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added nonhydrostatic capabilities to MPAS-O #21

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88fb291
added nonhydro to v2
scalandr Feb 8, 2022
4c0eeaa
internal wave and overflow run fine
scalandr Feb 9, 2022
28d6588
added seven modules for turbulence
scalandr Feb 14, 2022
e84e755
modified files in shared folder for les turbulence
scalandr Feb 15, 2022
91dff6b
added les turbulence changes in the time-stepping schemes, the code r…
scalandr Feb 16, 2022
dba0784
correction for RK4
scalandr Feb 17, 2022
7355644
removed a couple of print statements
scalandr Mar 24, 2022
5ca480c
changes in mpas_ocn_core_interface.F
scalandr May 12, 2022
a5fd43f
compiles with OpenMP
scalandr May 18, 2022
95295fa
got rid of two equation model (for now)
scalandr May 26, 2022
046ce71
addressed comments 1-5
scalandr May 26, 2022
650c6dd
changed name to nonhydrostaticPKG and added variables to package
scalandr Jun 10, 2022
c2b2412
changed name from verticalVelocity to vertVelocityNonhydro
scalandr Jun 28, 2022
3eacc9e
cleaned nonhydrostatic_pressure_solve.F and vel_hadv_coriolis.F
scalandr Jun 29, 2022
c9cf963
cleaned subroutine ocn_vert_transport_velocity_top
scalandr Jul 1, 2022
e81723c
cleaned mpas_ocn_vel_pressure_grad.F
scalandr Jul 1, 2022
2c5bcbf
now it compiles, fixed src/shared/Makefile
scalandr Jul 1, 2022
2f4fa64
fixed indentation in src/Registry.xml
scalandr Jul 5, 2022
c947a8e
added vertVelocityNonhydro to nonhydrostaticPKG
scalandr Jul 5, 2022
59bb822
added nonhydrostaticPressure to nonhydrostaticPKG
scalandr Jul 6, 2022
2f46b53
added blank lines in rk4 and fixed indentation
scalandr Jul 6, 2022
bc8290b
added tendVertVelocityNonhydro to nonhydrostaticPKG
scalandr Jul 6, 2022
fdb1d58
cleaned mpas_ocn_tendency.F and mpas_ocn_diagnostics.F
scalandr Jul 6, 2022
d55b293
now it compiles, fixed issues in split-implicit
scalandr Jul 7, 2022
1577b35
got rid of velocity*Tend variables
scalandr Jul 8, 2022
58ce136
got rid of unused flags
scalandr Jul 12, 2022
4fc4447
changed nonhydrostaticPressure name in time-steppers
scalandr Jul 12, 2022
5fc334c
cleaned split explicit and vel hmix del2
scalandr Jul 12, 2022
6b2320a
cleaned mpas_ocn_vel_pressure_grad.F
scalandr Jul 13, 2022
a111c41
inlined implicit vert mix in vert momentum
scalandr Jul 14, 2022
18a8b6e
fixes in ocean.cmake, mpas_ocn_nonhydrostatic_pressure_solve.F and mp…
scalandr Jan 20, 2023
e209e96
corrected ocn_vertVel_vmix_tend_implicit in mpas_ocn_vmix.F
scalandr Mar 10, 2023
1934c38
cleaned code
scalandr Mar 10, 2023
3e9778b
added nonhydro vars to restart file and corrected vvel coriolis
scalandr Mar 22, 2023
bc9cabc
changes to hmix for vertical momentum
scalandr Apr 6, 2023
9b31e2b
added flags in bld folder and corrected ocn_vel_coriolis_nonhydro_ten…
scalandr Apr 7, 2023
b94a4c0
added lines to build the e3sm way on Anvil
scalandr May 1, 2023
f9a76a1
added del4 in vertical momentum
scalandr May 1, 2023
2dec6bd
merged with most recent version of e3sm
scalandr May 2, 2023
707cc46
fixed building issue
scalandr May 2, 2023
a882fd9
Merge remote-tracking branch 'E3SM-Project/E3SM/master' into ocean/no…
scalandr May 19, 2023
3759f61
possible fix for e3sm tests
scalandr May 24, 2023
85718b4
possible fix for problem with ocn_vvel_hmix_del4
scalandr May 24, 2023
9052bc6
fixed omp pragma in mpas_ocn_vmix.F
scalandr May 31, 2023
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23 changes: 21 additions & 2 deletions components/mpas-framework/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -517,7 +517,26 @@ CPPINCLUDES =
FCINCLUDES =
LIBS =

#
# Add links to PETSC links if requested
ifeq "$(USE_PETSC)" "true"
ifndef PETSC
$(error PETSC is not set. Please set PETSC to the PETSC install directory when USE_PETSC=true)
endif
ifneq (, $(shell ls $(PETSC)/lib/libpetsc.*))
LIBS += -L$(PETSC)/lib
CPPINCLUDES += -I$(PETSC)/include
FCINCLUDES += -I$(PETSC)/include
else ifneq (, $(shell ls $(PETSC)/libpetsc.*))
LIBS += -L$(PETSC)
CPPINCLUDES += -I$(PETSC)
FCINCLUDES += -I$(PETSC)
else
$(error libpetsc.* does NOT exist in $(PETSC) or $(PETSC)/lib)
endif
LIBS += -lpetsc
override CPPFLAGS += -DUSE_PETSC
endif

# If user has indicated a PIO2 library, define USE_PIO2 pre-processor macro
#
ifeq "$(USE_PIO2)" "true"
Expand All @@ -533,7 +552,7 @@ ifneq ($(wildcard $(PIO)/lib), )
else
PIO_LIB = $(PIO)
endif
LIBS = -L$(PIO_LIB)
LIBS += -L$(PIO_LIB)

#
# Regardless of PIO library version, look for an include subdirectory of PIO path
Expand Down
16 changes: 16 additions & 0 deletions components/mpas-ocean/bld/build-namelist
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Expand Up @@ -797,6 +797,21 @@ add_default($nl, 'config_topographic_wave_drag_coeff');

add_default($nl, 'config_density0');

###########################################
# Namelist group: nonhydrostatic_pressure #
###########################################

add_default($nl, 'config_enable_nonhydrostatic_mode');
add_default($nl, 'config_nonhydrostatic_solve_surface_boundary_condition');
add_default($nl, 'config_enable_vertMomentum_disable_nonHydro');
add_default($nl, 'config_nonhydrostatic_remove_rhs_mean');
add_default($nl, 'config_nonhydrostatic_preconditioner');
add_default($nl, 'config_nonhydrostatic_solver_type');
add_default($nl, 'config_petsc_rtol');
add_default($nl, 'config_petsc_atol');
add_default($nl, 'config_petsc_maxit');
add_default($nl, 'config_use_constant_forced_pgf');

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@vanroekel vanroekel Jul 12, 2022

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were these added by the automated scripts? Or hand entered?

#####################################
# Namelist group: pressure_gradient #
#####################################
Expand Down Expand Up @@ -1695,6 +1710,7 @@ my @groups = qw(run_modes
advection
bottom_drag
ocean_constants
nonhydrostatic_pressure
pressure_gradient
eos
eos_linear
Expand Down
1 change: 1 addition & 0 deletions components/mpas-ocean/bld/build-namelist-group-list
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@ my @groups = qw(run_modes
advection
bottom_drag
ocean_constants
nonhydrostatic_pressure
pressure_gradient
eos
eos_linear
Expand Down
15 changes: 15 additions & 0 deletions components/mpas-ocean/bld/build-namelist-section
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Original file line number Diff line number Diff line change
Expand Up @@ -330,6 +330,21 @@ add_default($nl, 'config_topographic_wave_drag_coeff');

add_default($nl, 'config_density0');

###########################################
# Namelist group: nonhydrostatic_pressure #
###########################################

add_default($nl, 'config_enable_nonhydrostatic_mode');
add_default($nl, 'config_nonhydrostatic_solve_surface_boundary_condition');
add_default($nl, 'config_enable_vertMomentum_disable_nonHydro');
add_default($nl, 'config_nonhydrostatic_remove_rhs_mean');
add_default($nl, 'config_nonhydrostatic_preconditioner');
add_default($nl, 'config_nonhydrostatic_solver_type');
add_default($nl, 'config_petsc_rtol');
add_default($nl, 'config_petsc_atol');
add_default($nl, 'config_petsc_maxit');
add_default($nl, 'config_use_constant_forced_pgf');

#####################################
# Namelist group: pressure_gradient #
#####################################
Expand Down
12 changes: 12 additions & 0 deletions components/mpas-ocean/bld/namelist_files/namelist_defaults_mpaso.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -365,6 +365,18 @@
<!-- ocean_constants -->
<config_density0>1026.0</config_density0>

<!-- nonhydrostatic_pressure -->
<config_enable_nonhydrostatic_mode>.false.</config_enable_nonhydrostatic_mode>
<config_nonhydrostatic_solve_surface_boundary_condition>'noGradient'</config_nonhydrostatic_solve_surface_boundary_condition>
<config_enable_vertMomentum_disable_nonHydro>.false.</config_enable_vertMomentum_disable_nonHydro>
<config_nonhydrostatic_remove_rhs_mean>.true.</config_nonhydrostatic_remove_rhs_mean>
<config_nonhydrostatic_preconditioner>'jacobi'</config_nonhydrostatic_preconditioner>
<config_nonhydrostatic_solver_type>'pipecgrr'</config_nonhydrostatic_solver_type>
<config_petsc_rtol>1.0e-10</config_petsc_rtol>
<config_petsc_atol>1.0E-20</config_petsc_atol>
<config_petsc_maxit>10000</config_petsc_maxit>
<config_use_constant_forced_pgf>.false.</config_use_constant_forced_pgf>
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I'm not sure we want to retain this option long term. My feeling is to remove the constant_forced_pgf from this PR


<!-- pressure_gradient -->
<config_pressure_gradient_type>'Jacobian_from_TS'</config_pressure_gradient_type>
<config_common_level_weight>0.5</config_common_level_weight>
Expand Down
82 changes: 82 additions & 0 deletions components/mpas-ocean/bld/namelist_files/namelist_definition_mpaso.xml
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Expand Up @@ -1732,6 +1732,88 @@ Valid values: any positive real, but typically 1000-1035
Default: Defined in namelist_defaults.xml
</entry>

<!-- nonhydrostatic_pressure -->

<entry id="config_enable_nonhydrostatic_mode" type="logical"
category="nonhydrostatic_pressure" group="nonhydrostatic_pressure">
Flag to enable the nonhydrostatic pressure calculation

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

<entry id="config_nonhydrostatic_solve_surface_boundary_condition" type="char*1024"
category="nonhydrostatic_pressure" group="nonhydrostatic_pressure">
setting for surface boundary condition for the pressure correction solve

Valid values: noGradient or no pressure
Default: Defined in namelist_defaults.xml
</entry>

<entry id="config_enable_vertMomentum_disable_nonHydro" type="logical"
category="nonhydrostatic_pressure" group="nonhydrostatic_pressure">
flag to enable hydrostatic pressure with vertical momentum tendencies

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

<entry id="config_nonhydrostatic_remove_rhs_mean" type="logical"
category="nonhydrostatic_pressure" group="nonhydrostatic_pressure">
flag to enabling mean from the right hand side of the nonhydro solve

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

<entry id="config_nonhydrostatic_preconditioner" type="char*1024"
category="nonhydrostatic_pressure" group="nonhydrostatic_pressure">
String describing preconditioner to use, recommended options -- jacobi, bjacobi, ilu

Valid values: jacobi, bjacobi, ilu
Default: Defined in namelist_defaults.xml
</entry>

<entry id="config_nonhydrostatic_solver_type" type="char*1024"
category="nonhydrostatic_pressure" group="nonhydrostatic_pressure">
String describing the solver context, recommended types -- pipecgrr, pipecg, cg, bcgs, gmres

Valid values: pipecgrr, pipecg, cg, bcgs, gmres
Default: Defined in namelist_defaults.xml
</entry>

<entry id="config_petsc_rtol" type="real"
category="nonhydrostatic_pressure" group="nonhydrostatic_pressure">
relative tolerance for the norm in petsc convergence

Valid values: very small positive reals
Default: Defined in namelist_defaults.xml
</entry>

<entry id="config_petsc_atol" type="real"
category="nonhydrostatic_pressure" group="nonhydrostatic_pressure">
absolute tolerance for the norm in petsc convergence

Valid values: very small positive reals
Default: Defined in namelist_defaults.xml
</entry>

<entry id="config_petsc_maxit" type="integer"
category="nonhydrostatic_pressure" group="nonhydrostatic_pressure">
maximum number of iterations in petsc solve

Valid values: positive integers
Default: Defined in namelist_defaults.xml
</entry>

<entry id="config_use_constant_forced_pgf" type="logical"
category="nonhydrostatic_pressure" group="nonhydrostatic_pressure">
logical to enable a constant pressure gradient that is added to rest of PGF NOTE: need to remove after rebasing on to master...
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Here is actually a note (I'm guessing I made it) to remove this flag.


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


<!-- pressure_gradient -->

Expand Down
83 changes: 83 additions & 0 deletions components/mpas-ocean/src/Registry.xml
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Expand Up @@ -244,6 +244,14 @@
description="If true, Laplacian horizontal mixing is used on the tracer equation."
possible_values=".true. or .false."
/>
<nml_option name="config_use_vertMom_del2" type="logical" default_value=".false." units="unitless"
description="If true, Laplacian horizontal mixing is used on the vertical momentum equation."
possible_values=".true. or .false."
/>
<nml_option name="config_vertMom_del2" type="real" default_value="0.0" units="m^2 s^{-1}"
description="Horizontal viscosity, $\nu_{2h}$. If config_hmix_use_ref_cell_width = .true. then $\nu_h$ = config_mom_del2*(cellWidth / config_hmix_use_ref_cell_width). If config_hmix_use_ref_cell_width = .false. then it is referenced to the smallest cell."
possible_values="any positive real"
/>
<nml_option name="config_tracer_del2" type="real" default_value="10.0" units="m^2 s^{-1}"
description="Horizontal diffusion, $\kappa_{2h}$. If config_hmix_use_ref_cell_width = .true. then $\kappa_h$ = config_tracer_del2*(cellWidth / config_hmix_use_ref_cell_width). If config_hmix_use_ref_cell_width = .false. then it is referenced to the smallest cell."
possible_values="any positive real"
Expand Down Expand Up @@ -1108,6 +1116,48 @@
possible_values="any positive real, but typically 1000-1035"
/>
</nml_record>
<nml_record name="nonhydrostatic_pressure">
<nml_option name="config_enable_nonhydrostatic_mode" type="logical" default_value=".false." units="unitless"
description="Flag to enable the nonhydrostatic pressure calculation"
possible_values=".true. or .false."
/>
<nml_option name="config_nonhydrostatic_solve_surface_boundary_condition" type="character" default_value="noGradient" units="unitless"
description="setting for surface boundary condition for the pressure correction solve"
possible_values="noGradient or no pressure"
/>
<nml_option name="config_enable_vertMomentum_disable_nonHydro" type="logical" default_value=".false." units="unitless"
description="flag to enable hydrostatic pressure with vertical momentum tendencies"
possible_values=".true. or .false."
/>
<nml_option name="config_nonhydrostatic_remove_rhs_mean" type="logical" default_value=".true." units="unitless"
description="flag to enabling mean from the right hand side of the nonhydro solve"
possible_values=".true. or .false."
/>
<nml_option name="config_nonhydrostatic_preconditioner" type="character" default_value="jacobi" units="unitless"
description="String describing preconditioner to use, recommended options -- jacobi, bjacobi, ilu"
possible_values="jacobi, bjacobi, ilu"
/>
<nml_option name="config_nonhydrostatic_solver_type" type="character" default_value="pipecgrr" units="unitless"
description="String describing the solver context, recommended types -- pipecgrr, pipecg, cg, bcgs, gmres"
possible_values="pipecgrr, pipecg, cg, bcgs, gmres"
/>
<nml_option name="config_petsc_rtol" type="real" default_value="1.0e-10" units="unitless"
description="relative tolerance for the norm in petsc convergence"
possible_values="very small positive reals"
/>
<nml_option name="config_petsc_atol" type="real" default_value="1.0E-20" units="unitless"
description="absolute tolerance for the norm in petsc convergence"
possible_values="very small positive reals"
/>
<nml_option name="config_petsc_maxit" type="integer" default_value="10000" units="unitless"
description="maximum number of iterations in petsc solve"
possible_values="positive integers"
/>
<nml_option name="config_use_constant_forced_pgf" type="logical" default_value=".false." units="unitless"
description="logical to enable a constant pressure gradient that is added to rest of PGF NOTE: need to remove after rebasing on to master..."
possible_values=".true. or .false."
/>
</nml_record>
<nml_record name="pressure_gradient" mode="forward">
<nml_option name="config_pressure_gradient_type" type="character" default_value="pressure_and_zmid" units="unitless"
description="Form of pressure gradient terms in momentum equation. For most applications, the gradient of pressure and layer mid-depth are appropriate. For isopycnal coordinates, one may use the gradient of the Montgomery potential. The sea surface height gradient (ssh_gradient) option is for barotropic, depth-averaged pressure."
Expand Down Expand Up @@ -1305,6 +1355,10 @@
description="If true, $h^{hf}$ is included in the desired ALE thickness, and the prognostic equations for $D^{lf}$ and $h^{hf}$ are integrated in the code."
possible_values=".true. or .false."
/>
<nml_option name="config_disable_ALE" type="logical" default_value=".false." units="unitless"
description="flag to disable the ALE coordinate and revert to eulerian mode NOTE: only works for RK4 at present"
possible_values=".true. or .false."
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This is another really untested option that I would suggest we remove. I don't think we want this finding its way to e3sm master

/>
<nml_option name="config_thickness_filter_timescale" type="real" default_value="5.0" units="days"
description="Filter time scale for the low-frequency baroclinic divergence, $\tau_{Dlf}$."
possible_values="any positive real value, but typically 5 days."
Expand Down Expand Up @@ -1383,6 +1437,18 @@
description="Disables tendencies on the velocity field from the Coriolis force and momentum advection."
possible_values=".true. or .false."
/>
<nml_option name="config_disable_vvel_all_tend" type="logical" default_value=".false." units="unitless"
description="Disables all tendencies on the vertical velocity field."
possible_values=".true. or .false."
/>
<nml_option name="config_disable_vvel_coriolis" type="logical" default_value=".false." units="unitless"
description="Disables tendencies on the vertical velocity field from the Coriolis force."
possible_values=".true. or .false."
/>
<nml_option name="config_disable_vvel_adv" type="logical" default_value=".false." units="unitless"
description="Disables advection of vertical velocity"
possible_values=".true. or .false."
/>
<nml_option name="config_disable_vel_pgrad" type="logical" default_value=".false." units="unitless"
description="Disables tendencies on the velocity field from the horizontal pressure gradient."
possible_values=".true. or .false."
Expand Down Expand Up @@ -1491,6 +1557,7 @@
<package name="topographicWaveDragPKG" description="This package controls variables required for topographic wave drag"/>
<package name="gotmPKG" description="This package is for GOTM variables, which are only needed when using GOTM for the vertical turbulence closure."/>
<package name="verticalRemapPKG" description="This package is for variables required for vertical Lagrangian remapping."/>
<package name="nonhydrostaticPKG" description="This package is for variables needed for the nonhydrostatic capabilities"/>
</packages>

<streams>
Expand Down Expand Up @@ -2118,6 +2185,14 @@
<var name="ssh" type="real" dimensions="nCells Time" units="m"
description="sea surface height"
/>
<var name="vertVelocityNonhydro" type="real" dimensions="nVertLevelsP1 nCells Time" units="m s^{-1}"
description="prognostic vertical velocity, only used when config_enable_nonhydrostatic_mode = .true."
packages="nonhydrostaticPKG"
/>
<var name="nonhydrostaticPressure" type="real" dimensions="nVertLevels nCells Time" units="N m^{-2}"
description="nonhydrostatic pressure, set to zero if config_enable_nonhydrostatic_mode = .false."
packages="nonhydrostaticPKG"
/>
Comment on lines +2188 to +2276
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@xylar xylar Jul 5, 2022

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Can these variables be put in the nonhydrostaticPKG package? If they aren't used at all when the nonhydrostaticPKG is disabled, this should be possible. If not, this will add to the memory used in hydrostatic mode.


<!-- FIELDS FOR FREQUENCY FILTERED THICKNESS -->
<var name="highFreqThickness" type="real" dimensions="nVertLevels nCells Time" units="m"
Expand Down Expand Up @@ -2466,6 +2541,10 @@
description="time tendency of normal component of velocity"
packages="forwardMode"
/>
<var name="tendVertVelocityNonhydro" type="real" dimensions="nVertLevelsP1 nCells Time" units="m s^{-2}" name_in_code="vertVelocityNonhydroTend"
description="time tendency of the vertical velocity (Only active for non hydrostatic mode)"
packages="nonhydrostaticPKG"
/>
Comment on lines +2542 to +2631
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@xylar xylar Jul 5, 2022

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Same here, can this be in the nonhydrostaticPKG package?

<var name="tendLayerThickness" type="real" dimensions="nVertLevels nCells Time" units="m s^{-1}" name_in_code="layerThickness"
description="time tendency of layer thickness"
packages="forwardMode"
Expand Down Expand Up @@ -2493,6 +2572,10 @@
<var name="daysSinceStartOfSim" type="real" dimensions="Time" units="days"
description="Time since simulationStartTime, for plotting"
/>
<var name="nhPressureCorrection" type="real" dimensions="nVertLevels nCells Time" units="unitless"
description="the pressure correction coming from the poisson pressure equation"
packages="nonhydrostaticPKG"
/>
Comment on lines +2608 to +2671
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@xylar xylar May 22, 2022

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Add to nonhydrostaticPKG

<var name="salinitySurfaceRestoringTendency" type="real" dimensions="nCells Time" units="m PSU/s" packages="activeTracersSurfaceRestoringPKG"
description="salinity tendency due to surface restoring"
/>
Expand Down
11 changes: 11 additions & 0 deletions components/mpas-ocean/src/driver/mpas_ocn_core_interface.F
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Expand Up @@ -110,6 +110,7 @@ function ocn_setup_packages(configPool, packagePool, iocontext) result(ierr)!{{{
integer :: err_tmp

logical, pointer :: forwardModeActive
logical, pointer :: nonhydrostaticPKGActive
logical, pointer :: analysisModeActive
logical, pointer :: initModeActive
logical, pointer :: thicknessFilterActive
Expand Down Expand Up @@ -162,6 +163,7 @@ function ocn_setup_packages(configPool, packagePool, iocontext) result(ierr)!{{{
logical, pointer :: config_use_topographic_wave_drag
logical, pointer :: config_use_GM
logical, pointer :: config_use_Redi
logical, pointer :: config_enable_nonhydrostatic_mode
logical, pointer :: config_use_vegetation_drag
logical, pointer :: config_use_time_varying_atmospheric_forcing
logical, pointer :: config_use_time_varying_land_ice_forcing
Expand Down Expand Up @@ -345,6 +347,15 @@ function ocn_setup_packages(configPool, packagePool, iocontext) result(ierr)!{{{
topographicWaveDragPKGActive = .true.
end if

!
! test for nonHydrostatic pressure
!
call mpas_pool_get_package(packagePool, 'nonhydrostaticPKGActive', nonhydrostaticPKGActive)
call mpas_pool_get_config(configPool, 'config_enable_nonhydrostatic_mode', config_enable_nonhydrostatic_mode)
if (config_enable_nonhydrostatic_mode) then
nonhydrostaticPKGActive = .true.
end if

!
! test for use of gm
!
Expand Down
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