- This commit is the first attempt to add a (generic) tracer to the OBC.
- The tracer "gtr1" is added from the ocean_bgc module generic_CFC.F90
- It is to imitate "salt" as if it was a passive tracer.

- We always intended to use links so that we were not maintaining code
  that did not belong to us. `listpaths` used to not work as expected
  so Niki had placed copies here when adding TEOS10. Using links also
  avoids any license conflicts.

- Removed two git submodules and added bare interfaces to
  config_src/exernal/ODA_hooks/
- Added some missing documentation

- Updated Doxygen configuration to find files in config_src/external

- This version of FMS is a prerequisite to updating calls to FMS ready to
  try FMS2 I/O behind NOAA-GFDL/SIS2#117 and mom-ocean#1033

…nd salinity

- The -B option forced make to make all targets. This was to ensure
  that everything was remade when work in a shared work space which
  is no longer the case. We always have a clean work space in these
  tests and in order to invoke make twice to handle srun errors we
  can't use the -B option anymore.

…to fix-pkg

- Adding domain position arguments to diag_axis_init calls

Moved hooks from pkg to external

…testing

Use FMS tag 2019.01.02 in .testing

Due to unpredictable conflicts with flags, the realization that flag
testing would launch jobs on Slurm environment, and the fact that Slurm
launchers, OpenMPI, and MPICH all appear to pass environment variables
on default, we now just assume that "env=val $(MPIRUN)" will pass an
environment variable to the MPI job in all cases.

This may not be true on all systems, but for now we will assume this
works.

…MS2019.01.02

This is the minimum required update to use 2020.01 FMS & FMScoupler

Testing: Removed environment flag checks

  Corrected halo size in density derivative calculations in smoothed_dRdT_dRdS
This fixes an i-parallelization problem that was recently introduced (as a part
of MOM6 PR#1089) when VERTEX_SHEAR is True, and closes MOM6 issue mom-ocean#1146.  All
answers in the existing MOM6-examples test suite are bitwise identical, but this
does change (correct) answers when VERTEX_SHEAR is true.

- FMS2020 has newer cpu affinity work. These are mostly to fix the
  issues with thread placing and  hyperthreadng under slurm on gaea.
  But it also works on Orion.
- The new affinity module simplifies the thread-placing calls in the
  component models.
- The name of some functions has changed, that's the reason for crashes
  like:
      FATAL: input domain does not have an io_domain.
- This update fixes those issues.
- openmp runs with 1 and 2 threads gives the same answers as non-openmp
- NOTE: I don't rememer why we put the thread placing calls in MOM_domains.F90
        They look as unnecessary and the whole #ifndef NOT_SET_AFFINITY block
        can probably be removed. ocean_nthreads is either set in coupler
or solo_driver.

…_halo

(*)Corrected halo size in EOS call if VERTEX_SHEAR=T

FMS affinity operations, often used in OpenMP directives, require
explicit CPU affinities such that the number of available CPUs matches
the number of requested PEs.

To accommodate this, we explicit configure OpenMP to use cpu=0 for our
ARM tests.

  Removed old debugging code in blocks of code surrounded by #ifdef statements
and removed unnecessary #ifdef around other blocks of debugging code.  MOM6
standards discourage the use of CPP macros except for a limited set of uses
related to memory where this is unavoidable, so this commit is bringing MOM6
closer to its stated standards.  All answers and output are identical.

  Modified doc_module so that new lines are added only when modules are
documented, and are added in all parameter_doc files in which modules are
documented.  All answers and output are identical, but there are white space
changes in MOM_parameter_doc and SIS_parameter_doc files.

  Added the new optional argument like_default to the log_param and doc_param
routines to help control where the documentation appears.  This new argument is
used for logging EPBL_USTAR_MIN, the diagnosed output value of MAXIMUM_DEPTH
when the input value is negative, and the diagnosed number of columns where
sponges occur with MOM_ALE_sponge.  An '!' was also added to the logging of
EPBL_USTAR_MIN.  All answers are bitwise identical but there are minor changes
in the contents of some MOM_parameter_doc.short files.

…nto add_dens_deriv_diag

Added diagnostics for partial derivatives of density

Removed #ifdef debugging blocks

  Added code to determine whether all parameters in the MOM_grid, MOM_restart,
MOM_write_cputime and MOM_tracer_registry modules are being used with their
default settings, and added all_default arguments to the log_version calls for
these modules.  All answers and output are identical, but there are white space
changes in MOM_parameter_doc.short and SIS_parameter_doc.short files.

Testing: Explicit OpenMP CPU affinity

- Members of a type cannot be individually labelled as shared/private
- One variable was converted to shared since it was defiend in a non-OMP
  section and then labelled as private which meant it was uninitialized.

…A/MOM6 into Hallberg-NOAA-module_doc_newlines

…into dev/gfdl

…hub.com/nikizadehgfdl/MOM6 into nikizadehgfdl-fix_openmp_affinity_issues_with_FMS2020

…into dev/gfdl

- Stanley et al., 2020, adds the Brankart modification to volume mean
  density via linear corrections involving SGS sample variances and
  covariances of T and S. This commit adds the new interfaces that
  allow a call to calculate_density to include the variances and
  covariance as arguments. This correction sits above the particular
  EOS and thus can use any EOS so long as second derivatives are
  available within the EOS module.

- The routines pressure_gradient_plm() and pressure_gradient_ppm()
  were poorly named and had comments referring to the pressure gradient
  calculation even though the only calculate edge values in the vertical
  for T/S using ALE functions. The routines are actually more general
  and can be used outside of the PGF. The comments have been shortened
  and no longer refer to the PGF.

- The integrals of density routines used (mostly) by the PGF calculation
  were part of MOM_EOS. Originally, when writing the analytic FV PGF paper,
  this was the right place to put the integrals. The additional variants
  using the ALE reconstruction functions mean that it is cleaner to have
  these routines sit in a layer above EOS and ALE.

- ppoly_E meant something to someone a while ago but we felt it
  would be better to clean up the ALE APIs. This is a pre-cursor
  to switching to a more precise description of reconstructions.

- Undid nesting of if / select statemnent
- Changed FATAL messages

- Function had been moved to density_integrals already but not
  deleted
- Also ordered public statements in MOM_EOS to help find things.

- Order was frustratingly illogical

- When converting from the two hor_index types to one (HII and HIO
  became HI) I retained the HI%isd:... declaration statements. We
  normally use `SZI_(G)` or `SZI_(HI)` so this switches to that style.

- This adds elemental functions for cellwise operations within the PLM
  construction procedure which allows the operations to be accessed
  from outside of the ALE functions on different array shapes but recover
  bitwise identical results.
- The older subroutines now use the functions and some optimizations were
  obtained in the process.

- Out of curiosity I want to be sure these weren't implicated in the long
  initialization cost.

- Soft index convention was not properly implemented in original PLM
  density integrals. Fixed to avoid confusion.

- Probably makes no difference but we re-computed weights repeatedly
  even though we'd pre-computed them (and used only once).
  - Reduces number of local variables.

- Removes (now) unused functions for quadrature and polynomial evaluation
- Has been tested by setting the logical use_PPM=.false.
  - reproduces PLM mode bitwise

- Use of new PLM functions led to out of date directives

- Now passing in 3D structures and tv so that we can access other fields
  in tv%.
- Corrected calculation of curvatures s6, t6 for interpolated interior
  line integrals.
- Tested with use_PPM=.false. and PLM edge values.
  - Using PLM edge values with use_PPM=.true. does give different answers
    because t6,s6 are non-zero albeit tiny. This is due to FP truncation
    errors.

- Since the majority of code is not about the analytic integration
  I thought it time to rename this module

- Continuation of rename of module

- This routine was suffering from if's inside loops. I've removed this
  one since it was just obfuscation, pretending to care about performance
  and actually reducing it.

- Makes use of the Stanley equation of state to include effects of
  SGS temperature variance, salinity variance and T-S covariance.

- This now calculates the gradient of SGS temperature variance
  using the same discretization as used for the gradient of
  density along coordinate surfaces.
- Added run-time coefficient for Stanley parameterization
- Fixed openmp directives.
- Alters halo over which vert_fill_TS() is called.
- Add Stanley parameter to tc2 to test new code.

- Renamed STANLEY_DET_COEFF to STANLEY_PRM_DET_COEFF to indicate
  this is for the Stanley parameterization as opposed to a related
  approach by Stanley for implementing the Brankart PGF correction.

- PGF_STANLEY_T2_DET_COEFF>=0. now adds the temperature variance
  contribution to the Brankart correction using the Stanley linearization
  of the EOS and parameterization of SGS variance.

- After starting with allocatables and switching to pointers
  I'd forgotten to nullify them.

- Passing the scale= to calculate_density_second_derivs() was the
  double scaling the density contribution from SGS variance in the
  Stanley parameterization.

- select case statements were indented as if once inside a loop.

- The pressure scaling was wrong when trying to call
  calculate_density_second_derivs_array() from within
  calculate_stanley_density_array() because the latter should not do
  any scaling but the former always did. I had to call the lower level
  functions provided by WRIGHT, TEOS10, etc to avoid get the scaling
  tests to pass.

- In preparing to add Brankartc terms to PLM form of presure gradient
  I'm adapting the routine to look like the PPM routine which takes 3D
  arguments but only works on layer "k".

- The Brankart PGF terms are now implemented in the PLM recontruction
  routines, just as they were for the PPM form.

- Added documentation lines for PGF_STANLEY_T2_DET_COEFF

- Per feedback to mom-ocean#1156

- Per feedback on mom-ocean#1156, corrected scaling for calculate_stanley_density_scalar()
  and calculate_stanley_density_1d().

- Per feedback on mom-ocean#1156.

- Per feedback on mom-ocean#1156

  Set a hard-coded maximum value of CS%a_u and CS%a_v of 1e37 m s-1 so that
these can be represented in diagnostics that are written with 32-bit floating
point numbers.  These values are so large that all answers are bitwise identical
in the MOM6-examples test cases, but it is possible that answers could change.

- Per feedback on mom-ocean#1156.

  Eliminated the unused variables CS%uhbt_IC and CS%vhbt_IC from the barotropic
control structure and from the MOM6 restart files.  Also placed a logical test
for CS%Gradual_BT_ICs around all references to CS%ubt_IC and CS%vbt_IC and
eliminated these variables from the restart files when they would not be used.
Additionally some unused arguments were removed from internal subroutines and
some spelling or index case errors were corrected.  All answers are bitwise
identical, but the MOM6 restart files have fewer variables and some unused
entries in the MOM_parameter_doc files have changed.