import matplotlib.colors as cols
import matplotlib.pyplot as plt
import uxarray as ux
+from matplotlib import cm
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from pyremap.descriptor.utility import interp_extrap_corner
@@ -191,6 +192,13 @@ Source code for polaris.viz.spherical
projection = cartopy.crs.PlateCarree(central_longitude=central_longitude)
colormap = config.get(colormap_section, 'colormap_name')
+ cmap = cm.get_cmap(colormap)
+ if config.has_option(colormap_section, 'under_color'):
+ under_color = config.get(colormap_section, 'under_color')
+ cmap.set_under(under_color)
+ if config.has_option(colormap_section, 'over_color'):
+ over_color = config.get(colormap_section, 'over_color')
+ cmap.set_over(over_color)
norm_type = config.get(colormap_section, 'norm_type')
if norm_type == 'linear':
@@ -204,7 +212,7 @@ Source code for polaris.viz.spherical
dtype=float)
plot = gdf_data.hvplot.polygons(
- c=da.name, cmap=colormap, logz=logz,
+ c=da.name, cmap=cmap, logz=logz,
clim=tuple(colorbar_limits),
clabel=colorbar_label,
width=1600, height=800, title=title,
diff --git a/main/_sources/developers_guide/framework/visualization.md.txt b/main/_sources/developers_guide/framework/visualization.md.txt
index 7c5c4292d..ce15e0932 100644
--- a/main/_sources/developers_guide/framework/visualization.md.txt
+++ b/main/_sources/developers_guide/framework/visualization.md.txt
@@ -154,7 +154,13 @@ colormap).
The `colorbar_limits` are the lower and upper bound of the colorbar range.
+There are also two optional config options used to set the colors on either end of the colormap:
+```cfg
+# [optional] colormap set_under and set_over options
+under_color = k
+over_color = orange
+```
### plotting from lat/lon grids
You can use {py:func}`polaris.viz.plot_global_lat_lon_field()` to plot a field
diff --git a/main/_sources/developers_guide/ocean/tasks/correlated_tracers_2d.md.txt b/main/_sources/developers_guide/ocean/tasks/correlated_tracers_2d.md.txt
index 26d1cff6a..63c31402c 100644
--- a/main/_sources/developers_guide/ocean/tasks/correlated_tracers_2d.md.txt
+++ b/main/_sources/developers_guide/ocean/tasks/correlated_tracers_2d.md.txt
@@ -77,6 +77,10 @@ each resolution. The colormap is controlled by these options:
# colormap
colormap_name = viridis
+# [optional] colormap set_under and set_over options
+under_color = k
+over_color = orange
+
# the type of norm used in the colormap
norm_type = linear
diff --git a/main/_sources/developers_guide/ocean/tasks/divergent_2d.md.txt b/main/_sources/developers_guide/ocean/tasks/divergent_2d.md.txt
index b00faeb72..901936796 100644
--- a/main/_sources/developers_guide/ocean/tasks/divergent_2d.md.txt
+++ b/main/_sources/developers_guide/ocean/tasks/divergent_2d.md.txt
@@ -71,6 +71,10 @@ each resolution. The colormap is controlled by these options:
# colormap
colormap_name = viridis
+# [optional] colormap set_under and set_over options
+under_color = k
+over_color = orange
+
# the type of norm used in the colormap
norm_type = linear
diff --git a/main/_sources/developers_guide/ocean/tasks/nondivergent_2d.md.txt b/main/_sources/developers_guide/ocean/tasks/nondivergent_2d.md.txt
index 607e51db1..258396df9 100644
--- a/main/_sources/developers_guide/ocean/tasks/nondivergent_2d.md.txt
+++ b/main/_sources/developers_guide/ocean/tasks/nondivergent_2d.md.txt
@@ -77,6 +77,10 @@ each resolution. The colormap is controlled by these options:
# colormap
colormap_name = viridis
+# [optional] colormap set_under and set_over options
+under_color = k
+over_color = orange
+
# the type of norm used in the colormap
norm_type = linear
diff --git a/main/_sources/developers_guide/ocean/tasks/rotation_2d.md.txt b/main/_sources/developers_guide/ocean/tasks/rotation_2d.md.txt
index 3ebc2908a..4e2cd83a1 100644
--- a/main/_sources/developers_guide/ocean/tasks/rotation_2d.md.txt
+++ b/main/_sources/developers_guide/ocean/tasks/rotation_2d.md.txt
@@ -71,6 +71,10 @@ each resolution. The colormap is controlled by these options:
# colormap
colormap_name = viridis
+# [optional] colormap set_under and set_over options
+under_color = k
+over_color = orange
+
# the type of norm used in the colormap
norm_type = linear
diff --git a/main/developers_guide/framework/visualization.html b/main/developers_guide/framework/visualization.html
index 3ef9f11d5..b7ccd8154 100644
--- a/main/developers_guide/framework/visualization.html
+++ b/main/developers_guide/framework/visualization.html
@@ -253,6 +253,12 @@ plotting from spherical MPAS meshesnorm_type is one of linear (a linear colormap) or log (a logarithmic
colormap).
The colorbar_limits are the lower and upper bound of the colorbar range.
+There are also two optional config options used to set the colors on either end of the colormap:
+# [optional] colormap set_under and set_over options
+under_color = k
+over_color = orange
+
+
plotting from lat/lon grids
diff --git a/main/developers_guide/ocean/tasks/correlated_tracers_2d.html b/main/developers_guide/ocean/tasks/correlated_tracers_2d.html
index 9ba59172d..c3d57afe1 100644
--- a/main/developers_guide/ocean/tasks/correlated_tracers_2d.html
+++ b/main/developers_guide/ocean/tasks/correlated_tracers_2d.html
@@ -205,6 +205,10 @@ viz# colormap
colormap_name = viridis
+# [optional] colormap set_under and set_over options
+under_color = k
+over_color = orange
+
# the type of norm used in the colormap
norm_type = linear
diff --git a/main/developers_guide/ocean/tasks/divergent_2d.html b/main/developers_guide/ocean/tasks/divergent_2d.html
index 4b8cab202..ed2fe1362 100644
--- a/main/developers_guide/ocean/tasks/divergent_2d.html
+++ b/main/developers_guide/ocean/tasks/divergent_2d.html
@@ -199,6 +199,10 @@ viz# colormap
colormap_name = viridis
+# [optional] colormap set_under and set_over options
+under_color = k
+over_color = orange
+
# the type of norm used in the colormap
norm_type = linear
diff --git a/main/developers_guide/ocean/tasks/nondivergent_2d.html b/main/developers_guide/ocean/tasks/nondivergent_2d.html
index 50bdf22c9..24af536fe 100644
--- a/main/developers_guide/ocean/tasks/nondivergent_2d.html
+++ b/main/developers_guide/ocean/tasks/nondivergent_2d.html
@@ -205,6 +205,10 @@ viz# colormap
colormap_name = viridis
+# [optional] colormap set_under and set_over options
+under_color = k
+over_color = orange
+
# the type of norm used in the colormap
norm_type = linear
diff --git a/main/developers_guide/ocean/tasks/rotation_2d.html b/main/developers_guide/ocean/tasks/rotation_2d.html
index c0dcc5d73..b203d0675 100644
--- a/main/developers_guide/ocean/tasks/rotation_2d.html
+++ b/main/developers_guide/ocean/tasks/rotation_2d.html
@@ -199,6 +199,10 @@ viz# colormap
colormap_name = viridis
+# [optional] colormap set_under and set_over options
+under_color = k
+over_color = orange
+
# the type of norm used in the colormap
norm_type = linear
diff --git a/main/searchindex.js b/main/searchindex.js
index 2a6bd0835..39164b52f 100644
--- a/main/searchindex.js
+++ b/main/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["design_docs/index", "design_docs/shared_steps", "design_docs/template", "developers_guide/api", "developers_guide/building_docs", "developers_guide/command_line", "developers_guide/deploying_spack", "developers_guide/docs", "developers_guide/framework/commands", "developers_guide/framework/config", "developers_guide/framework/index", "developers_guide/framework/io", "developers_guide/framework/logging", "developers_guide/framework/mesh", "developers_guide/framework/model", "developers_guide/framework/mpas", "developers_guide/framework/provenance", "developers_guide/framework/remapping", "developers_guide/framework/validation", "developers_guide/framework/visualization", "developers_guide/generated/polaris.Component", "developers_guide/generated/polaris.Component.add_config", "developers_guide/generated/polaris.Component.add_step", "developers_guide/generated/polaris.Component.add_task", "developers_guide/generated/polaris.Component.remove_step", "developers_guide/generated/polaris.ModelStep", "developers_guide/generated/polaris.ModelStep.add_model_config_options", "developers_guide/generated/polaris.ModelStep.add_namelist_file", "developers_guide/generated/polaris.ModelStep.add_streams_file", "developers_guide/generated/polaris.ModelStep.add_yaml_file", "developers_guide/generated/polaris.ModelStep.dynamic_model_config", "developers_guide/generated/polaris.ModelStep.map_yaml_configs", "developers_guide/generated/polaris.ModelStep.map_yaml_options", "developers_guide/generated/polaris.ModelStep.map_yaml_to_namelist", "developers_guide/generated/polaris.ModelStep.partition", "developers_guide/generated/polaris.ModelStep.process_inputs_and_outputs", "developers_guide/generated/polaris.ModelStep.runtime_setup", "developers_guide/generated/polaris.ModelStep.set_model_resources", "developers_guide/generated/polaris.ModelStep.setup", "developers_guide/generated/polaris.ModelStep.update_namelist_pio", "developers_guide/generated/polaris.Step", "developers_guide/generated/polaris.Step.add_dependency", "developers_guide/generated/polaris.Step.add_input_file", "developers_guide/generated/polaris.Step.add_output_file", "developers_guide/generated/polaris.Step.constrain_resources", "developers_guide/generated/polaris.Step.run", "developers_guide/generated/polaris.Step.runtime_setup", "developers_guide/generated/polaris.Step.set_resources", "developers_guide/generated/polaris.Step.set_shared_config", "developers_guide/generated/polaris.Step.setup", "developers_guide/generated/polaris.Step.validate_baselines", "developers_guide/generated/polaris.Task", "developers_guide/generated/polaris.Task.add_step", "developers_guide/generated/polaris.Task.configure", "developers_guide/generated/polaris.Task.remove_step", "developers_guide/generated/polaris.Task.set_shared_config", "developers_guide/generated/polaris.__main__.main", "developers_guide/generated/polaris.cache.update_cache", "developers_guide/generated/polaris.components.get_components", "developers_guide/generated/polaris.config.PolarisConfigParser", "developers_guide/generated/polaris.config.PolarisConfigParser.setup", "developers_guide/generated/polaris.io.download", "developers_guide/generated/polaris.io.symlink", "developers_guide/generated/polaris.io.update_permissions", "developers_guide/generated/polaris.job.clean_up_whitespace", "developers_guide/generated/polaris.job.get_slurm_options", "developers_guide/generated/polaris.job.write_job_script", "developers_guide/generated/polaris.list.list_cases", "developers_guide/generated/polaris.list.list_machines", "developers_guide/generated/polaris.list.list_suites", "developers_guide/generated/polaris.logging.log_method_call", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.build_subdivisions_cell_width_lat_lon", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.get_cell_width", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.get_subdivisions", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.make_jigsaw_mesh", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.run", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.setup", "developers_guide/generated/polaris.mesh.QuasiUniformSphericalMeshStep", "developers_guide/generated/polaris.mesh.QuasiUniformSphericalMeshStep.build_cell_width_lat_lon", "developers_guide/generated/polaris.mesh.QuasiUniformSphericalMeshStep.make_jigsaw_mesh", "developers_guide/generated/polaris.mesh.QuasiUniformSphericalMeshStep.run", "developers_guide/generated/polaris.mesh.QuasiUniformSphericalMeshStep.setup", "developers_guide/generated/polaris.mesh.planar.compute_planar_hex_nx_ny", "developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep", "developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep.run", "developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width", "developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep.setup", "developers_guide/generated/polaris.model_step.make_graph_file", "developers_guide/generated/polaris.mpas.area_for_field", "developers_guide/generated/polaris.mpas.time_index_from_xtime", "developers_guide/generated/polaris.namelist.ingest", "developers_guide/generated/polaris.namelist.parse_replacements", "developers_guide/generated/polaris.namelist.replace", "developers_guide/generated/polaris.namelist.write", "developers_guide/generated/polaris.parallel.get_available_parallel_resources", "developers_guide/generated/polaris.parallel.get_parallel_command", "developers_guide/generated/polaris.parallel.run_command", "developers_guide/generated/polaris.parallel.set_cores_per_node", "developers_guide/generated/polaris.provenance.write", "developers_guide/generated/polaris.remap.MappingFileStep", "developers_guide/generated/polaris.remap.MappingFileStep.dst_from_lon_lat", "developers_guide/generated/polaris.remap.MappingFileStep.dst_from_mpas", "developers_guide/generated/polaris.remap.MappingFileStep.dst_from_points", "developers_guide/generated/polaris.remap.MappingFileStep.dst_from_proj", "developers_guide/generated/polaris.remap.MappingFileStep.dst_global_lon_lat", "developers_guide/generated/polaris.remap.MappingFileStep.get_remapper", "developers_guide/generated/polaris.remap.MappingFileStep.runtime_setup", "developers_guide/generated/polaris.remap.MappingFileStep.src_from_lon_lat", "developers_guide/generated/polaris.remap.MappingFileStep.src_from_mpas", "developers_guide/generated/polaris.remap.MappingFileStep.src_from_proj", "developers_guide/generated/polaris.run.complete_step_run", "developers_guide/generated/polaris.run.load_dependencies", "developers_guide/generated/polaris.run.serial.run_single_step", 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"developers_guide/generated/polaris.yaml.PolarisYaml.update", "developers_guide/generated/polaris.yaml.PolarisYaml.write", "developers_guide/generated/polaris.yaml.main_mpas_to_yaml", "developers_guide/generated/polaris.yaml.mpas_namelist_and_streams_to_yaml", "developers_guide/generated/polaris.yaml.yaml_to_mpas_streams", "developers_guide/machines/anvil", "developers_guide/machines/chicoma", "developers_guide/machines/chrysalis", "developers_guide/machines/compy", "developers_guide/machines/frontier", "developers_guide/machines/index", "developers_guide/machines/perlmutter", "developers_guide/ocean/api", "developers_guide/ocean/framework", "developers_guide/ocean/generated/polaris.ocean.Ocean", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis.compute_error", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis.convergence_parameters", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis.exact_solution", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis.get_output_field", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis.plot_convergence", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis.run", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis.setup", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceForward", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceForward.compute_cell_count", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceForward.dynamic_model_config", "developers_guide/ocean/generated/polaris.ocean.convergence.spherical.SphericalConvergenceForward", "developers_guide/ocean/generated/polaris.ocean.convergence.spherical.SphericalConvergenceForward.compute_cell_count", "developers_guide/ocean/generated/polaris.ocean.ice_shelf.IceShelfTask", "developers_guide/ocean/generated/polaris.ocean.ice_shelf.IceShelfTask.setup_ssh_adjustment_steps", "developers_guide/ocean/generated/polaris.ocean.ice_shelf.SshAdjustment", "developers_guide/ocean/generated/polaris.ocean.ice_shelf.SshAdjustment.run", "developers_guide/ocean/generated/polaris.ocean.ice_shelf.SshForward", "developers_guide/ocean/generated/polaris.ocean.ice_shelf.SshForward.compute_cell_count", "developers_guide/ocean/generated/polaris.ocean.ice_shelf.SshForward.dynamic_model_config", "developers_guide/ocean/generated/polaris.ocean.mesh.spherical.add_spherical_base_mesh_step", "developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep", "developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.compute_cell_count", "developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.constrain_resources", 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"developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.init.Init", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.init.Init.run", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.init.Init.setup", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.restart.Restart", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep.dynamic_model_config", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.rpe.Rpe", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.rpe.Rpe.configure", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.rpe.analysis.Analysis", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.rpe.analysis.Analysis.run", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.rpe.analysis.Analysis.setup", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.threads.Threads", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.validate.Validate", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.validate.Validate.run", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.viz.Viz", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.viz.Viz.run", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.CosineBell", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.CosineBell.configure", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.add_cosine_bell_tasks", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.analysis.Analysis", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.analysis.Analysis.exact_solution", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.forward.Forward", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.forward.Forward.compute_cell_count", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.forward.Forward.dynamic_model_config", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.init.Init", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.init.Init.run", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.init.cosine_bell", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.viz.Viz", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.viz.Viz.run", "developers_guide/ocean/generated/polaris.ocean.tasks.geostrophic.Geostrophic", "developers_guide/ocean/generated/polaris.ocean.tasks.geostrophic.Geostrophic.configure", "developers_guide/ocean/generated/polaris.ocean.tasks.geostrophic.add_geostrophic_tasks", 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260, 269, 283, 285, 290, 340, 342, 359, 360, 361, 362, 368, 369, 372, 376, 377, 378, 380, 385, 386, 389, 395], "whether": [5, 8, 13, 14, 17, 19, 25, 30, 40, 42, 50, 51, 52, 57, 61, 62, 63, 67, 113, 114, 118, 123, 124, 125, 126, 127, 131, 141, 156, 165, 166, 167, 180, 186, 197, 204, 210, 225, 249, 274, 276, 278, 280, 285, 290, 309, 310, 312, 328, 330, 334, 338, 340, 342, 358, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 372, 375, 376, 377, 378, 380, 382, 383, 384, 385, 386, 387, 388, 389, 393], "omega": [5, 25, 31, 32, 33, 129, 167, 170, 171, 236, 262, 318, 335, 341, 359, 361, 373, 379, 382, 384, 388, 389], "config": [5, 7, 8, 10, 11, 12, 13, 17, 19, 21, 25, 26, 29, 30, 31, 32, 33, 40, 41, 42, 48, 51, 53, 55, 61, 65, 66, 77, 79, 82, 95, 96, 97, 98, 99, 115, 117, 118, 123, 125, 126, 129, 130, 131, 132, 134, 135, 153, 154, 156, 157, 160, 165, 167, 170, 171, 173, 180, 186, 187, 197, 198, 204, 210, 211, 222, 225, 236, 249, 252, 262, 280, 281, 294, 296, 297, 298, 299, 300, 301, 305, 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"polaris.seaice.tasks.single_column.forward.Forward": [[350, "polaris-seaice-tasks-single-column-forward-forward"]], "polaris.seaice.tasks.single_column.standard_physics.StandardPhysics": [[351, "polaris-seaice-tasks-single-column-standard-physics-standardphysics"]], "polaris.seaice.tasks.single_column.standard_physics.viz.Viz": [[352, "polaris-seaice-tasks-single-column-standard-physics-viz-viz"]], "polaris.seaice.tasks.single_column.standard_physics.viz.Viz.run": [[353, "polaris-seaice-tasks-single-column-standard-physics-viz-viz-run"]], "SeaIce component": [[354, "seaice-component"]], "Supported Model: MPAS-Seaice": [[355, "supported-model-mpas-seaice"]], "standard_physics_test": [[357, "standard-physics-test"]], "exact_restart_test": [[357, "exact-restart-test"]], "Solver errors when configuring conda environment": [[358, "solver-errors-when-configuring-conda-environment"]], "Proxy on LANL Macs": [[358, "proxy-on-lanl-macs"]], "gethostbyname failed": [[358, "gethostbyname-failed"]], "Glossary": [[359, "glossary"], [360, null]], "Polaris": [[360, "polaris"]], "User's guide": [[360, null]], "Developer's guide": [[360, null]], "Tutorials": [[360, null]], "Compass": [[360, "compass"]], "Developer Tutorial: Adding a new test group": [[361, "developer-tutorial-adding-a-new-test-group"]], "Getting started": [[361, "getting-started"]], "Making a new test group": [[361, "making-a-new-test-group"]], "Adding a \u201cdefault\u201d task": [[361, "adding-a-default-task"]], "Varying resolution and other parameters": [[361, "varying-resolution-and-other-parameters"]], "Adding the init step": [[361, "adding-the-init-step"]], "Creating a horizontal mesh": [[361, "creating-a-horizontal-mesh"]], "Adding a config file": [[361, "adding-a-config-file"]], "Adding the step to the task": [[361, "adding-the-step-to-the-task"]], "Creating a vertical coordinate": [[361, "creating-a-vertical-coordinate"]], "Creating an initial condition": [[361, "creating-an-initial-condition"]], "Adding plots": [[361, "adding-plots"]], "Adding step outputs": [[361, "adding-step-outputs"]], "Adding validation": [[361, "adding-validation"], [361, "id1"]], "Test things out!": [[361, "test-things-out"]], "Adding the forward step": [[361, "adding-the-forward-step"]], "Defining model config options and streams": [[361, "defining-model-config-options-and-streams"]], "Adding the forward step to the task": [[361, "adding-the-forward-step-to-the-task"]], "Adding more validation": [[361, "adding-more-validation"]], "Test the task again!": [[361, "test-the-task-again"]], "Adding a visualization step": [[361, "adding-a-visualization-step"]], "Adding the viz step to the task": [[361, "adding-the-viz-step-to-the-task"]], "Test the task one more time!": [[361, "test-the-task-one-more-time"]], "Adding a second task": [[361, "adding-a-second-task"]], "Enhancements": [[361, "enhancements"]], "Adding model config options in code": [[361, "adding-model-config-options-in-code"]], "Adding dynamic model config options": [[361, "adding-dynamic-model-config-options"]], "Computing the cell count": [[361, "computing-the-cell-count"]], "Adding a shared \u201csuperclass\u201d for tasks": [[361, "adding-a-shared-superclass-for-tasks"]], "Adding a parameter study": [[361, "adding-a-parameter-study"]], "Adding the steps to the task": [[361, "adding-the-steps-to-the-task"]], "Adding the analysis step": [[361, "adding-the-analysis-step"]], "How to (and how not to) pass data between steps": [[361, "how-to-and-how-not-to-pass-data-between-steps"]], "Config Files": [[362, "config-files"]], "A \u201cuser\u201d config file": [[362, "a-user-config-file"]], "Test-case config files": [[362, "test-case-config-files"]], "config options": [[363, "config-options"], [364, "config-options"], [365, "config-options"], [366, "config-options"], [367, "config-options"], [368, "config-options"], [369, "config-options"], [370, "config-options"], [375, "config-options"], [375, "id7"], [375, "id14"], [375, "id22"], [375, "id30"], [375, "id37"], [376, "config-options"], [377, "config-options"], [378, "config-options"], [379, "config-options"], [380, "config-options"], [380, "id7"], [380, "id14"], [380, "id22"], [382, "config-options"], [383, "config-options"], [383, "id7"], [384, "config-options"], [385, "config-options"], [386, "config-options"], [387, "config-options"], [387, "id1"], [387, "id6"], [387, "id13"], [388, "config-options"], [392, "config-options"], [392, "id5"], [392, "id10"], [393, "config-options"]], "Loading and running Polaris on Anvil": [[363, "loading-and-running-polaris-on-anvil"]], "Chicoma-CPU": [[364, "chicoma-cpu"]], "Loading and running Polaris on Chicoma": [[364, "loading-and-running-polaris-on-chicoma"]], "Loading and running Polaris on Chrysalis": [[365, "loading-and-running-polaris-on-chrysalis"]], "Loading and running Polaris on CompyMcNodeFace": [[366, "loading-and-running-polaris-on-compymcnodeface"]], "Loading and running Polaris on Frontier": [[367, "loading-and-running-polaris-on-frontier"]], "Slurm job queueing": [[368, "slurm-job-queueing"]], "MPICH": [[368, "mpich"]], "OpenMPI": [[368, "openmpi"]], "No MPI from conda-forge": [[368, "no-mpi-from-conda-forge"]], "Perlmutter-CPU": [[369, "perlmutter-cpu"]], "Loading and running Polaris on Perlmutter": [[369, "loading-and-running-polaris-on-perlmutter"]], "Jupyter notebook on remote data": [[369, "jupyter-notebook-on-remote-data"]], "Ice shelf": [[370, "ice-shelf"]], "SSH adjustment steps": [[370, "ssh-adjustment-steps"]], "1D Grid type": [[372, "d-grid-type"]], "uniform": [[372, "uniform"]], "tanh_dz": [[372, "tanh-dz"]], "index_tanh_dz": [[372, "index-tanh-dz"]], "60layerPHC": [[372, "layerphc"]], "80layerE3SMv1": [[372, "layere3smv1"]], "100layerE3SMv1": [[372, "id1"]], "3D vertical coordinates": [[372, "d-vertical-coordinates"]], "z-star": [[372, "z-star"]], "z-level": [[372, "z-level"]], "sigma": [[372, "sigma"]], "cosine_bell and cosine_bell_cached_init suite": [[374, "cosine-bell-and-cosine-bell-cached-init-suite"]], "baroclinic channel": [[375, "baroclinic-channel"]], "description": [[375, "description"], [375, "id1"], [375, "id8"], [375, "id16"], [375, "id24"], [376, "description"], [377, "description"], [378, "description"], [379, "description"], [380, "description"], [380, "id1"], [380, "id8"], [380, "id16"], [382, "description"], [383, "description"], [383, "id1"], [384, "description"], [385, "description"], [386, "description"], [387, "description"], [387, "id2"], [387, "id7"], [388, "description"], [392, "description"], [393, "description"]], "suppported models": [[375, "suppported-models"], [376, "suppported-models"], [377, "suppported-models"], [378, "suppported-models"], [379, "suppported-models"], [380, "suppported-models"], [382, "suppported-models"], [383, "suppported-models"], [384, "suppported-models"], [385, "suppported-models"], [386, "suppported-models"], [387, "suppported-models"], [388, "suppported-models"]], "vertical grid": [[375, "vertical-grid"], [375, "id3"], [375, "id10"], [375, "id18"], [375, "id26"], [375, "id33"], [376, "vertical-grid"], [377, "vertical-grid"], [378, "vertical-grid"], [379, "vertical-grid"], [380, "vertical-grid"], [380, "id3"], [380, "id10"], [380, "id18"], [382, "vertical-grid"], [383, "vertical-grid"], [383, "id3"], [384, "vertical-grid"], [385, "vertical-grid"], [386, "vertical-grid"], [387, "vertical-grid"], [387, "id4"], [387, "id9"], [388, "vertical-grid"]], "initial conditions": [[375, "initial-conditions"], [375, "id4"], [375, "id11"], [375, "id19"], [375, "id27"], [375, "id34"], [376, "initial-conditions"], [377, "initial-conditions"], [378, "initial-conditions"], [379, "initial-conditions"], [380, "initial-conditions"], [380, "id4"], [380, "id11"], [380, "id19"], [382, "initial-conditions"], [383, "initial-conditions"], [383, "id4"], [384, "initial-conditions"], [385, "initial-conditions"], [386, "initial-conditions"], [387, "initial-conditions"], [387, "id5"], [387, "id10"], [388, "initial-conditions"], [392, "initial-conditions"], [392, "id2"], [392, "id7"], [393, "initial-conditions"]], "forcing": [[375, "forcing"], [375, "id5"], [375, "id12"], [375, "id20"], [375, "id28"], [375, "id35"], [376, "forcing"], [377, "forcing"], [378, "forcing"], [379, "forcing"], [380, "forcing"], [380, "id5"], [380, "id12"], [380, "id20"], [382, "forcing"], [383, "forcing"], [383, "id5"], [384, "forcing"], [385, "forcing"], [386, "forcing"], [387, "forcing"], [387, "id11"], [388, "forcing"], [392, "forcing"], [392, "id3"], [392, "id8"], [393, "forcing"]], "time step and run duration": [[375, "time-step-and-run-duration"], [375, "id6"], [375, "id13"], [375, "id21"], [375, "id29"], [375, "id36"], [376, "time-step-and-run-duration"], [377, "time-step-and-run-duration"], [378, "time-step-and-run-duration"], [379, "time-step-and-run-duration"], [380, "time-step-and-run-duration"], [380, "id6"], [380, "id13"], [380, "id21"], [382, "time-step-and-run-duration"], [383, "time-step-and-run-duration"], [383, "id6"], [384, "time-step-and-run-duration"], [385, "time-step-and-run-duration"], [386, "time-step-and-run-duration"], [387, "time-step-and-run-duration"], [387, "id12"], [388, "time-step-and-run-duration"], [393, "time-step-and-run-duration"]], "cores": [[375, "cores"], [375, "id15"], [375, "id23"], [375, "id31"], [375, "id38"], [376, "cores"], [377, "cores"], [378, "cores"], [379, "cores"], [380, "cores"], [380, "id15"], [380, "id23"], [382, "cores"], [383, "cores"], [384, "cores"], [385, "cores"], [386, "cores"], [387, "cores"], [387, "id14"], [388, "cores"], [392, "cores"], [392, "id4"], [392, "id9"], [393, "cores"]], "thread": [[375, "thread"]], "correlated tracers 2-d": [[376, "correlated-tracers-2-d"]], "cosine bell": [[377, "cosine-bell"]], "divergent 2-d": [[378, "divergent-2-d"]], "ice shelf 2d": [[380, "ice-shelf-2d"]], "default_with_restart": [[380, "default-with-restart"]], "default_tidal_forcing": [[380, "default-tidal-forcing"]], "inertial gravity wave": [[382, "inertial-gravity-wave"]], "internal wave": [[383, "internal-wave"]], "default task": [[383, "default-task"]], "RPE task": [[383, "rpe-task"]], "manufactured solution": [[384, "manufactured-solution"]], "convergence": [[384, "convergence"]], "nondivergent 2-d": [[385, "nondivergent-2-d"]], "rotation 2-d": [[386, "rotation-2-d"]], "single column": [[387, "single-column"], [392, "single-column"]], "": [[388, "ocean-category-of-task"], [393, "seaice-category-of-task"]], "task_name": [[388, "task-name"], [393, "task-name"]], "Quick Start for Users": [[389, "quick-start-for-users"]], "Quick Start for Users is not yet valid": [[389, null]], "Loading polaris conda and spack environments": [[389, "loading-polaris-conda-and-spack-environments"]], "E3SM supported machines": [[389, "e3sm-supported-machines"]], "Other machines": [[389, "other-machines"]], "Building supported E3SM components as standalone models": [[389, "building-supported-e3sm-components-as-standalone-models"]], "Setting up tasks": [[389, "setting-up-tasks"]], "Running a task": [[389, "running-a-task"]], "Running with a job script": [[389, "running-with-a-job-script"]], "Sea ice component": [[390, "sea-ice-component"]], "standard physics test": [[392, "standard-physics-test"]], "timestep and run duration": [[392, "timestep-and-run-duration"], [392, "id11"]], "visualization": [[392, "visualization"]], "exact restart test": [[392, "exact-restart-test"]]}, "indexentries": {"component (class in polaris)": [[20, "polaris.Component"]], "__init__() (polaris.component method)": [[20, "polaris.Component.__init__"]], "add_config() (polaris.component method)": [[21, "polaris.Component.add_config"]], "add_step() (polaris.component method)": [[22, "polaris.Component.add_step"]], "add_task() (polaris.component method)": [[23, "polaris.Component.add_task"]], "remove_step() (polaris.component method)": [[24, "polaris.Component.remove_step"]], "modelstep (class in polaris)": [[25, "polaris.ModelStep"]], "__init__() (polaris.modelstep method)": [[25, "polaris.ModelStep.__init__"]], "add_model_config_options() (polaris.modelstep method)": [[26, "polaris.ModelStep.add_model_config_options"]], "add_namelist_file() (polaris.modelstep method)": [[27, "polaris.ModelStep.add_namelist_file"]], "add_streams_file() (polaris.modelstep method)": [[28, "polaris.ModelStep.add_streams_file"]], "add_yaml_file() (polaris.modelstep method)": [[29, "polaris.ModelStep.add_yaml_file"]], "dynamic_model_config() (polaris.modelstep method)": [[30, "polaris.ModelStep.dynamic_model_config"]], "map_yaml_configs() (polaris.modelstep method)": [[31, "polaris.ModelStep.map_yaml_configs"]], "map_yaml_options() (polaris.modelstep method)": [[32, "polaris.ModelStep.map_yaml_options"]], "map_yaml_to_namelist() (polaris.modelstep method)": [[33, "polaris.ModelStep.map_yaml_to_namelist"]], "partition() (polaris.modelstep method)": [[34, "polaris.ModelStep.partition"]], "process_inputs_and_outputs() (polaris.modelstep method)": [[35, "polaris.ModelStep.process_inputs_and_outputs"]], "runtime_setup() (polaris.modelstep method)": [[36, "polaris.ModelStep.runtime_setup"]], "set_model_resources() (polaris.modelstep method)": [[37, "polaris.ModelStep.set_model_resources"]], "setup() (polaris.modelstep method)": [[38, "polaris.ModelStep.setup"]], "update_namelist_pio() (polaris.modelstep method)": [[39, "polaris.ModelStep.update_namelist_pio"]], "step (class in polaris)": [[40, "polaris.Step"]], "__init__() (polaris.step method)": [[40, "polaris.Step.__init__"]], "add_dependency() (polaris.step method)": [[41, "polaris.Step.add_dependency"]], "add_input_file() (polaris.step method)": [[42, "polaris.Step.add_input_file"]], "add_output_file() (polaris.step method)": [[43, "polaris.Step.add_output_file"]], "constrain_resources() (polaris.step method)": [[44, "polaris.Step.constrain_resources"]], "run() (polaris.step method)": [[45, "polaris.Step.run"]], "runtime_setup() (polaris.step method)": [[46, "polaris.Step.runtime_setup"]], "set_resources() (polaris.step method)": [[47, "polaris.Step.set_resources"]], "set_shared_config() (polaris.step method)": [[48, "polaris.Step.set_shared_config"]], "setup() (polaris.step method)": [[49, "polaris.Step.setup"]], "validate_baselines() (polaris.step method)": [[50, "polaris.Step.validate_baselines"]], "task (class in polaris)": [[51, "polaris.Task"]], "__init__() (polaris.task method)": [[51, "polaris.Task.__init__"]], "add_step() (polaris.task method)": [[52, "polaris.Task.add_step"]], "configure() (polaris.task method)": [[53, "polaris.Task.configure"]], "remove_step() (polaris.task method)": [[54, "polaris.Task.remove_step"]], "set_shared_config() (polaris.task method)": [[55, "polaris.Task.set_shared_config"]], "main() (in module polaris.__main__)": [[56, "polaris.__main__.main"]], "update_cache() (in module polaris.cache)": [[57, "polaris.cache.update_cache"]], "get_components() (in module polaris.components)": [[58, "polaris.components.get_components"]], "polarisconfigparser (class in polaris.config)": [[59, "polaris.config.PolarisConfigParser"]], "__init__() (polaris.config.polarisconfigparser method)": [[59, "polaris.config.PolarisConfigParser.__init__"]], "setup() (polaris.config.polarisconfigparser method)": [[60, "polaris.config.PolarisConfigParser.setup"]], "download() (in module polaris.io)": [[61, "polaris.io.download"]], "symlink() (in module polaris.io)": [[62, "polaris.io.symlink"]], "update_permissions() (in module polaris.io)": [[63, "polaris.io.update_permissions"]], "clean_up_whitespace() (in module polaris.job)": [[64, "polaris.job.clean_up_whitespace"]], "get_slurm_options() (in module polaris.job)": [[65, "polaris.job.get_slurm_options"]], "write_job_script() (in module polaris.job)": [[66, "polaris.job.write_job_script"]], "list_cases() (in module polaris.list)": [[67, "polaris.list.list_cases"]], "list_machines() (in module polaris.list)": [[68, "polaris.list.list_machines"]], "list_suites() (in module polaris.list)": [[69, "polaris.list.list_suites"]], "log_method_call() (in module polaris.logging)": [[70, "polaris.logging.log_method_call"]], "icosahedralmeshstep (class in polaris.mesh)": [[71, "polaris.mesh.IcosahedralMeshStep"]], "__init__() (polaris.mesh.icosahedralmeshstep method)": [[71, "polaris.mesh.IcosahedralMeshStep.__init__"]], "build_subdivisions_cell_width_lat_lon() (polaris.mesh.icosahedralmeshstep method)": [[72, "polaris.mesh.IcosahedralMeshStep.build_subdivisions_cell_width_lat_lon"]], "get_cell_width() (polaris.mesh.icosahedralmeshstep static method)": [[73, "polaris.mesh.IcosahedralMeshStep.get_cell_width"]], "get_subdivisions() (polaris.mesh.icosahedralmeshstep static method)": [[74, "polaris.mesh.IcosahedralMeshStep.get_subdivisions"]], "make_jigsaw_mesh() (polaris.mesh.icosahedralmeshstep method)": [[75, "polaris.mesh.IcosahedralMeshStep.make_jigsaw_mesh"]], "run() (polaris.mesh.icosahedralmeshstep method)": [[76, "polaris.mesh.IcosahedralMeshStep.run"]], "setup() (polaris.mesh.icosahedralmeshstep method)": [[77, "polaris.mesh.IcosahedralMeshStep.setup"]], "quasiuniformsphericalmeshstep (class in polaris.mesh)": [[78, "polaris.mesh.QuasiUniformSphericalMeshStep"]], "__init__() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[78, "polaris.mesh.QuasiUniformSphericalMeshStep.__init__"]], "build_cell_width_lat_lon() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[79, "polaris.mesh.QuasiUniformSphericalMeshStep.build_cell_width_lat_lon"]], "make_jigsaw_mesh() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[80, "polaris.mesh.QuasiUniformSphericalMeshStep.make_jigsaw_mesh"]], "run() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[81, "polaris.mesh.QuasiUniformSphericalMeshStep.run"]], "setup() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[82, "polaris.mesh.QuasiUniformSphericalMeshStep.setup"]], "compute_planar_hex_nx_ny() (in module polaris.mesh.planar)": [[83, "polaris.mesh.planar.compute_planar_hex_nx_ny"]], "sphericalbasestep (class in polaris.mesh.spherical)": [[84, "polaris.mesh.spherical.SphericalBaseStep"]], "__init__() (polaris.mesh.spherical.sphericalbasestep method)": [[84, "polaris.mesh.spherical.SphericalBaseStep.__init__"]], "run() (polaris.mesh.spherical.sphericalbasestep method)": [[85, "polaris.mesh.spherical.SphericalBaseStep.run"]], "save_and_plot_cell_width() (polaris.mesh.spherical.sphericalbasestep method)": [[86, "polaris.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width"]], "setup() (polaris.mesh.spherical.sphericalbasestep method)": [[87, "polaris.mesh.spherical.SphericalBaseStep.setup"]], "make_graph_file() (in module polaris.model_step)": [[88, "polaris.model_step.make_graph_file"]], "area_for_field() (in module polaris.mpas)": [[89, "polaris.mpas.area_for_field"]], "time_index_from_xtime() (in module polaris.mpas)": [[90, "polaris.mpas.time_index_from_xtime"]], "ingest() (in module polaris.namelist)": [[91, "polaris.namelist.ingest"]], "parse_replacements() (in module polaris.namelist)": [[92, "polaris.namelist.parse_replacements"]], "replace() (in module polaris.namelist)": [[93, "polaris.namelist.replace"]], "write() (in module polaris.namelist)": [[94, "polaris.namelist.write"]], "get_available_parallel_resources() (in module polaris.parallel)": [[95, "polaris.parallel.get_available_parallel_resources"]], "get_parallel_command() (in module polaris.parallel)": [[96, "polaris.parallel.get_parallel_command"]], "run_command() (in module polaris.parallel)": [[97, "polaris.parallel.run_command"]], "set_cores_per_node() (in module polaris.parallel)": [[98, "polaris.parallel.set_cores_per_node"]], "write() (in module polaris.provenance)": [[99, "polaris.provenance.write"]], "mappingfilestep (class in polaris.remap)": [[100, "polaris.remap.MappingFileStep"]], "__init__() (polaris.remap.mappingfilestep method)": [[100, "polaris.remap.MappingFileStep.__init__"]], "dst_from_lon_lat() (polaris.remap.mappingfilestep method)": [[101, "polaris.remap.MappingFileStep.dst_from_lon_lat"]], "dst_from_mpas() (polaris.remap.mappingfilestep method)": [[102, "polaris.remap.MappingFileStep.dst_from_mpas"]], "dst_from_points() (polaris.remap.mappingfilestep method)": [[103, "polaris.remap.MappingFileStep.dst_from_points"]], "dst_from_proj() (polaris.remap.mappingfilestep method)": [[104, "polaris.remap.MappingFileStep.dst_from_proj"]], "dst_global_lon_lat() (polaris.remap.mappingfilestep method)": [[105, "polaris.remap.MappingFileStep.dst_global_lon_lat"]], "get_remapper() (polaris.remap.mappingfilestep method)": [[106, "polaris.remap.MappingFileStep.get_remapper"]], "runtime_setup() (polaris.remap.mappingfilestep method)": [[107, "polaris.remap.MappingFileStep.runtime_setup"]], "src_from_lon_lat() (polaris.remap.mappingfilestep method)": [[108, "polaris.remap.MappingFileStep.src_from_lon_lat"]], "src_from_mpas() (polaris.remap.mappingfilestep method)": [[109, "polaris.remap.MappingFileStep.src_from_mpas"]], "src_from_proj() (polaris.remap.mappingfilestep method)": [[110, "polaris.remap.MappingFileStep.src_from_proj"]], "complete_step_run() (in module polaris.run)": [[111, "polaris.run.complete_step_run"]], "load_dependencies() (in module polaris.run)": [[112, "polaris.run.load_dependencies"]], "run_single_step() (in module polaris.run.serial)": [[113, "polaris.run.serial.run_single_step"]], "run_tasks() (in module polaris.run.serial)": [[114, "polaris.run.serial.run_tasks"]], "setup_config() (in module polaris.run)": [[115, "polaris.run.setup_config"]], "unpickle_suite() (in module polaris.run)": [[116, "polaris.run.unpickle_suite"]], "setup_task() (in module polaris.setup)": [[117, "polaris.setup.setup_task"]], "setup_tasks() (in module polaris.setup)": [[118, "polaris.setup.setup_tasks"]], "read() (in module polaris.streams)": [[119, "polaris.streams.read"]], "update_defaults() (in module polaris.streams)": [[120, "polaris.streams.update_defaults"]], "update_tree() (in module polaris.streams)": [[121, "polaris.streams.update_tree"]], "write() (in module polaris.streams)": [[122, "polaris.streams.write"]], "setup_suite() (in module polaris.suite)": [[123, "polaris.suite.setup_suite"]], "compare_variables() (in module polaris.validate)": [[124, "polaris.validate.compare_variables"]], "plot_global_lat_lon_field() (in module polaris.viz)": [[125, "polaris.viz.plot_global_lat_lon_field"]], "plot_global_mpas_field() (in module polaris.viz)": [[126, "polaris.viz.plot_global_mpas_field"]], "plot_horiz_field() (in module polaris.viz)": [[127, "polaris.viz.plot_horiz_field"]], "use_mplstyle() (in module polaris.viz)": [[128, "polaris.viz.use_mplstyle"]], "polarisyaml (class in polaris.yaml)": [[129, "polaris.yaml.PolarisYaml"]], "__init__() 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[[146, "polaris.ocean.convergence.ConvergenceAnalysis.__init__"]], "compute_error() (polaris.ocean.convergence.convergenceanalysis method)": [[147, "polaris.ocean.convergence.ConvergenceAnalysis.compute_error"]], "convergence_parameters() (polaris.ocean.convergence.convergenceanalysis method)": [[148, "polaris.ocean.convergence.ConvergenceAnalysis.convergence_parameters"]], "exact_solution() (polaris.ocean.convergence.convergenceanalysis method)": [[149, "polaris.ocean.convergence.ConvergenceAnalysis.exact_solution"]], "get_output_field() (polaris.ocean.convergence.convergenceanalysis method)": [[150, "polaris.ocean.convergence.ConvergenceAnalysis.get_output_field"]], "plot_convergence() (polaris.ocean.convergence.convergenceanalysis method)": [[151, "polaris.ocean.convergence.ConvergenceAnalysis.plot_convergence"]], "run() (polaris.ocean.convergence.convergenceanalysis method)": [[152, "polaris.ocean.convergence.ConvergenceAnalysis.run"]], "setup() (polaris.ocean.convergence.convergenceanalysis method)": [[153, "polaris.ocean.convergence.ConvergenceAnalysis.setup"]], "convergenceforward (class in polaris.ocean.convergence)": [[154, "polaris.ocean.convergence.ConvergenceForward"]], "__init__() (polaris.ocean.convergence.convergenceforward method)": [[154, "polaris.ocean.convergence.ConvergenceForward.__init__"]], "compute_cell_count() (polaris.ocean.convergence.convergenceforward method)": [[155, "polaris.ocean.convergence.ConvergenceForward.compute_cell_count"]], "dynamic_model_config() (polaris.ocean.convergence.convergenceforward method)": [[156, "polaris.ocean.convergence.ConvergenceForward.dynamic_model_config"]], "sphericalconvergenceforward (class in polaris.ocean.convergence.spherical)": [[157, "polaris.ocean.convergence.spherical.SphericalConvergenceForward"]], "__init__() (polaris.ocean.convergence.spherical.sphericalconvergenceforward method)": [[157, 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polaris.ocean.ice_shelf)": [[163, "polaris.ocean.ice_shelf.SshForward"]], "__init__() (polaris.ocean.ice_shelf.sshforward method)": [[163, "polaris.ocean.ice_shelf.SshForward.__init__"]], "compute_cell_count() (polaris.ocean.ice_shelf.sshforward method)": [[164, "polaris.ocean.ice_shelf.SshForward.compute_cell_count"]], "dynamic_model_config() (polaris.ocean.ice_shelf.sshforward method)": [[165, "polaris.ocean.ice_shelf.SshForward.dynamic_model_config"]], "add_spherical_base_mesh_step() (in module polaris.ocean.mesh.spherical)": [[166, "polaris.ocean.mesh.spherical.add_spherical_base_mesh_step"]], "oceanmodelstep (class in polaris.ocean.model)": [[167, "polaris.ocean.model.OceanModelStep"]], "__init__() (polaris.ocean.model.oceanmodelstep method)": [[167, "polaris.ocean.model.OceanModelStep.__init__"]], "compute_cell_count() (polaris.ocean.model.oceanmodelstep method)": [[168, "polaris.ocean.model.OceanModelStep.compute_cell_count"]], "constrain_resources() 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method)": [[209, "polaris.ocean.tasks.cosine_bell.viz.Viz.run"]], "geostrophic (class in polaris.ocean.tasks.geostrophic)": [[210, "polaris.ocean.tasks.geostrophic.Geostrophic"]], "__init__() (polaris.ocean.tasks.geostrophic.geostrophic method)": [[210, "polaris.ocean.tasks.geostrophic.Geostrophic.__init__"]], "configure() (polaris.ocean.tasks.geostrophic.geostrophic method)": [[211, "polaris.ocean.tasks.geostrophic.Geostrophic.configure"]], "add_geostrophic_tasks() (in module polaris.ocean.tasks.geostrophic)": [[212, "polaris.ocean.tasks.geostrophic.add_geostrophic_tasks"]], "analysis (class in polaris.ocean.tasks.geostrophic.analysis)": [[213, "polaris.ocean.tasks.geostrophic.analysis.Analysis"]], "__init__() (polaris.ocean.tasks.geostrophic.analysis.analysis method)": [[213, "polaris.ocean.tasks.geostrophic.analysis.Analysis.__init__"]], "exact_solution() (polaris.ocean.tasks.geostrophic.analysis.analysis method)": [[214, 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"polaris.ocean.tasks.inertial_gravity_wave.analysis.Analysis"]], "__init__() (polaris.ocean.tasks.inertial_gravity_wave.analysis.analysis method)": [[234, "polaris.ocean.tasks.inertial_gravity_wave.analysis.Analysis.__init__"]], "exact_solution() (polaris.ocean.tasks.inertial_gravity_wave.analysis.analysis method)": [[235, "polaris.ocean.tasks.inertial_gravity_wave.analysis.Analysis.exact_solution"]], "exactsolution (class in polaris.ocean.tasks.inertial_gravity_wave.exact_solution)": [[236, "polaris.ocean.tasks.inertial_gravity_wave.exact_solution.ExactSolution"]], "__init__() (polaris.ocean.tasks.inertial_gravity_wave.exact_solution.exactsolution method)": [[236, "polaris.ocean.tasks.inertial_gravity_wave.exact_solution.ExactSolution.__init__"]], "normal_velocity() (polaris.ocean.tasks.inertial_gravity_wave.exact_solution.exactsolution method)": [[237, "polaris.ocean.tasks.inertial_gravity_wave.exact_solution.ExactSolution.normal_velocity"]], "ssh() (polaris.ocean.tasks.inertial_gravity_wave.exact_solution.exactsolution method)": [[238, "polaris.ocean.tasks.inertial_gravity_wave.exact_solution.ExactSolution.ssh"]], "forward (class in polaris.ocean.tasks.inertial_gravity_wave.forward)": [[239, "polaris.ocean.tasks.inertial_gravity_wave.forward.Forward"]], "__init__() (polaris.ocean.tasks.inertial_gravity_wave.forward.forward method)": [[239, "polaris.ocean.tasks.inertial_gravity_wave.forward.Forward.__init__"]], "compute_cell_count() (polaris.ocean.tasks.inertial_gravity_wave.forward.forward method)": [[240, "polaris.ocean.tasks.inertial_gravity_wave.forward.Forward.compute_cell_count"]], "init (class in polaris.ocean.tasks.inertial_gravity_wave.init)": [[241, "polaris.ocean.tasks.inertial_gravity_wave.init.Init"]], "__init__() (polaris.ocean.tasks.inertial_gravity_wave.init.init method)": [[241, "polaris.ocean.tasks.inertial_gravity_wave.init.Init.__init__"]], "run() (polaris.ocean.tasks.inertial_gravity_wave.init.init method)": [[242, "polaris.ocean.tasks.inertial_gravity_wave.init.Init.run"]], "viz (class in polaris.ocean.tasks.inertial_gravity_wave.viz)": [[243, "polaris.ocean.tasks.inertial_gravity_wave.viz.Viz"]], "__init__() (polaris.ocean.tasks.inertial_gravity_wave.viz.viz method)": [[243, "polaris.ocean.tasks.inertial_gravity_wave.viz.Viz.__init__"]], "run() (polaris.ocean.tasks.inertial_gravity_wave.viz.viz method)": [[244, "polaris.ocean.tasks.inertial_gravity_wave.viz.Viz.run"]], "add_internal_wave_tasks() (in module polaris.ocean.tasks.internal_wave)": [[245, "polaris.ocean.tasks.internal_wave.add_internal_wave_tasks"]], "default (class in polaris.ocean.tasks.internal_wave.default)": [[246, "polaris.ocean.tasks.internal_wave.default.Default"]], "__init__() (polaris.ocean.tasks.internal_wave.default.default method)": [[246, "polaris.ocean.tasks.internal_wave.default.Default.__init__"]], "forward (class in polaris.ocean.tasks.internal_wave.forward)": [[247, "polaris.ocean.tasks.internal_wave.forward.Forward"]], "__init__() (polaris.ocean.tasks.internal_wave.forward.forward method)": [[247, "polaris.ocean.tasks.internal_wave.forward.Forward.__init__"]], "compute_cell_count() (polaris.ocean.tasks.internal_wave.forward.forward method)": [[248, "polaris.ocean.tasks.internal_wave.forward.Forward.compute_cell_count"]], "dynamic_model_config() (polaris.ocean.tasks.internal_wave.forward.forward method)": [[249, "polaris.ocean.tasks.internal_wave.forward.Forward.dynamic_model_config"]], "init (class in polaris.ocean.tasks.internal_wave.init)": [[250, "polaris.ocean.tasks.internal_wave.init.Init"]], "__init__() (polaris.ocean.tasks.internal_wave.init.init method)": [[250, "polaris.ocean.tasks.internal_wave.init.Init.__init__"]], "run() (polaris.ocean.tasks.internal_wave.init.init method)": [[251, "polaris.ocean.tasks.internal_wave.init.Init.run"]], "rpe (class in polaris.ocean.tasks.internal_wave.rpe)": [[252, "polaris.ocean.tasks.internal_wave.rpe.Rpe"]], "__init__() (polaris.ocean.tasks.internal_wave.rpe.rpe method)": [[252, "polaris.ocean.tasks.internal_wave.rpe.Rpe.__init__"]], "configure() (polaris.ocean.tasks.internal_wave.rpe.rpe method)": [[253, "polaris.ocean.tasks.internal_wave.rpe.Rpe.configure"]], "analysis (class in polaris.ocean.tasks.internal_wave.rpe.analysis)": [[254, "polaris.ocean.tasks.internal_wave.rpe.analysis.Analysis"]], "__init__() (polaris.ocean.tasks.internal_wave.rpe.analysis.analysis method)": [[254, "polaris.ocean.tasks.internal_wave.rpe.analysis.Analysis.__init__"]], "run() (polaris.ocean.tasks.internal_wave.rpe.analysis.analysis method)": [[255, "polaris.ocean.tasks.internal_wave.rpe.analysis.Analysis.run"]], "viz (class in polaris.ocean.tasks.internal_wave.viz)": [[256, "polaris.ocean.tasks.internal_wave.viz.Viz"]], "__init__() (polaris.ocean.tasks.internal_wave.viz.viz method)": [[256, "polaris.ocean.tasks.internal_wave.viz.Viz.__init__"]], "run() (polaris.ocean.tasks.internal_wave.viz.viz method)": [[257, "polaris.ocean.tasks.internal_wave.viz.Viz.run"]], "manufacturedsolution (class in polaris.ocean.tasks.manufactured_solution)": [[258, "polaris.ocean.tasks.manufactured_solution.ManufacturedSolution"]], "__init__() (polaris.ocean.tasks.manufactured_solution.manufacturedsolution method)": [[258, "polaris.ocean.tasks.manufactured_solution.ManufacturedSolution.__init__"]], "add_manufactured_solution_tasks() (in module polaris.ocean.tasks.manufactured_solution)": [[259, "polaris.ocean.tasks.manufactured_solution.add_manufactured_solution_tasks"]], "analysis (class in polaris.ocean.tasks.manufactured_solution.analysis)": [[260, "polaris.ocean.tasks.manufactured_solution.analysis.Analysis"]], "__init__() (polaris.ocean.tasks.manufactured_solution.analysis.analysis method)": [[260, "polaris.ocean.tasks.manufactured_solution.analysis.Analysis.__init__"]], "exact_solution() (polaris.ocean.tasks.manufactured_solution.analysis.analysis method)": [[261, "polaris.ocean.tasks.manufactured_solution.analysis.Analysis.exact_solution"]], "exactsolution (class in polaris.ocean.tasks.manufactured_solution.exact_solution)": [[262, "polaris.ocean.tasks.manufactured_solution.exact_solution.ExactSolution"]], "__init__() (polaris.ocean.tasks.manufactured_solution.exact_solution.exactsolution method)": [[262, "polaris.ocean.tasks.manufactured_solution.exact_solution.ExactSolution.__init__"]], "normal_velocity() (polaris.ocean.tasks.manufactured_solution.exact_solution.exactsolution method)": [[263, "polaris.ocean.tasks.manufactured_solution.exact_solution.ExactSolution.normal_velocity"]], "ssh() (polaris.ocean.tasks.manufactured_solution.exact_solution.exactsolution method)": [[264, "polaris.ocean.tasks.manufactured_solution.exact_solution.ExactSolution.ssh"]], "forward (class in polaris.ocean.tasks.manufactured_solution.forward)": [[265, "polaris.ocean.tasks.manufactured_solution.forward.Forward"]], "__init__() (polaris.ocean.tasks.manufactured_solution.forward.forward method)": [[265, "polaris.ocean.tasks.manufactured_solution.forward.Forward.__init__"]], "compute_cell_count() (polaris.ocean.tasks.manufactured_solution.forward.forward method)": [[266, "polaris.ocean.tasks.manufactured_solution.forward.Forward.compute_cell_count"]], "init (class in polaris.ocean.tasks.manufactured_solution.init)": [[267, "polaris.ocean.tasks.manufactured_solution.init.Init"]], "__init__() (polaris.ocean.tasks.manufactured_solution.init.init method)": [[267, "polaris.ocean.tasks.manufactured_solution.init.Init.__init__"]], "run() (polaris.ocean.tasks.manufactured_solution.init.init method)": [[268, "polaris.ocean.tasks.manufactured_solution.init.Init.run"]], "setup() (polaris.ocean.tasks.manufactured_solution.init.init method)": [[269, "polaris.ocean.tasks.manufactured_solution.init.Init.setup"]], "viz (class in polaris.ocean.tasks.manufactured_solution.viz)": [[270, "polaris.ocean.tasks.manufactured_solution.viz.Viz"]], "__init__() (polaris.ocean.tasks.manufactured_solution.viz.viz method)": [[270, "polaris.ocean.tasks.manufactured_solution.viz.Viz.__init__"]], "run() (polaris.ocean.tasks.manufactured_solution.viz.viz method)": [[271, "polaris.ocean.tasks.manufactured_solution.viz.Viz.run"]], "add_single_column_tasks() (in module polaris.ocean.tasks.single_column)": [[272, "polaris.ocean.tasks.single_column.add_single_column_tasks"]], "cvmix (class in polaris.ocean.tasks.single_column.cvmix)": [[273, "polaris.ocean.tasks.single_column.cvmix.CVMix"]], "__init__() (polaris.ocean.tasks.single_column.cvmix.cvmix method)": [[273, "polaris.ocean.tasks.single_column.cvmix.CVMix.__init__"]], "forward (class in polaris.ocean.tasks.single_column.forward)": [[274, "polaris.ocean.tasks.single_column.forward.Forward"]], "__init__() (polaris.ocean.tasks.single_column.forward.forward method)": [[274, "polaris.ocean.tasks.single_column.forward.Forward.__init__"]], "idealage (class in polaris.ocean.tasks.single_column.ideal_age)": [[275, "polaris.ocean.tasks.single_column.ideal_age.IdealAge"]], "__init__() (polaris.ocean.tasks.single_column.ideal_age.idealage method)": [[275, "polaris.ocean.tasks.single_column.ideal_age.IdealAge.__init__"]], "init (class in polaris.ocean.tasks.single_column.init)": [[276, "polaris.ocean.tasks.single_column.init.Init"]], "__init__() (polaris.ocean.tasks.single_column.init.init method)": [[276, "polaris.ocean.tasks.single_column.init.Init.__init__"]], "run() (polaris.ocean.tasks.single_column.init.init method)": [[277, "polaris.ocean.tasks.single_column.init.Init.run"]], "viz (class in polaris.ocean.tasks.single_column.viz)": [[278, "polaris.ocean.tasks.single_column.viz.Viz"]], "__init__() (polaris.ocean.tasks.single_column.viz.viz method)": [[278, "polaris.ocean.tasks.single_column.viz.Viz.__init__"]], "run() (polaris.ocean.tasks.single_column.viz.viz method)": [[279, "polaris.ocean.tasks.single_column.viz.Viz.run"]], "spheretransport (class in polaris.ocean.tasks.sphere_transport)": [[280, "polaris.ocean.tasks.sphere_transport.SphereTransport"]], "__init__() (polaris.ocean.tasks.sphere_transport.spheretransport method)": [[280, "polaris.ocean.tasks.sphere_transport.SphereTransport.__init__"]], "configure() (polaris.ocean.tasks.sphere_transport.spheretransport method)": [[281, "polaris.ocean.tasks.sphere_transport.SphereTransport.configure"]], "add_sphere_transport_tasks() (in module polaris.ocean.tasks.sphere_transport)": [[282, "polaris.ocean.tasks.sphere_transport.add_sphere_transport_tasks"]], "analysis (class in polaris.ocean.tasks.sphere_transport.analysis)": [[283, "polaris.ocean.tasks.sphere_transport.analysis.Analysis"]], "__init__() (polaris.ocean.tasks.sphere_transport.analysis.analysis method)": [[283, "polaris.ocean.tasks.sphere_transport.analysis.Analysis.__init__"]], "convergence_parameters() (polaris.ocean.tasks.sphere_transport.analysis.analysis method)": [[284, "polaris.ocean.tasks.sphere_transport.analysis.Analysis.convergence_parameters"]], "filamentanalysis (class in polaris.ocean.tasks.sphere_transport.filament_analysis)": [[285, "polaris.ocean.tasks.sphere_transport.filament_analysis.FilamentAnalysis"]], "__init__() (polaris.ocean.tasks.sphere_transport.filament_analysis.filamentanalysis method)": [[285, "polaris.ocean.tasks.sphere_transport.filament_analysis.FilamentAnalysis.__init__"]], "run() (polaris.ocean.tasks.sphere_transport.filament_analysis.filamentanalysis method)": [[286, "polaris.ocean.tasks.sphere_transport.filament_analysis.FilamentAnalysis.run"]], "forward (class in polaris.ocean.tasks.sphere_transport.forward)": [[287, "polaris.ocean.tasks.sphere_transport.forward.Forward"]], "__init__() (polaris.ocean.tasks.sphere_transport.forward.forward method)": [[287, "polaris.ocean.tasks.sphere_transport.forward.Forward.__init__"]], "init (class in polaris.ocean.tasks.sphere_transport.init)": [[288, "polaris.ocean.tasks.sphere_transport.init.Init"]], "__init__() (polaris.ocean.tasks.sphere_transport.init.init method)": [[288, "polaris.ocean.tasks.sphere_transport.init.Init.__init__"]], "run() (polaris.ocean.tasks.sphere_transport.init.init method)": [[289, "polaris.ocean.tasks.sphere_transport.init.Init.run"]], "mixinganalysis (class in polaris.ocean.tasks.sphere_transport.mixing_analysis)": [[290, "polaris.ocean.tasks.sphere_transport.mixing_analysis.MixingAnalysis"]], "__init__() (polaris.ocean.tasks.sphere_transport.mixing_analysis.mixinganalysis method)": [[290, "polaris.ocean.tasks.sphere_transport.mixing_analysis.MixingAnalysis.__init__"]], "run() (polaris.ocean.tasks.sphere_transport.mixing_analysis.mixinganalysis method)": [[291, "polaris.ocean.tasks.sphere_transport.mixing_analysis.MixingAnalysis.run"]], "viz (class in polaris.ocean.tasks.sphere_transport.viz)": [[292, "polaris.ocean.tasks.sphere_transport.viz.Viz"]], "__init__() (polaris.ocean.tasks.sphere_transport.viz.viz method)": [[292, "polaris.ocean.tasks.sphere_transport.viz.Viz.__init__"]], "run() (polaris.ocean.tasks.sphere_transport.viz.viz method)": [[293, "polaris.ocean.tasks.sphere_transport.viz.Viz.run"]], "generate_1d_grid() (in module polaris.ocean.vertical.grid_1d)": [[294, "polaris.ocean.vertical.grid_1d.generate_1d_grid"]], "write_1d_grid() (in module polaris.ocean.vertical.grid_1d)": [[295, "polaris.ocean.vertical.grid_1d.write_1d_grid"]], "init_vertical_coord() (in module polaris.ocean.vertical)": [[296, "polaris.ocean.vertical.init_vertical_coord"]], "alter_bottom_depth() (in module polaris.ocean.vertical.partial_cells)": [[297, "polaris.ocean.vertical.partial_cells.alter_bottom_depth"]], "alter_ssh() (in module polaris.ocean.vertical.partial_cells)": [[298, "polaris.ocean.vertical.partial_cells.alter_ssh"]], "init_sigma_vertical_coord() (in module polaris.ocean.vertical.sigma)": [[299, "polaris.ocean.vertical.sigma.init_sigma_vertical_coord"]], "update_sigma_layer_thickness() (in module polaris.ocean.vertical.sigma)": [[300, "polaris.ocean.vertical.sigma.update_sigma_layer_thickness"]], "update_layer_thickness() (in module polaris.ocean.vertical)": [[301, "polaris.ocean.vertical.update_layer_thickness"]], "compute_min_max_level_cell() (in module polaris.ocean.vertical.zlevel)": [[302, "polaris.ocean.vertical.zlevel.compute_min_max_level_cell"]], "compute_z_level_layer_thickness() (in module polaris.ocean.vertical.zlevel)": [[303, "polaris.ocean.vertical.zlevel.compute_z_level_layer_thickness"]], "compute_z_level_resting_thickness() (in module polaris.ocean.vertical.zlevel)": [[304, "polaris.ocean.vertical.zlevel.compute_z_level_resting_thickness"]], "init_z_level_vertical_coord() (in module polaris.ocean.vertical.zlevel)": [[305, "polaris.ocean.vertical.zlevel.init_z_level_vertical_coord"]], "update_z_level_layer_thickness() (in module polaris.ocean.vertical.zlevel)": [[306, "polaris.ocean.vertical.zlevel.update_z_level_layer_thickness"]], "init_z_star_vertical_coord() (in module polaris.ocean.vertical.zstar)": [[307, "polaris.ocean.vertical.zstar.init_z_star_vertical_coord"]], "update_z_star_layer_thickness() (in module polaris.ocean.vertical.zstar)": [[308, "polaris.ocean.vertical.zstar.update_z_star_layer_thickness"]], "compute_transect() (in module polaris.ocean.viz)": [[309, "polaris.ocean.viz.compute_transect"]], "plot_transect() (in module polaris.ocean.viz)": [[310, "polaris.ocean.viz.plot_transect"]], "find_planar_transect_cells_and_weights() (in module polaris.ocean.viz.transect.horiz)": [[311, "polaris.ocean.viz.transect.horiz.find_planar_transect_cells_and_weights"]], "find_spherical_transect_cells_and_weights() (in module polaris.ocean.viz.transect.horiz)": [[312, "polaris.ocean.viz.transect.horiz.find_spherical_transect_cells_and_weights"]], "make_triangle_tree() (in module polaris.ocean.viz.transect.horiz)": [[313, "polaris.ocean.viz.transect.horiz.make_triangle_tree"]], "mesh_to_triangles() (in module polaris.ocean.viz.transect.horiz)": [[314, "polaris.ocean.viz.transect.horiz.mesh_to_triangles"]], "find_transect_levels_and_weights() (in module polaris.ocean.viz.transect.vert)": [[315, "polaris.ocean.viz.transect.vert.find_transect_levels_and_weights"]], "interp_mpas_to_transect_cells() (in module polaris.ocean.viz.transect.vert)": [[316, "polaris.ocean.viz.transect.vert.interp_mpas_to_transect_cells"]], "interp_mpas_to_transect_nodes() (in module polaris.ocean.viz.transect.vert)": [[317, "polaris.ocean.viz.transect.vert.interp_mpas_to_transect_nodes"]], "seaice (class in polaris.seaice)": [[345, "polaris.seaice.SeaIce"]], "__init__() (polaris.seaice.seaice method)": [[345, "polaris.seaice.SeaIce.__init__"]], "add_single_column_tasks() (in module polaris.seaice.tasks.single_column)": [[346, "polaris.seaice.tasks.single_column.add_single_column_tasks"]], "exactrestart (class in polaris.seaice.tasks.single_column.exact_restart)": [[347, "polaris.seaice.tasks.single_column.exact_restart.ExactRestart"]], "__init__() (polaris.seaice.tasks.single_column.exact_restart.exactrestart method)": [[347, "polaris.seaice.tasks.single_column.exact_restart.ExactRestart.__init__"]], "validate (class in polaris.seaice.tasks.single_column.exact_restart.validate)": [[348, "polaris.seaice.tasks.single_column.exact_restart.validate.Validate"]], "__init__() (polaris.seaice.tasks.single_column.exact_restart.validate.validate method)": [[348, "polaris.seaice.tasks.single_column.exact_restart.validate.Validate.__init__"]], "run() (polaris.seaice.tasks.single_column.exact_restart.validate.validate method)": [[349, "polaris.seaice.tasks.single_column.exact_restart.validate.Validate.run"]], "forward (class in polaris.seaice.tasks.single_column.forward)": [[350, "polaris.seaice.tasks.single_column.forward.Forward"]], "__init__() (polaris.seaice.tasks.single_column.forward.forward method)": [[350, "polaris.seaice.tasks.single_column.forward.Forward.__init__"]], "standardphysics (class in polaris.seaice.tasks.single_column.standard_physics)": [[351, "polaris.seaice.tasks.single_column.standard_physics.StandardPhysics"]], "__init__() (polaris.seaice.tasks.single_column.standard_physics.standardphysics method)": [[351, "polaris.seaice.tasks.single_column.standard_physics.StandardPhysics.__init__"]], "viz (class in polaris.seaice.tasks.single_column.standard_physics.viz)": [[352, "polaris.seaice.tasks.single_column.standard_physics.viz.Viz"]], "__init__() (polaris.seaice.tasks.single_column.standard_physics.viz.viz method)": [[352, "polaris.seaice.tasks.single_column.standard_physics.viz.Viz.__init__"]], "run() (polaris.seaice.tasks.single_column.standard_physics.viz.viz method)": [[353, "polaris.seaice.tasks.single_column.standard_physics.viz.Viz.run"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["design_docs/index", "design_docs/shared_steps", "design_docs/template", "developers_guide/api", "developers_guide/building_docs", "developers_guide/command_line", "developers_guide/deploying_spack", "developers_guide/docs", "developers_guide/framework/commands", "developers_guide/framework/config", "developers_guide/framework/index", "developers_guide/framework/io", "developers_guide/framework/logging", "developers_guide/framework/mesh", "developers_guide/framework/model", "developers_guide/framework/mpas", "developers_guide/framework/provenance", "developers_guide/framework/remapping", "developers_guide/framework/validation", "developers_guide/framework/visualization", "developers_guide/generated/polaris.Component", "developers_guide/generated/polaris.Component.add_config", "developers_guide/generated/polaris.Component.add_step", "developers_guide/generated/polaris.Component.add_task", "developers_guide/generated/polaris.Component.remove_step", "developers_guide/generated/polaris.ModelStep", "developers_guide/generated/polaris.ModelStep.add_model_config_options", "developers_guide/generated/polaris.ModelStep.add_namelist_file", "developers_guide/generated/polaris.ModelStep.add_streams_file", "developers_guide/generated/polaris.ModelStep.add_yaml_file", "developers_guide/generated/polaris.ModelStep.dynamic_model_config", "developers_guide/generated/polaris.ModelStep.map_yaml_configs", "developers_guide/generated/polaris.ModelStep.map_yaml_options", "developers_guide/generated/polaris.ModelStep.map_yaml_to_namelist", "developers_guide/generated/polaris.ModelStep.partition", "developers_guide/generated/polaris.ModelStep.process_inputs_and_outputs", "developers_guide/generated/polaris.ModelStep.runtime_setup", "developers_guide/generated/polaris.ModelStep.set_model_resources", "developers_guide/generated/polaris.ModelStep.setup", "developers_guide/generated/polaris.ModelStep.update_namelist_pio", "developers_guide/generated/polaris.Step", "developers_guide/generated/polaris.Step.add_dependency", "developers_guide/generated/polaris.Step.add_input_file", "developers_guide/generated/polaris.Step.add_output_file", "developers_guide/generated/polaris.Step.constrain_resources", "developers_guide/generated/polaris.Step.run", "developers_guide/generated/polaris.Step.runtime_setup", "developers_guide/generated/polaris.Step.set_resources", "developers_guide/generated/polaris.Step.set_shared_config", "developers_guide/generated/polaris.Step.setup", "developers_guide/generated/polaris.Step.validate_baselines", "developers_guide/generated/polaris.Task", "developers_guide/generated/polaris.Task.add_step", "developers_guide/generated/polaris.Task.configure", "developers_guide/generated/polaris.Task.remove_step", "developers_guide/generated/polaris.Task.set_shared_config", "developers_guide/generated/polaris.__main__.main", "developers_guide/generated/polaris.cache.update_cache", "developers_guide/generated/polaris.components.get_components", "developers_guide/generated/polaris.config.PolarisConfigParser", "developers_guide/generated/polaris.config.PolarisConfigParser.setup", "developers_guide/generated/polaris.io.download", "developers_guide/generated/polaris.io.symlink", "developers_guide/generated/polaris.io.update_permissions", "developers_guide/generated/polaris.job.clean_up_whitespace", "developers_guide/generated/polaris.job.get_slurm_options", "developers_guide/generated/polaris.job.write_job_script", "developers_guide/generated/polaris.list.list_cases", "developers_guide/generated/polaris.list.list_machines", "developers_guide/generated/polaris.list.list_suites", "developers_guide/generated/polaris.logging.log_method_call", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.build_subdivisions_cell_width_lat_lon", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.get_cell_width", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.get_subdivisions", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.make_jigsaw_mesh", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.run", "developers_guide/generated/polaris.mesh.IcosahedralMeshStep.setup", "developers_guide/generated/polaris.mesh.QuasiUniformSphericalMeshStep", "developers_guide/generated/polaris.mesh.QuasiUniformSphericalMeshStep.build_cell_width_lat_lon", "developers_guide/generated/polaris.mesh.QuasiUniformSphericalMeshStep.make_jigsaw_mesh", "developers_guide/generated/polaris.mesh.QuasiUniformSphericalMeshStep.run", "developers_guide/generated/polaris.mesh.QuasiUniformSphericalMeshStep.setup", "developers_guide/generated/polaris.mesh.planar.compute_planar_hex_nx_ny", "developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep", "developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep.run", "developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width", "developers_guide/generated/polaris.mesh.spherical.SphericalBaseStep.setup", "developers_guide/generated/polaris.model_step.make_graph_file", "developers_guide/generated/polaris.mpas.area_for_field", "developers_guide/generated/polaris.mpas.time_index_from_xtime", "developers_guide/generated/polaris.namelist.ingest", "developers_guide/generated/polaris.namelist.parse_replacements", "developers_guide/generated/polaris.namelist.replace", "developers_guide/generated/polaris.namelist.write", "developers_guide/generated/polaris.parallel.get_available_parallel_resources", "developers_guide/generated/polaris.parallel.get_parallel_command", "developers_guide/generated/polaris.parallel.run_command", "developers_guide/generated/polaris.parallel.set_cores_per_node", "developers_guide/generated/polaris.provenance.write", "developers_guide/generated/polaris.remap.MappingFileStep", "developers_guide/generated/polaris.remap.MappingFileStep.dst_from_lon_lat", "developers_guide/generated/polaris.remap.MappingFileStep.dst_from_mpas", "developers_guide/generated/polaris.remap.MappingFileStep.dst_from_points", "developers_guide/generated/polaris.remap.MappingFileStep.dst_from_proj", "developers_guide/generated/polaris.remap.MappingFileStep.dst_global_lon_lat", "developers_guide/generated/polaris.remap.MappingFileStep.get_remapper", "developers_guide/generated/polaris.remap.MappingFileStep.runtime_setup", "developers_guide/generated/polaris.remap.MappingFileStep.src_from_lon_lat", "developers_guide/generated/polaris.remap.MappingFileStep.src_from_mpas", "developers_guide/generated/polaris.remap.MappingFileStep.src_from_proj", "developers_guide/generated/polaris.run.complete_step_run", "developers_guide/generated/polaris.run.load_dependencies", "developers_guide/generated/polaris.run.serial.run_single_step", "developers_guide/generated/polaris.run.serial.run_tasks", "developers_guide/generated/polaris.run.setup_config", "developers_guide/generated/polaris.run.unpickle_suite", "developers_guide/generated/polaris.setup.setup_task", "developers_guide/generated/polaris.setup.setup_tasks", "developers_guide/generated/polaris.streams.read", "developers_guide/generated/polaris.streams.update_defaults", "developers_guide/generated/polaris.streams.update_tree", "developers_guide/generated/polaris.streams.write", "developers_guide/generated/polaris.suite.setup_suite", "developers_guide/generated/polaris.validate.compare_variables", "developers_guide/generated/polaris.viz.plot_global_lat_lon_field", "developers_guide/generated/polaris.viz.plot_global_mpas_field", "developers_guide/generated/polaris.viz.plot_horiz_field", "developers_guide/generated/polaris.viz.use_mplstyle", "developers_guide/generated/polaris.yaml.PolarisYaml", "developers_guide/generated/polaris.yaml.PolarisYaml.read", "developers_guide/generated/polaris.yaml.PolarisYaml.update", "developers_guide/generated/polaris.yaml.PolarisYaml.write", "developers_guide/generated/polaris.yaml.main_mpas_to_yaml", "developers_guide/generated/polaris.yaml.mpas_namelist_and_streams_to_yaml", "developers_guide/generated/polaris.yaml.yaml_to_mpas_streams", "developers_guide/machines/anvil", "developers_guide/machines/chicoma", "developers_guide/machines/chrysalis", "developers_guide/machines/compy", "developers_guide/machines/frontier", "developers_guide/machines/index", "developers_guide/machines/perlmutter", "developers_guide/ocean/api", "developers_guide/ocean/framework", "developers_guide/ocean/generated/polaris.ocean.Ocean", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis.compute_error", "developers_guide/ocean/generated/polaris.ocean.convergence.ConvergenceAnalysis.convergence_parameters", 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"developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.map_yaml_configs", "developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.map_yaml_options", "developers_guide/ocean/generated/polaris.ocean.model.OceanModelStep.setup", "developers_guide/ocean/generated/polaris.ocean.model.get_time_interval_string", "developers_guide/ocean/generated/polaris.ocean.rpe.compute_rpe", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.add_baroclinic_channel_tasks", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.decomp.Decomp", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.default.Default", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.forward.Forward", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.forward.Forward.compute_cell_count", "developers_guide/ocean/generated/polaris.ocean.tasks.baroclinic_channel.forward.Forward.dynamic_model_config", 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"developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.forward.Forward", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.forward.Forward.compute_cell_count", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.forward.Forward.dynamic_model_config", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.init.Init", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.init.Init.run", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.init.cosine_bell", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.viz.Viz", "developers_guide/ocean/generated/polaris.ocean.tasks.cosine_bell.viz.Viz.run", "developers_guide/ocean/generated/polaris.ocean.tasks.geostrophic.Geostrophic", "developers_guide/ocean/generated/polaris.ocean.tasks.geostrophic.Geostrophic.configure", "developers_guide/ocean/generated/polaris.ocean.tasks.geostrophic.add_geostrophic_tasks", 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"developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.forward.Forward.compute_cell_count", "developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.forward.Forward.dynamic_model_config", "developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.init.Init", "developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.init.Init.run", "developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.validate.Validate", "developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.validate.Validate.run", "developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.viz.Viz", "developers_guide/ocean/generated/polaris.ocean.tasks.ice_shelf_2d.viz.Viz.run", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.InertialGravityWave", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.add_inertial_gravity_wave_tasks", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.analysis.Analysis", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.analysis.Analysis.exact_solution", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.exact_solution.ExactSolution", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.exact_solution.ExactSolution.normal_velocity", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.exact_solution.ExactSolution.ssh", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.forward.Forward", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.forward.Forward.compute_cell_count", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.init.Init", "developers_guide/ocean/generated/polaris.ocean.tasks.inertial_gravity_wave.init.Init.run", 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directory step paths are easily discoverable by users.": [[1, "implementation-working-directory-step-paths-are-easily-discoverable-by-users"]], "Implementation: The output of shared steps may be used by multiple tasks.": [[1, "implementation-the-output-of-shared-steps-may-be-used-by-multiple-tasks"]], "Implementation: tasks do not rely on outputs from steps in other tasks": [[1, "implementation-tasks-do-not-rely-on-outputs-from-steps-in-other-tasks"]], "Testing": [[1, "testing"], [2, "testing"]], "Testing And Validation: Shared steps are run once.": [[1, "testing-and-validation-shared-steps-are-run-once"]], "Testing And Validation: Shared steps are run before steps that depend on their output.": [[1, "testing-and-validation-shared-steps-are-run-before-steps-that-depend-on-their-output"]], "Testing And Validation: Shared steps are not daughters of a task": [[1, "testing-and-validation-shared-steps-are-not-daughters-of-a-task"]], "Testing And Validation: Working directory structure is intuitive.": [[1, "testing-and-validation-working-directory-structure-is-intuitive"]], "Testing And Validation: Working directory step paths are easily discoverable by users.": [[1, "testing-and-validation-working-directory-step-paths-are-easily-discoverable-by-users"]], "Testing And Validation: The output of shared steps may be used by multiple tasks.": [[1, "testing-and-validation-the-output-of-shared-steps-may-be-used-by-multiple-tasks"]], "Testing And Validation: tasks do not rely on outputs from steps in other tasks": [[1, "testing-and-validation-tasks-do-not-rely-on-outputs-from-steps-in-other-tasks"]], "Template": [[2, "template"]], "Requirement: name-of-topic-here": [[2, "requirement-name-of-topic-here"]], "Algorithm Design (optional)": [[2, "algorithm-design-optional"]], "Algorithm Design: name-of-topic-here (same as Requirement)": [[2, "algorithm-design-name-of-topic-here-same-as-requirement"]], "Implementation: name-of-topic-here (same as Requirement)": [[2, 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"polaris-suite"]], "polaris serial": [[5, "polaris-serial"]], "polaris cache": [[5, "polaris-cache"]], "Deploying a new spack environment": [[6, "deploying-a-new-spack-environment"]], "Where do we update polaris dependencies?": [[6, "where-do-we-update-polaris-dependencies"]], "Mache": [[6, "mache"], [6, "id1"]], "Spack": [[6, "spack"]], "Conda": [[6, "conda"]], "Identifying E3SM machines": [[6, "identifying-e3sm-machines"]], "Config options describing E3SM machines": [[6, "config-options-describing-e3sm-machines"]], "Modules, env. variables, etc. for E3SM machines": [[6, "modules-env-variables-etc-for-e3sm-machines"]], "Creating spack environments": [[6, "creating-spack-environments"]], "Updating spack from polaris with mache from a remote branch": [[6, "updating-spack-from-polaris-with-mache-from-a-remote-branch"]], "Testing spack with PETSc (and Netlib LAPACK)": [[6, "testing-spack-with-petsc-and-netlib-lapack"]], "Testing spack with Albany": [[6, "testing-spack-with-albany"]], 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"visualization"]], "common matplotlib style": [[19, "common-matplotlib-style"]], "horizontal fields from planar meshes": [[19, "horizontal-fields-from-planar-meshes"]], "global lat/lon plots": [[19, "global-lat-lon-plots"]], "plotting from spherical MPAS meshes": [[19, "plotting-from-spherical-mpas-meshes"]], "plotting from lat/lon grids": [[19, "plotting-from-lat-lon-grids"]], "polaris.Component": [[20, "polaris-component"]], "polaris.Component.add_config": [[21, "polaris-component-add-config"]], "polaris.Component.add_step": [[22, "polaris-component-add-step"]], "polaris.Component.add_task": [[23, "polaris-component-add-task"]], "polaris.Component.remove_step": [[24, "polaris-component-remove-step"]], "polaris.ModelStep": [[25, "polaris-modelstep"]], "polaris.ModelStep.add_model_config_options": [[26, "polaris-modelstep-add-model-config-options"]], "polaris.ModelStep.add_namelist_file": [[27, "polaris-modelstep-add-namelist-file"]], "polaris.ModelStep.add_streams_file": [[28, 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"polaris.provenance.write": [[99, "polaris-provenance-write"]], "polaris.remap.MappingFileStep": [[100, "polaris-remap-mappingfilestep"]], "polaris.remap.MappingFileStep.dst_from_lon_lat": [[101, "polaris-remap-mappingfilestep-dst-from-lon-lat"]], "polaris.remap.MappingFileStep.dst_from_mpas": [[102, "polaris-remap-mappingfilestep-dst-from-mpas"]], "polaris.remap.MappingFileStep.dst_from_points": [[103, "polaris-remap-mappingfilestep-dst-from-points"]], "polaris.remap.MappingFileStep.dst_from_proj": [[104, "polaris-remap-mappingfilestep-dst-from-proj"]], "polaris.remap.MappingFileStep.dst_global_lon_lat": [[105, "polaris-remap-mappingfilestep-dst-global-lon-lat"]], "polaris.remap.MappingFileStep.get_remapper": [[106, "polaris-remap-mappingfilestep-get-remapper"]], "polaris.remap.MappingFileStep.runtime_setup": [[107, "polaris-remap-mappingfilestep-runtime-setup"]], "polaris.remap.MappingFileStep.src_from_lon_lat": [[108, "polaris-remap-mappingfilestep-src-from-lon-lat"]], 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"polaris-yaml-mpas-namelist-and-streams-to-yaml"]], "polaris.yaml.yaml_to_mpas_streams": [[135, "polaris-yaml-yaml-to-mpas-streams"]], "Anvil": [[136, "anvil"], [363, "anvil"]], "intel": [[136, "intel"], [138, "intel"], [139, "intel"]], "gnu": [[136, "gnu"], [138, "gnu"], [139, "gnu"]], "Chicoma": [[137, "chicoma"], [364, "chicoma"]], "chicoma-cpu, gnu": [[137, "chicoma-cpu-gnu"]], "Chrysalis": [[138, "chrysalis"], [365, "chrysalis"]], "CompyMcNodeFace": [[139, "compymcnodeface"], [366, "compymcnodeface"]], "Frontier": [[140, "frontier"], [367, "frontier"]], "frontier, gnu": [[140, "frontier-gnu"]], "frontier, crayclang": [[140, "frontier-crayclang"]], "Machines": [[141, "machines"], [368, "machines"]], "Supported Machines": [[141, "supported-machines"], [368, "supported-machines"]], "Other Machines": [[141, "other-machines"], [368, "other-machines"]], "Adding a New Supported Machine": [[141, "adding-a-new-supported-machine"]], "Adding a Machine Config File": [[141, 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[[29, "polaris.ModelStep.add_yaml_file"]], "dynamic_model_config() (polaris.modelstep method)": [[30, "polaris.ModelStep.dynamic_model_config"]], "map_yaml_configs() (polaris.modelstep method)": [[31, "polaris.ModelStep.map_yaml_configs"]], "map_yaml_options() (polaris.modelstep method)": [[32, "polaris.ModelStep.map_yaml_options"]], "map_yaml_to_namelist() (polaris.modelstep method)": [[33, "polaris.ModelStep.map_yaml_to_namelist"]], "partition() (polaris.modelstep method)": [[34, "polaris.ModelStep.partition"]], "process_inputs_and_outputs() (polaris.modelstep method)": [[35, "polaris.ModelStep.process_inputs_and_outputs"]], "runtime_setup() (polaris.modelstep method)": [[36, "polaris.ModelStep.runtime_setup"]], "set_model_resources() (polaris.modelstep method)": [[37, "polaris.ModelStep.set_model_resources"]], "setup() (polaris.modelstep method)": [[38, "polaris.ModelStep.setup"]], "update_namelist_pio() (polaris.modelstep method)": [[39, "polaris.ModelStep.update_namelist_pio"]], "step (class in polaris)": [[40, "polaris.Step"]], "__init__() (polaris.step method)": [[40, "polaris.Step.__init__"]], "add_dependency() (polaris.step method)": [[41, "polaris.Step.add_dependency"]], "add_input_file() (polaris.step method)": [[42, "polaris.Step.add_input_file"]], "add_output_file() (polaris.step method)": [[43, "polaris.Step.add_output_file"]], "constrain_resources() (polaris.step method)": [[44, "polaris.Step.constrain_resources"]], "run() (polaris.step method)": [[45, "polaris.Step.run"]], "runtime_setup() (polaris.step method)": [[46, "polaris.Step.runtime_setup"]], "set_resources() (polaris.step method)": [[47, "polaris.Step.set_resources"]], "set_shared_config() (polaris.step method)": [[48, "polaris.Step.set_shared_config"]], "setup() (polaris.step method)": [[49, "polaris.Step.setup"]], "validate_baselines() (polaris.step method)": [[50, "polaris.Step.validate_baselines"]], "task (class in polaris)": [[51, "polaris.Task"]], "__init__() (polaris.task method)": [[51, "polaris.Task.__init__"]], "add_step() (polaris.task method)": [[52, "polaris.Task.add_step"]], "configure() (polaris.task method)": [[53, "polaris.Task.configure"]], "remove_step() (polaris.task method)": [[54, "polaris.Task.remove_step"]], "set_shared_config() (polaris.task method)": [[55, "polaris.Task.set_shared_config"]], "main() (in module polaris.__main__)": [[56, "polaris.__main__.main"]], "update_cache() (in module polaris.cache)": [[57, "polaris.cache.update_cache"]], "get_components() (in module polaris.components)": [[58, "polaris.components.get_components"]], "polarisconfigparser (class in polaris.config)": [[59, "polaris.config.PolarisConfigParser"]], "__init__() (polaris.config.polarisconfigparser method)": [[59, "polaris.config.PolarisConfigParser.__init__"]], "setup() (polaris.config.polarisconfigparser method)": [[60, "polaris.config.PolarisConfigParser.setup"]], "download() (in module polaris.io)": [[61, "polaris.io.download"]], "symlink() (in module polaris.io)": [[62, "polaris.io.symlink"]], "update_permissions() (in module polaris.io)": [[63, "polaris.io.update_permissions"]], "clean_up_whitespace() (in module polaris.job)": [[64, "polaris.job.clean_up_whitespace"]], "get_slurm_options() (in module polaris.job)": [[65, "polaris.job.get_slurm_options"]], "write_job_script() (in module polaris.job)": [[66, "polaris.job.write_job_script"]], "list_cases() (in module polaris.list)": [[67, "polaris.list.list_cases"]], "list_machines() (in module polaris.list)": [[68, "polaris.list.list_machines"]], "list_suites() (in module polaris.list)": [[69, "polaris.list.list_suites"]], "log_method_call() (in module polaris.logging)": [[70, "polaris.logging.log_method_call"]], "icosahedralmeshstep (class in polaris.mesh)": [[71, "polaris.mesh.IcosahedralMeshStep"]], "__init__() (polaris.mesh.icosahedralmeshstep method)": [[71, "polaris.mesh.IcosahedralMeshStep.__init__"]], "build_subdivisions_cell_width_lat_lon() (polaris.mesh.icosahedralmeshstep method)": [[72, "polaris.mesh.IcosahedralMeshStep.build_subdivisions_cell_width_lat_lon"]], "get_cell_width() (polaris.mesh.icosahedralmeshstep static method)": [[73, "polaris.mesh.IcosahedralMeshStep.get_cell_width"]], "get_subdivisions() (polaris.mesh.icosahedralmeshstep static method)": [[74, "polaris.mesh.IcosahedralMeshStep.get_subdivisions"]], "make_jigsaw_mesh() (polaris.mesh.icosahedralmeshstep method)": [[75, "polaris.mesh.IcosahedralMeshStep.make_jigsaw_mesh"]], "run() (polaris.mesh.icosahedralmeshstep method)": [[76, "polaris.mesh.IcosahedralMeshStep.run"]], "setup() (polaris.mesh.icosahedralmeshstep method)": [[77, "polaris.mesh.IcosahedralMeshStep.setup"]], "quasiuniformsphericalmeshstep (class in polaris.mesh)": [[78, "polaris.mesh.QuasiUniformSphericalMeshStep"]], "__init__() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[78, "polaris.mesh.QuasiUniformSphericalMeshStep.__init__"]], "build_cell_width_lat_lon() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[79, "polaris.mesh.QuasiUniformSphericalMeshStep.build_cell_width_lat_lon"]], "make_jigsaw_mesh() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[80, "polaris.mesh.QuasiUniformSphericalMeshStep.make_jigsaw_mesh"]], "run() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[81, "polaris.mesh.QuasiUniformSphericalMeshStep.run"]], "setup() (polaris.mesh.quasiuniformsphericalmeshstep method)": [[82, "polaris.mesh.QuasiUniformSphericalMeshStep.setup"]], "compute_planar_hex_nx_ny() (in module polaris.mesh.planar)": [[83, "polaris.mesh.planar.compute_planar_hex_nx_ny"]], "sphericalbasestep (class in polaris.mesh.spherical)": [[84, "polaris.mesh.spherical.SphericalBaseStep"]], "__init__() (polaris.mesh.spherical.sphericalbasestep method)": [[84, "polaris.mesh.spherical.SphericalBaseStep.__init__"]], "run() (polaris.mesh.spherical.sphericalbasestep method)": [[85, "polaris.mesh.spherical.SphericalBaseStep.run"]], "save_and_plot_cell_width() (polaris.mesh.spherical.sphericalbasestep method)": [[86, "polaris.mesh.spherical.SphericalBaseStep.save_and_plot_cell_width"]], "setup() (polaris.mesh.spherical.sphericalbasestep method)": [[87, "polaris.mesh.spherical.SphericalBaseStep.setup"]], "make_graph_file() (in module polaris.model_step)": [[88, "polaris.model_step.make_graph_file"]], "area_for_field() (in module polaris.mpas)": [[89, "polaris.mpas.area_for_field"]], "time_index_from_xtime() (in module polaris.mpas)": [[90, "polaris.mpas.time_index_from_xtime"]], "ingest() (in module polaris.namelist)": [[91, "polaris.namelist.ingest"]], "parse_replacements() (in module polaris.namelist)": [[92, "polaris.namelist.parse_replacements"]], "replace() (in module polaris.namelist)": [[93, "polaris.namelist.replace"]], "write() (in module polaris.namelist)": [[94, "polaris.namelist.write"]], "get_available_parallel_resources() (in module polaris.parallel)": [[95, "polaris.parallel.get_available_parallel_resources"]], "get_parallel_command() (in module polaris.parallel)": [[96, "polaris.parallel.get_parallel_command"]], "run_command() (in module polaris.parallel)": [[97, "polaris.parallel.run_command"]], "set_cores_per_node() (in module polaris.parallel)": [[98, "polaris.parallel.set_cores_per_node"]], "write() (in module polaris.provenance)": [[99, "polaris.provenance.write"]], "mappingfilestep (class in polaris.remap)": [[100, "polaris.remap.MappingFileStep"]], "__init__() (polaris.remap.mappingfilestep method)": [[100, "polaris.remap.MappingFileStep.__init__"]], "dst_from_lon_lat() (polaris.remap.mappingfilestep method)": [[101, "polaris.remap.MappingFileStep.dst_from_lon_lat"]], "dst_from_mpas() (polaris.remap.mappingfilestep method)": [[102, "polaris.remap.MappingFileStep.dst_from_mpas"]], "dst_from_points() (polaris.remap.mappingfilestep method)": [[103, "polaris.remap.MappingFileStep.dst_from_points"]], "dst_from_proj() (polaris.remap.mappingfilestep method)": [[104, "polaris.remap.MappingFileStep.dst_from_proj"]], "dst_global_lon_lat() (polaris.remap.mappingfilestep method)": [[105, "polaris.remap.MappingFileStep.dst_global_lon_lat"]], "get_remapper() (polaris.remap.mappingfilestep method)": [[106, "polaris.remap.MappingFileStep.get_remapper"]], "runtime_setup() (polaris.remap.mappingfilestep method)": [[107, "polaris.remap.MappingFileStep.runtime_setup"]], "src_from_lon_lat() (polaris.remap.mappingfilestep method)": [[108, "polaris.remap.MappingFileStep.src_from_lon_lat"]], "src_from_mpas() (polaris.remap.mappingfilestep method)": [[109, "polaris.remap.MappingFileStep.src_from_mpas"]], "src_from_proj() (polaris.remap.mappingfilestep method)": [[110, "polaris.remap.MappingFileStep.src_from_proj"]], "complete_step_run() (in module polaris.run)": [[111, "polaris.run.complete_step_run"]], "load_dependencies() (in module polaris.run)": [[112, "polaris.run.load_dependencies"]], "run_single_step() (in module polaris.run.serial)": [[113, "polaris.run.serial.run_single_step"]], "run_tasks() (in module polaris.run.serial)": [[114, "polaris.run.serial.run_tasks"]], "setup_config() (in module polaris.run)": [[115, "polaris.run.setup_config"]], "unpickle_suite() (in module polaris.run)": [[116, "polaris.run.unpickle_suite"]], "setup_task() (in module polaris.setup)": [[117, "polaris.setup.setup_task"]], "setup_tasks() (in module polaris.setup)": [[118, "polaris.setup.setup_tasks"]], "read() (in module polaris.streams)": [[119, "polaris.streams.read"]], "update_defaults() (in module polaris.streams)": [[120, "polaris.streams.update_defaults"]], "update_tree() (in module polaris.streams)": [[121, "polaris.streams.update_tree"]], "write() (in module polaris.streams)": [[122, "polaris.streams.write"]], "setup_suite() (in module polaris.suite)": [[123, "polaris.suite.setup_suite"]], "compare_variables() (in module polaris.validate)": [[124, "polaris.validate.compare_variables"]], "plot_global_lat_lon_field() (in module polaris.viz)": [[125, "polaris.viz.plot_global_lat_lon_field"]], "plot_global_mpas_field() (in module polaris.viz)": [[126, "polaris.viz.plot_global_mpas_field"]], "plot_horiz_field() (in module polaris.viz)": [[127, "polaris.viz.plot_horiz_field"]], "use_mplstyle() (in module polaris.viz)": [[128, "polaris.viz.use_mplstyle"]], "polarisyaml (class in polaris.yaml)": [[129, "polaris.yaml.PolarisYaml"]], "__init__() (polaris.yaml.polarisyaml method)": [[129, "polaris.yaml.PolarisYaml.__init__"]], "read() (polaris.yaml.polarisyaml class method)": [[130, "polaris.yaml.PolarisYaml.read"]], "update() (polaris.yaml.polarisyaml method)": [[131, "polaris.yaml.PolarisYaml.update"]], "write() (polaris.yaml.polarisyaml method)": [[132, "polaris.yaml.PolarisYaml.write"]], "main_mpas_to_yaml() (in module polaris.yaml)": [[133, "polaris.yaml.main_mpas_to_yaml"]], "mpas_namelist_and_streams_to_yaml() (in module polaris.yaml)": [[134, "polaris.yaml.mpas_namelist_and_streams_to_yaml"]], "yaml_to_mpas_streams() (in module polaris.yaml)": [[135, "polaris.yaml.yaml_to_mpas_streams"]], "ocean (class in polaris.ocean)": [[145, "polaris.ocean.Ocean"]], "__init__() (polaris.ocean.ocean method)": [[145, "polaris.ocean.Ocean.__init__"]], "convergenceanalysis (class in polaris.ocean.convergence)": [[146, "polaris.ocean.convergence.ConvergenceAnalysis"]], "__init__() (polaris.ocean.convergence.convergenceanalysis method)": [[146, "polaris.ocean.convergence.ConvergenceAnalysis.__init__"]], "compute_error() (polaris.ocean.convergence.convergenceanalysis method)": [[147, "polaris.ocean.convergence.ConvergenceAnalysis.compute_error"]], "convergence_parameters() (polaris.ocean.convergence.convergenceanalysis method)": [[148, "polaris.ocean.convergence.ConvergenceAnalysis.convergence_parameters"]], "exact_solution() (polaris.ocean.convergence.convergenceanalysis method)": [[149, "polaris.ocean.convergence.ConvergenceAnalysis.exact_solution"]], "get_output_field() (polaris.ocean.convergence.convergenceanalysis method)": [[150, "polaris.ocean.convergence.ConvergenceAnalysis.get_output_field"]], "plot_convergence() (polaris.ocean.convergence.convergenceanalysis method)": [[151, "polaris.ocean.convergence.ConvergenceAnalysis.plot_convergence"]], "run() (polaris.ocean.convergence.convergenceanalysis method)": [[152, "polaris.ocean.convergence.ConvergenceAnalysis.run"]], "setup() (polaris.ocean.convergence.convergenceanalysis method)": [[153, "polaris.ocean.convergence.ConvergenceAnalysis.setup"]], "convergenceforward (class in polaris.ocean.convergence)": [[154, "polaris.ocean.convergence.ConvergenceForward"]], "__init__() (polaris.ocean.convergence.convergenceforward method)": [[154, "polaris.ocean.convergence.ConvergenceForward.__init__"]], "compute_cell_count() (polaris.ocean.convergence.convergenceforward method)": [[155, "polaris.ocean.convergence.ConvergenceForward.compute_cell_count"]], "dynamic_model_config() (polaris.ocean.convergence.convergenceforward method)": [[156, "polaris.ocean.convergence.ConvergenceForward.dynamic_model_config"]], "sphericalconvergenceforward (class in polaris.ocean.convergence.spherical)": [[157, "polaris.ocean.convergence.spherical.SphericalConvergenceForward"]], "__init__() (polaris.ocean.convergence.spherical.sphericalconvergenceforward method)": [[157, "polaris.ocean.convergence.spherical.SphericalConvergenceForward.__init__"]], "compute_cell_count() (polaris.ocean.convergence.spherical.sphericalconvergenceforward method)": [[158, "polaris.ocean.convergence.spherical.SphericalConvergenceForward.compute_cell_count"]], "iceshelftask (class in polaris.ocean.ice_shelf)": [[159, "polaris.ocean.ice_shelf.IceShelfTask"]], "__init__() (polaris.ocean.ice_shelf.iceshelftask method)": [[159, "polaris.ocean.ice_shelf.IceShelfTask.__init__"]], "setup_ssh_adjustment_steps() (polaris.ocean.ice_shelf.iceshelftask method)": [[160, "polaris.ocean.ice_shelf.IceShelfTask.setup_ssh_adjustment_steps"]], "sshadjustment (class in polaris.ocean.ice_shelf)": [[161, "polaris.ocean.ice_shelf.SshAdjustment"]], "__init__() (polaris.ocean.ice_shelf.sshadjustment method)": [[161, "polaris.ocean.ice_shelf.SshAdjustment.__init__"]], "run() (polaris.ocean.ice_shelf.sshadjustment method)": [[162, "polaris.ocean.ice_shelf.SshAdjustment.run"]], "sshforward (class in polaris.ocean.ice_shelf)": [[163, "polaris.ocean.ice_shelf.SshForward"]], "__init__() (polaris.ocean.ice_shelf.sshforward method)": [[163, "polaris.ocean.ice_shelf.SshForward.__init__"]], "compute_cell_count() (polaris.ocean.ice_shelf.sshforward method)": [[164, "polaris.ocean.ice_shelf.SshForward.compute_cell_count"]], "dynamic_model_config() (polaris.ocean.ice_shelf.sshforward method)": [[165, "polaris.ocean.ice_shelf.SshForward.dynamic_model_config"]], "add_spherical_base_mesh_step() (in module polaris.ocean.mesh.spherical)": [[166, "polaris.ocean.mesh.spherical.add_spherical_base_mesh_step"]], "oceanmodelstep (class in polaris.ocean.model)": [[167, "polaris.ocean.model.OceanModelStep"]], "__init__() (polaris.ocean.model.oceanmodelstep method)": [[167, "polaris.ocean.model.OceanModelStep.__init__"]], "compute_cell_count() (polaris.ocean.model.oceanmodelstep method)": [[168, "polaris.ocean.model.OceanModelStep.compute_cell_count"]], "constrain_resources() (polaris.ocean.model.oceanmodelstep method)": [[169, "polaris.ocean.model.OceanModelStep.constrain_resources"]], "map_yaml_configs() (polaris.ocean.model.oceanmodelstep method)": [[170, "polaris.ocean.model.OceanModelStep.map_yaml_configs"]], "map_yaml_options() (polaris.ocean.model.oceanmodelstep method)": [[171, "polaris.ocean.model.OceanModelStep.map_yaml_options"]], "setup() (polaris.ocean.model.oceanmodelstep method)": [[172, "polaris.ocean.model.OceanModelStep.setup"]], "get_time_interval_string() (in module polaris.ocean.model)": [[173, "polaris.ocean.model.get_time_interval_string"]], "compute_rpe() (in module polaris.ocean.rpe)": [[174, "polaris.ocean.rpe.compute_rpe"]], "add_baroclinic_channel_tasks() (in module polaris.ocean.tasks.baroclinic_channel)": [[175, "polaris.ocean.tasks.baroclinic_channel.add_baroclinic_channel_tasks"]], "decomp (class in polaris.ocean.tasks.baroclinic_channel.decomp)": [[176, "polaris.ocean.tasks.baroclinic_channel.decomp.Decomp"]], "__init__() (polaris.ocean.tasks.baroclinic_channel.decomp.decomp method)": [[176, "polaris.ocean.tasks.baroclinic_channel.decomp.Decomp.__init__"]], "default (class in polaris.ocean.tasks.baroclinic_channel.default)": [[177, "polaris.ocean.tasks.baroclinic_channel.default.Default"]], "__init__() (polaris.ocean.tasks.baroclinic_channel.default.default method)": [[177, "polaris.ocean.tasks.baroclinic_channel.default.Default.__init__"]], "forward (class in polaris.ocean.tasks.baroclinic_channel.forward)": [[178, "polaris.ocean.tasks.baroclinic_channel.forward.Forward"]], "__init__() (polaris.ocean.tasks.baroclinic_channel.forward.forward method)": [[178, "polaris.ocean.tasks.baroclinic_channel.forward.Forward.__init__"]], "compute_cell_count() (polaris.ocean.tasks.baroclinic_channel.forward.forward method)": [[179, "polaris.ocean.tasks.baroclinic_channel.forward.Forward.compute_cell_count"]], "dynamic_model_config() (polaris.ocean.tasks.baroclinic_channel.forward.forward method)": [[180, "polaris.ocean.tasks.baroclinic_channel.forward.Forward.dynamic_model_config"]], "init (class in polaris.ocean.tasks.baroclinic_channel.init)": [[181, "polaris.ocean.tasks.baroclinic_channel.init.Init"]], "__init__() (polaris.ocean.tasks.baroclinic_channel.init.init method)": [[181, "polaris.ocean.tasks.baroclinic_channel.init.Init.__init__"]], "run() (polaris.ocean.tasks.baroclinic_channel.init.init method)": [[182, "polaris.ocean.tasks.baroclinic_channel.init.Init.run"]], "setup() (polaris.ocean.tasks.baroclinic_channel.init.init method)": [[183, "polaris.ocean.tasks.baroclinic_channel.init.Init.setup"]], "restart (class in polaris.ocean.tasks.baroclinic_channel.restart)": [[184, "polaris.ocean.tasks.baroclinic_channel.restart.Restart"]], "__init__() (polaris.ocean.tasks.baroclinic_channel.restart.restart method)": [[184, "polaris.ocean.tasks.baroclinic_channel.restart.Restart.__init__"]], "restartstep (class in polaris.ocean.tasks.baroclinic_channel.restart.restart_step)": [[185, "polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep"]], "__init__() (polaris.ocean.tasks.baroclinic_channel.restart.restart_step.restartstep method)": [[185, "polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep.__init__"]], "dynamic_model_config() (polaris.ocean.tasks.baroclinic_channel.restart.restart_step.restartstep method)": [[186, "polaris.ocean.tasks.baroclinic_channel.restart.restart_step.RestartStep.dynamic_model_config"]], "rpe (class in polaris.ocean.tasks.baroclinic_channel.rpe)": [[187, "polaris.ocean.tasks.baroclinic_channel.rpe.Rpe"]], "__init__() (polaris.ocean.tasks.baroclinic_channel.rpe.rpe method)": [[187, "polaris.ocean.tasks.baroclinic_channel.rpe.Rpe.__init__"]], "configure() (polaris.ocean.tasks.baroclinic_channel.rpe.rpe method)": [[188, "polaris.ocean.tasks.baroclinic_channel.rpe.Rpe.configure"]], "analysis (class in polaris.ocean.tasks.baroclinic_channel.rpe.analysis)": [[189, "polaris.ocean.tasks.baroclinic_channel.rpe.analysis.Analysis"]], "__init__() (polaris.ocean.tasks.baroclinic_channel.rpe.analysis.analysis method)": [[189, "polaris.ocean.tasks.baroclinic_channel.rpe.analysis.Analysis.__init__"]], "run() (polaris.ocean.tasks.baroclinic_channel.rpe.analysis.analysis method)": [[190, "polaris.ocean.tasks.baroclinic_channel.rpe.analysis.Analysis.run"]], "setup() (polaris.ocean.tasks.baroclinic_channel.rpe.analysis.analysis method)": [[191, "polaris.ocean.tasks.baroclinic_channel.rpe.analysis.Analysis.setup"]], "threads (class in polaris.ocean.tasks.baroclinic_channel.threads)": [[192, "polaris.ocean.tasks.baroclinic_channel.threads.Threads"]], "__init__() (polaris.ocean.tasks.baroclinic_channel.threads.threads method)": [[192, 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"polaris.ocean.tasks.cosine_bell.CosineBell"]], "__init__() (polaris.ocean.tasks.cosine_bell.cosinebell method)": [[197, "polaris.ocean.tasks.cosine_bell.CosineBell.__init__"]], "configure() (polaris.ocean.tasks.cosine_bell.cosinebell method)": [[198, "polaris.ocean.tasks.cosine_bell.CosineBell.configure"]], "add_cosine_bell_tasks() (in module polaris.ocean.tasks.cosine_bell)": [[199, "polaris.ocean.tasks.cosine_bell.add_cosine_bell_tasks"]], "analysis (class in polaris.ocean.tasks.cosine_bell.analysis)": [[200, "polaris.ocean.tasks.cosine_bell.analysis.Analysis"]], "__init__() (polaris.ocean.tasks.cosine_bell.analysis.analysis method)": [[200, "polaris.ocean.tasks.cosine_bell.analysis.Analysis.__init__"]], "exact_solution() (polaris.ocean.tasks.cosine_bell.analysis.analysis method)": [[201, "polaris.ocean.tasks.cosine_bell.analysis.Analysis.exact_solution"]], "forward (class in polaris.ocean.tasks.cosine_bell.forward)": [[202, "polaris.ocean.tasks.cosine_bell.forward.Forward"]], 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\ No newline at end of file