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Merged
gold2718 merged 4 commits into from
Jan 10, 2021
Merged

cam6_3_008: Fixes for PIO2 plus nudging I/O update #310

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f2ce7b4
Fix zonal mean map for PIO2 output
Dec 19, 2020
8429ad5
PIO2 mods incorporating changes from PR 247
Jan 3, 2021
a7c9031
Import nudging.F90 from patcal's PR #241
Jan 7, 2021
508ace0
Initialized output variable (from review comments) and update ChangeLog
Jan 10, 2021
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81 changes: 80 additions & 1 deletion doc/ChangeLog
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Original file line number Diff line number Diff line change
@@ -1,5 +1,84 @@
===============================================================

Tag name: cam6_3_008
Originator(s): patcal, jedwards, goldy
Date: 2020-01-10
One-line Summary: Fixes for PIO2 plus nudging I/O update
Github PR URL: https://github.com/ESCOMP/CAM/pull/310

Purpose of changes (include the issue number and title text for each
relevant GitHub issue):
#237: Replace deprecated physics grid interfaces in nudging input
#248: scam tests don't work with pio2
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@nusbaume nusbaume Jan 8, 2021

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It looks like there are no keywords in the main PR message for Issue #263. I assume there should be?

Also, Issue #237 isn't listed here.

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@gold2718 gold2718 Jan 8, 2021

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On the #263 issue, that issue was not important for PIO1 usage and has been properly addressed as part of the PIO2 fixes. I added a line in the PR description.

Thanks for noticing the missing #237 line.

#263: attempt to initialize variable prior to calling intent(out) subroutine
#282: ambiguous dof when writing FV zonal mean values

Describe any changes made to build system: NA

Describe any changes made to the namelist: NA

List any changes to the defaults for the boundary datasets: NA

Describe any substantial timing or memory changes: NA

Code reviewed by: cacraig, fvitt, goldy, nusbaume

List all files eliminated: NA

List all files added and what they do: NA

List all existing files that have been modified, and describe the changes:

doc/ChangeLog
- This is what has become of my aspiring rap career
src/chemistry/mozart/mo_drydep.F90
- Pass file_desc_t instead of file handle
src/control/cam_history.F90
- Add fill value info required by PIO2
- Explicitly handle conversion to 4-byte reals (req. by PIO2)
src/control/cam_restart.F90
- Call cam_pio_set_fill for the restart file
src/control/ncdio_atm.F90
- Return the fill value as an optional output
- Pass file_desc_t instead of file handle
src/dynamics/fv/dyn_grid.F90
- Make sure that zonal mean grid has no duplicate points
src/dynamics/se/dyn_comp.F90
- Detect fillvalue in input fields for reset to zero
src/physics/cam/nudging.F90
- Use infld instead of raw NetCDF for data input
- Code cleanup
src/utils/cam_pio_utils.F90
- Added interfaces for cam_pio_inq_var_fill and cam_pio_set_fill
These interfaces encapsulate PIO1 / PIO2 fill functionality

If there were any failures reported from running test_driver.sh on any test
platform, and checkin with these failures has been OK'd by the gatekeeper,
then copy the lines from the td.*.status files for the failed tests to the
appropriate machine below. All failed tests must be justified.

cheyenne/intel/aux_cam:

FAIL ERP_Ln9.ne30_ne30_mg17.FCnudged.cheyenne_intel.cam-outfrq9s BASELINE /glade/p/cesm/amwg/cesm_baselines/cam6_3_007: ERROR BFAIL some baseline files were missing
- This is an expected fail because this test failed to run in cam6_3_007
(fix is part of this PR). The baseline was verified by running this test
standalone with a compare to cam6_3_006.

izumi/nag/aux_cam:

FAIL DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae COMPARE_base_da
- Known (pre-existing) failure

izumi/pgi/aux_cam: ALL PASS

CAM tag used for the baseline comparison tests if different than previous
tag: NA

Summarize any changes to answers): BFB

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

Tag name: cam6_3_007
Originator(s): goldy
Date: 2020-12-06
Expand Down Expand Up @@ -208,7 +287,7 @@ This error should be fixed with PR #241

izumi/nag/aux_cam:
FAIL DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae COMPARE_base_da
Known (pre-existing) failure
- Known (pre-existing) failure
FAIL DAE.f45_f45_mg37.FHS94.izumi_nag.cam-dae NLCOMP
FAIL ERC_D_Ln9.f10_f10_mg37.FHS94.izumi_nag.cam-idphys NLCOMP
FAIL ERC_D_Ln9.f10_f10_mg37.QPC5.izumi_nag.cam-outfrq3s_carma NLCOMP
Expand Down
80 changes: 40 additions & 40 deletions src/chemistry/mozart/mo_drydep.F90
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
module mo_drydep

!---------------------------------------------------------------------
! ... Dry deposition
! ... Dry deposition
!---------------------------------------------------------------------

use shr_kind_mod, only : r8 => shr_kind_r8, shr_kind_cl
Expand Down Expand Up @@ -80,7 +80,7 @@ module mo_drydep
integer, parameter :: n_land_type = 11

integer, allocatable :: spc_ndx(:) ! nddvels
real(r8), public :: crb
real(r8), public :: crb

type lnd_dvel_type
real(r8), pointer :: dvel(:,:) ! deposition velocity over land (cm/s)
Expand All @@ -93,7 +93,7 @@ module mo_drydep

!---------------------------------------------------------------------------
!---------------------------------------------------------------------------
subroutine dvel_inti_fromlnd
subroutine dvel_inti_fromlnd
use mo_chem_utls, only : get_spc_ndx
use cam_abortutils, only : endrun

Expand All @@ -120,10 +120,10 @@ subroutine dvel_inti_fromlnd
!-------------------------------------------------------------------------------------
subroutine drydep_update( state, cam_in )
use physics_types, only : physics_state
use camsrfexch, only : cam_in_t
use camsrfexch, only : cam_in_t

type(physics_state), intent(in) :: state ! Physics state variables
type(cam_in_t), intent(in) :: cam_in
type(cam_in_t), intent(in) :: cam_in

if (nddvels<1) return

Expand All @@ -137,15 +137,15 @@ subroutine drydep_fromlnd( ocnfrac, icefrac, sfc_temp, pressure_sfc, &
wind_speed, spec_hum, air_temp, pressure_10m, rain, &
snow, solar_flux, dvelocity, dflx, mmr, &
tv, ncol, lchnk )

!-------------------------------------------------------------------------------------
! combines the deposition velocities provided by the land model with deposition
! velocities over ocean and sea ice
! combines the deposition velocities provided by the land model with deposition
! velocities over ocean and sea ice
!-------------------------------------------------------------------------------------

use ppgrid, only : pcols
use chem_mods, only : gas_pcnst

#if (defined OFFLINE_DYN)
use metdata, only: get_met_fields
#endif
Expand All @@ -154,8 +154,8 @@ subroutine drydep_fromlnd( ocnfrac, icefrac, sfc_temp, pressure_sfc, &
! ... dummy arguments
!-------------------------------------------------------------------------------------

real(r8), intent(in) :: icefrac(pcols)
real(r8), intent(in) :: ocnfrac(pcols)
real(r8), intent(in) :: icefrac(pcols)
real(r8), intent(in) :: ocnfrac(pcols)
integer, intent(in) :: ncol
integer, intent(in) :: lchnk ! chunk number
real(r8), intent(in) :: sfc_temp(pcols) ! surface temperature (K)
Expand All @@ -164,7 +164,7 @@ subroutine drydep_fromlnd( ocnfrac, icefrac, sfc_temp, pressure_sfc, &
real(r8), intent(in) :: spec_hum(pcols) ! specific humidity (kg/kg)
real(r8), intent(in) :: air_temp(pcols) ! surface air temperature (K)
real(r8), intent(in) :: pressure_10m(pcols) ! 10 meter pressure (Pa)
real(r8), intent(in) :: rain(pcols)
real(r8), intent(in) :: rain(pcols)
real(r8), intent(in) :: snow(pcols) ! snow height (m)
real(r8), intent(in) :: solar_flux(pcols) ! direct shortwave radiation at surface (W/m^2)
real(r8), intent(in) :: tv(pcols) ! potential temperature
Expand All @@ -180,17 +180,17 @@ subroutine drydep_fromlnd( ocnfrac, icefrac, sfc_temp, pressure_sfc, &

real(r8), dimension(ncol) :: term ! work array
integer :: ispec
real(r8) :: lndfrac(pcols)
real(r8) :: lndfrac(pcols)
#if (defined OFFLINE_DYN)
real(r8) :: met_ocnfrac(pcols)
real(r8) :: met_icefrac(pcols)
real(r8) :: met_icefrac(pcols)
#endif
integer :: i

lndfrac(:ncol) = 1._r8 - ocnfrac(:ncol) - icefrac(:ncol)

where( lndfrac(:ncol) < 0._r8 )
lndfrac(:ncol) = 0._r8
where( lndfrac(:ncol) < 0._r8 )
lndfrac(:ncol) = 0._r8
endwhere

#if (defined OFFLINE_DYN)
Expand All @@ -201,7 +201,7 @@ subroutine drydep_fromlnd( ocnfrac, icefrac, sfc_temp, pressure_sfc, &
! ... initialize
!-------------------------------------------------------------------------------------
dvelocity(:,:) = 0._r8

!-------------------------------------------------------------------------------------
! ... compute the dep velocities over ocean and sea ice
! land type 7 is used for ocean
Expand All @@ -226,7 +226,7 @@ subroutine drydep_fromlnd( ocnfrac, icefrac, sfc_temp, pressure_sfc, &
dvelocity(:ncol,spc_ndx(ispec)) = lnd(lchnk)%dvel(:ncol,ispec)*lndfrac(:ncol) &
+ ocnice_dvel(:ncol,spc_ndx(ispec))
enddo

!-------------------------------------------------------------------------------------
! ... special adjustments
!-------------------------------------------------------------------------------------
Expand All @@ -249,10 +249,10 @@ subroutine drydep_fromlnd( ocnfrac, icefrac, sfc_temp, pressure_sfc, &
dvelocity(:ncol,hcooh_ndx) = dvelocity(:ncol,ch3cooh_ndx)
end if
end if

!-------------------------------------------------------------------------------------
! ... assign CO tags to CO
! put this kludge in for now ...
! put this kludge in for now ...
! -- should be able to set all these via the table mapping in seq_drydep_mod
!-------------------------------------------------------------------------------------
if( cohc_ndx>0 .and. co_ndx>0 ) then
Expand Down Expand Up @@ -533,11 +533,11 @@ subroutine get_landuse_and_soilw_from_file()
use ncdio_atm, only : infld

logical :: readvar

type(file_desc_t) :: piofile
character(len=shr_kind_cl) :: locfn
logical :: lexist

call getfil (drydep_srf_file, locfn, 1, lexist)
if(lexist) then
call cam_pio_openfile(piofile, locfn, PIO_NOWRITE)
Expand Down Expand Up @@ -630,10 +630,10 @@ subroutine interp_map( plon, plat, nlon_veg, nlat_veg, npft_veg, lat_veg, lat_ve
if (single_column) then
if (scm_cambfb_mode) then
piofile => initial_file_get_id()
call shr_scam_getCloseLatLon(piofile%fh,scmlat,scmlon,closelat,closelon,latidx,lonidx)
call shr_scam_getCloseLatLon(piofile,scmlat,scmlon,closelat,closelon,latidx,lonidx)
ploniop=size(loniop)
platiop=size(latiop)
else
else
latidx=1
lonidx=1
ploniop=1
Expand Down Expand Up @@ -697,7 +697,7 @@ subroutine interp_map( plon, plat, nlon_veg, nlat_veg, npft_veg, lat_veg, lat_ve
write(iulog,*) 'interp_map : mapping_ext ',mapping_ext
#endif
do j = 1,plon+1
lon1 = lon_edge(j)
lon1 = lon_edge(j)
do i = -veg_ext,nlon_veg+veg_ext
dx = lon_veg_edge_ext(i ) - lon1
dy = lon_veg_edge_ext(i+1) - lon1
Expand Down Expand Up @@ -729,17 +729,17 @@ subroutine interp_map( plon, plat, nlon_veg, nlat_veg, npft_veg, lat_veg, lat_ve
fraction = 0._r8
do jj = ind_lat(j),ind_lat(j+1)
y1 = max( lat_edge(j),lat_veg_edge(jj) )
y2 = min( lat_edge(j+1),lat_veg_edge(jj+1) )
y2 = min( lat_edge(j+1),lat_veg_edge(jj+1) )
dy = (y2 - y1)/(lat_veg_edge(jj+1) - lat_veg_edge(jj))
do ii =ind_lon(i),ind_lon(i+1)
i_ndx = mapping_ext(ii)
x1 = max( lon_edge(i),lon_veg_edge_ext(ii) )
x2 = min( lon_edge(i+1),lon_veg_edge_ext(ii+1) )
x2 = min( lon_edge(i+1),lon_veg_edge_ext(ii+1) )
dx = (x2 - x1)/(lon_veg_edge_ext(ii+1) - lon_veg_edge_ext(ii))
area = dx * dy
total_area = total_area + area
!-----------------------------------------------------------------
! ... special case for ocean grid point
! ... special case for ocean grid point
!-----------------------------------------------------------------
if( nint(landmask(i_ndx,jj)) == 0 ) then
fraction(npft_veg+1) = fraction(npft_veg+1) + area
Expand Down Expand Up @@ -790,7 +790,7 @@ subroutine interp_map( plon, plat, nlon_veg, nlat_veg, npft_veg, lat_veg, lat_ve
tmp_frac_lu(i,11, j) = sum(fraction(10:12))
end do lon_loop
end do lat_loop

do lchnk = begchunk, endchunk
ncol = get_ncols_p(lchnk)
call get_rlat_all_p(lchnk, ncol, rlats(:ncol))
Expand Down Expand Up @@ -819,7 +819,7 @@ subroutine interp_map( plon, plat, nlon_veg, nlat_veg, npft_veg, lat_veg, lat_ve
end do

end subroutine interp_map

!-------------------------------------------------------------------------------------
!-------------------------------------------------------------------------------------
subroutine drydep_xactive( sfc_temp, pressure_sfc, &
Expand Down Expand Up @@ -860,7 +860,7 @@ subroutine drydep_xactive( sfc_temp, pressure_sfc, &
real(r8), intent(in) :: spec_hum(pcols) ! specific humidity (kg/kg)
real(r8), intent(in) :: air_temp(pcols) ! surface air temperature (K)
real(r8), intent(in) :: pressure_10m(pcols) ! 10 meter pressure (Pa)
real(r8), intent(in) :: rain(pcols)
real(r8), intent(in) :: rain(pcols)
real(r8), intent(in) :: snow(pcols) ! snow height (m)

real(r8), intent(in) :: solar_flux(pcols) ! direct shortwave radiation at surface (W/m^2)
Expand All @@ -874,8 +874,8 @@ subroutine drydep_xactive( sfc_temp, pressure_sfc, &
integer, intent(in), optional :: beglandtype
integer, intent(in), optional :: endlandtype

real(r8), intent(in), optional :: ocnfrc(pcols)
real(r8), intent(in), optional :: icefrc(pcols)
real(r8), intent(in), optional :: ocnfrc(pcols)
real(r8), intent(in), optional :: icefrc(pcols)

!-------------------------------------------------------------------------------------
! ... local variables
Expand Down Expand Up @@ -952,7 +952,7 @@ subroutine drydep_xactive( sfc_temp, pressure_sfc, &
logical :: fr_lnduse(ncol,n_land_type) ! wrking array
real(r8) :: dewm ! multiplier for rs when dew occurs

real(r8) :: lcl_frc_landuse(ncol,n_land_type)
real(r8) :: lcl_frc_landuse(ncol,n_land_type)

integer :: beglt, endlt

Expand All @@ -966,16 +966,16 @@ subroutine drydep_xactive( sfc_temp, pressure_sfc, &
0.005_r8, 0.000_r8, 0.000_r8, 0.000_r8, 0.075_r8, 0.002_r8 /)

if (present( beglandtype)) then
beglt = beglandtype
beglt = beglandtype
else
beglt = 1
endif
if (present( endlandtype)) then
endlt = endlandtype
endlt = endlandtype
else
endlt = n_land_type
endif

!-------------------------------------------------------------------------------------
! initialize
!-------------------------------------------------------------------------------------
Expand All @@ -1001,7 +1001,7 @@ subroutine drydep_xactive( sfc_temp, pressure_sfc, &
!-------------------------------------------------------------------------------------
! season index only for ocn and sea ice
!-------------------------------------------------------------------------------------
index_season = 4
index_season = 4
!-------------------------------------------------------------------------------------
! special case for snow covered terrain
!-------------------------------------------------------------------------------------
Expand Down Expand Up @@ -1141,7 +1141,7 @@ subroutine drydep_xactive( sfc_temp, pressure_sfc, &
!-------------------------------------------------------------------------------------
! revise calculation of friction velocity and z0 over water
!-------------------------------------------------------------------------------------
lt = 7
lt = 7
do i = 1,ncol
if( fr_lnduse(i,lt) ) then
if( unstable(i) ) then
Expand Down Expand Up @@ -1386,7 +1386,7 @@ subroutine drydep_xactive( sfc_temp, pressure_sfc, &
if( lt == 7 ) then
where( fr_lnduse(:ncol,lt) )
! assume no surface resistance for SO2 over water`
wrk(:) = wrk(:) + lnd_frc(:)/(dep_ra(:ncol,lt,lchnk) + dep_rb(:ncol,lt,lchnk))
wrk(:) = wrk(:) + lnd_frc(:)/(dep_ra(:ncol,lt,lchnk) + dep_rb(:ncol,lt,lchnk))
endwhere
else
where( fr_lnduse(:ncol,lt) )
Expand Down
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