Fairmat 2024: base classes to describe computational geometry

base_classes/NXcg_alpha_complex.nxdl.xml

@@ -3,7 +3,7 @@
 <!--
 # NeXus - Neutron and X-ray Common Data Format
 #
-# Copyright (C) 2022-2024 NeXus International Advisory Committee (NIAC)
+# Copyright (C) 2022-2025 NeXus International Advisory Committee (NIAC)
 #
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public

base_classes/NXcg_cylinder.nxdl.xml

@@ -3,7 +3,7 @@
 <!--
 # NeXus - Neutron and X-ray Common Data Format
 #
-# Copyright (C) 2022-2024 NeXus International Advisory Committee (NIAC)
+# Copyright (C) 2022-2025 NeXus International Advisory Committee (NIAC)
 #
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public

base_classes/NXcg_ellipsoid.nxdl.xml

@@ -3,7 +3,7 @@
 <!--
 # NeXus - Neutron and X-ray Common Data Format
 #
-# Copyright (C) 2022-2024 NeXus International Advisory Committee (NIAC)
+# Copyright (C) 2022-2025 NeXus International Advisory Committee (NIAC)
 #
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public

base_classes/NXcg_face_list_data_structure.nxdl.xml

@@ -3,7 +3,7 @@
 <!--
 # NeXus - Neutron and X-ray Common Data Format
 #
-# Copyright (C) 2022-2024 NeXus International Advisory Committee (NIAC)
+# Copyright (C) 2022-2025 NeXus International Advisory Committee (NIAC)
 #
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
@@ -64,13 +64,15 @@ duplicate of an NXoff_geometry ?-->
 
          Although this description is storage efficient, it is not well-suited for
          topological analyses. In this case using a half-edge data structure is
-         an alternative. 
+         an alternative.
 
          Having an own base class for the data structure how primitives are stored is
          useful to embrace both users with small or detailed specification demands.
+
+         Indices can be used as identifier and thus names for individual instances.
     </doc>
     <!--resulting in a design similar to that of NXoff_geometry and the XDMF mixed primitive topology-->
-    <field name="number_of_vertices" type="NX_INT" units="NX_UNITLESS">
+    <field name="number_of_vertices" type="NX_UINT" units="NX_UNITLESS">
         <doc>
              Number of vertices for each face.
 
@@ -81,7 +83,7 @@ duplicate of an NXoff_geometry ?-->
             <dim index="1" value="n_f"/>
         </dimensions>
     </field>
-    <field name="number_of_edges" type="NX_INT" units="NX_UNITLESS">
+    <field name="number_of_edges" type="NX_UINT" units="NX_UNITLESS">
         <doc>
              Number of edges for each face.
 
@@ -92,12 +94,12 @@ duplicate of an NXoff_geometry ?-->
             <dim index="1" value="n_e"/>
         </dimensions>
     </field>
-    <field name="number_of_faces" type="NX_INT" units="NX_UNITLESS">
+    <field name="number_of_faces" type="NX_UINT" units="NX_UNITLESS">
         <doc>
              Number of faces of the primitives.
         </doc>
     </field>
-    <field name="identifier_vertex_offset" type="NX_INT" units="NX_UNITLESS">
+    <field name="index_offset_vertex" type="NX_INT" units="NX_UNITLESS">
         <doc>
              Integer offset whereby the identifier of the first member
              of the vertices differs from zero.
@@ -106,7 +108,7 @@ duplicate of an NXoff_geometry ?-->
              Inspect the definition of NXcg_primitive for further details.
         </doc>
     </field>
-    <field name="identifier_edge_offset" type="NX_INT" units="NX_UNITLESS">
+    <field name="index_offset_edge" type="NX_INT" units="NX_UNITLESS">
         <doc>
              Integer offset whereby the identifier of the first member
              of the edges differs from zero.
@@ -115,7 +117,7 @@ duplicate of an NXoff_geometry ?-->
              Inspect the definition of NXcg_primitive for further details.
         </doc>
     </field>
-    <field name="identifier_face_offset" type="NX_INT" units="NX_UNITLESS">
+    <field name="index_offset_face" type="NX_INT" units="NX_UNITLESS">
         <doc>
              Integer offset whereby the identifier of the first member
              of the faces differs from zero.
@@ -124,23 +126,23 @@ duplicate of an NXoff_geometry ?-->
              Inspect the definition of NXcg_primitive for further details.
         </doc>
     </field>
-    <field name="identifier_vertex" type="NX_INT" units="NX_UNITLESS">
+    <field name="indices_vertex" type="NX_INT" units="NX_UNITLESS">
         <doc>
              Integer identifier to distinguish all vertices explicitly.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_v"/>
         </dimensions>
     </field>
-    <field name="identifier_edge" type="NX_INT" units="NX_UNITLESS">
+    <field name="indices_edge" type="NX_INT" units="NX_UNITLESS">
         <doc>
              Integer used to distinguish all edges explicitly.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_e"/>
         </dimensions>
     </field>
-    <field name="identifier_face" type="NX_INT" units="NX_UNITLESS">
+    <field name="indices_face" type="NX_INT" units="NX_UNITLESS">
         <doc>
              Integer used to distinguish all faces explicitly.
         </doc>
@@ -216,6 +218,7 @@ duplicate of an NXoff_geometry ?-->
              * 0 - undefined
              * 1 - counter-clockwise (CCW)
              * 2 - clock-wise (CW)
+
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_f"/>

base_classes/NXcg_grid.nxdl.xml

@@ -3,7 +3,7 @@
 <!--
 # NeXus - Neutron and X-ray Common Data Format
 #
-# Copyright (C) 2022-2024 NeXus International Advisory Committee (NIAC)
+# Copyright (C) 2022-2025 NeXus International Advisory Committee (NIAC)
 #
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
@@ -121,7 +121,7 @@ should constraints on the grid be place here or not-->
     <!--does it have to be a tight bounding box?
 a good example for a general bounding box description for such a grids of triclinic cells
 https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallelepiped-->
-    <field name="number_of_boundaries" type="NX_INT" units="NX_UNITLESS">
+    <field name="number_of_boundaries" type="NX_UINT" units="NX_UNITLESS">
         <doc>
              Number of boundaries distinguished
 

base_classes/NXcg_half_edge_data_structure.nxdl.xml

@@ -3,7 +3,7 @@
 <!--
 # NeXus - Neutron and X-ray Common Data Format
 #
-# Copyright (C) 2022-2024 NeXus International Advisory Committee (NIAC)
+# Copyright (C) 2022-2025 NeXus International Advisory Committee (NIAC)
 #
 # This library is free software; you can redistribute it and/or
 # modify it under the terms of the GNU Lesser General Public
@@ -25,95 +25,97 @@
     <!--holes in the polygon mesh can be handled-->
     <symbols>
         <doc>
-             The symbols used in the schema to specify e.g. dimensions of arrays.
+            The symbols used in the schema to specify e.g. dimensions of arrays.
         </doc>
         <symbol name="d">
             <doc>
-                 The dimensionality, which has to be at least 2.
+                The dimensionality, which has to be at least 2.
             </doc>
         </symbol>
         <symbol name="n_v">
             <doc>
-                 The number of vertices.
+                The number of vertices.
             </doc>
         </symbol>
         <symbol name="n_f">
             <doc>
-                 The number of faces.
+                The number of faces.
             </doc>
         </symbol>
         <symbol name="n_he">
             <doc>
-                 The number of half-edges.
+                The number of half-edges.
             </doc>
         </symbol>
     </symbols>
     <doc>
-         Computational geeometry description of a half-edge data structure.
-
-         Such a data structure can be used to efficiently circulate around faces
-         and iterate over vertices of a planar graph. The data structure is also
-         known as a doubly connected edge list.
+        Computational geometry description of a half-edge data structure.
+
+        Such a data structure can be used to efficiently circulate around faces
+        and iterate over vertices of a planar graph. The data structure is also
+        known as a doubly connected edge list.
+
+        Indices can be used as identifier and thus names for individual instances.
     </doc>
     <field name="dimensionality" type="NX_POSINT" units="NX_UNITLESS">
         <doc>
-             Dimensionality of the primitives described.
+            Dimensionality of the primitives described.
         </doc>
     </field>
     <!--resulting in a design similar to that of NXoff_geometry and the XDMF mixed primitive topology-->
-    <field name="number_of_vertices" type="NX_INT" units="NX_UNITLESS">
+    <field name="number_of_vertices" type="NX_UINT" units="NX_UNITLESS">
         <doc>
-             Number of vertices for each face.
-             
-             Each entry represents the total number of vertices for that face,
-             irrespectively whether vertices are shared among faces or not.
+            Number of vertices for each face.
+
+            Each entry represents the total number of vertices for that face,
+            irrespectively whether vertices are shared among faces or not.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_f"/>
         </dimensions>
     </field>
-    <field name="number_of_edges" type="NX_INT" units="NX_UNITLESS">
+    <field name="number_of_edges" type="NX_UINT" units="NX_UNITLESS">
         <doc>
-             Number of edges for each face.
-             
-             Each entry represents the total number of edges for that face,
-             irrespectively whether edges are shared across faces or not.
+            Number of edges for each face.
+
+            Each entry represents the total number of edges for that face,
+            irrespectively whether edges are shared across faces or not.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_he"/>
         </dimensions>
     </field>
-    <field name="identifier_vertex_offset" type="NX_INT" units="NX_UNITLESS">
+    <field name="index_offset_vertex" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             Integer offset whereby the identifier of the first member
-             of the vertices differs from zero.
-             
-             Identifier can be defined explicitly or implicitly.
-             Inspect the definition of :ref:`NXcg_primitive` for further details.
+            Integer offset whereby the identifier of the first member
+            of the vertices differs from zero.
+
+            Identifier can be defined explicitly or implicitly.
+            Inspect the definition of :ref:`NXcg_primitive` for further details.
         </doc>
     </field>
-    <field name="identifier_edge_offset" type="NX_INT" units="NX_UNITLESS">
+    <field name="index_offset_edge" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             Integer offset whereby the identifier of the first member
-             of the edges differs from zero.
-             
-             Identifier can be defined explicitly or implicitly.
-             Inspect the definition of :ref:`NXcg_primitive` for further details.
+            Integer offset whereby the identifier of the first member
+            of the edges differs from zero.
+
+            Identifier can be defined explicitly or implicitly.
+            Inspect the definition of :ref:`NXcg_primitive` for further details.
         </doc>
     </field>
-    <field name="identifier_face_offset" type="NX_INT">
+    <field name="index_offset_face" type="NX_INT">
         <doc>
-             Integer offset whereby the identifier of the first member
-             of the faces differs from zero.
-             
-             Identifier can be defined explicitly or implicitly.
-             Inspect the definition of :ref:`NXcg_primitive` for further details.
+            Integer offset whereby the identifier of the first member
+            of the faces differs from zero.
+
+            Identifier can be defined explicitly or implicitly.
+            Inspect the definition of :ref:`NXcg_primitive` for further details.
         </doc>
     </field>
-    <!--therefore, identifier_ -vertex, -face, -half_edge are implicit-->
+    <!--therefore, indices_ -vertex, -face, -half_edge are implicit-->
     <field name="position" type="NX_NUMBER" units="NX_ANY">
         <doc>
-             The position of the vertices.
+            The position of the vertices.
         </doc>
         <dimensions rank="2">
             <dim index="1" value="n_v"/>
@@ -122,72 +124,72 @@
     </field>
     <field name="vertex_incident_half_edge" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             Identifier of the incident half-edge.
+            Identifier of the incident half-edge.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_v"/>
         </dimensions>
     </field>
     <field name="face_half_edge" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             Identifier of the (starting)/associated half-edge of the face.
+            Identifier of the (starting)/associated half-edge of the face.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_f"/>
         </dimensions>
     </field>
     <field name="half_edge_vertex_origin" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             The identifier of the vertex from which this half-edge is outwards pointing.
+            The identifier of the vertex from which this half-edge is outwards pointing.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_he"/>
         </dimensions>
     </field>
     <field name="half_edge_twin" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             Identifier of the associated oppositely pointing half-edge.
+            Identifier of the associated oppositely pointing half-edge.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_he"/>
         </dimensions>
     </field>
     <field name="half_edge_incident_face" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             If the half-edge is a boundary half-edge the
-             incident face identifier is NULL, i.e. 0.
+            If the half-edge is a boundary half-edge the
+            incident face identifier is NULL, i.e. 0.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_he"/>
         </dimensions>
     </field>
     <field name="half_edge_next" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             Identifier of the next half-edge.
+            Identifier of the next half-edge.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_he"/>
         </dimensions>
     </field>
     <field name="half_edge_prev" type="NX_INT" units="NX_UNITLESS">
         <doc>
-             Identifier of the previous half-edge.
+            Identifier of the previous half-edge.
         </doc>
         <dimensions rank="1">
             <dim index="1" value="n_he"/>
         </dimensions>
     </field>
     <field name="weinberg_vector">
         <doc>
-             Users are referred to the literature for the background of L. Weinberg's
-             work about topological characterization of planar graphs:
-             
-             * `L. Weinberg 1966a, &lt;https://dx.doi.org/10.1109/TCT.1964.1082216&gt;`_
-             * `L. Weinberg, 1966b, &lt;https://dx.doi.org/10.1137/0114062&gt;`_
-             * `E. A. Lazar et al. &lt;https://doi.org/10.1103/PhysRevLett.109.095505&gt;`_
-             
-             and how this work can e.g. be applied in space-filling tessellations
-             of microstructural objects like crystals/grains.
+            Users are referred to the literature for the background of L. Weinberg's
+            work about topological characterization of planar graphs:
+
+            * `L. Weinberg 1966a, &lt;https://dx.doi.org/10.1109/TCT.1964.1082216&gt;`_
+            * `L. Weinberg, 1966b, &lt;https://dx.doi.org/10.1137/0114062&gt;`_
+            * `E. A. Lazar et al. &lt;https://doi.org/10.1103/PhysRevLett.109.095505&gt;`_
+
+            and how this work can e.g. be applied in space-filling tessellations
+            of microstructural objects like crystals/grains.
         </doc>
     </field>
 </definition>