Consolidated content of too small base classes by merging these definitions into meatier base classes for primitives, further Autumn NIAC 2024 refactoring

atomprobe-tc · atomprobe-tc · commit d892c17f5d3e · 2025-01-10T17:55:36.000+01:00
diff --git a/base_classes/NXcg_geodesic_mesh.nxdl.xml b/base_classes/NXcg_geodesic_mesh.nxdl.xml
diff --git a/base_classes/NXcg_grid.nxdl.xml b/base_classes/NXcg_grid.nxdl.xml
@@ -21,7 +21,7 @@
 #
 # For further information, see http://www.nexusformat.org
 -->
-<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXcg_grid" extends="NXcg_primitive_set" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXcg_grid" extends="NXcg_primitive" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <symbols>
         <doc>
              The symbols used in the schema to specify e.g. dimensions of arrays.
@@ -46,9 +46,10 @@
          Computational geometry description of a grid of Wigner-Seitz cells in Euclidean space.
          
          Three-dimensional grids with cubic cells are if not the most frequently used
-         example of such grids. Examples of numerical methods where grids are used
-         are spectral-solver based crystal plasticity or other stencil methods like
-         phase-field or cellular automata.
+         example of such grids. Numerical methods and models that use grids are used
+         in many cases in the natural sciences and engineering disciplines. Examples are
+         discretizations in space and time used for phase-field, cellular automata, or Monte Carlo
+         modeling.
     </doc>
     <field name="origin" type="NX_NUMBER" units="NX_ANY">
         <doc>
@@ -112,7 +113,7 @@ should constraints on the grid be place here or not-->
         </dimensions>
     </field>
     <!--this should be a ROI-->
-    <group name="bounding_box" type="NXcg_polyhedron_set">
+    <group name="bounding_box" type="NXcg_polyhedron">
         <doc>
              A tight bounding box about the grid.
         </doc>
@@ -152,4 +153,25 @@ https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallele
             <dim index="1" value="n_b"/>
         </dimensions>
     </field>
+    <field name="surface_reconstruction" type="NX_CHAR">
+        <doc>
+             Details about the computational geometry method and implementation
+             used for discretizing internal surfaces as e.g. obtained with marching methods,
+             like marching squares or marching cubes.
+             
+             Documenting which specific version was used helps with understanding how
+             robust the results are with respect to the topology of the triangulation.
+             Reference to the specific implementation of marching cubes used.
+             
+             See for example the following papers for details about how to identify a
+             DOI which specifies the implementation used:
+             
+             * `W. E. Lorensen &lt;https://doi.org/10.1109/MCG.2020.2971284&gt;`_
+             * `T. S. Newman and H. Yi &lt;https://doi.org/10.1016/j.cag.2006.07.021&gt;`_
+             
+             The value placed here should ideally be an identifier of a program.
+             If not possible an identifier for a paper, tech repor, or free-text description
+             is possible.
+        </doc>
+    </field>
 </definition>
diff --git a/base_classes/NXcg_hexahedron.nxdl.xml b/base_classes/NXcg_hexahedron.nxdl.xml
@@ -27,7 +27,7 @@ a polyhedron is a specific polytope in 3d, do we need
 higher-dimensional polytopes? that could be useful for simplicies though
 as they are used in numerics etc. maybe reach out here to our friends
 from MarDI, for now let's assume we do not need polytopes for d > 3-->
-<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXcg_hexahedron_set" extends="NXcg_primitive_set" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXcg_hexahedron" extends="NXcg_primitive" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <symbols>
         <doc>
              The symbols used in the schema to specify e.g. dimensions of arrays.
@@ -65,7 +65,7 @@ from MarDI, for now let's assume we do not need polytopes for d > 3-->
          Hexahedra are important geometrical primitives, which are among the most
          frequently used elements in finite element meshing/modeling.
          
-         As a specialization of the :ref:`NXcg_primitive_set` base class hexahedra
+         As a specialization of the :ref:`NXcg_primitive` base class hexahedra
          are assumed non-degenerated, closed, and built of polygons that are
          not self-intersecting.
          
@@ -169,23 +169,21 @@ from MarDI, for now let's assume we do not need polytopes for d > 3-->
             <dim index="1" value="c"/>
         </dimensions>
     </field>
-    <!--substantially more detailed descriptors of the shape, the mesh
-orientation(NXorientation_set):-->
-    <group name="vertex_normal" type="NXcg_unit_normal_set"/>
-    <group name="edge_normal" type="NXcg_unit_normal_set"/>
-    <group name="face_normal" type="NXcg_unit_normal_set"/>
+    <group name="vertex_normal" type="NXcg_unit_normal"/>
+    <group name="edge_normal" type="NXcg_unit_normal"/>
+    <group name="face_normal" type="NXcg_unit_normal"/>
     <!--detailed mesh-based representation-->
     <group name="hexahedra" type="NXcg_face_list_data_structure">
         <doc>
              Combined storage of all primitives of all hexahedra.
         </doc>
     </group>
-    <group name="hexahedronID" type="NXcg_face_list_data_structure">
+    <group name="hexahedronID" type="NXcg_face_list_data_structure" nameType="partial">
         <doc>
              Individual storage of each hexahedron.
         </doc>
     </group>
-    <group name="hexahedron_half_edgeID" type="NXcg_half_edge_data_structure">
+    <group name="hexahedron_half_edgeID" type="NXcg_half_edge_data_structure" nameType="partial">
         <doc>
              Individual storage of each hexahedron as a graph.
         </doc>
diff --git a/base_classes/NXcg_marching_cubes.nxdl.xml b/base_classes/NXcg_marching_cubes.nxdl.xml
diff --git a/base_classes/NXcg_primitive.nxdl.xml b/base_classes/NXcg_primitive.nxdl.xml
@@ -177,6 +177,52 @@
             <dim index="2" value="d"/>
         </dimensions>
     </field>
+    <field name="is_mesh" type="NX_BOOLEAN">
+      <doc>
+        Do the primitives define a mesh.
+      </doc>
+    </field>
+    <!--<field name="is_triangle_mesh" type="NX_BOOLEAN">
+      <doc>
+        Do the primitives define triangle mesh.
+      </doc>
+    </field>
+    <field name="is_surface_mesh" type="NX_BOOLEAN">
+      <doc>
+        Do the primitives discretize the surface of an object.
+      </doc>
+    </field>-->
+    <field name="is_geodesic_mesh" type="NX_BOOLEAN">
+      <doc>
+         Do the primitives define a geodesic mesh or not.
+         
+         A geodesic surface mesh is a triangulated surface mesh with metadata which
+         can be used as an approximation to describe the surface of a sphere.
+         Triangulation of spheres are commonly used in Materials Science
+         for quantifying texture of materials, i.e. the relative rotation of
+         crystals to sample directions.
+         
+         For additional details or an introduction into the topic of geodesic meshes
+         see (from which specifically the section on subdivision schemes is relevant).
+         
+         * `E. S. Popko and C. J. Kitrick &lt;https://doi.org/10.1201/9781003134114&gt;`_
+         
+         Earth scientists have specific demands and different views about what should
+         be included in such a base class, given that nested geodesic meshes are a key
+         component of climate modelling software. For now we propose to use this
+         base class as a container for organizing data related to geodesic meshes.
+         
+         Specifically an instance of this base class should detail the rule set how
+         e.g. a geodesic (surface) mesh was instantiated as there are many
+         possibilities to do so.
+       </doc>
+    </field>
+    <field name="description">
+      <doc>
+        Possibility to store details such as when primitives form a (specific) type
+        of mesh such as geodesic meshes.
+      </doc>
+    </field>
     <group name="vertex_normal" type="NXcg_unit_normal"/>
     <group name="edge_normal" type="NXcg_unit_normal"/>
     <group name="face_normal" type="NXcg_unit_normal"/>
diff --git a/base_classes/NXcg_unit_normal.nxdl.xml b/base_classes/NXcg_unit_normal.nxdl.xml
@@ -25,7 +25,7 @@
 the benefit of NXcg_point_set is that the origin is 0 by default
 how to resolve the association between the unit normal and its associated primitive?
 rather make this a set of vectors, irrespective whether these are unit or not-->
-<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXcg_unit_normal_set" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXcg_unit_normal" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
     <!--eventually remove this base class and make normal vector a property of the primitive-->
     <symbols>
         <doc>
