source: trunk/LMDZ.MARS/changelog.txt @ 3443

== 17/09/08 ==
>>> Build a version with new soil but old radiative transfer,
    but keeping possibility of switching back to new radiative transfer),
    which incorporates changes & improvements currently included in the
    'reference version' GCM (see /u/emlmd/LMDZ.MARS.mixdyn)

>>> start by modifying makegcm as in /u/emlmd/LMDZ.MARS.mixdyn, so that it runs
    without environment variables and set LIBOGCM to /tmp15/emlmd/libo

>>> directory contents of 'aeronomars', 'grid' and 'filtrez' are simillar
    to those in /u/emlmd/LMDZ.MARS.mixdyn

>>> in bibio , only file mxva.F needed be upgraded

>>> get phymars and dyn3d contents from /u/emlmd/LMDZ.MARS.mixdyn
    (and remove all *old files)

>>> check differences between dyn3d and /u/emlmd/LMDZ.MARS.170908/libf/dyn3d
    and upgrade when necessary:
    - removed 'netcdf.inc' file (has nothing to do there!)
    - comgeom.h and comgeom.h : made fortran90 compliant
    - control.h : made fortran90 compliant
    - dynredem.F : more read/write controls + comments in english
    - ini_archive.F : new soil/thermal inertia changes
    - integrd.F : added additional information to output when crashing
    - lect_start_archive.F : new soil/thermal inertia changes
    - newstart.F : new soil/thermal inertia changes + comments in english
    - start2archive.F : new soil/thermal inertia changes
    - vanleer.F : removed inapropriate 'external' statement
    - write_archive.F : enable writting a subterranean field

>>> check differences between phymars and /u/emlmd/LMDZ.MARS.170908/libf/phymars
    and upgrade when necessary:
    New soil stuff:
    - added comsoil.h
    - iniwrite.F : new soil changes
    - added iniwritesoil.F90 and writediagsoil.F90 for subterranean fields
    - added interp_line.F (for subterranean grid interpolation)
    - adapted phyetat0.F for subterranean temperature & inertia
    - adapted physdem1.F to include new soil stuff
    - physiq.F : added calls to writediagsoil 
    - soil.F : new routine (fixed vertical grid + variable thermal inertia)
    - added soil_settings.F (to read/initialize/interpolate soil properties)
    - updated surfdat.h (since thermal inertia is now in comsoil.h)
    - updated tabfi.F : include new soil properties
    - updated testphys1d.F
    - updated dimphys.h (set nsoil=18 as default)

== 18/09/08 ==
>>> add the possibility of easily switching to Tran radiative transfert
    - updated aerdust.h.ocke97 (changed some variables name) so it can
      replace aerdust.h (which is currently the same as aerdust.h.clan91).
    - imported Tran's 'gfluxv.F' routine
    - imported Trans' version of 'swr.F' routine, saved it as 'swr.F.toon'

>>> Backup of 'old' Morcrette swr.F is 'swr.F.morc'
    NB: to switch from one radiative transfer to the other, just copy
    swr.F.morc or swr.F.toon to swr.F (and eventually 'touch swr.F' so that
    makegcm recompiles swr.F)
    No other dependencies (swr.F.toon uses 'gfluxv.F' and swr.F.morc uses
    'dedd.F').

>>> Changed the latter, so that users can switch from one to the other
    - modified swr.F.toon to become swr_toon.F (and to include gfluxv.F)
    - modified swr.F.morc to become swr_fouquart.F (and to include dedd.F)
    - added a flag in callkeys.h, swrtype (parameter to be set/changed by
      the user 1=Fouquart and 2=Toon)
    - update readtesassim so that the coefficient by which opacity
      is multiplied is set according to the 'swrtype' parameter

== 25/09/08 ==
>>> Implement the use of tracer-by-name in physics
    - in phymars/tracer.h set 'noms' length to 20 (instead of 10)
    - in phymars/callsedim2q.F and phymars/callsedim.F, use tracers by name
    - in phymars/dustopacity.F, use tracers by name
    - in phymars/vdifc.F, use tracers by name

== 26/09/08 ==
>>> Change implementation strategy (for now); don't move surface tracer around
    i.e.: surface ice remains equivalent to qsurf(nqmx)=qsurf(i_h2o_vap)
          and likewise for surface tendencies ...
    - modified vdifc.F and callsedim.F back
    - modified initracer.F (so that water names are h2o_vap & h2o_ice)
    
== 29/09/08 ==
    - modified aeronomars/init_chimie_B (cosmetics)
    - corrected aeronomars/moldiff.F internal routine tridag; changed
      "pause" error messages to 'stop' messages
    - modified phymars/watercloud.F to use tracers by name
    - corrected aeronomars/molvis.F (undefined 'fac' and 'Akk' written to 
       output at first call)
    
== 30/09/08 ==
    - modified aeronomars/calchim.F to use tracers by name
    - adapted aeronomars/photochemist_B.F to use tracers by name
    - adapted aeronomars/chemtermos.F to use tracers by name
    - adapted aeronomars/concentrations.F to use tracers by name
    - corrected aeronomars/conduction.F (undefined 'Akk' written to output
      at first call)
    - adapted aeronomars/euvheat.F to use tracers by name
    - adapted aeronomars/moldiff.F and moldiffcoeff.F to use tracers by name

== 01/10/08 ==
    - For more compatibility with LMDZ4; mimic reading a 'traceur.def' file
      in the dynamics via a call to a routine 'iniadvtrac.F' and saving
      tracers names in 'advtrac.h'
     -> created 'iniadvtrac.F', 'advtrac.h' and modified gcm.F
    - modified 'dynetat0.F' so that tracers are loaded from 'start.nc' by name
    - modified 'dynredem.F' so that tracers are written to 'restart.nc'
      by name
    - modified 'initracer.F' tu use tracers by name

== 02/10/08 ==
    - removed use of 'nqchem_min' everywhere:
      adapted 'euvheat.F','inifis.F','physiq.F'
      (leave 'inichim.F' for later)
    - updated 'phyetat0' and 'physdem1.F' to read/write surface tracers by name
    - modify things so that surface water ice index is the same as
      atmospheric water ice (except when running without water ice; then
      simply set i_h2o_ice=i_h2o_vap).
      NB: the easiest is to have global storage of tracer names/indexes in
      tracer.h
      => changed initracer.F & tracer.h to have global igcm_something indexes

== 03/10/08 ==
    - adaptations for surface ice index, modified files:
      phyetat0.F : if there is a dynamical tracer 'h2o_vap' then load
                   surface tracer called 'h2o_ice' instead
      initracer.F : in 'old' tracer name case: move qsurf(nqmx)->qsurf(nqmx-1)
                    and set i_h2o_ice=i_h2o_vap if iceparty=.false.
      physdem1.F : if old tracer names: move qsurf(nqmx-1)->qsurf(nqmx)
                   if iceparty=.false., write surface tracer 'h2o_ice'
                   (and not 'h2o_vap') to file.
      adapted vdifc.F, callsedim.F & watercloud.F & physiq.F so that surface
      ice is now identified as qsurf(i_h2o_ice)
    - updated aeronomars/perosat.F (cosmetics)

== 06/10/08 ==
    - modify newstart.F and lect_start_archive.F to use tracers by name
== 07/10/08 ==
    - adapted inichim_newstart.F (added qsurf to arguments)
      and inichim_readcallphys.F
== 08/10/08 ==
    - implement reading traceur.def in dyn3d/iniadvtrac.F

== 16/10/08==
    -small change in inifis.F (only warn if too many tracers, compared
     to the expected number, not stop).
     - corrected bug in initracer.F
== 21/10/08 ==
    - modified newstart.F to load B.Diez subsurface ice maps.
    - corrected small bug (uninitialized variable) in interp_horiz.F
== 22/10/08 ==
    - updated iniwritediagsoil.F so that thermal inertia is written to
      diagsoil.nc
== 31/10/08 ==
    - changed xvik.F program so it works even if we don't have atmospheric
     temperature at hand (then it uses a 10km reference scale height) and so
     that it does surface pressure interpolation log-wise.
== 03/11/08 ==
    - modified physiq to compute (and output) co2 column.
    - added improvement by Francois in newcondens.F about computing CO2
      partial pressure. This behavior is turned on by setting internal logical
      flag 'improved_ztcond' to '.true.' (and running with a co2 tracer)
    - updated 'start2archive' to work with 'new' gcm output (soil, tracers ...)
== 04/11/08 ==
    - upgraded xvik program to look for temperature in 7th layer variable if
     there is no global atmospheric temperature field at hand.
== 05/11/08 ==
    - more modifs to newcondens.F: added another internal flag 'bound_qco2' to
     enforce (if set to .true.) that co2 mass mixing ratio remains bounded.
== 07/11/08 ==
    - corrected 'writediagfi' & 'writediagsoil' so that an error message is 
      issued if called with a variable name which is too long.
== 18/12/08 ==
    - corrected bug in dyn3d 'addfi.F', (dimensions of local array p())
== 23/02/09 ==
    - modified "aeronomars/param_read.F" to do strictly fortran data
     initialization (otherwise xlf compiler complains)
    - changed a few '1.e-30' to '1.d-30' in aeronomars/photochemist_B.F
     so that max functions has 2 doubles as arguments (otherwise xlf
     compiler complains)

==07/04/09 ==
    -cosmetic changes/minor improvements in the handling of tracers in:
     aeronomars/photochemist_B.F
     aeronomars/perosat.F
     aeronomoars/euvheat.F
     aeronomars/moldiffcoeff.F
     aeronomars/moldiff.F
     aeronomars/cocentrations.F
     aeronomars/chemtermos.F
     aeronomars/calchim.F

--> NB: still there are differences in outputs when order of tracers is changed

== 09/04/09 ==
>>> fixed problem in 'vdifc.F' which lead to different results when moving
    tracers around.

== 10/04/09 ==
>>> corrected small bug in diagnostic outputs of 'watercloud.F' (tendencies were
    not added to tracer values).

== 21/04/09 ==
>>> corrected small bug in "physdem1.F" about writing water ice surface tracer
    to file

== 07/05/09 ==
>>> very minor correction (firstcall not set to true after first call
    if no tracers) in convadj.F

== 30/06/09 ==
>>> Implement reading *def files with IOIPSL ersatz 'getin' function
   - import "ioipsl_errioipsl.F90","ioipsl_getincom.F90","ioipsl_stringop.F90"
     in bibio
   - adapted 'dyn3d/defrun_new.F' to use "getin" function
   - adapted 'phymars/inifis.F' to use "getin" function

== 01/07/09 ==
>>> Adapted 'create_make_gcm' so that the "use" in *.F files is identified and
    corresponding dependencies included in the makefile rules.

>>> Added the 3D scattering from aerosols by JB Madeleine:
    - minor changes in aerave.F
    - added the calls to aeropacity.F, and aeroptproperties.F in callradite.F
    - changed the calls to lwu.F and swr.F in lwmain.F and swmain.F, respectively
    - added 3D scattering properties in lwu.F and swr.F
    - added the new aeroptproperties.F, aeropacity.F and suaer.F90 routines
        (removed dustopacity.F)
    - updated aeropacity.F with new tracer names
    - changed the call to callradite.F in physiq.F, added the initialization 
        of reffrad and nueffrad (aerosol effective radius and variance)
    - removed all the lines relative to the old "activice" option, including
        temperature variation due to latent heat release (now in comments)
    - renamed nsize into naersize in watercloud.F, watersat.F and newsedim.F,
        to avoid conflicts with another "nsize" variable in the radiative transfer
    - added the statement of nuice in watercloud.F, which is the effective variance
        of the log-normal distribution for ice
    - updated yomaer.h and removed aerice.h (and corresponding "includes")

== 02/07/09 ==
>>> Adapted 'aeronomars/inichim_readcallphys.F' (called by newstart)
     to use "getin" routine.
    + minor correction in 'inifis.F' (close 'iradia.def' file)
>>> Minor correction in 'dyn3d/dynetat0.F' and 'phymars/phyetat0.F'; do not
    attempt to reindex tracers if none were found.

>>> in 'deftank' added examples of 'traceur.def' files (traceur.def.co2 : 1
    co2 tracer; traceur.def.watercycle : 2 traceurs, water vapour and water ice
    tracer.def.chemistry : all 15 species)

== 06/07/09 ==
>>> Modified 'makegcm' and makegcm_g95' so that modules files are put 
    with libraries (and not in current directory)
    
== 21/07/09 ==
>>> Added in "testphys1d.F" a check that the (required) 'run.def' file is
    around (that file should contain the "INCLUDEDEF=callphys.def" instruction
    otherwise getin() calls won't work.
    Also added reding of 'traceur.def' (or initialisation of tracer names
    to dummy values q01,q02, ...) in testphys1d.F

== 22-24/07/09 == JBM
>>> Removed "iceparty" everywhere (calchim.F, inichim_readcallphys.F,
        chimie_data.h, inichim_newstart.F, photochemist_B.F, callkeys.h,
        callradite.F, callsedim.F, aeropacity.F, inifis.F, initracer.F, physdem1.F,
        physiq.F, watercloud.F). Water = .true. now implies the use of two
        tracers, i.e. water vapor and water ice.

>>> Removed fisice.h and stated the corresponding variables in the right
        places (physiq.F, callsedim.F, watercloud.F, newcondens.F, calchim.F);
        also removed unused cltop and clsurf variables in physiq.F.

>>> Removed the variable's splitting, which is now obsolete, in callradite.F
        (and its subroutines lwi.F, lwxb.F, lwxn.F, lwflux.F, lwmain.F, lwxd.F).
        Also removed the variable's splitting in calldrag_noro.F. Finally removed
        ndomain from dimradmars.h.

>>> Removed useless tests in aeropacity.F.

== 27-30/07/09 == JBM
>>> Cleaned the WRITEDIAGFI section in physiq.F, and moved the "mtot",
        "icetot" and "tauTES" variables from watercloud.F to physiq.F. Also
        cleaned the albedo change due to water ice deposition.

>>> Renamed rdust into rnuclei in callsedim.F, physiq.F and watercloud.F.

>>> Added a logical test for (water.and..not.tracer) in inifis.F.

>>> Removed "qsurf","zls" and "icount" from the list of inputs in
        watercloud.F (these variables were not used by the subroutine).

>>> Added a call to watercloud.F at firstcall, using typical dust optical
        depth (taufirstcall), in order to correctly initialize the ice particle
        size distribution for the radiative transfer scheme. Also created a new
        subroutine to load the effective radius and variance of the aerosols used
        by the radiative transfer scheme. Its name is updatereffrad.F, and it is
        called before aeroptproperties.F in callradite.F.

== 05/08/09 == JBM
>>> TES water-ice opacity is now fully computed using the radiatively active
        aerosol scheme. Absorption coefficient is calculated using Qext and
        omega at the IR reference wavelength. Omega was not computed before; it
        was only computed in the GCM channels, not at the reference wavelength.
        Thus it has been added in suaer.F90, aerave.F, yomaer.h, callradite.F,
        aeropacity.F and aeroptproperties.F. If "activice" is false, the
        TES opacity is computed using the old method (fit of the Qabs as a
        function of reff curve).

== 07/08/09 == EM
>>> Removed "iceparty" option from callphys.def

>>> modified physiq.F and initracer.F so that building of array niqchem() which
    contains the indexes of all chemistry tracers + water vapour and water
    ice is done in initracer.F (array niqchem(:) is now a common
    in tracer.h ).
    Also had to adapt inichim_newstart.F to behave similarly.

== 24/08/09 == EM included corrections by JBM
>>> Added declaration of nqchem(nqmx) local array in
    aeronomars/inichim_newstart.F

>>> Encapsulated calls to writediagfi & wstats in if (ngrid.ne.1) clause
    in phymars/aeropacity.F (otherwise it crashes in 1D).

== 26/08/09 == EM
>>> modified tracer.h, initracer.F, inichim_newstart.F and physiq.F to not use
    an niqchem() array (added in 07/08/09 changes)

>>> modified phymars/readtesassim.F90 and phymars/aeropacity.F so that
    assimilated dust for MY24 or MY25 or MY26 may be used (with iaervar=
    24,25 or 26); we keep iaervar=4 to also read MY24 dust for compatibility
    with older versions of code.
    Modified deftank/callphys.def : added comments about new iaervar values

== 25/09/09 == EM
>>> modified phymars/testphys1D.F : added incrementation of tracer values
    after call to physiq().

== 27/11/09 == EM
>>> updated comments in makegcm (translated help to english)

>> shifted to reading file traceur.def
   (dyn3d/iniadvtrac.F) in an Earth-LMDZ4 like way:
   first line == number of tracers
   and then tracer name (1 per line; later we'll add advection scheme type)
>> also updated example 'traceur.def' files in deftank accordingly

== 02/12/09 == EM
>>> upgraded testphys1d.F and profile.F to load run parameters with getin()
    function (from run.def ; no need for a "testphys1d.def" any more)
    added an example 'run.def.1d' file to 'deftank'

==10/12/09 == EM
>>> minor correction in testphys1d.F (was still checking if there is a
    testphys1d.def file around ; which is not used anymore)

==15/01/10 == JBM
>>> aeropacity.F: implemented a weighting of the dust opacity profile
  by using the dust size vertical profile defined in updatereffrad.F.
>>> aeroptproperties.F: changed the integration scheme (Gauss-Legendre)
  of the scattering parameters.
>>> suaer.F90: removed the use of an ad-hoc "solsir" factor. It is now
  directly computed from the scattering properties read in the ASCII
  files. Consequently, the IR extinction coefficient has been divided
  by solsir=2 in the ASCII file (called optprop_dustir_x0.5.dat instead
  of optprop_dustir.dat to allow compatibility with the older version
  and avoid chaos).
>>> updatereffrad.F: changed the dust size vertical profile.
>>> yomaer.h: the particle radius variable is now in simple precision,
  because the new scattering property integration scheme has changed.
>>> aeronomars/inichim_readcallphys.F (small) bug correction load value of
    'water' before testing its value...

== 18/01/10 == EM
>> added possibility to read (in inifis.F and aeropacity.F) the value of
   dust opacity tauvis from callphys.def file

== 01/02/10 == EM
>> added JBM updates of "callradite.F" (coments) "aeroptproperties.F" (bug fix
   of bad array bounds) and "aeropacity.F" (encapsulate wstats calls in
   if (callstats) )
>> added implementation of TES Cap albedos: "albedocaps.F90" and adapted
   "newcondens.F"  (and physiq.F, because added 'zls' argument to newcondens)
   and surfdat.h
>> changed default settings for dust : set a 1.3 factor in readtesassim.F90
   when using Toon radiative transfer, use M.Wolff-T-Matrix files in suaer.F90
 
== 03/02/10 == EM
>> Updated newstart.F in dyn3d, so that sub-surface thermal inertia values may
   be different in North and South hemispheres.

>> Updated "makegcm" and "makegcm_g95" scripts (cosmetic + default compilation
   option changes)
   
>> Minor changes in aeronomars/init_chimie_B.F (do not use lnblnk(); F90
   trim() intrinsic is much safer and better), and in initracer.F (better
   control over a possible array bound underflow).
   Also, in dyn3d/iniadvtrac.F, close input file properly,
   and in infis.F, more verbose message to output.

== 26/02/10 == EM
>> Updated makegcm and makegcm_g95 : default usage is now to set everything
   ("environment variables") in the script. Changed some default compilation
   options.
>>> removed 'float()' instructions in tabfi.F and iniwrite.F
    use "real()" to be compliant with standards.
>> Corrected small bug in testphys1d.F (look for file traceur.def)
   also added initialisation of tracers
>> Cleaned up inifis.F and initracer.F (some sanity checks were obsolete
   and/or wrong)
>> Improved writediagfi.F so that 1D (individual column in the GCM, or
   fields in testphys1d) data can be written in the diagfi.nc file
>> Minor changes/improvements in calls to writediagfi from physiq.F for dust

== 08/03/10 == EM
>> Minor update of "makegcm" and "makegcm_g95": use instruction "./makdim"
   (instead of "makdim"; in case "." is not in user's path)
>> put "real()" instructions instead of "float()" in dyn3d routines:
   disvert.F , dynredem.F , fluxstoke.F , fxhyp.F , fxy.F ,
   fxysinus.F , fyhyp.F , gcm.F , grid_atob.F , grid_noro.F , grid_noro1.F ,
   ini_archive.F , inigeom.F , newstart.F , ran1.F , sortvarc.F ,
   sortvarc0.F
>> Minor update of aeropacity.F (added if (callstats) around call to wstats)

== 28/04/10 == EM
>> Put the splitting in radiative transfer back in the model (JB):
   updated calldrag_noro.F  callradite.F  dimradmars.h  lwflux.F 
   lwi.F lwmain.F lwxb.F lwxd.F lwxn.F swmain.F
>> Fix bug (AS) in callradite.F (wrong loop boundaries line 332)
>> Fix bug (AS+JB) in "swr_toon.F" to enable running with more than
   100 levels...
>> Fix bug (JBM) in callsedim2q.F about setting pdqs_sed(:niq(iq)) to zero

== 25/08/10 == EM
>> Add a 'makegcm_gfortran' for compiling with gfortran
   and a 'makegcm_ifort' for compiling with ifort (on Gnome)
   
== 03/09/10 == EM
>> Modifications to enable running in double precision (using starts in r4
   or r8); just add options '-r8 -DNC_DOUBLE' to compile GCM in double precision
   -> adapted dyn3d/dynetat0.F, physmars/physdem1.F, phymars/soil_settings.F,
      phymars/readtesassim.F90, phymars/writediagfi.F, phymars/def_var.F90,
      phymars/writediagsoil.F90, phymars/wstats.F90, phymars/inistats.F
>> Added dyn3d/writediagdyn.F90 routine (to output scalar dynamical fields),
   adapted 'comconst.h' and 'comvert.h' to be Fortran77/Fortran 90 compatible.

== 14/12/10 == EM
>> Add -f option to #!/bin/csh in makegcm* scripts (to make sure that it is
   the bash environment compiler that is used as a default)
>> Update convadj.F with RW's version (fixes bug of non conservation of tracers
   in cases where convection stops at one level and starts at the next).

== 13/12/10 == EM
>> Update testphys1d.F so that initial tracer profiles may be loaded at
   initialization 

== 24/01/11 == JBM(+ some cleanup by EM)
>> Reactivated the "doubleq" method (two-moment scheme for dust
   transport) and connected it with the radiative transfer code. The
   opacity is set constant below a level indicated by the variable
   cstdustlevel in aeropacity.F to remove the thick layer of
   dust near the surface created by the constant lifting rate.
   The "density scaled opacity" used by the MCS team is computed
   and saved in dsodust.
   Updated routines: callradite.F, aeropacity.F, updatereffrad.F,
   callsedim.F, newsedim.F, initracer.F, vdifc.F, suaer.F90.
>> Added the use of named scatterers (same method as tracer-by-name)
   in the radiative transfer code. Scatterers are declared at
   firstcall in callradite.F (which is the equivalent of traceur.def)
   and the corresponding indices are saved in the common called
   aerkind.h (the equivalent of tracer.h).
   Updated routines: callradite.F, updatereffrad.F, aeropacity.F,
   suaer.F90, aerkind.h.
   EM: aerdust.h, aerdata.h and aerice.h are not used any more 
>> Merged callsedim2q.F and callsedim.F in one single routine
   callsedim.F to allow doubleq to be used with other tracers.
>> Added an input parameter called beta to newsedim.F, that allows
   to account for the shape of the particles in the computation of
   the sedimentation velocity.
>> Added the ability to transport a radiatively active population of
   submicron dust particles (flag "submicron" in callphys.def).
   Updated routines: callradite.F, updatereffrad.F, aeropacity.F,
   initracer.F, vdifc.F, suaer.F90, inifis.F, callkeys.h.
>> Connected the predicted size and amount of dust to the water
   cycle. The size of the particles is now given by rdust in
   updatereffrad.F, and the amount of cloud condensation nuclei
   (CCN) is given by ccn in aeropacity.F. The calculation of ccn is
   done in aeropacity.F because it's deduced from the opacity when
   doubleq is not used. rnuclei and dustcores are removed from
   watercloud.F and replaced by rdust and ccn.
   Updated routines: physiq.F, callradite.F, updatereffrad.F,
   aeropacity.F, watercloud.F.
>> Removed the "fake" call to watercloud.F in physiq.F which was used
   to give the size of the ice particles to the radiative transfer
   code at firstcall. Instead, rice is computed in updatereffrad.F
   using a simple equation and a typical amount of dust nuclei (ccn0).
>> Increased the number of Gauss integration points in
   aeroptproperties.F.
>> Added the ability to write the 3D scattering parameters of a
   given aerosol in the outputs using the out_qwg flag in
   aeroptproperties.
>> Changed "DO iir=1,4" into "DO iir=1,nir-1" in suaer.F90 (in case
   the number of infrared channels is changed).
>> Added nuice_ref in tracer.h and initracer.F, which is the
   effective variance of the log-normal distribution used for water-ice
   particles in the radiative transfer code.
>> Updated the computation of rice, reffice and rsedice in
   updatereffrad.F and callsedim.F.
>> Added nuice_sed in callsedim.F, which is the effective variance
   of the lognormal distribution used for the sedimentation of
   water-ice particles.
>> Added ccn_factor in watercloud.F, which is the ratio of the total
   number of dust particles over the number of condensation nuclei.
>> The variable beta is not saved anymore in newsedim.F.
>> Corrected the BIG bug in lwu.F that was responsible for unstabilities
   when clouds were radiatively active (FF+EM+JBM!)
>> Turned ilwd, ilwn and ilwb to 1 in inifis.F.
>> Added dust and ice visible opacities in the outputs.
   Modified routine: aeropacity.F.
>> Named water cycle tuneable parameters (nuice_sed, nuice_ref,
   alb_surfice, ccn_factor) which are mentioned at firstcall by the GCM
   (flag "water_param"). Modified routines: callsedim.F, physiq.F,
   watercloud.F.

== 25/01/2011 == EM
>> updated testphys1d.F: removed #include "aerdust.h"
>> cleanup in suaer.F90: no more calls to zerophys; added test to check
   there is no overflow of isize index (in visible domain averaged properties
   case)
>> minor cleanup in newsedim.F (make it more F90 oriented)
>> added flag 'TESicealbedo' (set to .true. to impose polar surface
   albedos as observed by TES) in callphys.def 
   
== 28/01/2011 == EM
>> added additional tests (to check correct reading of input files) in suaer.F90
>> updated inifis.F  so that the directory where external data files are to
   be found (e.g. TES opacities, dust properties, etc.) can be specified in
   run.def (or callphys.def) as " datadir = /path/to/the/directory "

== 29/01/2011 == AS
>> added updated mesoscale-related routines in phymars:
   ----------------------------------------------------------------------------
   NAME                       CHANGES compared to GCM counterpart 
   ----------------------------------------------------------------------------
   meso_callkeys.h        --> one variable is added [consider merging w/ GCM?] 
   meso_dustlift.F        --> stress + alpha default, or read in a file 
                               stress.def if here [consider merging w/ GCM?]
   meso_newcondens.F      --> correction on U V T tendencies is switched 
                               off (unstable in mesoscale) 
   meso_physiq.F          --> major modifications mainly related to I/O
   meso_slope.h           --> additional common for slope scheme
   meso_dimphys.h_ref     --> reference common serving as a basis for a 
                               compilation script (makemeso)
   meso_inifis.F          --> major modifications mainly related to I/O
   meso_param_slope.F90   --> slope scheme by Spiga and Forget GRL 2008 
                               [consider adding to GCM?]
   meso_readtesassim.F90  --> an old version because the new F90-compliant 
                               version needs the new makegcm scripts [TBD]
   meso_testphys1d.F      --> similar to GCM except for routine names
   ----------------------------------------------------------------------------
    NB: in meso_dustlift.F and meso_readtesassim.F90, the subroutines 
         have the same name as in the GCM.
         this is because those files are supposed to be copied 
         in specific temporary folders for compilation
>> any future change in the following GCM routines in phymars:
      - callkeys.h
      - dustlift.F
      - newcondens.F
      - physiq.F
      - inifis.F
      - readtesassim.F90
      - testphys1d.F
   will be in need to be impacted to the corresponding meso_ routines 
   [hence it is important to document this README file]
>> any change in any other GCM routines than the ones listed will
   have an effect in mesoscale simulations as well:
     -- the two models are being kept updated at the same time :)
     -- the two models would be possibly broken at the same time :(

== 15/02/2011 == EM
>> updated dissipation coefficients in indissip.F

== 25/02/2011 == EM
>> corrected bug in 'inifis.F' and 'datafile.h' to really be able to
   specify (in callphys.def; using datadir=/whatever/path/to/use ) the path
   to external datafiles (topography, surface properties, etc.)

== 28/02/2011 == JBM + AS
>> used settings reached by JBM to obtain his PhD results
      alb_surfice = 0.45  ---  in physiq.F and meso_physiq.F
      ccn_factor = 4.5    ---  in watercloud.F
      nuice_sed = 0.45    ---  in callsedim.F
>> NB: this is supposed to be further refined in the future

== 01/03/2011 == AS + JBM
>> nasty bug in the water cycle when iradia != 1  [no problem when iradia = 1]
   --> mesoscale runs w/ water cycle had strange 5-hour fluctuations in RICE, from 80mic to 5mic
>> PB: calculation of ccn [condensation nuclei] is done in callradite.F
      * ccn must be saved 
        --> corrected in physiq.F and meso_physiq.F
      * ccn must not be modified elsewhere [e.g. in watercloud, when divided by ccn_factor] 
        --> all calculations on ccn are now moved in callradite

== 03/03/2011 == AS
>> Added a pre-compilation flag MESOSCALE so that the LMDZ.MARS GCM
will compile without stating errors because of mesoscale routines.
[meso_physiq.F, meso_inifis.F]
>> Now, this MESOSCALE precompilation flag can be used to lower
the number of meso_* routines when adaptations for mesoscale
applications are not very extended.
   --> meso_testphys1d.F, meso_testphys1d.F, meso_dustlift.F
       routines were deleted and changes are now moved under 
       the MESOSCALE flag in the original GCM routines
   --> Completely transparent for GCM compilation 
       since it is devoid of the -DMESOSCALE option
   --> Very good for syncing because changes in dustlift, newcondens
       will be directly available in the mesoscale model

== 04/03/2011 == AS + JBM
>> new version version for aeroptproperties.F in phymars to limit uncertainties and be able to play with ngau
>> this was coded by JBM in his personal reference version but not transmitted to the team reference version

== 10/05/2011 == AS + JF
>> in newsedim.F used for mesoscale computations, spurious values close to the surface
   --> this was related to 1 - exp(-x) calculated as zero in w(ig,l) if x is very small
   --> fix: when this happens, replace exp(-x) by 1 - x since x ~ 0
>> in newsedim.F, "if (dztop.gt.epaisseur(ig,l)) then" was closed too soon by an "endif"
   --> hence basically the simple method was never used 
       and useless calculations with the complex method were carried out
   --> fix by moving the closing "endif" [in addition to corrections mentioned in the previous point]

== 17/05/2011 == EM
>> set internal computations using double precision in growthrate.F and
   watercloud.F (otherwise we sometimes end up with Nans).
>> add extra checks in newcondens.F to avoid possibility of out of bounds
   evaluation of array masse()
  
== 25/05/2011 == AS
>> found that the 10/05/2011 bug fix in newsedim.F is also useful for GCM runs.
>> no more need to modify callradite.F prior to compilation [but still dimradmars.h must be modified] 
   --> in callradite.F we now have
       -- DEFAULT name_iaer(1) is "dust_conrath"
       -- IF (doubleq.AND.active) name_iaer(1) = "dust_doubleq"
       -- IF (water.AND.activice) name_iaer(2) = "h2o_ice"  

== 27/05/2011 == EM
>> minor bug correction in writeg1d (JYC)
>> add "-check" to debug option in makegcm_ifort

== 08/06/2011 == EM
>> minor bug fix in lect_start_archive.F (using wrong surface temp. array).
   + swiched output messages to english and added that tracers not found
   in file must be initialized by user.
>> minor bug fix in datareadnc.F : 'datafile' path must be initialized.

== 08/06/2011 == EM
>> Significant update on how the number of scatterers is managed:
   Instead of having to manualy change 'nearkind' in dimradmars.h, the
   number of scatterers must now be set when compiling, using makegcm
   "makegcm -s 1" for one scatterer (dust) or "makegcm -s 2" (e.g. dust
   and water ice), default behaviour (ie not specifying -s #) is -s 1
   Modified phymars/dimradmars.h , added directory phymars/scatterers
   with script make_scatterers , and adapted makegcm* scripts.

== 17/06/2011 == AC
================================================
======== IMPLEMENTATION OF THERMALS ============
================================================
The main goal of this revision is to start including the thermals into the model
for development purposes. Users should not use the thermals yet, as
several major configuration changes still need to be done.

This version includes :
- updraft and downdraft parametrizations
- velocity in the thermal, including drag
- plume height analysis
- closure equation
- updraft transport of heat, tracers and momentum
- downdraft transport of heat

This model should not be used without upcoming developments, namely :
- downdraft transport of tracers and momentum
- updraft & downdraft transport of q2 (tke)
- revision of vdif_kc to compute q2 for non-stratified cases

Thermals could also include in a later revision :
- momentum loss during transport (horizontal drag)

Compilation of the thermals has been successfully tested on ifort, gfortran and pgf90

================================================
================================================

M      libf/phymars/callkeys.h
M      libf/phymars/inifis.F

Added new control flags to call the thermals :
- calltherm (false by default) <- to call thermals
- outptherm (false by default) <- to output thermal-related diagnostics (for dev purposes)
================================================
M      libf/phymars/vdifc.F
^------> added a temporary output for thermal-related diagnostics
M      libf/phymars/testphys1d.F
^------> added treatment for a initialization from a profile of neutral gas (ar)
      -> will be transformed in a decaying tracer for thermal diagnostics
M      libf/phymars/physiq.F
^------> added a section to call the thermals
      -> changed the call to convadj
      -> added thermal-related outputs for diagnostics
M      libf/phymars/convadj.F
^------> takes now into account the height of thermals to execute convective adjustment
      => note : convective adjustment needs to be activated when using thermals, in case of a 
         second instable layer above the thermals
================================================
A      libf/phymars/calltherm_interface.F90
^------> Interface between physiq.F and the thermals
A      libf/phymars/calltherm_mars.F90
^------> Routine running the sub-timestep of the thermals
A      libf/phymars/thermcell_main_mars.F90
^------> Main thermals routine specific to Martian physics
A      libf/phymars/thermcell_dqupdown.F90
^------> Thermals subroutine computing transport of quantities by updrafts and downdrafts
A      libf/phymars/thermcell.F90
^------> Module including parameters from the Earth to Mars importation. Will disappear in future dev
================================================
================================================

== 17/06/2011 == EM
>>> Updates and corrections (to enable compiling/running in debug mode with
    ifort)
- removed option "-free-form" from makegcm_ifort and set mod_loc_dir="."
  so that module files (produced in local directory by ifort)
  are moved to LIBO
- updated initracer.F, physdem1.F, physiq.F, inichim_newstart.F
  to avoid referencing out-of-bound array indexes (even if unused)
- cosmetic updates on inwrite.F, datareadnc.F
- updated newstart.F to initialize and use 'datadir' when looking for files
- corrected bug on interpolation of sub-surface temperatures in
  lect_start_archive.F

== 17/06/2011 == AC
>>> Important updates to thermals parameters
- Tuned aspect ratio of thermals to suit Buoyancy estimations from LES in CLOSURE relation
- Renormalization of alim_star after plume
- Removed alimentation mixing of estimated Teta in plume
>>> Minor change in makegcm_ifort

== 22/06/2011 == EM
- added modifications (from JYC & FGG) to tracer.h & initracer.F for ions
- minor improvement to newstart.F (q=x option, check that tracer index 
  provided by user is valid).
- minor correction to callradite.F (to enable compilation in debug mode
  with ifort when there is only one tracer).

== 17/06/2011 == AC
- Added maximum vertical velocity and heat flux output from thermals
- Added buoyancy diagnostics
- Minor modifications in thermals routines 

== 23/06/2011 == EM
- correct bug (introduced previously) in lect_start_archive.F on loop
  boundaries for soil temperature.

== 01/07/2011 == AC
- Added new settings for the Martian thermals from new LES observations
- Revamped thermcell's module variables to allow it's removal
- Minor changes in physiq and meso_physiq for the call to thermals
- Switched from dynamic to static memory allocation for all thermals variable 
to gain computation speed

== 04/07/2011 == AC
- Minor setting modification to thermals
- Added new flux optimization in thermcell_main_mars.F90, to run properly in 3D

== 14/07/2011 == JBM
- Tidying up dust properties in DATAFILE for better consistency (cf. suaer.F90)
- Cosmetic changes in aeropacity.F (changed comment and put a print inside a water flag)

== 15/07/2011 == EM
>> Implemented using 'z0' roughness length map (important: 'z0' reference
   field is in datafile surface.nc, which has also been updated).
- made z0 a z0(ngridmx) array and moved 'z0' from 'planete.h' to 'surfdat.h';
  added a 'z0_default' (common in surfdat.h) corresponding to the 'control'
  array value (contole(19) in startfi.nc).
- adapted 'tabfi.F' to use 'z0_default'.
- adapted 'phyetat0.F' to look for a 'z0' field in startfi.nc. If 'z0' is not
  found in the startfi.nc file, then the uniform default value (z0_default)
  is used.
- modified 'physdem1.F' to write 'z0' field to restart.nc
- adapted use of z0() in 'physiq.F' (diagnostic computation of surface stress),
  'vdifc.F' and 'vdif_cd.F'.
- adapted 'dustdevil.F' to use 'z0_default'.
- 'testphys1d.F' now uses 'z0_default', and the value to use can be set
  in run.def (with "z0=TheValueYouWant").
- modified 'datareadnc.F' to load reference map of 'z0' from surface.nc, and
  added a 'z0' option in 'newstart.F' to force a uniform value of z0. Note
  that the use of the z0 map is automatic when using newstart, but only when
  it loads a start_archive.nc file.

== 15/07/2011 == AS
- Modified the mesoscale part so that the previous change by EM does not
  imply an error in the mesoscale case. More development is needed though
  to get the "varying z0" capability in the mesoscale model.
- Worked on versions of meso_physiq and meso_inifis as close as possible
  to physiq and inifis for more continuity in the process of impacting changes 
  (and even possibly to reach a common version of physiq and inifis).
  >>> The main point is to make the mesoscale significant specific parts 
  coded into include files in meso_inc so that meso_physiq and meso_inifis
  looks very close to physiq and inifis.
  >>> This is completely transparent for GCM users who does not need the
  contents of meso_inc.
- Slight cosmetic changes to physiq.f and inifis.F
  --- some of them e.g. to prepare convergence between meso_physiq and physiq
- Dropped the meso_ prefix from the slope routines
  (currently those are only used in the mesoscale model,
   but one could imagine using those in hi-res GCM runs)
- Added a MESOSCALE flag to writediagfi so that mesoscale simulations
  are not bothered with calls put in routines by GCM people

== 19/07/2011 == AS
- Finished converging meso_physiq.F and meso_inifis.F towards physiq.F and inifis.F
  --> see previous point 15/07/2011
  --> meso_ routines no longer exist (everything is in meso_inc and transparent to GCM users)
  --> GCM routines include mesoscale parts within MESOSCALE precompiler commands
  --> MESOSCALE parts are as hidden as possible not to mess up with GCM users/developers
- Cleaned inelegant or useless #ifdef [or] #ifndef MESOSCALE in physiq and inifis so that
  a minimum amount of such precompiler commands is now reached [mainly related to I/O]
- Added the SF08 slope insolation model in the general physics parameterizations.
  Added a callslope keyword in inifis.F and callkeys.h
  --> This keyword is False by default / True if you use -DMESOSCALE
- Removed the obsolete call to Viking Lander 1 diagnostic
  Replaced it with a diagnostic for opacity at the domain center [valid for GCM and mesoscale]

== 01/08/2011 == EM
- Fixed bug in readtesassim (timeflag was not always set before being used)

== 03/08/2011 == AC
- Modified physiq.F to interface new SL parametrization
- New SL parametrization based on a bulk Richardson Monin-Obukhov theory formulation
   Stability functions are taken from D.E. England et al. (95)
   Similarity functions coefficients based on Dyer and Hicks (70).
   Includes thermal roughness length computation, heat and momentum drag coefficient computation
   Can be used to output hydrodynamic-related SL quantities (bulk Richardson, turbulent Prandtl number estimation, Reynolds number)
- Minor modification in thermcell_dqupdown.F to suit picky compilers
- vdifc.F Now takes into account sub-grid gustiness, evaluated from thermals activity (it's proxy being the maximum vertical velocity)
- Minor modification in meso_inc_les.F: u* is now taken from the new vdifc and not recomputed from a simple law
== 08/08/2011 == AC
- Formula correction for the Reynolds in vdif_cd : will affect the thermal roughness length. Results obtained with the precedent formula (previous commit) probably underestimate by about 1K the temperature in the mixing layer.
- Added a new subroutine to libf/phymars called surflayer_interpol.F. This routine can be called as a diagnostic for interpolation of horizontal velocity norm and temperature in the surface layer, in 1D or 3D. The output height is controlled by a parameter z_out, to be set in physiq.F. This might be later added to a .def file. z_out is set to 0. by default, resulting in no call to this subroutine.

== 16/08/2011 == AC
- Minor modification in physiq.F to pass Ch from vdifc to meso_inc_les
- Major modification to the formulation of integrals in surflayer_interpol.F
  Now stable for most cases. Some cases with highly negative Monin Obukhov length
  remain to be explored.
- Added gustiness to the Richardson computation in vdif_cd.F. Gustiness factor is for now of beta=1., after
  several comparisons with LES aerodynamic conductances. May be subject to a minor change (+/- 0.1)
  in the near future. (almost transparent for the user)
- Minor modifications relative to variables in vdifc.F.
- Esthetic change to calltherm_mars.F
- Changed the definition for HFX computation in the LES in meso_inc/meso_inc_les.F. New definition yields
  very similar results to old one and follows a strict definition of what HFX should be.

== 24/08/11 == TN
Attempts to tune the water cycle by adding outliers 
       + A few structural changes !!
* watercap.h is now obsolete and removed -- all is in surfdat.h
* watercaptag initialized in surfini.F (up to 7 areas defined) instead of initracer.F
  - settings proposed by AS commented
  - experiments by TN decommented. use with caution.
* water ice albedo and thermal inertia in callphys.def and inifis.F
* water ice albedo in surfini.F
* water ice albedo computation in albedocaps.F90
* alb_surfice is now obsolete in physiq.F, albedo_h2o_ice is used instead
* frost_albedo_threshold defined in surfdat.h
* water ice thermal inertia in soil.F
TODO: * calibrate thermal inertia and ice albedo
      * have a look at subgrid-scale ice with dryness ?

== 07/09/2011 == AC

- Added new flag for the Richardson-based surface layer :

callrichsl, can be changed in callphys.def

One should always use the thermals model when using this surface layer model.
Somes cases (weakly unstable with low winds), when not using thermals, won't be well represented by the
Richardson surface layer. This stands for Mesoscale and Gcm but not for LES model.

Correct configs :

callrichsl = .true.
calltherm = .true.

callrichsl = .false.
calltherm = .false.

callrichsl = .false.
calltherm = .true.

Previously unstable config :

callrichsl = .true.
calltherm = .false.

- To be able to run without thermals and with the new surface layer, a modification has been made to
physiq.F to account for gustiness in GCM and MESOSCALE for negative Richardson, so that :

callrichsl = .true.
calltherm = .false.

can now be used without problems, but is not recommended.

- Consequently, callrichsl = .false. is now the default configuration for thermals.

We recall the available options in callphys.def for thermals :

outptherm = BOOLEAN (.false. by default) : outputs thermals related quantities (lots of diagfi)
nsplit_thermals = INTEGER (50 by default in gcm, 2 in mesoscale) : subtimestep for thermals model.
         It is recommended to use at least 40 in the gcm, and at least 2 in the mesoscale.
         The user can lower these values but should check it's log for anomalies or errors regarding
         tracer transport in the thermals, or "granulosity" in the outputs for wmax, lmax and hfmax.

== 08/09/11 == AS
LMDZ.MARS + MESOSCALE. 
---> Setting up a more realistic water ice source at the poles (notably outliers)

[[ surfini.F ]]
Main changes and bug fixes
* reference to comcstfi.h was wrong. big problem because e.g. pi was not known.
* commented about a problem to be fixed, due to surfini being called before initracer.
* MESOSCALE: put the mesoscale north cap definition into a precompiling flag #MESOSCALE
             for the moment: if [alb_mean_TES > 0.26 and lat > 70] then outliers
             (previously done in meso_inc_caps.F)
   
[[ inifis.F ]]
Just changed a comment with wrong formatting

--> below, only MESOSCALE

[[ soil.F ]]
if somewhere IT > IT_outliers, then makes it = IT_outliers

[[ physiq.F ]]
[[ meso_inc/meso_inc_caps.F ]]
[[ meso_inc/meso_inc_ini.F ]]
meso_inc_caps no longer called. keep for reference for the moment.

[[ meso_inc/meso_inc_var.F ]]
deleted lines with *_lim variables, now useless

== 08/09/11 == EM
-Fixed problem about undefined tracer names in 'surfini.F' by calling
 'initracer' before 'surfini' in physiq.F

== 09/09/11 == AS
--> Fixed a problem with .eq. used with booleans in physiq.F
[some good picky compilers complain about this]
--> Added a warning in inifis about using
callrichsl = .false.
calltherm = .true.
which is not recommended. The new surface layer has been built to go
with the new mixing layer scheme (thermals). And anyway it is a much
better scheme than the previous one.

== 09/09/11 == AC

 This is a major update for thermals and richardson layer parametrization. This update stabilizes thermals (further
 studies might show that we can reduce the value of nsplit in gcm. To be tested.), and prevent downdrafts from descending into
 the surface layer, which was acting as a cold feedback on the thermals. The Richardson surface layer now features
 different gustiness coefficients for Richardson, heat and momentum so that u* and t* are correctly represented.
 
 Upcoming updates will change surflayer_interpol.F90 to implement those changes in the interpolation scheme as well.
 
 ***************************
 IMPORTANT : several parts of the vdifc code might want to use these new definitions for gustiness, u* and t*. exemple : dust devil routines
 that recompute u* ? lifting routines ? TODO !
 **************************
 
 
 M             289   libf/phymars/thermcell_main_mars.F90
 ^-----------------> Added iterations to the velocity / buoyancy / entrainment / detrainment
                     computation to ensure correct convergence. Iteration number is for now set to
                     4, which is probably too much. This will be changed once several cases are tested.
                     The minimum is probably 2 iterations.
 
 M             289   libf/phymars/vdifc.F
 ^-----------------> Subgrid gustiness parametrization now uses different gustiness beta coefficients
                     for heat and momentum. Comparisons with LES at Exomars landing site, matching u*
                     and teta* suggests values of beta=0.7 for momentum and beta=1.2 for heat, where
                     the formula for large scale horizontal winds in the first layer is :
                          U0^2 = pu^2 + pv^2 + (beta*wmax_th)^2
 
 M             289   libf/phymars/vdif_cd.F
 ^-----------------> LES data suggests that Richardson number distribution during daytime has a very large
                     standart deviation due to highly negative Richardsons on several gridpoints. As a consequence,
                     the mean Richardson in daytime in the LES is much more negative than in LES. In the gcm,
                     parametrized subgrid turbulence prevents such cases, which can be dangerous in nearly unstable conditions.
                     Hence, we use beta=0.5 instead of one, so that we keep the anti-crazy-hfx function of beta and we increase the
                     norm of negative Richardsons in general for daytime conditions. This is set in conjonction with
                     beta settings for heat and momentum in vdifc.
 
 M             289   libf/phymars/meso_inc/meso_inc_les.F
 ^-----------------> HFX and USTM computations now uses the different betas for heat and momentum.

== 21/09/11 == AS
--> Added MESOINI precompiler flag so that all fields needed to initialize the mesoscale model
     are being output in the diagfi.nc file. Previously it was made through a separate physiq.F
     which needed to be updated every time...
--> This is completely transparent to the casual GCM users and only appears in the WRITEDIAGFI section of physiq.F

== 21/09/11 == AC

Revision on several settings for the thermals model. This version relies on fits done for an article to be published, and is more precise.

 M             299   libf/phymars/thermcell_main_mars.F90
 ^-----------------> Changed downdraft to updraft mass flux ratio from -1.8 to -1.9
                     Changed first level for downdraft mixing from k=3 to k=2. Only level 1 is non-mixed now.
                     Changed coefficients for downdraft to updraft thermal buoyancy ratios.

 M             299   libf/phymars/calltherm_mars.F90
 ^-----------------> Changed r_aspect_thermals from 2. to 1.5 for the GCM version to better match buoyancy profiles.

== 29/09/11 == AS
--> To easily explore sensitivity to lifting thresholds: in dustlift.F, ustar_seuil=sqrt(stress/rho) 
    and alpha_lift[dust_mass] can be prescribed through an external stress.def parameter file.
    --- alpha_lift[dust_number] is computed from alpha_lift[dust_mass] as in initracer.F
    --- ustar_seuil is more user-friendly than stress because direct comparison with ustar from model 
--> For the moment this is MESOSCALE only, but potentially useful to everyone

== 30/09/11 == TN
>> Bug correction in lect_start_archive.F ; in some cases layer(:) was not
   initialized.


== 10/10/2011 == AC

***********
This commit aims at increasing the thermals speed. Using these corrections, gcm performances in 64x48x32 using 1 tracer goes from 27.9% elapsed time in thermals to 18.76%.

***********
Additional work needs to be done in tracer advection to gain speed in high tracer number configuration. (tracer advection (but not momentum nor temperature) could be decoupled from sub-timestep, as they do not act on the thermals scheme (water vapor is neglected as we use theta and not theta_v, and radiative effect of dust is not computed in the thermals.))

***********
=> TOP 5 of routine contributions to gcm runtime :

Each sample counts as 0.01 seconds.
  %   cumulative   self              self     total
 time   seconds   seconds    calls   s/call   s/call  name
 18.76      6.33     6.33      960     0.01     0.01  thermcell_main_mars_
 17.19     12.13     5.80                             __svml_powf4.A
 13.72     16.76     4.63    10369     0.00     0.00  filtreg_
  3.94     18.09     1.33                             __intel_new_memset
  3.73     19.35     1.26     2880     0.00     0.00  thermcell_dqupdown_

note: thermcell_main_mars_ does call quite a lot power computations (see __svml_powf4.A), but this number will not increase with tracer numbers.

***********
=> LOG:

M             312   libf/phymars/thermcell_main_mars.F90
^------------------- removed (commented) computations on buoyancy which is purely diagnostic
                     tuned internal convergence loop and added convergence criterion

M             312   libf/phymars/thermcell_dqupdown.F90
^------------------- removed (commented) downdraft-related if-loops (as we do not advect tracers and momentum in downdrafts for now)

M             312   libf/phymars/calltherm_mars.F90
^------------------- removed (commented) diagnostic-related computations
                     changed default thermals spliting and aspect ratio
                     corrected a bug where maximum height was not correctly computed and could result in convective adjustment used in place of thermals
                     when using certains sets of nsplit and r_aspect (was not happening with the baseline version, so that this correction is transparent to
                     users)
********************

== 14/10/2011 == AS + AC
- Monin-Obukhov length is now output from surflay_interpol and written in diagfi if z_out not 0.
- in calltherm_interface, defaut settings for qtransport_thermals and dtke_thermals

== 20/10/2011 == EM
- added FF's upgrade of writediagfi. Now, if at runtime there is a diagfi.def
  file, it should contain the list of variables (1 per line) than will be put
  in the diagfi.nc file. If there is no diagfi.def file, then all variables
  are put in the diagfi.nc file (as was the case before).
 
== 21/10/2011 == EM
- Corrected small bug in newstart: initracer was not always used and thus
  some tracer indexes (igm_co2, igcm_h2o_vap,...) were not set. This
  however means that we now also call inifis from newstart and that we read
  in flags set in 'callphys.def' (required for sanity checks in initracer).
  Also adapted 'inichim_readcallphys': removed some obsolescent tests on
  number of tracers for given combinations of options.

== 21/10/2011 == AS
- Added possibility for CH4 tracer in tracer.h and initracer.F

== 27/10/11 == AS
--> Added geticecover.F90 which computes seasonal ice cover given ls, lati(ngrid), long(ngrid)
    as proposed by T. Titus from TES observations [fitting functions for crocus line] 
    ... output is icecover(ngrid) which value is 0 [no ice cover] or 1 [ice cover]
    ... no calculations are done for latitudes between -40 and +40 [ice cover is directly set to 0]
--> In physiq.F, co2ice is set to a dummy high value to simulate a CO2 cap 
    wherever icecover(ngrid) is 1. This is done at each timestep before newcondens is called.
--> For the moment this is MESOSCALE only, but potentially useful to everyone.

== 28/10/11 == FL + AS
ADDED THE NEW FRAMEWORK FOR PHOTOCHEMISTRY
This is not the last version. A new rewritten version of calchim.F [using LAPACK] is yet to be committed.
--> A new version for photochemistry routines : *_B.F no longer exists, new routines in aeronomars
D              333   libf/aeronomars/photochemist_B.F
D              333   libf/aeronomars/init_chimie_B.F
A                0   libf/aeronomars/read_phototable.F
M              333   libf/aeronomars/calchim.F
A                0   libf/aeronomars/photochemistry.F
M              333   libf/aeronomars/chimiedata.h
--> Changed calls to calchim and watercloud [surfdust and surfice needed] in physiq.F
--> Left commented code for outputs in physiq.F [search for FL]
--> Added settings which works for 35 levels in inidissip.F according to FL. Commented for the moment.
--> Checked compilation and run, looks fine. Note that 'jmars.20101220' is needed.

== 02/11/2011 == AC

***********
This commit aims at increasing the thermals speed, especially for large tracer number configurations. The idea behind this commit is to advect non-active conserved variables outside of the sub-timestep of the thermals. Because these variables are not used in thermals computation, we can decouple them:

momentum: can be decoupled because we assume a constant ratio between horizontal velocity in alimentation layer and maximum vertical velocity in the thermal
s.

tracer: can be decoupled because we do not take condensation of any tracer into account and hence do not liberate latent heat nor form clouds in the thermal
s.

temperature: cannot be decoupled (of course)
***********

D             336   libf/phymars/thermcell_dqupdown.F90
^----------------   Deleted and replaced by a simpler version. Notes about downdraft advection are still available from revision 336 of SVN in thermcell_dqu
pdown.

A               0   libf/phymars/thermcell_dqup.F90
^----------------   New upward advection for tracers and momentum in thermals. Several changes are done compared to the old approach:
                          - Updraft quantities are not longer computed by making hypothesis on the amount of advected air.
                          - In general, the formalism for updraft computation is much simpler and clearer.
                          - Tracer tendancies are no longer computed using the conservation equation. Instead, we use the divergence
                          of an approximated turbulent flux of the concerned quantity, where downdraft are also neglected.

M             336   libf/phymars/thermcell_main_mars.F90
^----------------   The Main does not call anymore thermcell_dqupdown, which it was doing 2+tracer_number times per subtimestep (140 times per physical step for a 2 tracer config)

M             336   libf/phymars/calltherm_mars.F90
^----------------   Entrainment, detrainment and mass-fluxes are recomputed in  the sub-timestep loop. Their final value after iterations is used by the new
 advection routine to compute tracer and momentum fluxes.

*********** Results

- Conservation of tracers has been assessed over 1 yr in 1D and found to be comparable to that obtained with the simple convective adjustment. (it actually
seems to be better by a factor of 10%!)
- GCM speed-up is of about 20% compared to the old thermal configuration, for a 2 tracer case.
- Advection of sharp tracer profiles has been successfully observed, similar to the old method.

== 07/11/11 == JBM
>>> Changed watercloud.F to call two separate routines,
simpleclouds.F or improvedclouds.F, which are a simplified and
full microphysical scheme for cloud formation, respectively.
Removed the tag called "improved" in watercloud.F, and added
another tag called "microphys" which is defined in callphys.F
instead. Changed routines: callkeys, inifis, physiq, watercloud.

>>> Reimplemented the use of typical profiles of dust particle sizes
and CCNs in simpleclouds.F. Corrected the previously used
analytical CCN profile. Moved ccn_factor to simpleclouds.F,
which won't be used in the new microphysical scheme. Changed
routines: aeropacity, physiq, simpleclouds, watercloud.

>>> Computed rdust at the end of callsedim instead of updatereffrad,
except at firstcall. Renamed rfall into rsedcloud and moved it
in simpleclouds. Moved nuice_sed to initracer.F and added it to
tracer.h. Changed routines: callsedim, physiq, tracer.h,
watercloud, initracer, simpleclouds, updatereffrad.

>>> Added two tracers for the CCNs. Added the different tests in
initracer.F to make sure that, for example, microphys is not
used without doubleq, etc. Corrected an inconsistency in
callsedim.F, and changed the way r0 is updated. Changes
routines: callsedim, inifis, initracer, physiq, testphys1d,
tracer.h.

>>> Added the ability to have a spatially variable density in
newsedim (same method as that used for the radius of
sedimentation). Required the addition of one input to newsedim,
which is the size of the density variable "rho". Changed
routines: callsedim, newsedim.

>>> Added an output to aeropacity called "tauscaling", which is a
factor to convert dust_mass and dust_number to true quantities,
based on tauvis. Removed ccn and qdust from aeropacity, which
are obsolete now.

>>> Wrote improvedcloud.F which includes all the microphysical
scheme, and connected it to the sedimentation scheme. Added and
changed routines: callsedim, physiq, growthrate, nuclea,
improvedclouds, initracer, watercloud, microphys.h.

== 07/11/11 == TN

>> Added CCN & dust tracers updates in physiq.F
Corrected a bug that can give negative CCN numbers, due to the 
use of single precision values (only 6 decimals) whereas up to 10E+10 
CCN can be formed or disappears...

>> Corrected physical bug that causes h2o_vap or h2o_ice 
to be negative in improvedclouds.F.

>> Corrected physical bug that causes CCN & dust tracers
to be negative in improvedclouds.F when all ice sublimates and 
releases dust

>> Added parameter contact mteta in callphys.def
Default value is still 0.95, see inifis.F

>> Changed tendancy computation for dust_number in improvedclouds.F
that was not the right one. Indeed, the scavenged dust_number tracer 
is computed from the dust_mass one, and its tendancy before scavenging 
must be taken into account to compute its scavenging's tendancy.

== 09/11/11 == AS

Added a more recent version of concentrations.F by FL

== 22/11/11 == EM
>> Added FL corrections to aeronomars/photochemistry.F :
- Bug correction on the chemistry time step (now set to 1/3rd of the
  physics time step)
- Updated kinetics coefficients (according to JPL 2011)

== 22/11/11 == TN

>>Changed scavenging in improvedclouds.F : CCNs are now virtual like dust
to avoid tauscaling divergence.

>>Water ice radius is now updated after sedimentation in callsedim.F.
Added tau, tauscaling and zzlay as arguments

>>Commented aggressive outputs at first call in suaer.F90, aeropacity.F

== 23/11/11 == FGG + MALV

>> New parameterization of the NLTE 15 micron cooling. The old parameterization is kept as an option, including or not variable atomic oxygen concentration. A new flag is introduced in callphys.def, nltemodel, to select which parameterization wants to be used (new one, old one with variable [O], or old one with fixed [O], see below). Includes many new subroutines and commons in phymars. Some existing routines are also modified:

-physiq.F. Call to the new subroutine NLTE_leedat in first call. Call to nltecool modified to allow for variable atomic oxygen. Depending on the value of nltemodel, the new subroutine NLTEdlvr09_TCOOL is called instead of nltecool.

-inifis.F. Reading of nltemodel is added.

-callkeys.h Declaration of nltemodel is added.

The following lines should be added to callphys.def (ideally after setting callnlte):

# NLTE 15um scheme to use.
# 0->  Old scheme, static oxygen
# 1->  Old scheme, dynamic oxygen
# 2->  New scheme
nltemodel = 2

A new directory, NLTEDAT, has to be included in datagcm.

>> Improvements into NLTE NIR heating parameterization to take into account variability with O/CO2 ratio and SZA. A new subroutine, NIR_leedat.F, and a new common, NIRdata.h, are included. A new flag, nircorr, is added in callphys.def, to include or not these corrections. The following files are modified:

-nirco2abs.F: nq and pq are added in the arguments. The corrections factors are interpolated to the GCM grid and included in the clculation. A new subroutine, interpnir, is added at the end of the file.

-physiq.F: Call to NIR_leedat added at first call. Modified call to nirco2abs

-inifis: Reading new flag nircorr.

-callkeys.h: Declaration of nircorr.

The following lines have to be added to callphys.def (ideally after callnirco2):

# NIR NLTE correction for variable SZA and O/CO2? 
# matters only if callnirco2=T
# 0-> no correction
# 1-> include correction
nircorr=1

A new data file, NIRcorrection_feb2011.dat, has to be included in datagcm.

>> Small changes to the molecular diffusion scheme to fix the number of species considered, to avoid problems when compiling with more than 15 tracers (for example, when CH4 is included). Modified subroutines: aeronomars/moldiff.F and aeronomars/moldiffcoeff.F

== 24/11/11 == TN

>> corrected minor bug in updatereffrad.F : reffdust was not saved

>> ccn_factor as not correctly used in sedimentation.
It is now initialized in inifis.F, declared in tracer.h and
used in both simpleclouds.F & callsedim.F to update ice radius.

>> Commented diagfi outputs in aeropacity.F & improvedclouds.F for 
non scavenging users.


== 06/12/11 == TN

>> tiny change : nuice_sed initialisation is now done in inifis. Also changed initracer and improvedclouds.


== 08/12/2011 == EM
>> Include changes and updates for photochemistry by FL:
- aeronomars/calchim.F : change in units of surface density.
- aeronomars/surfacearea.F : new routine to compute ice and dust surface area
                             (m2/m3) available for heterogeneous reactions.
- phymars/initracer.F : bug correction: initialize igcm_ch4 and change loop
                        bounds (when guessing tracer names/properties with
                        old input files).
- phymars/watercloud.F : cleanup.
- phymars/physiq.F : add call to surfacearea; photochemistry is now called
                     after sedimentation to take into acount updated rdust
                     and rice.
 
== 08/12/2011 == EM
>> more updates for photochemistry:
-aeronomars/inichim_newstart.F : add methane + bug correction in "oldnames" case
-aeronomars/read_phototable.F : adapt routine so that photolysis table file
                                name may be set in the def file with
                                phototable = filename
                                (default is "jmars.20111014")


== 09/12/2011 == EM
>> more updates for photochemistry from FL: improved aeronomars/surfacearea.F ,
  with a change in arguments.

== 14/12/2011 == EM
>> fixed bug in callsedim.F: recomputation of rdust and rice should only be done
   if the appropriate tracers and flags are set.
>> commented out call to uertst in ch.F (uertst crashes with gfortran and is
   moreover puerly diagnostic messages).
>> In nltecool.F: Enforced using igcm_* indexes to identify tracers and not
   hard coded fixed numbers (which would lead to a disaster in cases where the
   order of tracers was changed).

== 14/12/2011 == AC
>> Improved computation of mixing in vdifc for temperatures less than the saturation
   temperature.
   The scheme works by computing mixing of T and then liberating latent heat when T<Ts.
   Taking into account the mass of co2 ice condensated, a new mixing profile for T is computed.
   When the computation has converged, the tendancy for mixing of T is taken with respect to
   the initial T profile for which co2 ice has been condensated.
>> This scheme is based on initial work done by Melanie Vangvichith and has been adapted/tested/bug-fixed
   and improved to Mars.

== 15/12/2011 == EM
>> minor correction in aeronomars/calchim.F and aeronomars/surfacearea.F : 
   calls to wstats should always be embeded in if (callstats) condition.
   
== 19/12/2011 == TN
>> new option in newstart: 'ini_h2osurf', water ice surface initialisation to keep seasonal frost 
   but get rid of polar cap positive or negative values.

== 20/12/2011 == AS
>> new option possible in callphys.def: tituscap [logical]
.true. will call functions geticecover to yield a nice evolving CO2 cap as measured by Titus (mostly useful for mesoscale)
.false. is the default option, so this change is transparent to the casual user

== 11/01/2012 == AC
>> Corrections to the thermals scheme following latest revisions of the related paper. Replaced the surface layer interpolator by a more
complete routine, that will ultimately become a post-processing utility (and disappear from libf) and a subroutine in the MCD.

== 23/11/11 == FGG
>> Cleanup of the NLTE routines which have been packed together to limit the 
   number of files. Also enforced that file names are non-capitalized (needed
   by the create_make_gcm scripts to better evaluate dependencies when
   building the makefile).
   
== 07/02/12 == JYC
>> Adding the new molecular diffusion routines (old "moldiff" and "moldiffcoeff"
   are kept for now and if further tests are needed):
   moldiffcoeff_red.F, moldiff_red.F90, diffusion.h
   Also updated "phymars/comdiurn.h", "aeronomars/conc.h" and 
   "aeronomars/chimiedata.h" to be fixed/free form compatible.

== 09/02/12 == EM
>> Updated the makegcm(s) so that default behaviour is to set LMDGCM env variable
   to be the directory in which the makegcm script is. Updated the makegcm_*
   to use "SOURCE" to identify main program to compile
>> Adapted "create_make_gcm" script so that it can compile a main program that
   is either something.F or something.F90. Also added that object files are
   removed from archive before compiling a new version.

== 10/02/12 == TN
>> Major update on watercycle: a smaller integration timestep is now used
   in watercloud.F, sedimentation of clouds is done in watercloud instead of 
   callsedim.F
>> Temperature-dependant contact parameter in nuclea.F
>> No dust lifting if CO2 ice in vdif.c
>> Ice integrated column opacity is written in diagfi from physiq.F, instead
   of aeropacity.F. Mandatory if iradia is not 1.
>> New definition of permanent ice in surfini.F and possibility to have an ice 
   cap in it in 1d.
>> Update in deftank: callphys.def.outliers,run.def.1d; added traceur.def.scavenging

== 15/02/12 == AS
>> Optimization of watercycle new capabilities, e.g.:
   ... in nuclea, removed 'if' from function fshape, modified **, decrease number of overall variables
   ... in growthrate and newsedim, modified ** 
   ... in improvedclouds, modified **, improved recursive calls to erf (now loop w/ 2 erf + 1 log instead of 4 erf + 4 log)
>> Checked consistency with previous formulations
>> Code 35% faster with a Valles Marineris mesoscale run in springtime (set imicro=25)
   ... probably even better at cloudier seasons

== 23/02/12 == AS
>> In improvedclouds and waterclouds, added optimizations
   ... moved calculations to firstcall
   ... moved 'if' statement so that only useful calculations are performed
>> Code about 10% faster [tests carried out with mesoscale summer Tharsis run]
>> Check with a GCM run that results similar

== 27/02/12 == AC
>> Continuation of thermals setting, comparisons with mesoscale results on Case C
>> Added possibility to call gcm (or 1d) with constant prescribed sensible heat flux, in the spirit of direct comparisons with LES
   ... This is directly comparable to the variable tke_heat_flux in namelist.input
   ... Requires the use of yamada4.F from terrestrial GCM (mixes more, seem more numerically stable)
   ... Usually requires high timesteps (>1000) to avoids crashes. Best approach is to compare
   height of first model level z1 and teta_1 between LES and 1D, and increase the timesteps until results 
   between the two models are comparable (might require a slitghly different tke_heat_flux between the two models
   due to difference in vertical diffusion schemes and subgrid effects)
   ... Syntax for use is to add "tke_heat_flux = ..." in callphys.def
>> Corrected some stuff with tke transport in thermals (which is anyway deactivated but one day maybe...)

== 02/03/12 == EM
>> bug fix in "aeronomars/moldiff_red.F90" (wrong mmol array size in included
   subroutine) + adapted extreme limit test for H to altitudes of ~4000km
   (compatble with 50 layer model).
>> bug fix in "nirco2abs.F" index of "co2" and "o" tracers were hard coded as
   1 and 3!
>> updates from FGG of euvheat.F, callkeys.h and inifis.F to have the
   "euveff" parameter read from callphys.def
>> added missing call to surfacearea before call to calchim in physiq (mea
   culpa) and also moved photochemistry so it occurs after sedimentation.

== 06/03/12 == EM
>> Added option "q=profile" in newstart to initialize a given tracer with
   a profile specified in an ASCII file.
>> Minor fix on lect_start_archive : when tracers were not found, a default
   value was asked to user, but twice! Once is enough.

== 07/03/12 == AC
********************************************************
>> UPDATE ON PARAMETERS TO SET TO USE THE THERMALS MODEL 
********************************************************

>> IN CALLPHYS.DEF <<
---------------------

- calltherm = .true.       > activates the thermals
- callrichsl = .true.      > activate the Richardson Monin Obukhov surface layer
with subgrid gustiness, and the yamada4 diffusion model from earth (corrected version of vdif_kc)
- leave calladj = .true.   > so that the convective adjustment may work ABOVE the PBL.

>> IN RUN.DEF <<
----------------

- 96 physicial timesteps per day (the internal sub-timestep of thermals will adapt
so that it costs only 10% more CPU time to go from "48pdt+thermals" to "96pdt+thermals".)
> this has to be respected because of a coupling between the radiative transfer and thermals
> if you really wish to run with 48 pdt/day, you may want to deactive the thermals...

>> USEFULL DIAGNOSTICS <<
-------------------------

- activating the thermals will automatically add 3 2D-outputs to diagfi.nc files:
> zmax_th : interpolated boundary layer height (m)
> hfmax_th : maximum vertical eddy heat flux reached in thermals (K.m/s)
> wstar : free convection velocity reached in thermals (m/s)

A rule of thumb for determining the mean velocities in subgrid-scale structures is:

Mean updraft velocity : ~ wstar
Maximum updraft velocity : ~ 2 or 3.*wstar
Mean downdraft velocity : ~ 0.66*wstar
Maximum absolute value of downdraft velocity : ~ 2.*wstar

>> AT COMPILATION TIME <<
-------------------------

- +1 vertical level during the compilation, and then using the updated z2sig.def

>> UPDATED Z2SIG.DEF <<
-----------------------

- one level has been added in the PBL, so that to reach 150km you have to compile with
33 vertical levels instead of 32.

10.00000     H: atmospheric scale height (km) (used as a reference only)
0.0020736
0.015735
0.0600151
0.163344
0.36358
0.708007
1.25334 
2.06571
3.22069
4.80327
6.90787
9.63834
13.108
18.9666
25.0626
31.5527
38.4369
45.4369
52.4369
59.4369
66.4369
73.4369
80.4369
87.4369
94.4369
101.4369
108.437
115.437
122.437
129.437
136.437
143.437
150.437
157.437
164.437
171.437
178.437
185.437
192.437
199.437
206.437
213.437
220.437
227.437
234.437
241.437
248.437
255.437
262.437
269.437
276.437
283.437
290.437
297.437
304.437
311.437
318.437
325.437
332.437
339.437
346.437
353.437
360.437
367.437
374.437
381.437
388.437
395.437

********************************************************
>> END OF UPDATE ON PARAMETERS FOR THE THERMALS MODEL
********************************************************

== 12/03/12 == EM
>> correction in nirco2abs: io and ico2 should be declared as integers
>> Update sponge: remove posibility of specifying 'hsponge', all modes
   apply to the last upper "nsponge" layers (default nsponge=3) and
   sponge time scale doubles with every level, starting from top.

== 12/03/12 == FL + EM
>> update a coefficient in photochemistry.F and some cleanup in watercloud.F
  and physiq.F.

== 29/03/12 == JYC + EM
>> Update vertical grid resolution for diffusion.
 
== 30/03/12 == EM
>> Updated model so that 1) reference pressure for opacity is now 610 Pa (and
   not 700 Pa anymore) and 2) the new MY24-MY30 dust scenarios (input files
   dust_MY24.nc, dust_MY25.nc, ..., dust_MY30.nc) can be used
   (when setting iaervar=24,25,...,30 in callphys.def): changed
   "readtesassim.F90" into "read_dust_scenario.F90" and apadpted aeropacity.F.
   one can still use the "old" MY24-MY25-MY26 (input files dust_tes_MY24.nc,
   dust_tes_MY25.nc and dust_tes_MY26.nc) scenarios by setting
   iaervar=124, 125 or 126 in callphys.def.

== 31/03/12 == AS & FF
>> Deleted obsolete lines in solarlong   

== 13/04/12 == FL
>> Update of the chemistry package: 
- calchim.F90 :
  - upgraded from calchim.F
  - can run with or without CH4
  - fixed the mass conservation scheme
- photochemistry.F :
  -chemistry timestep is now independant from physics timestep
  -can run with or without a CH4 tracer
  - removed initial tests on species, since these are already done in calchim
- removed inichim_readcallphys.F (not used any more)
- concentrations.F: adaptated to better handle indexes and molar masses of
                    tracers. "ncomp" (in chimiedata.h) no longer needed.
- inichim_newstart.F90 : rewritten and cleaned (won't be compatible with
                         old start files where tracer names are q01,...).
                         Now handles hybrid levels and automaticaly adapts
                         depending on which tracers are available.
- newstart.F : adapted to followup changes in inchim_newstart.F90 and some
               cleanup around the initialization of tracer names and surface
               values.

== 18/04/12 == TN
>> New scheme in improvedclouds.F based on an analytical solution of the crystal radius growth equation
>> Sedimentation of clouds done in callsedim.F, as it was done before version 520
>> Latent heat release of sublimating ground ice in vdifc.F
>> Bug corrected in lwu.F, that was a source of NaN for very thick water ice clouds
>> Bug corrected in updatereffrad.F, ice and dust radius are now updated each timestep before radiative transfer

== 20/04/12 == EM
>> Some cleanup on messages and comments in code about the reference pressure
   for dust opacity which is now 610 Pa.

== 25/04/12 == TN
>> The new scheme does not work for now. Instead, use of a subtimestep for nucleation and growth.

== 26/04/12 == FGG+FL
>> Update of the chemistry package, including:
- 93 reactions are accounted for (instead of 22); tracking 28 species (instead
  of 11)
- computation of photoabsorption using raytracing
- improved time stepping in the photochemistry
- updated parameters (cross-sections); with this new version input files
   are in 'EUV/param_v5' of "datafile" directory.
- transition between lower and upper atmosphere chemistry set to 0.1 Pa
  (calchim.F90)
- Lots of code clean-up: removed obsolete files column.F, param_v3.h,
  flujo.F, phdisrate.F, ch.F, interpfast.F, paramfoto.F, getch.F
  Converted chemtermos.F -> chemthermos.F90 and euvheat.F -> euvheat.F90.
  Added paramfoto_compact.F , param_v4.h and iono.h
- Upadted surfacearea.F
- Cleaned initracer.F and callkeys.h (removed use of obsolete "nqchem"
  and "oldnames" case when initializing tracers).
- Minor correction in "callsedim": compute "rdust" and/or "rice" only when
  it makes sense.

== 03/05/12 == JYC+EM
- Update of molecular diffusion routines (diffusion.h, moldiff_red.F90
  and moldiffcoeff_red.F): optimized to run faster and diffuse only
  specific tracers (if they are present).
- bugs fixed in simpleclouds.F (extra arguments) and watercloud.F (wrong
  arguments in call to simpleclouds and rdust() should only be recomputed
  if dust_mass & dust_number tracers are available).

== 04/05/12 == JYC+EM
- some syntax corrections in thermcall_main_mars, vdif_cd, pbl_parameters
  which cause problems when compiling with some strict compilers (g95, gfortran)
- added an initialisation of 'varian' in initracer for cases when using
  conrath dust; because that value can be is used elsewhere (e.g. surfacearea)

== 11/05/12 == FGG+FL
- aeronomars/inichim_newstart.F : initialization of chemistry now handles
  nitrogen species and ions
- aeronomars/conc.h : cleanup of obsolete variables
- aeronomars/chimiedata.h : cleanup of obsolete variables

== 12/05/12 == FGG+JYC+EM
- updated high atmosphere photochemistry (jthermcalc.F, param_v4.h, iono.h,
  paramfoto_compact.F, param_read.F , thermosphere.F).
- minor change in calchim.F90 (to not use maxloc(zycol, dim = 2) function
  which seems to be a problem for g95) .
- minor bug fix in perosat.F; set tendency on pdqscloud for h2o2 to zero if
  none is computed.
- in "moldiff.F", changed "tridag" to "tridag_sp", "LUBKSB" to "LUBKSB_SP"
  and "LUDCMP" to "LUDCMP_SP" to avoid possible conflicts with same routines
  defined in "moldiff_red.F". Added use of automatic-sized array in "tridag"
  and "tridag_sp" local array "gam" (to avoid using an a priori oversized
  local array).

== 21/05/12 == JYC+FL
- corrected bug in computation of HCO2+ in paramfoto_compact.F
- avoid infinite H2O saturation ratio at very low temperatures in improvedclouds.F

== 29/05/12 == EM
- Added the possibility to use the "cold" (iaervar=6) or "warm" (iaervar=7)
  dust scenarios (derived from the 7 MY24 to MY30 scenarios) in
  aeropacity.F and read_dust_scenario.F

== 04/06/12 == AC
- Code re-organization in diverse parts of the GCM code. These are NOT cosmetic
changes, but are needed for compilation of the Mesoscale model in NESTED configuration
using the new physics.

== 05/06/12 == AS
- Change few function names in nlte_aux.F so that nesting is possible. This is 
completely transparent to GCM users.

== 06/06/12 == EM
- Minor cleanup in surfini.F
- Corrected the polar mesh surface area which was wrong in the physics (changes
  in phyetat0.F, calfis.F and newstart.F)

== 14/06/12 == EM
- update z2sig.def file in deftank with improved vertical discretization for
  better thermals (this update should should have been done a while back...)

== 14/06/12 == FGG
- Added possibility to run with a varying EUV cycle following real one.
  The flag solvarmod=1 triggers this behaviour, with companion flag
  solvaryear=## , where ## is the Mars Year (from 23 to 30).
  Setting solvarmod=0 reverts to 'old' behaviour, where there is a constant
  EUV forcing throughout the run, set by the "solarcondate" flag.
- Needs corresponding input data files ("param_v6" subdirectory of "EUV"
  subdirectory in "datadir").
- Added files jthermcalc_e107.F and param_read_e107.F in "aeronomars",
  modified files euvheat.F90, hrtherm.F, chemthermos.F90, param_v4.h and
  param_read.F in "aeronomars" and files inifis.F, physiq.F and callkeys.h
  in "phymars".

== 15/06/12 == EM
- Minor fix in "nuclea.F", max() and min() functions must have arguments
  of identical types.
- Bug correction in "physiq.F": only water (and possibly dust and cnn if
  using microphysics) tracer tendencies should be updated after call
  to watercloud.

== 22/06/12 == EM
- Enforce that imposed TES ice albedo can never be greater than 0.9

== 28/06/12 == JYC+EM
- Decreased time step for molecular diffusion (diffusion.h) for better stability
- Added test in moldiff_red.F90 to enforce that the system can't be stuck in an 
  infinite loop.
- The creation and output of coefficients in file 'coeffs.dat' in moldiff_red.F
  is now controled by an internal flag (by default set to false).

== 12/07/12 == TN
- Use of stats.def to write variables in stats.nc, same as diagfi.def
- some outputs in physiq.F

== 25/07/12 == TN
- Added module updaterad.F90, that computes ice and dust radius: 
  ---> for ice particles: typical profile (even if doubleq is used) or microphysics
  ---> for dust particles: geometric mean radius (sedimentation,radiative transfer) 
                           or mass mean radius (for heterogenous nucleation of microphysics)
- Possibility to use microphys without scavenging: 
     dust population will not be affected by nucleation and CCN release
- New ice definition in surfini, based on latest CO2 cycle parameters

== 07/08/12 == FGG + MALV
- Improvement of the NLTE 15um scheme (for running with nltemodel = 2); now
  MUCH faster than previously (by a factor 5 or so):
- Improvements included to the parameterization:
  - Cool-to-space calculation included above P(atm)=1e-10, with a soft
    merging to the full result (without the CTS approximation) below that
    level
  - exhaustive cleaning of the code, including FTNCHK and reordering of
    loops, subroutines and internal calls
  - simplification of the precomputed tables of CO2 bands' atmospheric
    transmittances
  - the two internal grids (the one used in the CTS region and the one
    below) have been , in order to reduce the CPU time consumption
  - reading of the spectroscopic histograms is made only once, at the
    beginning of the GCM, to avoid repetitive readings of ASCII files
  - F90 matrix operations (matmul,...) included.
- Changes in routines:
  - removed nlte_leedat.F
  - updated nlte_calc.F, nlte_tcool.F, nlte_aux.F
  - updated nlte_commons.h, nlte_paramdef.h
  - added nlte_setup.F
- Important: The input files (in the NLTEDAT directory) read as input by
  these routines have changed. the NLTEDAT directory should now on contain
  only the following files:
   deltanu26.dat  enelow27.dat  hid26-3.dat  parametp_Tstar_IAA1204.dat
   deltanu27.dat  enelow28.dat  hid26-4.dat  parametp_VC_IAA1204.dat
   deltanu28.dat  enelow36.dat  hid27-1.dat
   deltanu36.dat  hid26-1.dat   hid28-1.dat
   enelow26.dat   hid26-2.dat   hid36-1.dat

== 08/08/12 == EM
>> Some minor changes and adaptations for the MCDv5 runs:
- removed the 'nice' instruction from run0 script
- update dissipation factors in inidissip.F (fac_mid=3,fac_up=30,startalt=70)
- add some outputs in physiq.F
- put example def files used for MCDv5 simulations in deftank:
  callphys.def.MCD5 run.def.64x48x49.MCD5 traceur.def.MCD5

== 08/08/12 == FGG
>> commented out some messages in nlte_tcool.F (which were informations
   useful and meaningful during code development only)

== 27/08/12 == FGG
>> bug correction in the varying EUV case; now correctly account for things
   as the year cycles.

== 20/09/2012 == EM
>> update of zrecast utility: add possibility to have automatic "MCD/GCM"
   altitude above surface levels as well as the possibility to specify min,
   max and number of levels.

== 21/09/2012 == EM
>> Adapted code so that it can run fractions of days: e.g. if "nday=1.5" in
  run.def, then run a sol and a half, "nday=0.75" to run three quarters of
  a sol... Of course the fraction should correspond to a number of complete
  dynamics/physics cycles. The fraction of the sol that a (re)start.nc
  file corresponds to is (read)written as 'Time' in the file.

== 25/09/2012 == EM
>> Minor improvement for running fractions of sols; enforce some rounding of
   'Time' (ie: fraction of day) read from the start.nc file in order to limit

== 05/11/2012 == TN
>> Added new option : ndynstep in run.def, that allows to run for a specific number a dynamical timesteps.
   If ndynstep is not specified or is negative, nday is used. Otherwise nday value is discarded.
   The problem with nday alone is that one can only run the GCM for a decimal fraction of one sol.

== 06/11/2012 == EM
>> update of zrecast utility: now the planetary constants (radius, gravity,
   reduced gas constant) are read from the "controle" array in the file and
   not hard coded. That way zrecast can also be used for the generic model.
   Note that the "distance to center of Mars" and "MCD" options still contain
   some hard coded Mars constants.

== 15/02/2013 == TN
>> Various bugs
- watercloud.F : latent heat release was not correctly added
- updaterad.F90 : minimal rdust is changed from 0.1 to 0.01 microns
- vdifc.F : The scheme with potential temperature mixing that takes into acount CO2 condensation
            could not work without CO2 condensation (callcond=false) -- see commit r473
            This caused a quick GCM crash. Now there is no condensation at all with callcond=false
- physiq.F : pressure levels are now correctly used with surface pressure changes due to CO2
             condensation. Only zplev and zplay variables should be used in physiq.
             Bug corrected in case of scavenging=false that led to instabilities. CCN tracers were not checked.
- makegcm : use of phy$physique instead of phymars for scatterrers
 
== 25/02/2013 == EM
- added "-fp-model precise" option when compiling with ifort (fixes unexplained
  mass loss of tracer in the dynamics)
  
== 27/02/2013 == EM
- minor bug correction in newcondens.F and some code tidying (in co2snow.F also).

== 12/03/2013 == EM
- added possibility to set slope parameters in testphys1d

== 12/03/2013 == TN
- added possibility to use the radiative slope scheme in the 3D-GCM

== 10/05/2013 == FGG
- bug correction in "extract" utility

== 02/07/2013 == TN
>> Added the possibility to store multiple initial states in one start/startfi
>> New option 'ecrithist' in run.def to write data in start/startfi every ecrithist
   dynamical timestep (default is to write it at the end of the GCM run).
>> New option 'timestart' in run.def to initialize the GCM with the time timestart
   stored in start (default is last time).
>> This new feature is (supposedly) totally RETROCOMPATIBLE. Changes are:
  - Time axis added in startfi
  - Time axis can be longer than one in start/startfi
  - Possibility to initialize the GCM with old start/startfi
  - Compatibility with start2diagfi, newstart, testphys1d, expandstartfi
  - Absolute date is stored in diagfi for less-than-a-day runs
>> Quick documentation about dates :
  - Day at the beginning of the start (integer) is stored in controle(4) 
    for start and diagfi and controle(3) for startfi.
  - Fraction of the day at the beginning of the start (real between 0 included and 1 excluded) 
    is stored in controle(29) for start, controle(27) for diagfi and controle(4) for startfi.
  - The "Time" variable stores all the dates from the beginning of the start (positive real) 
    for start, startfi and diagfi
  - Time is stored in start_archive in the "Time" variable.
  - Time-related data in the controle field of start_archive are useless.
For instance the i-th date of diagfi is controle(4)+controle(27)+Time(i)

== 04/07/2013 == EM
- Removed options "-static" and "-xSSE4.2" from ifort default options from
  makegcm_ifort (-static not usable on Gnome computer, and not much benefit
  anyways, and -xSSE4.2 causes unexplained crashes with thermosphere on
  Gnome)

== 18/07/2013 == EM
- Bug fix: when running with photochemistry, ccns did not sediment! Fixed
  initracer.F. Also added that callsedim/newsedim use updated temperatures.
- Converted run0 and run_mcd scripts to bash.

== 26/07/2013 == FGG +JYC
- Upgrade on the thermospheric photochemical reaction rates. These are now
  read in from a file "chemthermos_reactionrates.def".

== 06/09/2013 == AC + EM + AS
- Cleaned and commented version of thermal plume model with automatic arrays
- Checked: exact same results than before modifications

== 11/09/2013 == EM
- Bug fix in vdifc.F: in some cases, some elements of pdqsdif() were not given
  any value. In all cases, it is safer to start with clean initialization of
  output tendencies to zero.
- Bug fix in concentration.F: error in cpi() and aki() indexes led to
  wrong computation of atmospheric conductivity and specific heat.

== 11/09/2013 == EM
- IMPORTANT CHANGE: Implemented dynamic tracers. It is no longer necessary to
  compile the model with the '-t #' option, number of tracers is simply read
  from tracer.def file (as before).
  Adapted makegcm_* scripts (and co.) accordingly.
  Technical aspects of the switch to dynamic tracers are:
  - advtrac.h (in dyn3d) removed and replaced by module infotrac.F
  - tracer.h (in phymars) removed and replaced by module tracer_mod.F90 (which
    contains nqmx, the number of tracers, etc. and can be used anywhere in the
    physics).
- Included some side cleanups: removed unused files (in dyn3d) anldoppler2.F,
  anl_mcdstats.F and anl_stats-diag.F, and all the unecessary dimensions.*
  files in grid/dimension.
- Checked that changes are clean and that GCM yields identical results (in
  debug mode) to previous svn version.

== 13/09/2013 == AS
- Performed the necessary modifications for dynamic tracers 
  to work with the mesoscale model
- Added precompiling flag MESOSCALE around pressure modifications
  done in revision 883. This makes the mesoscale model become crazy.

== 21/09/2013 == EM
- Bug fix in yamada4.F: values for near-surface diffusion coefficients were
  used but not set.
- NB: FH recommends updating to latest yamada4 from Earth GCM and using
  their iflag_pbl=11 scheme.

== 23/09/2013 == EM
- IMPORTANT CHANGE: Removed all reference/use of ngridmx (dimphys.h) in
  routines (necessary prerequisite to using parallel dynamics); in most 
  cases this just means adding 'ngrid' as routine argument, and making
  local saved variables allocatable (and allocated at first call).
  In the process, had to convert many *.h files to equivalent
  modules: yomaer.h => yomaer_h.F90 , surfdat.h => surfdat_h.F90 ,
  comsaison.h => comsaison_h.F90 , yomlw.h => yomlw_h.F90 ,
  comdiurn.h => comdiurn_h.F90 , dimradmars.h => dimradmars_mod.F90 ,
  comgeomfi.h => comgeomfi_h.F90, comsoil.h => comsoil_h.F90 ,
  slope.h => slope_mod.F90
- Also updated EOF routines, everything is now in eofdump_mod.F90
- Removed unused routine lectfux.F (in dyn3d)

== 31/10/2013 == TN
- Added a freedust mode, to be used with doubleq :
  Dust is not lifted, not rescaled, dust opacity is predicted instead of being forced.
  A corresponding freedust option is added in newstart to rescale dust to acceptable values
  before such a GCM run, although 'q=profile' could be used too.

== 13/11/2013 == AS
--> Added precompiling flag MESOSCALE around pressure modifications
    done in revision 883. This makes the mesoscale model become crazy.

== 20/11/2013 == EM
- Correction: in physiq.F, move newcondens (CO2 condensation routine) so that
  it is the last atmospheric physical process to be computed.
- Also corrected the setting of the South Pole surface temperature to
  CO2 condensation temperature (when obliquity < 27) to account for varying
  CO2 mixing ratio. This operation is now done in newcondens.

== 28/11/2013 == FGG
- Bug fix: Sun-Mars distance was not correctly taken into account in the
  solvarmod==1 (daily varying realistic EUV input) case.

== 10/12/2013 == FGG
- Improved 15um cooling routines, with also better handling of errors.

== 18/12/2013 == EM
- Bug fix in thermcall_main_mars, layer thickness "zdz" must be recomputed
  in every do ig=1,ngrid loop.

== 20/12/2013 == EM
Series of changes to enable running in parallel (using LMDZ.COMMON dynamics);
Current LMDZ.MARS can still notheless be compiled and run in serial mode
"as previously".
Summary of main changes:
- Main programs (newstart, start2archive, xvik) that used to be in dyn3d have
  been moved to phymars.
- dyn3d/control.h is now module control_mod.F90
- rearanged input/outputs routines everywhere to handle serial/MPI cases.
  physdem.F => phyredem.F90 , phyetat0.F => phyetat0.F90 ; all read/write
  routines for startfi files are gathered in module iostart.F90
- added parallelism related routines init_phys_lmdz.F90, comgeomphy.F90,
  dimphy.F90, iniphysiq.F90, mod_grid_phy_lmdz.F90, mod_phys_lmdz_mpi_data.F90,
  mod_phys_lmdz_mpi_transfert.F90, mod_phys_lmdz_omp_data.F90,
  mod_phys_lmdz_omp_transfert.F90, mod_phys_lmdz_para.F90,
  mod_phys_lmdz_transfert_para.F90 in phymars
  and mod_const_mpi.F90 in dyn3d (for compliance with parallel case)
- created generic routines 'planetwide_maxval' and 'planetwide_minval', in
  module "planetwide_mod", that enable obtaining the min and max of a field
  over the whole planet.

== 08/01/2014 == EM
- Update of the read_dust_scenario routine: when input dust scenarios file
  contain variable "dustop", it is assumed to be visible extinction opacity,
  and if it is "cdod" (recent change, for the MCDv5.1 dust scenarios), then
  it is IR absorption opacity (and is multiplied by 2.6 to be converted to
  visible extinction opacity).

== 12/03/2014 == EM
- Bug fix in surfini.F, nb_ice array should be the size of the full grid.
  Only was an issue when runiing in MPI and mode icelocationmode = 1
  Note that it would make more sense for the initialization of watercaptag and co.
  to be done in newstart, and that these values be stored in startfi.nc

== 12/03/2014 == TN
- Added tauscaling (the conversion factor from virtual to real dust) in startfi.nc file.
  It is needed for 3 cases:
  1. Compute ice particles size when using microphysics on the first physics step 
     before the call to the radiative transfer (updatereffrad)
  2. The conversion to real dust values with newstart, to be used for the freedust mode.
  3. It brings the necessary information for the calculation of the dust 3D opacity 
     from start & startfi files only when using virtual dust.
  If tauscaling is not present, the default value is 10^-3 everywhere when needed.
  If the freedust mode is used, tauscaling is equal to 1 everywhere. 
  Modified accordingly startfi and start_archive writing and reading routines.

== 24/03/2014 == AS
--> fixed a potential bug in thermal plume model because zlmax was computed both in thermcell_main_mars and calltherm_interface... so made it an OUT argument
 of calltherm_interface. also: changed the name to limz. and added precompiling flags to avoid the use of planetwide in MESOSCALE. in MESOSCALE we just go hi
gh enough (nlayer-5) and do not care about computational cost (although we certainly gain from not using MAXVAL).
--> moved allocations upward in inifis. does not change anything for GCM, but make MESOSCALE modifications simpler, and overall make inifis better organized:
 first allocations, then reading callphys.def file.
--> added precompiling flags around lines that are both useless for MESOSCALE (notably I/O) and recently adapted to parallel computations in the GCM
--> tidied up what is MESOSCALE vs. GCM in surfini

== 15/04/2014 == AS
1. No more SAVE,ALLOCATABLE arrays outside modules.
     This is important to solve the nesting conundrum in MESOSCALE.
     And overall this is good for the harmony of the universe.
     (Joke apart, this is good for any interfacing task. And compliant with a F90 spirit).
     Note that bit-to-bit compatibility of results in debug mode was checked.
2. inifis is split in two : phys_state_var_init + conf_phys
     This makes interfacing with MESOSCALE more transparent.
     This is also clearer for LMDZ.MARS. 
     Before, inifis has two very different tasks to do.
3. a bit of cleaning as far as modules and saves are concerned

== 15/04/2014 == AS
Replaced comcstfi and planete includes by modules

== 18/04/2014 == EM
Some minor fixes and cleanup.
- use surfdat_h, ... qsurf was missing in start2archive
- 'tauscaling' was missing from argument list when calling physdem1
  in testphys1d

== 19/04/2014 == FF+EM
Add "composition" option in newstart to enable global modification of
CO2,N2,Ar,O2 and CO mixing ratios. Plus some cleanup on physics variables
(saved arrays) which have been moved to modules.

== 01/05/2014 == AS
- Filling geom arrays is now out of phys_var_state_init. Done
  through a merged function ini_fillgeom within the comgeomfi_h module.
- Cosmetic changes
- New interface with the mesoscale model: lesser amount of dirty MESOSCALE includes

== 04/05/2014 == AS
- Further reduction of the amount of MESOSCALE precompiling steps and code bits
- Changed the I/O interface with the mesoscale model
  --> I are not longer arguments but are passed through modules
  --> O are no longer generated as additional includes
      but passed through the module comm_wrf.F90
      !! this new module is harmless 
      !!   in GCM applications 
      !!   (arrays are not allocated)
- Note: the easiest for interfacing is to put all fields 
        to be output in a module with allocatable arrays.
        see for instance in turb_mod for ustar.
        but this could conflict with GCM developers' habits
        so we use the comm_wrf.F90 strategy instead for
        several arrays (radiative transfer, clouds, etc...)

== 07/05/2014 == EM+FF
Some fixes and updates:
- addfi (dyn3d): Add correction on theta when surface pressure changes
- vdif_cd (phymars): Correction for coefficients in stable nighttime case
- jthermcalc (aeronomars): Fix for some pathological cases (further investigations
  on the origin of these is needed)

== 09/05/2014 == AS
- Added a flag callyamada4 in callphys.def to activate or not the latest version
for subgrid-scale mixing. It is T by default.
- Warnings in conf_phys modified accordingly.

== 10/05/2014 == AS
- Further reduction (or 'factorisation') of mesoscale includes
- ustar and tstar are calculated in vdifc. so no need to recalculate
  those elsewhere. use turb_mod module to store it. 

== 11/05/2014 == AS
- Number of scatterers no longer prescribed at compiling time
- Number of scatterers must now be set in callphys.def (keyword: naerkind)
- Added in dimradmars_mod a subroutine ini_scatterers to initialize arrays once naerkind is known
  -- NB: ini_scatterers is not called in phys_var_init
  --     but rather in conf_phys once naerkind is read in callphys.def
- Checks + names of scatterers moved from callradite to conf_phys
- Put what was in scatterers.h in dimradmars_mod
- Put what was in aerkind.h in dimradmars_mod
- Put what was in yomaer_h in dimradmars_mod
- Moved conc_mod in phymars rather than aeronomars. 
  Otherwise pb of cyclic dependencies (plus compiling without aeronomars is impossible).

== 14/05/2014 == FGG
- Bug fix in jthermcalc.F: rounding issues in computation of the solar zenith
  angle when SZA slightly greater than 90
- Corrected misleading warning in nlte_tcool.F

== 20/05/2014 == AS
IMPORTANT CHANGE
- Remove all reference/use of nlayermx and dimphys.h
- Made use of automatic arrays whenever arrays are needed with dimension nlayer
- Remove lots of obsolete reference to dimensions.h
- Converted iono.h and param_v4.h into corresponding modules
   (with embedded subroutine to allocate arrays)
   (no arrays allocated if thermosphere not used)
- Deleted param.h and put contents into module param_v4_h
- Adapted testphys1d, newstart, etc...
- Made DATA arrays in param_read to be initialized by subroutine 
   fill_data_thermos in module param_v4_h
- Optimized computations in paramfoto_compact (twice less dlog10 calculations)
- Checked consistency before/after modification in debug mode
- Checked performance is not impacted (same as before)

== 21/05/2014 == EM
- Bug fix in thermosphere.F, always initialize all tendencies to zero. (only
  really matters in cases when only some of the included parametrizations
  are used).

== 02/06/2014 == EM
- Add possibility to use clim or MY31 dust scenarios (and realistic EUV for MY31).

== 11/07/2014 == EM
- Changed the variable passed from LMDZ.MARS dynamics to physics: it is now
a mass flux (kg/s) which is then converted to a vertical velocity (m/s) in
the physics. This is to be consistent with what is done in LMDZ.COMMON.

== 26/08/2014 == FGG
- Bug fix: Enforce recomputation of reaction rates at every call of
  routine prodsandlosses (in paramfoto_compact.F)

== 06/10/2014 == TN
- New option dustiropacity in callphys.def to change the reference IR opacity
  of dust. Default is 'tes' (like before), the new one is 'mcs'. A new output,
  dsodust, is the density scaled opacity of dust, to be compared with MCS
  measurements, along with dustiropacity='mcs'. Future evolutions of this option
  could include other instruments, or be used for water ice.

== 20/10/2014 == JYC
- Update and bug correction on the escape fluxes of H and H2.

== 13/02/2015 == EM
- Update pbl_parameter with corrected version by Anne-Flore Moreau.

== 26/02/2015 == EM
- Update default location for "datadir" files, now at
  http://www.lmd.jussieu.fr/~lmdz/planets/mars/datadir
  or /u/lmdz/WWW/planets/mars/datadir for local users.

== 04/03/2015 == FF+EM
- Some cleanup in iniorbit.F

== 12/03/2015 == EM
- Some cleanup in the dynamics/physics interface.

== 23/03/2015 == EM
- Follow-up to cleanup in dynamics/physics interface. Add iniprint.h to be
  in line with what is done in LMDZ.COMMON dynamics.

== 31/03/2015 == EM
- Reorganizing the physics/dynamics interface, for better compatibility
  between models and with the parallel LMDZ.COMMON dyn core. Main structural
  changes are:
* misc: (replaces what was the "bibio" directory)
- Should only contain extremely generic (and non physics or
  dynamics-specific) routines
* dynlonlat_phylonlat: (new interface directory)
- This directory contains routines relevent to physics/dynamics grid
  interactions, e.g. routines gr_dyn_fi or gr_fi_dyn and calfis
- Moreover the dynlonlat_phylonlat contains directory "phymars".
  This subdirectories should only contain specific interfaces (e.g. 
  iniphysiq) or main programs (e.g. newstart or xvik).
* phymars/dyn1d: this subdirectory contains the 1D model.

== 24/06/2015 == EM
- Missing "use logic_mod" added in testphys1d
- Changed the "use comconst_mod" inistats to use information from physics
  (comconstfi_h module) rather than dynamics.
- Moved "iniprint.h" back to dyn3d (and added link to it in dyn1d), as it
  is preferable to not share modules/commons between physics and dynamics.

== 04/08/2015 == TN
- New option supersat to allow for the supersaturation of water vapor.
  Default value is True. The goal is to disable supersaturation even 
  with microphysics for comparison purposes.

== 19/11/2015 == EM
- Added option "-cpp" so that users can add the definition of specific
  precompiling flags in makegcm_* scripts (and added default BLAS and
  LAPACK flags for ifort on Gnome and Ada).
- Put calls to dgesv (Lapack) routine in photochemistry_asis.F90 under the
  LAPACK preprocessing flag. Moved secondary routines in photochemistry.F and 
  photochemistry_asis.F90 into the main (via contains instruction) to avoid
  multiple definitions of routines with identical names.

== 19/11/2015 == EM
- set things in param_read_e107.F and read_dust_scenario.F90 to read MY32
  EUV and dust forcings.

== 13/01/2016 == EM
- Improvement on planetwide_min/max/sum for the 3D fields which assumed the vertical dimension to be klev.
  Now works for any (klon,...) field.

== 25/03/2016 == EM
- Code reorganization (to mach comming evolutions on all planetary models),
  created a "phy_common" directory to contain routines common (wrt structural
  nature of underlying code/grid) to all LMDZ-related physics packages.
- Adapted "create_make_gcm" and "makegcm*" scripts accordingly
  (deleted obsolete makegcm_g95)

== 28/03/2016 == EM
- Added module "regular_lonlat_mod.F90" (to store information on global
  lon-lat grid) in phy_common.
- Turned iniphysiq (in dynlonlat_phylonlat/phymars)into module
  "iniphysiq_mod.F90".

== 29/03/2016 == EM
- Added "time_phylmdz_mod.F90" module to store information on time and
  calendar in the physics, should be used instead of accessing "temps_mod"
  from the dynamics. And moved daysec and dtphys from module "comcstfi_h"
  to module "time_phylmdz_mod".
- Made "phys_state_var_init" a module

== 30/03/2016 == EM
- Got rid of references to "control_mod" from the physics. Added a couple
  of relevent variables for outputs in time_phylmdz_mod.

== 02/04/2016 == EM
- Got rid of references to "dimensions.h" from physics packages:
  use nbp_lon (=iim), nbp_lat (==jjp1) and nbp_lev 
  from module mod_grid_phy_lmdz (in phy_common) instead.
- Added "ioipsl_getin_p_mod.F90" (getin_p routine) in phy_common to
  correctly read in parameters from *.def files in a parallel environment.

== 07/04/2016 == EM
- Some fixes for buggy outputs in 1D introduced by previous code modifications.
- made statto.h a module.
- ecritphy in dyn3d/control_mod.F90 should be an integer, not a real.

== 08/04/2016 == EM
- Fix for the 1D model initializations.

== 13/04/2016 == EM
- Some code reorganization: "dynlonlat_phylonlat" directory becomes
  "dynphy_lonlat".
- "iniprint.h" moved from "dyn3d" to "misc".

== 17/04/2016 == EM
- fix for 1D in writediagfi to enable writing at 
  "ecritphy" rate.
- removed iniprint.h from phymars/dyn1d since it is in "misc"
- Some code cleanup in anticipation of future updates:
 - changed variable names in comgeomphy.F90: give them more
   explicit names: rlond => longitude , 
   rlatd => latitude, airephy => cell_area,
   cuphy => dx , cvphy => dy
 - removed long(), lati() and area() from comgeomfi_h.F90,
   use longitude(), latitude() and cell_are() from
   comgeomphy.F90 instead

== 22/04/2016 == EM
- Updates and cleanup wrt dynamics/physics separation:
  Removed init_phys_lmdz.F90 and comgeomphy.F90 from phymars;
  comgeomphy is replaced by geometry_mod (located in phy_common).
  Added physics_distribution_mod.F90 in phy_common and
  mod_interface_dyn_phys.F90 in dynphy_lonlat.
  Added nrtype.F90 (contains math const. like PI, etc.) in "misc"

== 25/04/2016 == LS
- Bug fix in read_dust_scenario.F90 to handle the limit case
  of identical realday and time() values at the end of the year.

== 02/05/2016 == JL+EM
- bug fix in calfis: wrong array (pw) sent to physics: the transfered
  mass flux should be on the physics grid, not the dynamics grid.
  Moreover values at the poles needed to be correctly recomputed.

== 06/05/2016 == EM
- turn physiq.F into module physiq_mod.F

== 07/05/2016 == EM
- Bug fix in testphys1d, enforce iphysiq=1 after conf_phys (where its 
  value might be modified).

== 12/05/2016 == EM
- Fix in wstats: use "def_var_stats" and not "def_var" (intended for
  writediagfi) or else outputs are always single precision.

== 20/05/2016 == AS+EM
- cleanup around iniphysiq: separate things between planet-independent
  initializations (now done by inigeomphy in dynphy_lonlat) and
  mosre physics-package specific things (remain in iniphysiq).

== 27/05/2016 == EM
- missing libf/dynphy_lonlat/phymars/inigeomphy_mod.F90 in previous commit

== 12/07/2016 == EM
- move initialization of dimphy from inigeomphy to iniphysiq (initializations
related to routines in phy_common or dynphy_lonlat can be done in 
inigeomphy, but any initialization for modules/routines in a physics
package (directory phymars) must be done in the related phymars/iniphysiq
routine.

== 27/07/2016 == EM
- further cleanup in the dynamics/physics interface: stop sending information
  about tracer advection (tracerdyn) back from physics to dynamics as this
  input parameter can be read and set in the dynamics.

== 09/09/2016 == EM
- Some code cleanup (and harmonization with LMDZ.COMMON): remove "ecritphy"
  from the dynamics (since it is read/used in the physics) and remove
  "grireg" (unused) and "physic" (use iflag_phys instead) parameters from
  the dynamics.
- turn sponge.F into sponge_mod.F90 (and remove sponge.h)

== 13/09/2016 == EM
- Further cleanup to harmonize with LMDZ.COMMON turn "idissip" into
  "dissip_period".

== 10/10/16 == J. Audouard
- Added CO2 clouds : if co2clouds is set to .true., physiq_mod will call co2cloud.F which contains a co2 clouds microphysics scheme (improvedCO2clouds.F). 3 tracers are needed: co2_ice, ccnco2_mass and ccnco2_number. 
- Routines added:
 co2cloud.F (called by physiq_mod.F, contains the microtimestep)
 co2sat.F 
 improvedCO2clouds.F (called inside the microtimestep, contains the microphysics)
 massflowrateCO2.F (CO2 ice growth rate)
 nucleaCO2.F (CO2 ice nucleation)
 
- The following routines/files have been modified to take co2 clouds into account : 
 callkeys.h (added logicals co2clouds and microphysco2)
 callsedim.F (CO2 clouds tracers are ignored : their sedimentation is done in the microtimestep inside co2cloud.F)
 conf_phys.F (added CO2 clouds logicals and some variables needed by the CO2 microphysics)
 initracer.F (added CO2 clouds tracers)
 microphys.H (added some values needed by the CO2 microphysic scheme)
 physiq_mod.F (now calls co2cloud.F if co2cloud is set to .true.)
 tracer_mod.F90 (added some variables needed by CO2 microphysics)
 updaterad.F90 (added a routine for CO2 clouds)
 
== 25/10/2016 == EM
Updates for full physics/dynamics separation:
- introduced module vertical_layers_mod.F90 in phy_common to store information
  about the vertical grid to be used in the physics. Routines in the physics
  should "use vertical_layers_mod" and not "use comvert_mod".
- created an "ini_tracer_mod" routine in module "tracer_mod" for a cleaner
  initialization of the later. Module tracer_mod should be used in the
  physics, not infotrac (belongs to the dynamics).
- removed some purely dynamics-related outputs (etot0, zoom parameters, etc.)
  from diagfi.nc and stats.nc outputs as these informations are not available
  in the physics.
- added scalheight (atmospheric scale height) in comvert_mod

== 16/11/2016 == EM
Bug fix in 1D in physiq, missing "if (co2clouds)" around some operations to
be done only when that option is set.

== 22/11/2016 == JA
-  Bug fix concerning the "riceco2" variable which was declared as a double or as areal in different routines. riceco2 is now correctly declared as a double evrywhere (updaterad.F and co2cloud.F)
-  Moved CO2 clouds outuputs from physiq_mod.F to co2cloud.F
-  Removed some CO2 clouds properties computation in physiq_mod.F (now done in post-treatment)

== 24/01/2017 == JA
-Modification of CO2 clouds routines : removal of some screen ouputs, modification for 3D of the writediagfi outputs in co2cloud.F, improvedCO2clouds.F and physiq_mod.F
-callphys.def.co2clouds was added in deftank. It contains the necessary flags and constant for including co2clouds
-traceur.def.co2clouds was added in deftank. It supplies the necessary tracers for running the co2 clouds scheme

== 30/01/2017 == JA
-Modification of CO2 clouds microtimestep : now is set by imicro in callphys.def together with the water ice clouds microtimestep
-Addition of a meteoritic flux of dust is now possible:
          meteoriticflux_mod.F90 was added, it contains 3 variables that are provided in callphys.def (default values = no flux): meteo_flux_mass, meteo_flux_number and meteo_alt (in km)
          meteo_flux_mass and meteo_flux_number are added to the dust tracers at the z-level corresponding to meteo_alt at every timestep inside co2cloud.F
          conf_phys.F was modified to perform the initialization of the meteoritic flux with the callphys.def values (default values = no flux)
          callphys.def.co2clouds in deftank has been accordingly modified
          
== 08/02/2017 == JYC+EM
- Added possibility to run with an Helium "he" tracer (to be initialized
  at constant value of 3.6e-7 kg/kg_air, i.e. the 4ppm of Krasnopolsky 1996
  EUVE satellite, using newstart).
- corrected case for CH4 in aeronomars/photochemistry.F (was using undefined
  indexes when there is no CH4).
- updated aki/cpi coefficients for Argon used to compute mean atmospheric
  Cp and thermal conductivity in aeronomars/concentrations.F

== 30/03/2017 == EM
Keep up with updates in LMDZ.COMMON:
In dynphy_lonlat : 
- inigeomphy_mod.F90 : add ind_cell_glo computation and  transfer
                       to init_geometry
- mod_interface_dyn_phys.F90 : use is_north_pole_dyn and is_south_pole_dyn
                               (instead of is_north_pole, is_south_pole)
In phy_common:
- abort_physic.F90 : to properly abort from physics (to be used instead
                     of abort_gcm which is for within the dynamics)
- geometry_mod.F90 : add ind_cell_glo module variable to store global
                     column index
- mod_phys_lmdz_mpi_data.F90 : use print_control_mod (rather than iniprint.h)
                               and define is_north_pole_dyn, is_south_pole_dyn
                               (instead of is_north_pole, is_south_pole)
- mod_phys_lmdz_mpi_transfert.F90 : use is_north_pole_dyn, is_south_pole_dyn
                                    (instead of is_north_pole, is_south_pole)
- mod_phys_lmdz_omp_data.F90 : add is_omp_master (alias of is_omp_root) module
                               variable and use print_control_mod (rather than
                               iniprint.h), and introduce is_north_pole_phy
                               and is_south_pole_phy
- mod_phys_lmdz_para.F90 : use print_control_mod (rather than iniprint.h)
- physics_distribution_mod.F90 : add call to init_dimphy in
                                 init_physics_distribution
- init_print_control_mod.F90 : added to initialize print_control_mod module
                               variables
- print_control_mod.F90 : make initialization occur via init_print_control_mod
                          to avoid circular module dependencies

== 31/03/2017 == EM + FGG
Add possibility to fix EUV input as E10.7 value and remove previous system
(which used parameter solarcondate). The E10.7 value is now set via
callphys.def by parameter "fixed_euv_value" which is only used if 
solvarmod==0. 
Guidelines for min/ave/max EUV input:  fixed_euv_value=80/140/320.


== 03/04/2017 == JA
further work on the CO2 clouds scheme:
-water ice clouds can now serve as condensation nucleii for CO2 clouds. Memory of CO2 CCN origin is kept, but a study of the water cycle is needed to know ig further work is necessary.
-co2cloud.F, improvedCO2clouds.F, nucleaCO2.F, massflowrateCO2.F and physiq_mod.F have been modified accordingly.
-co2 cloud scheme tuning has been improved for more stability. 
-a new contact parameter for CO2 ice on silicate is used (mtetaco2=0.78) in microphys.h. Reference in microphysic.h
-CO2 ice temperature is computed as a function of temperature in CO2cloud.F and improvedCO2cloud.F. Reference is in initracer.F

== 07/04/2017 == EM
Fixing a big bug (dating from revision 1528) in wstats.

== 19/05/2017 == MV
- implementation of a sub-grid water cloud fraction scheme (by A. Pottier): If CLFvarying is set to true in callphys.def,
  then the sub-grid cloud fraction routine is applied in watercloud.F and aeropacity.F.
- accordingly modified files are: watercloud.F, aeropacity.F, callradite.F, conf_phys.F, phyetat0.F, phyredem.F90, physiq_mod.F, 
  testphys1d.F, callkeys.h, newtsart.F, start2archive.F, lect_start_archive.F
- added file: tcondwater.F90, used by watercloud.F to calculate the condensation temperature of water
- watercloud.F, aeropacity.F, callradite.F are converted to module files as watercloud_mod.F, aeropacity_mod.F, callradite_mod.F

== 24/05/2017 == EM
- remove writing a "nebuldata.out" file in physiq introduced by previous update.
  It is not necessary and causes issues when in parallel.

== 27/06/2017 == FGG
- add possibility to read in MY33 EUV forcing.

== 06/07/2017 == JA
- Update for CO2 clouds scheme.
- Several bugs have been corrected. 
- Two .dat files are necessary (1 containing the CO2 ice Extinction coefficients is mandatory). 
 They are in /data/jaudouard/datadir on ciclad if you need.
- Several logical can now be set in callphys.def. Explained in co2clouds.F:
 if co2useh2o=.true., water ice particles can serve as CCN for CO2 microphysics
 if meteo_flux=.true., meteoritic particles are supplied to the CO2 nucleation, according to John Plane values.
 if CLFvaryingCO2=.true, a sub-grid temperature distribution is applied for the CO2 
microphysics (just like water clouds). The amplitude is spantCO2, also read from callphys.def
- The previous logical microphysco2 has been removed.
- Cloud opacity at 1µm is now computed in the co2cloud.F routine
- Most of the co2 ice clouds scheme writediagfi are now in co2clouds.F
- Some cleaning of the CO2 ice clouds routine has been done. Not perfect yet!
 
== 02/11/2017 == JA
- Update for CO2 clouds scheme.
- Several bugs have been corrected, further cleaning performed.
- The main routine of co2 clouds is co2cloud.F. Please read its comments if interested.

== 03/11/2017 == JA
- Further cleaning of the CO2 ice clouds code
- We can now have different micro-timesteps bewteen the water ice clouds and the co2 ice clouds
- callphys.def needs imicroco2 = integer (typically 50) (water microtimestep is imicro=integer)
- A filter based on Spiga et al 2012 Saturation index has been implemented. It is supposed to represent
  if a gravity wave propagates to the mesosphere or not (wheter the wave saturates on its way or not). 
  The sub-grid temperature distribution is cancelled if the saturation index value of the column (between 12 and 80 km) is > 0.1, and is applied (+/- 3K) otherwise. if the keyword satindexco2=.true. in callphys.def (only applies if CLFvaryingCO2=.true. anyway). If set to .false., deactivate this filter and the sub grid T distribution applies everywhere and everytime. See comments in co2clouds.F
- All that you need to launch a GCM run with co2 clouds is described in co2clouds.F comments. Ehouarn Millour and Anni Määttänen have the files. 
 
== 15/11/2017 == EM
- Bug fix in co2cloud.F (in the computation of the saturation index) along
  with some code tidying.

== 18/12/2017 == EM
- Add possibility to load a dust MY33 scenario.

== 22/12/2017 == MV
-In the sub-grid scale cloud scheme zt is replaced is by ztclf and zq by zqclf ('clf' for 'cloud fraction') in order to avoid any confusion for the further schemes, which need initialization.
-zteff and pqeff are initialized in the first part of the CLFvarying scheme, section 0 of the code, instead of been initialized in section 1 (tendencies) with the sub-timesteps.
-The cloud fraction cannot be lower than the settled value mincloud.

== 05/01/2018 == CL+EM
- updated massflowrateCO2 routine which now uses an analytical formula rather
  than an iterative solver
- some code tidying in improvedCO2clouds.F

== 05/01/2018 == EM
- fix in co2cloud.F: use "co2cloudfrac" instead of "cloudfrac" to avoid
  output naming collisions with the water cycle.

== 09/01/2018 == FGG
Updated the calculation of the dissociation and ionization
branching ratios, using the values in the Schunk and Nagy book.
New datafiles *branchingratio_schunkandnagy2000_param.dat must be loaded
for the "EUVDAT" subdirectory of the standard "datadir" directory.
Main changes are:
- param_v4_h.F90  -> New definition for the O2 ionization branching ratio
- param_read_e107.F -> Read the new files containing the S&N branching ratios
- paramfoto_compact.F -> Mainly cleaning of the code and the comments.
Also correction of a bug affecting the calculation of CO losses
- chemthermos.F90 -> Small modification to add the possibility of including
NO and O2 nightglow rates to the outputs
- calchim.F90 and calchim_asis.F90 -> account for change in arguments in
calls to chemthermos

== 09/03/2018 == MV
"Cosmetics" changes in watercloud_mod and improvedclouds to better understand the roles of variables : 
- in watercloud_mod : change of variables subpdq and subpdt to sum_subpdq and sum_subpdt to make clear we are making the sum of the tendencies in the microphysics loop.
- in improvedclouds : change of the names of input and output variables according to their names in watercloud_mod in order to not confuse them (in improvedclouds "ptimestep" corresponds actually to "microtimestep").
- in watercloud_mod, CLFvarying block : change of the name zteff in pteff to be logical with the other variables names, and writediagfi lines have been moved to the CLFvarying block.

== 09/03/2018 == MV
"cosmetics" changes in co2cloud and improvedCO2clouds to better understand the role of the variables:
- in co2cloud : - change of variables subpdq and subpdt in sum_subpdq and sum_subpdt to make clear we are making the sum of the tendencies in the microphysics loop.
                - change of variables pdqsed in subpdqsed as these are tendencies inside the microphysics loop
                - flag "sedimentation" has been added for the sedimentation block
                - variables names in the sedimentation block have been changed (tempo_traceurs becomes zqsed, sav_trac becomes zqsed0)
                - variable sum_subpdqs_sedco2 was added in the microphysics loop to make clear we make the sum of the surface sedimentation flux, output variable is still pdqs_sedco2
                - variable sum_subpdqs_sedco2 has been initialized to zero
                - zteff has been changed to pteff to be logical with the other variables names
- in improvedCO2clouds : change of the names of input and output variables according to their names in co2cloud in order to not confuse them (in improvedCO2clouds "ptimestep" corresponds actually to "microtimestep").

== 03/04/2018 == EM
Tidying the gravity wave routines by turning them into modules:
orodrag.F -> orodrag_mod.F : note that the declared size of pvar(), which is
used in call to gwstress was wrong.
calldrag_noro.F -> calldrag_noro_mod.F
drag_noro.F -> drag_noro_mod.F
gwstress.F -> gwstress_mod.F

== 04/04/2018 == EM
- Forgotten in previous commit:  gwprofil.F -> gwprofil_mod.F (here also the
size of an argument, rho, was incorrect in caller orodrag).
- Turned newsedim.F into a module newsedim_mod.F
- Adapted co2cloud.F and improvedCO2clouds.F to not use "newunit" to open file
(it is perfectly legitimate F2008 Fortran, but older compiler such as gfortran
on local LMD machines are not there yet).

== 10/04/2018 == EM
Code cleanup: get rid of routine "zerophys".

== 12/04/2018 == EM
Code cleanup:
- remove "comorbit.h" since it is no longer used.
- turn "datafile.h" into module datafile_mod.F90 (and rename variable
  "datafile" as "datadir" since it stores the path to the datafile directory).

== 17/04/2018 == MV
1D code cleanup:
- in testphys1d.F variable totcloudfrac is directly called from dimradmars_mod (which notably prevents from errors when tracer=F)

== 17/04/2018 == MV
1D code cleanup:
- in testphys1d.F variable cell_area is intialized to 1 before being called

== 17/04/2018 == DB
CO2 code update:
- nucleaCO2.F: code cleanup and use co2useh2o flag to handle cases where
               h2o ccns have to be tracked and accounted for.
- co2cloud.F & improvedco2clouds.F: code cleanup and use co2useh2o flag to
               control updates on water variables if necessary.
- physiq.F : cleanup on outputs & compute mtotco2 and icetotco2

== 19/04/2018 == DB
CO2 code updates:
- make co2cloud a module and save mem_* variables (initialized via phys_state_var_init)
- make improvedCO2cloud a module
- read/write mem_* variables in phyetat0.F and phyredem.F

== 05/06/2018 == EM
A first step towards 1+1=2 (for now only works without tracers):
- store and load "albedo" (surface albedo) and wstar (thermals' max vertical
  velocity) in physics (re)start file.
- turn phyetat0 into a module in the process.

== 21/06/2018 == EM
- Make a "doc" subdirectory to store the documentation source files with the code

== 27/06/2018 == EM
- Fix problematic writediagfi call in physiq (should not write a "Time" variable
  as "Time" is already defined as a dimension) and added some extra tests in
  writediagfi to better detect similar issues.

== 05/07/2018 == MV
- callsedim.F changed to module callsedim_mod.F

== 05/07/2018 == MV
- improvedclouds.F changed to module improvedclouds_mod.F

== 11/07/2018 == EM
Some cosmetic changes:
- make watercloud less verbose
- turn vdifc.F into a module
- turn updatereffrad.F into a module

== 17/07/2018 == MV
Cosmetic changes:
- variables suffixes for sub-grid scale cloud scheme changed from --1 to --clf

== 18/07/2018 == EM+MV
Integration of the detached dust layer parametrizations (rocket dust storm, slope wind lifting, CW, and dust injection scheme, DB).
Still experimental, default behaviour (rdstorm=.false., dustinjection=0) identical to previous revision.
NB: Updated newstart requires an updated "surface.nc" containing the "hmons" field.

== 19/07/2018 == MV
Cosmetic/practical changes:
- Addition of the intent in/out characteristics of variables in watercloud_mod and improvedclouds_mod subroutines

== 27/07/2018 == EM
Update xvik.F main program to work with current diagfi outputs.

== 01/08/2018 == MV
Cosmetic/practical changes:
- swmain and lwmain become modules swmain_mod, lwmain_mod
- Addition of the intent in/out characteristics of variables in swmain_mod and lwmain_mod subroutines
Correction:
- in callsedim_mod, declaration of variable tau(ngrid,nlay) corrected to tau(ngrid,naerkind)

== 09/08/2018 == MV
Correction of the dust storm scheme:
- in rocketduststorm_mod.F90 the case of not daytime and no storm was not taken into account (it was actually in comment), which lead to NaNs in the calculation of pdqrds (scheme=0, division by alpha=0.)
Useful:
- in compute_dtau_mod.F90, the writediagfi of tauref_scenario has been added

== 13/09/2018 == DB + EM
- Turn watersat into a module.
CO2 cloud updates:
- compute co2 condensation tendencies in the co2 cloud scheme and pass them
  on to vdifc (for tests; they might not be needed) and adapt newcondens.

== 19/09/2018 == EM
- Bug fix in newstart. lon/lat and cell_area were not correctly sent to
  the restartfi.nc file.

== 18/10/2018 == FL
- Remove old (Euler Backward) photochemistry code

== 18/10/2018 == EM
- cleanup "newcondens" (remove obsolete options), change its name
  to co2condens and turn it into a module.

== 24/10/2018 == EM
- Fix writediagsoil so that it also works in parallel.

== 15/11/2018 == FGG
Modifications to use the parametrized photoabsorbtion coefficients;
a first step towards implementing ionospheric chemistry in the new
chemical solver:
- change in species indexes in chemthermos.F90, paramfoto_compact.F,
  hrtherm.F and euvheat.F90
- calchim.F90: added a variable in call to photochemistry
- photochemistry.F90: added calls to jthermcalc_e107 and phdisrate,
  with an additionlal flag, jparam (.false. by default). The
  computed photodissociation coefficents are sent to v_phot, which
  is used in the chemistry. Thus concentrations computed in
  chimtogcm are now done over all atmospheric layers.

et jthermcalc.F

== 22/01/2019 == MV
- Fix a typo in the Van Leer routine vlz_fi.F in the case of w < 0 (negative vertical velocity).

== 22/01/2019 == MV
- Update of rocketduststorm_mod.F90 : 
We want to separate both parametrizations related to the formation of the detached dust layers. Therefore, rocketduststorm_mod.F90 now only comprises the rocket dust storm scheme, whereas it contained also before the calculation of the vertical velocity induced by the presence of the sub-grid scale topography. This latter part is under development and will be integrated as a fully independant parametrization: the aim is to simulate the entrainment of dust by slope winds, from the boundary layer up to the top of the sub-grid scale topography.
- Addition of initial surface parameters "summit" and "base" to prepare the previously described slope wind parametrization

== 22/01/2019 == MV
- typo in vdifc.F (visible in debug mode) in the case of rdstorm=false, condition for defining pdqsdif(stormdust_mass/number)
- typo in physiq_mod.F (visible in debug mode): wrong indices for tracers in aerosol(:,:,:)

== 23/01/2019 == MV
- follow-up of the last change in physiq_mod.F: put iaer indices (defined in dimradmars_mod.F) for aerosol(:,:,:) in writediagfi calls.

== 23/01/2019 == MV
- follow-up of the last change in datareadnc.F

== 24/01/2019 == MV
- follow-up and correction of the last change in rocketduststorm_mod.F90: coefdetrain has to be a vector

== 05/02/2019 == MV
- follow-up of the last change in rocketduststorm_mod.F90

== 06/02/2019 == MV
- follow-up of the last change in rocketduststorm_mod.F90: corrections in vector definitions

== 14/02/2019 == MV
- handling of a particular case in Van Leer advection in rocketduststorm_mod.F90: when the vertical velocity is very large at a particular layer and null below or above, mass fluxes must not entrain more tracers than available in the layer

== 06/03/2019 == MV
- correction of the Van Leer scheme in vlz_fi.F, used by the sedimentation routine (particular case evoked previously)

== 02/04/2019 == MV
- correction of the Van Leer scheme in vlz_fi.F, used by the sedimentation routine, and rocketduststorm_mod.F90 (particular case evoked previously --> update)

== 24/04/09 == EM+FF
- Updated co2condens to correctly conserve tracer mass

== 10/05/2019 == EM
- updates in code to be able to read in the MY34 dust scenario and the MY34
  solar EUV input
 
== 14/06/2019 == EM
- minor updates: enable output of Ls in diagfi files and make an error
  message more verbose.

== 19/07/2019 == GG+EM
- Add F.Lott's non-orographic GW parametrization. Disabled by default for now,
  activated by setting calllott_nonoro=.true. in callphys.def

== 05/09/2019 == AS
- Changed dlog/dexp in log/exp
- Added a double() instance to improvedCO2clouds so that the model works in simple precision [e.g. mesoscale]

== 10/09/2019 == JYC
- Use Wilke's formulation for molecular diffusion

== 11/09/2019 == FGG
- Updated chemical core to include ionospheric chemistry

== 12/09/2019 == MV
- Update of compute_dtau_mod.F90: dtau is calculated in function of the dust opacity given by the dust scenario the day after

== 23/09/2019 == MV
Set adpatable parameters for the rocket dust storm scheme (parameters included in callkeys.h, and adaptable according to the callphys.def with the function "call getin" in conf_phys.F):
- ti_injection, tf_injection (by default: ti_injection=10. and tf_injection=12., impacted files: compute_dtau_mod.F90, vdifc_mod.F)
- coeff_detrainment (by default: coeff_detrainment=0., impacted files: rocketduststorm_mod.F90)

== 24/09/2019 == EM
- Reactivate output of density scaled opacity

== 24/09/2019 == AB+EM
Some code cleanup (and preparing next steps): 
- Turn calchim into a module and make tendencies module variables
  in calchim_mod and watercloud_mod
- Externalize in "physiq" the computation of solar zenithal angle
  (it should be computed at every physics timestep, regardless of iradia)

== 25/09/2019 == AB+EM
Add the possibility to super-cycle chemistry computations. Chemistry will
be computed every "ichemistry" physics step (but chemistry tendencies are
added every physics step). Default is ichemistry=1.

== 04/10/2019 == AB+EM
Handle case when injecting without dust scenario (iaervar=1) in compute_dtau_mod

== 09/10/2019 == EM
Big cleanup: remove obsolete compilation scripts (makgcm_*) and dynamical core
(since the one in LMDZ.COMMON should be used instead).

== 11/10/2019 == EM
Add new version of z2sig.def to "deftank" (and keep a copy of the old one
as z2sig.def.MCD5)

== 22/10/2019 == MV
Add z2sig.def.hr to "deftank" corresponding to the high vertical resolution with 177 levels from the surface to the exobase.  

== 05/11/2019 == EM
Update non orographic GW routine so that key parameter RUWMAX is read in
from callphys.def


== 07/11/2019 == JN 
File "newstart.F", option "composition". Added the possibility to change atmospheric
composition when non-co2 gases (ar, n2, co, o2) are implicit. When this case is met,
we assume the molar mass of non-co2 atmosphere to be the one measured by MSL at Ls~184.
Atmospheric composition is changed at a selected grid point, and horizontal and vertical
gradients are preserved.

== 14/11/2019 == MV
Add the sublimation/condensation latent heat release from the surface water ice in vdifc_mod.F. It can be activated or deactivated with the new flag "latentheat" (for now latentheat=false by default).

== 24/11/2019 == EM
Fix in surfini for the 1D model when imposing watercaptag.
Protect output of CO2 saturation in physiq to when there is a CO2 tracer.

== 04/12/2019 == AB
Add the instantaneous scavenging by CO2 of dust, ccn and water ice in co2condens_mod. It can be activated or deactivated with the new flag "scavco2cond" (=false by default). Expected to be replaced by the CO2 clouds microphysics in the future.

== 12/12/2019 == EM
Bug fix in the scavenging routine (missing initialisation of tendencies of
surface tracers) in co2condens.

== 13/12/2019 == MV
Implementation of a new parametrization of the dust entrainment by slope winds above the sub-grid scale topography. The parametrization is activated with the flag slpwind=.true. (set to "false" by default) in callphys.def. The new parametrization involves the new tracers topdust_mass and topdust_number.

== 18/12/2019 == MV
Update of the rocketduststorm parametrization: clean-up of the code + back to the sub-timesteps method for the Van Leer transport, homogeneous with the one used in topmons_mod.F.

== 20/12/2019 == AB
Add the observer simulator program simu_MCS_temp.F90 to the LMDZ.MARS/util/ directory, as well as a simu_MCS_temp.def. This program reads a MCS file (binned by Luca Montabone), extracts the daytime and nighttime temperatures from a GCM simulation file, and outputs a netcdf file in the same format as the MCS file.
More details in simu_MCS_temp.def and in the preface of simu_MCS_temp.F90.

== 07/01/2020 == AD
Correction of Mars GCM utility by EM (r2204):
(Bug fix for when input file of the localtime utility is the ouput of zrecast and has aps()/bps() arrays which may not be of the same size as number of vertical layers.)
Variables declaration changed in order to be compiled with ifort
Manual User Update: Old stuff removed from part4: Running the model

== 08/01/2020 == EM
Bug fix in calchim (only had an impact when computations include the
ionosphere), parameters should not be reset at every call.

== 10/01/2020 == EM
Fix a minor bug in the 1D model when initializing the time of day at the
begining of the run.

== 14/01/2020 == EM
Bug fix in newstart "composition" option; added option "q=factor" in
newstart to multiply a tracer mixing ratio by a constant factor.

== 16/01/2020 == EM
Change "latentheat" flag to a more descriptive "latentheat_surfwater" and
set its default value to .true.

== 22/01/2020 == DB (the return!)
Update the nonorographic gravity waves drag parametrization (from the r3599 of Earth s model LMDZ6): 1) add east_ and west_gwdstress variables, 2) delete aleas function: random waves are producted by the MOD function, 3) reproductibility concerning the number of procs is now validated, 4) changing name of some variables like RUW, RVW, ZOP, ZOM,..., 5) tendency of winds due to GW drag are now module variables and written in restart files. 

== 23/01/2020 == EM
First implementation of XIOS in the physics

== 24/01/2020 == BR+JN+AB
Bug fix in physiq_mod for 1D runs, where the routine getslopes reinitialized the slope inclination and orientation to 0, while they were assigned in the input files.

== 24/01/2020 == EM
Further cleanup of nonorographic gravity waves drag parametrization east_gwstress
and west_gwstress need be initialized and are better as module variables.

== 24/01/2020 == EM
Bug fix in rocketduststorm & topmons routines; "tauscaling" sould not be a local
(moreover uninitialized) variable. Added it to the arguments of the routines.

== 27/01/2020 == AB+EM
Bug fixes in localtime.F90 : 1) Following of the correction by EM (r2215), separation of the "valid_range" and "missing_value" indicators, which prevented localtime to write the missing_value attribute in the output file and was making r2215 useless ; 2) Altitude attributes written in the output file are no more specified by default but are read in input file (important for zrecasted files).

== 28/01/2020 == JN
Adding a new flag 'paleomars' (default false) in 1d GCM in order to use
eccentricity and solar longitude of perihelion as input parameters.
Added variables : halfaxe, excentric, Lsperi. New routine call_dayperi.F from FF to
compute perhelion date from prescribed eccentricity & Lsperi.

== 04/02/2020 == AB
Small improvements in simu_MCS_temp.F90 : 1) The binning method is now more consistent with the MCS file ; 2) stats files are more rigorously recognized.

== 10/02/2020 == CM
Initialization of mu0_int and ztim1 in 'nirco2abs.F' to prevent crash during debug mode simulations.

== 27/02/2020 == AB
Resolved ticket #32 : 1) dsodust is now calculated only once in the InfraRed by aeropacity_mod (used to be wrongly calculated twice, such as dsodust=IR_part+Visible_part) ; 2) dsords is now calculated in the IR by aeropacity_mod (used to be calculated in the Visible) ; 3) dsotop is added and calculated in the IR in aeropacity_mod
+ some cleaning and commenting of the code

== 04/03/2020 == AB
Resolved ticket #14 : when calling writediagfi for all kinds of dust Density-Scaled Opacity (dsodust,dsords,dsotop,dso), an information about the IR wavelength used by the GCM is added in the "title" attribute of the netcdf variable ("tes" = 9.3micron ; "mcs" = 21.6micron).
NB : these dust DSO calculated by the GCM are extinction opacities, hence not always corresponding to the actual opacity/optical depth measured by the instruments (ex: TES = 9.3micron absorption optical depth).

== 04/03/2020 == AB
Bug fixes in the slope winds parametrization and its interactions with rocketduststorm : now, it is considered that the sub-grid dust storm is decorrelated from the dust entrainment above the sub-grid scale topography, so that : 1) the background dust available for slope winds is updated after the rocketduststorm parametrization ; 2) the extra-heating on top of the mountains is calculated regarding topdust and background dust tracers' optical depths only (and not stormdust optical depth).

== 06/03/2020 == AB
Bug fix following r2248 in aeropacity_mod and topmons_mod : since dsodust, dsords and dsotop are diagnostic physiq_mod variables, we don't want them to be reinitialized at each call of aeropacity_mod and topmons_mod, but we initialize them once and for all at the beginning of physiq_mod instead.

== 10/03/2020 == AB
Bug fix in topmons_mod : the array rhobarz(ig,l) (density at interlayer levels) had only nlayer allocated instead of nlayer+1 (caused issues in calculating the topdust detrainment at the top of the model)

== 12/03/2020 == EM
Transparent adaptations to be able to compile using the PGI compiler:
- look for NaN using logical test a/=a instead of isnan() which is not standard
- use erf() function as it handles single/double precision (derf is obsolete)

== 12/03/2020 == FL+EM
Update newstart option "composition" with Trainer et al 2019. (and ACS)
values.
 
== 13/03/2020 == JN
Adding a new 2D variable "watercap", perennial ground water ice.
qsurf(ig,igcm_h2o_ice) can no longer be negative. 
When watercaptag=true, ie when there is an infinite amount of water avalaible for sublimation,
and there is no more h2o frost, sublimation digs into watercap reservoir.
For now watercap can't grow, even on watercaptag, and has same albedo than qsurf(h2o_ice).
When using old start file, watercap is automatically initiated as 0. 
Added watercap in newstart.F aswell.

== 19/03/2020 == JN
Adding watercap in start2archive. When absent in the start files, it is initialized at 0,
and qsurf(igcm_h2o_ice) can no longer be negative. The negative fraction of qsurf(h2o_ice),
if it exists, is set in watercap.

== 20/03/2020 == EM
Cleanup of phyetatO and only apply conversion of negative water ice surface
to the watercap variable if there was is initial "watercap" field in the
start file.

== 20/03/2020 == EM
Save "dtau", the opacity difference between model and target dust scenario
in the restartfi.nc file so that we have 1+1=2 when running with dust
injection schemes.

== 28/03/2020 == AD
Minor update to be able to compile Mars physics with Dynamico
Abort_physics (abort routine in LMDZ.MARS) instead of abort_gcm (in LMDZ.COMMON) in jthermcalc.F

== 02/04/2020 == FGG
A first step towards water ion chemistry. Add a new reaction and modify reaction
rates for HCO2+

== 02/04/2020 == EM
Some code cleanup:
- move profile.F to dyn1d since it is only used by the 1D model
- remove scatter.F, which is not used (and moreover a synonym of the scatter
  routine from the "mod_phys_lmdz_para" module)
- remove obsolete "multipl.F" routine, replace the calls to it in vdifc_mod
  by modern Fortran syntax.

== 07/04/2020 == AB
Add the program terminator.F90 to the LMDZ.MARS/util/ directory, as well as a terminator.def
This program can be used to interpolate GCM files at one terminator (morning or evening) all around the globe.
+ a fix of localtime.F90 which didn't work for stats files.

== 08/04/2020 == AD
Martian physics is now able to start without startfi.nc
Major update for phyetat0_mod and physiq_mod based on what have been done for the Generic physics

== 09/04/2020 == AB
Resolved Ticket #41 : the density-scaled opacities are now multiplied by tauscaling before being
written in the output files (have an effect only when working with freedust=false)

== 13/04/2020 == FGG
- Adding HCO+ ion chemistry.

== 14/04/2020 == AD
Minor update of revision 2281 in order to run martian physics with callsoil option when no startfi.nc

== 16/04/2020 == EM
Update reference run.def.64x48x49.MCD5 to keep up with recent (r2181) changes
dissip_fac_mid and dissip_fac_up are now read in from the run.def file.

== 16/04/2020 == AB
Add the program solzenangle.F90 to the LMDZ.MARS/util/ directory, as well as a solzenangle.def
This program actually replaces the former program terminator.F90, and can be used to interpolate GCM
files at one given solar zenith angle (on the morning-side or the evening-side) all around the globe
(the terminator corresponding to sza = 90deg)

== 20/04/2020 == EM
Fix for the 1D, follow up from the recent addition of watercap.

== 22/04/2020 == AD
Minor update of revision 2281 about initialisation of emissivity and albedo when no startfi
Now default emissivity/albedo is 0.95/0.1
Flags to change these fields are now more explicit: surfemis_without_startfi instead of surfemis (idem for surfalbedo)

== 24/04/2020 == MV
dyn3dpar: Implementation in the parallel version of the dynamics of the dynamical transport of the isotopes using the same scheme as the one implemented by Camille Risi in the Earth GCM (see LMDZ6/libf/dyn3dmem, and Risi et al. 2009: genealogy of the tracers+transport of the isotopic ratio). This is added to prepare the future implementation of the HDO cycle in the GCM. These changes had been already added in the sequential part.
dyn3d: corrections to prevent from dividing by zero in the case of the use of the isotopes scheme.
traceur.def.isotopes: example of how to write the traceur.def if you want to use the new dynamics with the genealogy of the isotopes: air is the father of all, H2O is the father of HDO.

== 27/04/2020 == MV
follow-up of the last commit: add the routine check_isotopes_p.F in dyn3dpar. Note: this routine is used in the Earth GCM to check the aberrant values but for now it is inactive in our version, as long as variable "ok_isotopes" in /dyn3d_common/infotrac.F90 remains "false". This routine was already present in the sequential version of the dynamics dyn3d.

== 28/04/2020 == FGG
Add H2O+ ion chemistry

== 28/04/2020 == AB
Resolved Ticket #46 : it is now possible to concatenate concat files with a coherent
time axis. NB : the program puts now a higher importance in respecting the controle
variable of all the input files (when there is one).
Example : concat[diagfi2 (66sols from sol 61); diagfi4 (65sols from sol 193)]
Old output Time: [61.08,..127,|127.08,..192]; New output Time: [61.08,..127,|193.08,..258]

== 28/04/2020 == EM
Some code tidying: use getin_p() instead of getin() and use "call abort_physic"
instead of "stop" or "call abort"

== 30/04/2020 == MV
follow-up of the commit regarding the dynamical transport of isotopes: new variables for the thresholds for zq(pere) and masseq in the transport of the isotopic Ratio

== 04/05/2020 == AB
Following r2303 (concatenate concat files) and truly resolving Ticket #46 :
1) little bugs fixed from the previous revision ; 2) add the possibility to change the
offset of the output file time axis by asking the user the new offset and the level of
priority to put on it over the starting day stored in the first input file
(NB: this last point also implies a change in concatnc.def, but retrocompatibility
with old concatnc.def files has been ensured)

== 06/05/2020 == EM
More code tidying: use getin_p() instead of getin() and use "call abort_physic"
instead of "stop" or "call abort"

== 06/05/2020 == LR
Implementation of HDO in the physics
New tracers hdo_vap and hdo_ice are added. Cf. traceur.def.isotopes in deftank for exemple of traceur.def.
All HDO related computations are activated by flag hdo=.true. in callphys.def. (see callphys.def.hdo in deftank for an example)
Additional option hdofrac (true by default) allows for turning on/off fractionation (for tests).
For now, only functional with simplified cloud scheme (so microphys=.false. and activice=.false. also recommended).
Initialisation of start files can be done with option 'inihdo' in newstart.

== 07/05/2020 == AB
Following r2303 and r2308 and truly truly resolving Ticket #46 on concatnc:
Improved ergonomics of the user interface, with no more request to the user
in the midst of computations

== 12/05/2020 == LR
Fixing some errors in vdifc_mod related to variable watercap. This variable was also integrated to the hdo cycle. 
Also added watercap output for the 1D model.

== 12/05/2020 == AB
Creation of the utilitary program aeroptical.F90, whose goal is to compute the opacities [1/km]
of dust and water ice aerosols, from their mass mixing ratios and their effective radius
stored in a GCM file, all at a wavelength given by the user. To that end, it reads optical
properties stored in files of the datadir/ directory.
+ associated aeroptical.def

== 13/05/2020 == FGG
- Finalized water ion chemisty (added H3O+ and OH+ ions). Added an example
  of relevent traceur.def file in deftank.
- Added the computation of NO nightglow.

== 13/05/2020 == MV
Extent of the transport of the isotopic ratio implemented in the dynamics to all the Van Leer transport schemes used in the physics (for now it only concerns the tracer HDO).
- libf/dynphy_lonlat/phymars/:
 iniphysiq_mod.F90: transmission of the content of variables describing the isotopes defined in the dynamics (precisely by dyn3d_common/infotrac.F90, which reads traceur.def) to the physics
- libf/phymars/:
  phys_state_var_init_mod.F90, tracer_mod.F : initialisation of the variables describing the isotopes in the physics
  callsedim_mod.F: implementation of the transport of the isotopic ratio in the Van Leer scheme used for sedimentation (applies to hdo ice)
  co2condens_mod.F: implementation of the transport of the isotopic ratio in the Van Leer scheme used for condensation of CO2 (applies to hdo ice and vapour)

== 14/05/2020 == MV
Follow-up of the last commit for the transport of the isotopic ratio: forgot the initialisation of zq0() in callsedim_mod.F !

== 15/05/2020 == MV
Follow-up of the last commit for the transport of the isotopic ratio: cleaning to help the user: 
-initracer.F: hdo must be defined as an isotope (meaning its "father" has to be precised in traceur.def) and must be placed at the end of the list of tracers in traceur.def.
-/deftank/traceur.def.isotopes: writing of traceur.def in the case of hdo=true has been simplified to match both the 3D and the 1D simulations.
-simpleclouds.F,hdo_surfex_mod.F,physiq_mod.F: thresholds of 1.e-16 have been replaced by the variable qperemin defined in tracer_mod.F.

== 18/05/2020 == TP
- Update of the program xvik.F 
- Useless code removed
- Add some comments about xvik outputs
- Declaration of physics constants inside the program as variable and not as inputs like before
- Temporal shift due to viking landing sol removed : xvik outputs are given in real sol
- Add the possibility to choose the format of time dimension for xvik outputs : ls, sol or both
- Path to input and output files removed from the code and put as input
- List of input files removed from code and put as input

== 18/05/2020 == AB
Some improvements in aeroptical.F90 :
1) add the possibility to input a diagfi_P.nc file (with pressure as altitude coordinates) ;
2) replace all "title" attributes into "long_name" attributes in accordance with ticket #48

== 26/05/2020 == MV
Follow-up of the last commit for the transport of the isotopic ratio: simplification of the transmission of variables from the dynamics to the physics:
- libf/dynphy_lonlat/phymars/:
 iniphysiq_mod.F90: transmission of the content of 2 variables describing the isotopes instead of 4 (nqperes: number of tracers "peres", nqfils: number of tracers "fils")
- libf/phymars/:
  phys_state_var_init_mod.F90, tracer_mod.F: idem
  callsedim_mod.F: idem
  co2condens_mod.F: idem
- libf/phymars/dyn1d:
  testphys1d.F: idem (the reading interface for traceur.def has been completed to fill the variables nqperes and nqfils).

== 29/05/2020 == AD
More outputs with xios from physics
physics is now able to transmit soil fields to xios
2334:Update of xios ouput file definition

== 08/06/2020 == TP
Add folder "xvik" in util that contains a program called "fit_Iceinertia_MONSicedepth.F" that is used to compute best-fit cap albedo, ICE DEPTH  and total CO2 inventory. The diretory also contains : 
- a file "VL1" of harmonics of VL1 surface pressure
- a file "compile_fit" to compile the main program
- a README explaining how to use the program
- a .def file to use as input for the main program

== 09/06/2020 == CM
Improvement in the reading of input profiles for 1D simulation.
 - add: dyn1d/read_profile_mod.F90

== 10/06/2020 == CM
CO2 microphysics is now available.
/!\ Add a new file: co2condens_mod4micro.F90 => It is a copy of co2condens_mod.F, but adapted to the case of co2
                                                microphysics. This could be temporary, but don't forget to modify
                                                these two subroutines if there is a change in one of them.

== 11/06/2020 == AD
New tool to convert a startarchive from LMDZ (lonlat) into start.nc and startfi.nc adapted to DYNAMICO
Still under development: be careful when using it

== 12/06/2020 == EM
Minor fix to r2362 (addition of CO2 microphysics): make CO2 conservation
tests only if CO2 microphysics is on.

== 18/06/2020 == LR
HDO
Correction of an error in newstart for inihdo.
Other minor corrections for HDO cycle.
Transition from fractionation coefficients from Merlivat et al. 1967 to Lamb et al. 2017

== 02/07/2020 == CM
CO2 microphysics: correction on improvedco2cloud.F90
                  sublimation of co2_ice if ccnco2 number < 1

== 03/07/2020 == EM
nirco2abs: handle the (rare) case when input O mixing ratio is negative to avoid
generating NaN heating rates.

== 06/07/2020 == EM
Some code cleanup: use "call abort_physic()" instead of "stop" or "call abort"

== 07/07/2020 == DB
Add kstar parameter to control kmin value. kmi=1/lambda_max, to ensure the "subgrid scale" characteristic, we have to constrain the GW's wavelength by the size of the mesh

== 07/07/2020 == EM
Improve "zrecast" utility: add possibility to transfer 3D (lon-lat-time)
variables to output file and add some extra sanity checks of user inputs.

== 10/07/2020 == AB
Add the new version of the MCS observer simulator program simu_MCS.F90, replacing the old version simu_MCS_temp.F90.
The program can now handle (ie, interpolate and bin like the MCS file) any 4D GCM variable, by linking them to
a MCS variable among temp (default), dust and water ice, serving as reference for the binning.
More details in the preface of simu_MCS.F90 and in simu_MCS.def

== 01/09/2020 == MV
Implementation of HDO in the microphysics of water ice clouds:
- improvedclouds_mod.F: calculation of the HDO flux
- growthrate.F, microphys.h: addings to take into account the effect of diffusion kinetics on fractionation
- callsedim_mod.F: sedimentation of HDO as an isotope of water in the microphysics case

== 17/09/2020 == EM
Code tidying : make a "dust_param_mod" module to store dust cycle relevant flags
and variables (and remove them from callkeys.h)

== 25/09/2020 == AB
In conf_phys.F :
Put the default value of rocketduststorm detrainment coefficient at 0.05 instead of 0. previously,
in order to have an column-integrated dust optical depth that better follows the scenario and doesn't
madly skyrocket in the dusty season.
+ correction of a comment for abort_physic

== 30/09/2020 == EM
Cleanup around "aeropacity" to prepare future evolutions; added module
dust_scaling_mod to handle computation of tauscaling.

== 06/10/2020 == AB
Correction of a bad unit for qdusttotal0 and qdusttotal1 (diagnostic outputs of the stormdust scheme)
+ some corrections of comments about aerosol and tauref in aeropacity

== 13/10/2020 == EM
Code cleanup: remove "tauref" and replace it with two distinct variables,
"tau_pref_gcm" and "tau_pref_scenario" which are repectively the visible
dust opacity column (at 610 Pa) in the GCM and prescribed by a dust scenario.

== 15/10/2020 == AB
Correction in solzenangle.F90 : the missing value was not initialized when the attribute was not
present in the input file.
+ Resolved Ticket #61 : add comments in the code and in the output file to make the program more
transparent for the users

== 16/10/2020 == EM
Add a new scheme to handle the dust and its radiative impact. Triggered using
a new flag dustscaling_mode=2 (dustscaling_mod=0: no rescaling at all, and
dustscaling_mode=1: full rescaling using tauscaling, GCMv5.3 style). Rescaling
is then only done on the radiative impact (see dust_scaling_mod.F90) of dust.
Moreover the scaling factor "dust_rad_adjust" is evaluated using the target dust
scenario opacity for the next sol and left to evolve linearly until then to not
impose the diurnal evolution of dust.
In practice, main changes or additions in the code are:
- renamed flag "tauscaling_mode" as "dustscaling_mode"
- moved parameter "t_scenario_sol" to "dust_param_mod"
- adapted "compute_dustscaling" routine in "dust_scaling_mod"
- added module "dust_rad_adjust_mod"
- 2D fields "dust_rad_adjust_prev" and "dust_rad_adjust_next" required to
  compute coefficient "dust_rad_adjust" need to be stored in (re)startfi files

==02/11/2020 == EM
Adaptation for when using dust injection and/or dustscaling_mode==2. The
dust scenarios are then meant to just hold one value per sol deemed to
be valid for a given local time (t_scenario_sol in dust_param_mod). Thus
to avoid unwanted temporal interpolation in read_dust_scenario, the time
axis there should simply contain integers.

== 05/11/2020 == FGG
Bug fix in jthermcalc_e107.F: correctly account for the actual Sun-Mars
distance.

== 14/11/2020 == FF + EM
- Make a single README file (get rid of REAME.exec) and update "compile"
  script to (hopefully) better illustrate how to compile utilities
- Update utilities zrecast and lslin:
  zrecast.F90: Force the vertical interpolation of any variable starting
  by "rho" to be in log space (as it should for density, molecular
  concentration in mol.cm-3 etc..). Set missing value to 1.E20
  lslin.F90: fix various problems in the output.
 
== 17/11/2020 == FF + AB
Update utilities :
concat.F90
- rewrite and simplify the handling of time and offset so that any file
  can be concatenated, including files from different years or stats file
- use modulo to shift starting sols in concat.nc to values between 0 and 669
- add a "adls" option in addition to "sol" or "ls" to add a Ls 1D variable
   while keeping "sol" as the Time axis
- add conservation of altitude attributes (long_name,units,positive)
- enable absence of both hybrid (aps,bps) and sigma levels

solzenangle.F90
- improve calculation for 1 sol file (stats) to use all local time data
- read the starting sol in the file instead of asking it to the user
  (except for stats file) ; keep the possibility for user to change it
- ask mean Ls value for stats file instead of sol number
- fix crash when using "all variable" option (ticket #66)
- fix bug on aps,bps by using GCM_layers dimension instead of altitude

localtime.F90
- fix crash when using "all variable" option (ticket #66)
- fix bug on aps,bps by using GCM_layers dimension instead of altitude

For all 3 utilities :
- handle all ndim cases for the variables (ticket #52)
- change "title" attribute into "long_name" by default (ticket #48)
- extend size of long_name character string (ticket #57)
- remove the use of #ifdef NC_DOUBLE (ticket #67)
 
== 23/11/2020 == AB
Add stormdust in the aerosol opacities computed by aeroptical.F90
+ add a description of aeroptical in util/README

== 01/12/2020 == MV
- improvedclouds_mod.F: update of the nucleation equation with its analytical resolution
- writediagmicrofi.F: makes it possible to get outputs from the microphysics (call example in watercloud_mod.F)

== 16/12/2020 == AB
Fix a typo made in r2434 in localtime.F90, that replaced the long_name attribute
of variables by "Time"

== 12/01/2021 == AB
Harmonization of the utility programs lslin, concatnc and localtime when dealing
with Solar longitude as the Time variable (for localtime, the check on long_name
attribute is still compliant with files from previous versions)

== 15/01/2021 == AB
Changes in aeroptical.F90 :
- add the flag nf90_64bit_offset when creating the output file. Without it, the 
  program couldn't deal with large files (concat) with multiple aerosols
- modify the code structure to make it a bit less memory-intensive
- add topdust in computed aerosol opacities
- add the possibility to compute absorption opacities, instead of extinction :
  the user must specify 'ext' or 'abs' in aeroptical.def
- update the description of aeroptical in util/README

+ adapt simu_MCS to take into account aeroptical output variables when choosing
  the binning reference
+ add outputs for topdust in physiq_mod

== 25/01/2021 == EM
- Minor cleanup and update in aeropacity_mod.F and read_dust_scenario.F90 to be
  able to use MY35 dust scenario

== 25/01/2021 == AB
Changes in lslin.F90 :
 - make sure the interpolation takes into account potential missing values in
   the input file fields, especially when the average/binning option is not used
   (ticket #68)
 - enable the averaging option even when the Ls timestep is set automatically
 /!\ previous lslin.def must be updated in consequence !
 - code clean-up, especially remove duplicates on controle field and altitude units
 - replace all the tests "if (ndim.ge.3) then" by a unique test at the beginning
   of the var loop
 - change "title" attribute into "long_name" by default (ticket #48)

+ add an indicative updated lslin.def
+ update util/README

== 16/02/2021 == FGG+JYC
- Adding the deuterium chemistry now that the HDO cycle is included.
- Chemistry still works as before if deuterium tracers are not present.
- Added handling of hdo in molecular diffusion (moldiff_red).

== 24/02/2021 == MV
Correction in lect_start_archive.F:
- adds the variable "watercap" to insure its transmission in the case newstart.F  
  uses start_archive.nc to create the start files.

== 03/03/2021 == FGG
- bug fix in the diagnostic of H, H2, and D total escape which was wrong
  when running in parallel. The escape rates can now also be included as
  outputs in diagfi.

== 18/03/2021 == EM
- change outputs names for species number densities (in molecules/cm3)
  from "rho_*" to "num_*" and add possibility to output only first layer
  atmospheric temperatures as "temp_layer1".

== 07/04/2021 == CM
- add co2_ice as scatterer in radiative transfert. Need co2clouds and
   activeco2ice .eqv. True. Files involved:
      - aeropacity_mod.F
      - callradite_mod.F
      - physiq_mod.F
      - updatereffrad_mod.F
      - suaer.F90
- determine co2_ice density from temperature. Used in riceco2 computation.
   Files involved:
      - co2cloud.F90
      - improvedco2clouds_mod.F90
      - updaterad.F90
      - updatereffrad_mod.F
- co2condens_mod4micro.F: variable initialization
- initracer.F: add nuiceco2_ref = 0.2
- phyredem.F: remove co2_ice from qsurf since co2_ice => co2ice
- watercloud_mod.F: tiny typo

== 21/04/2021 == AD
- update of ztime_fin (variable "Time" stored in startfi.nc) for Dynamico
  where the addition of a dynamical timestep is no longer needed
  
== 22/04/2021 == JN
- Adding a new option for icelocationmode in surfini.F, which uses the 
  predefined 64x48 water caps for any resolution. Now default option 
  should be icelocationmode=4.

== 25/04/2021 == EM
Code cleanup, remove unused routines in libf/dynphy_lonlat (those from
LMDZ.COMMON are used) and likewise make links to dynamics routines in "dyn1d"
point to LMDZ.COMMON routines

== 27/04/2021 == RV
- update of day_ini, time and hour_ini in restart and retstartfi. 
Hour_ini is obsolete. If we write one restart file: day_ini is the last day
of the simulation and the remaining time is in Time (often=0), if we write 
multiple restart nothing changes 

== 22/04/2021 == JN
 - The variable albedo_h2o_ice is now decomposed into albedo_h2o_cap 
and albedo_h2o_frost, in order to discriminate between perennial ice
and seasonnal frost. Retrocompatible with old callphys.def and 
albedo_h2o_ice. Current default values are 0.35 for both albedos.

== 30/04/2021 == AB
Some corrections of run scripts in deftank/ciclad/ :
the next run_monthX is now well written, with a formulation that is more coherent with deftank/occigen/run_month1 version
+ the PBS memory specifications for the CICLAD job are set to more relevant values

== 30/04/2021 == AS
update of changes by RV on 27/04/2021; streamlining day_end to avoid using a dynamical module in the physics.


== 1/05/2021 == JN
Added a "cap_albedo" flag (default false) in order to allow northern polar cap albedo to remain unchanged by water frost deposition.

== 3/05/2021 == LR
Bugfix for streamfunction tool. Now asks the user for another file in which to
find cv.

== 04/05/2021 == RV
- update of r2507: correct ztime_fin for dynamico
- Test for no writting Diagfi for Dynamico
- Correction for Xios output : Change of calendar : start_date=0 as a diagfi, timestep for output physic=1s, day_length=ndtphys, it is needed to have output in days in the xml to have the correct time

== 6/05/2021 == JN
vdifc_mod update !!
 - vdifc now treats separately h2o_vap and other tracers
 - water sublimation is now treated with an implicit scheme & adaptative subtimestep
 - latent heat of sublimation is working with the implicit scheme
 - the adaptative subtimestep is empirically calculated with a temperature variation criterion "dtmax"
 - hdo_vap is now treated independantly after h2o_vap (should be fine !)

== 06/05/2021 == MV
Correction of the threshold value used to prevent from negative values in watercloud_mod.F: the threshold is set to 1e-16 (=qperemin, an already existing parameter for the water cycle), instead of 1e-8. This former value was at the origin of a strong and unrealistic drying out of the upper atmosphere, when the photochemistry was active, during the first part of the martian year (months 3 and 4). (bug reported by Francisco Gonzalez-Galindo).

== 15/05/2021 == JN
Added a logical flag allowing for a temperature-dependant parametrization of the water contact parameter : "temp_dependant_m". Default value is false for now.

== 17/05/2021 == CM
minor fix in co2condens4micro; fix co2 sedimentation rate outputs

== 26/05/2021 == AB
Make a cleaner initialization of some variables in simu_MCS.F90

== 26/05/2021 == JN
Bug correction in testphys1d.F, when calling "phys_start_var_init"

== 27/05/2021 == FF+CM
Update zrecast utility:
 - conversion to pressure coordinate possible even if temperature is not available
 - phisinit added to the output file
 - vertical interpolation in log coordinates for variable with name starting with "num_"
 - mode 3 (above local surface): set to missing value when z > z_range

== 08/06/2021 == MV
re-commit of version 2526: testphys1d.F: Fix for the 1D, follow up from previous modifications of phys_state_var_init subroutine.

== 09/06/2021 == EM
Bug (wrong usage of surface pressure) fix in vdifc (bug was introduced in r2515)

== 22/06/2021 == CM
co2clouds: fix mtotco2, icetotco2, vaptotco2 outputs

== 29/06/2021 == AB
Make simu_MCS.F90 compatible with DYNAMICO lon-lat output files, with a check on the latitude array order when doing the interpolation

== 01/07/2021 == EM
Add possibility of additional tests (NaNs, but also of unrealistic values) of
fields at the begining of physics (i.e. coming from the dynamics) and at the
end of the physics integration. These are respectively triggered by seting
flags "check_physics_inputs" and "check_physics_outputs" to .true.

== 08/07/2021 == RV
- update of r2507: correction for time output in the case of multiple restart files

== 08/07/2021 == RV
tab_cntrl is written by Xios output. It is now a module variable of phyetat0_mod

== 08/07/2021 == RV
Utilitaire concatnc, localtime, zrecast can process Xios output

== 08/07/2021 == RV
Change in the context_lmdz_physics.xml and field_def_physics_mars.xml to be consistent with the changes of physiq_mod (new variables : cntrl_tab, ap, bp, aps, bps, phisinit...)

== 13/07/2021 == RV
Update of the revision 2545, physiq_mod is corrected to contain the modifications that were previously deleted by error

== 18/08/2021 == FGG
Make NO and O2 Nightglow emissions computations more flexible (reaction index
 no longer hard coded in photochemistry.F90).
 
== 07/09/2021 == AB
simu_MCS.F90 : now computes the column-integrated dust optical depths of the MCS and GCM files
(between levels with no missing values in both files, which vary with space and time) and outputs
the ratio tau_GCM/tau_MCS to be used to normalize the GCM dust opacity profiles when comparing to MCS

== 07/09/2021 == EM
Some code cleanup and refactoring around wstats:
- turn wstats.F90 into a module
- remove no useless statto_mod.F90
- incorporate auxilliary inistats and mkstats routines in wstats_mod.F90
- move flag "callstats" from callkeys.h to being a module variable of wstats_mod

== 13/09/2021 == JN
Water-cycle cleanup, clarifications and additions.
- flag "cap_albedo" renamed "cst_cap_albedo" for clarity. When set to true, watercaptag grid cells albedo
remains constant even when frost condensates on it. Only useful when albedo of frost and cap are different
(default is false)
- addition of two flags "refill_watercap" and "frost_metam_threshold". Refill_watercap is used to convert
h2o_ice_s into watercap if the amount of h2o_ice_s is above the frost_metam_threshold (on watercaptag only).
One could see it as water frost converted into perennial ice. 

== 20/09/2021 == CM
CO2 clouds microphysics improvements:
 - add sedimentation at the surface of CNs tracers
 - add tracers ccnco2_h2o_mass_ice, ccnco2_h2o_mass_ccn, ccnco2_h2o_number in place of mem_Nccn_co2, mem_Qccn_co2
 - modification of updaterice_microco2 to take into account water ice as CN and not only dust as CN
 
== 20/09/2021 == EM
Improve wstats: the callstats flag is now embedded within wstats and checked
internaly so no need to have some "if (callstats)" conditions around calls
to wstats anymore.
In addition: wstats now looks for an (optional) stats.def file in the
directory where the GCM is run to know which variable should be included
in the stats.nc file. The stats.def ASCII file should simply contain 
one variable name per line, in the same way as the diagfi.def file for
diagfi outputs. If there is no stats.def file then all variables sent to
wstats will be in the stats.nc file (which matches the behaviour prior to
this improvement).

== 24/09/2021 == CM
merge co2condens_mod4micro.F with co2condens_mod.F
variable used:
if (co2clouds)
  condens_layer, condens_column
else
  zcondicea, zfallice

== 22/10/2021 == EM
Improve tests by "check_physics_fields": also look for
negative values of tracers.


== 22/10/2021 == SF+AB
Clarify the description of extract

== 25/10/2021 == MW+EM
Fixes for the picky gfortran10 compiler which identifies using a scalar
instead of a one-element array as an error.

== 26/10/2021 == CM
Delete nucleaco2.F (old file), the good one is nucleaco2.F90 (better modular)

== 27/10/2021 == JL+EM
Fixes in the utilities for the picky gfortran 10+ compiler

== 29/10/2021 == RV
First stage of implementing Open_MP in the physic. 
So far it can initialyse physic and run with all routines at .FALSE.

== 29/10/2021 == LR
Fixing missing case for hdo_ice in inichim_newstart
Should fix issue #25 on gitlab

== 16/11/2021 == RV
Second stage of implementation of Open_MP in the physic. 
Run with callrad=.true.

== 18/11/2021 == RV
Third stage of implementation of Open_MP in the physic. 
Run with callnlte=callnirco2=calldifv=calladj=calltherm=callrichsl=callcond=callsoil=calllott=TESicealbedo=.true.

== 19/11/2021 == JN
Bug correction in vdifc caused by the computation of watercap tendency within the subtimestep of water ice sublimation.
This is now computed after the subtimestep (actually much simpler).
Local variables "zwatercap" and "zdwatercap_dif" used to monitor the evolution of watercap during the subtimestep
are now obsoletes and thus deleted.
Third stage of implementation of Open_MP in the physic. 
Run with callnlte=callnirco2=calldifv=calladj=calltherm=callrichsl=callcond=callsoil=calllott=TESicealbedo=.true.

== 30/11/2021 == CM
MPCO2: add meteoritic particles as condensation nuclei.
   => new flag: meteo_flux
   => new input file in datadir: Meteo_flux_Plane_v2.dat

== 03/12/2021 == LR
Utils: fixed a bug in concatnc. The program now properly carries over missing
values from the input files into the output file.

== 06/12/2021 == CM
MPCO2: remove old file Meteo_flux_Plane.dat, change file name Meteo_flux_Plane_v2.dat to Meteo_flux_Plane.dat

== 10/12/2021 == MV
hdo_surfex_mod.F, vdifc_mod.F: addings to account for the effect of kinetics in the fractionation by condensation of HDO at the surface

== 15/12/2021 == JL
Fixes and improvements in the Non-orographic GW scheme, namely:
- increments are not tendencies
- missing rho factor in EP flux computation
- missing rho at launch altitude
- changed inputs, because R and Cp are needed to compute rho and BV

== 17/12/2021 == JYC+EM
Move "zls" (solar longitude) from being a local variable of physiq
to module comsaison_h. This is for convenience (saving zls and making
it available to the "plasma dynamical core").
Also cleaned up and commented comsaison_h in the process.

== 04/01/2022 == CM
- Clean co2condens_mod.F
- remove dqsurf duplication after call co2condens

== 04/01/2022 == AB
Some further cleaning of co2condens following r2599 and r2600 that fixed the bug appearing when the scavenging by CO2 ice was activated.

== 04/01/2022 == CM
following r2600, remove use co2condens_mod4micro in physiq_mod.F

== 18/01/2022 == RV
Open_MP files reading for callnlte = .true.

== 18/01/2022 == RV
Open_MP files reading for NIR : callnirco2.and.nircorr.eq.1

== 18/01/2022 == RV
Open_MP files reading for Dustdevil : callddevil = .true.

== 18/01/2022 == RV
Open_MP files reading for albedocaps : TESicealbedo = .true.
New subroutine specific for the reading

== 18/01/2022 == RV
Open_MP files reading for thermosphere : callthermos = .true.

== 18/01/2022 == RV
Open_MP files reading for moldiff : callmoldiff = .true.

== 18/01/2022 == RV
Open_MP : Put all the "COMMON" of *.h file as "$OMP THREADPRIVATE"

== 18/01/2022 == RV
Open_MP files reading for PHOTOCHEMISTRY : photochem = .true.

== 18/01/2022 == RV
Open_MP Correction for previous commit: commision of photolysis_mod

== 18/01/2022 == RV
Put all the "save" variables as "!$OMP THREADPRIVATE" in phymars.
The code can now be tested (comparison between restart(fi), diagfi files)
Compile with the option : -parallel mpi_omp, add these lines in the bash: 
export OMP_NUM_THREADS= N
export OMP_STACKSIZE=200M
with "N" of the order of #levels/10

== 18/01/2022 == RV
Open_MP : In co2condens_mod : Remove emisref from THREADPRIVATE as it is not a saved variable

== 28/02/2022 == RV
Open_MP :Small OpenMP fixes in conf_phys for reading radia.def with ifort

== 28/02/2022 == AB
Big changes on mountain top dust flows for GCM6:
- the scheme now activates only in grid meshes that contain a mountain among
  a hard-written list, instead of every meshes. This is done to prevent strong
  artificial reinjections of dust in places that don't present huge converging
  slopes that concentrate dust (ex: Valles Marineris, Hellas).
  Topdust is now also detrained as soon as it leaves the column it originated from.
- the list of the 19 allowed mountains is used by the subroutine topmons_setup
  in module topmons_mod, to compute a logical array contains_mons(ngrid).
  alpha_hmons and hsummit are also set up once and for all by this subroutine,
  which is called in physiq_mod's firstcall.
- contains_mons, alpha_hmons and hsummit are now saved variables of the module
  surfdat_h, and are called as such and not as arguments in the subroutines
  using them.
- the logical flag "slpwind" and the comments in the code have also been updated
  to the new terminology "mountain top dust flows", accordingly to ticket #71.
  The new flag read in callphys.def is "topflows".

== 01/03/2022 == AB+LL
Fix ticket #93. start2archive now correctly stores the variable albedo from
startfi.nc in the output file start_archive.nc, and newstart reads the variable
albedo in start_archive.nc before outputing it in restartfi.nc

== 03/03/2022 == AB
Changes on dust_rad_adjust for GCM6:
- put an upper limit on dust_rad_adjust to avoid skyrocketing values when there are strong diurnal
  variations of opacity
- move the condition to compute dust_rad_adjust only once per time step before the whole call to
  compute_dust_rad_adjust, instead of repetitive local checks
- some cleaning

== 09/03/2022 == EM
Update inichim_newstart to be compatible with latest additions of non-chemistry
tracers.

== 09/03/2022 == AB
Update .def* files in LMDZ.MARS/deftank/
*.def.GCM6 files are bound to change later but are ready to use.

== 09/03/2022 == AB
Following r2637, change default values for dust cycle parameters to make them
consistent with callphys.def.GCM6

== 09/03/2022 == JL
Update for non-orographic Gravity Waves; some key parameters can now be
set via callphys.def

== 15/03/2022 == JL
Switching orographic GW routines to F90 and adding comments.

== 17/03/2022 == AB
Implementation of the IRabs-to-VISext dust scenario conversion, depending on the GCM effective radius :
- new flag 'reff_driven_IRtoVIS_scenario', false by default, must be set to true to use this dynamic conversion
  (otherwise, the coefficient takes the constant value of 2.6, eqv to reff=1.5\B5m, as before)
  A specific line is added in deftank/callphys.def.GCM6
- this flag requires the 'dustiropacity' to be set to 'tes' to match the IR scenario's wavelength.
  'mcs'-like dso diagnostics can only be produced by the use of the post-processing tool util/aeroptical.F90
- the variable IRtoVIScoef is computed in aeropacity via the GCM CDOD ratio : tau_pref_gcm_VIS/tau_pref_gcm_IR
  (only at the first call to callradite during each physical timestep)
- change read_dust_scenario into module read_dust_scenario_mod

== 21/03/2022 == RV
OMP : update the batch example for Occigen and the README associated

== 24/03/2022 == EM
Small update of the handling writing fields in the restartfi.nc; use a
dedicated flag to avoid calls to mod() with a zero argument which causes
recent gfortran (9+) to complain about a division by zero when in debug mode.

== 28/03/2022 == JL+EM
- turn sugwd.F to sugwd.F90 with extra comments
- turn yoegwd.h into a module

== 07/04/2022 == CM
initracer.F : remove nuice_ref, nuiceco2_ref (ticket 100)
              add some test for co2 microphysics

== 07/04/2022 == CM
co2cloud.F90 : correction on rsedcloudco2 computation (nuice instead of sigma)
               correction on opacities/riceco2 computation when using water ice CCN
improvedco2clouds_mod.F90 : add some comments
physiq_mod.F : add variable co2conservation
               add zdsc = 0 before  call co2condens
co2condens_mod.F : adapt zfallice outputs in accordance with co2cloud flag
                   otherwise we have not 1 day(1proc) = 1 day (24procs) test
updatereffrad_mod.F : deals with co2useh2o flag before riceco2 computation

== 08/04/2022 == EM
Follow-up to removal of nuice_ref default value in initracer.
Put nuice_ref=01 as default value in conf_phys to maintain default behaviour.

== 25/04/2022 == AB
Put the CO2 ice scavenging ratio for dust and water ice to 20 instead of 100, to prevent drying of the water cycle.

== 27/04/2022 == EM
Fixed option to initialize chemistry in testphys1d (inichim_newstart call
arguments were wrong).
Turned inichim_newstart.F90 into a module.

== 17/05/2022 == TP
Add incoming solar direct flux at surface in stats outputs for the MCD.
+ declare new variable "flux_1AU" for solar constant.

== 19/05/2022 == JL
Upate Non-Orographic GW scheme: cmax is not longer fixed but evaluated
as the zonal wind at launch altitude.

== 27/05/2022 == EM
Add possibility to output either upward or downward SW flux at the surface
and top of atmosphere from physiq. Required adding some output arguments
to callradite.

== 30/06/2022 == EM
Minor bug fix in co2condens, erroneous use of surface geopotential phisfi(),
wheras geoptential pphi() is already the geopotential relative to the surface.
Tests showed that this specific erroneous computation was only done in rare
cases and had overall little impact on the simulations.

== 01/07/2022 == EM
Fix a bug I introduced in r2681 (19/05/2022): surface tracers should only be 
initialized to zero if not found in the startfi.nc file.

== 01/07/2022 == JN
"caps" flag is no longer called in surfini.F to set the location of watercaptag.
It now only affects the temperature of south pole grid cell in co2condens.

== 31/08/2022 == JN
Added "atm_wat_profile" flag in 1d to force dry and wet atmospheric water vapor profiles.

== 1/09/2022 == JN
"atm_wat_profile" flag change in 1d. It is now a float directly prescribing the desired MMR of water vapor (0<atm_wat_profile=<1). If (atm_wat_profile > qsat) at a given timestep we have : (atm_wat_profile = qsat).
Other options are :
 - atm_wat_profile = -1 : water vapor and ice are free in the column. This is the default mode of the 1d model which conserves total water tracers (qsurf + watercap + h2o_ice + h2o_vap)
 - atm_wat_profile = 0 : dry atmosphere, where q(h2o_ice) = q(h2o_vap) = 0.

== 13/10/2022 == MV
watercloud_mod.F: implementation of the HDO ice and vapor fluxes computation in the case of supersat=false.

== 14/10/2022 == MV
watercloud_mod.F: follow-up of previous commit.
improvedclouds_mod.F: Lamb et al. 2017 formula set as default in the fractionation by condensation calculation.

== 20/10/2022 == EM
Add reference def files used to generate MCDv6.1 in deftank
(as a side note MCDv6.1 was generated using r2740 of the GCM)

== 20/10/2022 == AM
Bug fix in jthermcalc_e107 (wrong indexes used in some computations involving
NO2 and H2).

== 08/11/2022 == RV
Update startarchive2icosa repertory for new version of Dynamico

== 08/11/2022 == RV
Moving a modulo misplaced in start2archive

== 14/11/2022 == AB
Non-retrocompatible changes of the program util/aeroptical.F90 :
 - make the program more generic, as the user now specify in aeroptical.def
   the aerosols to be computed, as well as the necessary information for each
   aerosol, that are :
   aerosol_name,aerosol_mmr(GCM variable name),aerosol_reff(GCM variable name or single value in m),aerosol_rho(value in kg/m3),optpropfile_name
 - creation of a separate module aeropt_mod.F90 that can be used by other programs (e.g. for the MCD),
   with one subroutine reading the ASCII optical properties file,
   one subroutine interpolating optical properties at a given (wvl,reff) tuple,
   and one subroutine deallocating the module variables.
 - modify the compile program to compile this module aeropt_mod.F90 along 
   with the aeroptical.F90 program. There is no change for the user,
   which just has to run the command 'compile aeroptical' like before.
 - correct the handling of user's wavelength or particle sizes that do not lie
   within the boundaries of the optical properties file.

== 15/11/2022 == JN
 - Now allow seasonal frost to change albedo in 1d 
 - Can now output albedo in 1d with diagfi.def

== 18/11/2022 == EM
Remove the "tracer" (logical) flag as we now always run with at least
one tracer.

== 18/11/2022 == EM
A first step at cleaning/improving the xvik program: updated comments
and changed output yearly dates range to include sol=669.0 (i.e. last
time step of the year).

== 23/11/2022 == RV
Correct initialisation and outputting of variable to run the pcm and newstart in debug mode.
In topmons, zlaywmax=-1 by default, only positive values are correct.

== 23/11/2022 == RV
The variable co2ice is deleted. All the co2 ice on surface is now in qsurf(:,igcm_co2).
CO2 tracer is now mandatory. diagfi output is unchanged.

== 23/11/2022 == RV
Same as previous commit in 1D.

== 23/11/2022 == RV
Same as previous commit for newstart and startarchive.

== 23/11/2022 == RV
Cleaning of phyredem0. Argument passed to the subroutines were unused.

== 23/11/2022 == AB
The program util/aeroptical.F90 can now compute column-integrated optical depths
of the aerosols, in addition to the opacity profiles. The user has to specify it
('yes' or 'no') in aeroptical.def
Detailed changes :
 - update of the aeroptical.def file to ask the user if the column optical depth 
   should be computed (non-retrocompatible change)
 - add in the init2 subroutine a computation of the layers' height delta_z, with 
   adaptable method depending on the availability of some variables in the input file
   and on wether or not the input file has been zrecasted before. Preliminary validation
   shows that these different methods yield a +/-3% error on the output column optical
   depth tau_[aer]. The delta_z variable is also written in the output file.
 - add a log file for warnings in the interpolation subroutine in aeropt_mod.F90
   + add some comments in the code
 - add the ouput "zzlev" (= interlayer altitudes) in libf/phymars/physiq_mod.F
   so that it can be directly used by aeroptical.F90 to compute delta_z

== 29/11/2022 == AB
Add an example of setup in LMDZ.MARS/util/compile to compile utilitary programs
on Irene-Rome supercomputer.

== 02/12/2022 == JN
Add "surf_h2o_lh" output. This is the latent heat term from ground water ice
sublimation / condensation in W.m-2 
Also corrected units of shortwave & longwave heat rates in writediagfi

== 18/12/2022 == TP
Update xvik program. The program now interpolates surface pressure at 3 locations : Viking Lander 1, Viking Lander 2 and Insight.
Also add as outputs :
- Diurnal average
- Harmonics fit (Fourier series) of the diurnal average (6 harmonics)
Columns of each output are described at the top of each file. (Fourier coefficients are also given for harmonics fit) 
Total CO2 inventory is also caluclated now by xvik.

== 26/01/2023 == SF+AB
Fix a small error on co2ice in dynphy_lonlat/phymars/lect_start_archive.F (used by newstart)

== 31/01/2023 == RV
Small fix : move an endif misplaced for watercap

== 31/01/2023 == RV
Watercaptag is now outputed in the starfi.nc.
There is a new mode : icelocationmode=5 to read watercaptag from startfi and to do as iceloctaionmode=4 if the variable is not present.

== 31/01/2023 == RV
A file containing information about number of iteration and reason of stopping of the PEM can be outputed (info_run_PEM.def)

== 10/02/2023 == RV
Change back the modification of r2883 to its original form + Retrocompatibility for icelocation_mode.ne.5 in surfini

== 10/02/2023 == RV
Correction of recomp_tend_co2 formula and make it dependent on the presence of co2_ice.
Add different stopping criterion for water_ice and co2_ice called : water_ice_criterion and co2_ice_criterion.
Add the possibility to output a diagfi.nc each year for the amount of ice, the tendencies, tsurf and ps.
Remove useless variables (not sloped) 
Remove useless file
Some cleaning

== 10/02/2023 == RV
New Boolean options for following orbital parameters of ob_ex_lsp.asc: var_obl, var_ex, var_lsp.
If using evol_orbit_pem=true, you can specify which parameter to follow.
True by default: Do you want to change the parameter XXX during the PEM run as prescribed in ob_ex_lsp.asc.
If false, it is set to constant (to the value of the tab_cntrl in the start)

== 10/02/2023 == LL
PEM
Soil temperature initialisation has been updated
Conf_PEM improved by adding some options to the users (thermal regolith depend on the pressure, depth of the subsurface layers, etc.)
Minor edits then (+ svn update with RV had some issues, so there are some "artefact changes" ...)

== 14/02/2023 == RV
First modifications to introduce subslope parametrization in surface processes.
New variables are added in the new module comslope_mod to describe the subslopes: 
        _ nslope (number of subslope)
        _ subslope_dist (distribution  of the slopes)
        _ def_slope (bound of the slope statistics / repartitions) etc..
These variables are added to the starfi file.
Other GCM variables, outputs and subroutines are not modified yet.
Only nslope=1 is accepted so far (ie. same as no subslope parametrization)

== 16/02/2023 == RV
MARS PEM : Deep cleaning of variables name and allocate.
All the "dyn to phys" grid change is done in subroutines and not in the main program.

== 21/02/2023 == RV
Following r2896, further implementation of subslope parametrisation.
Carefull ! This is a devolpment revision and it still need improvements and tests. 
However, this commit should not change anything for nslope=1.
Only nslope=1 is possible for now!
Utilitaries are not adapted yet.
Dimension of some variables (30 listed below) is changed to add the nslope dimension.
Outputs (diagfi and restartfi) are not changed yet.
nslope is now read and written in the startfi.nc

== 22/02/2023 == LL
PEM: First implementation of a dynamic ice table (vs. static ice table at equilibrium) following Schorgofer (2010,Icarus)

== 23/02/2023 == AB
In aeroptical.F90, handle cases between :
- "all opacities in the column are missing values" (in which case we set column-integrated tau=missval)
and
- "at least one opacity is not a missing value but is 0" (in which case we set tau=0)

== 28/02/2023 == RV
Further implementation of subslope parametrisation.
Carefull ! This is a devolpment revision and it still need improvements and tests. 
However, this commit should not change anything for nslope=1. Only nslope=1 is possible for now!
Sloped variables in the startfi are outputed along the nslope dimension.
Possibility to output variables on a specific subslope in diagfi using VAR_slopeXX in the diagfi.def,
with VAR the variable name (ex: tsurf, co2ice...) and XX the slope number (ex: 04, 07...).
Without any specific mention to slope, variable named VAR in the diagfi.def will correspond to the variable in the flat slope, this can change in the future.
Other code changes for nslope.gt.1 (sometimes the grid mesh average is used instead of the value of the subslope)

== 28/02/2023 == RV
This commit can produce small differences in restartfi.nc due to numerical roundup even for the case nslope=1.
tsurf_mesh_avg is used for callradite, thermosphere and in a specific case with Richardson based surface layer.

== 09/03/2023 == RV
Newstart is now adapted to subslope parametrization and is compatible with the PCM.
It can create start with 1, 5 or 7 subslope abd needs mola64.nc to do so.
Correction in compute_mesh_avg for nslope=1: no average is done only a copy.

== 10/03/2023 == EM
Make subslope_mola a module and turn (extremely) large static arrays into
allocated ones and assume that the "mola64.nc" file is in "datadir" rather
than a hard coded location.

== 12/03/2023 == EM
Follow-up on the addition of an nslope dimension, also adapt XIOS outputs.

== 14/03/2023 == RV
Adapt start2archive.F to the subslope parametrisation.
Small correction for newstart.

== 14/03/2023 == RV
Adapt start2archive_SSO.F to the subslope parametrisation.

== 14/03/2023 == RV
Move the initialisation of inertiedat in the subslope dimension for the case where we start without startfi.

== 16/03/2023 == EM
Add a "diagsoil" flag to trigger outputing a diagsoil.nc file
(default is diagsoil=.false.)

== 16/03/2023 == EM
Some corrections to the 1D model to take into account recent changes
(removing co2ice and added islope dimension to some arrays).

== 25/03/2023 == EM
Add the possibility to use MY36 dust scenario and MY36 EUV inputs

==30/03/2023 == EM
Add illustrative execution job for spirit (aka MESOIPSL cluster) in deftank

==30/03/2023 == RV
Add the possibility to start the 1d model from a startfi (option startfile_1D in run.def false by default).
It will then write a restartfi at the end of the run.
+ Correction of r2919 for flux geo in 1D and initialize it to 0 by default.
+ Minor correction of iostart error message.

==31/03/2023 == RV
The 1D model always output a restarfi

== 31/03/2023 == AB
Replicate Venus commits r2927 and r2928 for Mars photochemistry :
Correction of the reaction N2+ + e- > N + N

== 02/04/2023 == EM
Adapt topmons_setup to handle both cartesian and icosahedral grids

==03/04/2023 == RV
Remove the test ngrid==1 for writediagfi. The routine can handle well the 1D case.

==03/04/2023 == RV
Add a new routine to write output called write_output.
It needs to be imported (for example : use write_output_mod, only: write_output)
Then, it requires only 4 arguments : the name of the variable, its title, its units and the variable itself.
It detects the dimension of the variable and decide to output either in diagfi or diagsoil.
It is also compatible with XIOS (xml file needs to be adapted)
Writediagfi and writediagsoil routines are still available in case.

==03/04/2023 == RV
Small correction in write_output_mod following r2932

== 10/04/2023 == EM
A first step in cleaning up outputs and adding field definitions for XIOS.
 
== 12/04/2023 == RV
Adapt routine lect_start_archive.F to the subslope param.
 
== 12/04/2023 == JN
Change default atw_wat_profile (1d model) to -1 instead of 0 : water is conserved on the column

== 14/03/2023 == AB
Update the setup example in util/compile to compile utilitary programs
on Irene-Rome supercomputer following OS upgrade to Red Hat 8.

== 26/04/23 == RV
Following r2942, small modification to output inertiesoil as a subslope variable in the startfi.nc

== 26/04/23 == LL
Following r2942, fix a bug in the 1D version (inertiesoil was not
written in the startfile).
Introduce the possibility to prescribe subsurface ice in the 1D model

== 27/04/2023 == EM
Fix OpenMP bug on inertiesoil, unnecessary loop and a line
too long for fixed fortran format.
Minor fix for picky gfortran compiler in testphys1d (no .eq. for logicals!)

== 28/04/2023 == RV
Correct writing of variables inertiesoil and fluxgeo following r2919 and r2942 

== 28/04/2023 == RV
Adapt vdifc, co2condens, rocketduststorm and topmons routines to the subslope parametrisation.

== 05/05/2023 == RV
Correct start2archive to write watercaptag correctly. 
Watercaptag will be set to false and correctly handle by the PCM in the case where we change resolution.
+ Correct inertiesoil writting in start2archive

== 12/05/2023 == RV
Create a new file "file_def_physics_mars.xml" in deftank. 
This is the place to define the output (file name, variable, frequency, operation...) of the physic when using XIOS.

== 17/05/2023 == AB
Fixed r2963 which was preventing to compile the model without XIOS
+ changed the computation of variables rhowater_* so that they are real densities (factor 1/rvap missing ; this doesn't affect the previous PEM results as these densities were only compared between each other)
+ added comments and units for ice table variables in physiq_mod.F
+ made Clapeyron coefficient names in physiq_mod.F coherent with how they are defined in the PEM
+ fixed a reference in constants_marspem_mod.F90
+ fixed unit attribute of surface/soil water densities in field_def_physics_mars.xml

== 19/05/2023 == JN
+ Architecture change in watercloud_mod.F, improvedclouds_mod.F :
Instead of computing all subtimesteps simultaneously, we now loop on
(ngrid,nlay) first. This is to allow for a future adaptative timestep.
+ Second architecture change in the computations of tendencies within
watercloud_mod.F : we now increment directly tracers and temperature instead
of tendencies. This may allow future developments for optimizations.
+ Because of second change, no bit by bit correspondance with previous
revision (truncature stuff)
+ "simpleclouds" routine should be broken in this build (microphys=.false.)
+ Introducing a flag "cloud_adapt_ts" (false by default) to set the adaptative timestep (not yet ready). Otherwise fully retrocompatible.


== 26/05/2023 == RV
Adapt write_output to be able to output integer and logical in diagfi.nc, but the variables are converted to real by the routine before being written in the netcdf.

== 30/05/2023 == RV
Adapt expandstartfi to subslope dimension and small correction regarding depreciated dimension "number_of_advected_field"

== 02/06/2023 == EM
Follow-up to r2970: output of integers/logicals also converted to reals with XIOS
Also updated "deftank/field_def_physics_mars.xml" to keep up with recently added
variables

== 09/06/2023 == AB
Adapt simu_MCS.F90 so that it also recognizes new dust opacity names from aeroptical (since r2817 : "opa_dust" instead of "opadust")
(retrocompatible with old names as well)

== 12/06/2023 == EV
+ Created an option to output the profiles in 1D using write_prof (default is false)
for the several years run mostly the PEM

== 12/06/2023 == JN
Following commit r2966 : 
+ adaptative subtimestep now ready and computed in improvedclouds using an
empirical powerlaw. Flag is "cloud_adapt_ts" (default false) with
retrocompatibility with imicro.
+ simpleclouds working 

== 03/07/2023 == JN
Bugfix in improvedclouds from previous commit (r2984) where loops on
(ngrid,nlay) where conducted within big (ngrid,nlay) loop. Two occurrences :
initialization of zq0 and preventing negative tracers. 

== 06/07/2023 == EM
Minor fix in utility "expandstartfi": correctly handle the case of
polar mesh areas.

== 07/07/2023 == JBC
Minor fix for initialization of tracers indices and rework of "atm_wat_profile" in testphys1d.F.

== 10/07/2023 == EM
Update reference field_def_physics_mars.xml to take into account recently
added outputs in improvedclouds.

== 18/07/2023 == EM
Some adaptations to enable running the 1D model with XIOS.
Note that this requires compiling with "-io xios -parallel mpi"
but the model should then be run using a single core, i.e. without mpirun

== 19/07/2023 == JBC
Some adaptations to make the 1D model run with XIOS and MPICH for use with 1D PEM.
Small fixes to compile and run 1D model related to the second to last commit.

== 21/07/2023 == EM
Some code cleanup. Remove obsolete "comg1d.h" and "writeg1d.F" (were used to
specifically output for Grads in 1D).
Also turned lwi and lwflux into modules while at it.

== 21/07/2023 == EM
More code cleanup. Turn "nirdata.h" common into module "nirdata.F90" and
include "nir_leedat.F" (reading/loading of the data) in the module.
Also turn nirco2abs.F in a module.

== 21/07/2023 == EM
Fix OpenMP bug in paleoclimate_mod; saved variables should be threadprivate.

== 22/07/2023 == EM
Some code cleanup around microphysics. Turn microphys.h into module 
microphys_h.F90, and while at it also turn nuclea.F, growthrate.F90 and
massflowrateco2.F90 into modules.

== 24/07/2023 == EM
Code cleanup concerning chemistry. Turn chimiedata.h into module
chemistrydata.F90 and integrate read_phototable.F in it.
Also fix an OpenMP issue with read_phototable; different OpenMP threads
should not simultaneously open/read a file. Let the master do the job
and then broadcast the result to all cores.
While at it, also turned nltecool.F and nlte_tcool.F into modules.

== 25/07/2023 == EM
Code cleanup in diffusion, turn variables from diffusion.h into module 
variables in moldiff_red.F90 (turn it into a module in the process).
Also turn moldiffcoeff_red.F and thermosphere.F into modules.

== 26/07/2023 == EM
Code cleanup: nltedata.h is only included in nltecool.F so turn this data
into module data there. Also convert lteparams.h into module nlteparams_h.F90.
And while at it also turn nlthermeq.F and blendrad.F into modules.

== 27/07/2023 == JN
Optimization for adaptative subtimestep of water-ice clouds : should now be
much faster. + small cleanup

== 28/07/2023 == EM
Further code cleanup with NLTE routines; converted nlte_paramdef.h to module
nlte_paramdef_h.F90 and nlte_commons.h to module nlte_commons_h.F90
(could not turn nlte_aux.F, nlte_setup.F and nlte_calc.F into modules due
to circular dependencies; would require further code reorganization).

== 31/07/2023 == JBC
Addition in 1D of relaxation towards a profile for atmospheric water. It needs the flag "atm_wat_tau" (real):
 - atm_wat_tau < 0. -> no relaxation (default);
 - atm_wat_tau >= 0. -> relaxation towards the value "atm_wat_profile" with relaxation time "atm_wat_tau".

== 07/08/2023 == EM
Fixed a bug in newstart call to lect_start_archive; missing perenial_co2ice
argument. Turned lect_start_archive into a module so this cant't happen again.

== 09/08/2023 == JBC
Small fixes to be able to run the Mars PCM 1D without "water".

== 14/08/2023 == JBC
Related to commit r3026: improvement of error message in initracer.F (now it gives correctly the only identified tracers) + one small correction to run PCM 1D without water.

== 8/09/2023 == JBC
In testphys1D.F, "dtphys" was renamed into a local variable "dttestphys" because "dtphys" is also a variable of time_phylmdz_mod.F90. Thus, it could have been modified by the physics through the module (for ex. by tabfi.F when reading startfi.nc) and affect the dynamics which is prohibited.
Some code cleaning in regards of tests in 1D.

== 12/09/2023 == JBC
The variable 'timeperi' (defined in "planete_h.F90" and computed in "iniorbit.F") is renamed into 'lsperi' and thus slightly changed to be coherent to the solar longitude of perihelion in radian. It can now be used out of the box by other subroutines/programs like the PEM.

== 21/09/2023 == JBC
Addition of the pressure profile to be able to run chained simulations in 1D. Like this, the surface pressure can be got from one run to the next.
Rework of "write_profile.F90" + correction of arguments in its call in "testphys1d.F": 'qsurf' was wrongly given!

== 26/09/2023 == JBC
Addition of the file "start1D.txt" which mimics a "start.nc" file to be able to run chained simulations in 1D. Like this, key variables and profiles can be got from one run to the next. As a consequence, the subroutine "write_profile.F90" is replaced by "writerestart1D.F90".

== 27/09/2023 == JBC
Upgrade of "testphys1d" to Fortran 90. Cleaning of the subroutine and minor optimizations of the code.
Correction of a bug: 'inertiedat(1,1)' was overwritten by 'inertieice'.
From now on, in "testphys1d.F90", initialization is entirely done by a new subroutine called 'init_testphys1d' ("init_testphys1d_mod.F90").

== 27/09/2023 == EM
Add extra tests for XIOS output: only combine and send fields to XIOS if the
user requests them in one of the output files.

== 27/09/2023 == YL+AB
Fix ticket #141 : when doing a log interpolation in zrecast (e.g. for density), negative and null values are changed into a very small positive value (below the numerical precision) so that the log interpolation yields a null value.
+ add '_FillValue' attribute (redundant with 'missing_value') checks and outputs in zrecast to comply with newest NCO versions (part of ticket #152)

== 28/09/2023 == EM
Update reference deftank files:
- remove obsolete callphys.def.notracers
- rename z2sig.def to z2sig.def.MCD6
- update callphys.def.GCM6 to include non-oro GW parametrization
- update callphys.def.MCD6 to disable Frost metamorphism option

== 28/09/2023 == JBC
Related to commit r3056, correction of bugs and some adaptations of the subroutine 'init_testphys1d'.

== 28/09/2023 == JN
Finalization of adaptative timestep of cloud microphysics :
- conf_phys.F : Checking that both flags "cloud_adapt_ts" and "temp_dependant_m" needs to be
activated in order to run with an acceptable water cycle
- nuclea.F : "temp_dependant_m" now actualized to be compatible with "cloud_adapt_ts" as
in the latest release
- improvedclouds.F : "cloud_adapt_ts" powerlaw coefficients actualized for conservative
present-day computations
- Explicit comments in several sections of the code with these infos

== 28/09/2023 == JN
Following previous commit, correction of a spelling mistake "temp_dependant_m"
is actually "temp_dependent_m". Sorry about that.

== 30/09/2023 == AB
Following r3061 and r3062 :
- adapt files callphys.def.GCM6 and callphys.def.MCD6 in deftank/ to match with the new orthograph of temp_dependent_m
- restore the possibility to run with a temperature-dependent contact parameter without using the cloud adaptative subtimestep
  (MCD6.1 configuration, mteta = linear fit of temp)

== 02/10/2023 == LL
Follwing -r 3056:
- Surface variables (tsurf, tsoil, albedo, emis, qsurf) are not defined and allocated in testphys1D but the routines testphys1D and init_testphys1D used what is defined in comsoil, surfdat_h, dimradmod. 
-surface variables in testphys1D and init_testphys1D have a slope dimension (set to 1 for now, hard-coded, will be improve later). 
Slight changes are expected for the PEM (TBC w/ JBC).

== 03/10/2023 == JBC
In 1D, 'q' has been converted from dimension (:,:) to (1,:,:) and 'q2' is now got through the module 'turb_mod'. It allows more generalization and to match dimension in the subroutines.
Related to commit r3066, correction of a bug to write/read a restart/start in 1D and more adaptations of the code.

== 05/10/2023 == AB
Add an example of setup in util/compile to compile utilitary programs on Adastra supercomputer.
Warning: on Adastra, you need to add the netcdf library path to LD_LIBRARY_PATH before running the executable
(export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$NETCDF_DIR/lib)

== 05/10/2023 == JBC
Correction of a bug introduced in commit r3069 when compiling with ifort.

== 06/10/2023 == JBC
Transformation of 'writerestart1D' into module.

== 06/10/2023 == JN
Bugfix : adaptative timestep now is insensitive to ptimestep

== 09/10/2023 == EM
Improve conctatnc's handling of XIOS output files (handle change in some
variable names, e.g. "area" or "phisfi").

== 10/10/2023 == EM
Enable outputing cell area with XIOS and make sure the polar grid point
is correctly handled (i.e. on lon-lat grid outputs polar mesh area must
be adjusted to account for the replicated polar meshes).

== 10/10/2023 == EM+JBC
Follow-up of r3078 which broke the 1D model.
Also added initialisation of non-oro GW tendencies stored in startfi.nc when in 1D.

== 18/10/2023 == JBC
    - Correction of a bug in "writediagfi.F": the case of using the 1D model with parallelization was not anticipated so that the "diagfi.nc" file was filled with NaNf;
    - Addition of the file "start1D.txt" as an example in the directory deftank/;
    - Some "cosmetic" modifications in "improvedclouds_mod.F", "write_output_mod.F90" and "testphys1d.F90".

== 22/10/2023 == EM
Fix issues with dates when in parallel with OpenMP (missing copyin
statement when opening parallel section in iniphysiq). Added some threadprivate
clauses in saved module variables in comcstfi_h.F90 and planete_h.F90.
Prettyfied solarlong.F and made it a module. Likewise for conf_phys.F

Some code tidying:
Made pi in module comcstfi_h a parameter (and not a variable recomputed at
various points by various routines) and added module routine init_comcstfi_h
to cleanly initialize module variables.
Moved iniorbit.F to be a module routine of planete_h since it initializes
(some of ) the module variables it contains.

== 23/10/2023 == EV
We added the to module vdifc the possibily of subsurface intercation, mostly to have the option of buried glaicer that can lose ice and create polar layers.
if no ice is on the surface the ice the atmosphere can directly interact with the subsurface ice.
if ice is on the surface it can interact with the subsurface ice.
**For now it is not working with more then one subslope. I will add this feature soon**
In order to use it there are two flags that needs to be set to true.
paleoclimate=.true.
lag_layer=.true.
in addition one need to give the following parametrs in startfi or run.def:
d_coef=X for the diffusion coeficent (4e-4 is the defualt)
<h2o_ice_depth=X> if its zero or lower there is no subsurface ice (default -1).
outputs: zdq_ssi, momentarily zdqsdif after the interaction with the SSIzdq_subtimestep,  momentarily flux after the interaction with the SSIzdq_ssi_frost momentarily zdqsdif after the interaction of the frost with the SSI
q1, atmospheric first layer water vapor quatity
qeq, SSI water vapor quantity

== 26/10/2023 == JBC
Few small fixes following r3098.

== 02/11/2023 == LL
Correction of a small bug in soil_settings: the interpolation on the new grid
for the thermal inertia was not used with the old thermal inertia vector but
only with the last value of the oldthermal inertia
Cleaning of the code

== 03/11/2023 == JBC
Small fix on "field_def_physics_mars.xml".

== 03/11/2023 == LL
Introducing qsoil to model H2O adsorption/desorption in the subsurface. For now, I've fixed the number of tracers in the subsurface to t
hree (H2O vap, H2O ice, H2O ads).
Changing the soil grid (better resolution) as given by Pierre Yves Meslin
Adding the possibility to compute H2O adsorption desorption and exchange with
the near-surface atmosphere, only works in 1D for now. By default, subtimestep
for water sublimation is 1 when adsorption is activated (otherwise it crashes)

== 08/11/2023 == JBC
Correction of the case when startfiles1D = .true. and there is no "startfi.nc": the flags used in "init_testphys1d_mod.F90" were not correct so the model crashed and didn't create a "startfi.nc" from scratch as intended.

== 08/11/2023 == LL
Following -r 3113, fixing newstart & startarchive by implementing the changes
in phyredem1 and phyetat0, i.e., adding qsoil and nqsoil in the arguments of
the subroutine

== 09/11/2023 == JBC + EV
Correction of a bug introduced in r3059: in case of 'watercaptag=.true.', 'watercap' was prevented to evolve as it should be because of 'zqsurf' in "vdifc_mod.F90" which was forced to be 0 if negative.

== 10/11/2023 == LL
* Fixing index bug in soilwater.F The adsorption/desorption model now run
with the subtimestep (but still not in 3D yet).
* Small changes for the boundary conditions when considering
adsorption/desorption

== 14/11/2023 == AB
Add a sanity check on tau_pref_gcm in aeropacity when running without rescaling (dustscaling_mode=/=1), hence resolving ticket #156
+ add some comments and a sanity check in conf_phys to ensure freedust flag is not used with dustscaling_mode=1.

== 15/11/2023 == LL
* Update in soilwater: adding the possibility to run without adsorption, but with the possibility to run with seasonal frost forming in the subsurface
* THe choice of the isotherm for adsorption can be now done by setting  the integer choice_ads in the callphys.def choice_ads = 1 adsorption rate is computed with the H2O thermal speed; choice_ads = 2 adsorption rate is computed based on exeperimental resutls, choice_ads =3 no adsorption

== 17/11/2023 == CS
* Bug fixes for improvedcloud_mod.F :
- Initialization of dMice when low ccn number
- Initialization of zdq at first sub time step (spenttime=0)
- Move 'coef' to fix the formula for zimicro

== 17/11/2023 == JBC
Correction of a bug related to r3126: 'choice_ads' did not have a default value which made the model crash. 'choice_ads = 0' is the default value (no adsorption).
Cleaning of the 1D initialization: any reference of the PEM has been removed from "init_testphys1D_mod.F90". This way is much cleaner even though it needs more code.

== 21/11/2023 == EM
Bug fix in phyetat0, igcm_co2_tmp was not initialed when paleoclimate==.false.
but used nonetheless. Added an if(paleoclimate) around computation of 
perennial_co2ice() as it should only be computed in that context; also added
an if(paleoclimate) around writting perennial_co2ice() to restartfi.nc in
physdem1 for the same reason.

== 24/11/2023 == LL
Bug fix in newstart, "perenial_co2ice" has been changed to "perennial_co2ice"
in -r3010 in the PCM without being changed in newstart. It is now corrected.

== 29/11/2023 == JBC
Small "cosmetic" cleanings in some subroutines for the readability and "surfini.F" is transformed into "surfini_mod.F90" (explicit module interface + Fortran 90 format).

== 29/11/2023 == JL
New scheme "nonoro_gwd_mix_mod" to simulate non-orographic gravity waves induced mixing. The scheme flag "calljliu_gwimix" has been put to "false" as default.
There are three tunable parameters that have been set up, as "nonoro_gwimixing_eff=0.1", "nonoro_gwimixing_eff1=0.1", "nonoro_gwimixing_vdl=1.5".
Remember to use full-layers model configuration (64x48x73) when you try to call this scheme because we need to evaluate the saturation altitude of each monochromatic wave.
More than ~75% of the waves saturated at altitude above 120 km.

== 02/12/2023 == LL
Bug fix in init_testphys and testphys. Index for water vapor and ice were not initialized
(but used in testphys1d when atm_wat_profile > 0). It is fixed by calling
initracer in init_testphys1d_mod.

== 06/12/2023 == EM
Minor fixes to ensure outputs of water cycle related variables are only
computed and made if the water cycle is computed.

== 06/12/2023 == JBC
Tiny fix from r3147 (Fortran fixed format).

== 06/12/2023 == LL
Switching vdif_cd to a module and convert it to F90.
Some cleaning have also been made (remove commented lines, outputs, etc.)
VDIFC: minor fix: zcdv_true zcdh_true are out and not in variables.

== 07/12/2023 == LL
Switching pbl_parameter.F into a module. Cleaning of unused variables/sections in it.
Correction in the computations of ustar, thetastar as it was done in a different way compare to vdif_cd. It is now self-consistent.
Maybe pbl_surface in the MCD needs also to be changed ? In discussion with Ehouarn and Aymeric.

== 09/12/2023 == LL
Add the possibility to compute Cd; Ch based on the virtual potential temperature to account for water flotability.
To do so, a boolean "virtual", set to false by default, must be set to true (for now hard coded as future modifications will follow).
Small change following previous commit: when computing the virtual surface temperature, if frost is at the surface, qvap_surf = qsat. else; it is qvap in the first layer

== 12/12/2023 == CS
rnew and cpnew are already initialized in physiq_mod.F with call concentrations.F if callthermos is true.

== 12/12/2023 == CS
* zzlay and zzlev are calculated at the begining of physics taking into account the evolution of gravitational acceleration with altitude (g becomes gz) and varying reduced gas constant with composition of the atmosphere (r becomes rnew).
* zzlay and zzlev are updated at the end of physics after call co2condens with updated pressure and temperature.
* call concentrations, when photochem or callthermos is true, has been moved before the first calculation of zzlay and zzlev to be able to use varying reduced gas constant rnew.

== 13/12/2023 == CS
Cleaning of conduction.F, euvheat.F90, moldiff.F and molvis.F, some commented lines referring to a local calculation of layers/levels altitudes have been removed.

== 19/12/2023 == JBC
Fixed an issue where the gfortran compilation failed due to rank mismatch of the 'field' argument when calling 'writediagfi' + cleaning of the subroutine.

== 19/12/2023 == CS
* A new call to vdifcd is done with updated winds (after inversion of wind u and wind v and before inversion of the potential temperature h) and zcdv / zcdh are also updated. It matches with what is done in the generic model. 
* Old commented lines with a call to vdifcd at the begining of the tracers part of vdifc_mod have been removed.

== 19/12/2023 == CS
Little bug fix with missing arguments for vdifcd that were added in r3153

== 19/12/2023 == CS
Small fix following r3163 

== 27/12/2023 == LL
The computation of Cdh; Cdv is now done for each sub-grid surfaces and not only the flat one.

== 30/12/2023 == EM
Fix typo in previous commit

== 03/01/2024 == EM
Minor fix for XIOS output of a scalar in write_output_mod.F90.
Also added more helpful error messages in xios_output_mod.F90.

== 11/01/2024 == JBC
Correction of a bug: 'perennial_co2ice' was not initialized if there was no "startfi.nc" file.

== 16/01/2024 == EM
Update reference traceur.def.MCD5 to include all ions (as in *.MCD6) since
runs including the ionosphere needs these.
While at it also from some callphys.def.* files and rename
callphys.def.watercycle as callphys.def.GCM5 to (hopefully) avoid confusions.

== 18/01/2024 == JBC
Improvement of the error message for tracers initialization with a 1D start file + update of "start1D.txt" in the deftank + small cleanings.

== 25/01/2024 == JBC
Some changes to prepare the introduction of slopes in 1D: in particular, the subroutine "getslopes.F90" and "param_slope.F90" are now inside the module "slope_mod.F90" + Few small cleanings throughout the code.

== 26/01/2024 == CS
- conc_mod.F : Added new subroutines init_r_cp_mu and update_r_cp_mu_ak to replace initialization of rnew, cpnew, mmean and akknew as constants and their update if callthermos or photochem (same update as in concentrations.F) that were done in physic_mod.F. 
- rnew, cpnew, mmean and akknew are now protected meaning they cannot be modified anywhere in the model other than in conc_mod.F .
- concentrations.F has been removed.
- Knowing where rnew, cpnew, mmean come from is now more explicit. These modifications respond to the need expressed in ticket #90.

== 26/01/2024 == CS
Following revision 3185 concentrations.F has been deleted from LMDZ.MARS/aeronomars/

== 29/01/2024 == JBC
Addition of the parameter 'CO2cond_ps' (= 1 by default) for 1D. This coefficient controls the surface pressure change. If 'CO2cond_ps = 1', then surface pressure varies normally. If 'CO2cond_ps = 0', then surface pressure is kept constant. The ratio of polar cap surface over planetary surface is a typical value (8.3e-4) for tests. To be defined in "callphys.def" so that both PCM and PEM can read it.

== 30/01/2024 == CS
Update of the reference to default values of coeff_detrainment, coeff_injection, ti_injection and tf_injection (following old revision r2639) in callphys.def.MCD6

== 02/02/2024 == JBC
Small update following r3188 to keep the CO2 mixing ration constant if "CO2cond_ps = 0" + Some cleanings.

== 05/02/2024 == JBC
Small modification of the change introduced in r3200 to make the code simpler and faster.

== 07/02/2024 == JBC
- Addition of the possibility to use subslopes parametrization in 1D. To do so, put 'nslope=x' in "run.def" where x (1, 3, 5 or 7) is the number of slopes you want to, or modify it in an appropriate "startfi.nc". Then, default subslopes definition and distribution are used by the model. The already existing case of using one slope whose inclination and orientation are defined in "run.def" is still possible.
- Some cleanings throughout the code, in particular related to unused variables.

== 08/02/2024 == JBC
Fix the situation where the 1D model read the "startfi.nc" or "start1D.txt" if they were present even though 'startfiles=.false', instead of initializing by default.

== 08/02/2024 == JBC
Modification of r3200 for the 1D model: the 'CO2cond_ps' coefficient (now defined in "co2condens_mod.F") is applied not only to update the surface pressure but also all the tracers and the winds from now on. It is done in "physiq_mod.F" just after the call to 'co2condens'.

== 08/02/2024 == JBC
Following r3203, initialization cases for subslopes parametrization in 1D have been settled: it can be done with 'nslope' in "run.def" or by using an appropriate "startfi.nc". Addition of error/warning messages for the different situations to be user-friendly.

== 09/02/2024 == JBC
- Addition in the deftank of a bash script "launch_1Dchained.sh" to make chained simulations of 1D PCM runs.
- Move the script "launch_orb_1Dchained.sh" from the PEM deftank to the Mars PCM deftank.

== 09/02/2024 == LL
- Update the computation of qsat for frost at high temperatures; following
what is done in the Generic PCM

== 12/02/2024 == JBC
Correction of a bug in "writediagsoil.F90": the case of using the 1D model with parallelization was not anticipated so that the "diagsoil.nc" file was filled with meaningless data.

== 13/02/2024 == EM
Fix start2archive; routine surfini is now in module surfini_mod.

== 13/02/2024 == EM
Move "Martian nogcm" from common dynamics to Mars dynamics-physics interface.

== 16/02/2024 == LL
Small correction for the surface layer scheme: the value of the critical Richardson varys if one used the classic yamada scheme (0.2 in this case) or can be a tunning parameter if one uses the atke scheme
Also add the possibily to write the tke in the diagfi.nc when calling pbl_parameter

== 16/02/2024 == LL
Adsorption: commit the last version developed by Pierre Yves Meslin

== 16/02/2024 == EM
Follow-up of r3217, remove some unused "use ..." in leapfrog_nogcm which
cause problems when compiling gcm in parallel mode

== 19/02/2024 == EM
Remove interactive checking with XIOS whether a field should be sent to it;
some yet unresolved issues arise when using this in mixed MPI-OpenMP mode...

== 20/02/2024 == LL
* Move soil_tifeedback into a module waterice_tifeedback_mod.F90
* The flag to call tifeedback has been changed from "tifeedback" to surfaceice_tifeedback for clarity
* Add the possibility to change the thermal inertia while pore ices is forming in the soil: to do so, use the flag poreice_tifeedback. The computation is done i
n waterice_tifeedback_mod.F90.
For now, surfaceice_tifeedback and poreice_tifeedback can not be called together
, we might think about how to merge later.

== 20/02/2024 == LL
Fixing a bug in 1D: atm_wat_profile should evolve freely when considering
relaxation, and should not be set to qsat in cold conditions. 

== 23/02/2024 == EM
Minor fix in topmons_setup: handle case when mount is "resolved" for high
resolution runs.

== 29/02/2024 == LL
Fixing bugs in soilwater (array size and indexes in loop)

== 01/03/2024 == LL
Following -r 3223, re-introduce the possibility to run the subsurface water ice
evolution without  adsorption

== 04/03/2024 == LL
*Fixing bug in initestphys: the soil depth were initialized using the old grid (but with 57 layers). It was not detected in soil_settings -to be investigated - and therefore soil thermal inertia, when adding subsurface ice, were completely wrong
* Fixing bug in initestphys and waterice_tifeedback: when changing the soil thermal properties to account for the high thermal inertia of subsurface ice, the wrong layer was considered as 'mixed' (it was the layer after the correct one which was modified). 

== 04/03/2024 == LL
Introduce the possibility to prescribe (in 1D) the soil water ice content when running with adsorption/desoprtion

== 05/03/2024 == LL
Following -r 3098; cleaning of vdfic for the management of subsurface water ice.
Fixing some errors (wrong interpolation to compute the water ice temperature, wrong boundary conditions to compute qvap(1))

== 12/03/2024 == LL
Reversing -r 3250 (the ""bug"" I fixed was not a bug but my mystake)

== 12/03/2024 == Jliu
Synchronize all default non-orographic gravity wave parameters in callphys.def with the ones in scheme. The parameters are as follows:
#Eliassen-Palm FLux(only if calllott_nonoro=.true.)
nonoro_gwd_epflux_max=5.E-4
# saturation parameter non-orographic gravity waves(only if calllott_nonoro=.true.)
nonoro_gwd_sat=1.5
# maximum of the phase speed of the gravity waves(only if calllott_nonoro=.true.)
nonoro_gwd_cmax=50
# value of the dissaption coefficiet(only if calllott_nonoro=.true.)
nonoro_gwd_rdiss=0.07
# value of the max wave number
nonoro_gwd_kmax=1.E-4
# value of the min wave number
nonoro_gwd_kmin=7.E-6
# value to control the launch altitude
nonoro_gwd_xlaunch=0.6
# effective factor
nonoro_gwimixing_eff=0.1
# effective factor
nonoro_gwimixing_eff1=0.1
# mixing vertical decrease rate
nonoro_gwimixing_vdl=1.5

== 19/03/2024 == LL
Adapt soil water to run with massive ice and not pore filling ice + constant diffusion coefficient
Small fixes in vdifc for the interaction between the subsurface and frost (the flux from the surface frost to the subsurface was oo large if one removes all the frost at the surface)

== 20/03/2024 == LL
Small update of soil properties (porosity) when running soilwater to simulate the evolution of massive water ice

== 21/03/2024 == EM
Fix a buggy behavior of wstats: it would fail when using a stats.def file and
when the first (at every time step) variable sent to wstats() was not part of 
those listed in stats.def

== 21/03/2024 == Jliu
Fix several bugs in photochemistry related to the submit-crash-resubmit
problem: Some of the integers in the related routines are not set in
privatethreads. Consequently, the additives such as n=n+1 are accumulated with
threads, causing systermatic problems in the routine. This update fixed the
submit-crash-resubmit problem. The simulated results are same with previous
simulations as tested.

== 21/03/2024 == Jliu
Found and fixed another small bug in photochemistry related to commit r3289.

== 05/04/2024 == EM
Code cleanup to prepare the addition of new schemes for dust lifting by
wind stress and dust devils. Renamed "dustlift" routine "dust_windstress_lift"
and made it a module; also made dustdevil a module.

== 15/04/2024 == JBC
Modification of "subslope_mola.F90" to take into account other longitude resolution than 64. It makes "newstart" be able to change the number of sub-slopes for low resolution.

== 15/04/2024 == JBC
Correction related to r3301: the variable 'resol' was not linked to longitude resolution.

== 16/04/2024 == JBC
Revert "subslope_mola.F90" to the version before r3301. The modification was a mistake.

== 16/04/2024 == CS
Correction of a misspelled stats output variable name.

== 18/04/2024 == JBC
- Addition of the "startfi" file name as an argument for "phys_state_var_init_mod.F90"/"iniphysiq_mod.F90" to be able to initialize correctly the 3D PEM with its dedicated "startfi" file name.
- Small update of xml files for XIOS in the deftank, mainly to make the 3D PEM run with slopes.
- Few cleanings in "phyetat0_mod.F90".

== 19/04/2024 == JBC
Correction of a missing argument due to changes introduced in r3305.

== 25/04/2024 == LL
Fixing a bug in the initialization of sub-grid surface temperatures in the 1D
(subgrid slope index was missing)

== 25/04/2024 == JBC
Reversion of r3305 and r3307.

== 13/05/2024 == LL
Some modifications in vdifc and pbl_parameters to include the effect of water buoyoncy on the sublimation of water ice.
Note: it only works with paleoclimate = .true. (since the model is not tuned with that ...).

== 17/05/2024 == LL
Fixing a bug in vdif_cd: a "residual", used as criterion to enter an iterative loop, was wrongly initialized. Hence, for some points, the algorithm does not go into the loop, and a wrong value of Cd, Ch was computed.
Also some cleaning/small fixing with save variables with OMP.

== 21/05/2024 == JBC
Addition of the paleoclimate variables in the change of the number of slopes by "newstart.F" + some simplifications of the way it is done.

== 21/05/2024 == JN
In vdifc_mod, adding a threshold on the subtimestep of water vapor
sublimation/condensation to avoid computation when surface ice is too low.
Also nsubtimestep is now stored in diagfi at the end of the subtimestep for
clarity of the code.

== 21/05/2024 == JBC
Addition of the paleoclimate variable 'd_coef' in the writing of the "restartfi.nc" file.

== 23/05/2024 == LL
Small correction of how qsurf of co2 is initialized in the south pole.
Some correction for the albedo of co2 ice when using paleoclimate: a uniform value (albedo_co2_cap) is used for both hemisphere for CO2 frost, and a different (higher) value is used for perennial ice.

== 23/05/2024 == JBC
Modification of "iniwritesoil.F90": 'nsoilmx' and 'mlayer' are now arguments + making it as a module.

== 23/05/2024 == JBC
Correction of a variable name in the xml definition file causing an XIOS error because of a change in r3337.

== 29/05/2024 == JN
Following commit r3337, threshold for vdifc subtimestep is no longer hardcoded
and explicitly commented.

== 31/05/2024 == JBC
- Correction for the script "launch_orb_1Dchained.sh" in the deftank.
- Small cleanings related to error detection.

== 12/06/2024 == EM
Change the way the rate of outputs for diagfi.nc files is specified:
IMPORTANT: Specifying "ecritphy" no longer possible and will trigger an error.
Use "outputs_per_sol" to specify output rate instead.
This should makes things (hopefully) clearer for users and also better
enforces a cleaner and clearer separation between dynamics and physics.

== 19/06/2024 == JBC
Update of the "run.def.1d" file in the deftank.

== 19/06/2024 == JL
Update of non-orographic gravity waves mixing scheme. 1)mixing in potential
temperature are added. 2)all mixing in q,u,theta now are implemented by AR-1 
algorithm. Tests (MY29,MY32-35) runs show that this implementation has limited
impact to the temperature/tides fields.

== 19/06/2024 == JL
Un petit bug fixed in mixing traceurs when doing AR-1: the last step q tendency 
was forgot to give to montainant step. Thus all mixing-induce tendency becomes 
zero due to initiallization values are zero.

== 06/08/2024 == LL
Correction of the computation of the water vapor flux from the subsurface ice
when thin frost is at the surface
cleaning testphys1d

== 12/08/2024 == LL
Following previous commit, fixing a bug: more frost than what is a the surface could sublimes (when working with lag layer only). It is corrected, not in a elegant way...

== 26/08/2024 == LL
Fixing bug: the emissivity of perenial CO2 ice was not correctly handled

== 20/09/2024 == EM
Update reference callphys.def.hdo.GCM5 in deftank

== 27/09/2024 == JYC+EM
Add new molecular diffusion routine moldiff_MPF (modified pass flow scheme)
But for intermetiate testing the legacy moldiff_red routine remains
the default. The "moldiff_scheme" flag (1: legacy, 2: MPF) can be used
to swich from one scheme to the other.