Merge pull request #756 from trhille/landice/add_crane_glacier_mesh

Add Crane Glacier mesh generation

This merge adds a Crane Glacier test group with a mesh generation test case.

compass/landice/__init__.py

@@ -1,6 +1,7 @@
 from compass.landice.tests.antarctica import Antarctica
 from compass.landice.tests.calving_dt_convergence import CalvingDtConvergence
 from compass.landice.tests.circular_shelf import CircularShelf
+from compass.landice.tests.crane import Crane
 from compass.landice.tests.dome import Dome
 from compass.landice.tests.eismint2 import Eismint2
 from compass.landice.tests.ensemble_generator import EnsembleGenerator
@@ -31,6 +32,7 @@ def __init__(self):
         self.add_test_group(Antarctica(mpas_core=self))
         self.add_test_group(CalvingDtConvergence(mpas_core=self))
         self.add_test_group(CircularShelf(mpas_core=self))
+        self.add_test_group(Crane(mpas_core=self))
         self.add_test_group(Dome(mpas_core=self))
         self.add_test_group(Eismint2(mpas_core=self))
         self.add_test_group(EnsembleGenerator(mpas_core=self))

compass/landice/tests/crane/Crane.geojson

@@ -0,0 +1,8 @@
+{
+"type": "FeatureCollection",
+"name": "crane",
+"crs": { "type": "name", "properties": { "name": "urn:ogc:def:crs:OGC:1.3:CRS84" } },
+"features": [
+{ "type": "Feature", "properties": { "name": "Crane", "tags": "Crane", "object": "region", "component": "landice", "author": "https://nsidc.org/data/nsidc-0709/versions/2" }, "geometry": { "type": "Polygon", "coordinates": [ [ [ -62.711133639719051, -65.201690711497449 ], [ -62.670350055324924, -65.222528990830909 ], [ -62.603459729541953, -65.242580535851928 ], [ -62.572933915847166, -65.263459838062047 ], [ -62.5447479615612, -65.280135328846143 ], [ -62.526497752286581, -65.28953644693928 ], [ -62.505122164004312, -65.302192318858971 ], [ -62.485513843643858, -65.307365058584693 ], [ -62.456050254898265, -65.306845472030545 ], [ -62.416719886631014, -65.301407479922261 ], [ -62.325208704931725, -65.295492600965616 ], [ -62.335693172886117, -65.281896177745708 ], [ -62.317445266252619, -65.267199412520284 ], [ -62.298527185097853, -65.256186534513901 ], [ -62.270881390790265, -65.25997099550591 ], [ -62.243281563118522, -65.273087823873411 ], [ -62.224460224612052, -65.281283149356511 ], [ -62.207546873139194, -65.287430270161053 ], [ -62.190867321049865, -65.293903404053424 ], [ -62.156665341547331, -65.292936788753778 ], [ -62.098387196049593, -65.288693547437447 ], [ -62.007252795520166, -65.281089453867637 ], [ -62.018859863281264, -65.375587463378082 ], [ -62.016600511940915, -65.379978412162856 ], [ -62.077136087381596, -65.380590210127849 ], [ -62.145699215470813, -65.372818470998254 ], [ -62.167281294498281, -65.375205553640882 ], [ -62.222861066440238, -65.371647482909793 ], [ -62.291680881779712, -65.372550024011389 ], [ -62.345048311349345, -65.367675194569742 ], [ -62.390573553751047, -65.370527255810515 ], [ -62.461664445041194, -65.389161881004426 ], [ -62.514312160790922, -65.402953390636739 ], [ -62.56636193602624, -65.414222755333114 ], [ -62.659506325283054, -65.431956710379481 ], [ -62.737637116748708, -65.454237931998676 ], [ -62.805918071586682, -65.482698633184754 ], [ -62.811183455537751, -65.484889234346724 ], [ -62.867708260649586, -65.511061365188823 ], [ -62.885804488291811, -65.542376342806179 ], [ -62.886691630407086, -65.569250665285935 ], [ -62.890670180308163, -65.576005754891469 ], [ -62.89831926564306, -65.588982307100196 ], [ -62.900773458184162, -65.589992247734628 ], [ -62.929764097326832, -65.601912856045203 ], [ -63.002567564209123, -65.629035378321959 ], [ -63.126602388643924, -65.631554288838103 ], [ -63.236318220802865, -65.63019217813239 ], [ -63.303819000409725, -65.599646937653191 ], [ -63.34925965578536, -65.569997824340518 ], [ -63.365154289162966, -65.55375966578741 ], [ -63.385548345064301, -65.53767854182712 ], [ -63.388604133476498, -65.516436113569014 ], [ -63.322626984854296, -65.457362380394201 ], [ -63.293553165044756, -65.420795970865555 ], [ -63.263005675425205, -65.393281566591043 ], [ -63.22118042805085, -65.379796313503746 ], [ -63.189035571735126, -65.375371224505727 ], [ -63.092184036117075, -65.343941847844178 ], [ -63.057623964387204, -65.307638195868762 ], [ -62.98940255786006, -65.283710009963457 ], [ -62.912046122160845, -65.275008725259099 ], [ -62.889459667642733, -65.25213604170456 ], [ -62.861455853629565, -65.239849619201379 ], [ -62.848620556551481, -65.21727944406112 ], [ -62.711133639719051, -65.201690711497449 ] ] ] } }
+]
+}

compass/landice/tests/crane/__init__.py

@@ -0,0 +1,16 @@
+from compass.landice.tests.crane.mesh_gen import MeshGen
+from compass.testgroup import TestGroup
+
+
+class Crane(TestGroup):
+    """
+    A test group for Crane Glacier test cases.
+    """
+    def __init__(self, mpas_core):
+        """
+        mpas_core : compass.landice.Landice
+            the MPAS core that this test group belongs to
+        """
+        super().__init__(mpas_core=mpas_core, name='crane')
+
+        self.add_test_case(MeshGen(test_group=self))

compass/landice/tests/crane/mesh.py

@@ -0,0 +1,59 @@
+from compass.landice.mesh import build_cell_width, build_mali_mesh
+from compass.model import make_graph_file
+from compass.step import Step
+
+
+class Mesh(Step):
+    """
+    A step for creating a mesh and initial condition for thwaites test cases
+    """
+    def __init__(self, test_case):
+        """
+        Create the step
+        Parameters
+        ----------
+        test_case : compass.TestCase
+            The test case this step belongs to
+        """
+        super().__init__(test_case=test_case, name='mesh', cpus_per_task=128,
+                         min_cpus_per_task=1)
+
+        self.add_output_file(filename='graph.info')
+        self.add_output_file(filename='Crane.nc')
+        self.add_input_file(filename='antarctica_8km_2024_01_29.nc',
+                            target='antarctica_8km_2024_01_29.nc',
+                            database='')
+        self.add_input_file(filename='Crane.geojson',
+                            package='compass.landice.tests.crane',
+                            target='Crane.geojson',
+                            database=None)
+        self.add_input_file(filename='antarctica_1km_2024_01_29_AP.nc',
+                            target='antarctica_1km_2024_01_29_AP.nc',
+                            database='')
+
+    # no setup() method is needed
+
+    def run(self):
+        """
+        Run this step of the test case
+        """
+        logger = self.logger
+        mesh_name = 'Crane.nc'
+        section_name = 'mesh'
+
+        logger.info('calling build_cell_width')
+        cell_width, x1, y1, geom_points, geom_edges, floodMask = \
+            build_cell_width(
+                self, section_name=section_name,
+                gridded_dataset='antarctica_8km_2024_01_29.nc')
+
+        build_mali_mesh(
+            self, cell_width, x1, y1, geom_points, geom_edges,
+            mesh_name=mesh_name, section_name=section_name,
+            gridded_dataset='antarctica_1km_2024_01_29_AP.nc',
+            projection='ais-bedmap2', geojson_file='Crane.geojson',
+            cores=self.cpus_per_task)
+
+        logger.info('creating graph.info')
+        make_graph_file(mesh_filename=mesh_name,
+                        graph_filename='graph.info')

compass/landice/tests/crane/mesh_gen/__init__.py

@@ -0,0 +1,39 @@
+from compass.landice.tests.crane.mesh import Mesh
+from compass.testcase import TestCase
+from compass.validate import compare_variables
+
+
+class MeshGen(TestCase):
+    """
+    The high resolution test case for the crane test
+    group simply creates the mesh and initial condition.
+    The basal friction optimization occurs separately,
+    outside of COMPASS.
+    """
+
+    def __init__(self, test_group):
+        """
+        Create the test case
+
+        Parameters
+        ----------
+        test_group : compass.landice.tests.crane.Crane
+            The test group that this test case belongs to
+        """
+        name = 'mesh_gen'
+        subdir = name
+        super().__init__(test_group=test_group, name=name,
+                         subdir=subdir)
+
+        self.add_step(
+            Mesh(test_case=self))
+
+    def validate(self):
+        """
+        Compare ``thickness``, ``bedTopography``, ``iceMask`` and
+        ``beta`` with a baseline if one was provided.
+        """
+        variables = ['thickness', 'bedTopography', 'iceMask',
+                     'beta']
+        compare_variables(test_case=self, variables=variables,
+                          filename1='mesh/Crane.nc')

compass/landice/tests/crane/mesh_gen/mesh_gen.cfg

@@ -0,0 +1,48 @@
+# config options for mesh_gen test case
+[mesh]
+
+# number of levels in the mesh
+levels = 10
+
+# Bounds of Crane regional mesh
+x_min = -2.442e6
+x_max = -2.246e6
+y_min = 1.124e6
+y_max = 1.334e6
+
+# distance from ice margin to cull (km).
+# Set to a value <= 0 if you do not want
+# to cull based on distance from margin.
+cull_distance = -1.0
+
+# mesh density parameters
+# minimum cell spacing (meters)
+min_spac = 5.e2
+# maximum cell spacing (meters)
+max_spac = 1.e3
+# log10 of max speed for cell spacing
+high_log_speed = 2.5
+# log10 of min speed for cell spacing
+low_log_speed = 0.75
+# distance at which cell spacing = max_spac
+high_dist = 1.e5
+# distance within which cell spacing = min_spac
+low_dist = 5.e4
+
+# mesh density parameters used if use_bed = True
+# These settings are taken from the Humboldt mesh
+# and have not yet been evaluated for Crane.
+# distance at which bed topography has no effect
+high_dist_bed = 1.e5
+# distance within which bed topography has maximum effect
+low_dist_bed = 5.e4
+# Bed elev beneath which cell spacing is minimized
+low_bed = 50.0
+# Bed elev above which cell spacing is maximized
+high_bed = 100.0
+
+# mesh density functions
+use_speed = True
+use_dist_to_grounding_line = True
+use_dist_to_edge = False
+use_bed = False

docs/developers_guide/landice/api.rst

@@ -67,6 +67,23 @@ circular_shelf
    visualize.visualize_circular_shelf
 
 
+crane
+~~~~
+
+.. currentmodule:: compass.landice.tests.crane
+
+.. autosummary::
+   :toctree: generated/
+
+   Crane
+
+   mesh_gen.MeshGen
+   mesh_gen.MeshGen.run
+
+   mesh.Mesh
+   mesh.Mesh.run
+
+
 dome
 ~~~~
 

docs/developers_guide/landice/framework.rst

@@ -31,8 +31,8 @@ mesh
 
 The landice framework module :py:mod:`compass.landice.mesh` provides functions
 used by all ``mesh_gen`` tests cases, which currently exist within the
-``antarctica``, ``greenland``, ``humboldt``, ``kangerlussuaq``, ``koge_bugt_s``,
-and ``thwaites`` test groups. These functions include:
+``antarctica``, ``crane``, ``greenland``, ``humboldt``, ``kangerlussuaq``,
+``koge_bugt_s``, and ``thwaites`` test groups. These functions include:
 
 :py:func:`compass.landice.mesh.gridded_flood_fill()` applies a flood-fill algorithm
 to the gridded dataset in order to separate the ice sheet from peripheral ice.

docs/developers_guide/landice/test_groups/crane.rst

@@ -0,0 +1,30 @@
+.. _dev_landice_crane:
+
+crane
+=============
+
+The ``crane`` test group (:py:class:`compass.landice.tests.crane.Crane`)
+creates a variable resolution (default 500 m - 1 km) mesh for a regional domain of Crane Glacier
+(see :ref:`landice_crane`).
+
+.. _dev_landice_crane_framework:
+
+framework
+---------
+
+The shared config options for the ``crane`` test group are described
+in :ref:`landice_crane` in the User's Guide.
+
+mesh
+~~~~
+
+The class :py:class:`compass.landice.tests.crane.mesh.Mesh`
+defines a step for creating a variable resolution Crane Glacier mesh.
+This is used by the ``mesh_gen`` test case.
+
+mesh_gen
+--------
+
+The :py:class:`compass.landice.tests.crane.mesh_gen.MeshGen`
+calls the :py:class:`compass.landice.tests.crane.mesh.Mesh` to create
+the variable resolution Crane Glacier mesh.

docs/developers_guide/landice/test_groups/index.rst

@@ -10,6 +10,7 @@ Test groups
    antarctica
    calving_dt_convergence
    circular_shelf
+   crane
    dome
    ensemble_generator
    enthalpy_benchmark

docs/users_guide/landice/test_groups/crane.rst

@@ -0,0 +1,82 @@
+.. _landice_crane:
+
+crane
+=============
+
+The ``landice/crane`` test group includes a test case for creating a
+mesh for Crane Glacier, Antarctica. The optimization for basal friction
+happens outside of COMPASS because it requires expert usage and takes a
+larger amount of computing resources than COMPASS is typically run with.
+
+.. figure:: images/crane_500mto1km.png
+   :width: 777 px
+   :align: center
+
+   Bed topography in meters above sea level on Crane 500m-1km mesh.
+
+The test group includes a single test case that creates the variable resolution mesh.
+
+config options
+--------------
+
+The test group uses the following default config options.  At this point only
+the mesh generation options are adjusted through the config file.
+
+.. code-block:: cfg
+
+    # config options for mesh_gen test case
+    [mesh]
+    
+    # number of levels in the mesh
+    levels = 10
+    
+    # Bounds of Crane regional mesh
+    x_min = -2.442e6
+    x_max = -2.246e6
+    y_min = 1.124e6
+    y_max = 1.334e6
+    
+    # distance from ice margin to cull (km).
+    # Set to a value <= 0 if you do not want
+    # to cull based on distance from margin.
+    cull_distance = -1.0
+    
+    # mesh density parameters
+    # minimum cell spacing (meters)
+    min_spac = 5.e2
+    # maximum cell spacing (meters)
+    max_spac = 1.e3
+    # log10 of max speed for cell spacing
+    high_log_speed = 2.5
+    # log10 of min speed for cell spacing
+    low_log_speed = 0.75
+    # distance at which cell spacing = max_spac
+    high_dist = 1.e5
+    # distance within which cell spacing = min_spac
+    low_dist = 5.e4
+    
+    # mesh density parameters used if use_bed = True
+    # These settings are taken from the Humboldt mesh
+    # and have not yet been evaluated for Crane.
+    # distance at which bed topography has no effect
+    high_dist_bed = 1.e5
+    # distance within which bed topography has maximum effect
+    low_dist_bed = 5.e4
+    # Bed elev beneath which cell spacing is minimized
+    low_bed = 50.0
+    # Bed elev above which cell spacing is maximized
+    high_bed = 100.0
+    
+    # mesh density functions
+    use_speed = True
+    use_dist_to_grounding_line = True
+    use_dist_to_edge = False
+    use_bed = False
+
+mesh_gen
+--------
+
+``landice/crane/default`` creates a variable resolution mesh.
+The default is 500m-1km resolution with mesh density determined by
+observed ice speed and distance to grounding line. There is no model
+integration step.

docs/users_guide/landice/test_groups/index.rst

@@ -15,6 +15,7 @@ physics but that are not run routinely.
    antarctica
    calving_dt_convergence
    circular_shelf
+   crane
    dome
    eismint2
    ensemble_generator