MPAS refactor notes

[hkershaw-brown]

Unresolved issues:

Surface elevation check
! Reject obs if the station height is far way from the model terrain.

but fwd operators (rttov) need these surface values
see discussion #332

Code:

branch (be aware I may force push to this)
https://github.com/NCAR/DART/tree/mpas-refactor

Spec (note 7 v 8)
https://docs.google.com/document/d/1wD4MKM5PquOUbxK3YxIjcbIaFThJfa318heDn_bFUbs/edit

[hkershaw-brown]

In compute_u_with_rbf there is a loop around ens_size, for get_reconstruct but uval(1:ens_size) is set to set to the single value ureconstructzonal/ureconstructmeridional so you are getting the whole ensemble set each step of the loop

whole ensemble == last value from the loop.

DART/models/mpas_atm/model_mod.f90

Lines 6214 to 6226 in e218864

	do e = 1, ens_size
	call get_reconstruct(nedges, lat*deg2rad, lon*deg2rad, &
	coeffs_reconstruct, on_a_sphere, veldata(:, e), &
	ureconstructx, ureconstructy, ureconstructz, &
	ureconstructzonal, ureconstructmeridional)
	if (zonal) then
	uval = ureconstructzonal
	else
	uval = ureconstructmeridional
	endif
	enddo

[hkershaw-brown]

todo can be different across the ensemble

DART/models/mpas_atm/model_mod.f90

Lines 6183 to 6192 in e218864

	!>@todo lower (upper) could be different levels in pressure
	!lowval = x(index1 + (edgelist(i)-1) * nvert + lower(i)-1)
	lowindx = int(index1,i8) + int((edgelist(i)-1) * nvert,i8) + int(lower(i,1)-1,i8)
	lowval = get_state(lowindx, state_handle)
	!uppval = x(index1 + (edgelist(i)-1) * nvert + upper(i)-1)
	upindx = int(index1,i8) + int((edgelist(i)-1) * nvert,i8) + int(upper(i,1)-1,i8)
	uppval = get_state(upindx, state_handle)
	veldata(i, :) = lowval*(1.0_r8 - fract(i, :)) + uppval*fract(i, :)

[hkershaw-brown]

on_bound? not used

DART/models/mpas_atm/model_mod.f90

Line 4871 in e218864

logical :: at_surf, do_norm, on_bound

DART/models/mpas_atm/model_mod.f90

Lines 4930 to 4938 in e218864

	! if the entire ensemble has missing vertical values we can return now.
	! otherwise we need to continue to convert the members with good vertical values.
	! boundary cells will be updated by the assimilation.
	! if all the vertical localization coord values are missing,
	! we don't call this routine again, and return.
	if (all(zin == missing_r8)) then ! .or. on_bound) then
	istatus(:) = 0
	return
	endif

[hkershaw-brown]

find_vert_indices is a wrap around find_vert_level. Remove

DART/models/mpas_atm/model_mod.f90

Line 6030 in e218864

subroutine find_vert_indices (state_handle, ens_size, loc, nc, c, lower, upper, fract, ier)

[hkershaw-brown]

convert_vert_distrib_state (state)
convert_vert_distrib (obs)

super repetitive & according to this comment state is calling the interpolation anyway:

DART/models/mpas_atm/model_mod.f90

Lines 4968 to 4972 in e218864

	!>@todo FIXME - this is the original code from the
	!> observation version which does horizontal interpolation.
	!> in this code we know we are on a state vector location
	!> so no interp is needed. we should be able to make this
	!> more computationally efficient.

[hkershaw-brown]

If rbf is depricated 11 years ago, possibly it is time to remove the code?

DART/models/mpas_atm/model_mod.f90

Line 119 in e218864

! RBF (radial basis function) modules, donated by LANL. currently deprecated

note see comment on incorrect rbf calulcaiton.

[hkershaw-brown]

Shells scripts are out of date, user complaints about cycling. Lots of csh (poor).

Documentation is poor, also points people to this MPAS page which sends people to non-existent documentation (https://svn-dares-dart.cgd.ucar.edu/)

[hkershaw-brown]

Nope:

DART/models/mpas_atm/model_mod.f90

Line 188 in e218864

! try adjusting what static_init_model does, before it is called.

DART/models/mpas_atm/model_mod.f90

Line 285 in e218864

! if set by: call force_u_into_state() *BEFORE* calling static_init_model(),

DART/models/mpas_atm/model_mod.f90

Lines 551 to 552 in e218864

	subroutine static_init_model()
	!>@todo FIXME - can we add an optional arg here for update_bc use?

Note, beware of whatever the regional stuff is doing. Seems like some bizarre choices here.

DART/models/mpas_atm/model_mod.f90

Lines 2097 to 2098 in e218864

	! modify what static_init_model does. this *must* be called before
	! calling static_init_model().

more nope:

DART/models/mpas_atm/update_bc.f90

Lines 100 to 102 in e218864

	! Note that force_u_into_state should be called before static_init_model, which is unusual.
	call force_u_into_state()
	call set_lbc_variables(bdy_template_filename)

[hkershaw-brown]

update_bc.f90 is calling use direct_netcdf_mod,only : read_variables directly. 🙃

[hkershaw-brown]

why is this compile time, rather than runtime:

DART/models/mpas_atm/model_mod.f90

Lines 238 to 243 in e218864

	! compile-time control over whether grid information is written to the
	! diagnostic files or not. if it is, the files are self-contained (e.g. for
	! ease of plotting), but are also much larger than they would be otherwise.
	! change this private variable to control whether the grid information is
	! written or not.
	logical :: add_static_data_to_diags = .false.

[hkershaw-brown]

why is this compile time, rather than runtime:

DART/models/mpas_atm/model_mod.f90

Lines 238 to 243 in e218864

	! compile-time control over whether grid information is written to the
	! diagnostic files or not. if it is, the files are self-contained (e.g. for
	! ease of plotting), but are also much larger than they would be otherwise.
	! change this private variable to control whether the grid information is
	! written or not.
	logical :: add_static_data_to_diags = .false.

oh add_static_data_to_diags is not used and there is also a compile time (namelist) option write_grid_to_diag_file

[hkershaw-brown]

! FIXME: it may be desirable to read in xCell(:), yCell(:), zCell(:)
! to keep from having to compute them on demand, especially since we
! have converted the radian lat/lon of the cell centers into degrees.
! we have to convert back, then take a few sin and cos to get xyz.
! time/space/accuracy tradeoff here.

https://github.com/NCAR/DART/blame/e2188646b97573f198c66f7ea63482ebc34afa11/models/mpas_atm/model_mod.f90#L416