feat(topology): vacuum coordinate and multi block

Two major changes in this version. First stroid now embeds a vacuum coordinate as part of its StroidMesh file (this is a packed set of mfem meshes and GridFunction). This is a logical coordinate from 0 at the stellar surface to 1 at the mesh surface / compactified infinity which can be used by consumers to much more stablly infer position in the vacuum region. Second, there is a new topology backend, multi_block, which has been made the default. See the readme for more information but the basic jist is that multi_block addes 6 transition blocks onto the edge of the core domain. This allows for a much more well conditioned transition from the internal cartesien region to the external spherical region. The mesh conditioning improves by roughly a factor of 1000 for the same refinement level when compared to the legacy topology. The legacy topology is maintained as a option if core_mapping is set to spherified in the config.

tests/python/core_mapping_smoke.py

@@ -0,0 +1,126 @@
+"""Focused core-mapping smoke checks for a built or staged STROID Python module.
+
+Example:
+    python core_mapping_smoke.py --module _stroid --module-dir build/build-python
+    python core_mapping_smoke.py --module-dir /path/to/staged/site-packages
+"""
+
+import argparse
+import importlib
+import json
+from pathlib import Path
+import sys
+import tempfile
+
+
+def element_counts(stroid, mesh):
+    result = stroid.stats.ComputeMeshStats(
+        mesh, stroid.stats.MeshStatFeatures.ELEMENT_COUNT
+    )
+    assert not result.errors, result.errors
+    assert result.element_counts is not None
+    return result.element_counts
+
+
+def run(stroid):
+    default = stroid.config.MeshConfig()
+    assert default.core_mapping == "spherified"
+    default.core_mapping = "multi_block"
+    assert default.core_mapping == "multi_block"
+    assert "core_mapping: multi_block" in repr(default)
+
+    summaries = []
+    with tempfile.TemporaryDirectory(prefix="stroid-python-smoke-") as output:
+        output_path = Path(output)
+        config_path = output_path / "multi_block.toml"
+        config_path.write_text(
+            '[main]\ncore_mapping = "multi_block"\nrefinement_levels = 0\n'
+            'order = 3\ninclude_external_domain = false\n'
+            'r_core = 0.25\nr_star = 1.0\nr_infinity = 6.0\n'
+            'flattening = 0.0\nr_instability = 1e-14\n'
+            'core_steepness = 1.0\ncontinuity_order = 2\n'
+            'surface_bdr_id = 1\ninf_bdr_id = 2\n'
+            'core_id = 1\nenvelope_id = 2\nvacuum_id = 3\n'
+            '[main.optimization_methods]\ntmop = false\nsmoothstep = true\n'
+        )
+        configured_mesh = stroid.GenerateMesh(str(config_path))
+        assert configured_mesh.config.core_mapping == "multi_block"
+        assert element_counts(stroid, configured_mesh).total == 13
+
+        for mapping in ("spherified", "multi_block"):
+            for external in (False, True):
+                config = stroid.config.MeshConfig(
+                    core_mapping=mapping,
+                    refinement_levels=0,
+                    order=3,
+                    include_external_domain=external,
+                    optimization_methods=stroid.config.OptimizationMethods(
+                        tmop=False, smoothstep=True
+                    ),
+                )
+                mesh = stroid.GenerateMesh(config)
+                assert mesh.has_mesh() and mesh.has_rmesh()
+                counts = element_counts(stroid, mesh)
+                expected_core = 7 if mapping == "multi_block" else 1
+                expected_total = expected_core + 6 + (6 if external else 0)
+                assert counts.total == expected_total
+                assert counts.core == expected_core
+                assert counts.envelope == 6
+                assert counts.vacuum == (6 if external else 0)
+
+                path = output_path / f"{mapping}-{external}.smesh"
+                stroid.IO.SaveStroidMesh(mesh, str(path), "Python core-mapping smoke")
+                loaded = stroid.IO.LoadStroidMesh(str(path))
+                assert loaded.config.core_mapping == mapping
+                assert element_counts(stroid, loaded).total == expected_total
+
+                stroid.refinement.UniformRefinement(loaded, 1)
+                assert loaded.config.core_mapping == mapping
+                assert loaded.refinement_levels == 1
+                refined_counts = element_counts(stroid, loaded)
+                assert refined_counts.total == expected_total * 8
+                assert refined_counts.core == expected_core * 8
+
+                if mapping == "spherified":
+                    legacy = "\n".join(
+                        line for line in path.read_text().splitlines()
+                        if not line.startswith("core_mapping:")
+                    )
+                    legacy_mesh = stroid.IO.ParseStroidMesh(legacy)
+                    assert legacy_mesh.config.core_mapping == "spherified"
+                    assert element_counts(stroid, legacy_mesh).total == expected_total
+
+                summaries.append({
+                    "mapping": mapping,
+                    "external": external,
+                    "initial_elements": expected_total,
+                    "refined_elements": refined_counts.total,
+                })
+
+        invalid = stroid.config.MeshConfig(
+            core_mapping="unknown", refinement_levels=0
+        )
+        try:
+            stroid.GenerateMesh(invalid)
+        except (ValueError, RuntimeError):
+            pass
+        else:
+            raise AssertionError("Unsupported core_mapping was accepted")
+
+    return summaries
+
+
+def main():
+    parser = argparse.ArgumentParser(description=__doc__)
+    parser.add_argument("--module", default="stroid")
+    parser.add_argument("--module-dir", type=Path)
+    args = parser.parse_args()
+    if args.module_dir is not None:
+        sys.path.insert(0, str(args.module_dir.resolve()))
+    stroid = importlib.import_module(args.module)
+    summaries = run(stroid)
+    print(json.dumps({"module": stroid.__file__, "cases": summaries}, indent=2))
+
+
+if __name__ == "__main__":
+    main()