Merge coastal to ocean/develop: COMPASS and sediment additions

docs/ocean/design_docs/harmonic_analysis/tides.bib

@@ -0,0 +1,48 @@
+@incollection{chassignet_primer_2018,
+	title = {A {Primer} on {Global} {Internal} {Tide} and {Internal} {Gravity} {Wave} {Continuum} {Modeling} in {HYCOM} and {MITgcm}},
+	isbn = {978-1-72054-997-0},
+	url = {http://purl.flvc.org/fsu/fd/FSU\_libsubv1\_scholarship\_submission\_1536242074\_55feafcc},
+	language = {en},
+	urldate = {2018-10-23},
+	booktitle = {New {Frontiers} in {Operational} {Oceanography}},
+	publisher = {GODAE OceanView},
+	author = {Arbic, Brian K. and Alford, Matthew H. and Ansong, Joseph K. and Buijsman, Maarten C. and Ciotti, Robert B. and Farrar, J. Thomas and Hallberg, Robert W. and Henze, Christopher E. and Hill, Christopher N. and Luecke, Conrad A. and Menemenlis, Dimitris and Metzger, E. Joseph and Müeller, Malte and Nelson, Arin D. and Nelson, Bron C. and Ngodock, Hans E. and Ponte, Rui M. and Richman, James G. and Savage, Anna C. and Scott, Robert B. and Shriver, Jay F. and Simmons, Harper L. and Souopgui, Innocent and Timko, Patrick G. and Wallcraft, Alan J. and Zamudio, Luis and Zhao, Zhongxiang},
+	editor = {Chassignet, Eric P. and Pascual, Ananda and Tintoré, Joaquin and Verron, Jacques},
+	month = aug,
+	year = {2018},
+	doi = {10.17125/gov2018.ch13},
+	file = {Arbic et al. - 2018 - A Primer on Global Internal Tide and Internal Grav.pdf:/Users/pwolfram/Zotero/storage/TEDRP9CP/Arbic et al. - 2018 - A Primer on Global Internal Tide and Internal Grav.pdf:application/pdf}
+}
+
+@article{Luettich1992ADCIRC,
+    author={Luettich, R.A. and Westerink, J.J. and Scheffner, N.W.},
+	title = {{ADCIRC}: {An} {Advanced} {Three}-{Dimensional} {Circulation} {Model} for {Shelves}, {Coasts}, and {Estuaries}. {Report} 1. {Theory} and {Methodology} of {ADCIRC-2DDI} and {ADCIRC-3DL}.},
+	language = {en},
+	pages = {143},
+	year={1992}
+}
+
+@article{arbic2004accuracy,
+  title={The accuracy of surface elevations in forward global barotropic and baroclinic tide models},
+  author={Arbic, Brian K and Garner, Stephen T and Hallberg, Robert W and Simmons, Harper L},
+  journal={Deep Sea Research Part II: Topical Studies in Oceanography},
+  volume={51},
+  number={25-26},
+  pages={3069--3101},
+  year={2004},
+  publisher={Elsevier}
+}
+
+@article{westerink_lsq,
+author = {Westerink, J. J. and Connor, J. J. and Stolzenbach, K. D.},
+title = {A frequency–time domain finite element model for tidal circulation based on the least-squares harmonic analysis method},
+journal = {International Journal for Numerical Methods in Fluids},
+volume = {8},
+number = {7},
+pages = {813-843},
+keywords = {Shallow Water Equations, Iterative, Harmonic Analysis, Least Squares, Finite Element, Tides},
+doi = {10.1002/fld.1650080706},
+url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/fld.1650080706},
+eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/fld.1650080706},
+year = {1988}
+}

src/core_ocean/Registry.xml

@@ -97,7 +97,11 @@
 		/>
 		<dim name="maxTidalConstituents"
 			description="Max number of tidal potential constituents"
-			definition="37"
+			definition="8"
+		/>
+		<dim name="maxTidalConstituentsX2"
+			description="Max number of tidal potential constituents"
+			definition="maxTidalConstituents+maxTidalConstituents"
 		/>
 	</dims>
 
@@ -544,6 +548,10 @@
 		/>
 	</nml_record>
 	<nml_record name="forcing" mode="init;forward">
+		<nml_option name="config_use_variable_drag" type="logical" default_value=".false." units="unitless"
+					description="Controls if variable drag is enabled."
+					possible_values=".true. or .false."
+		/>
 		<nml_option name="config_use_bulk_wind_stress" type="logical" default_value=".false." units="unitless"
 					description="Controls if zonal and meridional components of windstress are used to build surface wind stress."
 					possible_values=".true. or .false."
@@ -594,6 +602,10 @@
 			description="Number of days to ramp up time varying forcing"
 			possible_values="Any positive real number"
 		/>
+		<nml_option name="config_time_varying_atmospheric_forcing_ramp_delay" type="real" default_value="0.0" units="days"
+			description="Number of days to delay ramp time varying forcing"
+			possible_values="Any positive real number"
+		/>
 		<nml_option name="config_use_time_varying_land_ice_forcing" type="logical" default_value=".false." units="unitless"
 			description="If true calculate input forcing fields."
 			possible_values=".true. or .false."
@@ -668,6 +680,10 @@
 					description="Value of period of monochromatic tide."
 					possible_values="Any positive real number."
 		/>
+		<nml_option name="config_tidal_forcing_monochromatic_phaseLag" type="real" default_value="0.0" units=""
+					description="Value of phase of monochromatic tide."
+					possible_values="Any real number between."
+		/>
 		<nml_option name="config_tidal_forcing_monochromatic_baseline" type="real" default_value="0.0" units="days"
 					description="Value of baseline monochromatic tide, e.g., sea level rise."
 					possible_values="Any positive real number."
@@ -723,6 +739,20 @@
 					possible_values="0.0 to turn off, 0.09 is typical value to use for scalar approximation"
 		/>
 	</nml_record>
+	<nml_record name="vegetation_drag" mode="init;forward">
+		<nml_option name="config_use_vegetation_drag" type="logical" default_value=".false." units="unitless"
+					description="Controls if vegetation_drag is used."
+					possible_values=".true. or .false."
+		/>
+		<nml_option name="config_use_vegetation_manning_equation" type="logical" default_value=".false." units="unitless"
+					description="Compute vegetation drag force using vegetation-induced Manning roughness coefficient."
+					possible_values=".true. or .false."
+		/>
+		<nml_option name="config_vegetation_drag_coefficient" type="real" default_value="1.09" units="unitless"
+					description="Vegetation drag coefficient"
+					possible_values="O(1)"
+		/>
+	</nml_record>
 	<nml_record name="frazil_ice" mode="forward">
 		<nml_option name="config_use_frazil_ice_formation" type="logical" default_value=".false." units="unitless"
 					description="Controls if fluxes related to frazil ice process are computed."
@@ -859,6 +889,14 @@
 					description="Dimensionless bottom drag coefficient, $c_{drag}$."
 					possible_values="any positive real, typically 1.0e-3"
 		/>
+		<nml_option name="config_use_implicit_bottom_drag_variable" type="logical" default_value=".false." units="unitless"
+					description="If true, spatially-variable implicit bottom drag is used on the momentum equation."
+					possible_values=".true. or .false."
+		/>
+		<nml_option name="config_use_implicit_bottom_drag_variable_mannings" type="logical" default_value=".false." units="unitless"
+					description="If true, uses Mannings' n values for the computation of Cd=g*n^2*h^{-1/3}."
+					possible_values=".true. or .false."
+		/>
 		<nml_option name="config_use_explicit_bottom_drag" type="logical" default_value=".false." units="unitless"
 					description="If true, explicit bottom drag is used on the momentum equation."
 					possible_values=".true. or .false."
@@ -1228,12 +1266,14 @@
 		<package name="splitTimeIntegrator" description="This package includes variables required for either the split or unsplit explicit time integrators."/>
 		<package name="thicknessFilter" description="This package includes variables required for frequency filtered thickness."/>
 		<package name="windStressBulkPKG" description="This package includes varibles required for bulk wind stress forcing."/>
+		<package name="variableBottomDragPKG" description="This package includes varibles required for variable bottom drag."/>
 		<package name="thicknessBulkPKG" description="This package includes varibles required for bulk thickness forcing."/>
 		<package name="landIcePressurePKG" description="This package includes variables needed for runs with the sea surface depressed by land-ice pressure."/>
 		<package name="landIceFluxesPKG" description="This package includes varibles required for land ice thickness, momentum and tracer fluxes."/>
 		<package name="landIceCouplingPKG" description="This package includes varibles required for land ice coupling but not land ice fluxes in standalone mode."/>
 		<package name="frazilIce" description="This package includes variables required for frazil ice formation."/>
 		<package name="tidalForcing" description="This package includes variables required for tidal forcing on a boundary."/>
+		<package name="vegetationDragPKG" description="This package includes vegetation properties used for computing vegetation drag"/>
 		<package name="forwardMode" description="This package controls variables that are intended to be used within the forward run mode of the ocean model."/>
 		<package name="analysisMode" description="This package controls variables that are intended to be used within the analysis run mode of the ocean model."/>
 		<package name="initMode" description="This package controls variables that are intended to be used within the init run mode of the ocean model."/>
@@ -1354,6 +1394,7 @@
 			<var name="shortWaveHeatFlux"/>
 			<var name="evaporationFlux"/>
 			<var name="rainFlux"/>
+			<var name="bottomDrag"/>
 		</stream>
 
 		<!-- Forward mode streams -->
@@ -1760,6 +1801,7 @@
 			<var name="topDragMagnitude"/>
 			<var name="landIceFreshwaterFlux"/>
 			<var name="landIceHeatFlux"/>
+			<var name="bottomDrag"/>
 		</stream>
 
 		<stream name="Gent_McWilliams_spherical"
@@ -2771,6 +2813,10 @@
 			 description="Meridional (northward) component of wind stress at cell centers from coupler. Positive northward."
 			 packages="windStressBulkPKG"
 		/>
+		<var name="bottomDrag" type="real" dimensions="nCells" units="unitless"
+			 description="Bottom drag Cd coefficient in cells."
+			 packages="variableBottomDragPKG"
+		/>
 		<var name="nForcingGroupCounter"		type="integer"	dimensions="Time"/>
 		<var name="forcingGroupNames"			type="text"	dimensions="nForcingGroupsMax Time"/>
 		<var name="forcingGroupRestartTimes"		type="text"	dimensions="nForcingGroupsMax Time"/>
@@ -3008,6 +3054,27 @@
 			 packages="tidalForcing"
 		/>
 
+		<!-- Input fields for vegetation properties -->
+		<var name="vegetationHeight" type="real" dimensions="nCells" units="m"
+			 description="Stem height of the vegetation"
+			 packages="vegetationDragPKG"
+		/>
+		<var name="vegetationDiameter" type="real" dimensions="nCells" units="m"
+			 description="Stem diameter of the vegetation"
+			 packages="vegetationDragPKG"
+		/>
+		<var name="vegetationDensity" type="real" dimensions="nCells" units="m^{-2}"
+			 description="Stem density of the vegetation per unit area"
+			 packages="vegetationDragPKG"
+		/>
+		<var name="vegetationMask" type="integer" dimensions="nCells" units="unitless"
+			 description="Mask value 1 as vegetated cell, and 0 as non-vegetated cell"
+			 packages="vegetationDragPKG"
+		/>
+		<var name="vegetationManning" type="real" dimensions="nCells" units="unitless"
+			 description="Manning roughness coefficient induced by vegetation"
+			 packages="vegetationDragPKG"
+		/>
 		<!-- Output fields for forcing due to tides -->
 		<var name="tidalLayerThicknessTendency" type="real" dimensions="nVertLevels nCells Time" units="m s^{-1}"
 			 description="layer thickness tendency due to tidal forcing"

src/core_ocean/analysis_members/Makefile

@@ -27,7 +27,10 @@ MEMBERS = mpas_ocn_global_stats.o \
           mpas_ocn_eddy_product_variables.o\
           mpas_ocn_moc_streamfunction.o\
           mpas_ocn_ocean_heat_content.o\
-          mpas_ocn_mixed_layer_heat_budget.o
+          mpas_ocn_mixed_layer_heat_budget.o\
+          mpas_ocn_sediment_flux_index.o\
+          mpas_ocn_sediment_transport.o\
+          mpas_ocn_harmonic_analysis.o
 
 all: $(OBJS)
 

src/core_ocean/analysis_members/Registry_analysis_members.xml

@@ -31,3 +31,6 @@
 #include "Registry_moc_streamfunction.xml"
 #include "Registry_ocean_heat_content.xml"
 #include "Registry_mixed_layer_heat_budget.xml"
+#include "Registry_sediment_flux_index.xml"
+#include "Registry_sediment_transport.xml"
+#include "Registry_harmonic_analysis.xml"