Skip to content

Commit

Permalink
Merge pull request #250 from xylar/fix-manufactured-solution-viz
Browse files Browse the repository at this point in the history 
Fix manufactured solution viz step
  • Loading branch information
@xylar
xylar authored Dec 2, 2024
2 parents a44d4b8 + d97b0d4 commit e1ad8af
Show file tree
Hide file tree
Showing 4 changed files with 110 additions and 35 deletions.
1 change: 1 addition & 0 deletions polaris/ocean/convergence/analysis.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,7 @@ def setup(self):
Add input files based on resolutions, which may have been changed by
user config options
"""
super().setup()
config = self.config
dependencies = self.dependencies_dict
if self.refinement == 'time':
Expand Down
10 changes: 6 additions & 4 deletions polaris/ocean/tasks/manufactured_solution/__init__.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -119,10 +119,12 @@ def __init__(self, component, config, refinement='both'):

self.add_step(Analysis(component=component,
subdir=f'{self.subdir}/analysis',
refinement=refinement,
dependencies=analysis_dependencies))
self.add_step(Viz(component=component, resolutions=resolutions,
taskdir=self.subdir),
dependencies=analysis_dependencies,
refinement=refinement))
self.add_step(Viz(component=component,
dependencies=analysis_dependencies,
taskdir=self.subdir,
refinement=refinement),
run_by_default=False)
config.add_from_package('polaris.ocean.convergence',
'convergence.cfg')
Expand Down
5 changes: 0 additions & 5 deletions polaris/ocean/tasks/manufactured_solution/analysis.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,11 +8,6 @@ class Analysis(ConvergenceAnalysis):
"""
A step for analysing the output from the manufactured solution
test case
Attributes
----------
resolutions : list of float
The resolutions of the meshes that have been run
"""
def __init__(self, component, subdir, dependencies, refinement='both'):
"""
Expand Down
129 changes: 103 additions & 26 deletions polaris/ocean/tasks/manufactured_solution/viz.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,11 @@
import matplotlib.pyplot as plt
import numpy as np

from polaris.ocean.convergence import (
get_resolution_for_task,
get_timestep_for_task,
)
from polaris.ocean.model import OceanIOStep
from polaris.ocean.resolution import resolution_to_subdir
from polaris.ocean.tasks.manufactured_solution.exact_solution import (
ExactSolution,
)
Expand All @@ -19,10 +22,31 @@ class Viz(OceanIOStep):
Attributes
----------
resolutions : list of float
The resolutions of the meshes that have been run
dependencies_dict : dict of dict of polaris.Steps
The dependencies of this step must be given as separate keys in the
dict:
mesh : dict of polaris.Steps
Keys of the dict correspond to `refinement_factors`
Values of the dict are polaris.Steps, which must have the
attribute `path`, the path to `base_mesh.nc` of that
resolution
init : dict of polaris.Steps
Keys of the dict correspond to `refinement_factors`
Values of the dict are polaris.Steps, which must have the
attribute `path`, the path to `initial_state.nc` of that
resolution
forward : dict of polaris.Steps
Keys of the dict correspond to `refinement_factors`
Values of the dict are polaris.Steps, which must have the
attribute `path`, the path to `forward.nc` of that
resolution
refinement : str
Refinement type. One of 'space', 'time' or 'both' indicating both
space and time
"""
def __init__(self, component, resolutions, taskdir):
def __init__(self, component, dependencies, taskdir, refinement='both'):
"""
Create the step
Expand All @@ -31,37 +55,82 @@ def __init__(self, component, resolutions, taskdir):
component : polaris.Component
The component the step belongs to
resolutions : list of float
The resolutions of the meshes that have been run
dependencies : dict of dict of polaris.Steps
The dependencies of this step must be given as separate keys in the
dict:
mesh : dict of polaris.Steps
Keys of the dict correspond to `refinement_factors`
Values of the dict are polaris.Steps, which must have the
attribute `path`, the path to `base_mesh.nc` of that
resolution
init : dict of polaris.Steps
Keys of the dict correspond to `refinement_factors`
Values of the dict are polaris.Steps, which must have the
attribute `path`, the path to `initial_state.nc` of that
resolution
forward : dict of polaris.Steps
Keys of the dict correspond to `refinement_factors`
Values of the dict are polaris.Steps, which must have the
attribute `path`, the path to `forward.nc` of that
resolution
taskdir : str
The subdirectory that the task belongs to
refinement : str, optional
Refinement type. One of 'space', 'time' or 'both' indicating both
space and time
"""
super().__init__(component=component, name='viz', indir=taskdir)
self.resolutions = resolutions
self.dependencies_dict = dependencies
self.refinement = refinement
self.add_output_file('comparison.png')

for resolution in resolutions:
mesh_name = resolution_to_subdir(resolution)
def setup(self):
"""
Add input files based on resolutions, which may have been changed by
user config options
"""
super().setup()
config = self.config
dependencies = self.dependencies_dict

if self.refinement == 'time':
option = 'refinement_factors_time'
else:
option = 'refinement_factors_space'
refinement_factors = config.getlist('convergence', option,
dtype=float)

for refinement_factor in refinement_factors:
base_mesh = dependencies['mesh'][refinement_factor]
init = dependencies['init'][refinement_factor]
forward = dependencies['forward'][refinement_factor]
self.add_input_file(
filename=f'mesh_{mesh_name}.nc',
target=f'../init/{mesh_name}/culled_mesh.nc')
filename=f'mesh_r{refinement_factor:02g}.nc',
work_dir_target=f'{base_mesh.path}/base_mesh.nc')
self.add_input_file(
filename=f'init_{mesh_name}.nc',
target=f'../init/{mesh_name}/initial_state.nc')
filename=f'init_r{refinement_factor:02g}.nc',
work_dir_target=f'{init.path}/initial_state.nc')
self.add_input_file(
filename=f'output_{mesh_name}.nc',
target=f'../forward/{mesh_name}/output.nc')

self.add_output_file('comparison.png')
filename=f'output_r{refinement_factor:02g}.nc',
work_dir_target=f'{forward.path}/output.nc')

def run(self):
"""
Run this step of the test case
"""
plt.switch_backend('Agg')
config = self.config
resolutions = self.resolutions
nres = len(resolutions)
if self.refinement == 'time':
option = 'refinement_factors_time'
else:
option = 'refinement_factors_space'
refinement_factors = config.getlist('convergence', option,
dtype=float)

nres = len(refinement_factors)

section = config['manufactured_solution']
eta0 = section.getfloat('ssh_amplitude')
Expand All @@ -70,11 +139,14 @@ def run(self):
fig, axes = plt.subplots(nrows=nres, ncols=3, figsize=(12, 2 * nres))
rmse = []
error_range = None
for i, res in enumerate(resolutions):
mesh_name = resolution_to_subdir(res)
ds_mesh = self.open_model_dataset(f'mesh_{mesh_name}.nc')
ds_init = self.open_model_dataset(f'init_{mesh_name}.nc')
ds = self.open_model_dataset(f'output_{mesh_name}.nc')

for i, refinement_factor in enumerate(refinement_factors):
ds_mesh = self.open_model_dataset(
f'mesh_r{refinement_factor:02g}.nc')
ds_init = self.open_model_dataset(
f'init_r{refinement_factor:02g}.nc')
ds = self.open_model_dataset(
f'output_r{refinement_factor:02g}.nc')
exact = ExactSolution(config, ds_init)

t0 = datetime.datetime.strptime(ds.xtime.values[0].decode(),
Expand Down Expand Up @@ -110,8 +182,13 @@ def run(self):
axes[0, 2].set_title('Error (Numerical - Analytical)')

pad = 5
for ax, res in zip(axes[:, 0], resolutions):
ax.annotate(f'{res}km', xy=(0, 0.5),
for ax, refinement_factor in zip(axes[:, 0], refinement_factors):
timestep, _ = get_timestep_for_task(
config, refinement_factor, refinement=self.refinement)
resolution = get_resolution_for_task(
config, refinement_factor, refinement=self.refinement)

ax.annotate(f'{resolution}km\n{timestep}s', xy=(0, 0.5),
xytext=(-ax.yaxis.labelpad - pad, 0),
xycoords=ax.yaxis.label, textcoords='offset points',
size='large', ha='right', va='center')
Expand Down

0 comments on commit e1ad8af

Please sign in to comment.