Issue 1593 part 3 - Reads attenuation database by Rohit-Kakodkar · Pull Request #1628 · PrincetonUniversity/SPECFEMPP

Rohit-Kakodkar · 2026-02-03T17:00:13Z

Description

Refactors materials reader
Reads attenuation props
Adds a test for acoustic elastic w attenuation
Adds a test for poroelastic w attenuation

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

- [x] Refactors materials reader - [x] Reads attenuation props - [x] Adds a test for acoustic elastic w attenuation

- Updates ``TYPE_MATCH`` and ``SEQ_FOR_TAGS`` macros so that they are not dependent on naming schemes

Copilot

Pull request overview

Adds support for reading constant isotropic attenuation parameters from mesh material databases (2D and 3D), and introduces new 2D unit-test meshes/configurations to exercise attenuation reading.

Changes:

Refactors 2D material reading to populate a unified materials container via add_material() and to recognize constant isotropic attenuation.
Extends material/container plumbing to track attenuation tags and adds a debug materials::print() implementation (dim2).
Adds new 2D attenuation test datasets and new mesh test cases (acoustic/elastic and poroelastic).

Reviewed changes

Copilot reviewed 24 out of 27 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
tests/unit-tests/mesh/dim2/test_config.yaml	Adds new dim2 mesh test cases including attenuation datasets; re-enables EM mesh test entry.
tests/unit-tests/mesh/dim2/materials/properties.cpp	Changes derived-properties test behavior when ground truth is missing.
tests/unit-tests/mesh/dim2/materials/materials.cpp	Adds ground-truth expectations for attenuation materials; expands attenuation-tag iteration.
core/specfem/mesh/dim2/materials/materials.hpp	Adds `add_material()`, adds constant attenuation tag handling, adds `print()` declaration, ctor change.
core/specfem/mesh/dim2/materials/materials.cpp	Implements `materials<dim2>::print()`.
core/specfem/mesh/dim3/materials/materials.hpp	Initializes `n_materials` fields; expands to support constant attenuation containers.
core/specfem/io/mesh/impl/fortran/dim2/read_material_properties.cpp	Refactors dim2 materials reading to use `materials.add_material()` and handle attenuation.
core/specfem/io/mesh/impl/fortran/dim2/mesh.cpp	Updates material counting iteration to include constant attenuation tags.
core/specfem/io/mesh/impl/fortran/dim3/read_materials.cpp	Adds support for reading constant isotropic attenuation for acoustic/elastic in 3D.
core/specfem/medium/dim2/*/material.hpp	Adds default ctors for attenuation value structs.
core/specfem/macros/material_iterators.hpp	Removes unsupported constant-attenuation combinations from MATERIAL_SYSTEMS_DIM2.
tests/unit-tests/data/dim2/*	Adds new attenuation mesh datasets and provenance inputs (poroelastic + fluid/solid).

Comments suppressed due to low confidence (1)

core/specfem/io/mesh/impl/fortran/dim2/mesh.cpp:202

This FOR_EACH_IN_PRODUCT includes CONSTANT_ISOTROPIC for electromagnetic_te and elastic_psv_t/isotropic_cosserat combinations, but those medium_container::material specializations don't exist. This will not compile once the macro expands. Iterate only over supported material systems (e.g., MATERIAL_SYSTEMS_DIM2) or otherwise exclude unsupported medium/property combinations from the attenuation cartesian product.

  FOR_EACH_IN_PRODUCT(
      (DIMENSION_TAG(DIM2),
       MEDIUM_TAG(ELASTIC_PSV, ELASTIC_SH, ACOUSTIC, POROELASTIC, ELASTIC_PSV_T,
                  ELECTROMAGNETIC_TE),
       PROPERTY_TAG(ISOTROPIC, ANISOTROPIC, ISOTROPIC_COSSERAT),
       ATTENUATION_TAG(NONE, CONSTANT_ISOTROPIC)),
      {
        total_materials_read += mesh.materials
                                    .get_container<_medium_tag_, _property_tag_,
                                                   _attenuation_tag_>()
                                    .element_materials.size();
      })

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Copilot · 2026-02-03T21:47:17Z

tests/unit-tests/mesh/dim2/materials/properties.cpp

      const auto computed = mesh.materials;
+
+      // Check if Test.name is in properties_ground_truth
+      if (properties_ground_truth.find(Test.name) ==
+          properties_ground_truth.end()) {
+        std::ostringstream message;
+        message << "No ground truth available for properties of test '"
+                << Test.name << "' [" << __FILE__ << ":" << __LINE__ << "]\n";
+        specfem::Logger::info(message.str());
+        continue;
+      }


The test now logs and continues when no ground-truth entry exists for a test name. This makes it easy for new/renamed tests (including the newly added attenuation cases) to silently skip validation and still pass CI, reducing the value of the unit test. Prefer failing the test when ground truth is missing, or add ground-truth entries for the new attenuation meshes (even if the derived properties are identical to the non-attenuation cases).

Copilot · 2026-02-03T21:47:18Z

tests/unit-tests/mesh/dim2/materials/materials.cpp

                    ELASTIC_PSV_T, ELECTROMAGNETIC_TE),
         PROPERTY_TAG(ISOTROPIC, ANISOTROPIC, ISOTROPIC_COSSERAT),
-         ATTENUATION_TAG(NONE)),
+         ATTENUATION_TAG(NONE, CONSTANT_ISOTROPIC)),


The ATTENUATION_TAG cartesian product was expanded to include CONSTANT_ISOTROPIC for all medium/property combinations, which will instantiate unsupported material types (e.g., electromagnetic_te + constant_isotropic, elastic_psv_t/isotropic_cosserat + constant_isotropic). Those medium_container::material specializations don't exist, so this macro expansion will not compile. Limit iteration to supported material systems (e.g., MATERIAL_SYSTEMS_DIM2) or explicitly exclude unsupported combinations.

Suggested change

ATTENUATION_TAG(NONE, CONSTANT_ISOTROPIC)),

ATTENUATION_TAG(NONE)),

Copilot · 2026-02-03T21:47:18Z

core/specfem/io/mesh/impl/fortran/dim2/read_material_properties.cpp

    std::ifstream &stream, const int numat,
    const specfem::enums::elastic_wave elastic_wave,
    const specfem::enums::electromagnetic_wave electromagnetic_wave,
-    specfem::mesh::materials<specfem::dimension::type::dim2>::material<
-        acoustic, isotropic, no_attenuation> &acoustic_isotropic,
-    specfem::mesh::materials<specfem::dimension::type::dim2>::material<
-        elastic_psv, isotropic, no_attenuation> &elastic_psv_isotropic,
-    specfem::mesh::materials<specfem::dimension::type::dim2>::material<
-        elastic_sh, isotropic, no_attenuation> &elastic_sh_isotropic,
-    specfem::mesh::materials<specfem::dimension::type::dim2>::material<
-        elastic_psv, anisotropic, no_attenuation> &elastic_psv_anisotropic,
-    specfem::mesh::materials<specfem::dimension::type::dim2>::material<
-        elastic_sh, anisotropic, no_attenuation> &elastic_sh_anisotropic,
-    specfem::mesh::materials<specfem::dimension::type::dim2>::material<
-        poroelastic, isotropic, no_attenuation> &poroelastic_isotropic,
-    specfem::mesh::materials<specfem::dimension::type::dim2>::material<
-        electromagnetic_te, isotropic, no_attenuation>
-        &electromagnetic_te_isotropic,
-    specfem::mesh::materials<specfem::dimension::type::dim2>::material<
-        elastic_psv_t, isotropic_cosserat, no_attenuation>
-        &elastic_psv_t_isotropic_cosserat) {
+    specfem::mesh::materials<specfem::dimension::type::dim2> &materials) {

  // Define the elastic medium tag based on input elastic wave type
  const specfem::element::medium_tag elastic = [elastic_wave]() {


Within this refactor, electromagnetic_wave is validated via an immediately-invoked lambda (see the local electromagnetic = [electromagnetic_wave](){...}();) that throws for TM even if the database contains no electromagnetic materials, and the resulting variable is unused. That means non-EM runs can fail just because the config selects TM. Remove the unused variable and only validate/branch on electromagnetic_wave inside the indic == 4 (electromagnetic) parsing path.

lsawade

I didn't catch the add_material member in 3D when you originally implemented it. Nice!

Refactor implementation macros

Rohit-Kakodkar and others added 3 commits February 3, 2026 07:44

Issue 1593 - 3 - Read the database

d23889b

- [x] Refactors materials reader - [x] Reads attenuation props - [x] Adds a test for acoustic elastic w attenuation

Updated database

f0b8cff

Fixed tests | added poroelastic test

bde990c

Rohit-Kakodkar requested review from icui and lsawade February 3, 2026 17:00

Refactor implementation macros

9e6b3dc

- Updates ``TYPE_MATCH`` and ``SEQ_FOR_TAGS`` macros so that they are not dependent on naming schemes

Rohit-Kakodkar added the enhancement New feature or request label Feb 3, 2026

Merge branch 'devel' into issue-1593-part-3

decc4b7

Copilot AI review requested due to automatic review settings February 3, 2026 21:38

Copilot started reviewing on behalf of Rohit-Kakodkar February 3, 2026 21:39 View session

Copilot AI reviewed Feb 3, 2026

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icui approved these changes Feb 4, 2026

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lsawade approved these changes Feb 4, 2026

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Rohit-Kakodkar added 3 commits February 5, 2026 10:25

Merge pull request #1629 from PrincetonUniversity/refactor-impl-macro

d73e820

Refactor implementation macros

Merge branch 'devel' into issue-1593-part-3

d579eeb

Fixed compilation

8bffee0

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Issue 1593 part 3 - Reads attenuation database#1628

Issue 1593 part 3 - Reads attenuation database#1628
Rohit-Kakodkar wants to merge 8 commits intodevelfrom
issue-1593-part-3

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	ATTENUATION_TAG(NONE, CONSTANT_ISOTROPIC)),
	ATTENUATION_TAG(NONE)),

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Rohit-Kakodkar commented Feb 3, 2026

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