1675 cosserat implementation - Base branch by Rohit-Kakodkar · Pull Request #1753 · PrincetonUniversity/SPECFEMPP

Rohit-Kakodkar · 2026-03-25T13:13:26Z

Description

Creates a temporary branch for cosserat mesh. @maxlchien

Issue Number

If there is an issue created for these changes, link it here

Checklist

Please make sure to check developer documentation on specfem docs.

I ran the code through pre-commit to check style
THE DOCUMENTATION BUILDS WITHOUT WARNINGS/ERRORS
I have added labels to the PR (see right hand side of the PR page)
My code passes all the integration tests
I have added sufficient unittests to test my changes
I have added/updated documentation for the changes I am proposing
I have updated CMakeLists to ensure my code builds
My code builds across all platforms

…cept for receivers.hpp, receivers.cpp, info.tpp, and boundary_medium_container.hpp (see next commit)

…ls when reading mesh

… from issue #1675)

… is implemented

)

…until #1739 is merged)

1675 read cosserat mesh

Update Fortran 3D mesher to accommodate isotropic Cosserat

Copilot

Pull request overview

Adds a new 3D “EightNodeElasticCosserat” mesh test case and wires up dim3 material/tag plumbing so Cosserat (elastic spin + isotropic Cosserat) meshes can be exercised by the unit-test suite.

Changes:

Extend dim3 unit-test parameterization and expected-results maps to include EightNodeElasticCosserat.
Add dim3 Cosserat material container instantiations and a new material_id parsing branch in the Fortran mesh reader.
Add a new dim3 test dataset directory (provenance + generated database.bin) and a Snakemake workflow to regenerate it.

Reviewed changes

Copilot reviewed 18 out of 19 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
tests/unit-tests/mesh/dim3/test.cpp	Adds `EightNodeElasticCosserat` to the parameterized dim3 mesh test suite.
tests/unit-tests/mesh/dim3/tags.cpp	Adds expected tag entries for Cosserat elements.
tests/unit-tests/mesh/dim3/mesh.cpp	Adds expected mesh-size entry for the Cosserat dataset.
tests/unit-tests/mesh/dim3/materials.cpp	Adds expected Cosserat material entries.
tests/unit-tests/mesh/dim3/control_nodes.cpp	Adds expected control-node entry for the Cosserat dataset.
tests/unit-tests/mesh/dim3/boundaries.cpp	Adds expected boundary-face entry for the Cosserat dataset.
tests/unit-tests/mesh/dim3/adjacency_graph.cpp	Adds expected adjacency entry for the Cosserat dataset.
tests/unit-tests/data/dim3/EightNodeElasticCosserat/provenance/interfaces.txt	Adds provenance input describing interfaces for the Cosserat mesh.
tests/unit-tests/data/dim3/EightNodeElasticCosserat/provenance/interface1.txt	Adds provenance interface elevation file.
tests/unit-tests/data/dim3/EightNodeElasticCosserat/provenance/Mesh_Par_file	Adds provenance mesher parameter file for generating the Cosserat mesh.
tests/unit-tests/data/dim3/EightNodeElasticCosserat/database.bin	Adds the generated mesh database used by unit tests.
tests/unit-tests/data/dim3/EightNodeElasticCosserat/Snakefile	Adds a workflow to regenerate `database.bin`.
tests/unit-tests/data/dim3/EightNodeElasticCosserat/.gitignore	Ignores Snakemake’s executable check artifact.
core/specfem/mesh/dim3/materials/materials.hpp	Instantiates dim3 material containers/accessors for `elastic_spin` + `isotropic_cosserat`.
core/specfem/io/mesh/impl/fortran/dim3/read_materials.cpp	Adds parsing for Cosserat material ID and fixes an acoustic/elastic Vs error message.

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Copilot · 2026-03-25T13:22:21Z

@@ -190,8 +192,8 @@ template <> struct materials<specfem::element::dimension_tag::dim3> {
   * - Integration with SPECFEM++ template metaprogramming patterns
   */
  FOR_EACH_IN_PRODUCT(
-      (DIMENSION_TAG(DIM3), MEDIUM_TAG(ACOUSTIC, ELASTIC),
-       PROPERTY_TAG(ISOTROPIC, ANISOTROPIC),
+      (DIMENSION_TAG(DIM3), MEDIUM_TAG(ACOUSTIC, ELASTIC, ELASTIC_SPIN),
+       PROPERTY_TAG(ISOTROPIC, ANISOTROPIC, ISOTROPIC_COSSERAT),
       ATTENUATION_TAG(NONE, CONSTANT_ISOTROPIC)),


This doc block (and the @tparam descriptions in this struct) still describes only acoustic/elastic + isotropic/anisotropic combinations, but the implementation now supports elastic_spin and isotropic_cosserat. Please update the parameter/docs list so it matches the actual supported material systems in dim3.

Copilot · 2026-03-25T13:22:21Z

+          material(rho, kappa, mu, nu, j, lambda_c, mu_c, nu_c);
+      const int index = materials.add_material(material);
+      mapping.push_back({ specfem::element::medium_tag::elastic_spin,
+                          specfem::element::property_tag::isotropic_cosserat,
+                          specfem::element::attenuation_tag::none, index,
+                          imat });
+    }
    default:
      throw std::runtime_error("Unknown material ID: " +
                               std::to_string(material_id));


case 4 (Cosserat) falls through into default because it’s missing a break; at the end of the case block. As written, Cosserat materials will always be parsed and then immediately trigger the "Unknown material ID" exception.

Copilot · 2026-03-25T13:22:21Z

+      if (mu < 0.0 || mu_c < 0.0 || 3 * lambda + 2 * mu < 0.0 ||
+          3 * lambda_c + 2 * mu_c < 0.0) {
+        throw std::runtime_error(
+            "Invalid elastic parameters for Cosserat material. u, mu_c, "
+            "3*lambda + 2*mu, and 3*lambda_c + 2*mu_c must be non-negative.");


The Cosserat validation error message has a typo and is a bit unclear: it says "u" but the variable is mu. Consider correcting the parameter name(s) in the message (and potentially include the offending values) to make debugging material files easier.

Suggested change

if (mu < 0.0 || mu_c < 0.0 || 3 * lambda + 2 * mu < 0.0 ||

3 * lambda_c + 2 * mu_c < 0.0) {

throw std::runtime_error(

"Invalid elastic parameters for Cosserat material. u, mu_c, "

"3*lambda + 2*mu, and 3*lambda_c + 2*mu_c must be non-negative.");

const type_real first_combination = static_cast<type_real>(3.0) * lambda +

static_cast<type_real>(2.0) * mu;

const type_real second_combination =

static_cast<type_real>(3.0) * lambda_c +

static_cast<type_real>(2.0) * mu_c;

if (mu < 0.0 || mu_c < 0.0 || first_combination < 0.0 ||

second_combination < 0.0) {

throw std::runtime_error(

"Invalid elastic parameters for Cosserat material. mu, mu_c, "

"3*lambda + 2*mu, and 3*lambda_c + 2*mu_c must be non-negative. " +

std::string("Values are mu=") + std::to_string(mu) +

", mu_c=" + std::to_string(mu_c) +

", 3*lambda + 2*mu=" + std::to_string(first_combination) +

", 3*lambda_c + 2*mu_c=" + std::to_string(second_combination) +

".");

Copilot · 2026-03-25T13:22:22Z

+      {
+          "EightNodeElasticCosserat",
+          ExpectedMaterials3D(
+              TotalMaterials(1, 8),
+              { // Element 0
+                ElementMaterial(
+                    specfem::element::medium_tag::elastic_spin,
+                    specfem::element::property_tag::isotropic_cosserat, 0,
+                    specfem::medium_container::material<
+                        specfem::element::dimension_tag::dim3,
+                        specfem::element::medium_tag::elastic_spin,
+                        specfem::element::property_tag::isotropic_cosserat,
+                        specfem::element::attenuation_tag::none>(
+                        2300.0, 1500.0, 2800.0, 1e6, 1e4, 300.0, 25.0, 500.0)),
+                // Element 5
+                ElementMaterial(
+                    specfem::element::medium_tag::elastic_spin,
+                    specfem::element::property_tag::isotropic_cosserat, 5,
+                    specfem::medium_container::material<
+                        specfem::element::dimension_tag::dim3,
+                        specfem::element::medium_tag::elastic_spin,
+                        specfem::element::property_tag::isotropic_cosserat,
+                        specfem::element::attenuation_tag::none>(
+                        2300.0, 1500.0, 2800.0, 1e6, 1e4, 300.0, 25.0,
+                        500.0)) }),


This new Cosserat test case adds expected elastic_spin/isotropic_cosserat materials, but the current material-comparison logic in ExpectedMaterials3D::check() won’t validate them (the FOR_EACH_IN_PRODUCT call used for comparison doesn’t enumerate any combinations unless it includes an ATTENUATION_TAG(...) list, and it’s also limited to MEDIUM_TAG(ELASTIC)/PROPERTY_TAG(ISOTROPIC)). Please extend the comparison logic to iterate valid (medium, property, attenuation) combinations and validate Cosserat materials too, otherwise this test can pass without actually checking the computed materials.

Copilot · 2026-03-25T13:22:22Z

                                    specfem::element::property_tag::isotropic,
                                    specfem::element::attenuation_tag::none,
-                                    specfem::element::boundary_tag::none) }) }
+                                    specfem::element::boundary_tag::none) }) },


The surrounding documentation says the EightNodeElastic case “Spot-checks elements 0, 1, and 5”, but the expected tag list now only checks elements 0 and 5. Either re-add the element-1 check (to keep coverage consistent) or update the comment block so it matches what the test actually verifies.

Copilot · 2026-03-25T13:22:22Z

@@ -0,0 +1,45 @@
+# Snakemake workflow to generate database for 4-node elastic problem in 3D


The header comment doesn’t match this workflow/test case: it says “4-node elastic problem in 3D”, but this directory is EightNodeElasticCosserat and NGNOD = 8 in the provenance. Please update the comment to avoid confusion when regenerating the database.

Suggested change

# Snakemake workflow to generate database for 4-node elastic problem in 3D

# Snakemake workflow to generate database for 8-node elastic Cosserat problem in 3D

Copilot · 2026-03-25T13:22:22Z

+    shell:
+        "echo 'All tasks completed successfully.'"
+
+rule check_executible:


Typo in the rule name: check_executible should be check_executable (and update any references to it).

Suggested change

rule check_executible:

rule check_executable:

Copilot · 2026-03-25T13:22:23Z

+# define the different materials in the model as:
+# #material_id  #rho  #vp  #vs  #Q_Kappa  #Q_mu  #anisotropy_flag  #domain_id
+#     Q_Kappa          : Q_Kappa attenuation quality factor
+#     Q_mu             : Q_mu attenuation quality factor
+#     anisotropy_flag  : 0 = no anisotropy / 1,2,... check the implementation in file aniso_model.f90
+#     domain_id        : 1 = acoustic / 2 = elastic


The material-format comments are now misleading for this Cosserat case. The line defining the material has more fields than the documented “#rho #vp #vs #Q_Kappa #Q_mu #anisotropy_flag #domain_id”, and domain_id is shown as 4 even though the comment says it’s 1=acoustic / 2=elastic. Please update the inline documentation to reflect the Cosserat material parameter layout used here.

Suggested change

# define the different materials in the model as:

# #material_id #rho #vp #vs #Q_Kappa #Q_mu #anisotropy_flag #domain_id

# Q_Kappa : Q_Kappa attenuation quality factor

# Q_mu : Q_mu attenuation quality factor

# anisotropy_flag : 0 = no anisotropy / 1,2,... check the implementation in file aniso_model.f90

# domain_id : 1 = acoustic / 2 = elastic

# define the different materials in the model as (Cosserat elastic case):

# #material_id #rho #vp #vs #Q_Kappa #Q_mu #cosserat_param_1 #cosserat_param_2 #cosserat_param_3 #domain_id

# Q_Kappa : Q_Kappa attenuation quality factor

# Q_mu : Q_mu attenuation quality factor

# cosserat_param_* : additional Cosserat material parameters (see Cosserat model implementation)

# domain_id : 1 = acoustic / 2 = elastic / 4 = elastic Cosserat

… case

Co-authored-by: Rohit-Kakodkar <40695390+Rohit-Kakodkar@users.noreply.github.com>

…nto 1675-cosserat-mesh

…sts for inverse jacobian

…integrand tests

…rat-mesh

This interface now reuses code when possible, primarily moving to a tensor abstraction. - Store the stress tensor as a tensor type - Implement tensor operators for TensorPointViewType - Update stress and stress integrand routines I have tried to stick with the tests without much overhaul. However with this change the jacobian inverse test can now move to algorithms inverse.

Move stress integrand conversion logic to jacobian inverse

maxlchien and others added 19 commits March 6, 2026 05:43

Update Fortran 3D mesher to accommodate isotropic Cosserat

c8c8be8

Add ELASTIC_SPIN and ISOTROPIC_COSSERAT to all necessary products, ex…

524c248

…cept for receivers.hpp, receivers.cpp, info.tpp, and boundary_medium_container.hpp (see next commit)

Correct IDOMAIN_COSSERAT tag name in meshfem3d

b6fe2f3

Read elastic spin materials

8c6f6b3

Fix initialization parameters and add validation for cosserat materia…

09dcb22

…ls when reading mesh

Add unit tests for mesh reader with new EightNodeElasticCosserat case

9b64416

Merge branch 'devel' into 1676-update-cosserat-assembly

6fe7f14

Add assembly test case for EightNodeElasticCosserat (needs data files…

054159c

… from issue #1675)

Finish adding tag combinations to necessary locations

f199506

Remove tag combination from compute_wavefield, deferred until physics…

9c15ba9

… is implemented

Add unit testing for tag combinations (dependent on the data in pr #1743

1163942

)

Merge branch 'devel' into 1675-read-cosserat-mesh

23addf3

Update meshfem3d docs to add elastic isotropic coserat documentation

d41bd4c

Correct domain id ordering in test data

74dfa99

Remove superfluous line in documentation

233f2e4

Update example in docs

013533e

Register EightNodeElasticCosserat to test to be run (tests will fail …

1b6159b

…until #1739 is merged)

Merge branch 'devel' into 1676-update-cosserat-assembly

bc17ed5

Merge pull request #1743 from maxlchien/1675-read-cosserat-mesh

47b29ad

1675 read cosserat mesh

Copilot AI review requested due to automatic review settings March 25, 2026 13:13

Copilot started reviewing on behalf of Rohit-Kakodkar March 25, 2026 13:14 View session

Merge pull request #1739 from maxlchien/1673-cosserat-mesher-update

5832213

Update Fortran 3D mesher to accommodate isotropic Cosserat

Copilot AI reviewed Mar 25, 2026

View reviewed changes

maxlchien added 3 commits March 25, 2026 11:05

Changes following copilot review

d21a1c5

Edit read_mesh_parameter_file.f90 to handle cosserat

fa29151

Generate database and fix Snakefile for EightNodeElastiCosserat tests…

9a953ab

… case

maxlchien mentioned this pull request Mar 25, 2026

1675 cosserat mesh fixes #1755

Merged

8 tasks

Update tests/unit-tests/mesh/dim3/materials.cpp

2a24e1f

Co-authored-by: Rohit-Kakodkar <40695390+Rohit-Kakodkar@users.noreply.github.com>

icui requested review from icui and lsawade March 27, 2026 13:04

Update test database.

380b230

icui approved these changes Apr 28, 2026

View reviewed changes

maxlchien and others added 10 commits May 5, 2026 05:39

Merge branch '1675-cosserat-mesh' of github.com:maxlchien/SPECFEMPP i…

7cbc054

…nto 1675-cosserat-mesh

Fix Jacobian 3D internal assignment order

040f82d

Fix intrinsic rotation logging bug

fca909f

Merge branch 'devel' into 1675-cosserat-mesh

2459329

Update couple stress logic to use inverted jacobian, and adds unit te…

ee0741b

…sts for inverse jacobian

Fix some logic related to the determinant

4af8317

Add roundtrip stress integrand conversion tests, and cosserat stress …

a07e9dc

…integrand tests

A few includes

bfce018

Merge branch 'devel' into 1675-cosserat-mesh

3fb881c

Merge branch 'PrincetonUniversity:1675-cosserat-mesh' into 1675-cosse…

7f6a79e

…rat-mesh

lsawade approved these changes May 13, 2026

View reviewed changes

Rohit-Kakodkar added 3 commits May 13, 2026 14:20

removed unused member functions

dc4d319

Merge branch 'devel' into 1675-cosserat-mesh

0bbe75f

lsawade added the new physics This labels the introduction of new physics to the code label May 15, 2026

maxlchien and others added 7 commits May 18, 2026 10:13

Remove unused tests

b263949

Merge branch 'devel' into 1675-cosserat-mesh

a8525d4

Added some missing files

f2e89d4

Merge branch '1675-cosserat-mesh' into 1675-cosserat-mesh

0f8c7e0

A few updates for consistency

051028d

Remove superfluous docstring

c189003

Copilot review changes

4e0c038

lsawade linked an issue May 22, 2026 that may be closed by this pull request

Implement 3D Cosserat Media #1672

Open

Rohit-Kakodkar and others added 5 commits May 26, 2026 09:02

Merge pull request #1839 from maxlchien/1675-cosserat-mesh

abfa42a

Move stress integrand conversion logic to jacobian inverse

Merge branch 'devel' into 1675-cosserat-mesh

4c7906d

Merge branch 'devel' into 1675-cosserat-mesh

d49c88a

Merge branch 'devel' into 1675-cosserat-mesh

96852e3

Merge branch 'devel' into 1675-cosserat-mesh

47dcba6

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1675 cosserat implementation - Base branch#1753

1675 cosserat implementation - Base branch#1753
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-      if (mu < 0.0 || mu_c < 0.0 || 3 * lambda + 2 * mu < 0.0 ||
-* lambda_c + 2 * mu_c < 0.0) {
-        throw std::runtime_error(
-            "Invalid elastic parameters for Cosserat material. u, mu_c, "
-            "3*lambda + 2*mu, and 3*lambda_c + 2*mu_c must be non-negative.");
+      const type_real first_combination = static_cast<type_real>(3.0) * lambda +
+                                          static_cast<type_real>(2.0) * mu;
+      const type_real second_combination =
+          static_cast<type_real>(3.0) * lambda_c +
+          static_cast<type_real>(2.0) * mu_c;
+      if (mu < 0.0 || mu_c < 0.0 || first_combination < 0.0 ||
+          second_combination < 0.0) {
+        throw std::runtime_error(
+            "Invalid elastic parameters for Cosserat material. mu, mu_c, "
+            "3*lambda + 2*mu, and 3*lambda_c + 2*mu_c must be non-negative. " +
+            std::string("Values are mu=") + std::to_string(mu) +
+            ", mu_c=" + std::to_string(mu_c) +
+            ", 3*lambda + 2*mu=" + std::to_string(first_combination) +
+            ", 3*lambda_c + 2*mu_c=" + std::to_string(second_combination) +
+            ".");

		@@ -0,0 +1,45 @@
		# Snakemake workflow to generate database for 4-node elastic problem in 3D

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Rohit-Kakodkar commented Mar 25, 2026

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