From 85f713c1c0e3595afbe393de20c5ecc1c63f5839 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
<41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 26 Apr 2024 17:13:54 +0000
Subject: [PATCH] Update documentation
---
.../tests/ismip6_run/ismip6_ais_proj2300.html | 26 ++++++-
.../set_up_experiment.html | 65 ++++++++++++++++
.../landice/test_groups/ismip6_run.rst.txt | 29 ++++++-
.../landice/test_groups/ismip6_run.rst.txt | 76 ++++++++++++++++++-
.../landice/test_groups/ismip6_run.html | 29 ++++++-
latest/searchindex.js | 2 +-
.../landice/test_groups/ismip6_run.html | 73 +++++++++++++++++-
7 files changed, 290 insertions(+), 10 deletions(-)
diff --git a/latest/_modules/compass/landice/tests/ismip6_run/ismip6_ais_proj2300.html b/latest/_modules/compass/landice/tests/ismip6_run/ismip6_ais_proj2300.html
index c21d20cd7e..df48d248c9 100644
--- a/latest/_modules/compass/landice/tests/ismip6_run/ismip6_ais_proj2300.html
+++ b/latest/_modules/compass/landice/tests/ismip6_run/ismip6_ais_proj2300.html
@@ -114,6 +114,9 @@
Source code for compass.landice.tests.ismip6_run.ismip6_ais_proj2300
import os
+from compass.landice.tests.ismip6_run.ismip6_ais_proj2300.create_slm_mapping_files import ( # noqa
+ CreateSlmMappingFiles,
+)
from compass.landice.tests.ismip6_run.ismip6_ais_proj2300.set_up_experiment import ( # noqa
SetUpExperiment,
)
@@ -189,7 +192,23 @@ Source code for compass.landice.tests.ismip6_run.ismip6_ais_proj2300
subdir=exp_name, exp=exp))
# Do not add experiments to step to steps_to_run;
# each experiment (step) should be run manually
- self.steps_to_run = []
@@ -201,7 +220,10 @@
Source code for compass.landice.tests.ismip6_run.ismip6_ais_proj2300
raise ValueError("ERROR: 'compass run' has no functionality at the "
"test case level for this test. "
"Please submit the job script in "
- "each experiment's subdirectory manually instead.")
+ "each experiment's subdirectory manually instead."
+ "To create Sea-Level Model mapping files, submit"
+ "job script or execute 'compass run' from the"
+ "'mapping_files' subdirectory.")
diff --git a/latest/_modules/compass/landice/tests/ismip6_run/ismip6_ais_proj2300/set_up_experiment.html b/latest/_modules/compass/landice/tests/ismip6_run/ismip6_ais_proj2300/set_up_experiment.html
index 58f86e0fa4..07bbfe30da 100644
--- a/latest/_modules/compass/landice/tests/ismip6_run/ismip6_ais_proj2300/set_up_experiment.html
+++ b/latest/_modules/compass/landice/tests/ismip6_run/ismip6_ais_proj2300/set_up_experiment.html
@@ -117,6 +117,9 @@ Source code for compass.landice.tests.ismip6_run.ismip6_ais_proj2300.set_up_
import os
import shutil
import sys
+from importlib import resources
+
+from jinja2 import Template
from compass.io import symlink
from compass.job import write_job_script
@@ -171,6 +174,7 @@ Source code for compass.landice.tests.ismip6_run.ismip6_ais_proj2300.set_up_
region_mask_fname = os.path.split(region_mask_path)[-1]
calving_method = section.get('calving_method')
use_face_melting = section.getboolean('use_face_melting')
+ sea_level_model = section.getboolean('sea_level_model')
if self.exp == 'hist':
exp_fcg = 'ctrlAE'
@@ -341,6 +345,52 @@ Source code for compass.landice.tests.ismip6_run.ismip6_ais_proj2300.set_up_
self.add_namelist_options(options=options,
out_name='namelist.landice')
+ if sea_level_model:
+ # get config options
+ slm_input_ice = section.get('slm_input_ice')
+ slm_input_earth = section.get('slm_input_earth')
+ slm_earth_structure = section.get('slm_earth_structure')
+ slm_input_others = section.get('slm_input_others')
+ nglv = section.getint('nglv')
+
+ # complete the full paths to the SLM inputs
+ slm_input_ice = os.path.join(slm_input_ice,
+ f'GL{nglv}/ice_noGrIS_GL{nglv}/')
+ slm_input_others = os.path.join(slm_input_others,
+ f'GL{nglv}/')
+ # incorporate the SLM config in the landice namelist
+ options = {'config_uplift_method': "'sealevelmodel'"}
+ self.add_namelist_options(options=options,
+ out_name='namelist.landice')
+
+ # change the sealevel namelist
+ template = Template(resources.read_text
+ (resource_location,
+ 'namelist.sealevel.template'))
+ text = template.render(nglv=int(nglv), slm_input_ice=slm_input_ice,
+ slm_input_earth=slm_input_earth,
+ slm_earth_structure=slm_earth_structure,
+ slm_input_others=slm_input_others)
+
+ # write out the namelist.sealevel file
+ file_slm_nl = os.path.join(self.work_dir, 'namelist.sealevel')
+ with open(file_slm_nl, 'w') as handle:
+ handle.write(text)
+
+ # create SLM output paths
+ os.makedirs(os.path.join(self.work_dir, 'OUTPUT_SLM/'),
+ exist_ok='True')
+ os.makedirs(os.path.join(self.work_dir, 'ICELOAD_SLM/'),
+ exist_ok='True')
+
+ # link in SLM mapping files
+ # they don't exist yet, but we can create symlinks now
+ map_dir = os.path.join('..', 'mapping_files')
+ for map_file in ('mapfile_mali_to_slm.nc',
+ 'mapfile_slm_to_mali.nc'):
+ os.symlink(os.path.join(map_dir, map_file),
+ os.path.join(self.work_dir, map_file))
+
# For all projection runs, symlink the restart file for the
# historical run
# don't symlink restart_timestamp or you'll have a mighty mess
@@ -393,6 +443,21 @@ Source code for compass.landice.tests.ismip6_run.ismip6_ais_proj2300.set_up_
"""
Run this step of the test case
"""
+
+ config = self.config
+ section = config['ismip6_run_ais_2300']
+ sea_level_model = section.getboolean('sea_level_model')
+ if sea_level_model:
+ # Check if mapping files were generated
+ map_dir = os.path.join('..', 'mapping_files')
+ for map_file in ('mapfile_mali_to_slm.nc',
+ 'mapfile_slm_to_mali.nc'):
+ if not os.path.isfile(os.path.join(map_dir, map_file)):
+ sys.exit(f"ERROR: 'mapping_files/{map_file}'"
+ "does not exist in workdir."
+ "Please run the 'mapping_files' step"
+ "before proceeding.")
+
run_model(step=self, namelist='namelist.landice',
streams='streams.landice')
diff --git a/latest/_sources/developers_guide/landice/test_groups/ismip6_run.rst.txt b/latest/_sources/developers_guide/landice/test_groups/ismip6_run.rst.txt
index f26b936dc7..6a79f18a4e 100644
--- a/latest/_sources/developers_guide/landice/test_groups/ismip6_run.rst.txt
+++ b/latest/_sources/developers_guide/landice/test_groups/ismip6_run.rst.txt
@@ -5,6 +5,7 @@ ismip6_run
The ``ismip6_run`` test group (:py:class:`compass.landice.tests.ismip6_run`)
sets up experiments from the ISMIP6 experimental protocol.
+Additionally, the test group has an option to setup coupled MALI-Sea Level Model (SLM) simulations.
(see :ref:`landice_ismip6_run`).
framework
@@ -18,7 +19,7 @@ ismip6_ais_proj2300
-------------------
The :py:class:`compass.landice.tests.ismip6_run.ismip6_ais_proj2300.Ismip6AisProj2300`
-sets up an ensemble of ISMIP6 Antarctica 2300
+sets up an ensemble of ISMIP6 Antarctica 2300 (standalone MALI and coupled MALI-SLM)
simulations. The constructor (``__init__``) does nothing other than
allow the ``ismip6_ais_proj2300`` test case to be listed by ``compass list``
without having all individual experiments listed in a verbose listing.
@@ -54,5 +55,29 @@ submitted as an independent slurm job.
Finally, a symlink to the compass load script is added to the run work
directory, which compass does not do by default.
-The ``run`` method runs MALI for the given experiment.
+The ``run`` runs MALI for the given experiment. It also builds mapping files
+between MALI and the SLM by calling a local method ``_build_mapping_files``
+if the SLM option in the config file is enabled.
+Important notes for analyzing coupled MALI-SLM simulations
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Currently, MALI uses a planar mesh that projects the south pole with
+polar stereographic projection of ellipsoidal Earth, and the sea-level model
+uses a global grid of spherical Earth. This inconsistency in the Earth's
+assumed shape (ellipsoid vs. sphere) in MALI and the SLM causes discrepancies
+in the comparison of post-simulation ice mass calculations from the model outputs.
+To address this issue, an interim solution has been made to project the southern
+polar region onto the MALI planar mesh assuming a sphere (this is done by setting
+the lat/long in the MALI mesh using the 'aid-bedmap2-sphere' projection string in
+calling the function in 'set_lat_lon_fields_in_planar_grid.py'. Thus, the resulting
+MALI mesh for coupled MALI-SLM simulations that are setup from this testgroup have
+the lat/long values based off sphere. Once the simulation outputs are generated,
+it is necessary to calculate and apply the scaling factors to the MALI outputs
+to correct for the areal distortion arose from projecting the south pole on a sphere
+onto plane. Only after applying the scaling factor, the MALI outputs will be
+comparable to the SLM outputs. The equations to calculate the scaling factors are shown in
+Eqn. 21-4 in https://pubs.usgs.gov/pp/1395/report.pdf
+An example of the calculation for the MALI-SLM case can also be found in
+the ``compass`` testgroup/testcase/ ``compass/landice/test/slm/circ_icesheet/``,
+``visualize`` step (https://github.com/MPAS-Dev/compass/pull/748).
diff --git a/latest/_sources/users_guide/landice/test_groups/ismip6_run.rst.txt b/latest/_sources/users_guide/landice/test_groups/ismip6_run.rst.txt
index fd2ebf4e04..ac5b3390d3 100644
--- a/latest/_sources/users_guide/landice/test_groups/ismip6_run.rst.txt
+++ b/latest/_sources/users_guide/landice/test_groups/ismip6_run.rst.txt
@@ -89,6 +89,31 @@ for new runs
# Whether facemelting should be included in the runs
include_face_melting = False
+ # True if running coupled MALI-sea level model simulation
+ sea_level_model = True
+
+ # NOTE: for the directories related to the sea-level model input/outputs, the slash '/' at the end of the directory name is necessary.
+ # Path to the base directory containing globally defined ice thickness field for the sea-level model
+ slm_input_ice = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/icemodel/
+
+ # Path to the directory containing earth model for the sea-level model
+ slm_input_earth = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/earthmodel/
+
+ # Earth structure profile
+ # possible values: any file name string of earth model file.
+ # Note that there is no single representative earth model for the globe or
+ # any region of the globe (e.g., West Antarctica, East Antarctica, Greenland)
+ # But for this test, we use 'prem_512.l60K2C.sum18p6.dum19p2.tz19p4.lm22' for West Antarctica
+ # and 'prem_coll_512.l120C.ump5.lm10' for East Antarctica. Other earthmodels that can be used
+ # should exist in the path defined in the config option 'slm_input_earth'.
+ slm_earth_structure = prem_512.l60K2C.sum18p6.dum19p2.tz19p4.lm22
+
+ # Path to the diectory containing other input files (present-day global topography and sea-level model grid files)
+ slm_input_others = /global/cfs/cdirs/fanssie/MALI_projects/SeaLevelModel_Inputs/others/
+
+ # number of gauss-legendre nodes in latitude (typically an integer multiple of 512)
+ nglv = 2048
+
Additionally, a user should also include the following options (and possibly
others) that will be used for submitting the jobs for each ensemble member
(set to appropriate values for their usage situation):
@@ -100,10 +125,10 @@ others) that will be used for submitting the jobs for each ensemble member
qos = regular
[job]
- wall_time = 10:00:00
+ wall_time = 10:00:00
Steps for setting up and running experiments
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+--------------------------------------------
1. With a compass conda environment set up, run, e.g.,
``compass setup -t landice/ismip6_run/ismip6_ais_proj2300 -w WORK_DIR_PATH -f USER.cfg``
@@ -133,3 +158,50 @@ Steps for setting up and running experiments
Note that the ``hist`` run must be completed before any of the other
experiments can be run. A symlink to the ``hist`` restart file from year
2015 exists in each of the other experiment subdirectories.
+
+Important notes for running coupled MALI-SLM simulations
+--------------------------------------------------------
+
+Projection handling
+~~~~~~~~~~~~~~~~~~~
+
+Currently, MALI uses a planar mesh that projects the south pole with
+polar stereographic projection of ellipsoidal Earth, and the sea-level model
+uses a global grid of spherical Earth. This inconsistency in the Earth's
+assumed shape (ellipsoid vs. sphere) in MALI and the SLM causes discrepancies
+in the comparison of post-simulation ice mass calculations from the model outputs.
+To address this issue, an interim solution has been made to project the southern
+polar region onto the MALI planar mesh assuming a sphere (this is done by setting
+the lat/long in the MALI mesh using the 'aid-bedmap2-sphere' projection string in
+calling the function in 'set_lat_lon_fields_in_planar_grid.py'. Thus, the resulting
+MALI mesh for coupled MALI-SLM simulations that are setup from this testgroup have
+the lat/long values based off sphere. Once the simulation outputs are generated,
+it is necessary to calculate and apply the scaling factors to the MALI outputs
+to correct for the areal distortion arose from projecting the south pole on a sphere
+onto plane. Only after applying the scaling factor, the MALI outputs will be
+comparable to the SLM outputs. The equations to calculate the scaling factors are shown in
+Eqn. 21-4 in https://pubs.usgs.gov/pp/1395/report.pdf
+An example of the calculation for the MALI-SLM case can also be found in
+the ``compass`` testgroup/testcase/ ``compass/landice/test/slm/circ_icesheet/``,
+``visualize`` step (https://github.com/MPAS-Dev/compass/pull/748).
+
+Mapping files
+~~~~~~~~~~~~~
+
+Coupling between the Sea-Level Model and MALI requires the generation of mapping files
+before simulations are run. When ``sea_level_model=True`` in the cfg file, an
+additional test case step is created named ``mapping_files``. Before any MALI
+simulations are started, the user should run this step. It will generate the required
+mapping files, and they will be available in each experiment directory through symlinks.
+Once the mapping files have been generated, the user can proceed to running the ``hist``
+experiment.
+
+Restarts
+~~~~~~~~
+
+Additionally, for restarts with the SLM to work correctly, the entire history of the
+``OUTPUT_SLM`` and ``ICELOAD_SLM`` directories must be present. Because the projection
+experiments (ctrl and exp*) are branched off the hist run as restarts, this means these
+two directories from the hist run must be manually copied to each projection run before
+beginning it. There is not an easy way for this to happen automatically, so this step
+must be done manually.
diff --git a/latest/developers_guide/landice/test_groups/ismip6_run.html b/latest/developers_guide/landice/test_groups/ismip6_run.html
index bab1dfcef9..de389f4fea 100644
--- a/latest/developers_guide/landice/test_groups/ismip6_run.html
+++ b/latest/developers_guide/landice/test_groups/ismip6_run.html
@@ -147,6 +147,7 @@
ismip6_run
The ismip6_run test group (compass.landice.tests.ismip6_run)
sets up experiments from the ISMIP6 experimental protocol.
+Additionally, the test group has an option to setup coupled MALI-Sea Level Model (SLM) simulations.
(see ismip6_run).
framework
@@ -157,7 +158,7 @@ framework
+
+Important notes for analyzing coupled MALI-SLM simulations
+Currently, MALI uses a planar mesh that projects the south pole with
+polar stereographic projection of ellipsoidal Earth, and the sea-level model
+uses a global grid of spherical Earth. This inconsistency in the Earth’s
+assumed shape (ellipsoid vs. sphere) in MALI and the SLM causes discrepancies
+in the comparison of post-simulation ice mass calculations from the model outputs.
+To address this issue, an interim solution has been made to project the southern
+polar region onto the MALI planar mesh assuming a sphere (this is done by setting
+the lat/long in the MALI mesh using the ‘aid-bedmap2-sphere’ projection string in
+calling the function in ‘set_lat_lon_fields_in_planar_grid.py’. Thus, the resulting
+MALI mesh for coupled MALI-SLM simulations that are setup from this testgroup have
+the lat/long values based off sphere. Once the simulation outputs are generated,
+it is necessary to calculate and apply the scaling factors to the MALI outputs
+to correct for the areal distortion arose from projecting the south pole on a sphere
+onto plane. Only after applying the scaling factor, the MALI outputs will be
+comparable to the SLM outputs. The equations to calculate the scaling factors are shown in
+Eqn. 21-4 in https://pubs.usgs.gov/pp/1395/report.pdf
+An example of the calculation for the MALI-SLM case can also be found in
+the compass testgroup/testcase/ compass/landice/test/slm/circ_icesheet/,
+visualize step (https://github.com/MPAS-Dev/compass/pull/748).
diff --git a/latest/searchindex.js b/latest/searchindex.js
index 8bdbc49001..90abc405c7 100644
--- a/latest/searchindex.js
+++ b/latest/searchindex.js
@@ -1 +1 @@
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[[7, "deploying-spack-with-albany"]], "Deploying spack with PETSc (and Netlib LAPACK)": [[7, "deploying-spack-with-petsc-and-netlib-lapack"]], "Describing a Spack Environment": [[337, "describing-a-spack-environment"]], "Design": [[0, "design"]], "Design Documents": [[2, "design-documents"]], "Design: cached outputs": [[0, "design-cached-outputs"]], "Design: either \u201cnormal\u201d or \u201ccached\u201d versions of a step": [[0, "design-either-normal-or-cached-versions-of-a-step"]], "Design: selecting whether to use cached outputs": [[0, "design-selecting-whether-to-use-cached-outputs"]], "Design: unique identifier for cached outputs": [[0, "design-unique-identifier-for-cached-outputs"]], "Design: updating cached outputs": [[0, "design-updating-cached-outputs"]], "Developer Tutorial: Adding a new ocean/sea ice regionally refined mesh (RRM)": [[921, "developer-tutorial-adding-a-new-ocean-sea-ice-regionally-refined-mesh-rrm"]], "Developer Tutorial: Adding a new test group": [[922, "developer-tutorial-adding-a-new-test-group"]], "Developer Tutorial: Adding a parameter study": [[920, "developer-tutorial-adding-a-parameter-study"]], "Developer Tutorial: Porting a legacy COMPASS test group": [[923, "developer-tutorial-porting-a-legacy-compass-test-group"]], "Developer's guide": [[919, null]], "Directory structure": [[914, "directory-structure"]], "Docstrings": [[8, "docstrings"]], "Documentation": [[8, "documentation"], [920, "documentation"], [922, "documentation"], [923, "documentation"]], "Download": [[9, "download"]], "Downloading and symlinking input files": [[914, "downloading-and-symlinking-input-files"]], "DtConvergenceTest": [[314, "dtconvergencetest"]], "E3SM supported machines": [[983, "e3sm-supported-machines"]], "EC30to60": [[964, "ec30to60"]], "EC30to60 and ECwISC30to60": [[895, "ec30to60-and-ecwisc30to60"]], "ECwISC30to60": [[964, "ecwisc30to60"]], "Environments with Albany": [[916, "environments-with-albany"]], "Environments with PETSc and 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"implementation"], [1, "implementation"], [3, "implementation"]], "Implementation: Ability specify/modify core counts": [[1, "implementation-ability-specify-modify-core-counts"]], "Implementation: Considerations related to running test cases in parallel": [[1, "implementation-considerations-related-to-running-test-cases-in-parallel"]], "Implementation: Easy batch submission": [[1, "implementation-easy-batch-submission"]], "Implementation: Looser, more flexible directory structure": [[1, "implementation-looser-more-flexible-directory-structure"]], "Implementation: Machine-specific data": [[1, "implementation-machine-specific-data"]], "Implementation: Make test cases easy to understand, modify and and create": [[1, "implementation-make-test-cases-easy-to-understand-modify-and-and-create"]], "Implementation: Resolution can be a test case parameter": [[1, "implementation-resolution-can-be-a-test-case-parameter"]], "Implementation: Shared code": [[1, "implementation-shared-code"]], "Implementation: Shared configuration options": [[1, "implementation-shared-configuration-options"]], "Implementation: Support for pre-made initial condition files": [[1, "implementation-support-for-pre-made-initial-condition-files"]], "Implementation: Test case code is easy to alter and rerun": [[1, "implementation-test-case-code-is-easy-to-alter-and-rerun"]], "Implementation: User- and developer-friendly documentation": [[1, "implementation-user-and-developer-friendly-documentation"]], "Implementation: cached outputs": [[0, "implementation-cached-outputs"]], "Implementation: either \u201cnormal\u201d or \u201ccached\u201d versions of a step": [[0, "implementation-either-normal-or-cached-versions-of-a-step"]], "Implementation: name-of-topic-here (same as Requirement)": [[3, "implementation-name-of-topic-here-same-as-requirement"]], "Implementation: selecting whether to use cached outputs": [[0, "implementation-selecting-whether-to-use-cached-outputs"]], "Implementation: unique identifier for cached outputs": [[0, "implementation-unique-identifier-for-cached-outputs"]], "Implementation: updating cached outputs": [[0, "implementation-updating-cached-outputs"]], "In compass framework": [[915, "in-compass-framework"]], "Including a Floodplain": [[340, "including-a-floodplain"]], "Input files": [[914, "input-files"]], "Intel on Anvil": [[948, "intel-on-anvil"]], "Intel on Chrysalis": [[950, "intel-on-chrysalis"]], "Intel on CompyMcNodeFace": [[951, "intel-on-compymcnodeface"]], "Jupyter notebook on remote data": [[953, "jupyter-notebook-on-remote-data"]], "Kuroshio8to60 and Kuroshio12to60": [[895, "kuroshio8to60-and-kuroshio12to60"], [964, "kuroshio8to60-and-kuroshio12to60"]], "Land-ice Framework": [[78, "land-ice-framework"], [925, "land-ice-framework"]], "Landice Framework": [[77, "landice-framework"]], "Landice core": [[312, "landice-core"], [926, "landice-core"]], "Legacy COMPASS": [[919, "legacy-compass"]], "Logging": [[9, "logging"]], "MPAS Cores": [[4, "mpas-cores"], [914, "mpas-cores"]], "MPICH": [[952, "id4"]], "Mache": [[7, "mache"], [7, "id1"]], "Machines": [[337, "machines"], [952, "machines"]], "Making a graph file": [[9, "making-a-graph-file"]], "Making a new test group": [[922, "making-a-new-test-group"], [923, "making-a-new-test-group"]], "Making a new test group and \u201ccosine_bell\u201d test case": [[920, "making-a-new-test-group-and-cosine-bell-test-case"]], "Mesh": [[9, "mesh"], [340, "mesh"], [956, "mesh"]], "Meshes": [[964, "meshes"]], "Metadata": [[964, "metadata"]], "Mirroring MOAB on Chicoma": [[7, "mirroring-moab-on-chicoma"]], "Model": [[9, "model"]], "Modules": [[915, "modules"]], "Modules, env. variables, etc. for E3SM machines": [[7, "modules-env-variables-etc-for-e3sm-machines"]], "Namelist replacements and streams files": [[340, "namelist-replacements-and-streams-files"]], "No MPI from conda-forge": [[952, "no-mpi-from-conda-forge"]], "Norms": [[9, "norms"]], "Ocean core": [[890, "ocean-core"], [958, "ocean-core"]], "Ocean framework": [[340, "ocean-framework"]], "Ocean0": [[970, "ocean0"]], "Ocean1": [[970, "ocean1"]], "Ocean2": [[970, "ocean2"]], "OpenMPI": [[952, "id5"]], "Optional flags": [[916, "optional-flags"]], "Organization of Tests": [[914, "organization-of-tests"]], "Other Machines": [[337, "other-machines"], [952, "other-machines"]], "Output files": [[914, "output-files"]], "Overview": [[915, "overview"]], "Packages": [[915, "packages"]], "Packages and Modules": [[915, "packages-and-modules"]], "Particles": [[340, "particles"]], "Partitioning the mesh": [[9, "partitioning-the-mesh"]], "Performance run": [[970, "performance-run"]], "Perlmutter": [[338, "perlmutter"], [953, "perlmutter"]], "Perlmutter-CPU": [[953, "perlmutter-cpu"]], "Plotting": [[340, "plotting"]], "Provenance": [[9, "provenance"]], "Proxy on LANL Macs": [[917, "proxy-on-lanl-macs"]], "QU, Icos, QUwISC and IcoswISC": [[964, "qu-icos-quwisc-and-icoswisc"]], "QU, QUwISC, Icos and IcoswISC": [[895, "qu-quwisc-icos-and-icoswisc"]], "QU240 and Icos240": [[964, "qu240-and-icos240"]], "QU240 and QUwISC240": [[895, "qu240-and-quwisc240"]], "QUwISC240 and IcoswISC240": [[964, "quwisc240-and-icoswisc240"]], "Quick Start for Developers": [[916, "quick-start-for-developers"]], "Quick Start for Users": [[983, "quick-start-for-users"]], "RRS6to18 and RRSwISC6to18": [[895, "rrs6to18-and-rrswisc6to18"], [964, "rrs6to18-and-rrswisc6to18"]], "Remapping Topography": [[340, "remapping-topography"]], "Remapping topography": [[956, "remapping-topography"]], "Requirement: Ability specify/modify core counts": [[1, "requirement-ability-specify-modify-core-counts"]], "Requirement: Considerations related to running test cases in parallel": [[1, "requirement-considerations-related-to-running-test-cases-in-parallel"]], "Requirement: Easy batch submission": [[1, "requirement-easy-batch-submission"]], "Requirement: Looser, more flexible directory structure": [[1, "requirement-looser-more-flexible-directory-structure"]], "Requirement: Machine-specific data": [[1, "requirement-machine-specific-data"]], "Requirement: Make test cases easy to understand, modify and create": [[1, "requirement-make-test-cases-easy-to-understand-modify-and-create"]], "Requirement: Resolution can be a test case parameter": [[1, "requirement-resolution-can-be-a-test-case-parameter"]], "Requirement: Shared code": [[1, "requirement-shared-code"]], "Requirement: Shared configuration options": [[1, "requirement-shared-configuration-options"]], "Requirement: Support for pre-made initial condition files": [[1, "requirement-support-for-pre-made-initial-condition-files"]], "Requirement: Test case code is easy to alter and rerun": [[1, "requirement-test-case-code-is-easy-to-alter-and-rerun"]], "Requirement: User- and developer-friendly documentation": [[1, "requirement-user-and-developer-friendly-documentation"]], "Requirement: cached outputs": [[0, "requirement-cached-outputs"]], "Requirement: either \u201cnormal\u201d or \u201ccached\u201d versions of a step": [[0, "requirement-either-normal-or-cached-versions-of-a-step"]], "Requirement: name-of-topic-here": [[3, "requirement-name-of-topic-here"]], "Requirement: selecting whether to use cached outputs": [[0, "requirement-selecting-whether-to-use-cached-outputs"]], "Requirement: unique identifier for cached outputs": [[0, "requirement-unique-identifier-for-cached-outputs"]], "Requirement: updating cached outputs": [[0, "requirement-updating-cached-outputs"]], "Requirements": [[0, "requirements"], [1, "requirements"], [3, "requirements"]], "RestartTest": [[317, "restarttest"]], "RunModel": [[314, "runmodel"], [315, "runmodel"], [317, "runmodel"]], "Running MPAS": [[9, "running-mpas"]], "Running a test case": [[983, "running-a-test-case"]], "Running compass from the repo": [[916, "running-compass-from-the-repo"]], "Running the mesh test case": [[921, "running-the-mesh-test-case"]], "Running with a job script": [[983, "running-with-a-job-script"]], "SO12to60 and SOwISC12to60": [[895, "so12to60-and-sowisc12to60"], [964, "so12to60-and-sowisc12to60"]], "Sea surface height adjustment": [[954, "sea-surface-height-adjustment"]], "Set up a compass repository with worktrees: for advanced users": [[916, "set-up-a-compass-repository-with-worktrees-for-advanced-users"]], "Set up a compass repository: for beginners": [[916, "set-up-a-compass-repository-for-beginners"]], "Set up and run": [[922, "set-up-and-run"], [923, "set-up-and-run"]], "Setting config options based on resolution": [[922, "setting-config-options-based-on-resolution"], [922, "id2"]], "Setting the number of tasks and CPUs per task": [[920, "setting-the-number-of-tasks-and-cpus-per-task"]], "Setting up test cases": [[983, "setting-up-test-cases"]], "SetupMesh": [[315, "setupmesh"], [317, "setupmesh"]], "Shared config options": [[964, "shared-config-options"], [966, "shared-config-options"], [980, "shared-config-options"]], "Simulation run": [[970, "simulation-run"]], "Slurm job queueing": [[952, "slurm-job-queueing"]], "SmokeTest": [[317, "smoketest"]], "Solver errors when configuring conda environment": [[917, "solver-errors-when-configuring-conda-environment"]], "Spack": [[7, "spack"]], "Spherical Meshes": [[9, "spherical-meshes"]], "Step attributes": [[914, "step-attributes"]], "Steps": [[914, "steps"]], "Steps for setting up and running an ensmble": [[934, "steps-for-setting-up-and-running-an-ensmble"]], "Steps for setting up and running experiments": [[941, "steps-for-setting-up-and-running-experiments"]], "Summary": [[0, "summary"], [1, "summary"], [3, "summary"]], "Supported Machines": [[337, "supported-machines"], [952, "supported-machines"]], "Supported machines": [[916, "supported-machines"]], "Switching between different compass environments": [[916, "switching-between-different-compass-environments"]], "Switching to an EC30to60 base resolution": [[921, "switching-to-an-ec30to60-base-resolution"]], "Symlink to input files from compass": [[914, "symlink-to-input-files-from-compass"]], "Symlinks": [[9, "symlinks"]], "Symlinks to input files": [[914, "symlinks-to-input-files"]], "Template": [[3, "template"]], "Test Cases": [[984, "test-cases"]], "Test Groups": [[77, "test-groups"], [339, "test-groups"], [914, "test-groups"], [939, "test-groups"]], "Test Suites": [[914, "test-suites"], [983, "test-suites"], [985, "test-suites"]], "Test cases": [[325, "test-cases"], [331, "test-cases"], [895, "test-cases"], [914, "test-cases"], [964, "test-cases"]], "Test groups": [[324, "test-groups"], [899, "test-groups"], [968, "test-groups"]], "Test suites": [[927, "test-suites"], [959, "test-suites"]], "Test-case config files": [[924, "test-case-config-files"]], "TestCase attributes": [[914, "testcase-attributes"]], "Testing": [[0, "testing"], [1, "testing"], [3, "testing"]], "Testing MALI with Albany": [[7, "testing-mali-with-albany"]], "Testing MPAS-Ocean with PETSc": [[7, "testing-mpas-ocean-with-petsc"]], "Testing MPAS-Ocean without PETSc": [[7, "testing-mpas-ocean-without-petsc"]], "Testing and Validation: name-of-topic-here (same as Requirement)": [[3, "testing-and-validation-name-of-topic-here-same-as-requirement"]], "Testing compass": [[7, "testing-compass"]], "Testing spack with Albany": [[7, "testing-spack-with-albany"]], "Testing spack with PETSc (and Netlib LAPACK)": [[7, "testing-spack-with-petsc-and-netlib-lapack"]], "Testing: Ability specify/modify core counts": [[1, "testing-ability-specify-modify-core-counts"]], "Testing: Considerations related to running test cases in parallel": [[1, "testing-considerations-related-to-running-test-cases-in-parallel"]], "Testing: Easy batch submission": [[1, "testing-easy-batch-submission"]], "Testing: Looser, more flexible directory structure": [[1, "testing-looser-more-flexible-directory-structure"]], "Testing: Machine-specific data": [[1, "testing-machine-specific-data"]], "Testing: Make test cases easy to understand, modify and create": [[1, "testing-make-test-cases-easy-to-understand-modify-and-create"]], "Testing: Resolution can be a test case parameter": [[1, "testing-resolution-can-be-a-test-case-parameter"]], "Testing: Shared code": [[1, "testing-shared-code"]], "Testing: Shared configuration options": [[1, "testing-shared-configuration-options"]], "Testing: Support for pre-made initial condition files": [[1, "testing-support-for-pre-made-initial-condition-files"]], "Testing: Test case code is easy to alter and rerun": [[1, "testing-test-case-code-is-easy-to-alter-and-rerun"]], "Testing: User- and developer-friendly documentation": [[1, "testing-user-and-developer-friendly-documentation"]], "Testing: cached outputs": [[0, "testing-cached-outputs"]], "Testing: either \u201cnormal\u201d or \u201ccached\u201d versions of a step": [[0, "testing-either-normal-or-cached-versions-of-a-step"]], "Testing: selecting whether to use cached outputs": [[0, "testing-selecting-whether-to-use-cached-outputs"]], "Testing: unique identifier for cached outputs": [[0, "testing-unique-identifier-for-cached-outputs"]], "Testing: updating cached outputs": [[0, "testing-updating-cached-outputs"]], "The legacy COMPASS test group": [[923, "the-legacy-compass-test-group"]], "Troubleshooting": [[916, "troubleshooting"], [917, "troubleshooting"]], "Troubleshooting spack": [[7, "troubleshooting-spack"]], "Tutorials": [[919, null]], "Unix Shell": [[916, "unix-shell"]], "Unknown machines": [[916, "unknown-machines"]], "Updating PIO namelist options": [[9, "updating-pio-namelist-options"]], "Updating a streams file at runtime": [[914, "updating-a-streams-file-at-runtime"]], "Updating namelist options at runtime": [[914, "updating-namelist-options-at-runtime"]], "Updating spack from compass with mache from a remote branch": [[7, "updating-spack-from-compass-with-mache-from-a-remote-branch"]], "Updating the test case and test group": [[923, "updating-the-test-case-and-test-group"]], "User's guide": [[919, null]], "Validating timers": [[9, "validating-timers"]], "Validating variables": [[9, "validating-variables"]], "Validation": [[9, "validation"]], "Varying resolution (or other parameters)": [[922, "varying-resolution-or-other-parameters"], [923, "varying-resolution-or-other-parameters"]], "Versions": [[919, null]], "Vertical coordinate": [[340, "vertical-coordinate"], [957, "vertical-coordinate"]], "Visualize": [[315, "visualize"], [317, "visualize"]], "WC14 and WCwISC14": [[895, "wc14-and-wcwisc14"], [964, "wc14-and-wcwisc14"]], "What the script does": [[916, "what-the-script-does"]], "Where do we update compass dependencies?": [[7, "where-do-we-update-compass-dependencies"]], "Within a test case": [[915, "within-a-test-case"]], "Within a test group": [[915, "within-a-test-group"]], "Within an MPAS core": [[915, "within-an-mpas-core"]], "ais_observations": [[78, "ais-observations"]], "analysis": [[893, "analysis"], [894, "analysis"], [896, "analysis"], [897, "analysis"], [907, "analysis"], [908, "analysis"], [909, "analysis"], [909, "id4"], [909, "id8"], [909, "id12"], [910, "analysis"], [911, "analysis"]], "analysis step": [[966, "analysis-step"], [980, "analysis-step"]], "analysis_test test case": [[895, "analysis-test-test-case"], [964, "analysis-test-test-case"]], "antarctica": [[77, "antarctica"], [313, "antarctica"], [928, "antarctica"]], "atmosphere": [[325, "atmosphere"], [940, "atmosphere"]], "baroclinic_channel": [[339, "baroclinic-channel"], [891, "baroclinic-channel"], [960, "baroclinic-channel"]], "branch_ensemble": [[319, "branch-ensemble"], [934, "branch-ensemble"]], "cache": [[4, "cache"]], "cache module": [[9, "cache-module"]], "calving_dt_convergence": [[77, "calving-dt-convergence"], [314, "calving-dt-convergence"], [927, "calving-dt-convergence"], [929, "calving-dt-convergence"]], "chicoma-cpu, gnu": [[334, "chicoma-cpu-gnu"]], "circular_shelf": [[77, "circular-shelf"], [315, "circular-shelf"], [930, "circular-shelf"]], "clean": [[4, "clean"]], "clean module": [[9, "clean-module"]], "combine": [[912, "combine"], [912, "id1"]], "combine_topo": [[912, "combine-topo"], [981, "combine-topo"]], "compass cache": [[6, "compass-cache"]], "compass clean": [[6, "compass-clean"]], "compass conda environment": [[983, "compass-conda-environment"]], "compass conda environment, compilers and system modules": [[916, "compass-conda-environment-compilers-and-system-modules"]], "compass framework": [[1, "compass-framework"], [4, "compass-framework"]], "compass list": [[6, "compass-list"]], "compass python package": [[1, "compass-python-package"]], "compass run": [[6, "compass-run"]], "compass setup": [[6, "compass-setup"]], "compass suite": [[6, "compass-suite"]], "compass.MpasCore": [[10, "compass-mpascore"]], "compass.MpasCore.add_test_group": [[11, "compass-mpascore-add-test-group"]], "compass.Step": [[12, "compass-step"]], "compass.Step.add_input_file": [[13, 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"compass.ocean.tests.sphere_transport.correlated_tracers_2d.forward.Forward.get_timestep_str", false]], "get_timestep_str() (compass.ocean.tests.sphere_transport.divergent_2d.forward.forward method)": [[768, "compass.ocean.tests.sphere_transport.divergent_2d.forward.Forward.get_timestep_str", false]], "get_timestep_str() (compass.ocean.tests.sphere_transport.nondivergent_2d.forward.forward method)": [[782, "compass.ocean.tests.sphere_transport.nondivergent_2d.forward.Forward.get_timestep_str", false]], "get_timestep_str() (compass.ocean.tests.sphere_transport.rotation_2d.forward.forward method)": [[806, "compass.ocean.tests.sphere_transport.rotation_2d.forward.Forward.get_timestep_str", false]], "globalconvergence (class in compass.ocean.tests.global_convergence)": [[412, "compass.ocean.tests.global_convergence.GlobalConvergence", false]], "globalocean (class in compass.ocean.tests.global_ocean)": [[425, "compass.ocean.tests.global_ocean.GlobalOcean", false]], "gotm (class in compass.ocean.tests.gotm)": [[516, "compass.ocean.tests.gotm.Gotm", false]], "greenland (class in compass.landice.tests.greenland)": [[177, "compass.landice.tests.greenland.Greenland", false]], "gridded_flood_fill() (in module compass.landice.mesh)": [[88, "compass.landice.mesh.gridded_flood_fill", false]], "horizontaladvection (class in compass.ocean.tests.planar_convergence.horizontal_advection)": [[730, "compass.ocean.tests.planar_convergence.horizontal_advection.HorizontalAdvection", false]], "humboldt (class in compass.landice.tests.humboldt)": [[191, "compass.landice.tests.humboldt.Humboldt", false]], "hurricane (class in compass.ocean.tests.hurricane)": [[525, "compass.ocean.tests.hurricane.Hurricane", false]], "hydro (class in compass.ocean.tests.lock_exchange.hydro)": [[640, "compass.ocean.tests.lock_exchange.hydro.Hydro", false]], "hydroradial (class in compass.landice.tests.hydro_radial)": [[202, "compass.landice.tests.hydro_radial.HydroRadial", false]], "hydrovsnonhydro (class in compass.ocean.tests.overflow.hydro_vs_nonhydro)": [[684, "compass.ocean.tests.overflow.hydro_vs_nonhydro.HydroVsNonhydro", false]], "iceshelf2d (class in compass.ocean.tests.ice_shelf_2d)": [[566, "compass.ocean.tests.ice_shelf_2d.IceShelf2d", false]], "icosahedralmeshstep (class in compass.mesh)": [[45, "compass.mesh.IcosahedralMeshStep", false]], "icosmeshfromconfigstep (class in compass.ocean.tests.global_ocean.mesh.qu)": [[494, "compass.ocean.tests.global_ocean.mesh.qu.IcosMeshFromConfigStep", false]], "images_to_movies() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[623, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.images_to_movies", false]], "init (class in compass.ocean.tests.global_convergence.cosine_bell.init)": [[423, "compass.ocean.tests.global_convergence.cosine_bell.init.Init", false]], "init (class in compass.ocean.tests.global_ocean.init)": [[476, "compass.ocean.tests.global_ocean.init.Init", false]], "init (class in compass.ocean.tests.gotm.default.init)": [[523, "compass.ocean.tests.gotm.default.init.Init", false]], "init (class in compass.ocean.tests.hurricane.init)": [[539, "compass.ocean.tests.hurricane.init.Init", false]], "init (class in compass.ocean.tests.planar_convergence.horizontal_advection.init)": [[736, "compass.ocean.tests.planar_convergence.horizontal_advection.init.Init", false]], "init (class in compass.ocean.tests.sphere_transport.correlated_tracers_2d.init)": [[757, "compass.ocean.tests.sphere_transport.correlated_tracers_2d.init.Init", false]], "init (class in compass.ocean.tests.sphere_transport.divergent_2d.init)": [[771, "compass.ocean.tests.sphere_transport.divergent_2d.init.Init", false]], "init (class in compass.ocean.tests.sphere_transport.nondivergent_2d.init)": [[785, "compass.ocean.tests.sphere_transport.nondivergent_2d.init.Init", false]], "init (class in compass.ocean.tests.sphere_transport.rotation_2d.init)": [[809, "compass.ocean.tests.sphere_transport.rotation_2d.init.Init", false]], "init (class in compass.ocean.tests.tides.init)": [[832, "compass.ocean.tests.tides.init.Init", false]], "init_vertical_coord() (in module compass.ocean.vertical)": [[882, "compass.ocean.vertical.init_vertical_coord", false]], "init_z_level_vertical_coord() (in module compass.ocean.vertical.zlevel)": [[888, "compass.ocean.vertical.zlevel.init_z_level_vertical_coord", false]], "init_z_star_vertical_coord() (in module compass.ocean.vertical.zstar)": [[889, "compass.ocean.vertical.zstar.init_z_star_vertical_coord", false]], "initialstate (class in compass.ocean.tests.baroclinic_channel.initial_state)": [[370, "compass.ocean.tests.baroclinic_channel.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.dam_break.initial_state)": [[390, "compass.ocean.tests.dam_break.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.drying_slope.initial_state)": [[405, "compass.ocean.tests.drying_slope.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.global_ocean.init.initial_state)": [[479, "compass.ocean.tests.global_ocean.init.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.hurricane.init.initial_state)": [[545, "compass.ocean.tests.hurricane.init.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.ice_shelf_2d.initial_state)": [[574, "compass.ocean.tests.ice_shelf_2d.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.internal_wave.initial_state)": [[589, "compass.ocean.tests.internal_wave.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.isomip_plus.initial_state)": [[605, "compass.ocean.tests.isomip_plus.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.lock_exchange.initial_state)": [[641, "compass.ocean.tests.lock_exchange.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.merry_go_round.initial_state)": [[653, "compass.ocean.tests.merry_go_round.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.nonhydro.solitary_wave.initial_state)": [[663, "compass.ocean.tests.nonhydro.solitary_wave.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.nonhydro.stratified_seiche.initial_state)": [[674, "compass.ocean.tests.nonhydro.stratified_seiche.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.overflow.initial_state)": [[689, "compass.ocean.tests.overflow.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.parabolic_bowl.initial_state)": [[708, "compass.ocean.tests.parabolic_bowl.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.soma.initial_state)": [[743, "compass.ocean.tests.soma.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.tides.init.initial_state)": [[835, "compass.ocean.tests.tides.init.initial_state.InitialState", false]], "initialstate (class in compass.ocean.tests.ziso.initial_state)": [[875, "compass.ocean.tests.ziso.initial_state.InitialState", false]], "initialstatefrominitmode (class in compass.ocean.tests.overflow.initial_state_from_init_mode)": [[691, "compass.ocean.tests.overflow.initial_state_from_init_mode.InitialStateFromInitMode", false]], "inject_exact_solution() (compass.ocean.tests.parabolic_bowl.viz.viz method)": [[715, "compass.ocean.tests.parabolic_bowl.viz.Viz.inject_exact_solution", false]], "internalwave (class in compass.ocean.tests.internal_wave)": [[584, "compass.ocean.tests.internal_wave.InternalWave", false]], "interp_ais_bedmachine() (in module compass.landice.mesh)": [[89, "compass.landice.mesh.interp_ais_bedmachine", false]], "interp_ais_measures() (in module compass.landice.mesh)": [[90, "compass.landice.mesh.interp_ais_measures", false]], "interpolate_data_to_grid() (compass.ocean.tests.hurricane.init.interpolate_atm_forcing.interpolateatmforcing method)": [[549, "compass.ocean.tests.hurricane.init.interpolate_atm_forcing.InterpolateAtmForcing.interpolate_data_to_grid", false]], "interpolate_data_to_grid() (compass.ocean.tests.hurricane.lts.init.topographic_wave_drag.computetopographicwavedrag method)": [[554, "compass.ocean.tests.hurricane.lts.init.topographic_wave_drag.ComputeTopographicWaveDrag.interpolate_data_to_grid", false]], "interpolate_data_to_grid() (compass.ocean.tests.tides.init.interpolate_wave_drag.interpolatewavedrag method)": [[839, "compass.ocean.tests.tides.init.interpolate_wave_drag.InterpolateWaveDrag.interpolate_data_to_grid", false]], "interpolate_geom() (in module compass.ocean.tests.isomip_plus.geom)": [[603, "compass.ocean.tests.isomip_plus.geom.interpolate_geom", false]], "interpolate_ocean_mask() (in module compass.ocean.tests.isomip_plus.geom)": [[604, "compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask", false]], "interpolateatmforcing (class in compass.ocean.tests.hurricane.init.interpolate_atm_forcing)": [[548, "compass.ocean.tests.hurricane.init.interpolate_atm_forcing.InterpolateAtmForcing", false]], "interpolatewavedrag (class in compass.ocean.tests.tides.init.interpolate_wave_drag)": [[838, "compass.ocean.tests.tides.init.interpolate_wave_drag.InterpolateWaveDrag", false]], "ismip6aisproj2300 (class in compass.landice.tests.ismip6_run.ismip6_ais_proj2300)": [[259, "compass.landice.tests.ismip6_run.ismip6_ais_proj2300.Ismip6AisProj2300", false]], "ismip6forcing (class in compass.landice.tests.ismip6_forcing)": [[219, "compass.landice.tests.ismip6_forcing.Ismip6Forcing", false]], "ismip6run (class in compass.landice.tests.ismip6_run)": [[258, "compass.landice.tests.ismip6_run.Ismip6Run", false]], "isomipplus (class in compass.ocean.tests.isomip_plus)": [[598, "compass.ocean.tests.isomip_plus.IsomipPlus", false]], "isomipplustest (class in compass.ocean.tests.isomip_plus.isomip_plus_test)": [[607, "compass.ocean.tests.isomip_plus.isomip_plus_test.IsomipPlusTest", false]], "isunnguatasermia (class in compass.landice.tests.isunnguata_sermia)": [[265, "compass.landice.tests.isunnguata_sermia.IsunnguataSermia", false]], "kangerlussuaq (class in compass.landice.tests.kangerlussuaq)": [[270, "compass.landice.tests.kangerlussuaq.Kangerlussuaq", false]], "kogebugts (class in compass.landice.tests.koge_bugt_s)": [[275, "compass.landice.tests.koge_bugt_s.KogeBugtS", false]], "label_mesh() (in module compass.ocean.tests.hurricane.lts.mesh.lts_regions)": [[560, "compass.ocean.tests.hurricane.lts.mesh.lts_regions.label_mesh", false]], "landice (class in compass.landice)": [[79, "compass.landice.Landice", false]], "list_cases() (in module compass.list)": [[41, "compass.list.list_cases", false]], "list_machines() (in module compass.list)": [[42, "compass.list.list_machines", false]], "list_suites() (in module compass.list)": [[43, "compass.list.list_suites", false]], "lockexchange (class in compass.ocean.tests.lock_exchange)": [[637, "compass.ocean.tests.lock_exchange.LockExchange", false]], "log_method_call() (in module compass.logging)": [[44, "compass.logging.log_method_call", false]], "loglaw (class in compass.ocean.tests.drying_slope.loglaw)": [[407, "compass.ocean.tests.drying_slope.loglaw.LogLaw", false]], "ltsregionsstep (class in compass.ocean.tests.hurricane.lts.mesh.lts_regions)": [[557, "compass.ocean.tests.hurricane.lts.mesh.lts_regions.LTSRegionsStep", false]], "main() (in module compass.__main__)": [[34, "compass.__main__.main", false]], "make_convergence_arrays() (in module compass.ocean.tests.sphere_transport.process_output)": [[792, "compass.ocean.tests.sphere_transport.process_output.make_convergence_arrays", false]], "make_graph_file() (in module compass.model)": [[61, "compass.model.make_graph_file", false]], "make_jigsaw_mesh() (compass.mesh.icosahedralmeshstep method)": [[49, "compass.mesh.IcosahedralMeshStep.make_jigsaw_mesh", false]], "make_jigsaw_mesh() (compass.mesh.quasiuniformsphericalmeshstep method)": [[54, "compass.mesh.QuasiUniformSphericalMeshStep.make_jigsaw_mesh", false]], "make_region_masks() (in module compass.landice.mesh)": [[91, "compass.landice.mesh.make_region_masks", false]], "mark_cull_cells_for_mismip() (in module compass.landice.tests.mismipplus.setup_mesh)": [[292, "compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP", false]], "merrygoround (class in compass.ocean.tests.merry_go_round)": [[646, "compass.ocean.tests.merry_go_round.MerryGoRound", false]], "mesh (class in compass.landice.tests.antarctica.mesh)": [[97, "compass.landice.tests.antarctica.mesh.Mesh", false]], "mesh (class in compass.landice.tests.crane.mesh)": [[116, "compass.landice.tests.crane.mesh.Mesh", false]], "mesh (class in compass.landice.tests.greenland.mesh)": [[180, "compass.landice.tests.greenland.mesh.Mesh", false]], "mesh (class in compass.landice.tests.humboldt.mesh)": [[194, "compass.landice.tests.humboldt.mesh.Mesh", false]], "mesh (class in compass.landice.tests.isunnguata_sermia.mesh)": [[266, "compass.landice.tests.isunnguata_sermia.mesh.Mesh", false]], "mesh (class in compass.landice.tests.kangerlussuaq.mesh)": [[271, "compass.landice.tests.kangerlussuaq.mesh.Mesh", false]], "mesh (class in compass.landice.tests.koge_bugt_s.mesh)": [[276, "compass.landice.tests.koge_bugt_s.mesh.Mesh", false]], "mesh (class in compass.landice.tests.thwaites.mesh)": [[303, "compass.landice.tests.thwaites.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.global_ocean.mesh)": [[489, "compass.ocean.tests.global_ocean.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.hurricane.mesh)": [[561, "compass.ocean.tests.hurricane.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.sphere_transport.correlated_tracers_2d.mesh)": [[759, "compass.ocean.tests.sphere_transport.correlated_tracers_2d.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.sphere_transport.divergent_2d.mesh)": [[773, "compass.ocean.tests.sphere_transport.divergent_2d.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.sphere_transport.nondivergent_2d.mesh)": [[787, "compass.ocean.tests.sphere_transport.nondivergent_2d.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.sphere_transport.rotation_2d.mesh)": [[811, "compass.ocean.tests.sphere_transport.rotation_2d.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.tides.mesh)": [[845, "compass.ocean.tests.tides.mesh.Mesh", false]], "meshgen (class in compass.landice.tests.antarctica.mesh_gen)": [[99, "compass.landice.tests.antarctica.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.crane.mesh_gen)": [[118, "compass.landice.tests.crane.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.greenland.mesh_gen)": [[182, "compass.landice.tests.greenland.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.humboldt.mesh_gen)": [[196, "compass.landice.tests.humboldt.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.isunnguata_sermia.mesh_gen)": [[268, "compass.landice.tests.isunnguata_sermia.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.kangerlussuaq.mesh_gen)": [[273, "compass.landice.tests.kangerlussuaq.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.koge_bugt_s.mesh_gen)": [[278, "compass.landice.tests.koge_bugt_s.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.thwaites.mesh_gen)": [[305, "compass.landice.tests.thwaites.mesh_gen.MeshGen", false]], "meshmodifications (class in compass.landice.tests.mesh_modifications)": [[280, "compass.landice.tests.mesh_modifications.MeshModifications", false]], "mismipplus (class in compass.landice.tests.mismipplus)": [[283, "compass.landice.tests.mismipplus.MISMIPplus", false]], "misomip (class in compass.ocean.tests.isomip_plus.misomip)": [[610, "compass.ocean.tests.isomip_plus.misomip.Misomip", false]], "module": [[80, "module-compass.landice.ais_observations", false], [532, "module-compass.ocean.tests.hurricane.configure", false], [825, "module-compass.ocean.tests.tides.configure", false]], "movieplotter (class in compass.ocean.tests.isomip_plus.viz.plot)": [[622, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter", false]], "mpas_flood_fill() (in module compass.landice.mesh)": [[92, "compass.landice.mesh.mpas_flood_fill", false]], "mpascore (class in compass)": [[10, "compass.MpasCore", false]], "nondivergent2d (class in compass.ocean.tests.sphere_transport.nondivergent_2d)": [[776, "compass.ocean.tests.sphere_transport.nondivergent_2d.Nondivergent2D", false]], "nonhydro (class in compass.ocean.tests.lock_exchange.nonhydro)": [[643, "compass.ocean.tests.lock_exchange.nonhydro.Nonhydro", false]], "nonhydro (class in compass.ocean.tests.nonhydro)": [[657, "compass.ocean.tests.nonhydro.Nonhydro", false]], "nonhydro (class in compass.ocean.tests.overflow.nonhydro)": [[693, "compass.ocean.tests.overflow.nonhydro.Nonhydro", false]], "ocean (class in compass.ocean)": [[341, "compass.ocean.Ocean", false]], "oceanbasal (class in compass.landice.tests.ismip6_forcing.ocean_basal)": [[237, "compass.landice.tests.ismip6_forcing.ocean_basal.OceanBasal", false]], "oceangraphpartition (class in compass.ocean.tests.global_ocean.files_for_e3sm.ocean_graph_partition)": [[446, "compass.ocean.tests.global_ocean.files_for_e3sm.ocean_graph_partition.OceanGraphPartition", false]], "oceaninitialcondition (class in compass.ocean.tests.global_ocean.files_for_e3sm.ocean_initial_condition)": [[448, "compass.ocean.tests.global_ocean.files_for_e3sm.ocean_initial_condition.OceanInitialCondition", false]], "oceanmesh (class in compass.ocean.tests.global_ocean.files_for_e3sm.ocean_mesh)": [[450, "compass.ocean.tests.global_ocean.files_for_e3sm.ocean_mesh.OceanMesh", false]], "oceanthermal (class in compass.landice.tests.ismip6_forcing.ocean_thermal)": [[245, "compass.landice.tests.ismip6_forcing.ocean_thermal.OceanThermal", false]], "overflow (class in compass.ocean.tests.overflow)": [[680, "compass.ocean.tests.overflow.Overflow", false]], "package_path() (in module compass.io)": [[39, "compass.io.package_path", false]], "parabolicbowl (class in compass.ocean.tests.parabolic_bowl)": [[699, "compass.ocean.tests.parabolic_bowl.ParabolicBowl", false]], "partition() (in module compass.model)": [[62, "compass.model.partition", false]], "performancetest (class in compass.ocean.tests.global_ocean.performance_test)": [[506, "compass.ocean.tests.global_ocean.performance_test.PerformanceTest", false]], "planarconvergence (class in compass.ocean.tests.planar_convergence)": [[719, "compass.ocean.tests.planar_convergence.PlanarConvergence", false]], "plot() (compass.ocean.tests.tides.analysis.analysis method)": [[818, "compass.ocean.tests.tides.analysis.Analysis.plot", false]], 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\ No newline at end of file
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"Adding a template streams file": [[914, "adding-a-template-streams-file"]], "Adding a test case": [[923, "adding-a-test-case"]], "Adding a very high resolution region": [[921, "adding-a-very-high-resolution-region"]], "Adding a \u201cdefault\u201d test case": [[922, "adding-a-default-test-case"]], "Adding an initial condition and performance test": [[921, "adding-an-initial-condition-and-performance-test"]], "Adding an \u201canalysis\u201d step": [[920, "adding-an-analysis-step"]], "Adding an \u201crpe_test\u201d test case": [[922, "adding-an-rpe-test-test-case"]], "Adding namelist and streams files": [[914, "adding-namelist-and-streams-files"]], "Adding namelist options": [[914, "adding-namelist-options"]], "Adding regions of higher resolution": [[921, "adding-regions-of-higher-resolution"]], "Adding step outputs": [[922, "adding-step-outputs"]], "Adding the analysis step": [[922, "adding-the-analysis-step"], [923, "adding-the-analysis-step"]], "Adding the forward step": [[922, 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"Algorithm design: Test case code is easy to alter and rerun": [[1, "algorithm-design-test-case-code-is-easy-to-alter-and-rerun"]], "Algorithm design: User- and developer-friendly documentation": [[1, "algorithm-design-user-and-developer-friendly-documentation"]], "Anvil": [[333, "anvil"], [948, "anvil"]], "B": [[320, "b"], [935, "b"]], "Base Classes": [[4, "base-classes"]], "Building MPAS components": [[916, "building-mpas-components"], [983, "building-mpas-components"]], "Building the Documentation": [[5, "building-the-documentation"]], "Building the Spack Environment": [[337, "building-the-spack-environment"]], "Cached output files": [[914, "cached-output-files"]], "Caching outputs from compass steps": [[0, "caching-outputs-from-compass-steps"]], "Chicoma": [[334, "chicoma"], [949, "chicoma"]], "Chicoma-CPU": [[949, "chicoma-cpu"]], "Chrysalis": [[335, "chrysalis"], [950, "chrysalis"]], "Classes": [[915, "classes"]], "Code Style": [[915, "code-style"]], "Code and Documentation 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"perlmutter"]], "Perlmutter-CPU": [[953, "perlmutter-cpu"]], "Plotting": [[340, "plotting"]], "Projection handling": [[941, "projection-handling"]], "Provenance": [[9, "provenance"]], "Proxy on LANL Macs": [[917, "proxy-on-lanl-macs"]], "QU, Icos, QUwISC and IcoswISC": [[964, "qu-icos-quwisc-and-icoswisc"]], "QU, QUwISC, Icos and IcoswISC": [[895, "qu-quwisc-icos-and-icoswisc"]], "QU240 and Icos240": [[964, "qu240-and-icos240"]], "QU240 and QUwISC240": [[895, "qu240-and-quwisc240"]], "QUwISC240 and IcoswISC240": [[964, "quwisc240-and-icoswisc240"]], "Quick Start for Developers": [[916, "quick-start-for-developers"]], "Quick Start for Users": [[983, "quick-start-for-users"]], "RRS6to18 and RRSwISC6to18": [[895, "rrs6to18-and-rrswisc6to18"], [964, "rrs6to18-and-rrswisc6to18"]], "Remapping Topography": [[340, "remapping-topography"]], "Remapping topography": [[956, "remapping-topography"]], "Requirement: Ability specify/modify core counts": [[1, 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"interpolate_data_to_grid() (compass.ocean.tests.hurricane.init.interpolate_atm_forcing.interpolateatmforcing method)": [[549, "compass.ocean.tests.hurricane.init.interpolate_atm_forcing.InterpolateAtmForcing.interpolate_data_to_grid", false]], "interpolate_data_to_grid() (compass.ocean.tests.hurricane.lts.init.topographic_wave_drag.computetopographicwavedrag method)": [[554, "compass.ocean.tests.hurricane.lts.init.topographic_wave_drag.ComputeTopographicWaveDrag.interpolate_data_to_grid", false]], "interpolate_data_to_grid() (compass.ocean.tests.tides.init.interpolate_wave_drag.interpolatewavedrag method)": [[839, "compass.ocean.tests.tides.init.interpolate_wave_drag.InterpolateWaveDrag.interpolate_data_to_grid", false]], "interpolate_geom() (in module compass.ocean.tests.isomip_plus.geom)": [[603, "compass.ocean.tests.isomip_plus.geom.interpolate_geom", false]], "interpolate_ocean_mask() (in module compass.ocean.tests.isomip_plus.geom)": [[604, "compass.ocean.tests.isomip_plus.geom.interpolate_ocean_mask", false]], "interpolateatmforcing (class in compass.ocean.tests.hurricane.init.interpolate_atm_forcing)": [[548, "compass.ocean.tests.hurricane.init.interpolate_atm_forcing.InterpolateAtmForcing", false]], "interpolatewavedrag (class in compass.ocean.tests.tides.init.interpolate_wave_drag)": [[838, "compass.ocean.tests.tides.init.interpolate_wave_drag.InterpolateWaveDrag", false]], "ismip6aisproj2300 (class in compass.landice.tests.ismip6_run.ismip6_ais_proj2300)": [[259, "compass.landice.tests.ismip6_run.ismip6_ais_proj2300.Ismip6AisProj2300", false]], "ismip6forcing (class in compass.landice.tests.ismip6_forcing)": [[219, "compass.landice.tests.ismip6_forcing.Ismip6Forcing", false]], "ismip6run (class in compass.landice.tests.ismip6_run)": [[258, "compass.landice.tests.ismip6_run.Ismip6Run", false]], "isomipplus (class in compass.ocean.tests.isomip_plus)": [[598, "compass.ocean.tests.isomip_plus.IsomipPlus", false]], "isomipplustest (class in compass.ocean.tests.isomip_plus.isomip_plus_test)": [[607, "compass.ocean.tests.isomip_plus.isomip_plus_test.IsomipPlusTest", false]], "isunnguatasermia (class in compass.landice.tests.isunnguata_sermia)": [[265, "compass.landice.tests.isunnguata_sermia.IsunnguataSermia", false]], "kangerlussuaq (class in compass.landice.tests.kangerlussuaq)": [[270, "compass.landice.tests.kangerlussuaq.Kangerlussuaq", false]], "kogebugts (class in compass.landice.tests.koge_bugt_s)": [[275, "compass.landice.tests.koge_bugt_s.KogeBugtS", false]], "label_mesh() (in module compass.ocean.tests.hurricane.lts.mesh.lts_regions)": [[560, "compass.ocean.tests.hurricane.lts.mesh.lts_regions.label_mesh", false]], "landice (class in compass.landice)": [[79, "compass.landice.Landice", false]], "list_cases() (in module compass.list)": [[41, "compass.list.list_cases", false]], "list_machines() (in module compass.list)": [[42, "compass.list.list_machines", false]], "list_suites() (in module compass.list)": [[43, "compass.list.list_suites", false]], "lockexchange (class in compass.ocean.tests.lock_exchange)": [[637, "compass.ocean.tests.lock_exchange.LockExchange", false]], "log_method_call() (in module compass.logging)": [[44, "compass.logging.log_method_call", false]], "loglaw (class in compass.ocean.tests.drying_slope.loglaw)": [[407, "compass.ocean.tests.drying_slope.loglaw.LogLaw", false]], "ltsregionsstep (class in compass.ocean.tests.hurricane.lts.mesh.lts_regions)": [[557, "compass.ocean.tests.hurricane.lts.mesh.lts_regions.LTSRegionsStep", false]], "main() (in module compass.__main__)": [[34, "compass.__main__.main", false]], "make_convergence_arrays() (in module compass.ocean.tests.sphere_transport.process_output)": [[792, "compass.ocean.tests.sphere_transport.process_output.make_convergence_arrays", false]], "make_graph_file() (in module compass.model)": [[61, "compass.model.make_graph_file", false]], "make_jigsaw_mesh() (compass.mesh.icosahedralmeshstep method)": [[49, "compass.mesh.IcosahedralMeshStep.make_jigsaw_mesh", false]], "make_jigsaw_mesh() (compass.mesh.quasiuniformsphericalmeshstep method)": [[54, "compass.mesh.QuasiUniformSphericalMeshStep.make_jigsaw_mesh", false]], "make_region_masks() (in module compass.landice.mesh)": [[91, "compass.landice.mesh.make_region_masks", false]], "mark_cull_cells_for_mismip() (in module compass.landice.tests.mismipplus.setup_mesh)": [[292, "compass.landice.tests.mismipplus.setup_mesh.mark_cull_cells_for_MISMIP", false]], "merrygoround (class in compass.ocean.tests.merry_go_round)": [[646, "compass.ocean.tests.merry_go_round.MerryGoRound", false]], "mesh (class in compass.landice.tests.antarctica.mesh)": [[97, "compass.landice.tests.antarctica.mesh.Mesh", false]], "mesh (class in compass.landice.tests.crane.mesh)": [[116, "compass.landice.tests.crane.mesh.Mesh", false]], "mesh (class in compass.landice.tests.greenland.mesh)": [[180, "compass.landice.tests.greenland.mesh.Mesh", false]], "mesh (class in compass.landice.tests.humboldt.mesh)": [[194, "compass.landice.tests.humboldt.mesh.Mesh", false]], "mesh (class in compass.landice.tests.isunnguata_sermia.mesh)": [[266, "compass.landice.tests.isunnguata_sermia.mesh.Mesh", false]], "mesh (class in compass.landice.tests.kangerlussuaq.mesh)": [[271, "compass.landice.tests.kangerlussuaq.mesh.Mesh", false]], "mesh (class in compass.landice.tests.koge_bugt_s.mesh)": [[276, "compass.landice.tests.koge_bugt_s.mesh.Mesh", false]], "mesh (class in compass.landice.tests.thwaites.mesh)": [[303, "compass.landice.tests.thwaites.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.global_ocean.mesh)": [[489, "compass.ocean.tests.global_ocean.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.hurricane.mesh)": [[561, "compass.ocean.tests.hurricane.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.sphere_transport.correlated_tracers_2d.mesh)": [[759, "compass.ocean.tests.sphere_transport.correlated_tracers_2d.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.sphere_transport.divergent_2d.mesh)": [[773, "compass.ocean.tests.sphere_transport.divergent_2d.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.sphere_transport.nondivergent_2d.mesh)": [[787, "compass.ocean.tests.sphere_transport.nondivergent_2d.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.sphere_transport.rotation_2d.mesh)": [[811, "compass.ocean.tests.sphere_transport.rotation_2d.mesh.Mesh", false]], "mesh (class in compass.ocean.tests.tides.mesh)": [[845, "compass.ocean.tests.tides.mesh.Mesh", false]], "meshgen (class in compass.landice.tests.antarctica.mesh_gen)": [[99, "compass.landice.tests.antarctica.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.crane.mesh_gen)": [[118, "compass.landice.tests.crane.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.greenland.mesh_gen)": [[182, "compass.landice.tests.greenland.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.humboldt.mesh_gen)": [[196, "compass.landice.tests.humboldt.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.isunnguata_sermia.mesh_gen)": [[268, "compass.landice.tests.isunnguata_sermia.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.kangerlussuaq.mesh_gen)": [[273, "compass.landice.tests.kangerlussuaq.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.koge_bugt_s.mesh_gen)": [[278, "compass.landice.tests.koge_bugt_s.mesh_gen.MeshGen", false]], "meshgen (class in compass.landice.tests.thwaites.mesh_gen)": [[305, "compass.landice.tests.thwaites.mesh_gen.MeshGen", false]], "meshmodifications (class in compass.landice.tests.mesh_modifications)": [[280, "compass.landice.tests.mesh_modifications.MeshModifications", false]], "mismipplus (class in compass.landice.tests.mismipplus)": [[283, "compass.landice.tests.mismipplus.MISMIPplus", false]], "misomip (class in compass.ocean.tests.isomip_plus.misomip)": [[610, "compass.ocean.tests.isomip_plus.misomip.Misomip", false]], "module": [[80, "module-compass.landice.ais_observations", false], [532, "module-compass.ocean.tests.hurricane.configure", false], [825, "module-compass.ocean.tests.tides.configure", false]], "movieplotter (class in compass.ocean.tests.isomip_plus.viz.plot)": [[622, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter", false]], "mpas_flood_fill() (in module compass.landice.mesh)": [[92, "compass.landice.mesh.mpas_flood_fill", false]], "mpascore (class in compass)": [[10, "compass.MpasCore", false]], "nondivergent2d (class in compass.ocean.tests.sphere_transport.nondivergent_2d)": [[776, "compass.ocean.tests.sphere_transport.nondivergent_2d.Nondivergent2D", false]], "nonhydro (class in compass.ocean.tests.lock_exchange.nonhydro)": [[643, "compass.ocean.tests.lock_exchange.nonhydro.Nonhydro", false]], "nonhydro (class in compass.ocean.tests.nonhydro)": [[657, "compass.ocean.tests.nonhydro.Nonhydro", false]], "nonhydro (class in compass.ocean.tests.overflow.nonhydro)": [[693, "compass.ocean.tests.overflow.nonhydro.Nonhydro", false]], "ocean (class in compass.ocean)": [[341, "compass.ocean.Ocean", false]], "oceanbasal (class in compass.landice.tests.ismip6_forcing.ocean_basal)": [[237, "compass.landice.tests.ismip6_forcing.ocean_basal.OceanBasal", false]], "oceangraphpartition (class in compass.ocean.tests.global_ocean.files_for_e3sm.ocean_graph_partition)": [[446, "compass.ocean.tests.global_ocean.files_for_e3sm.ocean_graph_partition.OceanGraphPartition", false]], "oceaninitialcondition (class in compass.ocean.tests.global_ocean.files_for_e3sm.ocean_initial_condition)": [[448, "compass.ocean.tests.global_ocean.files_for_e3sm.ocean_initial_condition.OceanInitialCondition", false]], "oceanmesh (class in compass.ocean.tests.global_ocean.files_for_e3sm.ocean_mesh)": [[450, "compass.ocean.tests.global_ocean.files_for_e3sm.ocean_mesh.OceanMesh", false]], "oceanthermal (class in compass.landice.tests.ismip6_forcing.ocean_thermal)": [[245, "compass.landice.tests.ismip6_forcing.ocean_thermal.OceanThermal", false]], "overflow (class in compass.ocean.tests.overflow)": [[680, "compass.ocean.tests.overflow.Overflow", false]], "package_path() (in module compass.io)": [[39, "compass.io.package_path", false]], "parabolicbowl (class in compass.ocean.tests.parabolic_bowl)": [[699, "compass.ocean.tests.parabolic_bowl.ParabolicBowl", false]], "partition() (in module compass.model)": [[62, "compass.model.partition", false]], "performancetest (class in compass.ocean.tests.global_ocean.performance_test)": [[506, "compass.ocean.tests.global_ocean.performance_test.PerformanceTest", false]], "planarconvergence (class in compass.ocean.tests.planar_convergence)": [[719, "compass.ocean.tests.planar_convergence.PlanarConvergence", false]], "plot() (compass.ocean.tests.tides.analysis.analysis method)": [[818, "compass.ocean.tests.tides.analysis.Analysis.plot", false]], "plot_3d_field_top_bot_section() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[624, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.plot_3d_field_top_bot_section", false]], "plot_barotropic_streamfunction() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[625, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.plot_barotropic_streamfunction", false]], "plot_convergence() (in module compass.ocean.tests.sphere_transport.process_output)": [[793, "compass.ocean.tests.sphere_transport.process_output.plot_convergence", false]], "plot_filament() (in module compass.ocean.tests.sphere_transport.process_output)": [[794, "compass.ocean.tests.sphere_transport.process_output.plot_filament", false]], "plot_horiz_series() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[626, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.plot_horiz_series", false]], "plot_ice_shelf_boundary_variables() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[627, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.plot_ice_shelf_boundary_variables", false]], "plot_initial_state() (in module compass.ocean.plot)": [[357, "compass.ocean.plot.plot_initial_state", false]], "plot_interp_data() (compass.ocean.tests.hurricane.init.interpolate_atm_forcing.interpolateatmforcing method)": [[550, "compass.ocean.tests.hurricane.init.interpolate_atm_forcing.InterpolateAtmForcing.plot_interp_data", false]], "plot_interp_data() (compass.ocean.tests.tides.init.interpolate_wave_drag.interpolatewavedrag method)": [[840, "compass.ocean.tests.tides.init.interpolate_wave_drag.InterpolateWaveDrag.plot_interp_data", false]], "plot_layer_interfaces() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[628, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.plot_layer_interfaces", false]], "plot_melt_rates() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[629, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.plot_melt_rates", false]], "plot_melt_time_series() (compass.ocean.tests.isomip_plus.viz.plot.timeseriesplotter method)": [[635, "compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter.plot_melt_time_series", false]], "plot_over_and_undershoot_errors() (in module compass.ocean.tests.sphere_transport.process_output)": [[795, "compass.ocean.tests.sphere_transport.process_output.plot_over_and_undershoot_errors", false]], "plot_overturning_streamfunction() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[630, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.plot_overturning_streamfunction", false]], "plot_potential_density() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[631, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.plot_potential_density", false]], "plot_salinity() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[632, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.plot_salinity", false]], "plot_sol() (in module compass.ocean.tests.sphere_transport.process_output)": [[796, "compass.ocean.tests.sphere_transport.process_output.plot_sol", false]], "plot_temperature() (compass.ocean.tests.isomip_plus.viz.plot.movieplotter method)": [[633, "compass.ocean.tests.isomip_plus.viz.plot.MoviePlotter.plot_temperature", false]], "plot_time_series() (compass.ocean.tests.isomip_plus.viz.plot.timeseriesplotter method)": [[636, "compass.ocean.tests.isomip_plus.viz.plot.TimeSeriesPlotter.plot_time_series", false]], "plot_vertical_grid() (in module compass.ocean.plot)": [[358, "compass.ocean.plot.plot_vertical_grid", false]], "preprocess_ais_data() (in module compass.landice.mesh)": [[93, "compass.landice.mesh.preprocess_ais_data", false]], "print_data_as_csv() (in module compass.ocean.tests.sphere_transport.process_output)": [[797, "compass.ocean.tests.sphere_transport.process_output.print_data_as_csv", false]], "print_error_conv_table() (in module compass.ocean.tests.sphere_transport.process_output)": [[798, "compass.ocean.tests.sphere_transport.process_output.print_error_conv_table", false]], "processbasalmelt (class in compass.landice.tests.ismip6_forcing.ocean_basal.process_basal_melt)": [[239, "compass.landice.tests.ismip6_forcing.ocean_basal.process_basal_melt.ProcessBasalMelt", false]], "processgeom (class in compass.ocean.tests.isomip_plus.process_geom)": [[612, "compass.ocean.tests.isomip_plus.process_geom.ProcessGeom", false]], "processsmb (class in compass.landice.tests.ismip6_forcing.atmosphere.process_smb)": [[222, "compass.landice.tests.ismip6_forcing.atmosphere.process_smb.ProcessSMB", false]], "processsmbracmo (class in compass.landice.tests.ismip6_forcing.atmosphere.process_smb_racmo)": [[228, "compass.landice.tests.ismip6_forcing.atmosphere.process_smb_racmo.ProcessSmbRacmo", false]], "processthermalforcing (class in compass.landice.tests.ismip6_forcing.ocean_thermal.process_thermal_forcing)": [[247, "compass.landice.tests.ismip6_forcing.ocean_thermal.process_thermal_forcing.ProcessThermalForcing", false]], "quasiuniformsphericalmeshstep (class in compass.mesh)": [[52, "compass.mesh.QuasiUniformSphericalMeshStep", false]], "qumeshfromconfigstep (class in compass.ocean.tests.global_ocean.mesh.qu)": [[496, "compass.ocean.tests.global_ocean.mesh.qu.QUMeshFromConfigStep", false]], "read_ncl_rgb_file() (in module compass.ocean.tests.sphere_transport.process_output)": [[799, "compass.ocean.tests.sphere_transport.process_output.read_ncl_rgb_file", false]], "read_otps2_output() (compass.ocean.tests.tides.analysis.analysis method)": [[819, "compass.ocean.tests.tides.analysis.Analysis.read_otps2_output", false]], "read_pointstats() (compass.ocean.tests.hurricane.analysis.analysis method)": [[527, "compass.ocean.tests.hurricane.analysis.Analysis.read_pointstats", false]], "read_station_data() (compass.ocean.tests.hurricane.analysis.analysis method)": [[528, "compass.ocean.tests.hurricane.analysis.Analysis.read_station_data", false]], "read_station_file() (compass.ocean.tests.hurricane.analysis.analysis method)": [[529, "compass.ocean.tests.hurricane.analysis.Analysis.read_station_file", false]], "remap_adusumilli() (in module compass.ocean.tests.global_ocean.init.remap_ice_shelf_melt)": [[484, "compass.ocean.tests.global_ocean.init.remap_ice_shelf_melt.remap_adusumilli", false]], "remap_ismip6_basal_melt_to_mali_vars() (compass.landice.tests.ismip6_forcing.ocean_basal.process_basal_melt.processbasalmelt method)": [[241, "compass.landice.tests.ismip6_forcing.ocean_basal.process_basal_melt.ProcessBasalMelt.remap_ismip6_basal_melt_to_mali_vars", false]], "remap_ismip6_shelf_mask_to_mali_vars() (compass.landice.tests.ismip6_forcing.shelf_collapse.process_shelf_collapse.processshelfcollapse method)": [[254, "compass.landice.tests.ismip6_forcing.shelf_collapse.process_shelf_collapse.ProcessShelfCollapse.remap_ismip6_shelf_mask_to_mali_vars", false]], "remap_ismip6_smb_to_mali() (compass.landice.tests.ismip6_forcing.atmosphere.process_smb.processsmb method)": [[224, "compass.landice.tests.ismip6_forcing.atmosphere.process_smb.ProcessSMB.remap_ismip6_smb_to_mali", false]], "remap_ismip6_thermal_forcing_to_mali_vars() (compass.landice.tests.ismip6_forcing.ocean_thermal.process_thermal_forcing.processthermalforcing method)": [[248, "compass.landice.tests.ismip6_forcing.ocean_thermal.process_thermal_forcing.ProcessThermalForcing.remap_ismip6_thermal_forcing_to_mali_vars", false]], "remap_paolo() (in module compass.ocean.tests.global_ocean.init.remap_ice_shelf_melt)": [[485, "compass.ocean.tests.global_ocean.init.remap_ice_shelf_melt.remap_paolo", false]], "remap_particles() (in module compass.ocean.particles)": [[355, "compass.ocean.particles.remap_particles", false]], "remap_source_smb_to_mali() (compass.landice.tests.ismip6_forcing.atmosphere.process_smb_racmo.processsmbracmo method)": [[230, "compass.landice.tests.ismip6_forcing.atmosphere.process_smb_racmo.ProcessSmbRacmo.remap_source_smb_to_mali", false]], "remapbathymetry (class in compass.ocean.tests.tides.init.remap_bathymetry)": [[843, "compass.ocean.tests.tides.init.remap_bathymetry.RemapBathymetry", false]], "remapicebergclimatology (class in compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology)": [[454, "compass.ocean.tests.global_ocean.files_for_e3sm.remap_iceberg_climatology.RemapIcebergClimatology", false]], "remapiceshelfmelt (class in compass.ocean.tests.global_ocean.files_for_e3sm.remap_ice_shelf_melt)": [[452, "compass.ocean.tests.global_ocean.files_for_e3sm.remap_ice_shelf_melt.RemapIceShelfMelt", false]], "remapiceshelfmelt (class in compass.ocean.tests.global_ocean.init.remap_ice_shelf_melt)": [[482, "compass.ocean.tests.global_ocean.init.remap_ice_shelf_melt.RemapIceShelfMelt", false]], "remapseasurfacesalinityrestoring (class in compass.ocean.tests.global_ocean.files_for_e3sm.remap_sea_surface_salinity_restoring)": [[456, "compass.ocean.tests.global_ocean.files_for_e3sm.remap_sea_surface_salinity_restoring.RemapSeaSurfaceSalinityRestoring", false]], "remaptidalmixing (class in compass.ocean.tests.global_ocean.files_for_e3sm.remap_tidal_mixing)": [[458, "compass.ocean.tests.global_ocean.files_for_e3sm.remap_tidal_mixing.RemapTidalMixing", false]], "remaptopography (class in compass.ocean.mesh.remap_topography)": [[351, "compass.ocean.mesh.remap_topography.RemapTopography", false]], "remaptopography (class in compass.ocean.tests.utility.extrap_woa)": [[863, "compass.ocean.tests.utility.extrap_woa.RemapTopography", false]], "rename_ismip6_basal_melt_to_mali_vars() (compass.landice.tests.ismip6_forcing.ocean_basal.process_basal_melt.processbasalmelt method)": [[242, 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934], "spinup_test": [212, 213, 323, 938], "spinupensembl": [159, 160], "spinuptest": [212, 213], "ssh_adjust": [486, 487, 488, 579, 580, 581, 614, 615, 616, 898, 901], "sshadjust": [486, 487, 488, 579, 580, 581, 614, 615, 616], "standard_experi": [145, 146, 147, 148, 149, 318, 933], "standardexperi": [145, 146], "star": 957, "start": [916, 920, 921, 922, 923, 983], "state": [966, 980], "steady_state_drift_test": [214, 215, 323, 938], "steadystatedrifttest": [214, 215], "step": [0, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 339, 895, 914, 920, 922, 923, 934, 941, 963, 964, 966, 975, 976, 978, 980], "stratified_seich": [669, 670, 671, 672, 673, 674, 675, 676, 677, 678, 679, 904, 973], "stratifiedseich": [669, 670], "stream": [340, 914, 922, 923], "streamfunct": [617, 618, 901], "structur": [1, 914], "studi": 920, "style": [915, 916], "subdomain_extractor": [281, 282, 330, 945], "subdomainextractor": 281, "submiss": 1, "suit": [4, 6, 9, 73, 74, 914, 927, 959, 983, 985], "summari": [0, 1, 3], "support": [1, 337, 916, 952, 983], "surfac": 954, "surface_restor": 977, "switch": [916, 921], "symlink": [9, 40, 914], "system": 916, "tanh_dz": 957, "task": [297, 298, 299, 331, 512, 895, 920], "templat": [3, 914], "ten_day_test": [594, 595, 900, 969], "tendaytest": [594, 595], "test": [0, 1, 3, 7, 77, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 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873, 874, 875, 876, 877, 878, 879, 895, 899, 914, 915, 920, 921, 922, 923, 924, 927, 939, 959, 964, 966, 968, 980, 983, 984, 985], "testcas": [4, 27, 28, 29, 30, 31, 914], "testgroup": [4, 32, 33], "thin_film_ocean0": 970, "thin_film_tidal_forcing_ocean0": 970, "thread_test": 960, "threads_test": [382, 383, 384, 513, 514, 515, 891, 895, 964], "threadstest": [382, 383, 384, 513, 514, 515], "three_lay": 977, "threshold": 978, "thwait": [77, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 332, 947], "tide": [339, 814, 815, 816, 817, 818, 819, 820, 821, 822, 823, 824, 825, 826, 827, 828, 829, 830, 831, 832, 833, 834, 835, 836, 837, 838, 839, 840, 841, 842, 843, 844, 845, 846, 847, 911, 980], "time": [963, 975, 976, 978], "time_varying_ocean0": 970, "timer": 9, "timeseries_plot": 718, "timeseriesplott": [634, 635, 636], "topic": 3, "topograph": 966, "topographi": [340, 956], "topographic_wave_drag": [553, 554, 555, 556, 897], "troubleshoot": [7, 916, 917], "tutori": [919, 920, 921, 922, 923], "type": [894, 957], "understand": 1, "uniform": 957, "uniqu": 0, "unix": 916, "unknown": 916, "up": [916, 922, 923, 934, 941, 983], "updat": [0, 7, 9, 914, 916, 923], "update_cach": 35, "update_cor": [702, 725], "update_evaporation_flux": 599, "update_namelist_at_runtim": 24, "update_namelist_pio": 25, "update_streams_at_runtim": 26, "us": 0, "user": [1, 916, 919, 924, 983], "util": [339, 848, 849, 850, 851, 852, 853, 854, 855, 856, 857, 858, 859, 860, 861, 862, 863, 864, 865, 866, 912, 981], "valid": [3, 4, 9, 31, 75, 76, 102, 193, 199, 294, 398, 400, 402, 409, 436, 518, 586, 595, 650, 703, 746, 914, 923], "vari": [922, 923], "variabl": [7, 9], "veri": 921, "version": [0, 919, 986], "vertic": [340, 880, 881, 882, 883, 884, 885, 886, 887, 888, 889, 922, 957], "visual": [112, 113, 114, 132, 133, 134, 147, 148, 149, 164, 165, 169, 170, 216, 217, 218, 315, 317, 318, 323, 644, 645, 666, 667, 668, 677, 678, 679, 687, 688, 902, 904, 905], "visualize_circular_shelf": 114, "visualize_dom": 134, "visualize_eismint2": 149, "visualize_hydro_radi": 218, "viz": [392, 393, 410, 411, 582, 583, 596, 597, 619, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631, 632, 633, 634, 635, 636, 655, 656, 710, 711, 712, 713, 714, 715, 716, 717, 718, 892, 893, 898, 901, 906, 975], "wave": [966, 980], "wc14": [502, 503, 895, 964], "wc14basemesh": [502, 503], "wcwisc14": [895, 964], "we": 7, "what": 916, "when": 917, "where": 7, "whether": 0, "with_frazil": [877, 878, 879, 913, 982], "withfrazil": [877, 878, 879], "within": [1, 915], "without": 7, "worktre": 916, "write": [68, 356], "write_1d_grid": 881, "write_coeffs_reconstruct": [468, 469], "write_coordinate_fil": 824, "write_to_fil": [552, 556, 842], "writecoeffsreconstruct": [468, 469], "z": 957, "ziso": [339, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 913, 982], "ziso_test_cas": 913, "zisotestcas": [868, 869, 870], "zlevel": [885, 886, 887, 888], "zstar": 889}})
\ No newline at end of file
diff --git a/latest/users_guide/landice/test_groups/ismip6_run.html b/latest/users_guide/landice/test_groups/ismip6_run.html
index 4baf0b72c2..228f0ec5f4 100644
--- a/latest/users_guide/landice/test_groups/ismip6_run.html
+++ b/latest/users_guide/landice/test_groups/ismip6_run.html
@@ -68,6 +68,8 @@
ismip6_run
isunnguata_sermia
@@ -223,6 +225,31 @@ config options