Grid Topology Overview

Authors: Philip Chmielowiec, Orhan Eroglu

As discussed in our first notebook, UXarray uses the UGRID conventions as a foundation for represented Unstructured Grids. Here we’ll see how to access the underlying dimensions, coordinates, and connectivity variables that are available in UXarray.

Constructing the Grid Topology

The grid topology is defined as a Grid object in UXarray. A Grid object can be created in different ways.

Constructing through uxarray.open_grid()

If the intent is to explore only the grid topology instead of having any data sets with it, analyzing data variables, etc., a standalone Grid object can be instantiated as follows:

import uxarray
import uxarray as ux

# Base data path
base_path = "../../test/meshfiles/"

# Grid Path (MPAS Example)
grid_mpas_path = base_path + "/mpas/QU/mesh.QU.1920km.151026.nc"

grid_mpas = ux.open_grid(grid_mpas_path)
grid_mpas

<uxarray.Grid>
Original Grid Type: mpas
Grid Dimensions:
  * nMesh2_node: 320
  * nMesh2_face: 162
  * nMaxMesh2_face_nodes: 6
  * nMesh2_edge: 480
Grid Coordinate Variables:
  * Mesh2_node_x: (320,)
  * Mesh2_node_y: (320,)
  * Mesh2_face_x: (162,)
  * Mesh2_face_y: (162,)
Grid Connectivity Variables:
  * Mesh2_face_nodes: (162, 6)
  * Mesh2_edge_nodes: (480, 2)
  * nNodes_per_face: (162,)

Constructing through UxDataset

If the intent is to have an unstructured grid-aware dataset, i.e. UxDataset, and investigate the grid topology through it instead, the uxgrid property can be used. To be more precise, when a UxDataset object, or likewise UxDataArray object, is generated (e.g. through uxarray.open_dataset()), a Grid object via UxDataset.uxgrid, or UxDataArray.uxgrid, property is also created automatically and assigned to the dataset or variable.

The grid topology can be seen through this property as follows:

# Data File Path (UGRID Example)
grid_ne30_path = base_path + "/ugrid/outCSne30/outCSne30.ug"
data_ne30_path = base_path + "/ugrid/outCSne30/outCSne30_vortex.nc"

uxds = ux.open_dataset(grid_ne30_path, data_ne30_path)
uxds.uxgrid

<uxarray.Grid>
Original Grid Type: ugrid
Grid Dimensions:
  * nMesh2_face: 5400
  * nMaxMesh2_face_nodes: 4
  * nMesh2_node: 5402
Grid Coordinate Variables:
  * Mesh2_node_x: (5402,)
  * Mesh2_node_y: (5402,)
Grid Connectivity Variables:
  * Mesh2_face_nodes: (5400, 4)
  * nNodes_per_face: (5400,)

In addition, a previously-created Grid object can always be assigned to a new UxDataset as its uxgrid property as follows:

uxds_mpas = ux.UxDataset(uxgrid=grid_mpas)
uxds_mpas.uxgrid

<uxarray.Grid>
Original Grid Type: mpas
Grid Dimensions:
  * nMesh2_node: 320
  * nMesh2_face: 162
  * nMaxMesh2_face_nodes: 6
  * nMesh2_edge: 480
Grid Coordinate Variables:
  * Mesh2_node_x: (320,)
  * Mesh2_node_y: (320,)
  * Mesh2_face_x: (162,)
  * Mesh2_face_y: (162,)
Grid Connectivity Variables:
  * Mesh2_face_nodes: (162, 6)
  * Mesh2_edge_nodes: (480, 2)
  * nNodes_per_face: (162,)

Grid Attributes

All of the grid topology attributes such as coordinates, connectivity variables, dimensions, etc can be examined through the uxgrid property, i.e. Grid object:

uxds.uxgrid.Mesh2

<xarray.DataArray 'Mesh2' ()>
[1 values with dtype=int32]
Attributes:
    cf_role:                 mesh_topology
    long_name:               Topology data of 2D unstructured mesh
    topology_dimension:      2
    node_coordinates:        Mesh2_node_x Mesh2_node_y
    node_dimension:          nMesh2_node
    face_node_connectivity:  Mesh2_face_nodes
    face_dimension:          nMesh2_face

xarray.DataArray

'Mesh2'

• ...

  [1 values with dtype=int32]

• Coordinates: (0)
• Indexes: (0)
• Attributes: (7)

  cf_role :

  mesh_topology

  long_name :

  Topology data of 2D unstructured mesh

  topology_dimension :

  2

  node_coordinates :

  Mesh2_node_x Mesh2_node_y

  node_dimension :

  nMesh2_node

  face_node_connectivity :

  Mesh2_face_nodes

  face_dimension :

  nMesh2_face

If our input grid contained additional attributes that were not representable by the UGRID conventions, they would be stored here

uxds.uxgrid.parsed_attrs

{}

uxds_mpas.uxgrid.parsed_attrs

{'sphere_radius': 1.0, 'mesh_spec': '1.0', 'on_a_sphere': 'YES'}

Grid Coordinates

The coordinates by default are represented in terms of longitude and latitude.

uxds.uxgrid.Mesh2_node_x

<xarray.DataArray 'Mesh2_node_x' (nMesh2_node: 5402)>
[5402 values with dtype=float64]
Coordinates:
    Mesh2_node_x  (nMesh2_node) float64 ...
    Mesh2_node_y  (nMesh2_node) float64 ...
Dimensions without coordinates: nMesh2_node
Attributes:
    standard_name:  longitude
    long_name:      longitude of 2D mesh nodes
    units:          degrees_east

xarray.DataArray

'Mesh2_node_x'

• nMesh2_node: 5402

• ...

  [5402 values with dtype=float64]

• Coordinates: (2)
  • Mesh2_node_x
    (nMesh2_node)
    float64
    ...

    standard_name :

    longitude

    long_name :

    longitude of 2D mesh nodes

    units :

    degrees_east

    [5402 values with dtype=float64]

  • Mesh2_node_y
    (nMesh2_node)
    float64
    ...

    standard_name :

    latitude

    long_name :

    latitude of 2D mesh nodes

    units :

    degrees_north

    [5402 values with dtype=float64]

• Indexes: (0)
• Attributes: (3)

  standard_name :

  longitude

  long_name :

  longitude of 2D mesh nodes

  units :

  degrees_east

uxds.uxgrid.Mesh2_node_y

<xarray.DataArray 'Mesh2_node_y' (nMesh2_node: 5402)>
[5402 values with dtype=float64]
Coordinates:
    Mesh2_node_x  (nMesh2_node) float64 ...
    Mesh2_node_y  (nMesh2_node) float64 ...
Dimensions without coordinates: nMesh2_node
Attributes:
    standard_name:  latitude
    long_name:      latitude of 2D mesh nodes
    units:          degrees_north

xarray.DataArray

'Mesh2_node_y'

• nMesh2_node: 5402

• ...

  [5402 values with dtype=float64]

• Coordinates: (2)
  • Mesh2_node_x
    (nMesh2_node)
    float64
    ...

    standard_name :

    longitude

    long_name :

    longitude of 2D mesh nodes

    units :

    degrees_east

    [5402 values with dtype=float64]

  • Mesh2_node_y
    (nMesh2_node)
    float64
    ...

    standard_name :

    latitude

    long_name :

    latitude of 2D mesh nodes

    units :

    degrees_north

    [5402 values with dtype=float64]

• Indexes: (0)
• Attributes: (3)

  standard_name :

  latitude

  long_name :

  latitude of 2D mesh nodes

  units :

  degrees_north

If you wish to use the Cartesian coordinate system, you can access the following attributes, which will internally construct a set of Cartesian coordinates derived from the previous set.

uxds.uxgrid.Mesh2_node_cart_x

<xarray.DataArray 'Mesh2_node_cart_x' (nMesh2_node: 5402)>
array([ 0.57735027,  0.57735027, -0.57735027, ..., -0.58878977,
       -0.57332232, -0.55611709])
Coordinates:
    Mesh2_node_x  (nMesh2_node) float64 315.0 45.0 135.0 ... 141.1 138.0 135.0
    Mesh2_node_y  (nMesh2_node) float64 -35.26 -35.26 -35.26 ... 39.55 38.14
Dimensions without coordinates: nMesh2_node
Attributes:
    standard_name:  cartesian x
    units:          m

xarray.DataArray

'Mesh2_node_cart_x'

• nMesh2_node: 5402

• 0.5774 0.5774 -0.5774 -0.5774 ... -0.6026 -0.5888 -0.5733 -0.5561

  array([ 0.57735027,  0.57735027, -0.57735027, ..., -0.58878977,
         -0.57332232, -0.55611709])

• Coordinates: (2)
  • Mesh2_node_x
    (nMesh2_node)
    float64
    315.0 45.0 135.0 ... 138.0 135.0

    standard_name :

    longitude

    long_name :

    longitude of 2D mesh nodes

    units :

    degrees_east

    array([315.      ,  45.      , 135.      , ..., 141.09969 , 138.033171,
           135.      ])

  • Mesh2_node_y
    (nMesh2_node)
    float64
    -35.26 -35.26 ... 39.55 38.14

    standard_name :

    latitude

    long_name :

    latitude of 2D mesh nodes

    units :

    degrees_north

    array([-35.26439 , -35.26439 , -35.26439 , ...,  40.837604,  39.549078,
            38.143314])

• Indexes: (0)
• Attributes: (2)

  standard_name :

  cartesian x

  units :

  m

uxds.uxgrid.Mesh2_node_cart_y

<xarray.DataArray 'Mesh2_node_cart_y' (nMesh2_node: 5402)>
array([-0.57735027,  0.57735027,  0.57735027, ...,  0.47509872,
        0.51562103,  0.55611709])
Coordinates:
    Mesh2_node_x  (nMesh2_node) float64 315.0 45.0 135.0 ... 141.1 138.0 135.0
    Mesh2_node_y  (nMesh2_node) float64 -35.26 -35.26 -35.26 ... 39.55 38.14
Dimensions without coordinates: nMesh2_node
Attributes:
    standard_name:  cartesian y
    units:          m

xarray.DataArray

'Mesh2_node_cart_y'

• nMesh2_node: 5402

• -0.5774 0.5774 0.5774 -0.5774 -0.5774 ... 0.4346 0.4751 0.5156 0.5561

  array([-0.57735027,  0.57735027,  0.57735027, ...,  0.47509872,
          0.51562103,  0.55611709])

• Coordinates: (2)
  • Mesh2_node_x
    (nMesh2_node)
    float64
    315.0 45.0 135.0 ... 138.0 135.0

    standard_name :

    longitude

    long_name :

    longitude of 2D mesh nodes

    units :

    degrees_east

    array([315.      ,  45.      , 135.      , ..., 141.09969 , 138.033171,
           135.      ])

  • Mesh2_node_y
    (nMesh2_node)
    float64
    -35.26 -35.26 ... 39.55 38.14

    standard_name :

    latitude

    long_name :

    latitude of 2D mesh nodes

    units :

    degrees_north

    array([-35.26439 , -35.26439 , -35.26439 , ...,  40.837604,  39.549078,
            38.143314])

• Indexes: (0)
• Attributes: (2)

  standard_name :

  cartesian y

  units :

  m

uxds.uxgrid.Mesh2_node_cart_z

<xarray.DataArray 'Mesh2_node_cart_z' (nMesh2_node: 5402)>
array([-0.57735027, -0.57735027, -0.57735027, ...,  0.65391729,
        0.63673894,  0.6176306 ])
Coordinates:
    Mesh2_node_x  (nMesh2_node) float64 315.0 45.0 135.0 ... 141.1 138.0 135.0
    Mesh2_node_y  (nMesh2_node) float64 -35.26 -35.26 -35.26 ... 39.55 38.14
Dimensions without coordinates: nMesh2_node
Attributes:
    standard_name:  cartesian z
    units:          m

xarray.DataArray

'Mesh2_node_cart_z'

• nMesh2_node: 5402

• -0.5774 -0.5774 -0.5774 -0.5774 0.5774 ... 0.6693 0.6539 0.6367 0.6176

  array([-0.57735027, -0.57735027, -0.57735027, ...,  0.65391729,
          0.63673894,  0.6176306 ])

• Coordinates: (2)
  • Mesh2_node_x
    (nMesh2_node)
    float64
    315.0 45.0 135.0 ... 138.0 135.0

    standard_name :

    longitude

    long_name :

    longitude of 2D mesh nodes

    units :

    degrees_east

    array([315.      ,  45.      , 135.      , ..., 141.09969 , 138.033171,
           135.      ])

  • Mesh2_node_y
    (nMesh2_node)
    float64
    -35.26 -35.26 ... 39.55 38.14

    standard_name :

    latitude

    long_name :

    latitude of 2D mesh nodes

    units :

    degrees_north

    array([-35.26439 , -35.26439 , -35.26439 , ...,  40.837604,  39.549078,
            38.143314])

• Indexes: (0)
• Attributes: (2)

  standard_name :

  cartesian z

  units :

  m

Grid Connectivity

Connectivity variables are used to describe how various geometric elements (nodes, faces, edges) can be manipulated and interconnected to represent the topology of the unstructured grid.

As described in the UGRID conventions, these connectivity variables are stored as integer arrays and may contain a Fill Value. UXarray standardizes both of these at the data loading step, meaning that the data type and fill value can always be guaranteed to be the following:

ux.INT_DTYPE

numpy.int64

ux.INT_FILL_VALUE

-9223372036854775808

Below we can see how to access these connectivity variables.

uxds.uxgrid.Mesh2_face_nodes

<xarray.DataArray 'Mesh2_face_nodes' (nMesh2_face: 5400, nMaxMesh2_face_nodes: 4)>
array([[   0,    8,  356,  124],
       [   8,    9,  357,  356],
       [   9,   10,  358,  357],
       ...,
       [5399, 5400,  299,  300],
       [5400, 5401,  298,  299],
       [5401,  297,    6,  298]])
Dimensions without coordinates: nMesh2_face, nMaxMesh2_face_nodes
Attributes:
    cf_role:      face_node_connectivity
    start_index:  0
    _FillValue:   -9223372036854775808

xarray.DataArray

'Mesh2_face_nodes'

• nMesh2_face: 5400
• nMaxMesh2_face_nodes: 4

• 0 8 356 124 8 9 357 356 9 10 ... 300 5400 5401 298 299 5401 297 6 298

  array([[   0,    8,  356,  124],
         [   8,    9,  357,  356],
         [   9,   10,  358,  357],
         ...,
         [5399, 5400,  299,  300],
         [5400, 5401,  298,  299],
         [5401,  297,    6,  298]])

• Coordinates: (0)
• Indexes: (0)
• Attributes: (3)

  cf_role :

  face_node_connectivity

  start_index :

  0

  _FillValue :

  -9223372036854775808

uxds.uxgrid.nNodes_per_face

<xarray.DataArray 'nNodes_per_face' (nMesh2_face: 5400)>
array([4, 4, 4, ..., 4, 4, 4])
Dimensions without coordinates: nMesh2_face
Attributes:
    long_name:  number of non-fill value nodes for each face

xarray.DataArray

'nNodes_per_face'

• nMesh2_face: 5400

• 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 ... 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4

  array([4, 4, 4, ..., 4, 4, 4])

• Coordinates: (0)
• Indexes: (0)
• Attributes: (1)

  long_name :

  number of non-fill value nodes for each face

uxds.uxgrid

<uxarray.Grid>
Original Grid Type: ugrid
Grid Dimensions:
  * nMesh2_face: 5400
  * nMaxMesh2_face_nodes: 4
  * nMesh2_node: 5402
Grid Coordinate Variables:
  * Mesh2_node_x: (5402,)
  * Mesh2_node_y: (5402,)
  * Mesh2_node_cart_x: (5402,)
  * Mesh2_node_cart_y: (5402,)
  * Mesh2_node_cart_z: (5402,)
Grid Connectivity Variables:
  * Mesh2_face_nodes: (5400, 4)
  * nNodes_per_face: (5400,)

As we can see above, these are the only two connectivity variables listed. In addition to these, UXarray provides support for constructing additional connectivity variables.

uxds.uxgrid.Mesh2_edge_nodes

<xarray.DataArray 'Mesh2_edge_nodes' (nMesh2_edge: 10800, Two: 2)>
array([[   0,    8],
       [   0,  123],
       [   0,  124],
       ...,
       [5398, 5399],
       [5399, 5400],
       [5400, 5401]])
Dimensions without coordinates: nMesh2_edge, Two
Attributes:
    cf_role:          edge_node_connectivity
    _FillValue:       -9223372036854775808
    long_name:        Maps every edge to the two nodes that it connects
    start_index:      0
    inverse_indices:  [  0  25 369 ...  19  20 886]
    fill_value_mask:  [False False False ... False False False]

xarray.DataArray

'Mesh2_edge_nodes'

• nMesh2_edge: 10800
• Two: 2

• 0 8 0 123 0 124 1 36 1 ... 5397 5398 5398 5399 5399 5400 5400 5401

  array([[   0,    8],
         [   0,  123],
         [   0,  124],
         ...,
         [5398, 5399],
         [5399, 5400],
         [5400, 5401]])

• Coordinates: (0)
• Indexes: (0)
• Attributes: (6)

  cf_role :

  edge_node_connectivity

  _FillValue :

  -9223372036854775808

  long_name :

  Maps every edge to the two nodes that it connects

  start_index :

  0

  inverse_indices :

  [ 0 25 369 ... 19 20 886]

  fill_value_mask :

  [False False False ... False False False]

uxds.uxgrid.Mesh2_face_edges

<xarray.DataArray 'Mesh2_face_edges' (nMesh2_face: 5400, nMaxMesh2_face_edges: 4)>
array([[    0,    25,   369,     2],
       [   24,    28,  1056,    25],
       [   27,    31,  1058,    28],
       ...,
       [10798,   889,   887,   892],
       [10799,   886,   884,   889],
       [  883,    19,    20,   886]])
Dimensions without coordinates: nMesh2_face, nMaxMesh2_face_edges
Attributes:
    cf_role:      face_edges_connectivity
    start_index:  0
    long_name:    Maps every edge to the two nodes that it connects

xarray.DataArray

'Mesh2_face_edges'

• nMesh2_face: 5400
• nMaxMesh2_face_edges: 4

• 0 25 369 2 24 28 1056 25 27 31 ... 892 10799 886 884 889 883 19 20 886

  array([[    0,    25,   369,     2],
         [   24,    28,  1056,    25],
         [   27,    31,  1058,    28],
         ...,
         [10798,   889,   887,   892],
         [10799,   886,   884,   889],
         [  883,    19,    20,   886]])

• Coordinates: (0)
• Indexes: (0)
• Attributes: (3)

  cf_role :

  face_edges_connectivity

  start_index :

  0

  long_name :

  Maps every edge to the two nodes that it connects

uxds.uxgrid

<uxarray.Grid>
Original Grid Type: ugrid
Grid Dimensions:
  * nMesh2_face: 5400
  * nMaxMesh2_face_nodes: 4
  * nMesh2_node: 5402
  * nMesh2_edge: 10800
  * nMaxMesh2_face_edges: 4
Grid Coordinate Variables:
  * Mesh2_node_x: (5402,)
  * Mesh2_node_y: (5402,)
  * Mesh2_node_cart_x: (5402,)
  * Mesh2_node_cart_y: (5402,)
  * Mesh2_node_cart_z: (5402,)
Grid Connectivity Variables:
  * Mesh2_face_nodes: (5400, 4)
  * Mesh2_edge_nodes: (10800, 2)
  * Mesh2_face_edges: (5400, 4)
  * nNodes_per_face: (5400,)

These additional variables are constructed upon calling their respective attributes and are now stored under the uxgrid property. Additionally, the Mesh2_node_cart_x, Mesh2_node_cart_y, and Mesh2_node_cart_z that we constructed earlier are now also shown here.

Grid Dimensions

uxds.uxgrid.nMesh2_node

5402

uxds.uxgrid.nMesh2_edge

10800

uxds.uxgrid.nMesh2_face

5400

uxds.uxgrid.nMaxMesh2_face_nodes

4

uxds.uxgrid.nMaxMesh2_face_edges

4