Now register SSAlkAccum and SSAlkCoarse separately

The State_Chm%SSAlk array cannot be registered as a single array,
because it is has a 4th dimension of size 2, which is interpreted as per
species.

The solution is to register the two fields separately, as SSAlkAccum
and SSAlkCoarse.  This also requires a slight modification to the
HISTORY.rc files.

Signed-off-by: Bob Yantosca <[email protected]>

Remove obsolete, commented-out code from several modules

Removed commented-out blocks of code (tagged with "Prior to MM/DD/YY")
in several locations prior to the 12.0.0 release.

Signed-off-by: Bob Yantosca <[email protected]>

Add warning for larger timesteps when using MERRA-2 nested-grid CH4 a…

…nd CO2 simulations

Bram Maasakkers wrote:

   Melissa Sulprizio and I have been working on the methane simulation with
   MERRA-2 and the nested North America grid at 0.5x0.625. During our
   initial simulations, we found very high values in the stratosphere,
   originating at the edges of the domain and showing a checkerboard-like
   pattern in the domain. It appears this is caused by a violation of the
   CFL condition in the stratosphere due to strong stratospheric winds in
   MERRA-2. When the condition is violated at the boundaries, it leads to
   an out-of-bounds error but even preventing an out-of-bounds error there
   by capping the array index doesn’t prevent the high concentrations from
   originating. It seems that this previously occurred for the GEOS-5
   simulation but it did not seem to compromise simulation results
   significantly. For our purposes of comparing total column measurements
   of GOSAT to model output, it is a larger problem. We found it also
   occurs in the full-chem simulation.

  I think that a variable timestep could be implemented to prevent this
  from happening. For now, we recommend using a 5/10 transport/chemistry
  timestep with MERRA-2 nested grid simulations instead of 10/20.

Yuxuan Wang wrote:

   I agree with Lin and would also opt for a 10/20 mins time step as the
   default for full-chemistry nested-grid simulation. The reason is exactly
   as Daniel said. The nested-grid model users are predominantly using the
   full-chemistry option and concerns with tropospheric or surface
   concentration. The specialty nested-grid simulations, such as tagged CO,
   methane and CO2, used to require a separate development and model tuning,
   as least during the past before the HEMCO era. As a continuation of that
   ‘tradition’, the idea of putting a note or stop sign for the CH4 and CO2
   nested-grid code should work well.

Signed-off-by: Melissa Sulprizio <[email protected]>

Add warning for larger timesteps when using MERRA-2 nested-grid CH4 a…

…nd CO2 simulations

Bram Maasakkers wrote:

   Melissa Sulprizio and I have been working on the methane simulation with
   MERRA-2 and the nested North America grid at 0.5x0.625. During our
   initial simulations, we found very high values in the stratosphere,
   originating at the edges of the domain and showing a checkerboard-like
   pattern in the domain. It appears this is caused by a violation of the
   CFL condition in the stratosphere due to strong stratospheric winds in
   MERRA-2. When the condition is violated at the boundaries, it leads to
   an out-of-bounds error but even preventing an out-of-bounds error there
   by capping the array index doesn’t prevent the high concentrations from
   originating. It seems that this previously occurred for the GEOS-5
   simulation but it did not seem to compromise simulation results
   significantly. For our purposes of comparing total column measurements
   of GOSAT to model output, it is a larger problem. We found it also
   occurs in the full-chem simulation.

  I think that a variable timestep could be implemented to prevent this
  from happening. For now, we recommend using a 5/10 transport/chemistry
  timestep with MERRA-2 nested grid simulations instead of 10/20.

Yuxuan Wang wrote:

   I agree with Lin and would also opt for a 10/20 mins time step as the
   default for full-chemistry nested-grid simulation. The reason is exactly
   as Daniel said. The nested-grid model users are predominantly using the
   full-chemistry option and concerns with tropospheric or surface
   concentration. The specialty nested-grid simulations, such as tagged CO,
   methane and CO2, used to require a separate development and model tuning,
   as least during the past before the HEMCO era. As a continuation of that
   ‘tradition’, the idea of putting a note or stop sign for the CH4 and CO2
   nested-grid code should work well.

Signed-off-by: Melissa Sulprizio <[email protected]>

Updates to dustdead and megan HEMCO extensions previously missed

These updates are specific to the GEOS-5 CVS tag
cak_Icarus-1_0_GCCv1102e_v2_003. Differences from the main
GEOS-Chem branches are not blocked off with if defined DISCOVER
blocks.

Signed-off-by: Lizzie Lundgren <[email protected]>

Updated the README.md file for the v11-02/12.0.0 release

Now use Github markdown style.

Signed-off-by: Bob Yantosca <[email protected]>

Updated the README.md file for the v11-02/12.0.0 release

Now use Github markdown style.

Signed-off-by: Bob Yantosca <[email protected]>

Add ISOAAQ to AOD and PM2.5 diagnostics only if ComplexSOA is on

To avoid double-counting of SOA, we now add

  ISOAAQ = SOAGX + SOAMG + SOAIE + SOAME + LVOCOA + ISN10A

to the AOD diagnostics only when the complex SOA option is turned on.

Furthermore, for the PM2.5 diagnostic, we do the following:

(a) For simulations using Simple SOA only (Standard, Tropchem), then
    SOAS (but not ISOAAQ) will be added to the PM2.5 diagnostic;

(b) For simulations using Complex SOA only (complexSOA and
    complexSOA_SVPOA), then ISOAAQ (but not SOAS) will be added
    to the PM2.5 diagnostic;

(c) For the benchmark simulation (which turns on both simple and
    complex SOA simultaneously) SOAS but not ISOAAQ will be
    added to the PM2.5 diagnostic.  (This is to avoid double-counting.)

RESULTS:

This update will cause the Standard, Tropchem, and Benchmark
simulations to have differences in the PM2.5 diagnostic w/r/t the
prior commit (because SOAS and ISOAAQ together were added to the
PM2.5 diagnostic).

The complexSOA and complexSOA_SVPOA simulations will
have identical PM2.5 diagnostics w/r/t the prior commit (because
ISOAAQ was already being added to the PM2.5 diagnostic).

Signed-off-by: Bob Yantosca <[email protected]>

Restore FINNv1.5 modules

Barron Henderson wrote:

   It looks like v1.6 2015 and 2016 are probably okay, but switching to v1.6 for
   all years would be a problem.
   So, we should hold off on the system-wide implementation for now.

  -Barron

We have therefore restored the HEMCO/Extensions/hcox_include.H and
HEMCO/Extensions/hcox_finn_mod.F90 files that are consistent with the FINN v1.5
data.   Also we have renamed the FINN v1.6 files with the extension *.FINNv16 so that
when it comes time to restore FINNv1.6, we can add these quickly.

Signed-off-by: Bob Yantosca <[email protected]>

Updates to enable GCHP to compile with v11-02f

Signed-off-by: Lizzie Lundgren <[email protected]>