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Main departures from the standard distribution
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.. role:: bash(code)
   :language: bash

The sources for the CHIMERE in the CIF are in :bash:`model_sources/chimereGES/`. They are based on the sources of the standard CHIMERE distribution just before 2013a. Departures from the standard distribution are:
  - the elimination of aerosols
  - the 2013a development of the Van Leer scheme on the vertical has been added but not the other optimizations such as faster send/receive
  - the necessary changes to pass the information on observations to the model and to output the required information (e.g. simulated concentrations at the observations' time and location, pressures for satellite data)
  - the choices of the horizontal and vertical transport scheme and the choice of the final conversion factor are given in the chemical definitions of species
  - absolute value in :bash:`twostep.F90` because the analytics needs to transport negative increments also but this cannot work with chemistry
  - the sub-directory of LANDUSE files has been eliminated for shorter paths
  - the chemprep/data directory does not exist anymore
  - calendar.f90 needs update for types of days regarding dates and country
  - the use of the coordinates of the corners of the cells instead of only the centers
  - reading a file for the initial concentrations is mandatory. To chain simulations,  the \_o concentrations are read
  - lighter output files: a switch for writing or not netcdf files such as out, par, dep + do not re-write hlay, airm and others in out.nc
  - the BEMISSIONS files are in the same format as the AEMISSIONS files (instead of being more or less in the same format as BOUN\_CONCS with all the species in the same variable);  switch added to ignore biogenic emissions
  - changes in the geometry to allow domains including the pole
  - switches added to take or leave any of the five processes in prodloss i.e. chemistry, emissions, transmix, deposition and wet deposition
  - hpulse used to skip transport and chemistry calculations before pulses (used when computing response functions)
  - the possibility to convert dry air mole fractions CI/CL into total air mole fractions
  - **to be continued**


The tangent-linear and adjoint codes follow the forward one. Nevertheless, some features do not work yet in the adjoint **to be updated** :
  - more than one Gauss-Seidel iteration
  - refined time step more than 1?