[MedApplication] Preserve node and geometry IDs in MED I/O with SubModelParts by Marco1410 · Pull Request #14201 · KratosMultiphysics/Kratos

Marco1410 · 2026-02-12T12:15:48Z

📝 Description
This PR updates the MED I/O so that Kratos can write and read MED files preserving node and geometry IDs, including SubModelParts.

Main points:

Node IDs are preserved during write/read.
Geometry IDs are preserved.
SubModelParts in Kratos are saved as family groups in Salome and correctly reconstructed when reading.
Proper handling of SALOME points vs Kratos nodes to avoid creating unwanted point geometries.

I tested this with Python and C++ tests, and also with HROM potential flow models. So far everything works as expected.

🆕 Changelog

Updated 'med_model_part_io.cpp' (WriteModelPart and ReadModelPart)
Added/updated Python and C++ tests

…and geometry ids

philbucher

cool!

I have some concerns, but overall looks good

I leave approval to current users

philbucher · 2026-02-12T13:09:16Z

        for (int i = 0; i < num_groups; i++) {
-            group_names[i] = StringUtilities::Trim(c_group_names.substr(i * MED_LNAME_SIZE, MED_LNAME_SIZE), /*RemoveNullChar=*/true);
+            std::string raw_name( c_group_names.data() + i * MED_LNAME_SIZE, MED_LNAME_SIZE);
+            raw_name = StringUtilities::Trim(raw_name, true);


can you explain this change a bit? I thought the nullchars are already handled?

Thanks for your comments Philipp.

With the original version, the group names contain garbage characters at the end. To fix this, I trim the strings at the "\0" null terminator.

At least on Ubuntu, this works.

I trim the strings at the "\0" null terminator.

StringUtilities::Trim should already be doing this. What is the failing input?
Could you please add the failing input in this test so that it could be fixed there?

philbucher · 2026-02-12T13:10:10Z

            reorder_fct(geom_node_ids);

+            // Avoid using nodes or points as geometries
+            if (geo_type == MED_POINT1) {


why are those skipped? Structural cases need them! (e.g. pointloads)

I'm skipping the creation of point geometries, as they don't represent real geometries in Kratos.

Here, node families are used to construct SubModelParts that contain only nodes.

But they should represent real geometries. If you dont want them then you shouldnt create them in Salome.

See an example for a simple cantilever how they are used:
https://github.com/KratosMultiphysics/KratosSalomePlugin/blob/dce31197e15887b40174d27783ac2839b0134a2e/tui_examples/cantilever/salome_cantilever_hexa.py#L60

philbucher · 2026-02-12T13:13:14Z

        num_nodes,
        dimension);

+    // get global numbering for nodes, if the file contains them


ah man, despite my best efforts the IDs are always finding their way back :D

Main reason I am against using ids is that they are often (ab) used to get nodes from ModelParts. This is a search, which is expensive for large models
=> one should use position in the ModelPart instead with is O(1)
Also non-consecutive IDs can create problems for MPI-partitioning

personal rant aside, this should be optional, as some meshers dont even write the IDs
I would vote to not read the IDs by default, but that decision I leave to current users or the tech-committee

That’s true, but in any case, if we do nothing, the MED library enumerates them in its own way. This option is available in both Kratos and Salome, so for now, I think it is better to keep them synchronised. We can remove this later if needed.

well until now the Ids were just enuerated from the node position

In any case, I dont have a strong opinion

It's optional now, but locally just so we don't forget we're doing it until someone says something about it.

philbucher · 2026-02-13T17:00:36Z

+            << "Using MED implicit numbering." << std::endl;
+
+        for (med_int i = 0; i < num_nodes; ++i) {
+            node_ids[i] = i + 1;


I think you can use std::iota or sth similar

philbucher

I remembered some more potential conceptual issues with the export of SubModelParts

philbucher · 2026-02-20T10:20:54Z

+    med_int dimension = 0;
+    for (const auto& r_geom : rThisModelPart.Geometries()) {
+
+        dimension = std::max( dimension, static_cast<med_int>(r_geom.WorkingSpaceDimension()));
+    }
+    if (dimension == 0 || dimension == 1){
+        dimension = 3;
+    }


Suggested change

med_int dimension = 0;

for (const auto& r_geom : rThisModelPart.Geometries()) {

dimension = std::max( dimension, static_cast<med_int>(r_geom.WorkingSpaceDimension()));

}

if (dimension == 0 || dimension == 1){

dimension = 3;

}

med_int dimension = 2;

for (const auto& r_geom : rThisModelPart.Geometries()) {

dimension = std::max( dimension, static_cast<med_int>(r_geom.WorkingSpaceDimension()));

}

philbucher · 2026-02-20T10:28:36Z

+    CheckMEDErrorCode(err, "MEDmeshGlobalNumberWr (nodes)");
+
+    med_int next_family = 1;
+    std::unordered_map<std::string, med_int> smp_to_family;


I remembered part of why I didnt implement the writing of SubModelParts: A family in med is NOT the same as a SubModelPart in Kratos. A family contains only one type of geometry (e.g. only Triangle3 or Tetra4).
The med equivalent of a SubModelPart is a group, which consists of multiple families. (actually the relation is the other way round, each family has groups)

Also what I think is not considered is if a geometry belongs to multiple SubModelParts.

Back then I thought the solution would be to tag each entity like is done for the MMG-stuff, but not sure

philbucher · 2026-02-20T10:29:03Z

+
+    CheckMEDErrorCode(err, "MEDmeshGlobalNumberWr (nodes)");
+
+    med_int next_family = 1;


FYI by definition node-families are positive, whereas geometry families are negative

philbucher · 2026-02-20T10:29:27Z

+        CheckMEDErrorCode(err, "MEDmeshGlobalNumberWr (cells)");
+
+        const std::size_t nb_elem = conn.size();
+        std::vector<med_int> elem_family_numbers(nb_elem, 0);


Suggested change

std::vector<med_int> elem_family_numbers(nb_elem, 0);

std::vector<med_int> geom_family_numbers(nb_elem, 0);

philbucher · 2026-02-20T10:30:24Z

+
+    std::function<void(const ModelPart&)> collect_subparts =
+        [&](const ModelPart& mp) {
+            for (const auto& r_child : mp.SubModelParts()) {


med doesnt know SubSubModelParts, I am curious how you handle it. Have you tested it?

Marco1410 · 2026-03-24T12:59:21Z

Hi @philbucher!!, I’ve made some changes to support families and groups, and to use the hierarchical naming of model parts so it works with submodelparts and nested submodelparts.

I’ve been testing it, and so far everything works as expected.

Thanks for your feedback, and when you have time, I’d really appreciate it if you could take a look.

philbucher

Ok from my side 👍
I didnt review the algorithm in detail but I trust your tests

Approval I leave to some current users

philbucher · 2026-03-29T18:20:10Z

        for (int i = 0; i < num_groups; i++) {
-            group_names[i] = StringUtilities::Trim(c_group_names.substr(i * MED_LNAME_SIZE, MED_LNAME_SIZE), /*RemoveNullChar=*/true);
+            std::string raw_name( c_group_names.data() + i * MED_LNAME_SIZE, MED_LNAME_SIZE);
+            raw_name = StringUtilities::Trim(raw_name, true);


I trim the strings at the "\0" null terminator.

StringUtilities::Trim should already be doing this. What is the failing input?
Could you please add the failing input in this test so that it could be fixed there?

philbucher · 2026-03-31T14:41:03Z

    BuiltinTimer timer;

    const bool add_nodes_of_geometries = true; // TODO make this an input parameter
+    const bool preserve_global_numbering_for_nodes = true;


since this is a behavior change some current user should approve this PR
@sunethwarna @matekelemen

philbucher · 2026-03-31T14:43:49Z


+    std::vector<med_int> node_ids(num_nodes);
+    // get global numbering for nodes, if the file contains them
+    if (preserve_global_numbering_for_nodes) {


I actually like how its handled for the geometry
If the file contains the IDs then for me it would be fine to use them. If not issue a warning and do whats currently done

=> then you wouldnt need the preserve_global_numbering_for_nodes flag

philbucher · 2026-03-31T14:46:14Z


            KratosMed.MedTestingUtilities.CheckModelPartsAreEqual(
-                self.mp_read_1, self.mp_read_2, check_sub_model_parts=False  # until writing of SMPs is implemented
+                self.mp_read_1, self.mp_read_2, check_sub_model_parts=True  # until writing of SMPs is implemented


Suggested change

self.mp_read_1, self.mp_read_2, check_sub_model_parts=True # until writing of SMPs is implemented

self.mp_read_1, self.mp_read_2, check_sub_model_parts=True

now its implemented no?

…or_nodes flag

Marco1410 · 2026-04-07T09:00:59Z

@rubenzorrilla I've added the last changes.

philbucher

approving since the new behavior is optional wrt the numbering

Thanks!

Marco1410 added 4 commits February 12, 2026 12:35

main changes write-read modelpart with submodelparts preserving node …

ed19972

…and geometry ids

adding some changes for tests

cb0e374

fix cpp test

485779e

fix python tests

23c7bfa

Marco1410 requested review from matekelemen and philbucher February 12, 2026 12:15

Marco1410 assigned rubenzorrilla, riccardotosi and Rbravo555 Feb 12, 2026

Marco1410 added Enhancement IO MedApplication Salome labels Feb 12, 2026

philbucher reviewed Feb 12, 2026

View reviewed changes

Marco1410 assigned RiccardoRossi and unassigned riccardotosi Feb 12, 2026

philbucher reviewed Feb 13, 2026

View reviewed changes

Marco1410 added 5 commits February 19, 2026 11:47

Removed commented code

bf2e4ca

Replaced loop with std::iota

375f894

preserve global numbering for nodes ids optional

bb9d217

allow create submodelparts with point geometries

d4a5f25

fixed python tests

089a928

philbucher reviewed Feb 20, 2026

View reviewed changes

Marco1410 added 5 commits March 2, 2026 15:57

Merge branch 'master' into marco/med_application

e3d18aa

Merge branch 'master' into marco/med_application

99800cb

Updates --> Using families, groups and hierarchical names

2cb4ebf

small change

d0d7668

Avoid creating non-existent smp's

e2751c5

Marco1410 requested a review from philbucher March 24, 2026 12:59

philbucher reviewed Mar 31, 2026

View reviewed changes

Marco1410 added 2 commits April 7, 2026 10:55

Removing test comment

3fabb76

Going back group names split and removing preserve_global_numbering_f…

1def535

…or_nodes flag

philbucher reviewed Apr 7, 2026

View reviewed changes

Comment thread applications/MedApplication/custom_io/med_model_part_io.cpp Outdated

Removing omitted error line

c16a2c4

philbucher approved these changes Apr 7, 2026

View reviewed changes

Marco1410 merged commit 3f551a2 into master Apr 8, 2026
10 checks passed

Marco1410 deleted the marco/med_application branch April 8, 2026 08:09


		CheckMEDErrorCode(err, "MEDmeshGlobalNumberWr (nodes)");

		med_int next_family = 1;

	std::vector<med_int> elem_family_numbers(nb_elem, 0);
	std::vector<med_int> geom_family_numbers(nb_elem, 0);

	self.mp_read_1, self.mp_read_2, check_sub_model_parts=True # until writing of SMPs is implemented
	self.mp_read_1, self.mp_read_2, check_sub_model_parts=True

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Marco1410 commented Feb 12, 2026

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philbucher Feb 12, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Marco1410 commented Mar 24, 2026

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Marco1410 commented Apr 7, 2026

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philbucher Feb 12, 2026 •

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