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Add _FillValue to all active and debug tracer fields #571

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Add _FillValue to all active and debug tracer fields #571

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a111dc3
Replace -1e34 with _FillValue in active tracers
wenshanw May 24, 2020
b279208
Add _FillValue to all appropriate MPAS ocean fields
wenshanw Jun 19, 2020
70d4bee
remove _FillValue attribute from activeTracersTend
wenshanw Aug 26, 2020
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7 changes: 4 additions & 3 deletions src/core_ocean/shared/mpas_ocn_diagnostics.F
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Expand Up @@ -28,6 +28,7 @@ module ocn_diagnostics
use mpas_vector_reconstruction
use mpas_stream_manager
use mpas_io_units
use mpas_io, only : MPAS_REAL_FILLVAL

use ocn_constants
use ocn_config
Expand Down Expand Up @@ -168,7 +169,7 @@ subroutine ocn_diagnostic_solve(dt, statePool, forcingPool, meshPool, diagnostic
! (positive points from vertex1 to vertex2)
! units: s^{-1} m^{-1}
real (kind=RKIND), dimension(:,:), allocatable :: vorticityGradientTangentialComponent


real (kind=RKIND), dimension(:), pointer :: surfaceFluxAttenuationCoefficient
real (kind=RKIND), dimension(:), pointer :: surfaceFluxAttenuationCoefficientRunoff
Expand Down Expand Up @@ -331,8 +332,8 @@ subroutine ocn_diagnostic_solve(dt, statePool, forcingPool, meshPool, diagnostic

normalVelocity(:,nEdges+1) = -1e34
layerThickness(:,nCells+1) = -1e34
activeTracers(indexTemperature,:,nCells+1) = -1e34
activeTracers(indexSalinity,:,nCells+1) = -1e34
activeTracers(indexTemperature,:,nCells+1) = MPAS_REAL_FILLVAL
activeTracers(indexSalinity,:,nCells+1) = MPAS_REAL_FILLVAL

call ocn_relativeVorticity_circulation(relativeVorticity, circulation, meshPool, normalVelocity, err)

Expand Down
7 changes: 4 additions & 3 deletions src/core_ocean/shared/mpas_ocn_init_routines.F
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Expand Up @@ -27,6 +27,7 @@ module ocn_init_routines
use mpas_timer
use mpas_dmpar
use mpas_constants
use mpas_io, only : MPAS_REAL_FILLVAL

use mpas_rbf_interpolation
use mpas_vector_operations
Expand Down Expand Up @@ -539,7 +540,7 @@ subroutine ocn_init_routines_vert_coord(domain)!{{{
do iCell = 1,nCells
if (landIceMask(iCell)==0.and.abs(sum(layerThickness(1:maxLevelCell(iCell),iCell))-bottomDepth(iCell))>20.0_RKIND) then
consistentSSH = .false.
call mpas_log_write(' Warning: Sea surface height is outside of acceptable physical range, i.e. abs(sum(h)-bottomDepth)>20m.', &
call mpas_log_write(' Warning: Sea surface height is outside of acceptable physical range, i.e. abs(sum(h)-bottomDepth)>20m.', &
MPAS_LOG_ERR)
call mpas_log_write(' iCell: $i, maxLevelCell(iCell): $i, bottomDepth(iCell): $r, sum(h): $r', &
intArgs=(/iCell, maxLevelCell(iCell) /), &
Expand All @@ -550,7 +551,7 @@ subroutine ocn_init_routines_vert_coord(domain)!{{{
do iCell = 1,nCells
if (abs(sum(layerThickness(1:maxLevelCell(iCell),iCell))-bottomDepth(iCell))>20.0_RKIND) then
consistentSSH = .false.
call mpas_log_write(' Warning: Sea surface height is outside of acceptable physical range, i.e. abs(sum(h)-bottomDepth)>20m.', &
call mpas_log_write(' Warning: Sea surface height is outside of acceptable physical range, i.e. abs(sum(h)-bottomDepth)>20m.', &
MPAS_LOG_ERR)
call mpas_log_write(' iCell: $i, maxLevelCell(iCell): $i, bottomDepth(iCell): $r, sum(h): $r', &
intArgs=(/iCell, maxLevelCell(iCell) /), &
Expand Down Expand Up @@ -704,7 +705,7 @@ subroutine ocn_init_routines_block(block, dt, err)!{{{
call mpas_pool_get_array(tracersPool, groupItr % memberName, tracersGroup, 1)
if ( associated(tracersGroup) ) then
do iCell=1,nCells
tracersGroup(:, maxLevelCell(iCell)+1:nVertLevels,iCell) = -1.0e34_RKIND
tracersGroup(:, maxLevelCell(iCell)+1:nVertLevels,iCell) = MPAS_REAL_FILLVAL
end do
end if
end if
Expand Down
3 changes: 2 additions & 1 deletion src/core_ocean/shared/mpas_ocn_vmix.F
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Expand Up @@ -25,6 +25,7 @@ module ocn_vmix
use mpas_derived_types
use mpas_pool_routines
use mpas_timer
use mpas_io, only : MPAS_REAL_FILLVAL

use mpas_constants
use ocn_constants
Expand Down Expand Up @@ -986,7 +987,7 @@ subroutine ocn_tracer_vmix_tend_implicit(meshPool, dt, vertDiffTopOfCell, layerT
tracersTemp, N, nVertLevels, num_tracers)

tracers(:,1:N,iCell) = tracersTemp(:,1:N)
tracers(:,N+1:nVertLevels,iCell) = -1e34
tracers(:,N+1:nVertLevels,iCell) = MPAS_REAL_FILLVAL
end do
!$omp end do
!$omp end parallel
Expand Down
6 changes: 3 additions & 3 deletions src/core_ocean/tracer_groups/Registry_activeTracers.xml
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Expand Up @@ -61,7 +61,7 @@

<var_struct name="state" time_levs="2">
<var_struct name="tracers" time_levs="2">
<var_array name="activeTracers" dimensions="nVertLevels nCells Time" type="real" packages="activeTracersPKG" >
<var_array name="activeTracers" dimensions="nVertLevels nCells Time" type="real" packages="activeTracersPKG" missing_value="FILLVAL">
<var name="temperature" array_group="activeGRP" units="degrees Celsius"
description="potential temperature"
/>
Expand Down Expand Up @@ -139,15 +139,15 @@
</var_array>
</var_struct>
<var_struct name="tracersInteriorRestoringFields" time_levs="1">
<var_array name="activeTracersInteriorRestoringRate" type="real" dimensions="nVertLevels nCells Time" packages="activeTracersInteriorRestoringPKG">
<var_array name="activeTracersInteriorRestoringRate" type="real" dimensions="nVertLevels nCells Time" packages="activeTracersInteriorRestoringPKG" missing_value="FILLVAL">
<var name="temperatureInteriorRestoringRate" array_group="activeGRP" units="{s}^-1"
description="A non-negative field controlling the rate at which temperature is restored to temperatureInteriorRestoringValue"
/>
<var name="salinityInteriorRestoringRate" array_group="activeGRP" units="{s}^-1"
description="A non-negative field controlling the rate at which salinity is restored to salinityInteriorRestoringValue"
/>
</var_array>
<var_array name="activeTracersInteriorRestoringValue" type="real" dimensions="nVertLevels nCells Time" packages="activeTracersInteriorRestoringPKG">
<var_array name="activeTracersInteriorRestoringValue" type="real" dimensions="nVertLevels nCells Time" packages="activeTracersInteriorRestoringPKG" missing_value="FILLVAL">
<var name="temperatureInteriorRestoringValue" array_group="activeGRP" units="^\circ C"
description="Temperature is restored toward this field at a rate controlled by temperatureInteriorRestoringRate."
/>
Expand Down
2 changes: 1 addition & 1 deletion src/core_ocean/tracer_groups/Registry_debugTracers.xml
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Expand Up @@ -49,7 +49,7 @@

<var_struct name="state" time_levs="2">
<var_struct name="tracers" time_levs="2">
<var_array name="debugTracers" dimensions="nVertLevels nCells Time" type="real" packages="debugTracersPKG" default_value="1.0">
<var_array name="debugTracers" dimensions="nVertLevels nCells Time" type="real" packages="debugTracersPKG" default_value="1.0" missing_value="FILLVAL">
<var name="tracer1" array_group="debugGRP" units="tracer1"
description="tracer for debugging purposes"
/>
Expand Down