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Add Omega support to Cosine Bell tests
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xylar committed Dec 4, 2024
1 parent bdd5ae4 commit 52fc195
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Showing 6 changed files with 56 additions and 21 deletions.
2 changes: 1 addition & 1 deletion polaris/ocean/tasks/cosine_bell/analysis.py
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ def exact_solution(self, refinement_factor, field_name, time, zidx=None):
ds_mesh = xr.open_dataset(f'mesh_r{refinement_factor:02g}.nc')
sphere_radius = ds_mesh.sphere_radius

ds_init = xr.open_dataset(f'init_r{refinement_factor:02g}.nc')
ds_init = self.open_model_dataset(f'init_r{refinement_factor:02g}.nc')
latCell = ds_init.latCell.values
lonCell = ds_init.lonCell.values

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5 changes: 4 additions & 1 deletion polaris/ocean/tasks/cosine_bell/cosine_bell.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,10 @@ error_type = l2
# config options for convergence forward steps
[convergence_forward]

# time integrator: {'split_explicit', 'RK4'}
# time integrator
# either: {'RK4'}
# mpas-ocean: {'split_explicit'}
# omega: {'Forward-Backward', 'RungeKutta2'}
time_integrator = RK4

# RK4 time step per resolution (s/km), since dt is proportional to resolution
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10 changes: 10 additions & 0 deletions polaris/ocean/tasks/cosine_bell/forward.py
Original file line number Diff line number Diff line change
Expand Up @@ -46,3 +46,13 @@ def __init__(self, component, name, subdir, mesh, init,
graph_target=f'{mesh.path}/graph.info',
refinement_factor=refinement_factor,
refinement=refinement)

def setup(self):
"""
TEMP: symlink initial condition to name hard-coded in Omega
"""
super().setup()
model = self.config.get('ocean', 'model')
# TODO: remove as soon as Omega no longer hard-codes this file
if model == 'omega':
self.add_input_file(filename='OmegaMesh.nc', target='init.nc')
38 changes: 33 additions & 5 deletions polaris/ocean/tasks/cosine_bell/forward.yaml
Original file line number Diff line number Diff line change
@@ -1,14 +1,16 @@
mpas-ocean:
run_modes:
config_ocean_run_mode: forward
ocean:
time_management:
config_stop_time: none
config_run_duration: {{ run_duration }}
decomposition:
config_block_decomp_file_prefix: graph.info.part.
time_integration:
config_dt: {{ dt }}
config_time_integrator: {{ time_integrator }}

mpas-ocean:
run_modes:
config_ocean_run_mode: forward
decomposition:
config_block_decomp_file_prefix: graph.info.part.
debug:
config_disable_thick_all_tend: true
config_disable_thick_hadv: true
Expand Down Expand Up @@ -65,3 +67,29 @@ mpas-ocean:
- refLayerThickness
- kineticEnergyCell
- relativeVorticityCell

Omega:
Tendencies:
ThicknessFluxTendencyEnable : false
PVTendencyEnable : false
KETendencyEnable : false
SSHTendencyEnable : false
VelDiffTendencyEnable: false
VelHyperDiffTendencyEnable: false
TracerHorzAdvTendencyEnable : true
TracerDiffTendencyEnable : false
TracerHyperDiffTendencyEnable : false
Dimension:
NVertLevels: 1
IOStreams:
InitialState:
Filename: init.nc
History:
Filename: output.nc
Freq: {{ output_freq }}
FreqUnits: Seconds
Contents:
- Tracers
- LayerThickness
- NormalVelocity
RestartRead: {}
11 changes: 3 additions & 8 deletions polaris/ocean/tasks/cosine_bell/init.py
Original file line number Diff line number Diff line change
@@ -1,14 +1,13 @@
import numpy as np
import xarray as xr
from mpas_tools.io import write_netcdf
from mpas_tools.transects import lon_lat_to_cartesian
from mpas_tools.vector import Vector

from polaris import Step
from polaris.ocean.model import OceanIOStep
from polaris.ocean.vertical import init_vertical_coord


class Init(Step):
class Init(OceanIOStep):
"""
A step for an initial condition for for the cosine bell test case
"""
Expand Down Expand Up @@ -36,10 +35,6 @@ def __init__(self, component, name, subdir, base_mesh):
filename='mesh.nc',
work_dir_target=f'{base_mesh.path}/base_mesh.nc')

self.add_input_file(
filename='graph.info',
work_dir_target=f'{base_mesh.path}/graph.info')

self.add_output_file(filename='initial_state.nc')

def run(self):
Expand Down Expand Up @@ -107,7 +102,7 @@ def run(self):
ds['fEdge'] = xr.zeros_like(ds_mesh.xEdge)
ds['fVertex'] = xr.zeros_like(ds_mesh.xVertex)

write_netcdf(ds, 'initial_state.nc')
self.write_model_dataset(ds, 'initial_state.nc')


def cosine_bell(max_value, ri, r):
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11 changes: 5 additions & 6 deletions polaris/ocean/tasks/cosine_bell/viz.py
Original file line number Diff line number Diff line change
@@ -1,11 +1,10 @@
import cmocean # noqa: F401
import xarray as xr

from polaris import Step
from polaris.ocean.model import OceanIOStep
from polaris.viz import plot_global_mpas_field


class Viz(Step):
class Viz(OceanIOStep):
"""
A step for plotting fields from the cosine bell output
Expand Down Expand Up @@ -64,7 +63,7 @@ def run(self):
mesh_name = self.mesh_name
run_duration = config.getfloat('convergence_forward', 'run_duration')

ds_init = xr.open_dataset('initial_state.nc')
ds_init = self.open_model_dataset('initial_state.nc')
da = ds_init['tracer1'].isel(Time=0, nVertLevels=0)

plot_global_mpas_field(
Expand All @@ -73,11 +72,11 @@ def run(self):
title=f'{mesh_name} tracer at init', plot_land=False,
central_longitude=180.)

ds_out = xr.open_dataset('output.nc')
ds_out = self.open_model_dataset('output.nc')
da = ds_out['tracer1'].isel(Time=-1, nVertLevels=0)

plot_global_mpas_field(
mesh_filename='mesh.nc', da=da, out_filename='final.png',
config=config, colormap_section='cosine_bell_viz',
title=f'{mesh_name} tracer after {run_duration/24.:g} days',
title=f'{mesh_name} tracer after {run_duration / 24.:g} days',
plot_land=False, central_longitude=180.)

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