Skip to content

updated checkpoint_xdmf method save discontinuous fields properly #328

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
gthyagi wants to merge 2 commits into
base: development
Choose a base branch
from
+24 −9
Open

updated checkpoint_xdmf method save discontinuous fields properly #328

Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
17a12bf
updated checkpoint_xdmf method save discontinuous fields properly
gthyagi Jun 27, 2025
aa65291
added var as argument to def
gthyagi Jun 27, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
33 changes: 24 additions & 9 deletions src/underworld3/discretisation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2893,40 +2893,55 @@ def checkpoint_xdmf(
"""

## The mesh Var attributes

def get_cell_field_size(h5_filename):
with h5py.File(h5_filename, 'r') as f:
size = f[f'cell_fields/{var.clean_name}_{var.clean_name}'].shape[0]

@julesghub julesghub Jun 27, 2025

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

var is no longer in the scope of this function. This is not good.
Consider passing it in as an argument?

@gthyagi gthyagi Jun 27, 2025

Copy link
Copy Markdown
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Done ✅

return size

attributes = ""
for var in meshVars:
var_filename = filename + f"mesh.{var.clean_name}.{index:05}.h5"
var_filename = filename + f".mesh.{var.clean_name}.{index:05}.h5"

Copilot AI Jun 27, 2025

Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The helper function closes over var.clean_name from the outer scope, which may not refer to the intended variable when called. Consider passing the field name as an explicit parameter or defining this helper within the loop to avoid capturing the wrong var.

Copilot uses AI. Check for mistakes.

Copilot AI Jun 27, 2025

Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

[nitpick] Defining get_cell_field_size inside checkpoint_xdmf causes it to be redefined on every call. For clarity and efficiency, move this helper to the module level.

Copilot uses AI. Check for mistakes.

Copilot AI Jun 27, 2025

Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

[nitpick] Building filepaths via string concatenation can lead to errors (e.g. extra dots). Consider using os.path.join or at least a single f-string like f"{filename}.mesh.{var.clean_name}.{index:05}.h5" to improve readability and correctness.

Suggested change
var_filename = filename + f".mesh.{var.clean_name}.{index:05}.h5"
var_filename = f"{filename}.mesh.{var.clean_name}.{index:05}.h5"

Copilot uses AI. Check for mistakes.

if var.num_components == 1:
variable_type = "Scalar"
else:
variable_type = "Vector"
# We should add a tensor type here ...

# Determine if data is stored on nodes (vertex_fields) or cells (cell_fields)
if not getattr(var, "continuous") or getattr(var, "degree")==0:
center = "Cell"
numItems = get_cell_field_size(var_filename)
field_group = "cell_fields"
else:
center = "Node"
numItems = numVertices
field_group = "vertex_fields"

var_attribute = f"""
<Attribute
Name="{var.clean_name}"
Type="{variable_type}"
Center="Node">
Center="{center}">
<DataItem ItemType="HyperSlab"
Dimensions="1 {numVertices} {var.num_components}"
Type="HyperSlab">
Dimensions="1 {numItems} {var.num_components}"
Type="HyperSlab">
<DataItem
Dimensions="3 3"
Format="XML">
0 0 0
1 1 1
1 {numVertices} {var.num_components}
1 {numItems} {var.num_components}
</DataItem>
<DataItem
DataType="Float" Precision="8"
Dimensions="1 {numVertices} {var.num_components}"
Dimensions="1 {numItems} {var.num_components}"
Format="HDF">
&{var.clean_name+"_Data"};:/vertex_fields/{var.clean_name+"_"+var.clean_name}
&{var.clean_name+"_Data"};:/{field_group}/{var.clean_name+"_"+var.clean_name}
</DataItem>
</DataItem>
</Attribute>
"""
"""
attributes += var_attribute

for var in swarmVars:
Expand Down