hyperion.grid.AMRGrid¶

class hyperion.grid.AMRGrid(amr_grid=None)¶

An AMR grid.

Levels are stored in the levels attribute, which is a list of hyperion.grid.amr_grid.Level objects, which in turn contain a grids attribute which is a list of Grid objects.

Levels can be added with:

level = amr.add_level()

And grids can be added to a level with:

grid = level.add_grid()

Grid objects have the following attributes which should be set:

xmin - lower x position of the grid

xmax - upper x position of the grid

ymin - lower y position of the grid

ymax - upper y position of the grid

zmin - lower z position of the grid

zmax - upper z position of the grid

nx - number of cells in x direction

ny - number of cells in y direction

nz - number of cells in z direction

quantities - a dictionary containing physical quantities (see below)

AMRGrid 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 AMRGrid object, but a AMRGridView object. When setting this for the first time, this can be set either to another AMRGridView object, an external h5py link, or an empty list. For example, the following should work:

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

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

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

Which is also an AMRGridView object.

Methods

`read`(self, group[, quantities])	Read the geometry and physical quantities from an AMR grid
`read_geometry`(self, group)	Read in geometry information from an AMR grid
`read_quantities`(self, group[, quantities])	Read in physical quantities from an AMR grid
`write`(self, group[, quantities, copy, …])	Write out the AMR grid
`write_single_array`(self, group, name, amr_grid)	Write out a single quantity, checking for consistency with geometry
`add_derived_quantity`(self, name, function)
`to_yt`(self[, dust_id])	Convert AMR grid to a yt object (requires yt)
`from_yt`(ds[, quantity_mapping])	Convert a yt dataset to a Hyperion AMRGrid object

Methods (detail)

read(self, group, quantities='all')¶

Read the geometry and physical quantities from an AMR 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(self, group)¶

Read in geometry information from an AMR grid

Parameters

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

read_quantities(self, group, quantities='all')¶

Read in physical quantities from an AMR 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(self, group, quantities='all', copy=True, absolute_paths=False, compression=True, wall_dtype=<class 'float'>, physics_dtype=<class 'float'>)¶

Write out the AMR 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
physics_dtypetype: The datatype to use to write the physical quantities

write_single_array(self, group, name, amr_grid, 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
amr_gridAMRGridView: 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(self, name, function)¶

to_yt(self, 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).

classmethod from_yt(ds, quantity_mapping={})¶

Convert a yt dataset to a Hyperion AMRGrid object

Note

This method requires yt 3.0 or later

Parameters

dsyt Dataset: The yt dataset
quantity_mappingdict: A dictionary mapping the name of the quantity to use in Hyperion (the key) to the name of the field to extract in yt (the value).

Notes

The domain is always re-centered so that the position at ds.domain_center in yt becomes the origin in Hyperion.

Examples

Assuming that your dust opacities are defined per unit gas mass, and the simulation density is given in gas densities, converting is straightfoward (in this case we assume the density field is called ('gas', 'density')):

>>> from yt import load
>>> from hyperion.grid import AMRGrid
>>> ds = load('DD0010/moving7_0010')
>>> amr = AMRGrid.from_yt(ds, quantity_mapping={'density':('gas', 'density')})

However, you will need to take care if your dust opacities are defined in dust mass units. If the yt dataset does not contain dust densities, you can add a field yourself, for example:

>>> from yt import load
>>> from hyperion.grid import AMRGrid
>>> ds = load('DD0010/moving7_0010')
>>> def _dust_density(field, data):
...     return data[('gas', 'density')].in_units('g/cm**3') * 0.01
>>> ds.add_field(('gas', 'dust_density'), function=_dust_density, units='g/cm**3')

>>> amr = AMRGrid.from_yt(ds, quantity_mapping={'density':('gas', 'dust_density')})

class hyperion.grid.AMRGridView(amr_grid, quantity)¶

Methods

`append`(self, amr_grid_view)	Used to append quantities from another grid
`add`(self, amr_grid_view)	Used to add quantities from another grid

Methods (detail)

append(self, amr_grid_view)¶

Used to append quantities from another grid

Parameters

amr_gridAMRGridView instance: The grid to copy the quantity from

add(self, amr_grid_view)¶

Used to add quantities from another grid

Parameters

amr_gridAMRGridView instance: The grid to copy the quantity from

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hyperion.grid.AMRGrid¶