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updated checkpoint_xdmf method save discontinuous fields properly #328

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updated checkpoint_xdmf method save discontinuous fields properly #328

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updated checkpoint_xdmf method save discontinuous fields properly
gthyagi Jun 27, 2025
aa65291
added var as argument to def
gthyagi Jun 27, 2025
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33 changes: 24 additions & 9 deletions src/underworld3/discretisation.py
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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]
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var is no longer in the scope of this function. This is not good.
Consider passing it in as an argument?

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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"
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Copilot AI Jun 27, 2025

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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.

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Copilot AI Jun 27, 2025

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[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.

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Copilot AI Jun 27, 2025

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[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"

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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:
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