Merge branch 'master' of https://github.com/landlab/landlab into gt/i…

…cosphere-grid
landlab · Dec 6, 2023 · 03b9083 · 03b9083
2 parents c74becc + a520f6f
commit 03b9083
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diff --git a/.credits.toml b/.credits.toml
@@ -361,6 +361,14 @@ aliases = [
 alternate_emails = [
 ]
 
+[[tool.landlab.credits.author]]
+name = 'pre-commit-ci[bot]'
+email = '66853113+pre-commit-ci[bot]@users.noreply.github.com'
+aliases = [
+]
+alternate_emails = [
+]
+
 [[tool.landlab.credits.author]]
 name = 'root'
 email = 'root@093548ea-dc74-4ebb-8037-4be9f23db00a'

diff --git a/.mailmap b/.mailmap
@@ -194,4 +194,5 @@ Sebastien Lenard <sebastien.lenard@gmail.com> sebastien-lenard <91671955+sebasti
 Sebastien Lenard <sebastien.lenard@gmail.com> sebastien-lenard <sebastien.lenard@gmail.com>
 Shelby Ahrendt <36043125+shelbyahrendt@users.noreply.github.com> Shelby Ahrendt <36043125+shelbyahrendt@users.noreply.github.com>
 dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
+pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
 root <root@093548ea-dc74-4ebb-8037-4be9f23db00a> root <root@093548ea-dc74-4ebb-8037-4be9f23db00a>
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -14,7 +14,7 @@ repos:
       language: pygrep
 
 - repo: https://github.com/psf/black
-  rev: 23.10.1
+  rev: 23.11.0
   hooks:
   - id: black
     name: black
@@ -37,7 +37,7 @@ repos:
     additional_dependencies: [".[jupyter]"]
 
 - repo: https://github.com/keewis/blackdoc
-  rev: v0.3.8
+  rev: v0.3.9
   hooks:
   - id: blackdoc
     description: "Black for doctests"
@@ -52,7 +52,7 @@ repos:
     - flake8-simplify
 
 - repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.7.0
+  rev: 1.7.1
   hooks:
     - id: nbqa-pyupgrade
       args: ["--py310-plus"]

diff --git a/docs/index.toml b/docs/index.toml
@@ -22,7 +22,7 @@ doc = 'Link-parallel advection flux'
 dtype = 'float64'
 intent = 'out'
 mapping = 'link'
-optional = false
+optional = true
 units = 'm2/y'
 
 [components.AdvectionSolverTVD.info.advection__velocity]
@@ -422,6 +422,59 @@ mapping = 'node'
 optional = false
 units = '-'
 
+[components.ConcentrationTrackerForDiffusion]
+name = 'landlab.components.concentration_tracker.concentration_tracker_for_diffusion.ConcentrationTrackerForDiffusion'
+unit_agnostic = true
+summary = 'Track the concentration of any user-defined property.'
+
+[components.ConcentrationTrackerForDiffusion.info.bedrock_property__concentration]
+doc = 'Mass concentration of property per unit volume of bedrock'
+dtype = 'float64'
+intent = 'out'
+mapping = 'node'
+optional = false
+units = '-/m^3'
+
+[components.ConcentrationTrackerForDiffusion.info.sediment_property__concentration]
+doc = 'Mass concentration of property per unit volume of sediment'
+dtype = 'float64'
+intent = 'out'
+mapping = 'node'
+optional = false
+units = '-/m^3'
+
+[components.ConcentrationTrackerForDiffusion.info.soil__depth]
+doc = 'Depth of soil or weathered bedrock'
+dtype = 'float64'
+intent = 'in'
+mapping = 'node'
+optional = false
+units = 'm'
+
+[components.ConcentrationTrackerForDiffusion.info.soil__flux]
+doc = 'flux of soil in direction of link'
+dtype = 'float64'
+intent = 'in'
+mapping = 'link'
+optional = false
+units = 'm^2/yr'
+
+[components.ConcentrationTrackerForDiffusion.info.soil_production__rate]
+doc = 'rate of soil production at nodes'
+dtype = 'float64'
+intent = 'in'
+mapping = 'node'
+optional = false
+units = 'm/yr'
+
+[components.ConcentrationTrackerForDiffusion.info.topographic__elevation]
+doc = 'Land surface topographic elevation'
+dtype = 'float64'
+intent = 'in'
+mapping = 'node'
+optional = false
+units = 'm'
+
 [components.DepressionFinderAndRouter]
 name = 'landlab.components.depression_finder.lake_mapper.DepressionFinderAndRouter'
 unit_agnostic = true
@@ -2081,7 +2134,7 @@ units = 'm3'
 [components.LinearDiffuser]
 name = 'landlab.components.diffusion.diffusion.LinearDiffuser'
 unit_agnostic = true
-summary = 'This component implements linear diffusion of a Landlab field.'
+summary = 'Linear diffusion of a Landlab field.'
 
 [components.LinearDiffuser.info.hillslope_sediment__unit_volume_flux]
 doc = 'Volume flux per unit width along links'
@@ -2171,38 +2224,38 @@ units = 'm/s'
 [components.ListricKinematicExtender]
 name = 'landlab.components.tectonics.listric_kinematic_extender.ListricKinematicExtender'
 unit_agnostic = true
-summary = 'Apply tectonic extension and subsidence kinematically to a raster or'
+summary = 'Apply tectonic extension kinematically to a raster or'
 
-[components.ListricKinematicExtender.info.cumulative_subsidence_depth]
-doc = 'Cumulative depth of tectonic subsidence'
+[components.ListricKinematicExtender.info.advection__velocity]
+doc = 'Link-parallel advection velocity magnitude'
 dtype = 'float64'
-intent = 'out'
-mapping = 'node'
+intent = 'in'
+mapping = 'link'
 optional = true
-units = 'm'
+units = 'm/y'
 
-[components.ListricKinematicExtender.info.subsidence_rate]
-doc = 'Rate of tectonic subsidence in hangingwall area'
+[components.ListricKinematicExtender.info.fault_plane__elevation]
+doc = 'Elevation of fault plane'
 dtype = 'float64'
 intent = 'out'
 mapping = 'node'
 optional = false
 units = 'm'
 
-[components.ListricKinematicExtender.info.topographic__elevation]
-doc = 'Land surface topographic elevation'
+[components.ListricKinematicExtender.info.hangingwall__thickness]
+doc = 'Thickness of material in hangingwall block'
 dtype = 'float64'
-intent = 'inout'
+intent = 'out'
 mapping = 'node'
 optional = false
 units = 'm'
 
-[components.ListricKinematicExtender.info.upper_crust_thickness]
-doc = 'Thickness of upper crust (arbitrary datum)'
+[components.ListricKinematicExtender.info.topographic__elevation]
+doc = 'Land surface topographic elevation'
 dtype = 'float64'
 intent = 'inout'
 mapping = 'node'
-optional = true
+optional = false
 units = 'm'
 
 [components.LithoLayers]
@@ -3778,6 +3831,7 @@ provided_by = [
 desc = 'Link-parallel advection velocity magnitude'
 used_by = [
   'landlab.components.advection.advection_solver_tvd.AdvectionSolverTVD',
+  'landlab.components.tectonics.listric_kinematic_extender.ListricKinematicExtender',
 ]
 provided_by = []
 
@@ -3888,6 +3942,13 @@ provided_by = [
   'landlab.components.gravel_bedrock_eroder.gravel_bedrock_eroder.GravelBedrockEroder',
 ]
 
+[fields.bedrock_property__concentration]
+desc = 'Mass concentration of property per unit volume of bedrock'
+used_by = []
+provided_by = [
+  'landlab.components.concentration_tracker.concentration_tracker_for_diffusion.ConcentrationTrackerForDiffusion',
+]
+
 [fields.carbonate_production_rate]
 desc = 'Carbonate production rate'
 used_by = []
@@ -4001,13 +4062,6 @@ used_by = [
 ]
 provided_by = []
 
-[fields.cumulative_subsidence_depth]
-desc = 'Cumulative depth of tectonic subsidence'
-used_by = []
-provided_by = [
-  'landlab.components.tectonics.listric_kinematic_extender.ListricKinematicExtender',
-]
-
 [fields.depression__depth]
 desc = 'Depth of depression below its spillway point'
 used_by = []
@@ -4107,6 +4161,13 @@ provided_by = [
   'landlab.components.tidal_flow.tidal_flow_calculator.TidalFlowCalculator',
 ]
 
+[fields.fault_plane__elevation]
+desc = 'Elevation of fault plane'
+used_by = []
+provided_by = [
+  'landlab.components.tectonics.listric_kinematic_extender.ListricKinematicExtender',
+]
+
 [fields.flood_status_code]
 desc = 'Map of flood status (_PIT, _CURRENT_LAKE, _UNFLOODED, or _FLOODED).'
 used_by = []
@@ -4301,6 +4362,13 @@ provided_by = [
   'landlab.components.groundwater.dupuit_percolator.GroundwaterDupuitPercolator',
 ]
 
+[fields.hangingwall__thickness]
+desc = 'Thickness of material in hangingwall block'
+used_by = []
+provided_by = [
+  'landlab.components.tectonics.listric_kinematic_extender.ListricKinematicExtender',
+]
+
 [fields.height_above_drainage__elevation]
 desc = 'Elevation above the nearest channel node'
 used_by = []
@@ -4644,6 +4712,13 @@ provided_by = [
   'landlab.components.sink_fill.sink_fill_barnes.SinkFillerBarnes',
 ]
 
+[fields.sediment_property__concentration]
+desc = 'Mass concentration of property per unit volume of sediment'
+used_by = []
+provided_by = [
+  'landlab.components.concentration_tracker.concentration_tracker_for_diffusion.ConcentrationTrackerForDiffusion',
+]
+
 [fields.slope_coefficient]
 desc = 'Slope coefficient to define channels.'
 used_by = [
@@ -4669,6 +4744,7 @@ provided_by = []
 desc = 'Depth of soil or weathered bedrock'
 used_by = [
   'landlab.components.bedrock_landslider.bedrock_landslider.BedrockLandslider',
+  'landlab.components.concentration_tracker.concentration_tracker_for_diffusion.ConcentrationTrackerForDiffusion',
   'landlab.components.depth_dependent_diffusion.hillslope_depth_dependent_linear_flux.DepthDependentDiffuser',
   'landlab.components.depth_dependent_taylor_soil_creep.hillslope_depth_dependent_taylor_flux.DepthDependentTaylorDiffuser',
   'landlab.components.gravel_bedrock_eroder.gravel_bedrock_eroder.GravelBedrockEroder',
@@ -4689,7 +4765,9 @@ provided_by = [
 
 [fields.soil__flux]
 desc = 'flux of soil in direction of link'
-used_by = []
+used_by = [
+  'landlab.components.concentration_tracker.concentration_tracker_for_diffusion.ConcentrationTrackerForDiffusion',
+]
 provided_by = [
   'landlab.components.depth_dependent_diffusion.hillslope_depth_dependent_linear_flux.DepthDependentDiffuser',
   'landlab.components.depth_dependent_taylor_soil_creep.hillslope_depth_dependent_taylor_flux.DepthDependentTaylorDiffuser',
@@ -4797,6 +4875,7 @@ provided_by = [
 [fields.soil_production__rate]
 desc = 'rate of soil production at nodes'
 used_by = [
+  'landlab.components.concentration_tracker.concentration_tracker_for_diffusion.ConcentrationTrackerForDiffusion',
   'landlab.components.depth_dependent_diffusion.hillslope_depth_dependent_linear_flux.DepthDependentDiffuser',
   'landlab.components.depth_dependent_taylor_soil_creep.hillslope_depth_dependent_taylor_flux.DepthDependentTaylorDiffuser',
 ]
@@ -4821,13 +4900,6 @@ provided_by = [
   'landlab.components.priority_flood_flow_router.priority_flood_flow_router.PriorityFloodFlowRouter',
 ]
 
-[fields.subsidence_rate]
-desc = 'Rate of tectonic subsidence in hangingwall area'
-used_by = []
-provided_by = [
-  'landlab.components.tectonics.listric_kinematic_extender.ListricKinematicExtender',
-]
-
 [fields.surface__evapotranspiration]
 desc = 'actual sum of evaporation and plant transpiration'
 used_by = [
@@ -4982,6 +5054,7 @@ used_by = [
   'landlab.components.bedrock_landslider.bedrock_landslider.BedrockLandslider',
   'landlab.components.carbonate.carbonate_producer.CarbonateProducer',
   'landlab.components.chi_index.channel_chi.ChiFinder',
+  'landlab.components.concentration_tracker.concentration_tracker_for_diffusion.ConcentrationTrackerForDiffusion',
   'landlab.components.depression_finder.lake_mapper.DepressionFinderAndRouter',
   'landlab.components.depth_dependent_diffusion.hillslope_depth_dependent_linear_flux.DepthDependentDiffuser',
   'landlab.components.depth_dependent_taylor_soil_creep.hillslope_depth_dependent_taylor_flux.DepthDependentTaylorDiffuser',
@@ -5122,15 +5195,6 @@ provided_by = [
   'landlab.components.priority_flood_flow_router.priority_flood_flow_router.PriorityFloodFlowRouter',
 ]
 
-[fields.upper_crust_thickness]
-desc = 'Thickness of upper crust (arbitrary datum)'
-used_by = [
-  'landlab.components.tectonics.listric_kinematic_extender.ListricKinematicExtender',
-]
-provided_by = [
-  'landlab.components.tectonics.listric_kinematic_extender.ListricKinematicExtender',
-]
-
 [fields.user_d50]
 desc = 'Median grain size of the bed sediment in each link'
 used_by = [
@@ -5632,7 +5696,6 @@ uncategorized = [
   'landlab.grid.framed_voronoi.FramedVoronoiGrid.link_with_node_status',
   'landlab.grid.framed_voronoi.FramedVoronoiGrid.load',
   'landlab.grid.framed_voronoi.FramedVoronoiGrid.map_link_vector_components_to_node',
-  'landlab.grid.framed_voronoi.FramedVoronoiGrid.map_link_vector_to_nodes',
   'landlab.grid.framed_voronoi.FramedVoronoiGrid.map_node_to_link_lax_wendroff',
   'landlab.grid.framed_voronoi.FramedVoronoiGrid.map_node_to_link_linear_upwind',
   'landlab.grid.framed_voronoi.FramedVoronoiGrid.map_vectors_to_links',
@@ -6049,7 +6112,6 @@ uncategorized = [
   'landlab.grid.hex.HexModelGrid.link_with_node_status',
   'landlab.grid.hex.HexModelGrid.load',
   'landlab.grid.hex.HexModelGrid.map_link_vector_components_to_node',
-  'landlab.grid.hex.HexModelGrid.map_link_vector_to_nodes',
   'landlab.grid.hex.HexModelGrid.map_node_to_link_lax_wendroff',
   'landlab.grid.hex.HexModelGrid.map_node_to_link_linear_upwind',
   'landlab.grid.hex.HexModelGrid.map_vectors_to_links',
@@ -6394,7 +6456,6 @@ uncategorized = [
   'landlab.grid.base.ModelGrid.link_with_angle',
   'landlab.grid.base.ModelGrid.link_with_node_status',
   'landlab.grid.base.ModelGrid.map_link_vector_components_to_node',
-  'landlab.grid.base.ModelGrid.map_link_vector_to_nodes',
   'landlab.grid.base.ModelGrid.map_node_to_link_lax_wendroff',
   'landlab.grid.base.ModelGrid.map_node_to_link_linear_upwind',
   'landlab.grid.base.ModelGrid.map_vectors_to_links',
@@ -6763,7 +6824,6 @@ uncategorized = [
   'landlab.grid.radial.RadialModelGrid.link_with_node_status',
   'landlab.grid.radial.RadialModelGrid.load',
   'landlab.grid.radial.RadialModelGrid.map_link_vector_components_to_node',
-  'landlab.grid.radial.RadialModelGrid.map_link_vector_to_nodes',
   'landlab.grid.radial.RadialModelGrid.map_node_to_link_lax_wendroff',
   'landlab.grid.radial.RadialModelGrid.map_node_to_link_linear_upwind',
   'landlab.grid.radial.RadialModelGrid.map_vectors_to_links',
@@ -7318,7 +7378,6 @@ uncategorized = [
   'landlab.grid.raster.RasterModelGrid.looped_neighbors_at_patch',
   'landlab.grid.raster.RasterModelGrid.map_link_vector_components_to_node',
   'landlab.grid.raster.RasterModelGrid.map_link_vector_components_to_node_raster',
-  'landlab.grid.raster.RasterModelGrid.map_link_vector_to_nodes',
   'landlab.grid.raster.RasterModelGrid.map_node_to_link_lax_wendroff',
   'landlab.grid.raster.RasterModelGrid.map_node_to_link_linear_upwind',
   'landlab.grid.raster.RasterModelGrid.map_vectors_to_links',
@@ -7753,7 +7812,6 @@ uncategorized = [
   'landlab.grid.voronoi.VoronoiDelaunayGrid.link_with_node_status',
   'landlab.grid.voronoi.VoronoiDelaunayGrid.load',
   'landlab.grid.voronoi.VoronoiDelaunayGrid.map_link_vector_components_to_node',
-  'landlab.grid.voronoi.VoronoiDelaunayGrid.map_link_vector_to_nodes',
   'landlab.grid.voronoi.VoronoiDelaunayGrid.map_node_to_link_lax_wendroff',
   'landlab.grid.voronoi.VoronoiDelaunayGrid.map_node_to_link_linear_upwind',
   'landlab.grid.voronoi.VoronoiDelaunayGrid.map_vectors_to_links',

diff --git a/docs/source/reference/components/concentration_tracker.rst b/docs/source/reference/components/concentration_tracker.rst
@@ -0,0 +1,10 @@
+Concentration Tracker
+=====================
+
+ConcentrationTrackerForDiffusion: Track mass concentration of sediment properties based on flux from DepthDependentDiffuser or DepthDependentTaylorDiffuser
+-----------------------------------------------------------------------------------------------------------------------------------------------------------
+
+.. automodule:: landlab.components.concentration_tracker.concentration_tracker_for_diffusion
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/reference/components/index.rst b/docs/source/reference/components/index.rst
@@ -21,6 +21,7 @@ Hillslope geomorphology
    taylor_nonlinear_hillslope_flux
    depth_dependent_taylor_soil_creep
    threshold_eroder
+   concentration_tracker
 
 Fluvial geomorphology
 ---------------------