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Fairmat 2024: base classes to describe computational geometry #1421

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0cd4d80
Base class templates (#51)
mkuehbach Nov 30, 2023
b693886
Make nxdl
domna Jan 3, 2024
4ea902a
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
84eb726
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
2d1ceb7
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
a882d73
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
2cb86dc
Regenerate nxdls
domna Mar 4, 2024
950437b
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
5f93651
move new definitions to application and base_classes
lukaspie Sep 19, 2024
0b34306
Base class templates (#51)
mkuehbach Nov 30, 2023
b16ee17
Make nxdl
domna Jan 3, 2024
14f3b89
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
b054fdc
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
51acfc4
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
f625319
move new definitions to application and base_classes
lukaspie Sep 19, 2024
7881ae1
Base class templates (#51)
mkuehbach Nov 30, 2023
0471c66
Make nxdl
domna Jan 3, 2024
1eb89be
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
fbb2d99
Copyright updated to 2024 (#137)
domna Jan 4, 2024
6fa9f40
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
96c4267
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
2b659e8
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
b9fdf44
Regenerate nxdls
domna Mar 4, 2024
59cee3e
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
4874ed1
move new definitions to application and base_classes
lukaspie Sep 19, 2024
31e0126
Base class templates (#51)
mkuehbach Nov 30, 2023
cb64007
Make nxdl
domna Jan 3, 2024
53937d3
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
a7718ee
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
a071639
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
05d36e6
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
926d603
Regenerate nxdls
domna Mar 4, 2024
6d72295
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
037ea16
move new definitions to application and base_classes
lukaspie Sep 19, 2024
1500065
Base class templates (#51)
mkuehbach Nov 30, 2023
c2234b2
Make nxdl
domna Jan 3, 2024
cc80e84
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
a21b7b7
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
63328b0
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
34fcaa1
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
771a391
Regenerate nxdls
domna Mar 4, 2024
2dfcbf3
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
3bc8bd9
move new definitions to application and base_classes
lukaspie Sep 19, 2024
9440d9b
Base class templates (#51)
mkuehbach Nov 30, 2023
d68e489
Make nxdl
domna Jan 3, 2024
c180ae0
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
2928d6b
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
eac0ca0
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
8b0acd7
move new definitions to application and base_classes
lukaspie Sep 19, 2024
5f42ead
Base class templates (#51)
mkuehbach Nov 30, 2023
5a1b0b8
Make nxdl
domna Jan 3, 2024
e701652
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
68bca47
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
b90ea5b
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
b56519b
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
d710267
Regenerate nxdls
domna Mar 4, 2024
38e40b3
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
47649de
Fixed problems with formatting of math environments in rst
atomprobe-tc Apr 16, 2024
c9c2930
Clarified issues with depends_on, fixed typo pID for pfID in NXem_ebsd
atomprobe-tc Aug 30, 2024
e54306e
move new definitions to application and base_classes
lukaspie Sep 19, 2024
712bde4
Base class templates (#51)
mkuehbach Nov 30, 2023
95db291
Make nxdl
domna Jan 3, 2024
f11473f
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
309a35b
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
42a7925
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
ca1d4cb
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
72a54ed
Regenerate nxdls
domna Mar 4, 2024
52b890e
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
81c1782
Clarified issues with depends_on, fixed typo pID for pfID in NXem_ebsd
atomprobe-tc Aug 30, 2024
ec10c7d
move new definitions to application and base_classes
lukaspie Sep 19, 2024
13d88f2
Base class templates (#51)
mkuehbach Nov 30, 2023
e46f0b1
Make nxdl
domna Jan 3, 2024
227dd23
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
aee2a06
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
92dd74d
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
be2b542
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
e7831d5
Regenerate nxdls
domna Mar 4, 2024
4fdabcf
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
80214bc
move new definitions to application and base_classes
lukaspie Sep 19, 2024
cb00a76
Base class templates (#51)
mkuehbach Nov 30, 2023
2615623
Make nxdl
domna Jan 3, 2024
1910156
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
a280e2b
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
1dab87b
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
643564e
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
03e2519
Regenerate nxdls
domna Mar 4, 2024
c3466ff
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
4f16632
move new definitions to application and base_classes
lukaspie Sep 19, 2024
e045d40
Base class templates (#51)
mkuehbach Nov 30, 2023
b2079db
Make nxdl
domna Jan 3, 2024
7406512
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
6c9e07a
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
e72f30b
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
1b1c708
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
ad5e394
Regenerate nxdls
domna Mar 4, 2024
b3019b2
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
32cacc8
move new definitions to application and base_classes
lukaspie Sep 19, 2024
5c62f79
Base class templates (#51)
mkuehbach Nov 30, 2023
cb37e41
Make nxdl
domna Jan 3, 2024
7a9233a
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
7148e3e
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
17d0015
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
afea64c
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
cf1ef04
Regenerate nxdls
domna Mar 4, 2024
1f7f852
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
6d955cd
move new definitions to application and base_classes
lukaspie Sep 19, 2024
57cd3c0
Base class templates (#51)
mkuehbach Nov 30, 2023
ec467cf
Make nxdl
domna Jan 3, 2024
f0ad475
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
65b7ea8
Fixed issues detected during make local, manual builds successfully, …
atomprobe-tc Jan 8, 2024
74258a2
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
b23b135
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
179cba9
move new definitions to application and base_classes
lukaspie Sep 19, 2024
50eb894
Base class templates (#51)
mkuehbach Nov 30, 2023
d7d24d6
Make nxdl
domna Jan 3, 2024
0884c76
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
7a03f90
Copyright updated to 2024 (#137)
domna Jan 4, 2024
1e25411
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
c2f3703
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
6a51d87
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
53102c4
Regenerate nxdls
domna Mar 4, 2024
19dcef5
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
26c31cf
move new definitions to application and base_classes
lukaspie Sep 19, 2024
d8f8005
Base class templates (#51)
mkuehbach Nov 30, 2023
0ff46b1
Make nxdl
domna Jan 3, 2024
6df4654
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
18962ed
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
8d796d5
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
5e3e148
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
fb3787c
Regenerate nxdls
domna Mar 4, 2024
07052bd
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
86d3df2
Clarified issues with depends_on, fixed typo pID for pfID in NXem_ebsd
atomprobe-tc Aug 30, 2024
c296d58
move new definitions to application and base_classes
lukaspie Sep 19, 2024
19b95dd
Base class templates (#51)
mkuehbach Nov 30, 2023
10448a1
Make nxdl
domna Jan 3, 2024
f249898
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
390856e
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
e383312
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
ee91f00
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
985fc4b
Regenerate nxdls
domna Mar 4, 2024
010820b
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
97f4e44
Finalized data model for NXmicrostructure_imm
atomprobe-tc Jul 10, 2024
49ab8a6
move new definitions to application and base_classes
lukaspie Sep 19, 2024
bb8787c
Base class templates (#51)
mkuehbach Nov 30, 2023
09ff867
Make nxdl
domna Jan 3, 2024
126697b
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
46cc03b
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
5a68dbe
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
3cc5064
move new definitions to application and base_classes
lukaspie Sep 19, 2024
65bf96c
Base class templates (#51)
mkuehbach Nov 30, 2023
2f5786a
Make nxdl
domna Jan 3, 2024
a3fef52
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
7ba98b1
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
385deb6
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
ba543e9
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
6bc92ee
Regenerate nxdls
domna Mar 4, 2024
6091749
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
5d207bf
Clarified issues with depends_on, fixed typo pID for pfID in NXem_ebsd
atomprobe-tc Aug 30, 2024
595a340
move new definitions to application and base_classes
lukaspie Sep 19, 2024
afddfc9
Base class templates (#51)
mkuehbach Nov 30, 2023
77df860
Make nxdl
domna Jan 3, 2024
e1d56c9
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
c66df18
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
519243f
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
e58b2f9
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
4e58dc9
Regenerate nxdls
domna Mar 4, 2024
94a5225
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
7e456b9
move new definitions to application and base_classes
lukaspie Sep 19, 2024
39568c6
Base class templates (#51)
mkuehbach Nov 30, 2023
c5cc88f
Make nxdl
domna Jan 3, 2024
5b38c9b
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
0e831e3
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
584ae3f
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
de6620b
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
2081d76
Regenerate nxdls
domna Mar 4, 2024
18cf0bd
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
c3f494a
move new definitions to application and base_classes
lukaspie Sep 19, 2024
f4c77e4
Base class templates (#51)
mkuehbach Nov 30, 2023
bb41c43
Make nxdl
domna Jan 3, 2024
50d1602
Whitespace above and below copyright removed (new nyaml version)
domna Jan 3, 2024
6dcc33f
Added changes relevant to use the refactored NXapm parser of pynxtool…
atomprobe-tc Jan 10, 2024
262ce49
Recompiled NXDLs from YAML using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
3dc1ce5
Recompiled NXDLs from yaml using nyaml==0.0.9
atomprobe-tc Feb 28, 2024
01da8a9
Regenerate nxdls
domna Mar 4, 2024
deab0fe
Regenerate nxdls with nyaml==0.0.8 (#190)
domna Mar 5, 2024
56095d7
move new definitions to application and base_classes
lukaspie Sep 19, 2024
6267928
revert unintentional changes from cherry-pick
lukaspie Sep 24, 2024
27a9d4b
remove classes from contributed that have been moved to base_classes
lukaspie Sep 24, 2024
9dd6826
Refactored problematic attribute name depends on
atomprobe-tc Sep 25, 2024
740cea6
Merge remote-tracking branch 'origin/main' i.e. FAIRmat nexus_definit…
atomprobe-tc Jan 8, 2025
d2ad17f
Implement suggestion to drop suffix _set to avoid confusion with the …
atomprobe-tc Jan 8, 2025
8881995
Merge remote-tracking branch 'upstream/main' into fairmat-2024-comput…
atomprobe-tc Jan 9, 2025
9493eb5
Autumn NIAC 2024 edits
atomprobe-tc Jan 10, 2025
d892c17
Consolidated content of too small base classes by merging these defin…
atomprobe-tc Jan 10, 2025
09f1d6e
Refactored remaining docstrings to remove _set, and refactoring of re…
atomprobe-tc Jan 10, 2025
8c6786a
Indentation
atomprobe-tc Jan 10, 2025
3245ef3
Typo in xsd parameter
atomprobe-tc Jan 10, 2025
66f665d
Merge branch 'main' of github.com:nexusformat/definitions into fairma…
atomprobe-tc Jan 14, 2025
9a13cfa
Addressed comments from @PeterC-DLS
atomprobe-tc Jan 17, 2025
9ba70cf
Temporarily deactivated open flag for enumeration as #1521 not yet me…
atomprobe-tc Jan 17, 2025
9f6becc
Refactored remaining identifier to follow the identifier_* design to …
atomprobe-tc Jan 17, 2025
d417152
Implementation of feedback from the reviewers
atomprobe-tc Feb 3, 2025
3cbc467
Merge remote-tracking branch 'upstream/main' into fairmat-2024-comput…
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6 changes: 3 additions & 3 deletions base_classes/NXcg_alpha_complex.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -66,10 +66,10 @@ The so-called spectrum or sets of (weighted) alpha shapes includes the convex hu
Was the alpha complex regularized, i.e. have singular faces been removed, or not.
</doc>
</field>
<field name="alpha" type="NX_NUMBER" units="NX_LENGTH">
<field name="alpha" type="NX_NUMBER" units="NX_ANY">
<doc>
The alpha parameter, i.e. the radius of the alpha-sphere that
is used when computing the alpha complex.
The alpha parameter, i.e. the squared radius of the alpha-sphere
that is used when computing the alpha complex.
</doc>
</field>
<field name="offset" type="NX_NUMBER" units="NX_LENGTH">
Expand Down
16 changes: 9 additions & 7 deletions base_classes/NXcg_cylinder.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -21,9 +21,6 @@
#
# For further information, see http://www.nexusformat.org
-->
<!--
redundant as there is NXcsg, NXquadric, NXsolid_geometry with which
cylinder could be constructed, but NXcylinder is easier to understand-->
<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXcg_cylinder" extends="NXcg_primitive" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
<symbols>
<doc>
Expand All @@ -43,17 +40,22 @@ cylinder could be constructed, but NXcylinder is easier to understand-->
<doc>
Computational geometry description of a set of cylinders or (truncated) cones.

The radius can either be defined in the radii field or by filling both
the upper_cap_radii or lower_cap_radii field. The latter field case can
The radius can either be defined in the radii field or by filling the upper_cap_radii
and lower_cap_radii fields respectively. The latter field case can
thus be used to represent (truncated) cones.

It is possible to define only one of the cap_radii fields
to represent half-open cylinder.
</doc>
<field name="height" type="NX_NUMBER" units="NX_LENGTH">
<doc>
A direction vector which is parallel to the cylinder/cone axis
and whose magnitude is the height of the cylinder/cone.

The upper_cap is defined as the one that is farther away to the origin
when inspecting a parallel projection onto the direction vector.
The upper_cap is assumed to represent the end while the
lower_cap is assumed to represent the start of the
respective cylinder instances when inspecting along the
direction vector.
</doc>
<dimensions rank="2">
<dim index="1" value="c"/>
Expand Down
11 changes: 6 additions & 5 deletions base_classes/NXcg_ellipsoid.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -42,19 +42,20 @@ redundant as there is NXcsg, and NXquadric but easier to understand-->
<doc>
Computational geometry description of a set of ellipsoids.
</doc>
<field name="half_axes_radius" type="NX_NUMBER" units="NX_LENGTH">
<field name="semi_axes_value" type="NX_NUMBER" units="NX_LENGTH">
<doc>
Radius of the half axes.
Length of the semi-axes (e.g. semi-major and semi-minor
respectively for an ellipse).

Use if all ellipsoids in the set have the same half-axes.
</doc>
<dimensions rank="1">
<dim index="1" value="d"/>
</dimensions>
</field>
<field name="half_axes_radii" type="NX_NUMBER" units="NX_LENGTH">
<field name="semi_axes_values" type="NX_NUMBER" units="NX_LENGTH">
<doc>
Half-axes radii of each ellipsoid.
Length of the semi-axes if ellipsoids have individually different length.
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Suggested change
Length of the semi-axes if ellipsoids have individually different length.
Length of the semi-axes if ellipsoids have individually different lengths.

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Implemented

</doc>
<dimensions rank="2">
<dim index="1" value="c"/>
Expand All @@ -70,7 +71,7 @@ redundant as there is NXcsg, and NXquadric but easier to understand-->
<field name="radii" type="NX_NUMBER" units="NX_LENGTH">
<doc>
In the case that all ellipsoids are spheres whose radii differ.
For a mixture of spheres use half_axes_radii.
For a mixture of spheres use semi_axes_values.
</doc>
<dimensions rank="1">
<dim index="1" value="c"/>
Expand Down
17 changes: 6 additions & 11 deletions base_classes/NXcg_face_list_data_structure.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -53,11 +53,6 @@ duplicate of an NXoff_geometry ?-->
The total number of vertices of all faces. Faces are polygons.
</doc>
</symbol>
<symbol name="n_weinberg">
<doc>
The total number of Weinberg vector values of all faces.
</doc>
</symbol>
</symbols>
<doc>
Computational geometry of primitives via a face-and-edge-list data structure.
Expand Down Expand Up @@ -102,7 +97,7 @@ duplicate of an NXoff_geometry ?-->
Number of faces of the primitives.
</doc>
</field>
<field name="vertex_identifier_offset" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_vertex_offset" type="NX_INT" units="NX_UNITLESS">
<doc>
Integer offset whereby the identifier of the first member
of the vertices differs from zero.
Expand All @@ -111,7 +106,7 @@ duplicate of an NXoff_geometry ?-->
Inspect the definition of NXcg_primitive for further details.
</doc>
</field>
<field name="edge_identifier_offset" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_edge_offset" type="NX_INT" units="NX_UNITLESS">
<doc>
Integer offset whereby the identifier of the first member
of the edges differs from zero.
Expand All @@ -120,7 +115,7 @@ duplicate of an NXoff_geometry ?-->
Inspect the definition of NXcg_primitive for further details.
</doc>
</field>
<field name="face_identifier_offset" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_face_offset" type="NX_INT" units="NX_UNITLESS">
<doc>
Integer offset whereby the identifier of the first member
of the faces differs from zero.
Expand All @@ -129,23 +124,23 @@ duplicate of an NXoff_geometry ?-->
Inspect the definition of NXcg_primitive for further details.
</doc>
</field>
<field name="vertex_identifier" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_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="edge_identifier" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_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="face_identifier" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_face" type="NX_INT" units="NX_UNITLESS">
<doc>
Integer used to distinguish all faces explicitly.
</doc>
Expand Down
4 changes: 2 additions & 2 deletions base_classes/NXcg_grid.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -170,8 +170,8 @@ https://docs.lammps.org/Howto_triclinic.html NXcg_polyhedron because a parallele
* `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.
If not possible, an identifier for a paper, tech report, or free-text description
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Suggested change
If not possible, an identifier for a paper, tech report, or free-text description
If not possible, an identifier for a paper, technical report, or free-text description

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Corrected

can be used instead.
</doc>
</field>
</definition>
18 changes: 7 additions & 11 deletions base_classes/NXcg_half_edge_data_structure.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -52,7 +52,8 @@
Computational geeometry description of a half-edge data structure.

Such a data structure can be used to efficiently circulate around faces
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and iterate over vertices of a planar graph.
and iterate over vertices of a planar graph. The data structure is also
known as a doubly connected edge list.
</doc>
<field name="dimensionality" type="NX_POSINT" units="NX_UNITLESS">
<doc>
Expand All @@ -79,15 +80,10 @@
irrespectively whether edges are shared across faces or not.
</doc>
<dimensions rank="1">
<dim index="1" value="n_e"/>
<dim index="1" value="n_he"/>
</dimensions>
</field>
<field name="number_of_faces" type="NX_INT" units="NX_UNITLESS">
<doc>
Number of faces of the primitives.
</doc>
</field>
<field name="vertex_identifier_offset" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_vertex_offset" type="NX_INT" units="NX_UNITLESS">
<doc>
Integer offset whereby the identifier of the first member
of the vertices differs from zero.
Expand All @@ -96,7 +92,7 @@
Inspect the definition of :ref:`NXcg_primitive` for further details.
</doc>
</field>
<field name="edge_identifier_offset" type="NX_INT" units="NX_UNITLESS">
<field name="identifier_edge_offset" type="NX_INT" units="NX_UNITLESS">
<doc>
Integer offset whereby the identifier of the first member
of the edges differs from zero.
Expand All @@ -105,7 +101,7 @@
Inspect the definition of :ref:`NXcg_primitive` for further details.
</doc>
</field>
<field name="face_identifier_offset" type="NX_INT">
<field name="identifier_face_offset" type="NX_INT">
<doc>
Integer offset whereby the identifier of the first member
of the faces differs from zero.
Expand All @@ -114,7 +110,7 @@
Inspect the definition of :ref:`NXcg_primitive` for further details.
</doc>
</field>
<!--therefore, vertex_-, face_-, half_edge_-identifier are implicit-->
<!--therefore, identifier_ -vertex, -face, -half_edge are implicit-->
<field name="position" type="NX_NUMBER" units="NX_ANY">
<doc>
The position of the vertices.
Expand Down
18 changes: 8 additions & 10 deletions base_classes/NXcg_polyline.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -54,13 +54,13 @@ multiple vertices possible with the same point coordinates but different names.-

Each polyline is built from a sequence of vertices (points with identifiers).
Each polyline must have a start and an end point.
The sequence describes the positive traversal along the polyline when
The sequence describes the traversal along the polyline when
walking from the first to the last vertex.
</doc>
<field name="depends_on" type="NX_CHAR">
<doc>
Reference to an instance of :ref:`NXcg_point` which defines the
location of the vertices that are referred to in the
location of the vertices that are referred to in this
NXcg_polyline instance.
</doc>
</field>
Expand All @@ -78,8 +78,6 @@ multiple vertices possible with the same point coordinates but different names.-
<doc>
The total number of vertices of each polyline, irrespectively
whether vertices are shared by vertices or not.
See the docstring for polylines for further details about how
a set with different polyline members should be stored.
</doc>
<dimensions rank="1">
<dim index="1" value="c"/>
Expand Down Expand Up @@ -118,9 +116,9 @@ they share the same position in space but have different identifiers.-->
Sequence of identifier for vertices how they build each polyline.

A trivial example is a set with two polylines with three vertices each.
If the polylines meet in a junction, say the second vertex is shared
and marking the junction between the two polylines, it is possible that
there are only five unique positions. This suggests to store five
If the polylines meet at a vertex (assume for example that the second vertex
is shared and marking the junction between the two polylines), it is possible
that there are only five unique positions. This suggests to store five
unique vertices.

A non-trivial example is a set with several polylines. Assume that each
Expand All @@ -131,9 +129,9 @@ they share the same position in space but have different identifiers.-->
followed by the second vertex of the first polyline, until the last vertex
of the first polyline.
Thereafter, the first vertex of the second polyline, and so on and so forth.
Using the (cumulated) counts in number_of_vertices, the vertices of the
n-th polyline can be accessed on the following array index interval:
:math:`[\sum_{i=0}^{i=N-1}, \sum_{i=0}^{i=N}]`.
Using the (cumulated) counts in number_of_vertices (:math:`n^v_i`),
the vertices of the N-th polyline can be accessed on the array
index interval :math:`[\sum_{i=0}^{i=N-1} n^v_i, \sum_{i=0}^{i=N} n^v_i]`.
</doc>
<dimensions rank="1">
<dim index="1" value="n_total"/>
Expand Down
42 changes: 29 additions & 13 deletions base_classes/NXcg_primitive.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -51,17 +51,18 @@
</field>
<field name="dimensionality" type="NX_POSINT" units="NX_UNITLESS">
<doc>
The dimensionality of the primitive set.
The dimensionality of the primitive set with value up to d.
</doc>
<enumeration>
<!-- add when 1521 has been merged open="true"-->
<item value="1"/>
<item value="2"/>
<item value="3"/>
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</enumeration>
</field>
<field name="cardinality" type="NX_POSINT" units="NX_UNITLESS">
<doc>
The cardinality of the primitive set.
The cardinality of the primitive set. Value should be equal to c.
</doc>
</field>
<field name="identifier_offset" type="NX_INT" units="NX_UNITLESS">
Expand Down Expand Up @@ -92,7 +93,7 @@
</field>
<field name="center" type="NX_NUMBER" units="NX_ANY">
<doc>
The center of mass position of each primitive.
The center of each primitive
</doc>
<dimensions rank="2">
<dim index="1" value="c"/>
Expand All @@ -109,7 +110,7 @@
</field>
<field name="shape" type="NX_NUMBER" units="NX_LENGTH">
<doc>
A qualitative description of the shape of each primitive.
Shape of each primitive
</doc>
<dimensions rank="2">
<dim index="1" value="c"/>
Expand All @@ -118,9 +119,9 @@
</field>
<field name="length" type="NX_NUMBER" units="NX_LENGTH">
<doc>
Qualifier for the length of characteristic features of the primitive.
Length of each primitive

Often the term length is associated with the assumption that one
Often the term is associated with the assumption that one
edge is parallel to an axis of the coordinate system.
</doc>
<dimensions rank="1">
Expand All @@ -129,8 +130,21 @@
</field>
<field name="width" type="NX_NUMBER" units="NX_LENGTH">
<doc>
Qualifier often used to describe the length of one characteristic edge
within the coordinate system.
Width of each primitive

Often the term is associated with the assumption that one
edge is parallel to an axis of the coordinate system.
</doc>
<dimensions rank="1">
<dim index="1" value="c"/>
</dimensions>
</field>
<field name="height" type="NX_NUMBER" units="NX_LENGTH">
<doc>
Height of each primitive

Often the term is associated with the assumption that one
edge is parallel to an axis of the coordinate system.
</doc>
<dimensions rank="1">
<dim index="1" value="c"/>
Expand All @@ -144,11 +158,13 @@
<dim index="1" value="c"/>
</dimensions>
</field>
<field name="volume" type="NX_NUMBER" units="NX_VOLUME">
<field name="volume" type="NX_NUMBER" units="NX_ANY">
<doc>
Volume of each primitive.
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Set to NaN if does not apply for primitives for which is_closed is False.
Volume is an N-D concept for values of dimensionality larger than 1,
Area is a an alias for the two-dimensional case.
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Area is a an alias for the two-dimensional case.
Area is an alias for the two-dimensional case.

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Corrected

</doc>
<dimensions rank="1">
<dim index="1" value="c"/>
Expand Down Expand Up @@ -182,16 +198,16 @@
Do the primitives define a mesh.
</doc>
</field>
<!--<field name="is_triangle_mesh" type="NX_BOOLEAN">
<field name="is_triangle_mesh" type="NX_BOOLEAN">
<doc>
Do the primitives define triangle mesh.
Do the primitives define a triangle mesh or not.
</doc>
</field>
<field name="is_surface_mesh" type="NX_BOOLEAN">
<doc>
Do the primitives discretize the surface of an object.
Do the primitives discretize the surface of an object or not.
</doc>
</field>-->
</field>
<field name="is_geodesic_mesh" type="NX_BOOLEAN">
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<doc>
Do the primitives define a geodesic mesh or not.
Expand Down
2 changes: 1 addition & 1 deletion base_classes/NXcg_unit_normal.nxdl.xml
Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,7 @@ rather make this a set of vectors, irrespective whether these are unit or not-->
</field>
<field name="orientation" type="NX_INT" units="NX_UNITLESS">
<doc>
Qualifier which details the orientation of each normal vector
An indicator which details the orientation of each normal vector
in relation to its primitive, assuming the object is viewed
from a position outside the object.

Expand Down
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