! xmod = vmod/vdryair
+ !
+ ! where
+ ! cpri sum(vpri_i)
+ ! cakpri sum(a_i*vpri_i)
+ ! vdryair total column dry air
+ !
+ ! --------------------------------------------------
+
+ subroutine write_retrieval(settings,nretr,ncoord,xpoints,ypoints,idate,itime,&
+ cpri,cakpri,vmr_out,verr_out,cdryair,units)
+
+ type (settings_t), intent(in) :: settings
+ integer, intent(in) :: nretr, ncoord
+ real, dimension(maxretr,ncoord), intent(in) :: xpoints, ypoints
+ integer, dimension(maxretr), intent(in) :: idate, itime
+ real, dimension(maxretr), intent(in) :: vmr_out, verr_out
+ real, dimension(nretr), intent(in) :: cpri, cakpri, cdryair
+ character(len=6), dimension(4), intent(in) :: units
+
+ character(max_name_len) :: filename
+ character(len=8) :: adate
+ integer :: ncid, nrid, nlid, ncoid
+ integer :: xptid, yptid, dateid, timeid
+ integer :: cprid, cakprid, vmrid, verrid, cdairid
+
+ write(adate,fmt='(I8.8)') idate(1)
+ filename = 'retrieval_'//trim(settings%satname)//'_'//adate//'.nc'
+ write(logid,*) 'writing file: ',trim(settings%path_obsout)//trim(filename)
+
+ ! create file
+ call check( nf90_create(trim(settings%path_obsout)//trim(filename), nf90_clobber, ncid) )
+
+ ! define dimensions and variables
+ call check( nf90_def_dim(ncid, 'retrieval', nretr, nrid) )
+ call check( nf90_def_dim(ncid, 'ncoord', ncoord, ncoid) )
+ call check( nf90_def_var(ncid, 'xpoints', nf90_real, (/nrid, ncoid/), xptid) )
+ call check( nf90_put_att(ncid, xptid, 'units', 'degrees_east') )
+ call check( nf90_def_var(ncid, 'ypoints', nf90_real, (/nrid, ncoid/), yptid) )
+ call check( nf90_put_att(ncid, yptid, 'units', 'degrees_north') )
+ call check( nf90_def_var(ncid, 'idate', nf90_int, nrid, dateid) )
+ call check( nf90_put_att(ncid, dateid, 'units', 'none') )
+ call check( nf90_def_var(ncid, 'itime', nf90_int, nrid, timeid) )
+ call check( nf90_put_att(ncid, timeid, 'units', 'none') )
+ call check( nf90_def_var(ncid, 'cpri', nf90_real, nrid, cprid) )
+ call check( nf90_put_att(ncid, cprid, 'units', trim(units(3))) )
+ call check( nf90_def_var(ncid, 'cakpri', nf90_real, nrid, cakprid) )
+ call check( nf90_put_att(ncid, cakprid, 'units', trim(units(3))) )
+ call check( nf90_def_var(ncid, 'vmr', nf90_real, nrid, vmrid) )
+ call check( nf90_put_att(ncid, vmrid, 'units', trim(units(4))) )
+ call check( nf90_def_var(ncid, 'vmr_err', nf90_real, nrid, verrid) )
+ call check( nf90_put_att(ncid, verrid, 'units', trim(units(4))) )
+ call check( nf90_def_var(ncid, 'cdryair', nf90_real, nrid, cdairid) )
+ call check( nf90_put_att(ncid, cdairid, 'units', trim(units(2))) )
+
+ ! end define mode
+ call check( nf90_enddef(ncid) )
+
+ ! insert variables
+ call check( nf90_put_var(ncid, xptid, xpoints(1:nretr,:)) )
+ call check( nf90_put_var(ncid, yptid, ypoints(1:nretr,:)) )
+ call check( nf90_put_var(ncid, dateid, idate(1:nretr)) )
+ call check( nf90_put_var(ncid, timeid, itime(1:nretr)) )
+ call check( nf90_put_var(ncid, cprid, cpri) )
+ call check( nf90_put_var(ncid, cakprid, cakpri) )
+ call check( nf90_put_var(ncid, vmrid, vmr_out(1:nretr)) )
+ call check( nf90_put_var(ncid, verrid, verr_out(1:nretr)) )
+ call check( nf90_put_var(ncid, cdairid, cdryair) )
+
+ ! close file
+ call check( nf90_close(ncid) )
+
+ end subroutine write_retrieval
+
+ ! --------------------------------------------------
+
+end module mod_save
+
diff --git a/prep_satellite/mod_settings.f90 b/prep_satellite/mod_settings.f90
new file mode 100644
index 0000000..e03234e
--- /dev/null
+++ b/prep_satellite/mod_settings.f90
@@ -0,0 +1,567 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: mod_settings
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2022, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> mod_settings
+!!
+!! Purpose: Module for the construction of the settings data structure.
+!!
+!---------------------------------------------------------------------------------------
+
+module mod_settings
+
+ use mod_var
+
+ implicit none
+ private
+
+ public :: settings_t, read_settings, split, parse_string
+
+ ! settings_t contains all settings
+
+ type :: settings_t
+
+ character(len=max_name_len) :: satellite
+ character(len=max_name_len) :: satname
+ character(len=max_path_len) :: path_flexpart
+ character(len=max_path_len) :: path_options
+ character(len=max_path_len) :: path_output
+ character(len=max_path_len) :: path_ohfield
+ character(len=max_path_len) :: path_obs
+ character(len=max_path_len) :: path_obsout
+ character(len=max_name_len) :: suffix
+ character(len=max_path_len) :: file_avail
+ character(len=max_path_len) :: file_availnest
+ character(len=max_name_len) :: windfield
+
+ logical :: landonly
+ integer :: opmode_sel
+ character(len=max_name_len) :: nmeas_name
+ character(len=max_name_len) :: npixel_name
+ character(len=max_name_len) :: ncoord_name
+ character(len=max_name_len) :: nlevel_name
+ character(len=max_name_len) :: time_name
+ character(len=max_name_len) :: tdel_name
+ character(len=max_name_len) :: qa_name
+ character(len=max_name_len) :: oper_name
+ real :: qa_cutoff
+ character(len=max_name_len) :: vmr_name
+ character(len=max_name_len) :: verr_name
+ character(len=max_name_len) :: lat_name
+ character(len=max_name_len) :: lon_name
+ character(len=max_name_len) :: ak_name
+ character(len=max_name_len) :: apri_name
+ character(len=max_name_len) :: dryair_name
+ character(len=max_name_len) :: psurf_name
+ character(len=max_name_len) :: pdel_name
+ character(len=max_name_len) :: surfclass_name
+ character(len=max_name_len) :: landfrac_name
+
+ integer :: datei
+ integer :: datef
+ integer :: outrate
+ integer :: outaverage
+ integer :: outsample
+ integer :: ind_source
+ integer :: ind_receptor
+ integer :: lnested
+ integer :: linit_cond
+
+ real :: outlonleft
+ real :: outlatlower
+ integer :: numxgrid
+ integer :: numygrid
+ integer :: numzgrid
+ real :: dxout
+ real :: dyout
+ real :: outlonnest
+ real :: outlatnest
+ integer :: numxnest
+ integer :: numynest
+ real :: dxoutnest
+ real :: dyoutnest
+ real, dimension(:), allocatable :: zlevel
+
+ character(len=10) :: species
+ integer :: ageclass
+ integer :: npart
+ integer :: mass
+ logical :: avg_pixels
+ logical :: usegridfile
+ real :: dmin
+ integer :: nsteps
+ real :: cutoff
+ integer :: nmin
+ character(len=max_path_len) :: filegrid
+
+ end type settings_t
+
+ contains
+
+ ! --------------------------------------------------
+ ! check if input is numeric
+ ! --------------------------------------------------
+
+ logical function is_numeric(string)
+
+ character(len=200), intent(in) :: string
+ real :: var
+ integer :: ierr
+
+ read(string,*,iostat=ierr) var
+ if(ierr.eq.0) then
+ is_numeric=.true.
+ else
+ is_numeric=.false.
+ endif
+
+ end function is_numeric
+
+ ! --------------------------------------------------
+ ! check if input is logical
+ ! --------------------------------------------------
+
+ logical function is_logical(string)
+
+ character(len=200), intent(in) :: string
+ logical :: var
+ integer :: ierr
+
+ read(string,*,iostat=ierr) var
+ if(ierr.eq.0) then
+ is_logical=.true.
+ else
+ is_logical=.false.
+ endif
+
+ end function is_logical
+
+ ! --------------------------------------------------
+ ! split string
+ ! --------------------------------------------------
+
+ subroutine split(str,delims,before,sep)
+
+ ! Routine finds the first instance of a character from 'delims' in the
+ ! the string 'str'. The characters before the found delimiter are
+ ! output in 'before'. The characters after the found delimiter are
+ ! output in 'str'. The optional output character 'sep' contains the
+ ! found delimiter. A delimiter in 'str' is treated like an ordinary
+ ! character if it is preceded by a backslash (\). If the backslash
+ ! character is desired in 'str', then precede it with another backslash.
+
+ character(len=*) :: str, delims, before
+ character,optional :: sep
+ logical :: pres
+ character :: ch,cha
+ integer :: i, k, ibsl, ipos, iposa, lenstr
+
+ pres=present(sep)
+ str=adjustl(str)
+ lenstr=len_trim(str)
+ if(lenstr == 0) return ! string str is empty
+ k=0
+ ibsl=0 ! backslash initially inactive
+ before=' '
+ do i=1,lenstr
+ ch=str(i:i)
+ if(ibsl == 1) then ! backslash active
+ k=k+1
+ before(k:k)=ch
+ ibsl=0
+ cycle
+ end if
+ if(ch == '\') then ! backslash with backslash inactive
+ k=k+1
+ before(k:k)=ch
+ ibsl=1
+ cycle
+ end if
+ ipos=index(delims,ch)
+ if(ipos == 0) then ! character is not a delimiter
+ k=k+1
+ before(k:k)=ch
+ cycle
+ end if
+ if(ch /= ' ') then ! character is a delimiter that is not a space
+ str=str(i+1:)
+ if(pres) sep=ch
+ exit
+ end if
+ cha=str(i+1:i+1) ! character is a space delimiter
+ iposa=index(delims,cha)
+ if(iposa > 0) then ! next character is a delimiter
+ str=str(i+2:)
+ if(pres) sep=cha
+ exit
+ else
+ str=str(i+1:)
+ if(pres) sep=ch
+ exit
+ end if
+ end do
+ if(i >= lenstr) str=''
+ str=trim(str)
+ before=trim(before)
+ return
+
+ end subroutine split
+
+ ! --------------------------------------------------
+ ! routine to identify and read in content
+ ! --------------------------------------------------
+
+ subroutine read_content (line, identifier, cc, cn, cl, match)
+
+ character (len=200), intent (in) :: line, identifier
+ character (len=200), intent (out) :: cc ! character content
+ real(kind=8), intent (out) :: cn ! numeric content
+ logical, intent (out) :: cl ! logical content
+ logical, intent (out) :: match
+
+ integer :: n
+
+ n = len_trim (identifier)
+
+ ! default: line does not match, cc="", cn=-9900.0
+ cc = ""
+ cn = -9999.9
+ match = .false.
+ if ( len_trim (line) >= n ) then
+ if ( line(:n) == identifier(:n) ) then
+ cc = adjustl (line(n+1:))
+ if ( is_numeric(cc) ) then
+ read (line(n+1:),*) cn
+ else
+ if( is_logical(cc) ) read (line(n+1:),*) cl
+ endif
+ match = .true.
+ end if
+ end if
+
+ end subroutine read_content
+
+ ! --------------------------------------------------
+ ! routine to parse a string
+ ! --------------------------------------------------
+
+ subroutine parse_string (str, delims, args, nargs)
+
+ ! Parses the string 'str' into arguments args(1), ..., args(nargs) based on
+ ! the delimiters contained in the string 'delims'. Preceding a delimiter in
+ ! 'str' by a backslash (\) makes this particular instance not a delimiter.
+ ! The integer output variable nargs contains the number of arguments found.
+
+ character(len=*) :: str, delims
+ character(len=len_trim(str)) :: strsav
+ character(len=*), dimension(:) :: args
+ integer :: i, na, lenstr, nargs
+
+ strsav=str
+ na=size(args)
+
+ do i=1,na
+ args(i)=' '
+ end do
+ nargs=0
+ lenstr=len_trim(str)
+ if(lenstr==0) return
+
+ do
+ if(len_trim(str) == 0) exit
+ nargs=nargs+1
+ call split(str,delims,args(nargs))
+ end do
+ str=strsav
+
+ end subroutine parse_string
+
+ ! --------------------------------------------------
+ ! read settings
+ ! --------------------------------------------------
+
+ subroutine read_settings(filename, settings)
+
+ character(len=200), intent(in) :: filename
+ type(settings_t), intent(in out) :: settings
+
+ integer :: ierr, i, n
+ character(len=200) :: line, identifier, cc
+ real(kind=8) :: cn
+ logical :: match, cl
+ character(len=100), dimension(100) :: temp
+
+ ! default settings for logicals
+ settings%avg_pixels = .false.
+ settings%usegridfile = .false.
+ settings%landonly = .false.
+ settings%opmode_sel = -1
+
+ ! open file
+ open (100, file = trim (filename), status = 'old', iostat=ierr)
+ if(ierr.gt.0) then
+ write (*,*) 'ERROR: cannot find SETTINGS'
+ stop
+ endif
+
+ ! loop over lines
+ read_loop: do
+ read (100, fmt='(A)', iostat=ierr) line
+
+ ! first check if line exists or eof was reached
+ if ( ierr.gt.0 ) then
+ write (*,*) 'ERROR: check ', filename
+ exit read_loop
+ else if ( ierr.lt.0 ) then
+ exit read_loop
+ else
+
+ ! omit comments ("#") and empty lines
+ if ( index (trim (line), "#") .eq. 1 ) cycle read_loop
+ if ( len (trim (line)) .eq. 0 ) cycle read_loop
+
+ ! Path and file settings
+ identifier = "satellite:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%satellite = cc
+ identifier = "satname:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%satname = cc
+ identifier = "path_flexpart:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%path_flexpart = cc
+ identifier = "path_options:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%path_options = cc
+ identifier = "path_output:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%path_output = cc
+ identifier = "path_ohfield:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%path_ohfield = cc
+ identifier = "path_obs:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%path_obs = cc
+ identifier = "path_obsout:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%path_obsout = cc
+ identifier = "suffix:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%suffix = cc
+ identifier = "file_avail:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%file_avail = cc
+ identifier = "file_availnest:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%file_availnest = cc
+ identifier = "windfield:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%windfield = cc
+
+ ! satellite variables
+ identifier = "landonly:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%landonly = cl
+ identifier = "opmode_sel:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%opmode_sel = cn
+ identifier = "nmeas_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%nmeas_name = cc
+ identifier = "npixel_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%npixel_name = cc
+ identifier = "ncoord_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%ncoord_name = cc
+ identifier = "nlevel_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%nlevel_name = cc
+ identifier = "oper_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%oper_name = cc
+ identifier = "time_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%time_name = cc
+ identifier = "tdel_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%tdel_name = cc
+ identifier = "qa_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%qa_name = cc
+ identifier = "qa_cutoff:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%qa_cutoff = cn
+ identifier = "vmr_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%vmr_name = cc
+ identifier = "verr_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%verr_name = cc
+ identifier = "lat_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%lat_name = cc
+ identifier = "lon_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%lon_name = cc
+ identifier = "ak_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%ak_name = cc
+ identifier = "apri_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%apri_name = cc
+ identifier = "dryair_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%dryair_name = cc
+ identifier = "psurf_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%psurf_name = cc
+ identifier = "pdel_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%pdel_name = cc
+ identifier = "surfclass_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%surfclass_name = cc
+ identifier = "landfrac_name:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%landfrac_name = cc
+
+ ! COMMAND settings
+ identifier = "datei:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%datei = int(cn)
+ identifier = "datef:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%datef = int(cn)
+ identifier = "outrate:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%outrate = int(cn)
+ identifier = "outaverage:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%outaverage = int(cn)
+ identifier = "outsample:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%outsample = int(cn)
+ identifier = "ind_source:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%ind_source = int(cn)
+ identifier = "ind_receptor:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%ind_receptor = int(cn)
+ identifier = "lnested:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%lnested = int(cn)
+ identifier = "linit_cond:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%linit_cond = int(cn)
+
+ ! OUTGRID settings
+ identifier = "outlonleft:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%outlonleft = real(cn)
+ identifier = "outlatlower:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%outlatlower = real(cn)
+ identifier = "numxgrid:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%numxgrid = real(cn)
+ identifier = "numygrid:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%numygrid = real(cn)
+ identifier = "dxout:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%dxout = real(cn)
+ identifier = "dyout:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%dyout = real(cn)
+ identifier = "outlonnest:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%outlonnest = real(cn)
+ identifier = "outlatnest:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%outlatnest = real(cn)
+ identifier = "numxnest:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%numxnest = real(cn)
+ identifier = "numynest:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%numynest = real(cn)
+ identifier = "dxoutnest:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%dxoutnest = real(cn)
+ identifier = "dyoutnest:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%dyoutnest = real(cn)
+ identifier = "zlevel:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) then
+ call parse_string (cc, ",", temp(:), n)
+ if( .not.allocated(settings%zlevel) ) allocate( settings%zlevel(n) )
+ settings%numzgrid = n
+ do i = 1, n
+ read(temp(i),*) settings%zlevel(i)
+ enddo
+ endif
+
+ ! RELEASES settings
+ identifier = "species:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%species = cc
+ identifier = "ageclass:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%ageclass = int(cn)
+ identifier = "npart:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%npart = int(cn)
+ identifier = "mass:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%mass = int(cn)
+
+ ! AVERAGING settings
+ identifier = "avg_pixels:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%avg_pixels = cl
+ identifier = "usegridfile:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%usegridfile = cl
+ identifier = "dmin:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%dmin = cn
+ identifier = "nsteps:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%nsteps = cn
+ identifier = "cutoff:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%cutoff = cn
+ identifier = "nmin:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%nmin = int(cn)
+ identifier = "filegrid:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) settings%filegrid = cc
+
+ endif
+
+ end do read_loop
+
+ end subroutine read_settings
+
+ ! --------------------------------------------------
+
+end module mod_settings
+
diff --git a/prep_satellite/mod_var.f90 b/prep_satellite/mod_var.f90
new file mode 100644
index 0000000..aed88d6
--- /dev/null
+++ b/prep_satellite/mod_var.f90
@@ -0,0 +1,39 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: mod_var
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2022, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> mod_var
+!!
+!---------------------------------------------------------------------------------------
+
+module mod_var
+
+ implicit none
+
+ ! general variables
+ ! -----------------
+
+ integer, parameter :: max_path_len = 200
+ integer, parameter :: max_name_len = 200
+ integer, parameter :: maxretr = 1000000
+ integer, parameter :: logid = 500
+ integer, parameter :: maxbox = 500000
+
+end module mod_var
+
+
diff --git a/prep_satellite/prep_ageclass.f90 b/prep_satellite/prep_ageclass.f90
new file mode 100644
index 0000000..50c60dc
--- /dev/null
+++ b/prep_satellite/prep_ageclass.f90
@@ -0,0 +1,69 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: prep_ageclass
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2017, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> prep_ageclass
+!!
+!! Purpose: Prepares the options file AGECLASS.
+!!
+!! Interface:
+!!
+!! Inputs
+!! settings - settings data structure
+!! jd - julian day of start of month
+!!
+!! Externals
+!! caldate
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine prep_ageclass(settings, jd)
+
+ use mod_var
+ use mod_settings
+ use mod_dates
+
+ implicit none
+
+ type (settings_t), intent(in) :: settings
+ real(kind=8), intent(in) :: jd
+
+ character(len=max_path_len) :: filename
+ character(len=8) :: adate
+ integer :: jjjjmmdd, hhmiss
+ integer :: ierr
+ integer :: nageclass, lage
+
+ namelist /ageclass/ &
+ nageclass, &
+ lage
+
+ ! preset namelist variables
+ nageclass = 1
+ lage = settings%ageclass
+
+ call caldate(jd, jjjjmmdd, hhmiss)
+ write(adate,fmt='(I8.8)') jjjjmmdd
+ filename = trim(settings%path_options)//adate//'/options/AGECLASSES'
+
+ ! write namelist file format
+ open(100,file=trim(filename),status='replace',action='write',iostat=ierr)
+ write(100,nml=ageclass)
+ close(100)
+
+end subroutine prep_ageclass
diff --git a/prep_satellite/prep_command.f90 b/prep_satellite/prep_command.f90
new file mode 100644
index 0000000..5e5b27d
--- /dev/null
+++ b/prep_satellite/prep_command.f90
@@ -0,0 +1,171 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: prep_command
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2017, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> prep_command
+!!
+!! Purpose: Prepares the options file COMMAND.
+!!
+!! Interface:
+!!
+!! Inputs
+!! settings - settings data structure
+!! jd - julian day for start of month
+!!
+!! Externals
+!! caldate
+!! juldate
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine prep_command(settings, jd)
+
+ use mod_var
+ use mod_settings
+ use mod_dates
+
+ implicit none
+
+ type (settings_t), intent(in) :: settings
+ real(kind=8), intent(in) :: jd
+
+ character(len=max_path_len) :: filename
+ character(len=8) :: adate
+ integer :: jjjjmm, jjjjmmdd, hhmiss
+ integer :: datei, datef
+ integer :: ierr
+
+ integer :: ldirect ! runtime mode (currently only backwards: ldirect = -1)
+ integer :: ibdate, ibtime
+ integer :: iedate, ietime
+ integer :: partsplit
+ integer :: loutstep
+ integer :: loutaver
+ integer :: loutsample
+ integer :: itsplit ! time constant for particle splitting (secs)
+ integer :: lsynctime ! synchronisation interval of flexpart (secs)
+ real :: ctl ! factor by which time step must be smaller than tl
+ integer :: ifine ! factor by which to decrease time step for vertical motion
+ integer :: iout ! output type (1 = concentration/residence time, 2 = mixing ratio, 3 = both, 4 = plume trajectory)
+ integer :: ipout ! particle dump (0 = never, 1 = every output interval, 2 = only at end)
+ integer :: lsubgrid ! use subgrid terrain effect parameterization (0 = no, 1 = yes)
+ integer :: lconvection ! use convection (0 = no, 1 = yes)
+ integer :: lagespectra ! calculate age spectra (0 = no, 1 = yes)
+ integer :: ipin ! continue simulation with dumped particle data (0 = no, 1 = yes)
+ integer :: ioutputforeachrelease ! create output file for each release location (0 = no, 1 = yes)
+ integer :: mdomainfill ! domain filling option (0 = no, 1 = yes)
+ integer :: mquasilag ! quasilagrangian mode to track particles (0 = no, 1 = yes)
+ integer :: surf_only ! save only surface layer in grid_time files = 1, full resolution = 0
+ integer :: lnetcdfout ! netcdf output (0 = no, 1 = yes)
+ integer :: cblflag !
+ integer :: linversionout ! one grid_time file per release = 1, or per timestep (original format) = 0
+ integer :: satellite_releases ! releases for satellite retrievals
+ integer :: iflux ! calculate fluxes (0 = no, 1 = yes)
+ integer :: ind_source
+ integer :: ind_receptor
+ integer :: nested_output
+ integer :: linit_cond
+ character(len=max_path_len) :: ohfields_path
+
+ namelist /command/ &
+ ldirect, &
+ ibdate,ibtime, &
+ iedate,ietime, &
+ loutstep, &
+ loutaver, &
+ loutsample, &
+ itsplit, &
+ lsynctime, &
+ ctl, &
+ ifine, &
+ iout, &
+ ipout, &
+ lsubgrid, &
+ lconvection, &
+ lagespectra, &
+ ipin, &
+ ioutputforeachrelease, &
+ iflux, &
+ mdomainfill, &
+ ind_source, &
+ ind_receptor, &
+ mquasilag, &
+ nested_output, &
+ linit_cond, &
+ lnetcdfout, &
+ surf_only, &
+ cblflag, &
+ linversionout, &
+ satellite_releases, &
+ ohfields_path
+
+ ! initialize command file path and name
+ call caldate(jd, jjjjmmdd, hhmiss)
+ write(adate,fmt='(I8.8)') jjjjmmdd
+ filename = trim(settings%path_options)//adate//'/options/COMMAND'
+
+ call system('mkdir -p '//trim(settings%path_options)//adate//'/options/')
+
+ ! get dates
+ ! correct start date for length of back trajectory
+ call caldate((jd-settings%ageclass/3600d0/24d0), jjjjmmdd, hhmiss)
+ datei = jjjjmmdd
+ call caldate(jd+1d0, jjjjmmdd, hhmiss)
+ datef = jjjjmmdd
+
+ ! preset namelist variables
+ ldirect = -1
+ ibdate = datei
+ ibtime = 0
+ iedate = datef
+ ietime = 0
+ loutstep = settings%outrate
+ loutaver = settings%outaverage
+ loutsample = settings%outsample
+ itsplit = 999999999
+ lsynctime = 600
+ ctl = -5
+ ifine = 4
+ iout = 1
+ ipout = 2
+ lsubgrid = 1
+ lconvection = 1
+ lagespectra = 1
+ ipin = 0
+ ioutputforeachrelease = 1
+ iflux = 0
+ mdomainfill = 0
+ ind_source = settings%ind_source
+ ind_receptor = settings%ind_receptor
+ mquasilag = 0
+ nested_output = settings%lnested
+ linit_cond = settings%linit_cond
+ lnetcdfout = 0
+ surf_only = 1
+ cblflag = 0
+ linversionout = 1
+ satellite_releases = 1
+ ohfields_path = trim(settings%path_ohfield)
+
+ ! write command file
+ open(100,file=trim(filename),status='replace',action='write',iostat=ierr)
+ write(100,nml=command)
+ close(100)
+
+end subroutine prep_command
+
diff --git a/prep_satellite/prep_outgrid.f90 b/prep_satellite/prep_outgrid.f90
new file mode 100644
index 0000000..a659157
--- /dev/null
+++ b/prep_satellite/prep_outgrid.f90
@@ -0,0 +1,131 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: prep_outgrid
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2017, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> prep_outgrid
+!!
+!! Purpose: Prepares the options file OUTGRID
+!!
+!! Interface:
+!!
+!! Inputs
+!! settings - settings data structure
+!! jd - julian day for start of month
+!!
+!! Externals
+!! caldate
+!! skiplines
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine prep_outgrid(settings, jd)
+
+ use mod_var
+ use mod_settings
+ use mod_dates
+
+ implicit none
+
+ type (settings_t), intent(in) :: settings
+ real(kind=8), intent(in) :: jd
+
+ character(len=max_path_len) :: filename
+ character(len=8) :: adate
+ integer :: jjjjmmdd, hhmiss
+ integer :: ierr, n
+
+ real :: outlon0, outlat0, outlon0n, outlat0n
+ integer :: numxgrid, numygrid, numxgridn, numygridn
+ real :: dxout, dyout, dxoutn, dyoutn
+ real, dimension(settings%numzgrid) :: outheights
+
+ namelist /outgrid/ &
+ outlon0, &
+ outlat0, &
+ numxgrid, &
+ numygrid, &
+ dxout, &
+ dyout, &
+ outheights
+
+ namelist /outgridn/ &
+ outlon0n, &
+ outlat0n, &
+ numxgridn, &
+ numygridn, &
+ dxoutn, &
+ dyoutn
+
+ ! write OUTGRID
+
+ ! preset namelist variables
+ outlon0 = settings%outlonleft
+ ! correction for FLEXPART windfields
+ if ( settings%outlonleft.le.-180. ) then
+ if ( settings%windfield.eq.'oper' ) then
+ outlon0 = -179.
+ else if ( settings%windfield.eq.'era5' ) then
+ outlon0 = -179.5
+ else
+ write(logid,*) 'ERROR: prep_outgrid: unknown windfield type'
+ stop
+ endif
+ endif
+ outlat0 = settings%outlatlower
+ numxgrid = settings%numxgrid
+ numygrid = settings%numygrid
+ dxout = settings%dxout
+ dyout = settings%dyout
+ do n = 1, settings%numzgrid
+ outheights(n) = settings%zlevel(n)
+ end do
+
+ call caldate(jd, jjjjmmdd, hhmiss)
+ write(adate,fmt='(I8.8)') jjjjmmdd
+ filename = trim(settings%path_options)//adate//'/options/OUTGRID'
+
+ ! write namelist file format
+ open(100,file=trim(filename),status='replace',action='write',iostat=ierr)
+ write(100,nml=outgrid)
+ close(100)
+
+ ! write OUTGRID_NEST
+
+ if( settings%lnested.eq.1 ) then
+
+ ! preset namelist variables
+ outlon0n = settings%outlonnest
+ outlat0n = settings%outlatnest
+ numxgridn = settings%numxnest
+ numygridn = settings%numynest
+ dxoutn = settings%dxoutnest
+ dyoutn = settings%dyoutnest
+
+ call caldate(jd, jjjjmmdd, hhmiss)
+ write(adate,fmt='(I8.8)') jjjjmmdd
+ filename = trim(settings%path_options)//adate//'/options/OUTGRID_NEST'
+
+ ! write namelist file format
+ open(100,file=trim(filename),status='replace',action='write',iostat=ierr)
+ write(100,nml=outgridn)
+ close(100)
+
+ endif
+
+end subroutine prep_outgrid
+
diff --git a/prep_satellite/prep_pathnames.f90 b/prep_satellite/prep_pathnames.f90
new file mode 100644
index 0000000..9f7a839
--- /dev/null
+++ b/prep_satellite/prep_pathnames.f90
@@ -0,0 +1,75 @@
+!---------------------------------------------------------------------------------------
+! PREP_SATELLITE: prep_pathnames
+!---------------------------------------------------------------------------------------
+! FLEXINVERT 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.
+!
+! FLEXINVERT 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 FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
+!
+! Copyright 2017, Rona Thompson
+!---------------------------------------------------------------------------------------
+!
+!> prep_pathnames
+!!
+!! Purpose: Prepares the file pathnames
+!!
+!! Interface:
+!!
+!! Inputs
+!! settings - settings data structure
+!! jd - julian day for start of month
+!!
+!! Externals
+!! caldate
+!!
+!---------------------------------------------------------------------------------------
+
+subroutine prep_pathnames(settings, jd)
+
+ use mod_var
+ use mod_settings
+ use mod_dates
+
+ implicit none
+
+ type (settings_t), intent(in) :: settings
+ real(kind=8), intent(in) :: jd
+
+ character(len=max_path_len) :: filename
+ character(len=8) :: adate
+ integer :: jjjjmmdd, hhmiss
+ integer :: ierr
+
+ call caldate(jd, jjjjmmdd, hhmiss)
+ write(adate,fmt='(I8.8)') jjjjmmdd
+ filename = trim(settings%path_options)//adate//'/pathnames'
+
+ call system('mkdir -p '//trim(settings%path_options)//adate)
+ call system('mkdir -p '//trim(settings%path_output)//adate)
+
+ open(100,file=trim(filename),status='replace',action='write',iostat=ierr)
+
+ write(100,fmt='(A)') trim(settings%path_options)//adate//'/options/'
+ write(100,fmt='(A)') trim(settings%path_output)//adate//'/'
+ write(100,fmt='(A1)') '/'
+ write(100,fmt='(A)') trim(settings%file_avail)
+
+ if( settings%lnested.eq.1 ) then
+ write(100,fmt='(A1)') '/'
+ write(100,fmt='(A)') trim(settings%file_availnest)
+ write(100,fmt='(A)') '============================================'
+ write(100,fmt='(A1)') ' '
+ endif
+
+ close(100)
+
+end subroutine prep_pathnames
+
diff --git a/prep_satellite/run_flexpart.sh b/prep_satellite/run_flexpart.sh
new file mode 100755
index 0000000..3a771c7
--- /dev/null
+++ b/prep_satellite/run_flexpart.sh
@@ -0,0 +1,97 @@
+#!/bin/bash
+#---------------------------------------------------
+# Run FLEXPART jobs for satellite observations
+#---------------------------------------------------
+# Guide to use:
+# 1. edit the directories, exename, list of stations
+# months and year below
+# 2. for slurm set SLURM = 1 otherwise uses nohup
+# 3. the meteorology used for flexpart can be
+# specified by METEO
+# 4. run the script:
+# ./run_flexpart.sh
+#---------------------------------------------------
+
+# User settings
+SLURM=1
+PRIORITY=normal
+TIMELIM=2-00:00:00
+PARTITION=nilu
+EXENAME=FLEXPART
+DIRFLEX=/mypath/FLEXPART_v104/
+DIROPTIONS=/mypath/flexpart_input/
+PREFIX=releases_s5p_ch4
+YEAR=2020
+MONLIST=07
+DAYLIST=(01 02 03 04 05 06 07 08 09 10 11 12 13 14 15
+ 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31)
+
+#---------------------------------------------------
+
+NDAY=${#DAYLIST[@]}
+echo "number of days: "${NDAY}
+ARRAYDAY=`seq 1 ${NDAY}`
+
+NMON=${#MONLIST[@]}
+echo "number of months: "${NMON}
+ARRAYMON=`seq 1 ${NMON}`
+
+# check FLEXPART executable
+
+cd ${DIRFLEX}src/
+if [ ! `ls ${DIRFLEX}src/${EXENAME}` ]; then
+ make -j serial ncf=yes
+ if [ ! `ls ${DIRFLEX}src/${EXENAME}` ]; then
+ echo "cannot create exec: "${DIRFLEX}src/${EXENAME}
+ exit -1
+ fi
+fi
+chmod u+x ${EXENAME}
+
+# loop over FLEXPART runs
+
+for k in ${ARRAYMON}
+do
+ j=`expr $k - 1`
+ MON=${MONLIST[$j]}
+ for i in ${ARRAYDAY}
+ do
+ l=`expr $i - 1`
+ DAY=${DAYLIST[$l]}
+
+ # check RELEASES NCDF file exists if not go to next iteration
+ echo ${DIROPTIONS}${YEAR}${MON}${DAY}/options/${PREFIX}_${YEAR}${MON}${DAY}.nc
+ if [ ! `ls ${DIROPTIONS}${YEAR}${MON}${DAY}/options/${PREFIX}_${YEAR}${MON}${DAY}.nc` ]; then
+ continue
+ fi
+
+ # set-up job
+ cd ${DIROPTIONS}${YEAR}${MON}${DAY}
+ rm -f job_${MON}${DAY}
+ rm -f flex.log
+ cp -f ${DIRFLEX}src/${EXENAME} job_${MON}${DAY}
+ OUTPUT=flex.log
+ echo "submitting job for: "${YEAR}${MON}${DAY}
+
+ if [ ${SLURM} -eq 1 ]; then
+ # create submit.sh for submitting to slurm
+cat <<EOF > submit.sh
+#!/bin/bash
+./job_${MON}${DAY}
+EOF
+#sbatch --job-name=job_${MON}${DAY} --qos=${PRIORITY} --partition=${PARTITION} --time=${TIMELIM} --mem-per-cpu=50000 --output=${OUTPUT} submit.sh
+sbatch --job-name=job_${MON}${DAY} --partition=${PARTITION} --time=${TIMELIM} --mem-per-cpu=50000 --output=${OUTPUT} submit.sh
+ sleep 2
+ rm -f submit.sh
+ else
+ # use nohup
+ nohup ./job_${MON}${DAY} > ${OUTPUT}
+ sleep 2
+ fi
+
+ done
+done
+
+# the end
+
+
diff --git a/prep_satellite/sbatch_satellite.sh b/prep_satellite/sbatch_satellite.sh
new file mode 100755
index 0000000..1dd544e
--- /dev/null
+++ b/prep_satellite/sbatch_satellite.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+#---------------------------------------------------
+partition=nilu
+settings_file='./SETTINGS_tropomi'
+logfile='prep_satellite_tropomi.log'
+#---------------------------------------------------
+
+cat <<EOF > run_job.sh
+#!/bin/bash
+./prep_satellite ${settings_file} ${logfile}
+EOF
+
+sbatch --job-name=prep_sat --mem-per-cpu=6000 --partition=${partition} run_job.sh
+
+rm -f run_job.sh
diff --git a/prep_syndata/get_obs.f90 b/prep_syndata/get_obs.f90
index e248e4c..03c82d4 100644
--- a/prep_syndata/get_obs.f90
+++ b/prep_syndata/get_obs.f90
@@ -49,7 +49,7 @@ subroutine get_obs(config, files, obs, obserr)
logical :: lexist
integer :: jjjjmmdd, hhmiss, i, ierr
real :: jdate, conc, post, delta, cinipos
- real, dimension(maxobs) :: cini, bkg, nee, fff, ocn, prior, ghg
+ real, dimension(maxobs) :: cini, bkg, nee, fff, ocn, prior, ghg, cpri, cakpri
character(len=3) :: recs
obs(:) = 0.
@@ -60,6 +60,8 @@ subroutine get_obs(config, files, obs, obserr)
ocn(:) = 0.
prior(:) = 0.
ghg(:) = 0.
+ cpri(:) = 0.
+ cakpri(:) = 0.
filename = trim(files%path_output)//'monitor.txt'
inquire(file=trim(filename), exist=lexist)
@@ -72,17 +74,17 @@ subroutine get_obs(config, files, obs, obserr)
open(100,file=trim(filename),status='old',action='read',iostat=ierr)
read(100,fmt='(A)') dump
if ( config%spec.eq.'co2' ) then
- write(rowfmt,'(A,I6,A)') '(A3,1X,I8,1X,I6,1X,F14.6,1X,',11,'(F10.4,1X))'
+ write(rowfmt,'(A,I1,A,I6,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,',13,'(F10.4,1X))'
do i = 1, maxobs
read(100,fmt=rowfmt,iostat=ierr) recs, jjjjmmdd, hhmiss, jdate, conc, cini(i), cinipos, bkg(i), &
- nee(i), fff(i), ocn(i), prior(i), post, delta, obserr(i)
+ nee(i), fff(i), ocn(i), prior(i), post, cpri(i), cakpri(i), delta, obserr(i)
if ( ierr.ne.0 ) exit
end do
else
- write(rowfmt,'(A,I6,A)') '(A3,1X,I8,1X,I6,1X,F14.6,1X,',9,'(F10.4,1X))'
+ write(rowfmt,'(A,I1,A,I6,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,',11,'(F10.4,1X))'
do i = 1, maxobs
read(100,fmt=rowfmt,iostat=ierr) recs, jjjjmmdd, hhmiss, jdate, conc, cini(i), cinipos, bkg(i), &
- ghg(i), prior(i), post, delta, obserr(i)
+ ghg(i), prior(i), post, cpri(i), cakpri(i), delta, obserr(i)
if ( ierr.ne.0 ) exit
end do
endif
@@ -98,14 +100,14 @@ subroutine get_obs(config, files, obs, obserr)
end do
if ( config%spec.eq.'co2' ) then
- obs = cini + bkg + nee + fff + ocn
+ obs = cini + bkg + nee + fff + ocn + cpri - cakpri
else
if ( config%lognormal ) then
! lognormal
- obs = cini + bkg + prior
+ obs = cini + bkg + prior + cpri - cakpri
else
! normal
- obs = cini + bkg + ghg + prior
+ obs = cini + bkg + ghg + prior + cpri - cakpri
endif
endif
diff --git a/prep_syndata/initialize.f90 b/prep_syndata/initialize.f90
index 81f4c26..a2dbb47 100644
--- a/prep_syndata/initialize.f90
+++ b/prep_syndata/initialize.f90
@@ -41,6 +41,7 @@ subroutine initialize(files, config)
logical :: lexist
integer :: yyyymm, yyyymmdd, hhmiss
character(6) :: adate
+ character(8) :: areldate
character(4) :: ayear
integer :: numpoint
integer :: ibdate, ibtime
@@ -59,27 +60,36 @@ subroutine initialize(files, config)
filename = trim(files%file_recept)
inquire(file=trim(filename),exist=lexist)
- if (.not.lexist) then
+ if ( .not.lexist.and.config%ground ) then
write(logid,*) 'ERROR: cannot find '//trim(filename)
stop
+ else if ( lexist.and.config%ground ) then
+ write(logid,*) 'Reading receptor list: '//trim(filename)
+ call read_reclist(filename)
endif
- write(logid,*) 'Reading receptor list: '//trim(filename)
- call read_reclist(filename)
! initialize flexpart variables
! -----------------------------
! read header
- yyyymm=config%datei/100
- write(adate,'(i6)') yyyymm
- lexist = .false.
- i = 1
- do while ( (.not.lexist).and.(i.le.nrec) )
- if ( .not.config%nested ) filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header'
- if ( config%nested ) filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header_nest'
+ if ( config%satellite.and.nrec.eq.0 ) then
+ ! satellite only
+ write(areldate,'(I8)') config%datei
+ filename = trim(files%path_flexsat)//areldate//'/header'
inquire(file=trim(filename),exist=lexist)
- i = i + 1
- end do
+ else
+ ! read from ground-based output
+ yyyymm=config%datei/100
+ write(adate,'(i6)') yyyymm
+ lexist = .false.
+ i = 1
+ do while ( (.not.lexist).and.(i.le.nrec) )
+ if ( .not.config%nested ) filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header'
+ if ( config%nested ) filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header_nest'
+ inquire(file=trim(filename),exist=lexist)
+ i = i + 1
+ end do
+ endif ! satellite
if ( .not.lexist ) then
write(logid,*) 'ERROR initialize: cannot find flexpart header'
stop
@@ -138,7 +148,6 @@ subroutine initialize(files, config)
statres_hr = config%statres_hr
ndt = int(24./statres_hr)
ntstate = int(real(nday)/statres)
-! nflx = nday*nd_nee
else
! statres is time resolution of state variables
! ntstate is also number of state time invervals
@@ -146,7 +155,6 @@ subroutine initialize(files, config)
statres = config%statres
ntstate = int(real(nday)/statres)
ndt = 1
-! nflx = nday*24/nt_flx
endif
! adjust nday to match number of state time steps
diff --git a/prep_syndata/job_prep_syndata.sh b/prep_syndata/job_prep_syndata.sh
index 18a1741..6f8c2a4 100755
--- a/prep_syndata/job_prep_syndata.sh
+++ b/prep_syndata/job_prep_syndata.sh
@@ -1,8 +1,8 @@
#!/bin/bash
#---------------------------------------------------
-settings_files='/mypath/settings/SETTINGS_ghg_files'
-settings_config='/mypath/settings/SETTINGS_ghg_config'
+settings_files='/mypath/settings/SETTINGS_files'
+settings_config='/mypath/settings/SETTINGS_config'
./prep_syndata ${settings_files} ${settings_config}
diff --git a/prep_syndata/mod_save.f90 b/prep_syndata/mod_save.f90
index a06c678..9ad81e3 100644
--- a/prep_syndata/mod_save.f90
+++ b/prep_syndata/mod_save.f90
@@ -299,6 +299,7 @@ module mod_save
subroutine save_obs(config, files, obs, obserr)
use mod_var
+ use mod_dates
use mod_settings
implicit none
@@ -309,12 +310,22 @@ module mod_save
character(len=max_path_len) :: filename
character(len=max_name_len) :: rowfmt, dump
+ character(len=50) :: satname, string, before, sep, species, prefix
character(len=recname_len), dimension(nobs) :: recs
integer, dimension(nobs) :: jjjjmmdd, hhmiss
+ integer :: currentdate, currenttime
real(kind=8), dimension(nobs) :: jdate
+ real(kind=8) :: jd, jdobs
real :: conc, cini, cinipos, bkg, nee, fff, ocn, ghg, prior, post, delta, err
+ real, dimension(nobs) :: cpri, cakpri
integer :: i, ierr
- logical :: lexist
+ logical :: lexist, lsatellite
+
+ ! satellites
+ integer :: nretr, numretr, cnt, nfiles, nf
+ real, dimension(nobs) :: vmr
+ character(len=8) :: adate
+ integer :: ncid, dimid, varid
! read monitor
! ------------
@@ -329,34 +340,118 @@ module mod_save
open(100,file=trim(filename),status='old',action='read',iostat=ierr)
read(100,fmt='(A)') dump
if ( config%spec.eq.'co2' ) then
- write(rowfmt,'(A,I6,A)') '(A3,1X,I8,1X,I6,1X,F14.6,1X,',11,'(F10.4,1X))'
+ write(rowfmt,'(A,I1,A,I6,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,',13,'(F10.4,1X))'
do i = 1, nobs
read(100,fmt=rowfmt) recs(i), jjjjmmdd(i), hhmiss(i), jdate(i), conc, cini, cinipos, bkg, &
- nee, fff, ocn, prior, post, delta, err
+ nee, fff, ocn, prior, post, cpri(i), cakpri(i), delta, err
end do
else
- write(rowfmt,'(A,I6,A)') '(A3,1X,I8,1X,I6,1X,F14.6,1X,',9,'(F10.4,1X))'
+ write(rowfmt,'(A,I1,A,I6,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,',11,'(F10.4,1X))'
do i = 1, nobs
read(100,fmt=rowfmt) recs(i), jjjjmmdd(i), hhmiss(i), jdate(i), conc, cini, cinipos, bkg, &
- ghg, prior, post, delta, err
+ ghg, prior, post, cpri(i), cakpri(i), delta, err
end do
endif
close(100)
- ! write obs for each receptor
- ! ---------------------------
+ ! write ground-based obs
+ ! ----------------------
+ write(rowfmt,'(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,F10.4,1X,F10.4,1X,I4)'
do i = 1, nobs
- filename=trim(files%path_output)//trim(recs(i))//'_'//trim(config%spec)//'.txt'
- inquire(file=trim(filename),exist=lexist)
- if ( .not.lexist ) then
- open(100,file=trim(filename),action='write',status='replace',iostat=ierr)
+ ! check if observation is a satellite retrieval
+ read(recs(i),*,iostat=ierr) nretr
+ if ( ierr.eq.0 ) then
+ lsatellite = .true.
else
- open(100,file=trim(filename),action='write',status='old',access='append',iostat=ierr)
+ lsatellite = .false.
endif
- write(100,fmt='(A3,1X,I8,1X,I6,1X,F14.6,1X,F10.4,1X,F10.4,1X,I4)',iostat=ierr) &
- recs(i), jjjjmmdd(i), hhmiss(i), jdate(i), obs(i), obserr(i), 1
+ if ( .not.lsatellite ) then
+ filename=trim(files%path_output)//trim(recs(i))//'_'//trim(config%spec)//'.txt'
+ inquire(file=trim(filename),exist=lexist)
+ if ( .not.lexist ) then
+ open(100,file=trim(filename),action='write',status='replace',iostat=ierr)
+ else
+ open(100,file=trim(filename),action='write',status='old',access='append',iostat=ierr)
+ endif
+ write(100,fmt=rowfmt,iostat=ierr) recs(i), jjjjmmdd(i), hhmiss(i), jdate(i), obs(i), obserr(i), 1
+ close(100)
+ endif
+ end do
+
+ ! write satellite obs
+ ! -------------------
+
+ ! get prefix for satellite ncdf files
+ inquire(file=trim(files%path_output)//'obsfiles.txt',exist=lexist)
+ if ( lexist ) then
+ open(100,file=trim(files%path_output)//'obsfiles.txt',action='read',status='old',iostat=ierr)
+ read(100,*,iostat=ierr) nfiles
+ do nf = 1, nfiles
+ read(100,fmt='(A)',iostat=ierr) filename
+ if (ierr.ne.0) exit
+ string = trim(filename)
+ call split(string,".",before,sep)
+ if ( string.eq.'nc' ) then
+ ! assume ncdf file is for satellite obs
+ string = trim(filename)
+ ! first instance of delim
+ call split(string,"_",before,sep)
+ ! second instance of delim
+ call split(string,"_",prefix,sep)
+ ! third instance of delim
+ call split(string,"_",species,sep)
+ satname = trim(prefix)//'_'//trim(species)
+ write(logid,*) 'prefix satellite file = ',satname
+ exit
+ endif
+ end do
close(100)
+ else
+ write(logid,*) 'ERROR save_obs: obsfiles.txt not found'
+ stop
+ endif
+
+ ! loop over days writing one file per day
+ jd = juldatei
+ do while ( jd .le. juldatef )
+ cnt = 0
+ do i = 1, nobs
+ ! check if observation is a satellite retrieval
+ read(recs(i),*,iostat=ierr) nretr
+ if ( ierr.eq.0 ) then
+ lsatellite = .true.
+ else
+ lsatellite = .false.
+ endif
+ if ( lsatellite ) then
+ ! check if observation is for current day
+ jdobs = juldate(jjjjmmdd(i), 0)
+ if ( jdobs.ne.jd ) cycle
+ cnt = cnt + 1
+ vmr(cnt) = obs(i)
+ endif
+ end do ! nobs
+ ! copy original ncdf file and replace vmr with obs
+ call caldate(jd, currentdate, currenttime)
+ write(adate,fmt='(I8.8)') currentdate
+ filename = 'retrieval_'//trim(satname)//'_'//adate//'.nc'
+ print*, 'mod_save: filename = ',filename
+ call system('cp '//trim(files%path_satobs)//trim(filename)//' '//trim(files%path_output)//trim(filename))
+ call check( nf90_open(trim(files%path_output)//trim(filename),nf90_WRITE,ncid) )
+ call check( nf90_inq_dimid(ncid,'retrieval',dimid) )
+ call check( nf90_inquire_dimension(ncid,dimid,len=numretr) )
+ ! check consistent number of retrievals
+ if ( cnt.ne.numretr ) then
+ write(logid,*) 'ERROR: inconsistent number of retrievals for day ',currentdate,': numretr, cnt = ',numretr,cnt
+ stop
+ endif
+ call check( nf90_inq_varid(ncid,'vmr',varid) )
+ call check( nf90_put_var(ncid, varid, vmr(1:numretr)) )
+ call check( nf90_close(ncid) )
+ ! next day
+ jd = jd + 1d0
+ vmr(:) = 0.
end do
end subroutine save_obs
diff --git a/prep_syndata/mod_settings.f90 b/prep_syndata/mod_settings.f90
index 15d09a1..d3061cf 100644
--- a/prep_syndata/mod_settings.f90
+++ b/prep_syndata/mod_settings.f90
@@ -31,7 +31,7 @@ module mod_settings
implicit none
private
- public :: files_t, config_t, read_file_settings, read_config_settings, parse_string
+ public :: files_t, config_t, read_file_settings, read_config_settings, parse_string, split
! files_t contains information on paths and files
@@ -39,9 +39,11 @@ module mod_settings
character(len=max_path_len) :: path_prior ! path to prior fluxes
character(len=max_path_len) :: path_obs ! path to observations
+ character(len=max_path_len) :: path_satobs ! path to satellite observations
character(len=max_path_len) :: path_output ! path to output
character(len=max_name_len) :: suffix ! observation file name suffix
character(len=max_path_len) :: path_flexpart ! path to flexpart output
+ character(len=max_path_len) :: path_flexsat ! path to flexpart output for satellite obs
character(len=max_name_len) :: file_log ! log file name
character(len=max_path_len) :: file_regions ! region definitions file
character(len=max_name_len) :: varname_regs ! regions variable name
@@ -97,6 +99,8 @@ module mod_settings
real :: statres_hr ! sub-daily temporal resolution of state vector (e.g. 6, 12 or 24h)
real :: measerr ! measurement error
logical :: lognormal ! use lognormal distribution in state space (true or false)
+ logical :: satellite ! use satellite observations (true or false)
+ logical :: ground ! use ground-based observations (true or false)
real :: trunc ! truncation factor for eigenvalues of B
end type config_t
@@ -325,12 +329,18 @@ module mod_settings
identifier = "path_obs:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_obs = cc
+ identifier = "path_satobs:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) files%path_satobs = cc
identifier = "suffix:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%suffix = cc
identifier = "path_flexpart:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_flexpart = cc
+ identifier = "path_flexsat:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) files%path_flexsat = cc
identifier = "path_output:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_output = cc
@@ -462,6 +472,8 @@ module mod_settings
! logical defaults
config%lognormal = .false.
+ config%satellite = .false.
+ config%ground = .false.
config%trunc = 1.e-3
! open file
@@ -514,6 +526,14 @@ module mod_settings
identifier = "lognormal:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) config%lognormal = cl
+ identifier = "satellite:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) config%satellite = cl
+ identifier = "ground:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) config%ground = cl
+
+ ! other settings
identifier = "trunc:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) config%trunc = cn
@@ -561,6 +581,10 @@ module mod_settings
print*, 'WARNING read_config_settings: for CO2 cannot use lognormal -> changing to normal'
config%lognormal = .false.
endif
+ if ( .not.config%ground.and..not.config%satellite ) then
+ print*, 'ERROR: at least one of satellite or ground must be true'
+ stop
+ endif
end subroutine read_config_settings
diff --git a/prep_syndata/mod_strings.f90 b/prep_syndata/mod_strings.f90
index 342df59..b360d14 100644
--- a/prep_syndata/mod_strings.f90
+++ b/prep_syndata/mod_strings.f90
@@ -111,17 +111,26 @@ module mod_strings
character(*), intent(in) :: repstr
character(max_path_len) :: string_out
character(max_path_len) :: strtmp1, strtmp2
- integer :: strlen, replen, n
+ integer :: strlen, substrlen, replen, n
strlen = len_trim(string_in)
replen = len_trim(repstr)
+ substrlen = len_trim(substr)
! find first position of substr in string_in
n = index( string_in, substr, back=.false. )
- strtmp1 = string_in(1:n-1)
+ if ((n-1).gt.0) then
+ strtmp1 = string_in(1:n-1)
+ else
+ ! empty string
+ strtmp1 = ''
+ n = 1
+ endif
+! print*, 'str_replace first pos n, strtmp1 = ',n, strtmp1
! find last position of substr in string_in
- n = index( string_in, substr, back=.true. )
- strtmp2 = string_in(n+replen:strlen)
- string_out = trim(strtmp1)//trim(repstr)//trim(strtmp2)
+ n = index( string_in, substr, back=.true. )
+ strtmp2 = string_in(n+substrlen:strlen)
+! print*, 'str_replace last pos n, strtmp2 = ',n, strtmp2
+ string_out = trim(strtmp1)//trim(repstr)//trim(strtmp2)
end function str_replace
diff --git a/prep_syndata/sbatch.sh b/prep_syndata/sbatch.sh
index c9a2770..b74a4e8 100755
--- a/prep_syndata/sbatch.sh
+++ b/prep_syndata/sbatch.sh
@@ -2,8 +2,8 @@
#---------------------------------------------------
priority=0
partition=nilu
-settings_files='/mypath/settings/SETTINGS_ghg_files'
-settings_config='/mypath/settings/SETTINGS_ghg_config'
+settings_files='/mypath/settings/SETTINGS_files'
+settings_config='/mypath/settings/SETTINGS_config'
#---------------------------------------------------
cat <<EOF > run_job.sh
diff --git a/settings/SETTINGS_ghg_nest_config b/settings/SETTINGS_ch4sat_config
similarity index 78%
rename from settings/SETTINGS_ghg_nest_config
rename to settings/SETTINGS_ch4sat_config
index ca53281..ccc7bfb 100644
--- a/settings/SETTINGS_ghg_nest_config
+++ b/settings/SETTINGS_ch4sat_config
@@ -20,8 +20,8 @@ seed: 100
# Run dates: format yyyymmdd
# datei = start date
# datef = end date
-datei: 20120101
-datef: 20120131
+datei: 20200701
+datef: 20200731
# Use lognormal distribution (true or false) (only for non-CO2 species)
# if true need to use m1qn3 method
@@ -31,17 +31,17 @@ lognormal: .false.
trunc: 1.e-4
# Inversion method ('analytic', 'congrad' or 'm1qn3')
-method: congrad
+method: congrad
# Average/select flexpart releases (true or false)
-average_fp: .true.
+average_fp: .false.
# Number of iterations
# only used if method is 'congrad' or 'm1qn3'
maxiter: 10
# Optimize ocean boxes (true or false)
-inc_ocean: .true.
+inc_ocean: .false.
# Optimize initial mixing ratios (true or false)
opt_cini: .false.
@@ -55,9 +55,9 @@ spa_corr: .true.
# 1 = use prior best guess (file must be specified in SETTINGS_files)
prior_bg: 0
-# Restart a crashed run
-# for congrad/m1qn3 will pick-up from last iteration
-# for analytic will only use pre-calculated covariance matrix and boundary conditions
+# Restart a crashed run
+# for congrad will pick-up from last iteration
+# for other methods will only use pre-calculated covariance matrix and boundary conditions
# 0 = new run
# 1 = restart crashed run
restart: 0
@@ -69,14 +69,23 @@ verbose: .false.
# Species ("co2" or "ghg")
spec: ghg
+# Use satellite observations (true or false)
+satellite: .true.
+
+# Use ground-based observations (true or false)
+ground: .false.
+
# Molar mass (in flux files, e.g. CO2-C=12, CH4=16)
-molarmass: 16.
+molarmass: 16.
# Coefficient to convert from grid units of ppt to ppb
coeff: 1.e-3
+# Coefficient to convert satellite data to units of ppbv or ppmv
+coeffsat: 1.
+
# Use nested flexpart output (true or false)
-nested: .true.
+nested: .false.
# Inversion domain:
# if using nested output it must match the inversion domain
@@ -86,12 +95,12 @@ nested: .true.
# n_edge_lat = lat of northern inversion grid
# xres = longitudinal grid resolution
# yres = latitudinal grid resolution
-w_edge_lon: -15
-s_edge_lat: 30
-e_edge_lon: 35
-n_edge_lat: 75
-xres: 0.5
-yres: 0.5
+w_edge_lon: -180
+s_edge_lat: -90
+e_edge_lon: 180
+n_edge_lat: 90
+xres: 2.0
+yres: 2.0
# Spatial aggregation of grid (true or false)
regions: .true.
@@ -99,9 +108,9 @@ regions: .true.
# State vector (days):
# temporal resolution at which NEE fluxes are optimized
# must be an integer multiple of 1 day
-statres: 10.
+statres: 30.
-# prior fluxes:
+# other prior fluxes:
# nstep_flx = time step of other fluxes (integer hours, for monthly data use 720)
nstep_flx: 720
@@ -109,33 +118,32 @@ nstep_flx: 720
# used if error in obs input <= zero
measerr: 5.0
-# Initial mixing ratio error: fraction
+# Initial mixing ratio scalar error: fraction
cinierr: 0.005
# Prior flux error: fraction
-flxerr: 0.5
+flxerr: 1.0
# Lower limit flux error: unit (kg/m2/h)
-flxerr_ll: 1.e-8
+flxerr_ll: 1.e-9
# Spatial correlation length for land: unit (km)
-sigma_land: 250.
+sigma_land: 200.
# Spatial correlation length for ocean: unit (km)
sigma_ocean: 1000.
# Temporal correlation length: unit (days)
-sigmatime: 30.
+sigmatime: 90.
# Total error for inversion domain (Tg/y)
-# globerr <= 0: prior error covariance matrix not scaled
-globerr: 10.
+globerr: 100.
# Settings for optimization of initial mixing ratios
# comma separated list of northern edges of latitude bands
cini_lat: -30.,0.,30.,90.
# comma separated list of upper level of vertical bands (upper most level > outheight(nzgrid))
-#cini_alt: 2000., 10000., 55000.
-cini_alt: 55000.
+cini_alt: 2000., 10000., 55000.
# time resolution for initial mixing ratio scalars (days)
cinires: 30.
+
diff --git a/settings/SETTINGS_ghg_nest_files b/settings/SETTINGS_ch4sat_files
similarity index 71%
rename from settings/SETTINGS_ghg_nest_files
rename to settings/SETTINGS_ch4sat_files
index 9d1574b..b50b2ee 100644
--- a/settings/SETTINGS_ghg_nest_files
+++ b/settings/SETTINGS_ch4sat_files
@@ -29,47 +29,51 @@
# ==================================================
# Paths:
-path_obs: /mypath/TEST_OUTPUT/OBS/GHG/
-path_prior: /mypath/TEST_OUTPUT/FLUXES/GHG/
-path_output: /mypath/TEST_OUTPUT/RESULTS/GHG/NEST/
-path_flexpart: /mypath/TEST_OUTPUT/FLEXOUT/GHG/NEST/
-path_flexncdf: /mypath/TEST_OUTPUT/RESULTS/GHG/NEST/
+path_satobs: /mypath/satellite_obs/
+# path_obs is for ground observations
+path_obs: /mypath/ground_obs/
+path_prior: /mypath/flux/
+path_output: /mypath/output/
+path_flexsat: /mypath/flexpart_output_sat/
+# path_flexpart is for ground observations
+path_flexpart: /mypath/flexpart_output/
+path_flexncdf: /mypath/flexpart_ncdf_out/
# Prior best guess file (if prior_bg = 1 in SETTINGS_config)
file_bg:
# Suffix by which to identify observation files
-suffix: CH4.txt
+suffix: .txt
# Log file:
file_log: flexinvert.log
-# Regions mask file:
-# needs to correspond to flexpart domain and resolution (if using nested output needs to correspond to nest)
-file_regions: /mypath/TEST_OUTPUT/regions_ghg_nest.nc
-varname_regs: regions
-lonname_regs: longitude
-latname_regs: latitude
-
# Orography file:
# needs to correspond to global flexpart domain and resolution
-file_orog: /mypath/TEST_OUTPUT/elev.2-deg.nc
+file_orog: /mypath/input/elev.2-deg.nc
varname_orog: data
lonname_orog: lon
latname_orog: lat
+# Regions mask file:
+# needs to correspond to flexpart domain and resolution (if using nested output needs to correspond to nest)
+file_regions: /mypath/output/regions_2x2.nc
+varname_regs: regions
+lonname_regs: longitude
+latname_regs: latitude
+
# Land-sea mask file:
# needs to correspond to flexpart domain and resolution (if using nested output needs to correspond to nest)
-file_lsm: /mypath/TEST_INPUT/lsm_0.5x0.5.nc
-varname_lsm: lsm
-lonname_lsm: lon
-latname_lsm: lat
+file_lsm: /mypath/input/lsm_2x2.nc
+varname_lsm: mask
+lonname_lsm: longitude
+latname_lsm: latitude
# Global prior flux file: flux kg/m2/h
# needs to correspond to flexpart domain and resolution
# generic name with year YYYY
filename_flx: CH4_TOTAL_YYYY_20x20.nc
-varname_flx: emisch4
+varname_flx: emi_ch4
lonname_flx: longitude
latname_flx: latitude
timename_flx: time
@@ -77,21 +81,22 @@ timename_flx: time
# Regional prior flux file: flux kg/m2/h
# only needed if using nested output (needs to correspond to nest)
# generic name with year YYYY
-filenest_flx: CH4_TOTAL_YYYY_05x05.nc
-varnest_flx: emisch4
-lonnest_flx: longitude
-latnest_flx: latitude
-timenest_flx: time
+filenest_flx:
+varnest_flx:
+lonnest_flx:
+latnest_flx:
+timenest_flx:
# Initial concentrations: conc ppb
# file_initconc given as generic name with year and month YYYYMM
-path_initconc: /mypath/TEST_INPUT/INIT_CONC/GHG/
-file_initconc: ch4_noaa_YYYYMM.nc
+path_initconc: /mypath/init_conc/
+file_initconc: cams73_v20r1_ch4_conc_surface_dm_YYYYMM.nc
varname_init: CH4
# type of product (1 = CAMS CH4, 2 = EGG4, 3 = CAMS N2O, 4 = FP-CTM (daily), 5 = NOAA interpolated (monthly), 6 = FP-CTM (monthly))
-init_type: 5
+init_type: 1
+
+# Receptor list file (only needed if ground observations are used):
+file_recept: /mypath/input/stnlist_global_ch4.txt
-# Receptor list file:
-file_recept: /mypath/TEST_INPUT/reclist_ghg.txt
diff --git a/settings/SETTINGS_co2_config b/settings/SETTINGS_co2_config
index 011642e..c35647a 100644
--- a/settings/SETTINGS_co2_config
+++ b/settings/SETTINGS_co2_config
@@ -67,6 +67,12 @@ restart: 0
# only use for debugging small runs
verbose: .false.
+# Use satellite observations (true or false)
+satellite: .false.
+
+# Use ground-based observations (true or false)
+ground: .true.
+
# Species ("co2" or "ghg")
spec: co2
diff --git a/settings/SETTINGS_co2_files b/settings/SETTINGS_co2_files
index 4af6a1f..b8deaab 100644
--- a/settings/SETTINGS_co2_files
+++ b/settings/SETTINGS_co2_files
@@ -29,11 +29,11 @@
# ==================================================
# Paths:
-path_obs: /mypath/TEST_OUTPUT/OBS/CO2/
-path_prior: /mypath/TEST_OUTPUT/FLUXES/CO2/
-path_output: /mypath/TEST_OUTPUT/RESULTS/CO2/NO_NEST/
-path_flexpart: /mypath/TEST_OUTPUT/FLEXOUT/CO2/NO_NEST/
-path_flexncdf: /mypath/TEST_OUTPUT/RESULTS/CO2/NO_NEST/
+path_obs: /mypath/obs/
+path_prior: /mypath/flux/
+path_output: /mypath/output/
+path_flexpart: /mypath/flexpart_output/
+path_flexncdf: /mypath/flexpart_ncdf_out/
# Prior best guess file (if prior_bg = 1)
file_bg:
@@ -46,21 +46,21 @@ file_log: flexinvert.log
# Regions mask file:
# needs to correspond to flexpart resolution (for nested output needs to correspond to nested resolution)
-file_regions: /mypath/TEST_OUTPUT/regions_co2.nc
+file_regions: /mypath/output/regions_co2.nc
varname_regs: regions
lonname_regs: longitude
latname_regs: latitude
# Orography file:
# needs to correspond to global flexpart domain and resolution
-file_orog: /mypath/TEST_INPUT/elev.1-deg.nc
+file_orog: /mypath/input/elev.1-deg.nc
varname_orog: data
lonname_orog: lon
latname_orog: lat
# Land-sea mask file:
# needs to correspond to flexpart resolution (for nested output needs to correspond to nested resolution)
-file_lsm: /mypath/TEST_INPUT/lsm_1x1.nc
+file_lsm: /mypath/input/lsm_1x1.nc
varname_lsm: lsm
lonname_lsm: lon
latname_lsm: lat
@@ -74,7 +74,7 @@ lonname_nee: longitude
latname_nee: latitude
timename_nee: time
-# Global prior fossil fuel (and bio-fuel/mass burning) flux file: flux kg/m2/h
+# Global prior fossil fuel (and bio-fuel/bio-mass burning) flux file: flux kg/m2/h
# needs to correspond to flexpart domain and resolution
# generic name with year and month YYYYMM
filename_ff: CO2_FF_YYYYMM_10x10.nc
@@ -101,7 +101,7 @@ lonnest_nee:
latnest_nee:
timenest_nee:
-# Regional prior fossil fuel (and bio-fuel/mass burning) flux file: flux kg/m2/h
+# Regional prior fossil fuel (and bio-fuel/bio-mass burning) flux file: flux kg/m2/h
# only specify if using nested output (needs to correspond to nested resolution)
# generic name with year and month YYYYMM
filenest_ff:
@@ -122,13 +122,13 @@ timenest_ocn:
# Initial concentrations: conc (default is ppm)
# file_initconc given as generic name with year and month YYYYMM
# also need months preceding and proceeding inversion interval
-path_initconc: /mypath/TEST_INPUT/INIT_CONC/CO2/
+path_initconc: /mypath/init_conc/
file_initconc: co2_noaa_YYYYMM.nc
varname_init: CO2
# type of product (1 = CAMS CH4, 2 = EGG4, 3 = CAMS N2O and CO2, 4 = FP-CTM (daily), 5 = NOAA interpolated (monthly), 6 = FP-CTM (monthly))
init_type: 5
# Receptor list file:
-file_recept: /mypath/TEST_INPUT/reclist_co2.txt
+file_recept: /mypath/input/reclist_co2.txt
diff --git a/settings/SETTINGS_co2_nest_config b/settings/SETTINGS_co2_nest_config
deleted file mode 100644
index 54ca08a..0000000
--- a/settings/SETTINGS_co2_nest_config
+++ /dev/null
@@ -1,161 +0,0 @@
-# ==================================================
-#
-# FLEXINVERT CONFIGURATION SETTINGS
-#
-# comment lines start with '#'
-# each parameter line starts with 'parameter name:'
-#
-# ==================================================
-
-# Run mode:
-# 0 = run forward model
-# 1 = run optimization
-# 2 = randomly perturb for MC
-run_mode: 1
-
-# Random number seed
-# (only used if run_mode = 2)
-seed: 100
-
-# Run dates: format yyyymmdd
-# datei = start date
-# datef = end date
-datei: 20120101
-datef: 20120131
-
-# Use lognormal distribution (true or false) (only for non-CO2 species)
-# if true need to use m1qn3 method
-lognormal: .false.
-
-# Truncation of eigenvalues of B (cut at trunc x largest eigenvalue)
-trunc: 1.e-6
-
-# Inversion method ('analytic', 'congrad' or 'm1qn3')
-method: m1qn3
-
-# Average/select flexpart releases (true or false)
-average_fp: .false.
-
-# Number of iterations
-# only used if method is 'congrad' or 'm1qn3'
-maxiter: 20
-
-# Optimize ocean boxes (true or false)
-# currently only for ghg species (CO2 ocean fluxes not optimized)
-inc_ocean: .false.
-
-# Optimize initial mixing ratios (true or false)
-opt_cini: .true.
-
-# Use spatial correlation in error covariance matrix (true or false)
-# if use regions based ecosystems then should be false
-spa_corr: .true.
-
-# Use best guess estimate from previous inversion (congrad only)
-# 0 = no best guess
-# 1 = use best guess (file must be specified in SETTINGS_files)
-prior_bg: 0
-
-# Restart a crashed run
-# for congrad/m1qn3 will pick-up from last iteration
-# for analytic will only use pre-calculated covariance matrix and boundary conditions
-# 0 = new run
-# 1 = restart crashed run
-restart: 0
-
-# Verbose output
-# only use for debugging small runs
-verbose: .false.
-
-# Species ("co2" or "ghg")
-spec: co2
-
-# Molar mass (in flux files, e.g. C=12, CH4=16)
-molarmass: 12.
-
-# Coefficient to convert from grid units of ppt to observation unit (e.g. ppm)
-coeff: 1.e-6
-
-# Use nested flexpart output (true or false)
-nested: .true.
-
-# Inversion domain:
-# if using nested output it must match the inversion domain
-# w_edge_lon = lon of western edge of inversion grid
-# s_edge_lat = lat of southern edge inversion grid
-# e_edge_lon = lon of eastern edge of inversion grid
-# n_edge_lat = lat of northern inversion grid
-# xres = longitudinal grid resolution
-# yres = latitudinal grid resolution
-w_edge_lon: -15
-s_edge_lat: 30
-e_edge_lon: 35
-n_edge_lat: 75
-xres: 0.5
-yres: 0.5
-
-# Spatial aggregation of grid (true or false)
-regions: .true.
-
-# State vector time resolution:
-# time resolution at which NEE fluxes are optimized
-# statres determines averaging interval over 1 or more days (given in days)
-# statres_hr determines time resolution within 1 day (given in hours)
-# e.g. statres = 10, statres_hr = 6 give 4 time intervals per day that are averaged over 10 days
-statres: 10
-statres_hr: 12
-
-# NEE prior fluxes:
-# nstep_nee = time step of NEE fluxes (integer hours)
-nstep_nee: 3
-nstep_nee_reg: 3
-
-# Fossil fuel prior fluxes:
-# nstep_ff = time step of fossil fuel emissions (integer hours, for monthly data use 720)
-# coef_ff = coefficient to convert from input flux units to kg/m2/h
-nstep_ff: 720
-nstep_ff_reg: 720
-coeff_ff: 1.
-coeff_ff_reg: 1.
-
-# Ocean prior fluxes:
-# nstep_ocn = time step of other fluxes (integer hours, for monthly data use 720)
-nstep_ocn: 720
-
-# Measurement error: unit same as obs
-# used if error in obs input <= zero
-measerr: 0.5
-
-# Initial mixing ratio error: fraction
-cinierr: 0.005
-
-# Prior flux error: fraction
-flxerr: 0.25
-
-# Fossil fuel error: fraction
-# only used to calculate uncertainty projected into observation space
-ffferr: 0.05
-
-# Spatial correlation length for land: unit (km)
-sigma_land: 50.
-
-# Spatial correlation length for ocean: unit (km)
-sigma_ocean: 2000.
-
-# Temporal correlation length: unit (days)
-sigmatime: 30.
-
-# Total error for domain (Tg/y)
-# globerr <= 0: prior error covariance matrix not scaled
-globerr: 300.
-
-# Settings for optimization of initial mixing ratios
-# comma separated list of northern edges of latitude bands
-cini_lat: -30.,0.,30.,90.
-# comma separated list of upper level of vertical bands (upper most level > outheight(nzgrid))
-#cini_alt: 2000., 10000., 55000.
-cini_alt: 55000.
-# time resolution for initial mixing ratio scalars (days)
-cinires: 30.
-
-
diff --git a/settings/SETTINGS_co2_nest_files b/settings/SETTINGS_co2_nest_files
deleted file mode 100644
index 2420049..0000000
--- a/settings/SETTINGS_co2_nest_files
+++ /dev/null
@@ -1,133 +0,0 @@
-# ==================================================
-#
-# FLEXINVERT FILE SETTINGS
-#
-# comment lines start with '#'
-# each parameter line starts with 'parameter name:'
-#
-# Prior fluxes file dimensions:
-# time : days since 1900
-# latitude : latitude degrees north midpoints
-# longitude : longitude degrees east midpoints
-#
-# Regional mask file dimensions:
-# latitude : latitude degrees north midpoints
-# longitude : longitude degrees east midpoints
-#
-# Land-sea mask file dimensions:
-# latitude : latitude degrees north midpoints
-# longitude : longitude degrees east midpoints
-#
-# Initial concentrations file dimensions:
-# latitude : latitude degrees north south boundary
-# longitude : longitude degrees east west boundary
-#
-# Receptor list file:
-# ascii file containing one column list of
-# receptor names
-#
-# ==================================================
-
-# Paths:
-path_obs: /mypath/TEST_OUTPUT/OBS/CO2/
-path_prior: /mypath/TEST_OUTPUT/FLUXES/CO2/
-path_output: /mypath/TEST_OUTPUT/RESULTS/CO2/NEST/
-path_flexpart: /mypath/TEST_OUTPUT/FLEXOUT/CO2/NEST/
-
-# Prior best guess file (if prior_bg = 1)
-file_bg:
-
-# Suffix by which to identify observation files
-suffix: .txt
-
-# Log file:
-file_log: flexinvert.log
-
-# Regions mask file:
-# needs to correspond to flexpart resolution (for nested output needs to correspond to nested resolution)
-file_regions: /mypath/TEST_OUTPUT/regions_co2_nest.nc
-varname_regs: regions
-lonname_regs: longitude
-latname_regs: latitude
-
-# Orography file:
-# needs to correspond to global flexpart domain and resolution
-file_orog: /mypath/TEST_INPUT/elev.2-deg.nc
-varname_orog: data
-lonname_orog: lon
-latname_orog: lat
-
-# Land-sea mask file:
-# needs to correspond to flexpart resolution (for nested output needs to correspond to nested resolution)
-file_lsm: /mypath/TEST_INPUT/lsm_0.5x0.5.nc
-varname_lsm: lsm
-lonname_lsm: lon
-latname_lsm: lat
-
-# Global prior NEE flux file: flux kg/m2/h
-# needs to correspond to flexpart domain and resolution
-# generic name with year YYYY
-filename_nee: CO2_NEE_YYYY_20x20.nc
-varname_nee: nee
-lonname_nee: longitude
-latname_nee: latitude
-timename_nee: time
-
-# Global prior fossil fuel (and bio-fuel/mass burning) flux file: flux kg/m2/h
-# needs to correspond to flexpart domain and resolution
-# generic name with year and month YYYYMM
-filename_ff: CO2_FF_YYYYMM_20x20.nc
-varname_ff: emisco2
-lonname_ff: longitude
-latname_ff: latitude
-timename_ff: time
-
-# Global prior ocean flux file: flux kg/m2/h
-# needs to correspond to flexpart domain and resolution
-# generic name with year YYYY
-filename_ocn: CO2_OCEAN_YYYY_20x20.nc
-varname_ocn: emisco2
-lonname_ocn: longitude
-latname_ocn: latitude
-timename_ocn: time
-
-# Regional prior NEE flux file: flux kg/m2/h
-# only specify if using nested output (needs to correspond to nested resolution)
-# generic name with year YYYY
-filenest_nee: CO2_NEE_YYYY_05x05.nc
-varnest_nee: nee
-lonnest_nee: longitude
-latnest_nee: latitude
-timenest_nee: time
-
-# Regional prior fossil fuel (and bio-fuel/mass burning) flux file: flux kg/m2/h
-# only specify if using nested output (needs to correspond to nested resolution)
-# generic name with year and month YYYYMM
-filenest_ff: CO2_FF_YYYYMM_05x05.nc
-varnest_ff: emission
-lonnest_ff: lon
-latnest_ff: lat
-timenest_ff: time
-
-# Regional prior ocean flux file: flux kg/m2/h
-# only specify if using nested output (needs to correspond to nested resolution)
-# generic name with year YYYY
-filenest_ocn: CO2_OCEAN_YYYY_05x05.nc
-varnest_ocn: emisco2
-lonnest_ocn: longitude
-latnest_ocn: latitude
-timenest_ocn: time
-
-# Initial concentrations: conc (default is ppm)
-# file_initconc given as generic name with year and month YYYYMM
-# also need months preceding and proceeding inversion interval
-path_initconc: /mypath/TEST_INPUT/INIT_CONC/CO2/
-file_initconc: co2_noaa_YYYYMM.nc
-varname_init: CO2
-# type of product (1 = CAMS CH4, 2 = EGG4, 3 = CAMS N2O and CO2, 4 = FP-CTM (daily), 5 = NOAA interpolated (monthly), 6 = FP-CTM (monthly))
-init_type: 5
-
-# Receptor list file:
-file_recept: /mypath/TEST_INPUT/reclist_co2.txt
-
-
diff --git a/settings/SETTINGS_ghg_config b/settings/SETTINGS_ghg_config
index f684ff0..225cc30 100644
--- a/settings/SETTINGS_ghg_config
+++ b/settings/SETTINGS_ghg_config
@@ -31,14 +31,14 @@ lognormal: .false.
trunc: 1.e-4
# Inversion method ('analytic', 'congrad' or 'm1qn3')
-method: analytic
+method: congrad
# Average/select flexpart releases (true or false)
average_fp: .true.
# Number of iterations
# only used if method is 'congrad' or 'm1qn3'
-maxiter: 2
+maxiter: 10
# Optimize ocean boxes (true or false)
inc_ocean: .true.
@@ -66,6 +66,12 @@ restart: 0
# only use for debugging small runs
verbose: .true.
+# Use satellite observations (true or false)
+satellite: .false.
+
+# Use ground-based observations (true or false)
+ground: .true.
+
# Species ("co2" or "ghg")
spec: ghg
diff --git a/settings/SETTINGS_ghg_files b/settings/SETTINGS_ghg_files
index 663abb9..9685143 100644
--- a/settings/SETTINGS_ghg_files
+++ b/settings/SETTINGS_ghg_files
@@ -29,11 +29,11 @@
# ==================================================
# Paths:
-path_obs: /mypath/TEST_OUTPUT/OBS/GHG/
-path_prior: /mypath/TEST_OUTPUT/FLUXES/GHG/
-path_output: /mypath/TEST_OUTPUT/RESULTS/GHG/NO_NEST/congrad/
-path_flexpart: /mypath/TEST_OUTPUT/FLEXOUT/GHG/NO_NEST/
-path_flexncdf: /mypath/TEST_OUTPUT/RESULTS/GHG/NO_NEST/congrad/
+path_obs: /mypath/obs/
+path_prior: /mypath/flux/
+path_output: /mypath/output/
+path_flexpart: /mypath/flexpart_output/
+path_flexncdf: /mypath/flexpart_ncdf_out/
# Prior best guess file (if prior_bg = 1 in SETTINGS_config)
file_bg:
@@ -46,21 +46,21 @@ file_log: flexinvert.log
# Regions mask file:
# needs to correspond to flexpart domain and resolution (if using nested output needs to correspond to nest)
-file_regions: /mypath/TEST_OUTPUT/regions_ghg.nc
+file_regions: /mypath/output/regions_ghg.nc
varname_regs: regions
lonname_regs: longitude
latname_regs: latitude
# Orography file:
# needs to correspond to global flexpart domain and resolution
-file_orog: /xnilu_wrk/users/rlt/LANDCOVER/elev.1-deg.nc
+file_orog: /mypath/input/elev.1-deg.nc
varname_orog: data
lonname_orog: lon
latname_orog: lat
# Land-sea mask file:
# needs to correspond to flexpart domain and resolution (if using nested output needs to correspond to nest)
-file_lsm: /mypath/TEST_INPUT/lsm_1x1.nc
+file_lsm: /mypath/input/lsm_1x1.nc
varname_lsm: lsm
lonname_lsm: lon
latname_lsm: lat
@@ -85,13 +85,13 @@ timenest_flx:
# Initial concentrations: conc ppb
# file_initconc given as generic name with year and month YYYYMM
-path_initconc: /mypath/TEST_INPUT/INIT_CONC/GHG/
+path_initconc: /mypath/init_conc/
file_initconc: ch4_noaa_YYYYMM.nc
varname_init: CH4
# type of product (1 = CAMS CH4, 2 = EGG4, 3 = CAMS N2O, 4 = FP-CTM (daily), 5 = NOAA interpolated (monthly), 6 = FP-CTM (monthly))
init_type: 5
# Receptor list file:
-file_recept: /mypath/TEST_INPUT/reclist_ghg.txt
+file_recept: /mypath/input/reclist_ghg.txt
diff --git a/source/README_source.txt b/source/README_source.txt
index ec2f2b3..b978b3a 100644
--- a/source/README_source.txt
+++ b/source/README_source.txt
@@ -1,11 +1,11 @@
================================================================
- FLEXINVERT-Plus
+ FLEXINVERT source code
================================================================
Description:
- FLEXINVERT-Plus is a Bayesian inversion framework
+ FLEXINVERT is a Bayesian inversion framework
for optimizing fluxes of different atmospheric
species (e.g. CO2, CH4, BC).
diff --git a/source/average_fp.f90 b/source/average_fp.f90
index fc854fa..4600328 100755
--- a/source/average_fp.f90
+++ b/source/average_fp.f90
@@ -76,13 +76,14 @@ subroutine average_fp(files, config, obs)
real, dimension(nnxgrid,nnygrid,maxngrid):: gridnest_tmp ! flexpart nest flux sensitivity (or footprints), temporary to later calculate average
real(kind=8), dimension(maxngrid) :: gtime ! flux sensitivity time stamp (julian days)
real(kind=8), dimension(maxngrid) :: gtime_tmp ! flux sensitivity time stamp (julian days) of first footprint per observation
- integer :: ngrid
+ integer :: ngrid, nretr, ierr
real :: bndx, bndy, delx, dely
integer :: numx, numy, xshift, new_grid_time, standard_grid_time
integer :: numpoint, release_nr, nr_footprints
integer :: ibdate, ibtime
real(kind=8), dimension(maxpoint,2) :: releases
+ logical :: lsatellite ! logical indicating if observation is from satellite
! loop over observations
! ----------------------
@@ -91,6 +92,15 @@ subroutine average_fp(files, config, obs)
do i = 1, nobs
+ ! check if observation is from satellite and if so skip
+ read(obs%recs(i),*,iostat=ierr) nretr
+ if ( ierr.eq.0 ) then
+ lsatellite = .true.
+ else
+ lsatellite = .false.
+ endif
+ if ( lsatellite ) cycle
+
! reset values
gtime_tmp(:) = 0d0
grid_tmp(:,:,:) = 0.
diff --git a/source/calc_conc.f90 b/source/calc_conc.f90
index e8f74af..d08fdd0 100644
--- a/source/calc_conc.f90
+++ b/source/calc_conc.f90
@@ -54,7 +54,7 @@ subroutine calc_conc(config, fluxes, obs, ngrid, gtime, hnest, hbkg, iobs, ix1,
real, dimension(nxgrid,nygrid), intent (in) :: hbkg
integer, intent (in) :: ngrid, iobs, ix1, ix2, jy1, jy2
- integer :: n, ns, ni, flag, ind, ilo, ihi
+ integer :: n, ns, ni, flag, ind, ilo, ihi, ierr
real, dimension(nxgrid,nygrid) :: flxbg
real :: bkgerr, ffferr
@@ -149,9 +149,11 @@ subroutine calc_conc(config, fluxes, obs, ngrid, gtime, hnest, hbkg, iobs, ix1,
! -----------------------
if ( trim(config%spec).eq.'co2' ) then
- obs%err(iobs) = sqrt(obs%measerr(iobs)**2 + bkgerr + ffferr)
+ ! CO2
+ obs%err(iobs) = sqrt(obs%measerr(iobs)**2 + (sum(obs%cini(iobs,:))*config%cinierr)**2 + bkgerr + ffferr)
else
- obs%err(iobs) = sqrt(obs%measerr(iobs)**2 + bkgerr)
+ ! GHG
+ obs%err(iobs) = sqrt(obs%measerr(iobs)**2 + (sum(obs%cini(iobs,:))*config%cinierr)**2 + bkgerr)
endif
end subroutine calc_conc
diff --git a/source/congrad.f90 b/source/congrad.f90
index e88fd53..e1ef950 100644
--- a/source/congrad.f90
+++ b/source/congrad.f90
@@ -14,7 +14,7 @@
! You should have received a copy of the GNU General Public License
! along with FLEXINVERT. If not, see <http://www.gnu.org/licenses/>.
!
-! Copyright 2017, Rona Thompson
+! Adapted from the code of Mike Fisher (ECMWF) by Rona Thompson, 2017
!---------------------------------------------------------------------------------------
!
!> congrad
@@ -43,7 +43,9 @@
!!
!! References: Lanczos, C., J. Res. Natl. Bur. Standards, 45, 255-282, 1950
!! Paige, C. C. & Saunders, M. A., SIAM J. Numerical Aanalysis, 12(4), 1975
-!! Based on the code of Mike Fisher, ECMWF
+!!
+!! Based on the code of Mike Fisher, ECMWF, 2002
+!! and the adaptation of Frederic Chevallier, LSCE, 2004
!
!---------------------------------------------------------------------------------------
@@ -184,6 +186,10 @@ subroutine congrad(iter, grad, files, config, fluxes, obs, states, covar)
cost = 0.5*(cost_p + cost_o)
write(aiter,'(I2.2)') iter
write(logid,*) 'Cost iteration '//aiter//': ',cost
+ if ( isnan(cost) ) then
+ write(logid,*) 'ERROR congrad: cost is nan'
+ stop
+ endif
endif
! transform gradient to chi space
diff --git a/source/get_initconc.f90 b/source/get_initconc.f90
index 35dc1ab..f4b335a 100644
--- a/source/get_initconc.f90
+++ b/source/get_initconc.f90
@@ -207,7 +207,7 @@ subroutine get_initconc(files, config, filename, ntime, concini)
mpres = mpres*100.
case (3)
! CAMS N2O and CO2
- if ( config%spec.eq.'n2o' ) then
+ if ( config%spec.eq.'ghg' ) then
! vertical coordinate is pressure
allocate( mpres(nz) )
call check( nf90_inq_varid(ncid,trim(prsname),varid) )
@@ -313,7 +313,7 @@ subroutine get_initconc(files, config, filename, ntime, concini)
zkind = 0
case (3)
! CAMS N2O and CO2
- if ( config%spec.eq.'n2o' ) then
+ if ( config%spec.eq.'ghg' ) then
do n = 1, nz
! at present temp not included so use estimate
geoh(:,:,n) = (gasc*ts/gc/mmol)*log(psurf/mpres(n))
@@ -330,9 +330,9 @@ subroutine get_initconc(files, config, filename, ntime, concini)
rpres = sum(surfp(:,:,:),dim=3)/real(nt)/pres(:,:,n)
geoh(:,:,n) = (gasc*ts/gc/mmol)*log(rpres)
end do
+ deallocate( rpres )
+ deallocate( surfp )
endif
- deallocate( rpres )
- deallocate( surfp )
zkind = 0
case (4)
! FP-CTM
diff --git a/source/init_cini.f90 b/source/init_cini.f90
index 19a493d..9577c63 100644
--- a/source/init_cini.f90
+++ b/source/init_cini.f90
@@ -63,7 +63,7 @@ subroutine init_cini(files, config, obs)
integer :: jjjjmm, jjjjmmdd, hhmiss, eomday
integer :: lasttime, startmonth
integer :: month, prevmonth
- integer :: ix, jy, kz, i, n, nt, nz, nhours, ntime, ierr
+ integer :: ix, jy, kz, i, iz, n, nt, nz, nhours, ntime, ierr
real(kind=8) :: jdi
real(kind=8), dimension(nobs) :: jdates
real, dimension(nobs,ncini) :: cini
@@ -76,6 +76,7 @@ subroutine init_cini(files, config, obs)
integer :: numpoint, release_nr, nr_init
integer :: ibdate, ibtime
real(kind=8), dimension(maxpoint,2) :: releases
+ logical :: lsatellite
integer :: nretr
character(len=recname_len) :: anretr
@@ -113,18 +114,31 @@ subroutine init_cini(files, config, obs)
gridini(:,:,:) = 0.
nr_init = 0
- print*, 'obs%recs(i) = ',obs%recs(ind(i))
+ ! check if observation is a satellite retrieval
+ read(obs%recs(ind(i)),*,iostat=ierr) nretr
+ if ( ierr.eq.0 ) then
+ lsatellite = .true.
+ else
+ lsatellite = .false.
+ endif
+
+ print*, 'init_cini: obs%recs(i) = ',obs%recs(ind(i))
! check month of observation
call caldate(jdates(i), jjjjmmdd, hhmiss)
write(adate,'(I6.6)') jjjjmmdd/100
write(areldate,'(I8.8)') jjjjmmdd
month = jjjjmmdd/100
- path_flexrec = trim(files%path_flexpart)//trim(obs%recs(ind(i)))//'/'//trim(adate)//'/'
+ if ( lsatellite ) then
+ path_flexrec = trim(files%path_flexsat)//trim(areldate)//'/'
+ else
+ path_flexrec = trim(files%path_flexpart)//trim(obs%recs(ind(i)))//'/'//trim(adate)//'/'
+ endif
- if ( config%average_fp ) then
+ if ( config%average_fp.and..not.lsatellite ) then
! match and, if needed, average grid_initial files to observation timestamp
+ ! note: average_fp is not possible for satellite observations
! get header and release information related to current observation location
! (if not already read and same for previous observation)
@@ -176,6 +190,8 @@ subroutine init_cini(files, config, obs)
end do ! finished summing grid_initial
! convert from ppt to fraction of one
gridini = gridini*1.e-12
+ ! normalize to one
+ gridini = gridini/sum(gridini)
gridini = gridini/real(nr_init)
else
! filename not found
@@ -190,7 +206,13 @@ subroutine init_cini(files, config, obs)
! define file name
write(areldate,'(I8.8)') jjjjmmdd
write(areltime,'(I6.6)') hhmiss
- filename = trim(path_flexrec)//'grid_initial_'//trim(areldate)//trim(areltime)//'_001'
+ if ( lsatellite ) then
+ ! satellite observation
+ write(anretr,'(I6.6)') nretr
+ filename = trim(path_flexrec)//'grid_initial_'//trim(areldate)//'_'//trim(anretr)
+ else
+ filename = trim(path_flexrec)//'grid_initial_'//trim(areldate)//trim(areltime)//'_001'
+ endif
print*, 'init_cini: filename = ',filename
! read flexpart grid_init file
inquire(file=trim(filename),exist=lexist)
@@ -198,6 +220,11 @@ subroutine init_cini(files, config, obs)
call read_init(filename, gridini)
! convert from ppt to fraction of one
gridini = gridini*1.e-12
+ if ( lsatellite ) then
+ ! satellite convert to mole fraction
+ ! NO LONGER NEEDED WITH NEW FP VERSION
+! gridini = gridini/obs%cdryair(ind(i))
+ endif
else
write(logid,*) 'WARNING: cannot find ',filename
go to 10
@@ -253,10 +280,12 @@ subroutine init_cini(files, config, obs)
print*, 'init_cini: nhours = ',nhours
print*, 'init_cini: nt = ',nt
do kz = 1, nzgrid
- nz = 0
- do while(.true.)
- nz = nz + 1
- if ( outheight(kz).lt.cini_alt(nz) ) exit
+ nz = nzcini
+ do iz = 1, nzcini
+ if ( outheight(kz).lt.cini_alt(iz) ) then
+ nz = iz
+ exit
+ endif
end do
do jy = 1, nygrid
n = 0
@@ -283,6 +312,7 @@ subroutine init_cini(files, config, obs)
if (allocated( concini )) deallocate( concini )
+
end subroutine init_cini
diff --git a/source/init_cini_month.f90 b/source/init_cini_month.f90
index d709da6..f2f56d9 100644
--- a/source/init_cini_month.f90
+++ b/source/init_cini_month.f90
@@ -59,7 +59,7 @@ subroutine init_cini_month(files, config, obs)
logical :: lexist
integer :: lastjjjjmm, prejjjjmm, projjjjmm
integer :: jjjjmm, jjjjmmdd, hhmiss, mm, eomday
- integer :: ix, jy, kz, i, n, nz, ntime
+ integer :: ix, jy, kz, i, iz, n, nz, ntime
integer :: month, prevmonth
real :: conc
real(kind=8) :: jdmid, jdpre, jdlast
@@ -74,6 +74,7 @@ subroutine init_cini_month(files, config, obs)
integer :: numpoint, release_nr, nr_init
integer :: ibdate, ibtime
real(kind=8), dimension(maxpoint,2) :: releases
+ logical :: lsatellite
integer :: nretr, ierr
character(len=6) :: anretr
@@ -98,16 +99,31 @@ subroutine init_cini_month(files, config, obs)
gridini(:,:,:) = 0.
nr_init = 0
+ ! check if observation is a satellite retrieval
+ read(obs%recs(ind(i)),*,iostat=ierr) nretr
+ if ( ierr.eq.0 ) then
+ lsatellite = .true.
+ else
+ lsatellite = .false.
+ endif
+
! check month of observation
call caldate(jdates(i), jjjjmmdd, hhmiss)
write(adate,'(I6.6)') jjjjmmdd/100
write(areldate,'(I8.8)') jjjjmmdd
month = jjjjmmdd/100
- path_flexrec = trim(files%path_flexpart)//trim(obs%recs(ind(i)))//'/'//trim(adate)//'/'
+ if ( lsatellite ) then
+ ! satellite
+ path_flexrec = trim(files%path_flexsat)//trim(areldate)//'/'
+ else
+ ! ground-based
+ path_flexrec = trim(files%path_flexpart)//trim(obs%recs(ind(i)))//'/'//trim(adate)//'/'
+ endif
- if ( config%average_fp ) then
+ if ( config%average_fp.and..not.lsatellite ) then
! match and, if needed, average grid_initial files to observation timestamp
+ ! note: average_fp is not possible for satellite observations
! get header and release information related to current observation location
! (if not already read and same for previous observation)
@@ -159,6 +175,8 @@ subroutine init_cini_month(files, config, obs)
end do ! finished summing grid_initial
! convert from ppt to fraction of one
gridini = gridini*1.e-12
+ ! normalize to one
+ gridini = gridini/sum(gridini)
gridini = gridini/real(nr_init)
else
! filename not found
@@ -173,7 +191,14 @@ subroutine init_cini_month(files, config, obs)
! define file name
write(areldate,'(I8.8)') jjjjmmdd
write(areltime,'(I6.6)') hhmiss
- filename = trim(path_flexrec)//'grid_initial_'//trim(areldate)//trim(areltime)//'_001'
+ if ( lsatellite ) then
+ ! satellite observation
+ write(anretr,'(I6.6)') nretr
+ filename = trim(path_flexrec)//'grid_initial_'//trim(areldate)//'_'//trim(anretr)
+ else
+ ! ground based observation
+ filename = trim(path_flexrec)//'grid_initial_'//trim(areldate)//trim(areltime)//'_001'
+ endif
print*, 'init_cini_month: filename = ',filename
! read flexpart grid_init file
inquire(file=trim(filename),exist=lexist)
@@ -181,6 +206,11 @@ subroutine init_cini_month(files, config, obs)
call read_init(filename, gridini)
! convert from ppt to fraction of one
gridini = gridini*1.e-12
+ if ( lsatellite ) then
+ ! satellite convert to mole fraction
+ ! NO LONGER NEEDED WITH NEW FP VERSION
+! gridini = gridini/obs%cdryair(ind(i))
+ endif
else
write(logid,*) 'WARNING: cannot find ',filename
go to 10
@@ -220,11 +250,11 @@ subroutine init_cini_month(files, config, obs)
write(adate,'(I6.6)') projjjjmm
write(ayear,'(I4.4)') projjjjmm/100
select case ( files%init_type )
- case (4)
+ case (5)
pathname = str_replace(files%path_initconc, 'YYYY', ayear)
filename = str_replace(files%file_initconc, 'YYYYMM', adate)
filename = trim(pathname)//trim(filename)
- case (5)
+ case (6)
filename = str_replace(files%file_initconc, 'YYYYMM', adate)
filename = trim(files%path_initconc)//trim(filename)
end select
@@ -242,11 +272,11 @@ subroutine init_cini_month(files, config, obs)
write(adate,'(I6.6)') jjjjmm
write(ayear,'(I4.4)') jjjjmm/100
select case ( files%init_type )
- case (4)
+ case (5)
pathname = str_replace(files%path_initconc, 'YYYY', ayear)
filename = str_replace(files%file_initconc, 'YYYYMM', adate)
filename = trim(pathname)//trim(filename)
- case (5)
+ case (6)
filename = str_replace(files%file_initconc, 'YYYYMM', adate)
filename = trim(files%path_initconc)//trim(filename)
end select
@@ -262,11 +292,11 @@ subroutine init_cini_month(files, config, obs)
write(adate,'(I6.6)') prejjjjmm
write(ayear,'(I4.4)') prejjjjmm/100
select case ( files%init_type )
- case (4)
+ case (5)
pathname = str_replace(files%path_initconc, 'YYYY', ayear)
filename = str_replace(files%file_initconc, 'YYYYMM', adate)
filename = trim(pathname)//trim(filename)
- case (5)
+ case (6)
filename = str_replace(files%file_initconc, 'YYYYMM', adate)
filename = trim(files%path_initconc)//trim(filename)
end select
@@ -282,11 +312,11 @@ subroutine init_cini_month(files, config, obs)
write(adate,'(I6.6)') projjjjmm
write(ayear,'(I4.4)') projjjjmm/100
select case ( files%init_type )
- case (4)
+ case (5)
pathname = str_replace(files%path_initconc, 'YYYY', ayear)
filename = str_replace(files%file_initconc, 'YYYYMM', adate)
filename = trim(pathname)//trim(filename)
- case (5)
+ case (6)
filename = str_replace(files%file_initconc, 'YYYYMM', adate)
filename = trim(files%path_initconc)//trim(filename)
end select
@@ -304,10 +334,12 @@ subroutine init_cini_month(files, config, obs)
! calculate contribution of initial concentration to receptor
do kz = 1, nzgrid
- nz = 0
- do while(.true.)
- nz = nz + 1
- if ( outheight(kz).lt.cini_alt(nz) ) exit
+ nz = nzcini
+ do iz = 1, nzcini
+ if ( outheight(kz).lt.cini_alt(nz) ) then
+ nz = iz
+ exit
+ endif
end do
do jy = 1, nygrid
n = 0
diff --git a/source/init_co2.f90 b/source/init_co2.f90
index 2c3032f..ba580d1 100644
--- a/source/init_co2.f90
+++ b/source/init_co2.f90
@@ -85,7 +85,7 @@ subroutine init_co2(files, config, fluxes, obs, states, covar)
real, dimension(:,:,:), allocatable :: flx, flxnee, flxff, flxocn
real, dimension(:), allocatable :: xerr
integer, dimension(ndt) :: cnt
- integer :: nread, num
+ integer :: nread, num, numocn
integer :: eomday, eomday_save
integer :: jjjjmmdd, hhmiss, hh
real :: area
@@ -94,7 +94,7 @@ subroutine init_co2(files, config, fluxes, obs, states, covar)
integer :: n, nb, nd, nt, nts, i
integer :: ierr, lenstr
real(kind=8), dimension(:), allocatable :: jdate
- character(len=3), dimension(:), allocatable :: recs
+ character(len=recname_len), dimension(:), allocatable :: recs
real :: conc
character(len=20) :: dump
real, dimension(:,:), allocatable :: datain, dataout
@@ -398,10 +398,11 @@ subroutine init_co2(files, config, fluxes, obs, states, covar)
write(logid,*) 'Reading regional ocean fluxes'
! nested
fluxes%flxocn_nest(:,:,:) = 0.
- print*, 'init_co2: ocn reg timesteps input to read = ',(nday*24)/nt_ocn
- allocate( flxocn(nxregrid,nyregrid,(nday*24)/nt_ocn), stat = ierr )
+ numocn = max(1,(nday*24)/nt_ocn)
+ print*, 'init_co2: ocn reg timesteps input to read = ',numocn
+ allocate( flxocn(nxregrid,nyregrid,numocn), stat = ierr )
if ( ierr.ne.0 ) stop 'ERROR init_co2: not enough memory'
- allocate( timeocn((nday*24)/nt_ocn) )
+ allocate( timeocn(numocn) )
n = 0
jd = juldatei
do while ( jd.le.juldatef )
@@ -438,7 +439,7 @@ subroutine init_co2(files, config, fluxes, obs, states, covar)
flx)
! timestamp in julian days
do i = 1, nread
- if ( (n+i).gt.(nday*24)/nt_ocn ) exit
+ if ( (n+i).gt.numocn ) exit
timeocn(n+i) = jd + dble((i-1)*nt_ocn)/24d0
flxocn(:,:,n+i) = flx(:,:,i)
end do
@@ -446,7 +447,7 @@ subroutine init_co2(files, config, fluxes, obs, states, covar)
n = n + nread
jd = jd + dble(eomday_save)
end do
- n = min(n, (nday*24)/nt_ocn)
+ n = min(n, numocn)
print*, 'init_co2: ocnreg n = ',n
print*, 'init_co2: timeocn = ',timeocn
@@ -804,7 +805,7 @@ subroutine init_co2(files, config, fluxes, obs, states, covar)
endif
allocate( recs(nobs) )
allocate( jdate(nobs) )
- write(rowfmt,'(A,I6,A)') '(A3,1X,F14.6,1X,F10.4,1X,',ncini,'(F10.4,1X))'
+ write(rowfmt,'(A,I1,A,I6,A)') '(A',recname_len,',1X,F14.6,1X,F10.4,1X,',ncini,'(F10.4,1X))'
read(100,*) dump
do n = 1, nobs
read(100,rowfmt,iostat=ierr) recs(n), jdate(n), conc, obs%cini(n,:)
@@ -816,6 +817,10 @@ subroutine init_co2(files, config, fluxes, obs, states, covar)
! check consistency
if ( recs(1).ne.obs%recs(1).or.recs(nobs).ne.obs%recs(nobs).or.jdate(1).ne.obs%jdate(1).or.jdate(nobs).ne.obs%jdate(nobs) ) then
write(logid,*) 'ERROR init_co2: data in obsdatatype.txt inconsistent with run'
+ print*, recs(1), obs%recs(1)
+ print*, recs(nobs), obs%recs(nobs)
+ print*, jdate(1), obs%jdate(1)
+ print*, jdate(nobs), obs%jdate(nobs)
stop
endif
deallocate( recs )
diff --git a/source/init_ghg.f90 b/source/init_ghg.f90
index 3ad2314..63cb925 100644
--- a/source/init_ghg.f90
+++ b/source/init_ghg.f90
@@ -89,7 +89,7 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
integer :: i, n, nb, nread, num, eomday
integer :: ierr
real(kind=8), dimension(:), allocatable :: jdate, timeghg
- character(len=3), dimension(:), allocatable:: recs
+ character(len=recname_len), dimension(:), allocatable:: recs
real :: conc
character(len=20) :: dump
real, parameter :: smallnum=1.e-15
@@ -107,9 +107,9 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
! loop over prior flux files
- allocate( flxghg(nxgrid,nygrid,(nday*24/nt_flx)), stat = ierr )
+ allocate( flxghg(nxgrid,nygrid,max(1,(nday*24/nt_flx))), stat = ierr )
if ( ierr.ne.0 ) stop 'ERROR init_ghg: not enough memory'
- allocate( timeghg(nday*24/nt_flx) )
+ allocate( timeghg(max(1,nday*24/nt_flx)) )
n = 0
jd = juldatei
@@ -144,7 +144,7 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
jd, nread, num, &
flx)
do i = 1, nread
- if ( (n+i).gt.(nday*24/nt_flx) ) exit
+ if ( ((n+i).gt.(nday*24/nt_flx)).and.(nday*24/nt_flx.ne.0) ) exit
flxghg(:,:,n+i) = flx(:,:,i)
timeghg(n+i) = jd + dble((i-1)*nt_flx)/24d0
end do
@@ -153,6 +153,7 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
jd = jd + dble(eomday)
end do
n = min(n, nday*24/nt_flx)
+ n = max(n, 1)
print*, 'init_ghg: n = ',n
print*, 'init_ghg: timeghg = ',timeghg
@@ -174,7 +175,7 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
call average(nxgrid, n, timeghg, datain, ntstate, fluxes%time, dataout)
fluxes%flx(:,jy,:) = dataout(:,:)
end do
- else if ( statres.gt.real(nt_flx/24) ) then
+ else if ( statres.lt.real(nt_flx/24) ) then
! interpolate flux
do jy = 1, nygrid
datain = flxghg(:,jy,:)
@@ -207,9 +208,9 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
if ( config%nested ) then
- allocate( flxghg(nxregrid,nyregrid,(nday*24/nt_flx)), stat = ierr )
+ allocate( flxghg(nxregrid,nyregrid,(max(1,nday*24/nt_flx))), stat = ierr )
if ( ierr.ne.0 ) stop 'ERROR init_ghg: not enough memory'
- allocate( timeghg(nday*24/nt_flx) )
+ allocate( timeghg(max(1,nday*24/nt_flx)) )
n = 0
jd = juldatei
@@ -244,7 +245,7 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
jd, nread, num, &
flx)
do i = 1, nread
- if ( (n+i).gt.(nday*24)/nt_flx ) exit
+ if ( ((n+i).gt.(nday*24)/nt_flx).and.((nday*24)/nt_flx.ne.0) ) exit
timeghg(n+i) = jd + dble((i-1)*nt_flx)/24d0
flxghg(:,:,n+i) = flx(:,:,i)
end do
@@ -253,6 +254,7 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
jd = jd + dble(eomday)
end do
n = min(n, (nday*24)/nt_flx)
+ n = max(n, 1)
print*, 'init_ghg: reg n = ',n
print*, 'init_ghg: reg timeghg = ',timeghg
@@ -271,7 +273,7 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
call average(nxregrid, n, timeghg, datain, ntstate, fluxes%time, dataout)
fluxes%flx_nest(:,jy,:) = dataout(:,:)
end do
- else if ( statres.gt.real(nt_flx/24) ) then
+ else if ( statres.lt.real(nt_flx/24) ) then
! interpolate flux
do jy = 1, nyregrid
datain = flxghg(:,jy,:)
@@ -513,7 +515,7 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
endif
allocate( recs(nobs) )
allocate( jdate(nobs) )
- write(rowfmt,'(A,I6,A)') '(A3,1X,F14.6,1X,F10.4,1X,',ncini,'(F10.4,1X))'
+ write(rowfmt,'(A,I1,A,I6,A)') '(A',recname_len,',1X,F14.6,1X,F10.4,1X,',ncini,'(F10.4,1X))'
read(100,*) dump
do n = 1, nobs
read(100,rowfmt,iostat=ierr) recs(n), jdate(n), conc, obs%cini(n,:)
@@ -525,6 +527,10 @@ subroutine init_ghg(files, config, fluxes, obs, states, covar)
! check consistency
if ( recs(1).ne.obs%recs(1).or.recs(nobs).ne.obs%recs(nobs).or.jdate(1).ne.obs%jdate(1).or.jdate(nobs).ne.obs%jdate(nobs) ) then
write(logid,*) 'ERROR init_ghg: data in obsdatatype.txt inconsistent with run'
+ print*, recs(1), obs%recs(1)
+ print*, recs(nobs), obs%recs(nobs)
+ print*, jdate(1), obs%jdate(1)
+ print*, jdate(nobs), obs%jdate(nobs)
stop
endif
deallocate( recs )
diff --git a/source/initialize.f90 b/source/initialize.f90
index 64e4ef4..adbb03d 100644
--- a/source/initialize.f90
+++ b/source/initialize.f90
@@ -49,6 +49,7 @@ subroutine initialize(files, config)
logical :: lexist
integer :: yyyymm
character(len=6) :: adate
+ character(len=8) :: areldate
character(len=2) :: aiter
integer :: numpoint
integer :: ibdate, ibtime, jjjjmmdd, hhmiss
@@ -110,26 +111,35 @@ subroutine initialize(files, config)
filename = trim(files%file_recept)
inquire(file=trim(filename),exist=lexist)
- if (.not.lexist) then
+ if ( .not.lexist.and.config%ground ) then
write(logid,*) 'ERROR: cannot find '//trim(filename)
stop
+ else if ( lexist.and.config%ground ) then
+ write(logid,*) 'Reading receptor list: '//trim(filename)
+ call read_reclist(config, filename)
endif
- write(logid,*) 'Reading receptor list: '//trim(filename)
- call read_reclist(filename)
! initialize flexpart variables
! -----------------------------
! read header for global output
- yyyymm=config%datei/100
- write(adate,'(i6)') yyyymm
- lexist = .false.
- i = 1
- do while ( (.not.lexist).and.(i.le.nrec) )
- filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header'
+ if ( config%satellite.and.nrec.eq.0 ) then
+ ! satellite only
+ write(areldate,'(I8)') config%datei
+ filename = trim(files%path_flexsat)//areldate//'/header'
inquire(file=trim(filename),exist=lexist)
- i = i + 1
- end do
+ else
+ ! read from ground-based output
+ yyyymm=config%datei/100
+ write(adate,'(I6)') yyyymm
+ lexist = .false.
+ i = 1
+ do while ( (.not.lexist).and.(i.le.nrec) )
+ filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header'
+ inquire(file=trim(filename),exist=lexist)
+ i = i + 1
+ end do
+ endif ! satellite
if ( .not.lexist ) then
write(logid,*) 'ERROR initialize: cannot find flexpart header'
stop
@@ -137,6 +147,7 @@ subroutine initialize(files, config)
write(logid,*) 'Reading flexpart header: '//trim(filename)
call read_header(filename, numpoint, ibdate, ibtime, releases, &
numx, numy, bndx, bndy, delx, dely, xshift)
+
! global domain variables
nxgrid = numx
nygrid = numy
@@ -156,13 +167,21 @@ subroutine initialize(files, config)
! read header for nested output
if ( config%nested ) then
- lexist = .false.
- i = 1
- do while ( (.not.lexist).and.(i.le.nrec) )
- filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header_nest'
+ if ( config%satellite.and.nrec.eq.0 ) then
+ ! satellite only
+ write(areldate,'(I8)') config%datei
+ filename = trim(files%path_flexsat)//areldate//'/header_nest'
inquire(file=trim(filename),exist=lexist)
- i = i + 1
- end do
+ else
+ ! read from ground-based output
+ lexist = .false.
+ i = 1
+ do while ( (.not.lexist).and.(i.le.nrec) )
+ filename = trim(files%path_flexpart)//trim(recname(i))//'/'//adate//'/header_nest'
+ inquire(file=trim(filename),exist=lexist)
+ i = i + 1
+ end do
+ endif ! satellite
if ( .not.lexist ) then
write(logid,*) 'ERROR initialize: cannot find flexpart header_nest'
stop
@@ -170,6 +189,7 @@ subroutine initialize(files, config)
write(logid,*) 'Reading flexpart header_nest: '//trim(filename)
call read_header(filename, numpoint, ibdate, ibtime, releases, &
numx, numy, bndx, bndy, delx, dely, xshift)
+
! nested domain variables
nnxgrid = numx
nnygrid = numy
@@ -188,6 +208,25 @@ subroutine initialize(files, config)
end do
endif
+ ! some checks for CO2
+ ! -------------------
+
+ if (config%spec.eq.'co2') then
+ if (ndgrid.lt.6) then
+ write(logid,*) 'ERROR initialize: footprints in flexpart runs not'
+ write(logid,*) 'adequately resolved, ndgrid = ',ndgrid
+ stop
+ endif
+ if ( (mod((24/ndgrid),config%nstep_nee_reg).ne.0).and. &
+ (mod(config%nstep_nee_reg,(24/ndgrid)).ne.0) ) then
+ write(logid,*) 'ERROR initialize: footprint resolution and NEE prior resolution'
+ write(logid,*) 'should be an integral multiple of one or the other'
+ write(logid,*) 'ntstep_nee_reg = ',config%nstep_nee_reg
+ write(logid,*) 'ndgrid = ',ndgrid
+ stop
+ endif
+ endif
+
! nzgrid is z dimension of grid_init files (read from header)
! nzlev is z dimension of grid_time files with surface only
nzlev = 1
diff --git a/source/m1qn3_interface.f90 b/source/m1qn3_interface.f90
index 884d458..3fcbb38 100644
--- a/source/m1qn3_interface.f90
+++ b/source/m1qn3_interface.f90
@@ -209,6 +209,10 @@ subroutine m1qn3_interface(iter, grad, files, config, fluxes, obs, states, covar
write(logid,*) 'Cost 2Jo iteration '//aiter//' = ',cost_o
write(logid,*) 'Cost 2Jp iteration '//aiter//' = ',cost_p
write(logid,*) 'Cost iteration '//aiter//': ',cost
+ if ( isnan(cost) ) then
+ write(logid,*) 'ERROR congrad: cost is nan'
+ stop
+ endif
! save cost in case of a restart
open(100,file=trim(files%path_output)//'cost.txt',status='unknown',access='append',action='write',iostat=ierr)
write(100,fmt='(F13.4)') cost
diff --git a/source/mod_flexpart.f90 b/source/mod_flexpart.f90
index 7438cb1..08780c0 100755
--- a/source/mod_flexpart.f90
+++ b/source/mod_flexpart.f90
@@ -189,7 +189,7 @@ module mod_flexpart
real(kind=8), dimension(maxngrid), intent(in out) :: gtime
real, parameter :: scaleconc=1.e12
- real, parameter :: smallnum=1.e-38
+ real, parameter :: smallnum=tiny(0.)
logical :: lexist
integer :: ierr
integer :: nread
@@ -284,6 +284,12 @@ module mod_flexpart
! reverse order in time dimension
do nt = 1, ngrid
n = ngrid - nt + 1
+ ! remove spurious grid cells in footprint
+ do jy = 1, numy
+ do ix = 1, numx
+ if ( work(ix,jy,nt)>huge(0.) ) work(ix,jy,nt) = 0.
+ end do
+ end do
grid(:,:,n) = work(:,:,nt)
gtime(n) = jdtime(nt)
end do
@@ -366,7 +372,7 @@ module mod_flexpart
real, dimension(nxgrid,nygrid,nzgrid), intent(in out) :: gridinit
real, parameter :: scaleconc=1.e12
- real, parameter :: smallnum=1.e-38
+ real, parameter :: smallnum=tiny(0.)
logical :: lexist
integer :: ierr
integer :: sp_count_i, sp_count_r
@@ -443,7 +449,7 @@ module mod_flexpart
integer, intent(in) :: numx, numy, xshift
real, dimension(numx,numy,nread), intent(in out) :: factor
- real, parameter :: smallnum=1.e-38
+ real, parameter :: smallnum=tiny(0.)
logical :: lexist
integer :: ierr
integer :: sp_count_i, sp_count_r
diff --git a/source/mod_obs.f90 b/source/mod_obs.f90
index feaa559..c4f3f28 100644
--- a/source/mod_obs.f90
+++ b/source/mod_obs.f90
@@ -39,7 +39,7 @@ module mod_obs
type :: obs_t
real(kind=8), dimension(:), allocatable :: jdate ! julian dates
- character(len=max_name_len), dimension(:), allocatable :: recs ! receptor names
+ character(len=recname_len), dimension(:), allocatable :: recs ! receptor names
real, dimension(:), allocatable :: conc ! observed concentrations
real(kind=8), dimension(:), allocatable :: avetime ! time over which observation was made or averaged
real, dimension(:), allocatable :: ghg ! ghg best guess contribution to mixing ratio
@@ -54,6 +54,10 @@ module mod_obs
real, dimension(:), allocatable :: cinipos ! posterior inital concentrations
real, dimension(:), allocatable :: measerr ! measurement error
real, dimension(:), allocatable :: err ! total observation error
+ real, dimension(:), allocatable :: cpri ! prior total column mixing ratio for satellite
+ real, dimension(:), allocatable :: cakpri ! prior total column mixing ratio convolved with AK for satellite
+ real, dimension(:), allocatable :: cdryair ! total column moles of dry air (mol/m2)
+ real, dimension(:), allocatable :: cakav ! mean of column averaging kernel
end type
@@ -139,6 +143,26 @@ module mod_obs
write(logid,*) 'ERROR alloc_obs: not enough memory'
stop
endif
+ allocate( obs%cpri(nobs), stat = ierr )
+ if ( ierr.ne.0 ) then
+ write(logid,*) 'ERROR alloc_obs: not enough memory'
+ stop
+ endif
+ allocate( obs%cakpri(nobs), stat = ierr )
+ if ( ierr.ne.0 ) then
+ write(logid,*) 'ERROR alloc_obs: not enough memory'
+ stop
+ endif
+ allocate( obs%cdryair(nobs), stat = ierr )
+ if ( ierr.ne.0 ) then
+ write(logid,*) 'ERROR alloc_obs: not enough memory'
+ stop
+ endif
+ allocate( obs%cakav(nobs), stat = ierr )
+ if ( ierr.ne.0 ) then
+ write(logid,*) 'ERROR alloc_obs: not enough memory'
+ stop
+ endif
if ( config%spec.eq.'co2' ) then
allocate( obs%nee(nobs), stat = ierr )
@@ -166,6 +190,10 @@ module mod_obs
obs%measerr(:) = 0.
obs%err(:) = 0.
obs%ocn(:) = 0.
+ obs%cpri(:) = 0.
+ obs%cakpri(:) = 0.
+ obs%cdryair(:) = 0.
+ obs%cakav(:) = 1.
if ( config%spec.eq.'co2' ) then
obs%nee(:) = 0.
@@ -197,6 +225,10 @@ module mod_obs
if ( allocated(obs%ocn) ) deallocate(obs%ocn)
if ( allocated(obs%nee) ) deallocate(obs%nee)
if ( allocated(obs%fff) ) deallocate(obs%fff)
+ if ( allocated(obs%cpri) ) deallocate(obs%cpri)
+ if ( allocated(obs%cakpri) ) deallocate(obs%cakpri)
+ if ( allocated(obs%cdryair) ) deallocate(obs%cdryair)
+ if ( allocated(obs%cakav) ) deallocate(obs%cakav)
end subroutine dealloc_obs
@@ -212,11 +244,11 @@ module mod_obs
type (files_t), intent(in) :: files
type (obs_t), intent(in out) :: obs
- character(len=max_path_len) :: header
+ character(len=max_path_len) :: header, rowfmt
integer :: yyyymmdd, hhmiss
- character(len=4) :: recs
+ character(len=recname_len) :: recs
real(kind=8) :: jdate, avetime
- real :: conc, err
+ real :: conc, err, cpri, cakpri, cdryair, cakav
integer :: ierr
integer :: i
@@ -226,17 +258,19 @@ module mod_obs
! read all observations
open(200,file=trim(files%path_output)//'obsread.txt',action='read',status='old',iostat=ierr)
read(200,*) header
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,D14.6,1X,F10.6,1X,F10.4,1X,F10.4,F10.5,1X,F10.5,1X,F10.2,1X,F6.4)'
do i = 1, nobs
-! read(200,fmt='(A4,1X,I8,1X,I6,1X,D14.7,1X,F10.6,1X,F10.4,1X,F10.4)') &
-! recs, yyyymmdd, hhmiss, jdate, avetime, conc, err
- read(200,fmt='(A4,1X,I8,1X,I6,1X,D14.6,1X,F10.6,1X,F10.4,1X,F10.4)') &
- recs, yyyymmdd, hhmiss, jdate, avetime, conc, err
- obs%recs(i) = recs
+ read(200,fmt=rowfmt) recs, yyyymmdd, hhmiss, jdate, avetime, conc, err, cpri, cakpri, cdryair, cakav
+ obs%recs(i) = trim(recs)
obs%jdate(i) = jdate
obs%avetime(i) = avetime
obs%conc(i) = conc
obs%measerr(i) = err
obs%err(i) = err
+ obs%cpri(i) = cpri
+ obs%cakpri(i) = cakpri
+ obs%cdryair(i) = cdryair
+ obs%cakav(i) = cakav
end do
close(200)
diff --git a/source/mod_save.f90 b/source/mod_save.f90
index 94a61e6..aed5666 100644
--- a/source/mod_save.f90
+++ b/source/mod_save.f90
@@ -76,32 +76,30 @@ module mod_save
if ( config%spec.eq.'co2' ) then
! CO2 species
- write(100,*) 'rec yyyymmdd hhmmss juldate conc cini cinipos bkg nee fff ocn prior post diff error'
+ write(100,*) 'rec yyyymmdd hhmmss juldate conc cini cinipos bkg nee fff ocn prior post cpri cakpri diff error'
do i = 1, nobs
cinipri = sum(obs%cini(i,:))
call caldate(obs%jdate(i), jjjjmmdd, hhmiss)
- write(rowfmt,'(A,I6,A)') '(A3,1X,I8,1X,I6,1X,F14.6,1X,',11,'(F10.4,1X))'
+ write(rowfmt,'(A,I1,A,I6,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,',13,'(F10.4,1X))'
+ print*, 'save_obs: ',rowfmt
write(100,fmt=rowfmt) obs%recs(i), jjjjmmdd, hhmiss, obs%jdate(i), &
obs%conc(i), cinipri, obs%cinipos(i), obs%bkg(i), &
- obs%nee(i), obs%fff(i), obs%ocn(i), obs%prior(i), obs%model(i), obs%delta(i), obs%err(i)
+ obs%nee(i), obs%fff(i), obs%ocn(i), obs%prior(i), &
+ obs%model(i), obs%cpri(i), obs%cakpri(i), obs%delta(i), obs%err(i)
end do
else
! GHG species
- write(100,*) 'rec yyyymmdd hhmmss juldate conc cini cinipos bkg ghg prior post diff error'
- write(rowfmt,'(A,I6,A)') '(A3,1X,I8,1X,I6,1X,F14.6,1X,',9,'(F10.4,1X))'
+ write(100,*) 'rec yyyymmdd hhmmss juldate conc cini cinipos bkg ghg prior post cpri cakpri diff error'
+ write(rowfmt,'(A,I1,A,I6,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,',11,'(F10.4,1X))'
do i = 1, nobs
cinipri = sum(obs%cini(i,:))
call caldate(obs%jdate(i), jjjjmmdd, hhmiss)
- if ( config%lognormal.and..not.config%inc_ocean ) then
- ! if ocean grid cells not optimized include ocean contribution in prior and posterior model
- write(100,fmt=rowfmt) obs%recs(i), jjjjmmdd, hhmiss, obs%jdate(i), &
- obs%conc(i), cinipri, obs%cinipos(i), obs%bkg(i), &
- obs%ghg(i), obs%prior(i)+obs%ocn(i), obs%model(i)+obs%ocn(i), obs%delta(i), obs%err(i)
- else
- write(100,fmt=rowfmt) obs%recs(i), jjjjmmdd, hhmiss, obs%jdate(i), &
- obs%conc(i), cinipri, obs%cinipos(i), obs%bkg(i), &
- obs%ghg(i), obs%prior(i), obs%model(i), obs%delta(i), obs%err(i)
- endif
+ ! if log-normal and ocean grid cells not optimized include ocean contribution in prior and posterior model
+ ! in other case obs%ocn is zero
+ write(100,fmt=rowfmt) obs%recs(i), jjjjmmdd, hhmiss, obs%jdate(i), &
+ obs%conc(i), cinipri, obs%cinipos(i), obs%bkg(i), &
+ obs%ghg(i), obs%prior(i)+obs%ocn(i), obs%model(i)+obs%ocn(i), &
+ obs%cpri(i), obs%cakpri(i), obs%delta(i), obs%err(i)
end do
endif
@@ -138,7 +136,7 @@ module mod_save
call save_ghg(files, config, fluxes, states)
endif
if ( config%opt_cini ) then
- call save_scalar_cini(files, states)
+ call save_scalar_cini(files, config, states)
endif
end subroutine save_state
@@ -299,10 +297,16 @@ module mod_save
do jy = 1, nyregrid
! average to state vector timestamp
datain = fluxes%flxnee_nest(:,jy,:)
- call average(nxregrid, nday*ndgrid, fluxes%timefp, datain, ntstate, states%xtime, dataout)
+ if ((nday*ndgrid).gt.1.and.ntstate.gt.1) then
+ call average(nxregrid, nday*ndgrid, fluxes%timefp, datain, ntstate, states%xtime, dataout)
+ else if ((nday*ndgrid).gt.1) then
+ n = minloc(fluxes%timefp,dim=1,mask=abs(fluxes%timefp-states%xtime(1)).eq.minval(abs(fluxes%timefp-states%xtime(1))))
+ dataout(:,ntstate) = datain(:,n)
+ endif
fpri(:,jy,:) = fpri(:,jy,:) + dataout(:,:)/numscale
fpos(:,jy,:) = fpos(:,jy,:) + dataout(:,:)/numscale
end do
+ print*, 'completed NEE'
deallocate( datain )
deallocate( dataout )
@@ -328,12 +332,18 @@ module mod_save
do jy = 1, nyregrid
! average to state vector timestamp
datain = fluxes%flxff_nest(:,jy,:)
- call average(nxregrid, nday*ndgrid, fluxes%timefp, datain, ntstate, states%xtime, dataout)
+ if ((nday*ndgrid).gt.1.and.ntstate.gt.1) then
+ call average(nxregrid, nday*ndgrid, fluxes%timefp, datain, ntstate, states%xtime, dataout)
+ else if ((nday*ndgrid).gt.1) then
+ n = minloc(fluxes%timefp,dim=1,mask=abs(fluxes%timefp-states%xtime(1)).eq.minval(abs(fluxes%timefp-states%xtime(1))))
+ dataout(:,ntstate) = datain(:,n)
+ endif
fff_reg(:,jy,:) = dataout(:,:)/numscale
end do
+ print*, 'completed fossil fuel'
deallocate( datain )
deallocate( dataout )
-
+
! write ncdf file
! ---------------
@@ -793,24 +803,30 @@ module mod_save
!!
! --------------------------------------------------
- subroutine save_scalar_cini(files, states)
+ subroutine save_scalar_cini(files, config, states)
use mod_settings
use mod_states
use mod_var
type (files_t), intent(in) :: files
+ type (config_t), intent(in) :: config
type (states_t), intent(in) :: states
character(len=max_path_len) :: rowfmt
integer :: n, ierr
! write to file
- ! for lognormal these are the log transformed scalars
open(100,file=trim(files%path_output)//'scalars_cini.txt',status='replace',action='write',iostat=ierr)
write(rowfmt,'(A,I6,A)') '(',4,'(E11.4,1X))'
write(100,*) 'prior, pri_err, post, pos_err'
do n = 1, ntcini*ncini
- write(100,rowfmt) states%px0(npvar+n), states%pxerr0(npvar+n), states%px(npvar+n), states%pxerr(npvar+n)
+ if (config%lognormal) then
+ ! for lognormal these are the log transformed scalars
+ ! so undo the log transformation here
+ write(100,rowfmt) exp(states%px0(npvar+n)), exp(states%pxerr0(npvar+n)), exp(states%px(npvar+n)), exp(states%pxerr(npvar+n))
+ else
+ write(100,rowfmt) states%px0(npvar+n), states%pxerr0(npvar+n), states%px(npvar+n), states%pxerr(npvar+n)
+ endif
end do
close(100)
@@ -839,7 +855,7 @@ module mod_save
! write to file
open(100,file=trim(files%path_output)//'obsdatatype.txt',status='replace',action='write',iostat=ierr)
- write(rowfmt,'(A,I6,A)') '(A3,1X,F14.6,1X,F10.4,1X,',ncini,'(F10.4,1X))'
+ write(rowfmt,'(A,I1,A,I6,A)') '(A',recname_len,',1X,F14.6,1X,F10.4,1X,',ncini,'(F10.4,1X))'
write(100,*) 'recs jdate conc cini'
do i = 1, nobs
write(100,rowfmt) obs%recs(i), obs%jdate(i), obs%conc(i), obs%cini(i,:)
diff --git a/source/mod_settings.f90 b/source/mod_settings.f90
index 2df1248..7f847fd 100644
--- a/source/mod_settings.f90
+++ b/source/mod_settings.f90
@@ -38,10 +38,13 @@ module mod_settings
type :: files_t
character(len=max_path_len) :: path_obs ! path to observations
+ character(len=max_path_len) :: path_satobs ! path to satellite observations
character(len=max_path_len) :: path_prior ! path to prior fluxes
character(len=max_path_len) :: path_output ! path to output
- character(len=max_path_len) :: path_flexpart ! path to flexpart output
+ character(len=max_path_len) :: path_flexpart ! path to flexpart output for ground-based obs
+ character(len=max_path_len) :: path_flexsat ! path to flexpart output for satellite obs
character(len=max_path_len) :: path_flexncdf ! path to flexpart netcdf output (from previous run)
+! character(len=max_path_len) :: path_satrel ! path to satellite releases info
character(len=max_path_len) :: file_bg ! prior best guess file
character(len=max_name_len) :: suffix ! observation file suffix
character(len=max_name_len) :: file_log ! log file name
@@ -127,6 +130,9 @@ module mod_settings
integer :: restart ! restart a run that crashed (0=false, 1=true)
real :: molarmass ! molar mass of species (corresponds to flux files, e.g. C=12, CH4=16)
real :: coeff ! conversion coefficient from ppt to ppm or ppbv
+ logical :: satellite ! use satellite observations (true or false)
+ logical :: ground ! use ground-based observations (true or false)
+ real :: coeffsat ! conversion coefficient for satellite data to ppm or ppbv
logical :: nested ! use nested flexpart output (true or false)
real :: w_edge_lon ! lon of western edge of inversion grid
real :: s_edge_lat ! lat of southern edge of inversion grid
@@ -378,15 +384,24 @@ module mod_settings
identifier = "path_obs:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_obs = cc
+ identifier = "path_satobs:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) files%path_satobs = cc
identifier = "path_prior:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_prior = cc
identifier = "path_flexpart:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_flexpart = cc
+ identifier = "path_flexsat:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) files%path_flexsat = cc
identifier = "path_flexncdf:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_flexncdf = cc
+! identifier = "path_satrel:"
+! call read_content (line, identifier, cc, cn, cl, match)
+! if ( match ) files%path_satrel = cc
identifier = "path_output:"
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) files%path_output = cc
@@ -625,6 +640,8 @@ module mod_settings
config%spa_corr = .false.
config%verbose = .false.
config%lognormal = .false.
+ config%satellite = .false.
+ config%ground = .false.
config%trunc = 1.e-3
! open file
@@ -720,6 +737,17 @@ module mod_settings
call read_content (line, identifier, cc, cn, cl, match)
if ( match ) config%coeff = real(cn,kind=4)
+ ! read observation settings
+ identifier = "satellite:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) config%satellite = cl
+ identifier = "ground:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) config%ground = cl
+ identifier = "coeffsat:"
+ call read_content (line, identifier, cc, cn, cl, match)
+ if ( match ) config%coeffsat = real(cn,kind=4)
+
! read inversion domain settings
identifier = "nested:"
call read_content (line, identifier, cc, cn, cl, match)
@@ -893,6 +921,10 @@ module mod_settings
print*, 'WARNING read_config_settings: for CO2 ocean fluxes are not optimized inc_ocean -> false'
config%inc_ocean = .false.
endif
+ if ( .not.config%ground.and..not.config%satellite ) then
+ print*, 'ERROR: at least one of satellite or ground must be true'
+ stop
+ endif
end subroutine read_config_settings
diff --git a/source/mod_strings.f90 b/source/mod_strings.f90
index ed4d3a7..826b3de 100644
--- a/source/mod_strings.f90
+++ b/source/mod_strings.f90
@@ -111,16 +111,25 @@ module mod_strings
character(*), intent(in) :: repstr
character(max_path_len) :: string_out
character(max_path_len) :: strtmp1, strtmp2
- integer :: strlen, replen, n
+ integer :: strlen, substrlen, replen, n
strlen = len_trim(string_in)
replen = len_trim(repstr)
+ substrlen = len_trim(substr)
! find first position of substr in string_in
n = index( string_in, substr, back=.false. )
- strtmp1 = string_in(1:n-1)
+ if ((n-1).gt.0) then
+ strtmp1 = string_in(1:n-1)
+ else
+ ! empty string
+ strtmp1 = ''
+ n = 1
+ endif
+! print*, 'str_replace first pos n, strtmp1 = ',n, strtmp1
! find last position of substr in string_in
n = index( string_in, substr, back=.true. )
- strtmp2 = string_in(n+replen:strlen)
+ strtmp2 = string_in(n+substrlen:strlen)
+! print*, 'str_replace last pos n, strtmp2 = ',n, strtmp2
string_out = trim(strtmp1)//trim(repstr)//trim(strtmp2)
end function str_replace
diff --git a/source/read_obs.f90 b/source/read_obs.f90
index 28c5cf0..a237704 100755
--- a/source/read_obs.f90
+++ b/source/read_obs.f90
@@ -25,32 +25,52 @@
subroutine read_obs(config, files)
+ use netcdf
use mod_settings
use mod_var
use mod_dates
use mod_strings
+ use mod_save, only : check
implicit none
type (config_t), intent(in) :: config
type (files_t), intent(in) :: files
character(len=max_path_len), dimension(:), allocatable :: filelist
- character(len=4) :: recs
- character(len=20) :: species, before, sep
+ character(len=max_path_len) :: rowfmt, numfmt, filerelease
+ character(len=recname_len) :: recs
+ character(len=50) :: species, before, sep
character(len=200) :: header, string
+ character(len=8) :: adate
integer :: ierr
integer :: cnt
- integer :: nr, nf, nfiles
+ integer :: i, nr, nf, nfiles, strlen
integer :: yyyymmdd, hhmiss, hl, hh
real(kind=8) :: jdate, avetime
real :: conc, err, measerr, lon, alt
- integer :: num, reclen
+ integer :: num, reclen, nretr, nrelease, nlayer
+ integer :: ncid, varid, dimid
+ integer, dimension(:), allocatable :: idate, itime
+ real, dimension(:), allocatable :: cpri, cakpri, cdryair, vmr, vmr_err
+! real, dimension(:,:), allocatable :: cak
+ real :: xcpri, xcakpri, scl_cpri, scl_cakpri, scl_cdryair !, cak_av
+ logical :: lexist
! list observation files
! ----------------------
- call system('ls '//trim(files%path_obs)//'*'//trim(files%suffix)//' | wc -l > '//trim(files%path_output)//'obsfiles.txt')
- call system('ls '//trim(files%path_obs)//' | grep '//trim(files%suffix)//' >> '//trim(files%path_output)//'obsfiles.txt')
+ if ( config%ground.and.config%satellite ) then
+ call system('ls '//trim(files%path_obs)//'*'//trim(files%suffix)//&
+ ' '//trim(files%path_satobs)//'*.nc'//' | wc -l > '//trim(files%path_output)//'obsfiles.txt')
+ call system('ls '//trim(files%path_obs)//' | grep '//trim(files%suffix)//' >> '//trim(files%path_output)//'obsfiles.txt')
+ call system('ls '//trim(files%path_satobs)//' | grep .nc >> '//trim(files%path_output)//'obsfiles.txt')
+ else if ( config%ground ) then
+ call system('ls '//trim(files%path_obs)//'*'//trim(files%suffix)//' | wc -l > '//trim(files%path_output)//'obsfiles.txt')
+ call system('ls '//trim(files%path_obs)//' | grep '//trim(files%suffix)//' >> '//trim(files%path_output)//'obsfiles.txt')
+ else if ( config%satellite ) then
+ call system('ls '//trim(files%path_satobs)//'*.nc'//' | wc -l > '//trim(files%path_output)//'obsfiles.txt')
+ call system('ls '//trim(files%path_satobs)//' | grep .nc >> '//trim(files%path_output)//'obsfiles.txt')
+ endif
open(100,file=trim(files%path_output)//'obsfiles.txt',action='read',status='old',iostat=ierr)
if ( ierr.ne. 0 ) then
@@ -74,94 +94,195 @@ subroutine read_obs(config, files)
write(logid,*) 'ERROR: cannot open obsread.txt'
stop
endif
- write(200,*) 'rec yyyymmdd hhmmss juldate avetime conc error'
+! write(200,*) 'rec yyyymmdd hhmmss juldate avetime conc error cpri cakpri cdryair cakav'
+ write(200,*) 'rec yyyymmdd hhmmss juldate avetime conc error cpri cakpri cdryair'
cnt = 0
do nf = 1, nfiles
- ! check this file belongs to receptor in reclist
+ ! check if ground-based or satellite observation
string = filelist(nf)
call split(string,".",before,sep)
- call split(before,"_",recs,sep)
- species = trim(before)
- reclen = len_trim(recs)
-
- if ( .not.( any(recname(:)(1:reclen).eq.to_upper(recs)) ) ) go to 10
-
- ! open input file
- open(100,file=trim(files%path_obs)//trim(filelist(nf)),action='read',status='old',iostat=ierr)
- if ( ierr.ne.0 ) then
- write(logid,*) 'WARNING: cannot open: '//trim(files%path_obs)//trim(filelist(nf))
- go to 10
- endif
- write(logid,*) 'Reading file: '//trim(files%path_obs)//trim(filelist(nf))
-
- ! read header
- read (100, fmt='(A)', iostat=ierr) header
-
- ! station coordinates for data selection
- do nr = 1, nrec
- if ( to_upper(recs).eq.recname(nr) ) then
- lon = reclon(nr)
- alt = recalt(nr)
- go to 20
- endif
- end do
-20 continue
- if ( lon.eq.0.and.alt.eq.0 ) then
- write(logid,*) 'ERROR: read_obs: lon and alt are both zero -> check recepter list file'
- stop
- endif
-
- ! read data
- read_loop: do
- ! if avetime included in obs file
- if (reclen.eq.4) then
- read(100,fmt='(A4,1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)',iostat=ierr) &
- recs, yyyymmdd, hhmiss, jdate, avetime, conc, err, num
- elseif (reclen.eq.3) then
- read(100,fmt='(A3,1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)',iostat=ierr) &
- recs, yyyymmdd, hhmiss, jdate, avetime, conc, err, num
- endif
- ! if avetime not included (backwards compatability with observations prepared before update)
-! avetime = 0d0
-! if (reclen.eq.4) then
-! read(100,fmt='(A4,1X,I8,1X,I6,1X,F14.6,1X,F10.4,1X,F10.4,1X,I4)',iostat=ierr) &
-! recs, yyyymmdd, hhmiss, jdate, conc, err, num
-! elseif (reclen.eq.3) then
-! read(100,fmt='(A3,1X,I8,1X,I6,1X,F14.6,1X,F10.4,1X,F10.4,1X,I4)',iostat=ierr) &
-! recs, yyyymmdd, hhmiss, jdate, conc, err, num
+
+ if ( string.eq.'nc' ) then
+
+ ! satellite
+ ! ---------
+
+ ! check if data is in inversion time interval
+ read(before(19:26),*) yyyymmdd
+ print*, 'readobs: string before = ',before(19:26)
+ jdate = juldate(yyyymmdd, 0)
+ if ( jdate.lt.juldatei.or.jdate.gt.juldatef ) cycle
+
+ ! read ncdf file
+ call check( nf90_open(trim(files%path_satobs)//trim(filelist(nf)),nf90_NOWRITE,ncid) )
+ call check( nf90_inq_dimid(ncid,'retrieval',dimid) )
+ call check( nf90_inquire_dimension(ncid,dimid,len=nretr) )
+ allocate( idate(nretr), stat=ierr )
+ allocate( itime(nretr), stat=ierr )
+ allocate( cpri(nretr), stat=ierr )
+ allocate( cakpri(nretr), stat=ierr )
+ allocate( cdryair(nretr), stat=ierr )
+ allocate( vmr(nretr), stat=ierr )
+ allocate( vmr_err(nretr), stat=ierr )
+ call check( nf90_inq_varid(ncid,'idate',varid) )
+ call check( nf90_get_var(ncid,varid,idate) )
+ call check( nf90_inq_varid(ncid,'itime',varid) )
+ call check( nf90_get_var(ncid,varid,itime) )
+ call check( nf90_inq_varid(ncid,'cpri',varid) )
+ call check( nf90_get_var(ncid,varid,cpri) )
+ call check( nf90_inq_varid(ncid,'cakpri',varid) )
+ call check( nf90_get_var(ncid,varid,cakpri) )
+ call check( nf90_inq_varid(ncid,'cdryair',varid) )
+ call check( nf90_get_var(ncid,varid,cdryair) )
+ call check( nf90_inq_varid(ncid,'vmr',varid) )
+ call check( nf90_get_var(ncid,varid,vmr) )
+ call check( nf90_inq_varid(ncid,'vmr_err',varid) )
+ call check( nf90_get_var(ncid,varid,vmr_err) )
+ call check( nf90_close(ncid) )
+
+ ! read ncdf file of releases (for AK info)
+ ! this is not needed
+! write(adate,'(I8)') yyyymmdd
+! print*, trim(filelist(nf))
+! filerelease=str_replace(trim(filelist(nf)),'retrieval','releases')
+! inquire(file=trim(files%path_satrel)//adate//'/options/'//trim(filerelease),exist=lexist)
+! if (.not.lexist) then
+! write(logid,*) 'ERROR: file not found ',trim(files%path_satrel)//adate//'/options/'//trim(filerelease)
+! stop
! endif
- if ( ierr.ne.0 ) exit read_loop
- if ( jdate.ge.(juldatef+1d0) ) exit read_loop
- if ( jdate.lt.juldatei ) cycle read_loop
- ! select day/night for low/high alt sites
- hh = hhmiss/10000
- hl = hh + int(lon*24./360.)
- if ( hl.lt.0 ) then
- hl = hl + 24
- else if ( hl.ge.24 ) then
- hl = hl - 24
- endif
- if ( alt.le.1000. ) then
-! if ( (hl.lt.11).or.(hl.gt.15) ) cycle read_loop
- else
-! if ( (hl.gt.3).and.(hl.lt.23) ) cycle read_loop
+! call check( nf90_open(trim(files%path_satrel)//adate//'/options/'//trim(filerelease),nf90_NOWRITE,ncid) )
+! call check( nf90_inq_dimid(ncid,'retrieval',dimid) )
+! call check( nf90_inquire_dimension(ncid,dimid,len=nrelease) )
+! call check( nf90_inq_dimid(ncid,'nlayer',dimid) )
+! call check( nf90_inquire_dimension(ncid,dimid,len=nlayer) )
+! if (nrelease.ne.nretr) then
+! write(logid,*) 'ERROR: number of releases does not much number of retrievals'
+! stop
+! endif
+! allocate( cak(nretr,nlayer), stat=ierr )
+! call check( nf90_inq_varid(ncid,'cak',varid) )
+! call check( nf90_get_var(ncid,varid,cak) )
+! call check( nf90_close(ncid) )
+
+ ! loop over retrievals
+ avetime = 0d0
+ write(numfmt,fmt='(A,I1,A,I1,A)') '(I',recname_len,'.',recname_len,')'
+! write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,F10.5,1X,F10.5,1X,F10.2,1X,F6.4)'
+ write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,F10.5,1X,F10.5,1X,F10.2)'
+ do nr = 1, nretr
+ cnt = cnt + 1
+ write(recs,fmt=numfmt) nr
+ ! convert from input unit (e.g. mol/m2) to mole fraction
+ xcpri = cpri(nr)*config%coeffsat/cdryair(nr)
+ xcakpri = cakpri(nr)*config%coeffsat/cdryair(nr)
+! cak_av = sum(cak(nr,:))/real(nlayer)
+ print*, 'read_obs: xcpri, xcakpri = ',xcpri, xcakpri
+ print*, 'read_obs: cpri, cdryair = ',cpri(nr), cdryair(nr)
+ print*, 'read_obs: coeffsat = ',config%coeffsat
+ ! julian time
+ jdate = juldate(idate(nr), itime(nr))
+ write(200,fmt=rowfmt) recs, idate(nr), itime(nr), jdate, avetime, vmr(nr), vmr_err(nr), &
+ xcpri, xcakpri, cdryair(nr) !, cak_av
+ end do
+
+! deallocate( idate, itime, cpri, cakpri, cdryair, vmr, vmr_err, cak )
+ deallocate( idate, itime, cpri, cakpri, cdryair, vmr, vmr_err )
+
+ else
+
+ ! check if this file is one to read
+ strlen = len_trim(files%suffix)
+ string = filelist(nf)
+ do i = 1, len_trim(string)
+ if ( string(i:(i+strlen)).eq.trim(files%suffix) ) then
+ lexist = .true.
+ endif
+ end do
+ if ( .not.lexist ) cycle
+
+ ! ground-based
+ ! ------------
+
+ ! check this file belongs to receptor in reclist
+ call split(before,"_",recs,sep)
+ species = trim(before)
+ reclen = len_trim(recs)
+
+ if ( .not.( any(recname(:)(1:reclen).eq.to_upper(recs)) ) ) go to 10
+
+ ! open input file
+ open(100,file=trim(files%path_obs)//trim(filelist(nf)),action='read',status='old',iostat=ierr)
+ if ( ierr.ne.0 ) then
+ write(logid,*) 'WARNING: cannot open: '//trim(files%path_obs)//trim(filelist(nf))
+ go to 10
+ endif
+ write(logid,*) 'Reading file: '//trim(files%path_obs)//trim(filelist(nf))
+
+ ! read header
+ read (100, fmt='(A)', iostat=ierr) header
+
+ ! station coordinates for data selection
+ do nr = 1, nrec
+ if ( to_upper(recs).eq.recname(nr) ) then
+ lon = reclon(nr)
+ alt = recalt(nr)
+ go to 20
+ endif
+ end do
+20 continue
+ if ( lon.eq.0.and.alt.eq.0 ) then
+ write(logid,*) 'ERROR: read_obs: lon and alt are both zero -> check recepter list file'
+ stop
endif
- if ( conc.le.-999. ) cycle read_loop
- measerr = max(config%measerr, err)
- cnt = cnt + 1
- ! write to output file
- write(200,fmt='(A4,1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4)') &
- recs, yyyymmdd, hhmiss, jdate, avetime, conc, measerr
- end do read_loop
- ! close input file
- close(100)
+ ! read data
+ read_loop: do
+ ! if avetime included in obs file
+ write(rowfmt,'(A,I1,A)') '(A',reclen,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,1X,I4)'
+ read(100,fmt=rowfmt,iostat=ierr) recs, yyyymmdd, hhmiss, jdate, avetime, conc, err, num
+ ! if avetime not included (backwards compatability with observations prepared before update)
+! avetime = 0d0
+! write(rowfmt,'(A,I1,A)') '(A',reclen,',1X,I8,1X,I6,1X,F14.6,1X,F10.4,1X,F10.4,1X,I4)'
+! read(100,fmt=rowfmt,iostat=ierr) recs, yyyymmdd, hhmiss, jdate, conc, err, num
+ if ( ierr.ne.0 ) exit read_loop
+ if ( jdate.ge.(juldatef+1d0) ) exit read_loop
+ if ( jdate.lt.juldatei ) cycle read_loop
+ ! select day/night for low/high alt sites
+ hh = hhmiss/10000
+ hl = hh + int(lon*24./360.)
+ if ( hl.lt.0 ) then
+ hl = hl + 24
+ else if ( hl.ge.24 ) then
+ hl = hl - 24
+ endif
+ if ( alt.le.1000. ) then
+ if ( (hl.lt.11).or.(hl.gt.15) ) cycle read_loop
+ else
+ if ( (hl.gt.3).and.(hl.lt.23) ) cycle read_loop
+ endif
+ if ( conc.le.-999. ) cycle read_loop
+ measerr = max(config%measerr, err)
+ scl_cpri = 0.
+ scl_cakpri = 0.
+ scl_cdryair = 0.
+! cak_av = 1.
+ cnt = cnt + 1
+ ! write to output file
+! write(rowfmt,'(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,F10.5,1X,F10.5,1X,F10.2,1X,F6.4)'
+ write(rowfmt,'(A,I1,A)') '(A',recname_len,',1X,I8,1X,I6,1X,F14.6,1X,F10.6,1X,F10.4,1X,F10.4,F10.5,1X,F10.5,1X,F10.2)'
+ write(200,fmt=rowfmt) recs, yyyymmdd, hhmiss, jdate, avetime, conc, measerr, scl_cpri, scl_cakpri, scl_cdryair !, cak_av
+ end do read_loop
+
+ ! close input file
+ close(100)
10 continue
- end do
+ endif ! satellite of ground-based
+
+ end do ! loop over files
! close output file
close(200)
diff --git a/source/read_reclist.f90 b/source/read_reclist.f90
index 17c3d27..f9490b3 100644
--- a/source/read_reclist.f90
+++ b/source/read_reclist.f90
@@ -23,7 +23,7 @@
!!
!---------------------------------------------------------------------------------------
-subroutine read_reclist(filename)
+subroutine read_reclist(config, filename)
use mod_var
use mod_settings
@@ -31,7 +31,9 @@ subroutine read_reclist(filename)
implicit none
+ type (config_t), intent(in) :: config
character(len=max_path_len), intent(in) :: filename
+ character(len=max_path_len) :: rowfmt
character(len=200) :: line
character(len=10) :: foo, sep
integer :: ierr
@@ -39,10 +41,14 @@ subroutine read_reclist(filename)
! count number of receptors
+ nrec = 0
open(100,file=trim(filename),action='read',status='old',iostat=ierr)
- if(ierr.gt.0) then
+ if( ierr.gt.0.and..not.config%satellite ) then
write(logid,*) 'ERROR: cannot open: '//trim(filename)
stop
+ else if ( ierr.gt.0.and.config%satellite ) then
+ write(logid,*) 'WARNING: no ground-based observations found'
+ go to 20
endif
write(logid,*) 'Reading receptors file: '//trim(filename)
@@ -69,18 +75,17 @@ subroutine read_reclist(filename)
open(100,file=trim(filename),action='read',status='old',iostat=ierr)
write(logid,*) 'Receptors: '
+! write(rowfmt,fmt='(A,I1,A)') '(A',recname_len,',1X,F7.2,1X,F7.2,1X,F7.2)'
+ write(rowfmt,fmt='(A,I1,A)') '(A',3,',1X,F7.2,1X,F7.2,1X,F7.2)'
do cnt = 1, nrec
- if ( reclen.eq.4 ) then
- read(100,fmt='(A4,1X,F6.2,1X,F6.2,1X,F7.2)') recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
- write(logid,*) recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
- else if ( reclen.eq.3 ) then
- read(100,fmt='(A3,1X,F6.2,1X,F6.2,1X,F7.2)') recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
- endif
+ read(100,fmt=rowfmt) recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
write(logid,*) recname(cnt), reclat(cnt), reclon(cnt), recalt(cnt)
end do
close(100)
+20 continue
+
end subroutine read_reclist
diff --git a/source/sbatch_flexinvert.sh b/source/sbatch_flexinvert.sh
index c29c2f7..b82c3b9 100755
--- a/source/sbatch_flexinvert.sh
+++ b/source/sbatch_flexinvert.sh
@@ -1,9 +1,9 @@
#!/bin/bash
#---------------------------------------------------
partition=nilu
-jobname=testco2
-settings_files='/home/rthompson/REPOS/GITHUB/FLEXINVERTplus_clean/settings/SETTINGS_co2_files'
-settings_config='/home/rthompson/REPOS/GITHUB/FLEXINVERTplus_clean/settings/SETTINGS_co2_config'
+jobname=ghg
+settings_files='/mypath/settings/SETTINGS_ghg_files'
+settings_config='/mypath/settings/SETTINGS_ghg_config'
#---------------------------------------------------
cat <<EOF > run_job.sh
diff --git a/source/simulate.f90 b/source/simulate.f90
index d55f4c6..be349b7 100644
--- a/source/simulate.f90
+++ b/source/simulate.f90
@@ -75,6 +75,7 @@ subroutine simulate(iter, files, config, fluxes, obs, states, grad_o, cost_o)
character(len=max_path_len) :: filedates, filefactor
character(len=max_path_len) :: rowfmt
character(len=6) :: adate
+ character(len=recname_len) :: anretr
character(len=2) :: aiter
character(len=8) :: areldate, areltime
logical :: lexist
@@ -87,13 +88,14 @@ subroutine simulate(iter, files, config, fluxes, obs, states, grad_o, cost_o)
integer :: ind, ihi, ilo, flag, ntstep
integer :: countrate
integer :: tloop1, tloop2, time1, time2
- integer :: nread, ngrid
+ integer :: nread, ngrid, nretr
integer, dimension(:), allocatable :: istate, istateuni ! indices to state vector
real, dimension(:), allocatable :: rstateuni ! indices to state vector
real, dimension(nxgrid,nygrid,maxngrid) :: grid ! flexpart flux sensitivity (or footprints)
real, dimension(nnxgrid,nnygrid,maxngrid):: gridnest ! flexpart nest flux sensitivity (or footprints)
real, dimension(:,:,:), allocatable :: factor ! correction factor for dry air
+ real, dimension(:,:,:), allocatable :: factor_nest ! correction factor for dry air for regional domain
real(kind=8), dimension(maxngrid) :: gtime ! flux sensitivity time stamp (julian days)
real(kind=8), dimension(:), allocatable :: ftime ! correction factor time stamp (julian days)
real(kind=8), dimension(:), allocatable :: dates ! correction factor time stamp (jjjjmmddhhmiss)
@@ -102,7 +104,7 @@ subroutine simulate(iter, files, config, fluxes, obs, states, grad_o, cost_o)
real, dimension(nxgrid,nygrid) :: hbkg ! flux sensitivity for global minus regional domain
real, dimension(:), allocatable :: px ! state variables corresponding to back trajectory time
real, dimension(:), allocatable :: hx ! transport operator at state vector resolution
-! real, dimension(nxregrid*nyregrid) :: gridnestvec ! vectorized form of grid or gridnest for one timestep
+ logical :: lsatellite ! logical indicating if observation is from satellite
! initialize
! ----------
@@ -142,32 +144,61 @@ subroutine simulate(iter, files, config, fluxes, obs, states, grad_o, cost_o)
write(areldate,'(I8.8)') jjjjmmdd
write(areltime,'(I6.6)') hhmiss
+ ! check if observation is a satellite retrieval
+ read(obs%recs(i),*,iostat=ierr) nretr
+ if ( ierr.eq.0 ) then
+ lsatellite = .true.
+ else
+ lsatellite = .false.
+ endif
+ print*, 'simulate: lsatellite = ',lsatellite
+
! read correction factor for dry dir (ratio rho_wet/rho_dry)
-! if ( month.ne.prevmonth ) then
-! if ( allocated(dates) ) deallocate(dates)
-! if ( allocated(ftime) ) deallocate(ftime)
-! if ( allocated(factor) ) deallocate(factor)
-! call get_nread(filedates, nread)
-! allocate ( dates(nread) )
-! allocate ( ftime(nread) )
-! allocate ( factor(nxgrid,nygrid,nread) )
-! call read_dates(filedates, nread, dates)
-! do n = 1, nread
-! ftime(n) = juldate(int(dates(n)/1d6),int(dates(n)-floor(dates(n)/1d6)*1d6))
-! end do
-! factor(:,:,:) = 1.
-! filefactor = trim(path_flexrec)//'factor_drygrid'
-! inquire ( file=trim(filefactor),exist=lexist )
-! if ( lexist ) then
-! write(logid,*) 'Reading correction factor :'//trim(filefactor)
-! call read_factor(filefactor, nread, nxgrid, nygrid, nxshift, factor)
-! endif
-! endif
- ! for nested fp run: assume dry air correction is negligible
+ if ( month.ne.prevmonth ) then
+ if ( lsatellite ) then
+ path_flexrec = trim(files%path_flexsat)//trim(areldate)//'/'
+ else
+ path_flexrec = trim(files%path_flexpart)//trim(obs%recs(i))//'/'//trim(adate)//'/'
+ endif
+ filedates = trim(path_flexrec)//'dates'
+ if ( allocated(dates) ) deallocate(dates)
+ if ( allocated(ftime) ) deallocate(ftime)
+ if ( allocated(factor) ) deallocate(factor)
+ call get_nread(filedates, nread)
+ allocate ( dates(nread) )
+ allocate ( ftime(nread) )
+ allocate ( factor(nxgrid,nygrid,nread) )
+ call read_dates(filedates, nread, dates)
+ do n = 1, nread
+ ftime(n) = juldate(int(dates(n)/1d6),int(dates(n)-floor(dates(n)/1d6)*1d6))
+ end do
+ factor(:,:,:) = 1.
+ filefactor = trim(path_flexrec)//'factor_drygrid'
+ inquire ( file=trim(filefactor),exist=lexist )
+ if ( lexist ) then
+ write(logid,*) 'Reading correction factor :'//trim(filefactor)
+ call read_factor(filefactor, nread, nxgrid, nygrid, nxshift, factor)
+ endif
+ endif
! read flexpart footprints
call system_clock(time1, countrate)
- if ( .not.config%average_fp ) then
+ if ( lsatellite ) then
+ ! footprint for satellite retrieval
+ write(anretr,'(I6.6)') nretr
+ path_flexrec = trim(files%path_flexsat)//trim(areldate)//'/'
+ filename = trim(path_flexrec)//'grid_time_'//trim(areldate)//'_'//trim(anretr)
+ filedates = trim(path_flexrec)//'dates'
+ inquire ( file=trim(filename),exist=lexist )
+ if ( lexist ) then
+ write(logid,*) 'Reading flexpart :'//trim(filename)
+ ! read footprints from binary files
+ call read_grid(filename, filedates, obs%jdate(i), nxgrid, nygrid, nxshift, ngrid, grid, gtime)
+ else
+ write(logid,*) 'WARNING: cannot find '//trim(filename)
+ go to 10
+ endif
+ else if ( .not.config%average_fp ) then
! footprint times match observation timestamps
path_flexrec = trim(files%path_flexpart)//trim(obs%recs(i))//'/'//trim(adate)//'/'
filename = trim(path_flexrec)//'grid_time_'//trim(areldate)//trim(areltime)//'_001'
@@ -200,20 +231,49 @@ subroutine simulate(iter, files, config, fluxes, obs, states, grad_o, cost_o)
if (i.lt.10.and.iter.eq.0) write(logid,*) 'simulate: time to read grid (ms) = ',(time2-time1)*1000/countrate
! correction for dry air (only if obs are mixing ratios)
-! do n = 1, ngrid
-! ind = minloc(ftime,dim=1,mask=abs(ftime-gtime(n)).eq.minval(abs(ftime-gtime(n))))
-! grid(:,:,n) = grid(:,:,n)*factor(:,:,ind)
-! end do
- ! convert from ppt to ppmv or ppbv
- grid = grid*config%coeff*mmair/config%molarmass
+ do n = 1, ngrid
+ ind = minloc(ftime,dim=1,mask=abs(ftime-gtime(n)).eq.minval(abs(ftime-gtime(n))))
+ grid(:,:,n) = grid(:,:,n)*factor(:,:,ind)
+ end do
! convert s.m3/kg to s.m2/kg
grid = grid/outheight(1)
+ ! convert from equivalent ppt to observation units (e.g. ppmv)
+ grid = grid*config%coeff*mmair/config%molarmass
! apply numerical scaling
grid = grid/numscale
+! if ( lsatellite ) then
+ ! convert from column SRR units to that consistent with mole fractions
+ ! NO LONGER NEEDED WITH NEW FP CODE
+! grid = grid/obs%cdryair(i)
+! endif
- ! read nested flexpart footprints
+ ! read nested flexpart output
if ( config%nested ) then
- if ( .not.config%average_fp ) then
+ ! read correction factor for dry dir (ratio rho_wet/rho_dry)
+ if ( month.ne.prevmonth ) then
+ if ( allocated(factor_nest) ) deallocate(factor_nest)
+ allocate ( factor_nest(nnxgrid,nnygrid,nread) )
+ factor(:,:,:) = 1.
+ filefactor = trim(path_flexrec)//'factor_drygrid_nest'
+ inquire ( file=trim(filefactor),exist=lexist )
+ if ( lexist ) then
+ write(logid,*) 'Reading correction factor for nest :'//trim(filefactor)
+ call read_factor(filefactor, nread, nnxgrid, nnygrid, nnxshift, factor_nest)
+ endif
+ endif
+ if ( lsatellite ) then
+ ! footprint for satellite retrieval
+ filenest = trim(path_flexrec)//'grid_time_nest_'//trim(areldate)//'_'//trim(anretr)
+ inquire ( file=trim(filenest),exist=lexist )
+ if ( lexist ) then
+ write(logid,*) 'Reading flexpart :'//trim(filenest)
+ ! read footprints from binary files
+ call read_grid(filenest, filedates, obs%jdate(i), nnxgrid, nnygrid, nnxshift, ngrid, gridnest, gtime)
+ else
+ write(logid,*) 'WARNING: cannot find '//trim(filenest)
+ go to 10
+ endif
+ else if ( .not.config%average_fp ) then
! footprint times match observation timestamps
filenest = trim(path_flexrec)//'grid_time_nest_'//trim(areldate)//trim(areltime)//'_001'
inquire ( file=trim(filenest),exist=lexist )
@@ -238,12 +298,22 @@ subroutine simulate(iter, files, config, fluxes, obs, states, grad_o, cost_o)
go to 10
endif
endif
- ! convert from ppt to ppmv or ppbv
- gridnest = gridnest*config%coeff*mmair/config%molarmass
+ ! correction for dry air (only if obs are mixing ratios)
+ do n = 1, ngrid
+ ind = minloc(ftime,dim=1,mask=abs(ftime-gtime(n)).eq.minval(abs(ftime-gtime(n))))
+ gridnest(:,:,n) = gridnest(:,:,n)*factor_nest(:,:,ind)
+ end do
! convert s.m3/kg to s.m2/kg
gridnest = gridnest/outheight(1)
+ ! convert from equivalent ppt to observation units (e.g. ppmv)
+ gridnest = gridnest*config%coeff*mmair/config%molarmass
! apply numerical scaling
gridnest = gridnest/numscale
+! if ( lsatellite ) then
+ ! convert column SRR units to that consistent with mole fractions
+ ! NO LONG NEEDED WITH NEW FP CODE
+! gridnest = gridnest/obs%cdryair(i)
+! endif
endif
! calculate indices to state vector for footprint times
@@ -442,7 +512,7 @@ subroutine simulate(iter, files, config, fluxes, obs, states, grad_o, cost_o)
! model mixing ratios
! -------------------
- if ( iter.eq.0.or.(config%restart.eq.1.and.iter.eq.(lastiter+1)) ) then
+ if ( iter.eq.0.or.(config%restart.eq.1.and.((iter.eq.(lastiter+1)).or.(iter.eq.99))) ) then
call system_clock(time1, countrate)
! compute fixed mixing ratios
call calc_conc(config, fluxes, obs, ngrid, gtime, hnest, hbkg, i, ix1, ix2, jy1, jy2)
@@ -490,16 +560,19 @@ subroutine simulate(iter, files, config, fluxes, obs, states, grad_o, cost_o)
! model-observation difference
! ydel = Hf(p) + Hf_fix - yobs + yini + ybkg
if (config%spec.eq.'co2') then
- obs%delta(i) = obs%model(i) + obs%nee(i) + obs%fff(i) + obs%ocn(i) - &
- obs%conc(i) + obs%bkg(i) + obs%cinipos(i)
+ obs%delta(i) = obs%cpri(i) - obs%cakpri(i) + &
+ obs%model(i) + obs%nee(i) + obs%fff(i) + obs%ocn(i) + &
+ obs%bkg(i) + obs%cinipos(i) - obs%conc(i)
else
if ( config%lognormal ) then
! optimize scalar of fluxes so no contribution from best guess fluxes (ghg)
! but add ocn contribution (zero if ocean pixels optimized)
- obs%delta(i) = obs%model(i) - obs%conc(i) + obs%bkg(i) + obs%cinipos(i) + obs%ocn(i)
+ obs%delta(i) = obs%cpri(i) - obs%cakpri(i) + &
+ obs%model(i) + obs%ocn(i) + obs%bkg(i) + obs%cinipos(i) - obs%conc(i)
else
! optimize offsets so account for contribution from best guess fluxes (ghg)
- obs%delta(i) = obs%model(i) + obs%ghg(i) - obs%conc(i) + obs%bkg(i) + obs%cinipos(i)
+ obs%delta(i) = obs%cpri(i) - obs%cakpri(i) + &
+ obs%model(i) + obs%ghg(i) + obs%bkg(i) + obs%cinipos(i) - obs%conc(i)
endif
endif
@@ -590,7 +663,6 @@ subroutine simulate(iter, files, config, fluxes, obs, states, grad_o, cost_o)
filename = trim(files%path_output)//'grad_'//aiter//'.txt'
open(100,file=trim(filename),status='replace',action='write',iostat=ierr)
do i = 1, nvar
-! write(100,fmt='(E11.4)') grad_o(i)
write(100,fmt='(E13.6)') grad_o(i)
end do
close(100)
@@ -602,6 +674,7 @@ subroutine simulate(iter, files, config, fluxes, obs, states, grad_o, cost_o)
if ( allocated(dates) ) deallocate(dates)
if ( allocated(ftime) ) deallocate(ftime)
if ( allocated(factor) ) deallocate(factor)
+ if ( allocated(factor_nest) ) deallocate(factor_nest)
end subroutine simulate
--
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