hyperion.grid.OctreeGrid#

class hyperion.grid.OctreeGrid(*args)#

An octree grid.

To initialize an Octree object, use:

>>> grid = OctreeGrid(x, y, z, dx, dy, dz, refined)

where x, y, and z are the cartesian coordinates of the center of the grid, dx, dy, and dz are the half-widths of the grid, and refined is a sequence of boolean values that indicate whether a given cell is refined.

The first value of the refined sequence indicates whether the parent cell is sub-divided. If it is, then the the second element indicates whether the first cell of the parent cell is sub-divided. If it isn’t, then the next value indicates whether the second cell of the parent cell is sub-divided. If it is, then we need to specify the booleans for all the children of that cell before we move to the third cell of the parent cell.

For example, the simplest grid is a single cell that is not sub-divided:

refined = [False]

The next simplest grid is a single grid cell that is only sub-divided once:

refined = [True, False, False, False, False, False, False, False, False]

It is easier to picture this as a hierarchy:

refined = [True,
             False,
             False,
             False,
             False,
             False,
             False,
             False,
             False,
             ]

If we sub-divide the third sub-cell in the parent cell into cells that are themselves not sub-divided, we get:

refined = [True,
             False,
             False,
             True,
               False,
               False,
               False,
               False,
               False,
               False,
               False,
               False,
             False,
             False,
             False,
             False,
             False,
             ]

and so on. The order of the sub-cells is first along x, then along y, then along z.

OctreeGrid objects may contain multiple quantities (e.g. density, specific energy). To access these, you can specify the name of the quantity as an item:

>>> grid['density']

which is no longer an OctreeGrid object, but a OctreeGridView object. When setting this for the first time, this can be set either to another OctreeGridView object, an external h5py link, or an empty list. For example, the following should work:

>>> grid['density_new'] = grid['density']

OctreeGridView objects allow the specific dust population to be selected as an index:

>>> grid['density'][0]

Which is also an OctreeGridView object.

Methods

`set_walls`(x, y, z, dx, dy, dz, refined)
`read`(group[, quantities])	Read the geometry and physical quantities from an octree grid
`read_geometry`(group)	Read in geometry information from a cartesian grid
`read_quantities`(group[, quantities])	Read in physical quantities from a cartesian grid
`write`(group[, quantities, copy, ...])	Write out the octree grid
`write_single_array`(group, name, array[, ...])	Write out a single quantity, checking for consistency with geometry
`add_derived_quantity`(name, function)
`to_yt`([dust_id])	Convert AMR grid to a yt object (requires yt)

Methods (detail)

set_walls(x, y, z, dx, dy, dz, refined)#

read(group, quantities='all')#

Read the geometry and physical quantities from an octree grid

Parameters:

grouph5py.Group: The HDF5 group to read the grid from. This group should contain groups named ‘Geometry’ and ‘Quantities’.
quantities‘all’ or list: Which physical quantities to read in. Use ‘all’ to read in all quantities or a list of strings to read only specific quantities.

read_geometry(group)#

Read in geometry information from a cartesian grid

Parameters:

grouph5py.Group: The HDF5 group to read the grid geometry from.

read_quantities(group, quantities='all')#

Read in physical quantities from a cartesian grid

Parameters:

grouph5py.Group: The HDF5 group to read the grid quantities from
quantities‘all’ or list: Which physical quantities to read in. Use ‘all’ to read in all quantities or a list of strings to read only specific quantities.

write(group, quantities='all', copy=True, absolute_paths=False, compression=True, wall_dtype=<class 'float'>, physics_dtype=<class 'float'>)#

Write out the octree grid

Parameters:

grouph5py.Group: The HDF5 group to write the grid to
quantities‘all’ or list: Which physical quantities to write out. Use ‘all’ to write out all quantities or a list of strings to write only specific quantities.
copybool: Whether to copy external links, or leave them as links.
absolute_pathsbool: If copy is False, then this indicates whether to use absolute or relative paths for links.
compressionbool: Whether to compress the arrays in the HDF5 file
wall_dtypetype: The datatype to use to write the wall positions (ignored for this kind of grid)
physics_dtypetype: The datatype to use to write the physical quantities

write_single_array(group, name, array, copy=True, absolute_paths=False, compression=True, physics_dtype=<class 'float'>)#

Write out a single quantity, checking for consistency with geometry

Parameters:

grouph5py.Group: The HDF5 group to write the grid to
namestr: The name of the array in the group
arraynp.ndarray: The array to write out
copybool: Whether to copy external links, or leave them as links.
absolute_pathsbool: If copy is False, then this indicates whether to use absolute or relative paths for links.
compressionbool: Whether to compress the arrays in the HDF5 file
wall_dtypetype: The datatype to use to write the wall positions
physics_dtypetype: The datatype to use to write the physical quantities

add_derived_quantity(name, function)#

to_yt(dust_id=0)#

Convert AMR grid to a yt object (requires yt)

Parameters:

dust_idint, optional: The ID of the dust population to extract. If not set, this defaults to 0 (the first dust population).

class hyperion.grid.OctreeGridView(grid, quantity)#

Methods

`append`(grid)	Used to append quantities from another grid
`add`(grid)	Used to add quantities from another grid

Methods (detail)

append(grid)#

Used to append quantities from another grid

Parameters:

grid1D Numpy array or OctreeGridView instance: The grid to copy the quantity from

add(grid)#

Used to add quantities from another grid

Parameters:

grid1D Numpy array or OctreeGridView instance: The grid to copy the quantity from

hyperion.grid.OctreeGrid

Contents

hyperion.grid.OctreeGrid#