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Minor clean-up namelists to match new versions of mpas components #1862

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Nov 1, 2017
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Merged

Minor clean-up namelists to match new versions of mpas components #1862

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11c58db
Minor clean-up namelists to match new versions of mpas components
jonbob Oct 23, 2017
f498146
changes for MPAS online MOC analysis member
vanroekel Oct 23, 2017
6be60b2
Remove unused variables
mark-petersen Oct 23, 2017
e78ab2d
Correct stream close bracket
mark-petersen Oct 23, 2017
db259b5
Update MPAS-O submodule for bug fix
mark-petersen Oct 24, 2017
8d9b3ab
Update MPAS-O submodule for Sal restore tend output
mark-petersen Oct 24, 2017
30f634e
Corrects MOC streams and adds salinity restoring output variable
vanroekel Oct 25, 2017
354197f
Whitespace cleanup in buildnml
vanroekel Oct 25, 2017
4dc979d
Update MPAS-O to nonlocal KPP and OpenMP fix.
mark-petersen Oct 25, 2017
a360d89
Enables MOC AM for mpas and cleans namelist
vanroekel Oct 25, 2017
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1 change: 0 additions & 1 deletion components/mpas-cice/bld/build-namelist-section
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Original file line number Diff line number Diff line change
Expand Up @@ -384,7 +384,6 @@ add_default($nl, 'config_boundary_layer_iteration_number');
add_default($nl, 'config_use_ocean_mixed_layer');
add_default($nl, 'config_min_friction_velocity');
add_default($nl, 'config_ocean_heat_transfer_type');
add_default($nl, 'config_ocean_surface_type');
add_default($nl, 'config_sea_freezing_temperature_type');
add_default($nl, 'config_ocean_surface_type');

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1 change: 0 additions & 1 deletion components/mpas-cice/bld/namelist_files/namelist_defaults_mpas-cice.xml
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Expand Up @@ -337,7 +337,6 @@
<config_use_ocean_mixed_layer>false</config_use_ocean_mixed_layer>
<config_min_friction_velocity>0.0005</config_min_friction_velocity>
<config_ocean_heat_transfer_type>'constant'</config_ocean_heat_transfer_type>
<config_ocean_surface_type>'free'</config_ocean_surface_type>
<config_sea_freezing_temperature_type>'mushy'</config_sea_freezing_temperature_type>
<config_ocean_surface_type>'free'</config_ocean_surface_type>

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8 changes: 0 additions & 8 deletions components/mpas-cice/bld/namelist_files/namelist_definition_mpas-cice.xml
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Expand Up @@ -2256,14 +2256,6 @@ Valid values: MISSING POSSIBLE VALUES
Default: Defined in namelist_defaults.xml
</entry>

<entry id="config_ocean_surface_type" type="char*1024"
category="ocean" group="ocean">
MISSING DESCRIPTION

Valid values: MISSING POSSIBLE VALUES
Default: Defined in namelist_defaults.xml
</entry>

<entry id="config_sea_freezing_temperature_type" type="char*1024"
category="ocean" group="ocean">
MISSING DESCRIPTION
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2 changes: 2 additions & 0 deletions components/mpas-o/bld/build-namelist
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Expand Up @@ -1328,11 +1328,13 @@ if ($OCN_FORCING eq 'core_forced_restoring') {
add_default($nl, 'config_use_surface_salinity_monthly_restoring', 'val'=>".true.");
add_default($nl, 'config_salinity_restoring_constant_piston_velocity', 'val'=>"1.585e-6");
add_default($nl, 'config_salinity_restoring_max_difference', 'val'=>"100.");
add_default($nl, 'config_salinity_restoring_under_sea_ice', 'val'=>".false.");
} else {
add_default($nl, 'config_use_activeTracers_surface_restoring');
add_default($nl, 'config_use_surface_salinity_monthly_restoring');
add_default($nl, 'config_salinity_restoring_constant_piston_velocity');
add_default($nl, 'config_salinity_restoring_max_difference');
add_default($nl, 'config_salinity_restoring_under_sea_ice');
}
add_default($nl, 'config_use_activeTracers_interior_restoring');
add_default($nl, 'config_use_activeTracers_exponential_decay');
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1 change: 1 addition & 0 deletions components/mpas-o/bld/build-namelist-section
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Expand Up @@ -896,6 +896,7 @@ add_default($nl, 'config_use_activeTracers_ttd_forcing');
add_default($nl, 'config_use_surface_salinity_monthly_restoring');
add_default($nl, 'config_salinity_restoring_constant_piston_velocity');
add_default($nl, 'config_salinity_restoring_max_difference');
add_default($nl, 'config_salinity_restoring_under_sea_ice');

###############################################
# Namelist group: tracer_forcing_debugTracers #
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1 change: 1 addition & 0 deletions components/mpas-o/bld/namelist_files/namelist_defaults_mpas-o.xml
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Expand Up @@ -796,6 +796,7 @@
<config_use_surface_salinity_monthly_restoring>.false.</config_use_surface_salinity_monthly_restoring>
<config_salinity_restoring_constant_piston_velocity>0.0</config_salinity_restoring_constant_piston_velocity>
<config_salinity_restoring_max_difference>0.5</config_salinity_restoring_max_difference>
<config_salinity_restoring_under_sea_ice>.false.</config_salinity_restoring_under_sea_ice>

<!-- tracer_forcing_debugTracers -->
<config_use_debugTracers>.false.</config_use_debugTracers>
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11 changes: 10 additions & 1 deletion components/mpas-o/bld/namelist_files/namelist_definition_mpas-o.xml
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Expand Up @@ -1185,7 +1185,7 @@ Default: Defined in namelist_defaults.xml

<entry id="config_ssh_grad_relax_timescale" type="real"
category="coupling" group="coupling">
Timescale for relaxation of the ssh gradient for coupling. A value of 0.0 removes any relaxation and gives instantaneous response.
Timescale for relaxation of the ssh gradient for coupling. A value of 0.0 (default) removes any relaxation and gives instantaneous response.

Valid values: Any positive real number.
Default: Defined in namelist_defaults.xml
Expand Down Expand Up @@ -1218,6 +1218,7 @@ Valid values: Real Values greater than zero less than bottomDepth
Default: Defined in namelist_defaults.xml
</entry>


<!-- frazil_ice -->

<entry id="config_use_frazil_ice_formation" type="logical"
Expand Down Expand Up @@ -5157,6 +5158,14 @@ Valid values: any non-negative number
Default: Defined in namelist_defaults.xml
</entry>

<entry id="config_salinity_restoring_under_sea_ice" type="logical"
category="tracer_forcing_activeTracers" group="tracer_forcing_activeTracers">
flag to enable salinity restoring under sea ice

Valid values: .true. or .false.
Default: Defined in namelist_defaults.xml
</entry>


<!-- tracer_forcing_debugTracers -->

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63 changes: 58 additions & 5 deletions components/mpas-o/cime_config/buildnml
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Expand Up @@ -48,6 +48,7 @@ my $decomp_prefix = '';
my $ic_date = '';
my $ic_prefix = '';
my $restoring_file = '';
my $moc_mask_file = '';

if ( $OCN_GRID eq 'oEC60to30' ) {
$ic_date .= '151031';
Expand All @@ -65,11 +66,13 @@ if ( $OCN_GRID eq 'oEC60to30' ) {
$decomp_date .= '161222';
$decomp_prefix .= 'mpas-o.graph.info.';
$restoring_file .= 'sss.monthlyClimatology.PHC2_salx_040803.oEC60to30v3.nc';
$moc_mask_file .= 'oEC60to30v3_Atlantic_region_and_southern_transect.nc';
} elsif ( $OCN_GRID eq 'oEC60to30v3_ICG' ) {
$ic_date .= '170905';
$ic_prefix .= 'oEC60to30v3_60layer.restartFrom_anvil0824';
$decomp_date .= '161222';
$decomp_prefix .= 'mpas-o.graph.info.';
$moc_mask_file .= 'oEC60to30v3_Atlantic_region_and_southern_transect.nc';
} elsif ( $OCN_GRID eq 'oEC60to30wLI' ) {
$ic_date .= '160830';
$ic_prefix .= 'oEC60to30wLI';
Expand Down Expand Up @@ -127,11 +130,13 @@ if ( $OCN_GRID eq 'oEC60to30' ) {
$decomp_date .= '170111';
$decomp_prefix .= 'mpas-o.graph.info.';
$restoring_file .= 'sss.monthlyClimatology.PHC2_salx_040803.oRRS18to6v3.nc';
$moc_mask_file .= 'oRRS18to6v3.170111.SingleRegionAtlanticWTransportTransects_masks.nc';
} elsif ( $OCN_GRID eq 'oRRS18to6v3_ICG' ) {
$ic_date .= '170622';
$ic_prefix .= 'oRRS18to6v3.restartFrom_titan0228';
$decomp_date .= '170111';
$decomp_prefix .= 'mpas-o.graph.info.';
$moc_mask_file .= 'oRRS18to6v3.170111.SingleRegionAtlanticWTransportTransects_masks.nc';
} elsif ( $OCN_GRID eq 'oRRS15to5' ) {
$ic_date .= '151209';
$ic_prefix .= 'ocean.RRS.15-5km';
Expand Down Expand Up @@ -160,6 +165,9 @@ if ($OCN_FORCING eq 'core_forced') {
open(my $input_list, "+>", "$CASEBUILD/mpas-o.input_data_list");
print $input_list "mesh = $DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$ic_prefix.$ic_date.nc\n";
print $input_list "ic = $DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$ic_prefix.$ic_date.nc\n";
if ($moc_mask_file ne '') {
print $input_list "moc = $DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$moc_mask_file\n";
}
if ( $OCN_FORCING eq 'core_forced_restoring' ) {
print $input_list "sss = $DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$restoring_file\n";
}
Expand Down Expand Up @@ -413,7 +421,7 @@ if ( -e "$CASEROOT/SourceMods/src.mpaso/$STREAM_NAME" ) {
print $stream_file 'the analysis data.' . "\n";
print $stream_file '-->' . "\n";
print $stream_file '' . "\n";
if ($OCN_FORCING eq 'core_forced_restoring') {
if ($OCN_FORCING eq 'core_forced_restoring') {
print $stream_file '<stream name="surface_salinity_monthly_data"' . "\n";
print $stream_file ' type="input"' . "\n";
print $stream_file " filename_template=" . '"'
Expand All @@ -426,7 +434,44 @@ if ( -e "$CASEROOT/SourceMods/src.mpaso/$STREAM_NAME" ) {
print $stream_file ' <var name="surfaceSalinityMonthlyClimatologyValue"/>' . "\n";
print $stream_file '</stream>' . "\n";
print $stream_file '' . "\n";
}
}
print $stream_file '<stream name="transects"' . "\n";
print $stream_file ' type="input"' . "\n";
print $stream_file " filename_template=" . '"'
. "$DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$moc_mask_file"
. '"' . "\n";
print $stream_file ' input_interval="initial_only"' . "\n";
print $stream_file ' packages="mocStreamfunctionAMPKG"/>' . "\n";
print $stream_file '' . "\n";
print $stream_file '<stream name="regionalMasksInput"' . "\n";
print $stream_file ' type="input"' . "\n";
print $stream_file " filename_template=" . '"'
. "$DIN_LOC_ROOT/ocn/mpas-o/$OCN_MASK/$moc_mask_file"
. '"' . "\n";
print $stream_file ' input_interval="initial_only"' . "\n";
print $stream_file ' packages="mocStreamfunctionAMPKG"/>' . "\n";
print $stream_file '' . "\n";
print $stream_file '<stream name="mocStreamfunctionOutput"' . "\n";
print $stream_file ' type="output"' . "\n";
print $stream_file ' filename_template="mpaso.hist.am.mocStreamfunctionOutput.$Y-$M-$D.nc"'. "\n";
print $stream_file ' filename_interval="01-00-00_00:00:00"' . "\n";
print $stream_file ' clobber_mode="truncate"' . "\n";
print $stream_file ' reference_time="01-01-01_00:00:00"' . "\n";
print $stream_file ' output_interval="00-01-00_00:00:00"' . "\n";
print $stream_file ' packages="mocStreamfunctionAMPKG">' . "\n";
print $stream_file '' . "\n";
print $stream_file ' <var name="xtime"/>' . "\n";
print $stream_file ' <var name="mocStreamvalLatAndDepth"/>' . "\n";
print $stream_file ' <var name="mocStreamvalLatAndDepthRegion"/>' . "\n";
print $stream_file ' <var name="binBoundaryMocStreamfunction"/>' . "\n";
print $stream_file ' <var name="refBottomDepth"/>' . "\n";
print $stream_file ' <var name="regionGroupNames"/>' . "\n";
print $stream_file ' <var name="minMaxLatRegion"/>' . "\n";
print $stream_file ' <var name="regionNames"/>' . "\n";
print $stream_file ' <var name="nRegionsInGroup"/>' . "\n";
print $stream_file ' <var name="regionsInGroup"/>' . "\n";
print $stream_file '</stream>' . "\n";
print $stream_file '' . "\n";
print $stream_file '<stream name="globalStatsOutput"' . "\n";
print $stream_file ' type="output"' . "\n";
print $stream_file ' io_type="netcdf"' . "\n";
Expand Down Expand Up @@ -552,7 +597,7 @@ if ( -e "$CASEROOT/SourceMods/src.mpaso/$STREAM_NAME" ) {
print $stream_file ' filename_template="mpaso.hist.am.highFrequencyOutput.$Y-$M-$D_$h.$m.$s.nc"' . "\n";
print $stream_file ' filename_interval="00-01-00_00:00:00"' . "\n";
print $stream_file ' reference_time="01-01-01_00:00:00"' . "\n";
print $stream_file ' output_interval="00-00-05_00:00:00"' . "\n";
print $stream_file ' output_interval="00-00-01_00:00:00"' . "\n";
print $stream_file ' clobber_mode="truncate"' . "\n";
print $stream_file ' packages="highFrequencyOutputAMPKG">' . "\n";
print $stream_file '' . "\n";
Expand Down Expand Up @@ -663,8 +708,10 @@ if ( -e "$CASEROOT/SourceMods/src.mpaso/$STREAM_NAME" ) {
print $stream_file ' <var name="vertVelocityTop"/>' . "\n";
print $stream_file ' <var name="normalTransportVelocity"/>' . "\n";
print $stream_file ' <var name="vertTransportVelocityTop"/>' . "\n";
print $stream_file ' <var name="normalGMBolusVelocity"/>' . "\n";
print $stream_file ' <var name="vertGMBolusVelocityTop"/>' . "\n";
if ( $OCN_GRID !~ m/^oRRS1/ ) {
print $stream_file ' <var name="normalGMBolusVelocity"/>' . "\n";
print $stream_file ' <var name="vertGMBolusVelocityTop"/>' . "\n";
}
print $stream_file ' <var_struct name="tracersSurfaceFlux"/>' . "\n";
print $stream_file ' <var name="penetrativeTemperatureFlux"/>' . "\n";
print $stream_file ' <var name="latentHeatFlux"/>' . "\n";
Expand All @@ -681,6 +728,9 @@ if ( -e "$CASEROOT/SourceMods/src.mpaso/$STREAM_NAME" ) {
print $stream_file ' <var name="rainFlux"/>' . "\n";
print $stream_file ' <var name="snowFlux"/>' . "\n";
print $stream_file ' <var name="vertNonLocalFlux"/>' . "\n";
print $stream_file ' <var_array name="activeTracerHorizontalAdvectionTendency"/>' . "\n";
print $stream_file ' <var_array name="activeTracerVerticalAdvectionTendency"/>' . "\n";
print $stream_file ' <var_array name="activeTracerVertMixTendency"/>' . "\n";
print $stream_file ' <var_array name="activeTracerSurfaceFluxTendency"/>' . "\n";
print $stream_file ' <var_array name="temperatureShortWaveTendency"/>' . "\n";
print $stream_file ' <var_array name="activeTracerNonLocalTendency"/>' . "\n";
Expand All @@ -705,6 +755,9 @@ if ( -e "$CASEROOT/SourceMods/src.mpaso/$STREAM_NAME" ) {
print $stream_file ' <var name="landIceFreshwaterFlux"/>' . "\n";
print $stream_file ' <var name="landIceHeatFlux"/>' . "\n";
print $stream_file ' <var name="heatFluxToLandIce"/>' . "\n";
print $stream_file ' <var name="mocStreamvalLatAndDepth"/>' . "\n";
print $stream_file ' <var name="mocStreamvalLatAndDepthRegion"/>' . "\n";
print $stream_file ' <var name="binBoundaryMocStreamfunction"/>' . "\n";
if ( $OCN_BGC eq 'eco_only' || $OCN_BGC eq 'eco_and_dms' || $OCN_BGC eq 'eco_and_macromolecules' || $OCN_BGC eq 'eco_and_dms_and_macromolecules') {
print $stream_file ' <var_struct name="ecosysDiagFieldsLevel1"/>' . "\n";
print $stream_file ' <var_struct name="ecosysAuxiliary"/>' . "\n";
Expand Down
9 changes: 0 additions & 9 deletions components/mpas-o/driver/ocn_comp_mct.F
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Expand Up @@ -79,18 +79,9 @@ module ocn_comp_mct
!
! !PRIVATE MODULE VARIABLES

logical :: ldiag_cpl = .false.

integer, private :: &
cpl_write_restart, &! flag id for write restart
cpl_write_history, &! flag id for write history
cpl_write_tavg, &! flag id for write tavg
cpl_diag_global, &! flag id for computing diagnostics
cpl_diag_transp, &! flag id for computing diagnostics
my_task

real (kind=RKIND) :: tlast_coupled

integer :: nsend, nrecv

character(len=StrKIND) :: runtype, coupleTimeStamp
Expand Down
2 changes: 1 addition & 1 deletion components/mpas-o/model
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Submodule model updated from 169557 to 738a74
9 changes: 0 additions & 9 deletions components/mpasli/driver/glc_comp_mct.F
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Expand Up @@ -67,17 +67,8 @@ module glc_comp_mct

! !PRIVATE MODULE VARIABLES

logical :: ldiag_cpl = .false.

integer, private :: my_task

integer, private :: &
cpl_write_restart, &! flag id for write restart
cpl_write_history, &! flag id for write history
cpl_write_tavg, &! flag id for write tavg
cpl_diag_global, &! flag id for computing diagnostics
cpl_diag_transp ! flag id for computing diagnostics

integer :: nsend, nrecv

character(len=StrKIND) :: runtype !< ACME run type: initial, continue, branch
Expand Down