Feature: Feature mesh deformation by Lena-Richter · Pull Request #2196 · DLR-AMR/t8code

Lena-Richter · 2026-03-02T13:08:13Z

Describe your changes here:
Added mesh deformation support using the new t8_cmesh_mesh_deformation files. This allows moving mesh vertices to new positions defined by a CAD geometry.
The calculation is currently done by focusing on surface vertices and comparing their current locations with the target CAD shape. The displacement for internal vertices is not yet included. A new example, t8_cmesh_mesh_deformation_example.cxx, was added to show how the deformation works.

All these boxes must be checked by the AUTHOR before requesting review:

The PR is small enough to be reviewed easily. If not, consider splitting up the changes in multiple PRs.
The title starts with one of the following prefixes: Documentation:, Bugfix:, Feature:, Improvement: or Other:.
If the PR is related to an issue, make sure to link it.
The author made sure that, as a reviewer, he/she would check all boxes below.

All these boxes must be checked by the REVIEWERS before merging the pull request:

As a reviewer please read through all the code lines and make sure that the code is fully understood, bug free, well-documented and well-structured.

General

The reviewer executed the new code features at least once and checked the results manually.
The code follows the t8code coding guidelines.
New source/header files are properly added to the CMake files.
The code is well documented. In particular, all function declarations, structs/classes and their members have a proper doxygen documentation. Make sure to add a file documentation for each file!
All new algorithms and data structures are sufficiently optimal in terms of memory and runtime (If this should be merged, but there is still potential for optimization, create a new issue).

Tests

The code is covered in an existing or new test case using Google Test.
The code coverage of the project (reported in the CI) should not decrease. If coverage is decreased, make sure that this is reasonable and acceptable.
Valgrind doesn't find any bugs in the new code. This script can be used to check for errors; see also this wiki article.

If the Pull request introduces code that is not covered by the github action (for example coupling with a new library):

Should this use case be added to the github action?
If not, does the specific use case compile and all tests pass (check manually).

Scripts and Wiki

If a new directory with source files is added, it must be covered by the script/find_all_source_files.scp to check the indentation of these files.
If this PR introduces a new feature, it must be covered in an example or tutorial and a Wiki article.

License

The author added a BSD statement to doc/ (or already has one).

codecov · 2026-03-16T17:38:37Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.42%. Comparing base (3ed7e51) to head (374ecd6).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2196   +/-   ##
=======================================
  Coverage   79.42%   79.42%           
=======================================
  Files         115      115           
  Lines       19285    19285           
=======================================
  Hits        15318    15318           
  Misses       3967     3967

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

sandro-elsweijer · 2026-03-17T12:30:06Z

@@ -0,0 +1,121 @@
+#include <fstream>


Please include the license statement and file documentation

sandro-elsweijer · 2026-03-17T12:32:33Z

+#include <fstream>
+#include <iostream>
+#include <string>
+#include <algorithm>
+#include <t8_cmesh/t8_cmesh.h>
+#include <t8_cmesh/t8_cmesh.hxx>
+#include <t8_cmesh/t8_cmesh_vertex_connectivity/t8_cmesh_vertex_connectivity.hxx>
+#include <t8_cmesh/t8_cmesh_mesh_deformation/t8_cmesh_mesh_deformation.hxx>
+#include <t8_schemes/t8_default/t8_default.hxx>
+#include <t8_cmesh/t8_cmesh_io/t8_cmesh_readmshfile.h>
+#include <t8_cad/t8_cad_handle.hxx>
+#include <t8_vtk/t8_vtk_writer.h>
+#include <vector>
+#include <array>
+#include <mpi.h>
+#include <unordered_set>
+#include <sc_options.h>


Do you really need all those includes?
Can you also split them between t8code and std includes?

sandro-elsweijer · 2026-03-17T12:36:38Z

+  SC_CHECK_MPI (mpiret);
+
+  /* Initialize the sc library, has to happen before we initialize t8code. */
+  sc_init (sc_MPI_COMM_WORLD, 1, 1, NULL, SC_LP_PRODUCTION);


Suggested change

sc_init (sc_MPI_COMM_WORLD, 1, 1, NULL, SC_LP_PRODUCTION);

sc_init (sc_MPI_COMM_WORLD, 1, 1, NULL, SC_LP_ESSENTIAL);

sandro-elsweijer · 2026-03-17T12:52:53Z

+  /** Update the CAD manager with a new one. 
+   * \param[in] new_cad_handle The new CAD handle to be used.
+   */


Suggested change

/** Update the CAD manager with a new one.

* \param[in] new_cad_handle The new CAD handle to be used.

*/

/** Update the CAD handle with a new one.

* \param[in] new_cad_handle The new CAD handle to be used.

*/

sandro-elsweijer · 2026-03-17T12:53:50Z

    t8_forest/t8_forest_partition_for_coarsening.cxx
    t8_forest/t8_forest_pfc_helper.cxx
-    t8_forest/t8_forest.cxx
+    t8_forest/t8_forest.cxx  


Suggested change

t8_forest/t8_forest.cxx

t8_forest/t8_forest.cxx

sandro-elsweijer · 2026-03-17T12:54:14Z

  /* Moving plane loop */
  while (adapt_data.t < steps) {
-    /* Adapt and balance the forest.
+    /* Adapt and balance the forest. 


Suggested change

/* Adapt and balance the forest.

/* Adapt and balance the forest.

sandro-elsweijer · 2026-03-17T12:54:27Z

+#include <t8_geometry/t8_geometry_implementations/t8_geometry_cad.hxx>      /* Curved geometry calculation of trees */
+#include <t8_cmesh/t8_cmesh_mesh_deformation/t8_cmesh_mesh_deformation.hxx> /* Mesh deformation struct */
+#include <t8_cad/t8_cad_handle.hxx>                                         /* CAD data structure */


Suggested change

#include <t8_geometry/t8_geometry_implementations/t8_geometry_cad.hxx> /* Curved geometry calculation of trees */

#include <t8_cmesh/t8_cmesh_mesh_deformation/t8_cmesh_mesh_deformation.hxx> /* Mesh deformation struct */

#include <t8_cad/t8_cad_handle.hxx> /* CAD data structure */

#include <t8_geometry/t8_geometry_implementations/t8_geometry_cad.hxx> /* Curved geometry calculation of trees */

sandro-elsweijer · 2026-03-25T14:47:23Z

@@ -0,0 +1,156 @@
+


Suggested change

sandro-elsweijer · 2026-03-25T14:48:04Z

+  sc_options_destroy (opt);
+
+#else
+  t8_global_productionf ("\n\t ERROR: This example requires OpenCASCADE support to be enabled in t8code.\n\n");


Suggested change

t8_global_productionf ("\n\t ERROR: This example requires OpenCASCADE support to be enabled in t8code.\n\n");

t8_global_errorf ("ERROR: This example requires OpenCASCADE support to be enabled in t8code.\n");

sandro-elsweijer · 2026-03-25T14:49:12Z

+    /* Cleanup. */
+    t8_forest_unref (&forest);
+
+    std::cout << "Mesh deformation completed." << std::endl;


Suggested change

std::cout << "Mesh deformation completed." << std::endl;

t8_global_productionf ("Mesh deformation completed.");

sandro-elsweijer · 2026-03-25T15:09:57Z

+    /* The usage string or help message was truncated */
+    /* Note: gcc >= 7.1 prints a warning if we 
+     * do not check the return value of snprintf. */
+    t8_debugf ("Warning: Truncated usage string and help message to '%s' and '%s'\n", usage, help);


Suggested change

t8_debugf ("Warning: Truncated usage string and help message to '%s' and '%s'\n", usage, help);

t8_debugf ("WARNING: Truncated usage string and help message to '%s' and '%s'\n", usage, help);

sandro-elsweijer · 2026-03-26T10:00:17Z

+  /* Initialize t8code with log level SC_LP_ESSENTIAL. See sc.h for more info on the log levels. */
+  t8_init (SC_LP_ESSENTIAL);
+
+#ifdef T8CODE_ENABLE_OCC


Suggested change

#ifdef T8CODE_ENABLE_OCC

#if T8CODE_ENABLE_OCC

sandro-elsweijer · 2026-03-26T10:00:55Z

+  int dim = 0;
+  int level = 2;


The default values are assigned by the options

Suggested change

int dim = 0;

int level = 2;

int dim, level;

… deformation example

sandro-elsweijer · 2026-03-30T06:30:58Z

+#if T8CODE_ENABLE_OCC
+#include <t8_cad/t8_cad_handle.hxx>
+#include <t8_cmesh/t8_cmesh_mesh_deformation/t8_cmesh_mesh_deformation.hxx>
+#endif


Suggested change

#endif

#endif /* T8CODE_ENABLE_OCC */

sandro-elsweijer · 2026-03-30T06:31:24Z

+  mpiret = sc_MPI_Finalize ();
+  SC_CHECK_MPI (mpiret);
+
+#else


Suggested change

#else

#else /* !T8CODE_ENABLE_OCC */

sandro-elsweijer · 2026-03-30T06:31:32Z

+
+#else
+  t8_global_errorf ("ERROR: This example requires OpenCASCADE support to be enabled in t8code.\n\n");
+#endif


Suggested change

#endif

#endif /* T8CODE_ENABLE_OCC */

sandro-elsweijer · 2026-03-30T06:31:45Z

+  SC_CHECK_MPI (mpiret);
+
+#else
+  t8_global_errorf ("ERROR: This example requires OpenCASCADE support to be enabled in t8code.\n\n");


Suggested change

t8_global_errorf ("ERROR: This example requires OpenCASCADE support to be enabled in t8code.\n\n");

t8_global_errorf ("ERROR: This example requires OpenCASCADE support to be enabled in t8code.\n");

sandro-elsweijer · 2026-03-30T06:36:25Z

+#if T8_ENABLE_DEBUG
+    /* Iterate over all trees and compare to the reference tree. */
+    for (const auto &[tree_id, local_corner_index] : tree_list) {
+
+      const int *geom_attribute = static_cast<const int *> (
+        t8_cmesh_get_attribute (associated_cmesh, t8_get_package_id (), T8_CMESH_NODE_GEOMETRY_ATTRIBUTE_KEY, tree_id));
+
+      const int entity_dim = geom_attribute[2 * local_corner_index];
+      const int entity_tag = geom_attribute[2 * local_corner_index + 1];
+
+      /* Check if the attribute of the vertex is the same in all trees. */
+      if (!(entity_dim == first_tree_entity_dim && entity_tag == first_tree_entity_tag)) {
+        t8_errorf (
+          "Error: Inconsistent entity info for global vertex %li: tree %d: dim=%d tag=%d, expected dim=%d tag=%d\n",
+          global_vertex_id, tree_id, entity_dim, entity_tag, first_tree_entity_dim, first_tree_entity_tag);
+        SC_ABORTF ("Inconsistency in vertex info.\n");
+      }
+    }
+#endif /*T8_ENABLE_DEBUG */


Can you add a comment at the start explaining what this check does?

sandro-elsweijer

almost there!

sandro-elsweijer · 2026-04-28T08:35:25Z

+  /* Initialize t8code with log level SC_LP_ESSENTIAL. See sc.h for more info on the log levels. */
+  t8_init (SC_LP_ESSENTIAL);


With this log level your t8_productionf prints wont work.

Suggested change

/* Initialize t8code with log level SC_LP_ESSENTIAL. See sc.h for more info on the log levels. */

t8_init (SC_LP_ESSENTIAL);

/* Initialize t8code with log level SC_LP_PRODUCTION. See sc.h for more info on the log levels. */

t8_init (SC_LP_PRODUCTION);

sandro-elsweijer · 2026-04-28T08:40:19Z

+    t8_global_errorf ("ERROR: Invalid mesh dimension: dim=%d. Dimension must be 1, 2 or 3.\n\n", dim);
+    sc_options_print_usage (t8_get_package_id (), SC_LP_ERROR, opt, NULL);
+  }
+  else if (parsed >= 0) {


What would happen if parsed was -1? The program would terminate and the user has no clue why

Suggested change

else if (parsed >= 0) {

else {

sandro-elsweijer · 2026-04-28T08:40:54Z

+    t8_global_productionf ("%s\n", help);
+    sc_options_print_usage (t8_get_package_id (), SC_LP_ERROR, opt, NULL);
+  }
+  else if (msh_file == NULL || brep_file == NULL || dim == 0) {


if the user provides unknown options this also is a wrong usage

Suggested change

else if (msh_file == NULL || brep_file == NULL || dim == 0) {

else if (msh_file == NULL || brep_file == NULL || dim == 0 || parsed >= 0) {

sandro-elsweijer · 2026-04-28T08:42:52Z

+    sc_options_print_usage (t8_get_package_id (), SC_LP_ERROR, opt, NULL);
+  }
+  else if (msh_file == NULL || brep_file == NULL || dim == 0) {
+    t8_global_errorf ("ERROR: Missing required arguments: -m, -b, and -d are mandatory.\n\n");


We would have to keep this list updated twice, once in the options and once in this message. But the list is also in the usage you print in the next line

Suggested change

t8_global_errorf ("ERROR: Missing required arguments: -m, -b, and -d are mandatory.\n\n");

t8_global_errorf ("\n\t ERROR: Wrong usage.\n\n");

sandro-elsweijer · 2026-04-28T08:46:23Z

+      /* Check if the coordinates are available. */
+      if (old_coords == nullptr) {
+        t8_errorf ("Error: Coordinates attribute missing for tree %d\n.", first_tree_id);
+        SC_ABORTF ("Vertex coordinates are missing.");


Suggested change

SC_ABORTF ("Vertex coordinates are missing.");

SC_ABORTF ("Vertex coordinates are missing.\n");

sandro-elsweijer · 2026-04-28T08:46:32Z

+      /* Check if the (u,v)-parameters are available. */
+      if (uv_attribute == nullptr) {
+        t8_errorf ("Error: (u,v)-parameters are missing for tree %d\n.", first_tree_id);
+        SC_ABORT ("(u,v)-parameters are missing.");


Suggested change

SC_ABORT ("(u,v)-parameters are missing.");

SC_ABORT ("(u,v)-parameters are missing.\n");

sandro-elsweijer · 2026-04-28T08:46:46Z

+    /* Check if the geometry attribute is available for this tree. */
+    if (first_tree_geom_attribute == nullptr) {
+      t8_errorf ("Error: Geometry attribute missing for tree %d\n.", first_tree_id);
+      SC_ABORTF ("Geometry attribute is missing.");


Suggested change

SC_ABORTF ("Geometry attribute is missing.");

SC_ABORTF ("Geometry attribute is missing.\n");

Lena-Richter and others added 8 commits February 25, 2026 14:54

Implement mesh deformation: add new file and adjust related code

52dbb3d

implement sc_options for command line

afee13d

fix doxygen warnings

04959e2

fix doxygen warnings again

820f1e7

add doxygen file header for mesh deformation

bd3f549

Merge branch 'main' into feature-mesh_deformation

2d3af8f

add missing documentation for cad manager and iterators

fa8e214

Merge branch 'main' into feature-mesh_deformation

59a421e

Lena-Richter changed the title ~~Feature mesh deformation~~ Feature: Feature mesh deformation Mar 8, 2026

Lena-Richter marked this pull request as ready for review March 8, 2026 20:18

Lena-Richter marked this pull request as draft March 9, 2026 18:19

Lena-Richter added 2 commits March 9, 2026 20:24

add T8_ENABLE_OCC guards to t8_cad class

f0b2182

chore: restart CI tests

f13f6fb

Lena-Richter marked this pull request as ready for review March 10, 2026 20:00

Lena-Richter marked this pull request as draft March 10, 2026 21:06

Lena-Richter added 3 commits March 11, 2026 17:54

compile mesh deformation only if OCC is enabled

6a8cafa

merge main and resolve conflicts

1749a48

fix doxygen param name in t8_geometry_cad

7214e89

Lena-Richter marked this pull request as ready for review March 12, 2026 19:58

Merge branch 'main' into feature-mesh_deformation

8105450

spenke91 assigned sandro-elsweijer Mar 16, 2026

spenke91 requested a review from sandro-elsweijer March 16, 2026 14:38

Lena-Richter and others added 3 commits March 16, 2026 18:04

Merge branch 'main' into feature-mesh_deformation

8b535bb

move deformation logic to member functions

c11a6cc

fix gp_Pnt.hxx error

3f4fe39

Lena-Richter added 2 commits March 16, 2026 19:20

fix gp_Pnt.hxx error for example

b20b36a

fix MPI error for example

53a09de

sandro-elsweijer requested changes Mar 17, 2026

View reviewed changes

sandro-elsweijer assigned Lena-Richter Mar 17, 2026

sandro-elsweijer removed their assignment Mar 17, 2026

Lena-Richter and others added 2 commits March 23, 2026 16:06

Merge branch 'main' into feature-mesh_deformation

c99f5b5

address review comments for mesh deformation and clean up

b82fa7e

Lena-Richter assigned sandro-elsweijer and unassigned Lena-Richter Mar 25, 2026

sandro-elsweijer requested changes Mar 26, 2026

View reviewed changes

Lena-Richter added 2 commits March 26, 2026 11:55

clean up mesh deformation example

504e60d

wrap t8_mesm_mesh_deformation.hxx include with OCC guards in the emsh…

78fd6b2

… deformation example

Lena-Richter assigned sandro-elsweijer and unassigned sandro-elsweijer Mar 26, 2026

sandro-elsweijer previously approved these changes Mar 30, 2026

View reviewed changes

sandro-elsweijer assigned Lena-Richter Mar 30, 2026

address review and add comments

14a07c6

Lena-Richter dismissed sandro-elsweijer’s stale review via 14a07c6 March 30, 2026 07:49

Lena-Richter unassigned sandro-elsweijer and Lena-Richter Mar 30, 2026

Merge branch 'main' into feature-mesh_deformation

374ecd6

Lena-Richter assigned sandro-elsweijer Apr 24, 2026

sandro-elsweijer approved these changes Apr 28, 2026

View reviewed changes

sandro-elsweijer assigned Lena-Richter and unassigned sandro-elsweijer Apr 28, 2026

	sc_init (sc_MPI_COMM_WORLD, 1, 1, NULL, SC_LP_PRODUCTION);
	sc_init (sc_MPI_COMM_WORLD, 1, 1, NULL, SC_LP_ESSENTIAL);

	/* Adapt and balance the forest.
	/* Adapt and balance the forest.

	t8_global_productionf ("\n\t ERROR: This example requires OpenCASCADE support to be enabled in t8code.\n\n");
	t8_global_errorf ("ERROR: This example requires OpenCASCADE support to be enabled in t8code.\n");

	std::cout << "Mesh deformation completed." << std::endl;
	t8_global_productionf ("Mesh deformation completed.");

	t8_debugf ("Warning: Truncated usage string and help message to '%s' and '%s'\n", usage, help);
	t8_debugf ("WARNING: Truncated usage string and help message to '%s' and '%s'\n", usage, help);

		/* Initialize t8code with log level SC_LP_ESSENTIAL. See sc.h for more info on the log levels. */
		t8_init (SC_LP_ESSENTIAL);

	else if (msh_file == NULL \|\| brep_file == NULL \|\| dim == 0) {
	else if (msh_file == NULL \|\| brep_file == NULL \|\| dim == 0 \|\| parsed >= 0) {

	t8_global_errorf ("ERROR: Missing required arguments: -m, -b, and -d are mandatory.\n\n");
	t8_global_errorf ("\n\t ERROR: Wrong usage.\n\n");

	SC_ABORTF ("Vertex coordinates are missing.");
	SC_ABORTF ("Vertex coordinates are missing.\n");

	SC_ABORT ("(u,v)-parameters are missing.");
	SC_ABORT ("(u,v)-parameters are missing.\n");

	SC_ABORTF ("Geometry attribute is missing.");
	SC_ABORTF ("Geometry attribute is missing.\n");

Conversation

Lena-Richter commented Mar 2, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

General

Tests

Scripts and Wiki

License

Uh oh!

codecov Bot commented Mar 16, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Lena-Richter commented Mar 2, 2026 •

edited

Loading

codecov Bot commented Mar 16, 2026 •

edited

Loading