Check what has been done in the :bash:`workdir`:
===================================================

.. _chimere_check_inputs_readymade:

Checking the input files:
-------------------------

Check-list of basics:

  - the yaml file is copied here
  - the logfile is written here and its last line indicates "The forward mode has been successfully executed"
  - the chemical scheme stored in :bash:`chemical_scheme`
  - directory :bash:`controlvect` is empty
  - directory :bash:`model` contains the three CHIMERE's exectuables (even though only fwdchimere.e is used so far)
  - directory :bash:`transforms` is empty if using only ready-made CHIMERE input files
  - file VERSION indicates the IDs of the branch and commit of the CIF used for the simulation


In directory :bash:`datavect`, the files used for the components of the data vector are stored, in one directory per component. 
Therefore, for CHIMERE, there must be:

  - sub-directory :bash:`meteo`: contains links to the ready-made METEO files indicated in the yaml
  - sub-directories :bash:`flux` and :bash:`bioflux`: contain links to the ready-made A/BEMISSIONS files indicated in the yaml
  - sub-directory :bash:`inicond`: contains the link to the ready-made INI_CONCS file indicated in the yaml
  - sub-directories :bash:`latcond` and :bash:`topcond`: contain links to the ready-made BOUN_CONCS files indicated in the yaml
  - sub-directory :bash:`concs`: sub-directories for each ACTIVE_SPECIES that is measured contain :doc:`input monitor.nc files for in-situ data in our example</documentation/input-outputs/monitor>`.
  
If a link does not point to the right file, there is an issue, probably in the yaml (check typos!).

Checking the output files:
--------------------------

In directory :bash:`obsoperator`, three files are written to give details on the treatment done by the CIF:
  
  - :doc:`pipe_inputs.txt</documentation/input-outputs/check>`
  - :doc:`transform_description.txtt</documentation/input-outputs/check>`
  - :doc:`transform_pipe.txtt</documentation/input-outputs/check>`
  
Sub-directory :bash:`fwd_0000` contains:
  
  - the directories for all the periods in the simulation. They are usual CHIMERE execution directories, with links to the input files, the  executable as well as chimere.nml, a log and an error log files, if activated, various nectdf files as out.nc for hourly concentration outputs, dep.nc, etc. They do not contain the end.nc file. They also contain the specific mod.txt and obs.txt files which are used for extracting from CHIMERE the data to compute the equivalent of the observations. A text file name all_good is touched by CHIMERE when the period has been simulated without error. 
  - sub-directory :bash:`chain` contains the end.nc files to chain the periods one to another for covering the whole simulation.
  - in sub-directory :bash:`obsvect`, in :bash:`concs`, a sub-directory per species available in the observations contains the matching monitor.nc with the equivalent computed by CHIMERE. In this simple case, check that the columns i, j, level, sim, tstep, tstep\_glo and dtstep are filled.
  - a pickle file for the control vector is written.

In directory :bash:`obsvect`: XX???XX