Export average surface temperature #949
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
RemDelaporteMathurin
requested changes
Feb 26, 2025
There was a problem hiding this comment.
Hi @kaelyndunnell thanks for this, this is very much needed!
However I think it should be implemented differently:
- It doesn't make sense to ask users to provide
temperature_fieldas an argument ofSurfaceTemperaturesince they don't have access to the fenics object (fem.Constantorfem.Temperature) before callinginitialiseand since exports are defined before callinginitialise. Instead, I believe the class should not have this argument at all, andtemperature_fieldis set as an attribute only insideHTransportProblem
for export in self.exports:
if isinstance(export, SurfaceTemperature):
export.temperature_field = self.temperature_fenicsSurfaceTemperatureshares a lot of functionality withSurfaceQuantity: it should inherit from it- I'm thinking by looking at this we should revisit the design of these quantities @JonathanGSDUFOUR , I'll open an issue to describe my idea but here's the rough pitch
class SurfaceQuantity:
def __init__(self, surface, filename):
self.surface = surface
self.filename = filename
self.field = None # this is no longer a user argument but only an attribute
...
class AverageSurfaceConcentration(SurfaceQuantity):
def __init__(self, species, surface, filename):
self.species = species
super.__init__(surface, filename)Inside HTransportProblem
def initialise_exports(self):
for export in self.exports:
if not hasattr(export, "species"): # appropriate fenics functions are already stored in F.Species objects
export.field = self.temperature_fenics
Comment on lines
831
to
838
| elif isinstance(export, exports.SurfaceTemperature): | ||
| export.compute(self.ds) # compute surface temp | ||
|
|
||
| export.t.append(float(self.t)) # update export time | ||
|
|
||
| # if filename given write export data to file | ||
| if export.filename is not None: | ||
| export.write(t=float(self.t)) |
There was a problem hiding this comment.
These lines are not tested. That's because by design, it's impossible to use SurfaceTemperature in combination with HTransportProblem
RemDelaporteMathurin
added
enhancement
Co-authored-by: Rémi Delaporte-Mathurin <[email protected]>
RemDelaporteMathurin
requested changes
Mar 4, 2025
| @@ -415,6 +418,9 @@ def initialise_exports(self): | |||
| export.D = D | |||
| export.D_expr = D_expr | |||
|
|
|||
| if isinstance(export, exports.AverageSurfaceTemperature): | |||
| export.temperature_field = self.temperature_fenics | |||
There was a problem hiding this comment.
This should be tested!
There was a problem hiding this comment.
See comment below about integration test
Comment on lines
+93
to
+191
| def test_write_overwrite(tmp_path): | ||
| """Test that the write method overwrites the file if it already exists""" | ||
| filename = os.path.join(tmp_path, "my_export.csv") | ||
| my_model = F.HydrogenTransportProblem( | ||
| mesh=F.Mesh1D(np.linspace(0, 6.0, 10000)), temperature=500 | ||
| ) | ||
| my_model.define_temperature() | ||
|
|
||
| my_export = F.AverageSurfaceTemperature( | ||
| filename=filename, | ||
| surface=F.SurfaceSubdomain1D(id=35, x=1), | ||
| ) | ||
| my_export.value = 2.0 | ||
| my_export.write(0) | ||
| my_export.write(1) | ||
|
|
||
| my_export2 = F.AverageSurfaceTemperature( | ||
| filename=filename, | ||
| surface=F.SurfaceSubdomain1D(id=1, x=1), | ||
| ) | ||
| my_export2.value = 3.0 | ||
| my_export2.write(1) | ||
| my_export2.write(2) | ||
| my_export2.write(3) | ||
|
|
||
| data = np.genfromtxt(filename, delimiter=",", names=True) | ||
| file_length = data.size | ||
| expected_length = 3 | ||
|
|
||
| assert file_length == expected_length | ||
|
|
||
|
|
||
| def test_filename_setter_raises_TypeError(): | ||
| """Test that a TypeError is raised when the filename is not a string""" | ||
|
|
||
| with pytest.raises(TypeError, match="filename must be of type str"): | ||
| my_model = F.HydrogenTransportProblem( | ||
| mesh=F.Mesh1D(np.linspace(0, 6.0, 10000)), temperature=500 | ||
| ) | ||
| my_model.define_temperature() | ||
|
|
||
| F.AverageSurfaceTemperature( | ||
| filename=1, | ||
| surface=F.SurfaceSubdomain1D(id=1, x=1), | ||
| ) | ||
|
|
||
|
|
||
| def test_filename_setter_raises_ValueError(tmp_path): | ||
| """Test that a ValueError is raised when the filename does not end with .csv or .txt""" | ||
|
|
||
| with pytest.raises(ValueError): | ||
| my_model = F.HydrogenTransportProblem( | ||
| mesh=F.Mesh1D(np.linspace(0, 6.0, 10000)), temperature=500 | ||
| ) | ||
| my_model.define_temperature() | ||
|
|
||
| F.AverageSurfaceTemperature( | ||
| filename=os.path.join(tmp_path, "my_export.xdmf"), | ||
| surface=F.SurfaceSubdomain1D(id=1, x=1), | ||
| ) | ||
|
|
||
|
|
||
| @pytest.mark.parametrize("value", ["my_export.csv", "my_export.txt"]) | ||
| def test_writer(tmp_path, value): | ||
| """Test that the writes values at each timestep to either a csv or txt file""" | ||
| my_model = F.HydrogenTransportProblem( | ||
| mesh=F.Mesh1D(np.linspace(0, 6.0, 10000)), temperature=500 | ||
| ) | ||
| my_model.define_temperature() | ||
|
|
||
| my_export = F.AverageSurfaceTemperature( | ||
| filename=os.path.join(tmp_path, f"{value}"), | ||
| surface=F.SurfaceSubdomain1D(id=1, x=0), | ||
| ) | ||
| my_export.value = 2.0 | ||
|
|
||
| for i in range(10): | ||
| my_export.write(i) | ||
| file_length = len(np.genfromtxt(my_export.filename, delimiter=",")) | ||
|
|
||
| expected_length = i + 2 | ||
|
|
||
| assert file_length == expected_length | ||
|
|
||
|
|
||
| def test_surface_setter_raises_TypeError(): | ||
| """Test that a TypeError is raised when the surface is not a | ||
| F.SurfaceSubdomain""" | ||
|
|
||
| with pytest.raises( | ||
| TypeError, match="surface should be an int or F.SurfaceSubdomain" | ||
| ): | ||
| my_model = F.HydrogenTransportProblem( | ||
| mesh=F.Mesh1D(np.linspace(0, 6.0, 10000)), temperature=500 | ||
| ) | ||
| my_model.define_temperature() | ||
| F.AverageSurfaceTemperature( | ||
| surface="1", | ||
| ) |
There was a problem hiding this comment.
These tests aren't need as it tests the functionality in the parent class SurfaceQuantity
Comment on lines
+49
to
+51
| my_export = F.AverageSurfaceTemperature(surface=dummy_surface) | ||
| my_export.temperature_field = my_model.temperature_fenics | ||
| my_export.compute(ds) |
There was a problem hiding this comment.
Good, but we also need to test the full integration with HydrogenTransportProblem ie. just do
my_model.exports = [....]
my_model.initialise()
my_model.run()
# test value of export after run
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Proposed changes
Adds export for average surface temperature.
Types of changes
What types of changes does your code introduce to FESTIM?
Checklist
Further comments
If this is a relatively large or complex change, kick off the discussion by explaining why you chose the solution you did and what alternatives you considered, etc...