Merge pull request #745 from xylar/update-redi-and-ab2

Update namelist options for recent changes to Redi and Adams-Bashforth 2

compass/ocean/tests/global_ocean/__init__.py

@@ -63,7 +63,7 @@ def _add_tests(self, mesh_names, high_res_topography=True,
         """ Add test cases for the given mesh(es) """
 
         default_ic = 'WOA23'
-        default_time_int = 'split_explicit'
+        default_time_int = 'split_explicit_ab2'
 
         for mesh_name in mesh_names:
             mesh_test = Mesh(test_group=self, mesh_name=mesh_name,

compass/ocean/tests/global_ocean/analysis_test/__init__.py

@@ -36,7 +36,7 @@ def __init__(self, test_group, mesh, init, time_integrator):
         init : compass.ocean.tests.global_ocean.init.Init
             The test case that produces the initial condition for this run
 
-        time_integrator : {'split_explicit', 'RK4'}
+        time_integrator : {'split_explicit_ab2', 'RK4'}
             The time integrator to use for the forward run
         """
         super().__init__(test_group=test_group, mesh=mesh, init=init,

compass/ocean/tests/global_ocean/daily_output_test/__init__.py

@@ -1,6 +1,8 @@
+from compass.ocean.tests.global_ocean.forward import (
+    ForwardStep,
+    ForwardTestCase,
+)
 from compass.validate import compare_variables
-from compass.ocean.tests.global_ocean.forward import ForwardTestCase, \
-    ForwardStep
 
 
 class DailyOutputTest(ForwardTestCase):
@@ -25,7 +27,7 @@ def __init__(self, test_group, mesh, init, time_integrator):
         init : compass.ocean.tests.global_ocean.init.Init
             The test case that produces the initial condition for this run
 
-        time_integrator : {'split_explicit', 'RK4'}
+        time_integrator : {'split_explicit_ab2', 'RK4'}
             The time integrator to use for the forward run
         """
         super().__init__(test_group=test_group, mesh=mesh, init=init,

compass/ocean/tests/global_ocean/decomp_test/__init__.py

@@ -1,6 +1,8 @@
+from compass.ocean.tests.global_ocean.forward import (
+    ForwardStep,
+    ForwardTestCase,
+)
 from compass.validate import compare_variables
-from compass.ocean.tests.global_ocean.forward import ForwardTestCase, \
-    ForwardStep
 
 
 class DecompTest(ForwardTestCase):
@@ -24,7 +26,7 @@ def __init__(self, test_group, mesh, init, time_integrator):
         init : compass.ocean.tests.global_ocean.init.Init
             The test case that produces the initial condition for this run
 
-        time_integrator : {'split_explicit', 'RK4'}
+        time_integrator : {'split_explicit_ab2', 'RK4'}
             The time integrator to use for the forward run
         """
         super().__init__(test_group=test_group, mesh=mesh, init=init,

compass/ocean/tests/global_ocean/dynamic_adjustment/__init__.py

@@ -44,14 +44,14 @@ def __init__(self, test_group, mesh, init, time_integrator):
         init : compass.ocean.tests.global_ocean.init.Init
             The test case that produces the initial condition for this run
 
-        time_integrator : {'split_explicit', 'RK4'}
+        time_integrator : {'split_explicit_ab2', 'RK4'}
             The time integrator to use for the forward run
         """
         super().__init__(test_group=test_group, mesh=mesh, init=init,
                          time_integrator=time_integrator,
                          name='dynamic_adjustment')
 
-        if time_integrator == 'split_explicit':
+        if time_integrator == 'split_explicit_ab2':
             yaml_filename = 'dynamic_adjustment.yaml'
         else:
             yaml_filename = f'dynamic_adjustment_{time_integrator}.yaml'
@@ -145,7 +145,7 @@ def _add_step(self, step_name, options, get_dt_from_min_res,
         required = ['run_duration', 'output_interval', 'restart_interval']
         if not get_dt_from_min_res:
             required.append('dt')
-            if time_integrator == 'split_explicit':
+            if time_integrator == 'split_explicit_ab2':
                 required.append('btr_dt')
         for option in required:
             if option not in options:

compass/ocean/tests/global_ocean/files_for_e3sm/write_coeffs_reconstruct/__init__.py

@@ -30,7 +30,7 @@ def __init__(self, test_case, mesh, init):
             The test case that produces the initial condition for this run
         """
         super().__init__(test_case=test_case, mesh=mesh, init=init,
-                         time_integrator='split_explicit',
+                         time_integrator='split_explicit_ab2',
                          name='write_coeffs_reconstruct')
 
         package = 'compass.ocean.tests.global_ocean.files_for_e3sm.' \

compass/ocean/tests/global_ocean/forward.py

@@ -24,7 +24,7 @@ class ForwardStep(Step):
     init : compass.ocean.tests.global_ocean.init.Init
         The test case that produces the initial condition for this run
 
-    time_integrator : {'split_explicit', 'RK4'}
+    time_integrator : {'split_explicit_ab2', 'RK4'}
         The time integrator to use for the forward run
 
     dynamic_ntasks : bool
@@ -51,7 +51,7 @@ def __init__(self, test_case, mesh, time_integrator, init=None,
         mesh : compass.ocean.tests.global_ocean.mesh.Mesh
             The test case that produces the mesh for this run
 
-        time_integrator : {'split_explicit', 'RK4'}
+        time_integrator : {'split_explicit_ab2', 'RK4'}
             The time integrator to use for the forward run
 
         init : compass.ocean.tests.global_ocean.init.Init, optional
@@ -173,7 +173,7 @@ def setup(self):
 
         if self.get_dt_from_min_res:
             dt, btr_dt = self._get_dts()
-            if self.time_integrator == 'split_explicit':
+            if self.time_integrator == 'split_explicit_ab2':
                 self.add_namelist_options({'config_dt': dt,
                                            'config_btr_dt': btr_dt})
             else:
@@ -201,7 +201,7 @@ def runtime_setup(self):
         """
         if self.get_dt_from_min_res:
             dt, btr_dt = self._get_dts()
-            if self.time_integrator == 'split_explicit':
+            if self.time_integrator == 'split_explicit_ab2':
                 self.update_namelist_at_runtime({'config_dt': dt,
                                                  'config_btr_dt': btr_dt})
             else:
@@ -252,7 +252,7 @@ class ForwardTestCase(TestCase):
     init : compass.ocean.tests.global_ocean.init.Init
         The test case that produces the initial condition for this run
 
-    time_integrator : {'split_explicit', 'RK4'}
+    time_integrator : {'split_explicit_ab2', 'RK4'}
         The time integrator to use for the forward run
     """
 
@@ -271,7 +271,7 @@ def __init__(self, test_group, mesh, init, time_integrator, name):
         init : compass.ocean.tests.global_ocean.init.Init
             The test case that produces the initial condition for this run
 
-        time_integrator : {'split_explicit', 'RK4'}
+        time_integrator : {'split_explicit_ab2', 'RK4'}
             The time integrator to use for the forward run
 
         name : str
@@ -295,7 +295,7 @@ def get_forward_subdir(init_subdir, time_integrator, name):
     Get the subdirectory for a test case that is based on a forward run with
     a time integrator
     """
-    if time_integrator == 'split_explicit':
+    if time_integrator == 'split_explicit_ab2':
         # this is the default so we won't make a subdir for the time
         # integrator
         subdir = os.path.join(init_subdir, name)

compass/ocean/tests/global_ocean/init/ssh_adjustment.py

@@ -19,7 +19,7 @@ def __init__(self, test_case):
             The test case this step belongs to
         """
         super().__init__(test_case=test_case, mesh=test_case.mesh,
-                         time_integrator='split_explicit',
+                         time_integrator='split_explicit_ab2',
                          name='ssh_adjustment')
 
         self.add_namelist_options({'config_AM_globalStats_enable': '.false.'})

compass/ocean/tests/global_ocean/mesh/arrm10to60/namelist.split_explicit → compass/ocean/tests/global_ocean/mesh/arrm10to60/namelist.split_explicit_ab2

@@ -1,4 +1,4 @@
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_dt = '00:01:00'
 config_btr_dt = '00:00:03'
 config_run_duration = '0000_01:00:00'
@@ -7,4 +7,3 @@ config_mom_del2 = 10.0
 config_mom_del4 = 1.5e10
 config_hmix_scaleWithMesh = .true.
 config_use_GM = .true.
-config_Redi_min_layers_diag_terms = 15

compass/ocean/tests/global_ocean/mesh/ec30to60/namelist.split_explicit → compass/ocean/tests/global_ocean/mesh/ec30to60/namelist.split_explicit_ab2

@@ -1,4 +1,4 @@
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_dt = '00:05:00'
 config_btr_dt = '00:00:10'
 config_run_duration = '0000_00:15:00'

compass/ocean/tests/global_ocean/mesh/kuroshio12to60/namelist.split_explicit → compass/ocean/tests/global_ocean/mesh/kuroshio12to60/namelist.split_explicit_ab2

@@ -1,4 +1,4 @@
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_dt = '00:10:00'
 config_btr_dt = '00:00:10'
 config_run_duration = '0000_01:00:00'

compass/ocean/tests/global_ocean/mesh/kuroshio8to60/namelist.split_explicit → compass/ocean/tests/global_ocean/mesh/kuroshio8to60/namelist.split_explicit_ab2

@@ -1,4 +1,4 @@
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_dt = '00:05:00'
 config_btr_dt = '00:00:10'
 config_run_duration = '0000_01:00:00'

compass/ocean/tests/global_ocean/mesh/qu/namelist.split_explicit → compass/ocean/tests/global_ocean/mesh/qu/namelist.split_explicit_ab2

@@ -1,4 +1,4 @@
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_run_duration = '0000_06:00:00'
 config_hmix_use_ref_cell_width = .true.
 config_write_output_on_startup = .false.

compass/ocean/tests/global_ocean/mesh/qu240/namelist.split_explicit → compass/ocean/tests/global_ocean/mesh/qu240/namelist.split_explicit_ab2

@@ -1,4 +1,4 @@
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_dt = '02:00:00'
 config_btr_dt = '00:06:00'
 config_run_duration = '0000_06:00:00'

compass/ocean/tests/global_ocean/mesh/rrs6to18/namelist.split_explicit → compass/ocean/tests/global_ocean/mesh/rrs6to18/namelist.split_explicit_ab2

@@ -1,4 +1,4 @@
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_dt = '00:01:00'
 config_btr_dt = '00:00:03'
 config_run_duration = '0000_01:30:00'

compass/ocean/tests/global_ocean/mesh/so12to60/namelist.split_explicit → compass/ocean/tests/global_ocean/mesh/so12to60/namelist.split_explicit_ab2

@@ -1,4 +1,4 @@
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_dt = '00:01:00'
 config_btr_dt = '00:00:02'
 config_run_duration = '0000_01:00:00'

compass/ocean/tests/global_ocean/mesh/wc14/__init__.py

@@ -1,13 +1,14 @@
-import numpy as np
-import matplotlib.pyplot as plt
 import cartopy.crs as ccrs
 import cartopy.feature as cfeature
-
+import matplotlib.pyplot as plt
 import mpas_tools.mesh.creation.mesh_definition_tools as mdt
-from mpas_tools.mesh.creation.signed_distance import \
-    signed_distance_from_geojson, mask_from_geojson
+import numpy as np
 from geometric_features import read_feature_collection
 from mpas_tools.cime.constants import constants
+from mpas_tools.mesh.creation.signed_distance import (
+    mask_from_geojson,
+    signed_distance_from_geojson,
+)
 from mpas_tools.viz.colormaps import register_sci_viz_colormaps
 
 from compass.mesh import QuasiUniformSphericalMeshStep
@@ -25,7 +26,7 @@ def setup(self):
         inputs = ['coastline_CUSP.geojson',
                   'land_mask_Kamchatka.geojson',
                   'land_mask_Mexico.geojson',
-                  'namelist.split_explicit',
+                  'namelist.split_explicit_ab2',
                   'region_Arctic_Ocean.geojson',
                   'region_Bering_Sea.geojson',
                   'region_Bering_Sea_reduced.geojson',
@@ -58,8 +59,8 @@ def build_cell_width_lat_lon(self):
         dlon = 0.1
         dlat = dlon
         earth_radius = constants['SHR_CONST_REARTH']
-        print('\nCreating cellWidth on a lat-lon grid of: {0:.2f} x {0:.2f} '
-              'degrees'.format(dlon, dlat))
+        print(f'\nCreating cellWidth on a lat-lon grid of: '
+              f'{dlon:.2f} x {dlat:.2f} degrees')
         print('This can be set higher for faster test generation\n')
         nlon = int(360. / dlon) + 1
         nlat = int(180. / dlat) + 1
@@ -144,16 +145,16 @@ def build_cell_width_lat_lon(self):
                                                       earth_radius,
                                                       max_length=0.25)
         maskSmoothEast = 0.5 * (
-                    1 + np.tanh((transitionOffset - signedDistance) /
-                                (transitionWidth / 2.)))
+            1 + np.tanh((transitionOffset - signedDistance) /
+                        (transitionWidth / 2.)))
 
         fc = read_feature_collection('region_Bering_Sea_reduced.geojson')
         signedDistance = signed_distance_from_geojson(fc, lon, lat,
                                                       earth_radius,
                                                       max_length=0.25)
         maskSmoothWest = 0.5 * (
-                    1 + np.tanh((transitionOffset - signedDistance) /
-                                (transitionWidth / 2.)))
+            1 + np.tanh((transitionOffset - signedDistance) /
+                        (transitionWidth / 2.)))
 
         fc = read_feature_collection('land_mask_Kamchatka.geojson')
         maskWest = mask_from_geojson(fc, lon, lat)

compass/ocean/tests/global_ocean/mesh/wc14/namelist.split_explicit → compass/ocean/tests/global_ocean/mesh/wc14/namelist.split_explicit_ab2

@@ -1,4 +1,4 @@
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_dt = '00:01:00'
 config_btr_dt = '00:00:03'
 config_run_duration = '0000_01:00:00'

compass/ocean/tests/global_ocean/monthly_output_test/__init__.py

@@ -1,6 +1,8 @@
+from compass.ocean.tests.global_ocean.forward import (
+    ForwardStep,
+    ForwardTestCase,
+)
 from compass.validate import compare_variables
-from compass.ocean.tests.global_ocean.forward import ForwardTestCase, \
-    ForwardStep
 
 
 class MonthlyOutputTest(ForwardTestCase):
@@ -24,7 +26,7 @@ def __init__(self, test_group, mesh, init, time_integrator):
         init : compass.ocean.tests.global_ocean.init.Init
             The test case that produces the initial condition for this run
 
-        time_integrator : {'split_explicit', 'RK4'}
+        time_integrator : {'split_explicit_ab2', 'RK4'}
             The time integrator to use for the forward run
         """
         super().__init__(test_group=test_group, mesh=mesh, init=init,

compass/ocean/tests/global_ocean/namelist.forward

@@ -1,6 +1,6 @@
 config_ocean_run_mode = 'forward'
 config_block_decomp_file_prefix = 'graph.info.part.'
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_use_mom_del2 = .true.
 config_use_mom_del4 = .true.
 config_use_cvmix_convection = .true.
@@ -13,7 +13,7 @@ config_implicit_constant_bottom_drag_coeff = 1.0e-3
 config_use_bulk_wind_stress = .true.
 config_use_bulk_thickness_flux = .true.
 config_use_Redi = .true.
-config_Redi_min_layers_diag_terms = 8
+config_Redi_min_layers_diag_terms = 0
 config_use_GM = .true.
 config_AM_mixedLayerDepths_enable = .true.
 config_AM_mixedLayerDepths_compute_interval = 'dt'

compass/ocean/tests/global_ocean/performance_test/__init__.py

@@ -28,7 +28,7 @@ def __init__(self, test_group, mesh, init, time_integrator):
         init : compass.ocean.tests.global_ocean.init.Init
             The test case that produces the initial condition for this run
 
-        time_integrator : {'split_explicit', 'RK4'}
+        time_integrator : {'split_explicit_ab2', 'RK4'}
             The time integrator to use for the forward run
         """
         super().__init__(test_group=test_group, mesh=mesh, init=init,

compass/ocean/tests/global_ocean/restart_test/__init__.py

@@ -26,15 +26,15 @@ def __init__(self, test_group, mesh, init, time_integrator):
         init : compass.ocean.tests.global_ocean.init.Init
             The test case that produces the initial condition for this run
 
-        time_integrator : {'split_explicit', 'RK4'}
+        time_integrator : {'split_explicit_ab2', 'RK4'}
             The time integrator to use for the forward run
         """
         super().__init__(test_group=test_group, mesh=mesh, init=init,
                          time_integrator=time_integrator,
                          name='restart_test')
         module = __name__
 
-        restart_time = {'split_explicit': '0001-01-01_04:00:00',
+        restart_time = {'split_explicit_ab2': '0001-01-01_04:00:00',
                         'RK4': '0001-01-01_00:10:00'}
         restart_filename = '../restarts/rst.{}.nc'.format(
             restart_time[time_integrator].replace(':', '.'))

compass/ocean/tests/global_ocean/threads_test/__init__.py

@@ -1,6 +1,8 @@
+from compass.ocean.tests.global_ocean.forward import (
+    ForwardStep,
+    ForwardTestCase,
+)
 from compass.validate import compare_variables
-from compass.ocean.tests.global_ocean.forward import ForwardTestCase, \
-    ForwardStep
 
 
 class ThreadsTest(ForwardTestCase):
@@ -24,7 +26,7 @@ def __init__(self, test_group, mesh, init, time_integrator):
         init : compass.ocean.tests.global_ocean.init.Init
             The test case that produces the initial condition for this run
 
-        time_integrator : {'split_explicit', 'RK4'}
+        time_integrator : {'split_explicit_ab2', 'RK4'}
             The time integrator to use for the forward run
         """
         super().__init__(test_group=test_group, mesh=mesh, init=init,

compass/ocean/tests/gotm/default/namelist.forward

@@ -1,6 +1,6 @@
 config_dt = '000:00:25'
 config_btr_dt = '000:00:25'
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_run_duration = '0000_12:00:00'
 config_zonal_ssh_grad = -1.0e-5
 config_pressure_gradient_type = 'constant_forced'

compass/ocean/tests/isomip_plus/namelist.forward_and_ssh_adjust

@@ -4,7 +4,7 @@ config_btr_dt = '00:00:10'
 config_run_duration = '0000-01-00_00:00:00'
 config_write_output_on_startup = .false.
 config_block_decomp_file_prefix = 'graph.info.part.'
-config_time_integrator = 'split_explicit'
+config_time_integrator = 'split_explicit_ab2'
 config_use_mom_del2 = .true.
 config_use_tracer_del2 = .true.
 config_mom_del2 = 6.0

compass/ocean/tests/sphere_transport/correlated_tracers_2d/correlated_tracers_2d.cfg

@@ -14,7 +14,7 @@ goal_cells_per_core = 300
 # few cores are available)
 max_cells_per_core = 3000
 
-# time integrator (RK4 or split_explicit)
+# time integrator (RK4 or split_explicit_ab2)
 time_integrator = RK4
 
 # convergence threshold below which the test fails