Check what has been done in the workdir:

5. Check what has been done in the workdir:#

5.1. Checking the input files:#

Check-list of basics:

  • the YAML file is copied here

  • the logfile is written here and its last line reads “The forward mode has been successfully executed”

  • the chemical scheme is stored in chemical_scheme

  • directory controlvect is empty

  • directory model contains the three CHIMERE executables (even though only fwdchimere.e is used at this stage)

  • directory transforms is empty when using only ready-made CHIMERE input files

  • file VERSION records the branch and commit ID of the CIF used for the simulation

Directory datavect stores the files used for each data vector component, one sub-directory per component. For CHIMERE, the following must be present:

  • meteo: symlinks to the ready-made METEO files specified in the YAML

  • flux and bioflux: symlinks to the ready-made A/BEMISSIONS files specified in the YAML

  • inicond: a symlink to the ready-made INI_CONCS file specified in the YAML

  • latcond and topcond: symlinks to the ready-made BOUN_CONCS files specified in the YAML

  • concs: for each measured ACTIVE_SPECIES, a sub-directory containing input monitor.nc files.

If a symlink does not point to the correct file, there is likely an error in the YAML (check for typos).

5.2. Checking the output files:#

Directory obsoperator contains three files describing the processing done by the CIF:

Sub-directory fwd_0000 contains:

  • one directory per simulation period. These are standard CHIMERE execution directories containing symlinks to input files and the executable, along with chimere.nml, a log file, an error log, and (if activated) various NetCDF files such as out.nc for hourly concentration outputs and dep.nc. The end.nc file is not present here. The directories also contain mod.txt and obs.txt, used to extract CHIMERE output at observation locations. A file named all_good is written by CHIMERE when a period completes without error.

  • sub-directory chain: contains the end.nc files used to chain successive periods across the full simulation window.

  • sub-directory obsvect/concs: one sub-directory per observed species, each containing a monitor.nc file with the CHIMERE-simulated equivalents. In this simple case, verify that the columns i, j, level, sim, tstep, tstep_glo, and dtstep are populated.

  • a pickle file for the control vector.

In directory obsvect: XX???XX