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Merge branch 'xylar/ocn/fix-registry-for-docs' into next (PR #6293)
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Fix some formatting in MPAS-Ocean Registry for generating docs

To generate Latex documentation from the Registry, we need to escape
Latex in the namelist and variable descriptions.

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@jonbob
jonbob committed Mar 27, 2024
2 parents 5fe46fe + 87e358b commit 3cfb975
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Showing 2 changed files with 11 additions and 11 deletions.
10 changes: 5 additions & 5 deletions components/mpas-ocean/bld/namelist_files/namelist_definition_mpaso.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -245,7 +245,7 @@ Default: Defined in namelist_defaults.xml

<entry id="config_hmix_ref_cell_width" type="real"
category="hmix" group="hmix">
Reference cell width. If config_hmix_use_ref_cell_width = .true., then hmix coefficients are set to be nu_{2h} = config_mom_del2*(cellWidth / config_hmix_use_ref_cell_width) and nu_{4h} = config_mom_del4*(cellWidth / config_hmix_use_ref_cell_width)^3 where cellWidth is the effective cell width computed as 2*sqrt(areaCell/pi). See Hoch et al 2020 JAMES eq 1,2. This relation applies within a simulation, but also generally among multiple simulations, so the parameters config_mom_del2, config_mom_del4, and config_hmix_use_ref_cell_width can generally remain at their standard values, and just be adjusted for fine tuning.
Reference cell width. If config_hmix_use_ref_cell_width = .true., then hmix coefficients are set to be $nu_{2h}$ = config_mom_del2*(cellWidth / config_hmix_use_ref_cell_width) and $nu_{4h}$ = config_mom_del4*(cellWidth / config_hmix_use_ref_cell_width)$^3$ where cellWidth is the effective cell width computed as 2*sqrt(areaCell/pi). See Hoch et al 2020 JAMES eq 1,2. This relation applies within a simulation, but also generally among multiple simulations, so the parameters config_mom_del2, config_mom_del4, and config_hmix_use_ref_cell_width can generally remain at their standard values, and just be adjusted for fine tuning.

Valid values: Any positive real number, but typically a resolution number such as 30km.
Default: Defined in namelist_defaults.xml
Expand Down Expand Up @@ -307,7 +307,7 @@ Default: Defined in namelist_defaults.xml

<entry id="config_mom_del4" type="real"
category="hmix_del4" group="hmix_del4">
Coefficient for horizontal biharmonic operator on momentum. If config_hmix_use_ref_cell_width = .true. then $\nu_{4h}$ = config_mom_del4*(cellWidth / config_hmix_use_ref_cell_width)^3. If config_hmix_use_ref_cell_width = .false. then it is referenced to the smallest cell.
Coefficient for horizontal biharmonic operator on momentum. If config_hmix_use_ref_cell_width = .true. then $\nu_{4h}$ = config_mom_del4*(cellWidth / config_hmix_use_ref_cell_width)$^3$. If config_hmix_use_ref_cell_width = .false. then it is referenced to the smallest cell.

Valid values: any positive real
Default: Defined in namelist_defaults.xml
Expand All @@ -331,7 +331,7 @@ Default: Defined in namelist_defaults.xml

<entry id="config_tracer_del4" type="real"
category="hmix_del4" group="hmix_del4">
Coefficient for horizontal biharmonic operator on tracers. If config_hmix_use_ref_cell_width = .true. then $\nu_{4h}$ = config_tracer_del4*(cellWidth / config_hmix_use_ref_cell_width)^3. If config_hmix_use_ref_cell_width = .false. then it is referenced to the smallest cell.
Coefficient for horizontal biharmonic operator on tracers. If config_hmix_use_ref_cell_width = .true. then $\nu_{4h}$ = config_tracer_del4*(cellWidth / config_hmix_use_ref_cell_width)$^3$. If config_hmix_use_ref_cell_width = .false. then it is referenced to the smallest cell.

Valid values: any positive real
Default: Defined in namelist_defaults.xml
Expand Down Expand Up @@ -1188,7 +1188,7 @@ Default: Defined in namelist_defaults.xml

<entry id="config_sw_absorption_type" type="char*1024"
category="shortwaveRadiation" group="shortwaveRadiation">
Name of shortwave absorption type used in simulation.
Name of shortwave absorption type used in simulation.

Valid values: 'jerlov' or 'ohlmann00' or 'none'
Default: Defined in namelist_defaults.xml
Expand Down Expand Up @@ -1809,7 +1809,7 @@ Default: Defined in namelist_defaults.xml

<entry id="config_Rayleigh_damping_depth_variable" type="logical"
category="Rayleigh_damping" group="Rayleigh_damping">
If true applies r h^-1 instead of just r.
If true applies r h$^-1$ instead of just r.

Valid values: .true. or .false.
Default: Defined in namelist_defaults.xml
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12 changes: 6 additions & 6 deletions components/mpas-ocean/src/Registry.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -223,7 +223,7 @@
possible_values=".true. or .false."
/>
<nml_option name="config_hmix_ref_cell_width" type="real" default_value="30.0e3" units="m"
description="Reference cell width. If config_hmix_use_ref_cell_width = .true., then hmix coefficients are set to be nu_{2h} = config_mom_del2*(cellWidth / config_hmix_use_ref_cell_width) and nu_{4h} = config_mom_del4*(cellWidth / config_hmix_use_ref_cell_width)^3 where cellWidth is the effective cell width computed as 2*sqrt(areaCell/pi). See Hoch et al 2020 JAMES eq 1,2. This relation applies within a simulation, but also generally among multiple simulations, so the parameters config_mom_del2, config_mom_del4, and config_hmix_use_ref_cell_width can generally remain at their standard values, and just be adjusted for fine tuning."
description="Reference cell width. If config_hmix_use_ref_cell_width = .true., then hmix coefficients are set to be $nu_{2h}$ = config_mom_del2*(cellWidth / config_hmix_use_ref_cell_width) and $nu_{4h}$ = config_mom_del4*(cellWidth / config_hmix_use_ref_cell_width)$^3$ where cellWidth is the effective cell width computed as 2*sqrt(areaCell/pi). See Hoch et al 2020 JAMES eq 1,2. This relation applies within a simulation, but also generally among multiple simulations, so the parameters config_mom_del2, config_mom_del4, and config_hmix_use_ref_cell_width can generally remain at their standard values, and just be adjusted for fine tuning."
possible_values="Any positive real number, but typically a resolution number such as 30km."
/>
<nml_option name="config_apvm_scale_factor" type="real" default_value="0.0"
Expand Down Expand Up @@ -255,7 +255,7 @@
possible_values=".true. or .false."
/>
<nml_option name="config_mom_del4" type="real" default_value="1.2e11" units="m^4 s^-1"
description="Coefficient for horizontal biharmonic operator on momentum. If config_hmix_use_ref_cell_width = .true. then $\nu_{4h}$ = config_mom_del4*(cellWidth / config_hmix_use_ref_cell_width)^3. If config_hmix_use_ref_cell_width = .false. then it is referenced to the smallest cell."
description="Coefficient for horizontal biharmonic operator on momentum. If config_hmix_use_ref_cell_width = .true. then $\nu_{4h}$ = config_mom_del4*(cellWidth / config_hmix_use_ref_cell_width)$^3$. 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_mom_del4_div_factor" type="real" default_value="1.0" units="non-dimensional"
Expand All @@ -267,7 +267,7 @@
possible_values=".true. or .false."
/>
<nml_option name="config_tracer_del4" type="real" default_value="0.0" units="m^4 s^-1"
description="Coefficient for horizontal biharmonic operator on tracers. If config_hmix_use_ref_cell_width = .true. then $\nu_{4h}$ = config_tracer_del4*(cellWidth / config_hmix_use_ref_cell_width)^3. If config_hmix_use_ref_cell_width = .false. then it is referenced to the smallest cell."
description="Coefficient for horizontal biharmonic operator on tracers. If config_hmix_use_ref_cell_width = .true. then $\nu_{4h}$ = config_tracer_del4*(cellWidth / config_hmix_use_ref_cell_width)$^3$. If config_hmix_use_ref_cell_width = .false. then it is referenced to the smallest cell."
possible_values="any positive real"
/>
</nml_record>
Expand Down Expand Up @@ -762,7 +762,7 @@
</nml_record>
<nml_record name="shortwaveRadiation" mode="init;forward">
<nml_option name="config_sw_absorption_type" type="character" default_value="none"
description="Name of shortwave absorption type used in simulation. "
description="Name of shortwave absorption type used in simulation."
possible_values="'jerlov' or 'ohlmann00' or 'none'"
/>
<nml_option name="config_jerlov_water_type" type="integer" default_value="3"
Expand Down Expand Up @@ -1123,7 +1123,7 @@
possible_values="Any positive real value."
/>
<nml_option name="config_Rayleigh_damping_depth_variable" type="logical" default_value=".false."
description="If true applies r h^-1 instead of just r."
description="If true applies r h$^-1$ instead of just r."
possible_values=".true. or .false."
/>
<nml_option name="config_Rayleigh_bottom_friction" type="logical" default_value=".false."
Expand Down Expand Up @@ -3878,7 +3878,7 @@
packages="tidalPotentialForcingPKG"
/>
<var name="tidalPotentialLatitudeFunction" type="real" dimensions="nCells R3 Time" units="1"
description="Latitude function for tidal constituents: long-period = 3\sin^2(\phi)-1, diurnal = \sin(2\phi), semi-diurnal = \cos^2(\phi)"
description="Latitude function for tidal constituents: long-period = $3\sin^2(\phi)-1$, diurnal = $\sin(2\phi)$, semi-diurnal = $\cos^2(\phi)$"
packages="tidalPotentialForcingPKG"
/>
<var name="sshSubcycleCurWithTides" type="real" dimensions="nCells Time" units="m"
Expand Down

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