def test_adding_untracked_layer():
layers = MaterialLayers(3)
layers.add(1., type=3., size='sand')
layers.add([0., 0., 1.], type=3., size='sand')
with pytest.raises(ValueError):
layers.add([1.], type=3., size='sand', spam='eggs')
class Lithology(object):
"""Create a Lithology object.
A Lithology is a three dimentional representation of material operated on
by landlab components. Material can be removed through erosion or added to
through deposition. Rock types can have multiple attributes (e.g. age,
erodability or other parameter values, etc).
If the tracked properties are model grid fields, they will be updated to
the surface values of the Lithology. If the properties are not grid fields
then at-node grid fields will be created with their names. Lithology and
its derived versions will make a at-node grid field called `rock_type__id`
to store the rock type id.
Lithology was designed to be used on its own and to be inherited from and
improved. Currently one other Lithology variant exists: LithoLayers
which makes it easy to specify parallel layers of rock with generic layer
geometries.
It is constructed by specifying a series of thicknesses and a series of
rock type IDs. Thicknesses and IDs are both specified in order of closest
to the surface to furthest from the surface. Thicknesses can either be a
single value (cooresponding to a layer of uniform thickness) or a number-of
-nodes length array (cooresponding to a non-uniform layer).
Additionally, an attribute dictionary specifies the properties of each
rock type. This dictionary is expected to have the form of:
.. code-block:: python
attrs = {'K_sp': {1: 0.001,
2: 0.0001},
'D': {1: 0.01,
2: 0.001}}
Where ``'K_sp'`` and ``'D'`` are properties to track, and ``1`` and ``2``
are rock type IDs. The rock type IDs can be any type that is valid as a
python dictionary key.
Attributes
----------
z_top
z_bottom
thickness
dz
tracked_properties
properties
Methods
-------
add_rock_type
add_rock_property
update_rock_properties
add_layer
run_one_step
rock_cube_to_xarray
"""
_name = 'Lithology'
_cite_as = """ """
def __init__(self,
grid,
thicknesses,
ids,
attrs,
layer_type="MaterialLayers"):
"""Create a new instance of Lithology.
Parameters
----------
grid : Landlab ModelGrid
thicknesses : ndarray of shape `(n_layers, )` or `(n_layers, n_nodes)`
Values of layer thicknesses from surface to depth. Layers do not
have to have constant thickness. Layer thickness can be zero,
though the entirety of Lithology must have non-zero thickness.
ids : ndarray of shape `(n_layers, )` or `(n_layers, n_nodes)`
Values of rock type IDs cooresponding to each layer specified in
**thicknesses**. A single layer may have multiple rock types if
specified by the user.
attrs : dict
Rock type property dictionary. See class docstring for example of
required format.
layer_type : str, optional
Type of Landlab layers object used to store the layers. If
MaterialLayers (default) is specified, then erosion removes material
and does not create a layer of thickness zero. If EventLayers is
used, then erosion removes material and creates layers of thickness
zero. Thus, EventLayers may be appropriate if the user is interested
in chronostratigraphy.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
Create a Lithology with uniform thicknesses that alternates between
layers of type 1 and type 2 rock.
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
After creating a Lithology, the model grid will have an at-node grid
field set to the surface values of 'K_sp'.
>>> mg.at_node['K_sp']
array([ 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001,
0.001])
The surface values are also properties of the Lithology.
>>> lith['K_sp']
array([ 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001,
0.001])
We can access information about the Lithology like the total thickness
or layer thicknesses.
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
This might look confusing -- that the layers are in reverse order, but
it is OK. The last layers in the Lithology are those that are closest
to the surface.
The layers don't all have to have the same thickness as in the prior
example. If the layers have non-uniform thickness, then they must be
specified in an array of shape `(n_layer, n_nodes)`. In this case, the
layer IDs must be specified in either an array of `(n_layer)` or
`(n_layer, n_nodes)`.
Here we make a layer that gets thicker as a function of the x value of
the model grid.
>>> layer_pattern = (0.5 * mg.x_of_node) + 1.0
>>> thicknesses = [1*layer_pattern, 2*layer_pattern, 4*layer_pattern]
>>> ids = [1, 2, 1]
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.thickness
array([ 7. , 10.5, 14. , 7. , 10.5, 14. , 7. , 10.5, 14. ])
>>> lith.dz
array([[ 4. , 6. , 8. , 4. , 6. , 8. , 4. , 6. , 8. ],
[ 2. , 3. , 4. , 2. , 3. , 4. , 2. , 3. , 4. ],
[ 1. , 1.5, 2. , 1. , 1.5, 2. , 1. , 1.5, 2. ]])
"""
# save reference to the grid and the last time steps's elevation.
self._grid = grid
try:
self.last_elevation = self._grid['node'][
'topographic__elevation'][:].copy()
except KeyError:
msg = ('Lithology requires that topographic__elevation already '
'exists as an at-node field.')
raise ValueError(msg)
# save inital information about thicknesses, layers, attributes, and ids.
self._init_thicknesses = np.asarray(thicknesses)
self._attrs = attrs
self._number_of_init_layers = self._init_thicknesses.shape[0]
self._properties = list(attrs.keys())
self._rock_id_name = 'rock_type__id'
# assert that thicknesses and ids are correct and consistent shapes
# if thickness is a 2d array.
if self._init_thicknesses.ndim == 2:
# assert that the 2nd dimension is the same as the number of nodes.
if self._init_thicknesses.shape[1] != self._grid.number_of_nodes:
msg = ('Thicknesses provided to Lithology are ',
'inconsistent with the ModelGrid.')
raise ValueError(msg)
# if IDs is a 2d array assert that it is the same size as thicknesses
if np.asarray(ids).ndim == 2:
if self._init_thicknesses.shape != np.asarray(ids).shape:
msg = ('Thicknesses and IDs provided to Lithology are ',
'inconsistent with each other.')
raise ValueError(msg)
# if tests pass set value of IDs.
self._layer_ids = np.asarray(ids)
# if IDS is a 1d array
elif np.asarray(ids).ndim == 1:
if np.asarray(ids).size != self._number_of_init_layers:
msg = ('Number of IDs provided to Lithology is ',
'inconsistent with number of layers provided in '
'thicknesses.')
raise ValueError(msg)
# if tests pass, broadcast ids to correct shape.
self._layer_ids = np.broadcast_to(
np.atleast_2d(np.asarray(ids)).T,
self._init_thicknesses.shape)
else:
msg = ('IDs must be of shape `(n_layers, )` or `(n_layers, '
'n_nodes)`. Passed array has more than 2 dimensions.')
raise ValueError(msg)
elif self._init_thicknesses.ndim == 1:
if self._init_thicknesses.shape != np.asarray(ids).shape:
msg = ('Thicknesses and IDs provided to Lithology are ',
'inconsistent with each other.')
raise ValueError(msg)
self._layer_ids = np.asarray(ids)
else:
msg = (
'Thicknesses must be of shape `(n_layers, )` or `(n_layers, '
'n_nodes)`. Passed array has more than 2 dimensions.')
raise ValueError(msg)
# assert that attrs are pointing to fields (or create them)
for at in self._properties:
if at not in grid.at_node:
self._grid.add_empty('node', at)
# add a field for the rock type id
if self._rock_id_name not in self._grid.at_node:
self._grid.add_empty('node', self._rock_id_name)
# verify that all IDs have attributes.
self._check_property_dictionary()
# create a EventLayers instance
if layer_type == 'EventLayers':
self._layers = EventLayers(grid.number_of_nodes,
self._number_of_init_layers)
elif layer_type == 'MaterialLayers':
self._layers = MaterialLayers(grid.number_of_nodes,
self._number_of_init_layers)
else:
raise ValueError(('Lithology passed an invalid option for '
'layer type.'))
# From bottom to top, add layers to the Lithology with attributes.
for i in range(self._number_of_init_layers - 1, -1, -1):
try:
self.add_layer(self._init_thicknesses[i, :],
self._layer_ids[i, :])
except IndexError:
self.add_layer(self._init_thicknesses[i], self._layer_ids[i])
def __getitem__(self, name):
return self._get_surface_values(name)
@property
def ids(self):
"""Rock type IDs used by Lithology."""
return list(self._ids)
@property
def tracked_properties(self):
"""Properties tracked by Lithology.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.tracked_properties
['K_sp']
"""
self._properties.sort()
return self._properties
@property
def properties(self):
"""Properties dictionary used by Lithology.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.properties
{'K_sp': {1: 0.001, 2: 0.0001}}
"""
return self._attrs
@property
def thickness(self):
"""Total thickness of the Lithology at each node.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
"""
return self._layers.thickness
@property
def dz(self):
"""Thickness of each layer in the Lithology at each node.
The thickness of each layer in the Lithology as an array of shape
`(number_of_layers, number_of_nodes)`.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
"""
return self._layers.dz
@property
def z_bottom(self):
"""Thickness from the surface to the bottom of each layer in Lithology.
Thickness from the topographic surface to the bottom of each layer as
an array of shape `(number_of_layers, number_of_nodes)`.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.z_bottom
array([[ 8., 8., 8., 8., 8., 8., 8., 8., 8.],
[ 7., 7., 7., 7., 7., 7., 7., 7., 7.],
[ 3., 3., 3., 3., 3., 3., 3., 3., 3.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
"""
thick = np.broadcast_to(self._layers.thickness, self._layers.z.shape)
return thick - self._layers.z + self._layers.dz
@property
def z_top(self):
"""Thickness from the surface to the top of each layer in Lithology.
Thickness from the topographic surface to the top of each layer as
an array of shape `(number_of_layers, number_of_nodes)`.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.z_top
array([[ 7., 7., 7., 7., 7., 7., 7., 7., 7.],
[ 3., 3., 3., 3., 3., 3., 3., 3., 3.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 0., 0., 0., 0., 0., 0., 0., 0., 0.]])
"""
thick = np.broadcast_to(self._layers.thickness, self._layers.z.shape)
return thick - self._layers.z
def _check_property_dictionary(self):
"""Check compatibility of Lithology and property dictionary."""
ids = []
for at in self._properties:
ids.extend(self._attrs[at].keys())
self._ids = frozenset(np.unique(ids))
for at in self._properties:
for i in self._ids:
if i not in self._attrs[at]:
msg = ('A rock type with ID value ' + str(i) + 'was '
'specified in Lithology. No value '
'for this ID was provided in property ' + at + '.')
raise ValueError(msg)
def _update_surface_values(self):
"""Update Lithology surface values"""
# Update surface values for each attribute.
self._grid['node'][self._rock_id_name][:] = self._surface_rock_type
for at in self._properties:
self._grid['node'][at][:] = self[at]
def add_layer(self, thickness, rock_id=None):
"""Add a new layer to Lithology.
Parameters
----------
thickness : float or `(n_nodes,)` array
Positive values deposit material on to Lithology while negative
values erode Lithology.
rock_id : single value or `n_nodes` long itterable, optional if only erosion occurs
Rock type ID for new deposits. Can be single value or an number-
of-nodes array.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
We can instantiate Lithology with rock type properties we know we will
use in the future.
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001,
... 3: 0.01}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
Add a layer of thickness 3 and rock type 3.
>>> lith.add_layer(3, rock_id=3)
The value of K_sp at node is now updated to the value of rock type 3
>>> mg.at_node['K_sp']
array([ 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01])
A negative value will erode. We can also pass a `(n_nodes,) long array
to erode unevenly. If all parts of the layer erode, then no rock_id
needs to be passed.
>>> erosion_amount = [-2., -2., -2., -4., -4., -4., -6., -6., -6.]
>>> lith.add_layer(erosion_amount)
>>> mg.at_node['K_sp']
array([ 0.01 , 0.01 , 0.01 , 0.0001, 0.0001, 0.0001, 0.001 ,
0.001 , 0.001 ])
Now different layers are exposed at the surface and the value of K_sp
is spatially variable.
"""
thickness = np.array(thickness)
# verify that Lithology will still have thickness after change
if np.any((self._layers.thickness + thickness) <= 0):
msg = ('add_layer will result in Lithology having a thickness of '
'zero at at least one node.')
raise ValueError(msg)
# verify that rock type added exists.
try:
all_ids_present = self._ids.issuperset(rock_id)
new_ids = rock_id
except TypeError:
all_ids_present = self._ids.issuperset([rock_id])
new_ids = [rock_id]
if all_ids_present == False:
missing_ids = set(new_ids).difference(self._ids)
if np.any(thickness > 0):
msg = (
'Lithology add_layer was given a rock type id that does '
'not yet exist and will need to deposit. Use a valid '
'rock type or add_rock_type. ' + str(missing_ids))
raise ValueError(msg)
# add_rock_type
if rock_id is not None:
# add layer
attributes = {self._rock_id_name: rock_id}
self._layers.add(thickness, **attributes)
else:
self._layers.add(thickness)
# update surface rock type
self._surface_rock_type = self._layers.get_surface_values(
self._rock_id_name)
# update surface values
self._update_surface_values()
def add_property(self, attrs):
"""Add new property to Lithology
Parameters
----------
attrs : dict
Rock attribute dictionary for the new property(s).
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.add_property({'D': {1: 0.03,
... 2: 0.004}})
>>> lith.tracked_properties
['D', 'K_sp']
>>> mg.at_node['D']
array([ 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03])
"""
for at in attrs:
if at in self._properties:
msg = ('add_property is trying to add an existing '
'attribute, this is not permitted. ' + str(at))
raise ValueError(msg)
new_rids = attrs[at].keys()
for rid in new_rids:
if rid not in self._ids:
msg = ('add_property has an attribute(' + str(at) + ')'
' for rock type ' + str(rid) +
' that no other. Rock '
' type has. This is not permitted.')
raise ValueError(msg)
for rid in self._ids:
if rid not in new_rids:
msg = ('add_property needs a value for id ' + str(rid) + ''
' and attribute ' + str(at) + '.')
raise ValueError(msg)
for at in attrs:
if at not in self._grid.at_node:
self._grid.add_empty('node', at)
self._attrs[at] = attrs[at]
self._properties.append(at)
# update surface values
self._update_surface_values()
def add_rock_type(self, attrs):
"""Add rock type to Lithology.
Parameters
----------
attrs : dict
Rock attribute dictionary for the new rock type(s).
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.add_rock_type({'K_sp': {4: 0.03,
... 6: 0.004}})
>>> lith.ids
[1, 2, 4, 6]
>>> lith.properties
{'K_sp': {1: 0.001, 2: 0.0001, 4: 0.03, 6: 0.004}}
"""
# Check that the new rock type has all existing attributes
for at in self._properties:
if at not in attrs:
msg = 'The new rock type is missing attribute ' + str(at) + '.'
raise ValueError(msg)
# And no new attributes
for at in attrs:
if at not in self._properties:
msg = ('The new rock type has an attribute (e' + str(at) + ') '
'that no other rock type has. This is not permitted.')
raise ValueError(msg)
new_ids = []
for at in attrs:
att_dict = attrs[at]
rids = att_dict.keys()
for rid in rids:
if rid in self._layer_ids:
msg = ('Rock type ID ' + str(rid) + ' for attribute '
'' + str(at) + ' has already been added. This is '
'not allowed')
raise ValueError(msg)
else:
new_ids.append(rid)
self._attrs[at][rid] = att_dict[rid]
self._ids = self._ids.union(new_ids)
# update surface values
self._update_surface_values()
def update_rock_properties(self, at, rock_id, value):
"""Update rock type attribute.
Paramters
---------
at : str
Attribute name
rock_id : value
Rock type ID
value : value
New value for rock type attribute
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> mg.at_node['K_sp']
array([ 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001,
0.001])
>>> lith.update_rock_properties('K_sp', 1, 0.03)
>>> mg.at_node['K_sp']
array([ 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03])
"""
if at not in self._properties:
msg = ('Lithology cannot update the value of ' + str(at) + 'as '
'this attribute does not exist.')
raise ValueError(msg)
if self._ids.issuperset([rock_id]) == False:
msg = ('Lithology cannot update the value of rock type '
'' + str(rock_id) + 'for attribute ' + str(at) + ' as '
'this rock type is not yet defined.')
raise ValueError(msg)
# set the value in the attribute dictionary
self._attrs[at][rock_id] = value
# update surface values
self._update_surface_values()
def _get_surface_values(self, at):
"""Get surface values for attribute."""
return np.array(list(map(self._attrs[at].get,
self._surface_rock_type)))
def rock_cube_to_xarray(self, depths):
"""Construct a 3D rock cube of rock type ID as an xarray dataset.
Create an xarray dataset in (x, y, z) that shows the rock type with
depth relative to the current topographic surface.
Here the z dimension is depth relative to the current topographic
surface, NOT depth relative to an absolute datum.
Note also that when this method is called, it will construct the current
values of lithology with depth, NOT the initial values.
Paramters
---------
depths : array
Returns
-------
ds : xarray dataset
"""
depths = np.asarray(depths)
rock_type = self._layers[self._rock_id_name]
rock_cube = np.empty(
(depths.size, self._grid.shape[0], self._grid.shape[1]))
# at each node point, interpolate between ztop/bottomo correct.y
for sid in range(self._layers.number_of_stacks):
coord = np.unravel_index(
sid, (self._grid.shape[0], self._grid.shape[1]))
real_layers = self.dz[:, sid] > 0
f = interp1d(np.flipud(self.z_top[real_layers, sid]),
np.flipud(rock_type[real_layers, sid]),
kind='previous')
vals = f(depths)
rock_cube[:, coord[0], coord[1]] = vals
ds = xr.Dataset(
data_vars={
'rock_type__id': (('z', 'y', 'x'), rock_cube, {
'units': '-',
'long_name': 'Rock Type ID Code'
})
},
coords={
'x':
(('x'), self._grid.x_of_node.reshape(self._grid.shape)[0, :], {
'units': 'meters'
}),
'y':
(('y'), self._grid.y_of_node.reshape(self._grid.shape)[:, 1], {
'units': 'meters'
}),
'z': (('z'), depths, {
'units': 'meters',
'long_name': 'Depth Below Topographic Surface'
})
})
return ds
def run_one_step(self, dz_advection=0, rock_id=None):
"""Update Lithology.
The ``run_one_step`` method calculates elevation change of the
Lithology surface (taking into account any advection due to external
processes) and then either deposits or erodes based on elevation
change.
Parameters
----------
dz_advenction : float or `(n_nodes, ) shape array, optional
Change in rock elevation due to advection by some external process.
rock_id : value or `(n_nodes, ) shape array, optional
Rock type id for new material if deposited.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_ones('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
If we erode the surface, and then update Lithology, the thickness will
change.
>>> z -= 0.5
>>> lith.run_one_step(dz_advection=0)
>>> lith.thickness
array([ 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5])
The default of Lithology is to use MaterialLayers from the Landlab
layers submodule. This means that when we erode, we will remove a layer
from the layers datastructure if it has no material anywhere.
>>> lith.dz
array([[ 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ],
[ 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. ],
[ 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. ],
[ 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]])
We can see the value of the rock type at the surface.
>>> mg.at_node['rock_type__id']
array([ 1., 1., 1., 1., 1., 1., 1., 1., 1.])
If you deposit, a valid rock_id must be provided. If the rock type
is the same as the current surface value everywhere, then the layers
will be combined.
>>> z += 1.5
>>> lith.run_one_step(dz_advection=0, rock_id = 1)
>>> lith.thickness
array([ 9., 9., 9., 9., 9., 9., 9., 9., 9.])
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.]])
This contrasts with the behavior of Lithology if we use EventLayers.
Next we repeat this example with EventLayers. Note that no matter which
method you use, the values of the model grid fields will be the same.
These two methods differ only in the details of the data structure they
use to store the layer information.
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_ones('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs,
... layer_type='EventLayers')
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
If we erode the surface, and then update Lithology, the thickness
will change. However, with EventLayers, the ``lith.dz`` structure
will be different. It will have a layer with thickness zero that
represents the event of erosion.
>>> z -= 0.5
>>> lith.run_one_step(dz_advection=0)
>>> lith.thickness
array([ 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5])
>>> lith.dz
array([[ 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ],
[ 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. ],
[ 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. ],
[ 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[ 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ]])
We can see the value of the rock type at the surface. As expected,
it is just the same as if we used MaterialLayers.
>>> mg.at_node['rock_type__id']
array([ 1., 1., 1., 1., 1., 1., 1., 1., 1.])
If you deposit, a valid rock_id must be provided. Unlike
MaterialLayers, these two layers will not be combined, even if they
have the same properties.
>>> z += 1.5
>>> lith.run_one_step(dz_advection=0, rock_id = 1)
>>> lith.thickness
array([ 9., 9., 9., 9., 9., 9., 9., 9., 9.])
>>> lith.dz
array([[ 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ],
[ 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. ],
[ 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. ],
[ 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[ 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
[ 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5]])
"""
# calculate amount of erosion
elevation_change = (self._grid['node']['topographic__elevation'] -
(self.last_elevation + dz_advection))
# add layer
self.add_layer(elevation_change, rock_id=rock_id)
# update the last elevation.
self.last_elevation = self._grid['node'][
'topographic__elevation'][:].copy()
class Lithology(Component):
"""Create a Lithology object.
A Lithology is a three dimentional representation of material operated on
by landlab components. Material can be removed through erosion or added to
through deposition. Rock types can have multiple attributes (e.g. age,
erodability or other parameter values, etc).
If the tracked properties are model grid fields, they will be updated to
the surface values of the Lithology. If the properties are not grid fields
then at-node grid fields will be created with their names. Lithology and
its derived versions will make a at-node grid field called `rock_type__id`
to store the rock type id.
Lithology was designed to be used on its own and to be inherited from and
improved. Currently one other Lithology variant exists: LithoLayers
which makes it easy to specify parallel layers of rock with generic layer
geometries.
It is constructed by specifying a series of thicknesses and a series of
rock type IDs. Thicknesses and IDs are both specified in order of closest
to the surface to furthest from the surface. Thicknesses can either be a
single value (corresponding to a layer of uniform thickness) or a number-of
-nodes length array (corresponding to a non-uniform layer).
Additionally, an attribute dictionary specifies the properties of each
rock type. This dictionary is expected to have the form of:
.. code-block:: python
attrs = {'K_sp': {1: 0.001,
2: 0.0001},
'D': {1: 0.01,
2: 0.001}}
Where ``'K_sp'`` and ``'D'`` are properties to track, and ``1`` and ``2``
are rock type IDs. The rock type IDs can be any type that is valid as a
python dictionary key.
"""
_name = "Lithology"
_cite_as = """@article{barnhart2018lithology,
title = "Lithology: A Landlab submodule for spatially variable rock properties",
journal = "Journal of Open Source Software",
volume = "",
pages = "",
year = "2018",
doi = "10.21105/joss.00979",
author = "Katherine R. Barnhart and Eric Hutton and Nicole M. Gasparini and Gregory E. Tucker",
}"""
def __init__(self, grid, thicknesses, ids, attrs, layer_type="MaterialLayers"):
"""Create a new instance of Lithology.
Parameters
----------
grid : Landlab ModelGrid
thicknesses : ndarray of shape `(n_layers, )` or `(n_layers, n_nodes)`
Values of layer thicknesses from surface to depth. Layers do not
have to have constant thickness. Layer thickness can be zero,
though the entirety of Lithology must have non-zero thickness.
ids : ndarray of shape `(n_layers, )` or `(n_layers, n_nodes)`
Values of rock type IDs corresponding to each layer specified in
**thicknesses**. A single layer may have multiple rock types if
specified by the user.
attrs : dict
Rock type property dictionary. See class docstring for example of
required format.
layer_type : str, optional
Type of Landlab layers object used to store the layers. If
MaterialLayers (default) is specified, then erosion removes material
and does not create a layer of thickness zero. If EventLayers is
used, then erosion removes material and creates layers of thickness
zero. Thus, EventLayers may be appropriate if the user is interested
in chronostratigraphy.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
Create a Lithology with uniform thicknesses that alternates between
layers of type 1 and type 2 rock.
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
After creating a Lithology, the model grid will have an at-node grid
field set to the surface values of 'K_sp'.
>>> mg.at_node['K_sp']
array([ 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001,
0.001])
The surface values are also properties of the Lithology.
>>> lith['K_sp']
array([ 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001,
0.001])
We can access information about the Lithology like the total thickness
or layer thicknesses.
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
This might look confusing -- that the layers are in reverse order, but
it is OK. The last layers in the Lithology are those that are closest
to the surface.
The layers don't all have to have the same thickness as in the prior
example. If the layers have non-uniform thickness, then they must be
specified in an array of shape `(n_layer, n_nodes)`. In this case, the
layer IDs must be specified in either an array of `(n_layer)` or
`(n_layer, n_nodes)`.
Here we make a layer that gets thicker as a function of the x value of
the model grid.
>>> layer_pattern = (0.5 * mg.x_of_node) + 1.0
>>> thicknesses = [1*layer_pattern, 2*layer_pattern, 4*layer_pattern]
>>> ids = [1, 2, 1]
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.thickness
array([ 7. , 10.5, 14. , 7. , 10.5, 14. , 7. , 10.5, 14. ])
>>> lith.dz
array([[ 4. , 6. , 8. , 4. , 6. , 8. , 4. , 6. , 8. ],
[ 2. , 3. , 4. , 2. , 3. , 4. , 2. , 3. , 4. ],
[ 1. , 1.5, 2. , 1. , 1.5, 2. , 1. , 1.5, 2. ]])
"""
# save reference to the grid and the last time steps's elevation.
self._grid = grid
try:
self.last_elevation = self._grid["node"]["topographic__elevation"][:].copy()
except KeyError:
msg = (
"Lithology requires that topographic__elevation already "
"exists as an at-node field."
)
raise ValueError(msg)
# save inital information about thicknesses, layers, attributes, and ids.
self._init_thicknesses = np.asarray(thicknesses)
self._attrs = attrs
self._number_of_init_layers = self._init_thicknesses.shape[0]
self._properties = list(attrs.keys())
self._rock_id_name = "rock_type__id"
# assert that thicknesses and ids are correct and consistent shapes
# if thickness is a 2d array.
if self._init_thicknesses.ndim == 2:
# assert that the 2nd dimension is the same as the number of nodes.
if self._init_thicknesses.shape[1] != self._grid.number_of_nodes:
msg = (
"Thicknesses provided to Lithology are ",
"inconsistent with the ModelGrid.",
)
raise ValueError(msg)
# if IDs is a 2d array assert that it is the same size as thicknesses
if np.asarray(ids).ndim == 2:
if self._init_thicknesses.shape != np.asarray(ids).shape:
msg = (
"Thicknesses and IDs provided to Lithology are ",
"inconsistent with each other.",
)
raise ValueError(msg)
# if tests pass set value of IDs.
self._layer_ids = np.asarray(ids)
# if IDS is a 1d array
elif np.asarray(ids).ndim == 1:
if np.asarray(ids).size != self._number_of_init_layers:
msg = (
"Number of IDs provided to Lithology is ",
"inconsistent with number of layers provided in "
"thicknesses.",
)
raise ValueError(msg)
# if tests pass, broadcast ids to correct shape.
self._layer_ids = np.broadcast_to(
np.atleast_2d(np.asarray(ids)).T, self._init_thicknesses.shape
)
else:
msg = (
"IDs must be of shape `(n_layers, )` or `(n_layers, "
"n_nodes)`. Passed array has more than 2 dimensions."
)
raise ValueError(msg)
elif self._init_thicknesses.ndim == 1:
if self._init_thicknesses.shape != np.asarray(ids).shape:
msg = (
"Thicknesses and IDs provided to Lithology are ",
"inconsistent with each other.",
)
raise ValueError(msg)
self._layer_ids = np.asarray(ids)
else:
msg = (
"Thicknesses must be of shape `(n_layers, )` or `(n_layers, "
"n_nodes)`. Passed array has more than 2 dimensions."
)
raise ValueError(msg)
# assert that attrs are pointing to fields (or create them)
for at in self._properties:
if at not in grid.at_node:
self._grid.add_empty("node", at)
# add a field for the rock type id
if self._rock_id_name not in self._grid.at_node:
self._grid.add_empty("node", self._rock_id_name)
# verify that all IDs have attributes.
self._check_property_dictionary()
# create a EventLayers instance
if layer_type == "EventLayers":
self._layers = EventLayers(
grid.number_of_nodes, self._number_of_init_layers
)
elif layer_type == "MaterialLayers":
self._layers = MaterialLayers(
grid.number_of_nodes, self._number_of_init_layers
)
else:
raise ValueError(("Lithology passed an invalid option for " "layer type."))
# From bottom to top, add layers to the Lithology with attributes.
for i in range(self._number_of_init_layers - 1, -1, -1):
try:
self.add_layer(self._init_thicknesses[i, :], self._layer_ids[i, :])
except IndexError:
self.add_layer(self._init_thicknesses[i], self._layer_ids[i])
def __getitem__(self, name):
return self._get_surface_values(name)
@property
def ids(self):
"""Rock type IDs used by Lithology."""
return list(self._ids)
@property
def tracked_properties(self):
"""Properties tracked by Lithology.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.tracked_properties
['K_sp']
"""
self._properties.sort()
return self._properties
@property
def properties(self):
"""Properties dictionary used by Lithology.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.properties
{'K_sp': {1: 0.001, 2: 0.0001}}
"""
return self._attrs
@property
def thickness(self):
"""Total thickness of the Lithology at each node.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
"""
return self._layers.thickness
@property
def dz(self):
"""Thickness of each layer in the Lithology at each node.
The thickness of each layer in the Lithology as an array of shape
`(number_of_layers, number_of_nodes)`.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
"""
return self._layers.dz
@property
def z_bottom(self):
"""Thickness from the surface to the bottom of each layer in Lithology.
Thickness from the topographic surface to the bottom of each layer as
an array of shape `(number_of_layers, number_of_nodes)`.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.z_bottom
array([[ 8., 8., 8., 8., 8., 8., 8., 8., 8.],
[ 7., 7., 7., 7., 7., 7., 7., 7., 7.],
[ 3., 3., 3., 3., 3., 3., 3., 3., 3.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
"""
thick = np.broadcast_to(self._layers.thickness, self._layers.z.shape)
return thick - self._layers.z + self._layers.dz
@property
def z_top(self):
"""Thickness from the surface to the top of each layer in Lithology.
Thickness from the topographic surface to the top of each layer as
an array of shape `(number_of_layers, number_of_nodes)`.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.z_top
array([[ 7., 7., 7., 7., 7., 7., 7., 7., 7.],
[ 3., 3., 3., 3., 3., 3., 3., 3., 3.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 0., 0., 0., 0., 0., 0., 0., 0., 0.]])
"""
thick = np.broadcast_to(self._layers.thickness, self._layers.z.shape)
return thick - self._layers.z
def _check_property_dictionary(self):
"""Check compatibility of Lithology and property dictionary."""
ids = []
for at in self._properties:
ids.extend(self._attrs[at].keys())
self._ids = frozenset(np.unique(ids))
for at in self._properties:
for i in self._ids:
if i not in self._attrs[at]:
msg = (
"A rock type with ID value " + str(i) + "was "
"specified in Lithology. No value "
"for this ID was provided in property " + at + "."
)
raise ValueError(msg)
def _update_surface_values(self):
"""Update Lithology surface values"""
# Update surface values for each attribute.
self._grid["node"][self._rock_id_name][:] = self._surface_rock_type
for at in self._properties:
self._grid["node"][at][:] = self[at]
def add_layer(self, thickness, rock_id=None):
"""Add a new layer to Lithology.
Parameters
----------
thickness : float or `(n_nodes,)` array
Positive values deposit material on to Lithology while negative
values erode Lithology.
rock_id : single value or `n_nodes` long itterable, optional if only erosion occurs
Rock type ID for new deposits. Can be single value or an number-
of-nodes array.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
We can instantiate Lithology with rock type properties we know we will
use in the future.
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001,
... 3: 0.01}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
Add a layer of thickness 3 and rock type 3.
>>> lith.add_layer(3, rock_id=3)
The value of K_sp at node is now updated to the value of rock type 3
>>> mg.at_node['K_sp']
array([ 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01])
A negative value will erode. We can also pass a `(n_nodes,) long array
to erode unevenly. If all parts of the layer erode, then no rock_id
needs to be passed.
>>> erosion_amount = [-2., -2., -2., -4., -4., -4., -6., -6., -6.]
>>> lith.add_layer(erosion_amount)
>>> mg.at_node['K_sp']
array([ 0.01 , 0.01 , 0.01 , 0.0001, 0.0001, 0.0001, 0.001 ,
0.001 , 0.001 ])
Now different layers are exposed at the surface and the value of K_sp
is spatially variable.
"""
thickness = np.array(thickness)
# verify that Lithology will still have thickness after change
if np.any((self._layers.thickness + thickness) <= 0):
msg = (
"add_layer will result in Lithology having a thickness of "
"zero at at least one node."
)
raise ValueError(msg)
# verify that rock type added exists.
try:
all_ids_present = self._ids.issuperset(rock_id)
new_ids = rock_id
except TypeError:
all_ids_present = self._ids.issuperset([rock_id])
new_ids = [rock_id]
if not all_ids_present:
missing_ids = set(new_ids).difference(self._ids)
if np.any(thickness > 0):
msg = (
"Lithology add_layer was given a rock type id that does "
"not yet exist and will need to deposit. Use a valid "
"rock type or add_rock_type. " + str(missing_ids)
)
raise ValueError(msg)
# add_rock_type
if rock_id is not None:
# add layer
attributes = {self._rock_id_name: rock_id}
self._layers.add(thickness, **attributes)
else:
self._layers.add(thickness)
# update surface rock type
self._surface_rock_type = self._layers.get_surface_values(self._rock_id_name)
# update surface values
self._update_surface_values()
def add_property(self, attrs):
"""Add new property to Lithology
Parameters
----------
attrs : dict
Rock attribute dictionary for the new property(s).
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.add_property({'D': {1: 0.03,
... 2: 0.004}})
>>> lith.tracked_properties
['D', 'K_sp']
>>> mg.at_node['D']
array([ 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03])
"""
for at in attrs:
if at in self._properties:
msg = (
"add_property is trying to add an existing "
"attribute, this is not permitted. " + str(at)
)
raise ValueError(msg)
new_rids = attrs[at].keys()
for rid in new_rids:
if rid not in self._ids:
msg = (
"add_property has an attribute(" + str(at) + ")"
" for rock type " + str(rid) + " that no other rock "
" type has. This is not permitted."
)
raise ValueError(msg)
for rid in self._ids:
if rid not in new_rids:
msg = (
"add_property needs a value for id " + str(rid) + ""
" and attribute " + str(at) + "."
)
raise ValueError(msg)
for at in attrs:
if at not in self._grid.at_node:
self._grid.add_empty("node", at)
self._attrs[at] = attrs[at]
self._properties.append(at)
# update surface values
self._update_surface_values()
def add_rock_type(self, attrs):
"""Add rock type to Lithology.
Parameters
----------
attrs : dict
Rock attribute dictionary for the new rock type(s).
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.add_rock_type({'K_sp': {4: 0.03,
... 6: 0.004}})
>>> lith.ids
[1, 2, 4, 6]
>>> lith.properties
{'K_sp': {1: 0.001, 2: 0.0001, 4: 0.03, 6: 0.004}}
"""
# Check that the new rock type has all existing attributes
for at in self._properties:
if at not in attrs:
msg = "The new rock type is missing attribute " + str(at) + "."
raise ValueError(msg)
# And no new attributes
for at in attrs:
if at not in self._properties:
msg = (
"The new rock type has an attribute (e" + str(at) + ") "
"that no other rock type has. This is not permitted."
)
raise ValueError(msg)
new_ids = []
for at in attrs:
att_dict = attrs[at]
rids = att_dict.keys()
for rid in rids:
if rid in self._layer_ids:
msg = (
"Rock type ID " + str(rid) + " for attribute "
"" + str(at) + " has already been added. This is "
"not allowed"
)
raise ValueError(msg)
else:
new_ids.append(rid)
self._attrs[at][rid] = att_dict[rid]
self._ids = self._ids.union(new_ids)
# update surface values
self._update_surface_values()
def update_rock_properties(self, at, rock_id, value):
"""Update rock type attribute.
Paramters
---------
at : str
Attribute name
rock_id : value
Rock type ID
value : value
New value for rock type attribute
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_zeros('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> mg.at_node['K_sp']
array([ 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001,
0.001])
>>> lith.update_rock_properties('K_sp', 1, 0.03)
>>> mg.at_node['K_sp']
array([ 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03])
"""
if at not in self._properties:
msg = (
"Lithology cannot update the value of " + str(at) + "as "
"this attribute does not exist."
)
raise ValueError(msg)
if not self._ids.issuperset([rock_id]):
msg = (
"Lithology cannot update the value of rock type "
"" + str(rock_id) + "for attribute " + str(at) + " as "
"this rock type is not yet defined."
)
raise ValueError(msg)
# set the value in the attribute dictionary
self._attrs[at][rock_id] = value
# update surface values
self._update_surface_values()
def _get_surface_values(self, at):
"""Get surface values for attribute."""
return np.array(list(map(self._attrs[at].get, self._surface_rock_type)))
def rock_cube_to_xarray(self, depths):
"""Construct a 3D rock cube of rock type ID as an xarray dataset.
Create an xarray dataset in (x, y, z) that shows the rock type with
depth relative to the current topographic surface.
Here the z dimension is depth relative to the current topographic
surface, NOT depth relative to an absolute datum.
Note also that when this method is called, it will construct the current
values of lithology with depth, NOT the initial values.
Paramters
---------
depths : array
Returns
-------
ds : xarray dataset
"""
depths = np.asarray(depths)
rock_type = self._layers[self._rock_id_name]
rock_cube = np.empty((depths.size, self._grid.shape[0], self._grid.shape[1]))
# at each node point, interpolate between ztop/bottomo correct.y
for sid in range(self._layers.number_of_stacks):
coord = np.unravel_index(sid, (self._grid.shape[0], self._grid.shape[1]))
real_layers = self.dz[:, sid] > 0
f = interp1d(
np.flipud(self.z_top[real_layers, sid]),
np.flipud(rock_type[real_layers, sid]),
kind="previous",
)
vals = f(depths)
rock_cube[:, coord[0], coord[1]] = vals
ds = xr.Dataset(
data_vars={
"rock_type__id": (
("z", "y", "x"),
rock_cube,
{"units": "-", "long_name": "Rock Type ID Code"},
)
},
coords={
"x": (
("x"),
self._grid.x_of_node.reshape(self._grid.shape)[0, :],
{"units": "meters"},
),
"y": (
("y"),
self._grid.y_of_node.reshape(self._grid.shape)[:, 1],
{"units": "meters"},
),
"z": (
("z"),
depths,
{"units": "meters", "long_name": "Depth Below Topographic Surface"},
),
},
)
return ds
def run_one_step(self, dz_advection=0, rock_id=None):
"""Update Lithology.
The ``run_one_step`` method calculates elevation change of the
Lithology surface (taking into account any advection due to external
processes) and then either deposits or erodes based on elevation
change.
Parameters
----------
dz_advection : float or `(n_nodes, ) shape array, optional
Change in rock elevation due to advection by some external process.
rock_id : value or `(n_nodes, ) shape array, optional
Rock type id for new material if deposited.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_ones('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
If we erode the surface, and then update Lithology, the thickness will
change.
>>> z -= 0.5
>>> lith.run_one_step(dz_advection=0)
>>> lith.thickness
array([ 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5])
The default of Lithology is to use MaterialLayers from the Landlab
layers submodule. This means that when we erode, we will remove a layer
from the layers datastructure if it has no material anywhere.
>>> lith.dz
array([[ 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ],
[ 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. ],
[ 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. ],
[ 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]])
We can see the value of the rock type at the surface.
>>> mg.at_node['rock_type__id']
array([ 1., 1., 1., 1., 1., 1., 1., 1., 1.])
If you deposit, a valid rock_id must be provided. If the rock type
is the same as the current surface value everywhere, then the layers
will be combined.
>>> z += 1.5
>>> lith.run_one_step(dz_advection=0, rock_id = 1)
>>> lith.thickness
array([ 9., 9., 9., 9., 9., 9., 9., 9., 9.])
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.]])
This contrasts with the behavior of Lithology if we use EventLayers.
Next we repeat this example with EventLayers. Note that no matter which
method you use, the values of the model grid fields will be the same.
These two methods differ only in the details of the data structure they
use to store the layer information.
>>> mg = RasterModelGrid(3, 3)
>>> z = mg.add_ones('node', 'topographic__elevation')
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs,
... layer_type='EventLayers')
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
If we erode the surface, and then update Lithology, the thickness
will change. However, with EventLayers, the ``lith.dz`` structure
will be different. It will have a layer with thickness zero that
represents the event of erosion.
>>> z -= 0.5
>>> lith.run_one_step(dz_advection=0)
>>> lith.thickness
array([ 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5])
>>> lith.dz
array([[ 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ],
[ 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. ],
[ 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. ],
[ 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[ 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ]])
We can see the value of the rock type at the surface. As expected,
it is just the same as if we used MaterialLayers.
>>> mg.at_node['rock_type__id']
array([ 1., 1., 1., 1., 1., 1., 1., 1., 1.])
If you deposit, a valid rock_id must be provided. Unlike
MaterialLayers, these two layers will not be combined, even if they
have the same properties.
>>> z += 1.5
>>> lith.run_one_step(dz_advection=0, rock_id = 1)
>>> lith.thickness
array([ 9., 9., 9., 9., 9., 9., 9., 9., 9.])
>>> lith.dz
array([[ 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ],
[ 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. ],
[ 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. ],
[ 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[ 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
[ 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5]])
"""
# calculate amount of erosion
elevation_change = self._grid["node"]["topographic__elevation"] - (
self.last_elevation + dz_advection
)
# add layer
self.add_layer(elevation_change, rock_id=rock_id)
# update the last elevation.
self.last_elevation = self._grid["node"]["topographic__elevation"][:].copy()
class Lithology(Component):
"""Create a Lithology object.
A Lithology is a three dimentional representation of material operated on
by landlab components. Material can be removed through erosion or added to
through deposition. Rock types can have multiple attributes (e.g. age,
erodability or other parameter values, etc).
If the tracked properties are model grid fields, they will be updated to
the surface values of the Lithology. If the properties are not grid fields
then at-node grid fields will be created with their names. Lithology and
its derived versions will make a at-node grid field called `rock_type__id`
to store the rock type id.
Lithology was designed to be used on its own and to be inherited from and
improved. Currently one other Lithology variant exists: LithoLayers
which makes it easy to specify parallel layers of rock with generic layer
geometries.
It is constructed by specifying a series of thicknesses and a series of
rock type IDs. Thicknesses and IDs are both specified in order of closest
to the surface to furthest from the surface. Thicknesses can either be a
single value (corresponding to a layer of uniform thickness) or a number-of
-nodes length array (corresponding to a non-uniform layer).
Additionally, an attribute dictionary specifies the properties of each
rock type. This dictionary is expected to have the form of:
.. code-block:: python
attrs = {'K_sp': {1: 0.001,
2: 0.0001},
'D': {1: 0.01,
2: 0.001}}
Where ``'K_sp'`` and ``'D'`` are properties to track, and ``1`` and ``2``
are rock type IDs. The rock type IDs can be any type that is valid as a
python dictionary key.
References
----------
**Required Software Citation(s) Specific to this Component**
Barnhart, K., Hutton, E., Gasparini, N., Tucker, G. (2018). Lithology: A
Landlab submodule for spatially variable rock properties. Journal of Open
Source Software 3(30), 979 - 2. https://dx.doi.org/10.21105/joss.00979
**Additional References**
None Listed
"""
_name = "Lithology"
_unit_agnostic = True
_cite_as = """@article{barnhart2018lithology,
title = "Lithology: A Landlab submodule for spatially variable rock properties",
journal = "Journal of Open Source Software",
volume = "",
pages = "",
year = "2018",
doi = "10.21105/joss.00979",
author = "Katherine R. Barnhart and Eric Hutton and Nicole M. Gasparini and Gregory E. Tucker",
}"""
_info = {}
def __init__(
self,
grid,
thicknesses,
ids,
attrs,
layer_type="MaterialLayers",
dz_advection=0,
rock_id=None,
):
"""Create a new instance of Lithology.
Parameters
----------
grid : Landlab ModelGrid
thicknesses : ndarray of shape `(n_layers, )` or `(n_layers, n_nodes)`
Values of layer thicknesses from surface to depth. Layers do not
have to have constant thickness. Layer thickness can be zero,
though the entirety of Lithology must have non-zero thickness.
ids : ndarray of shape `(n_layers, )` or `(n_layers, n_nodes)`
Values of rock type IDs corresponding to each layer specified in
**thicknesses**. A single layer may have multiple rock types if
specified by the user.
attrs : dict
Rock type property dictionary. See class docstring for example of
required format.
layer_type : str, optional
Type of Landlab layers object used to store the layers. If
MaterialLayers (default) is specified, then erosion removes material
and does not create a layer of thickness zero. If EventLayers is
used, then erosion removes material and creates layers of thickness
zero. Thus, EventLayers may be appropriate if the user is interested
in chronostratigraphy.
dz_advection : float, `(n_nodes, )` shape array, or at-node field array optional
Change in rock elevation due to advection by some external process.
This can be changed using the property setter. Dimensions are in
length, not length per time.
rock_id : value or `(n_nodes, )` shape array, optional
Rock type id for new material if deposited.
This can be changed using the property setter.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
Create a Lithology with uniform thicknesses that alternates between
layers of type 1 and type 2 rock.
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
After creating a Lithology, the model grid will have an at-node grid
field set to the surface values of 'K_sp'.
>>> mg.at_node['K_sp']
array([ 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001,
0.001])
The surface values are also properties of the Lithology.
>>> lith['K_sp']
array([ 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001,
0.001])
We can access information about the Lithology like the total thickness
or layer thicknesses.
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
This might look confusing -- that the layers are in reverse order, but
it is OK. The last layers in the Lithology are those that are closest
to the surface.
The layers don't all have to have the same thickness as in the prior
example. If the layers have non-uniform thickness, then they must be
specified in an array of shape `(n_layer, n_nodes)`. In this case, the
layer IDs must be specified in either an array of `(n_layer)` or
`(n_layer, n_nodes)`.
Here we make a layer that gets thicker as a function of the x value of
the model grid.
>>> layer_pattern = (0.5 * mg.x_of_node) + 1.0
>>> thicknesses = [1*layer_pattern, 2*layer_pattern, 4*layer_pattern]
>>> ids = [1, 2, 1]
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.thickness
array([ 7. , 10.5, 14. , 7. , 10.5, 14. , 7. , 10.5, 14. ])
>>> lith.dz
array([[ 4. , 6. , 8. , 4. , 6. , 8. , 4. , 6. , 8. ],
[ 2. , 3. , 4. , 2. , 3. , 4. , 2. , 3. , 4. ],
[ 1. , 1.5, 2. , 1. , 1.5, 2. , 1. , 1.5, 2. ]])
"""
super().__init__(grid)
try:
self._last_elevation = self._grid["node"]["topographic__elevation"][
:
].copy()
except KeyError:
msg = (
"Lithology requires that topographic__elevation already "
"exists as an at-node field."
)
raise ValueError(msg)
# save inital information about thicknesses, layers, attributes, and ids.
self._init_thicknesses = np.asarray(thicknesses)
self._attrs = attrs
self._number_of_init_layers = self._init_thicknesses.shape[0]
self._properties = list(attrs.keys())
self._rock_id_name = "rock_type__id"
# assert that thicknesses and ids are correct and consistent shapes
# if thickness is a 2d array.
if self._init_thicknesses.ndim == 2:
# assert that the 2nd dimension is the same as the number of nodes.
if self._init_thicknesses.shape[1] != self._grid.number_of_nodes:
msg = (
"Thicknesses provided to Lithology are ",
"inconsistent with the ModelGrid.",
)
raise ValueError(msg)
# if IDs is a 2d array assert that it is the same size as thicknesses
if np.asarray(ids).ndim == 2:
if self._init_thicknesses.shape != np.asarray(ids).shape:
msg = (
"Thicknesses and IDs provided to Lithology are ",
"inconsistent with each other.",
)
raise ValueError(msg)
# if tests pass set value of IDs.
self._layer_ids = np.asarray(ids)
# if IDS is a 1d array
elif np.asarray(ids).ndim == 1:
if np.asarray(ids).size != self._number_of_init_layers:
msg = (
"Number of IDs provided to Lithology is ",
"inconsistent with number of layers provided in "
"thicknesses.",
)
raise ValueError(msg)
# if tests pass, broadcast ids to correct shape.
self._layer_ids = np.broadcast_to(
np.atleast_2d(np.asarray(ids)).T, self._init_thicknesses.shape
)
else:
msg = (
"IDs must be of shape `(n_layers, )` or `(n_layers, "
"n_nodes)`. Passed array has more than 2 dimensions."
)
raise ValueError(msg)
elif self._init_thicknesses.ndim == 1:
if self._init_thicknesses.shape != np.asarray(ids).shape:
msg = (
"Thicknesses and IDs provided to Lithology are ",
"inconsistent with each other.",
)
raise ValueError(msg)
self._layer_ids = np.asarray(ids)
else:
msg = (
"Thicknesses must be of shape `(n_layers, )` or `(n_layers, "
"n_nodes)`. Passed array has more than 2 dimensions."
)
raise ValueError(msg)
# assert that attrs are pointing to fields (or create them)
for at in self._properties:
if at not in grid.at_node:
self._grid.add_empty(at, at="node")
# add a field for the rock type id
if self._rock_id_name not in self._grid.at_node:
self._grid.add_empty(self._rock_id_name, at="node")
# verify that all IDs have attributes.
self._check_property_dictionary()
# create a EventLayers instance
if layer_type == "EventLayers":
self._layers = EventLayers(
grid.number_of_nodes, self._number_of_init_layers
)
elif layer_type == "MaterialLayers":
self._layers = MaterialLayers(
grid.number_of_nodes, self._number_of_init_layers
)
else:
raise ValueError(("Lithology passed an invalid option for " "layer type."))
# From bottom to top, add layers to the Lithology with attributes.
for i in range(self._number_of_init_layers - 1, -1, -1):
try:
self.add_layer(self._init_thicknesses[i, :], self._layer_ids[i, :])
except IndexError:
self.add_layer(self._init_thicknesses[i], self._layer_ids[i])
self.dz_advection = dz_advection
self.rock_id = rock_id
def __getitem__(self, name):
return self._get_surface_values(name)
@property
def dz_advection(self):
"""Rate of vertical advection.
Parameters
----------
dz_advection : float, `(n_nodes, )` shape array, or at-node field array optional
Change in rock elevation due to advection by some external process.
This can be changed using the property setter. Dimensions are in
length, not length per time.
Returns
-------
current rate of vertical advection
"""
return return_array_at_node(self._grid, self._dz_advection)
@dz_advection.setter
def dz_advection(self, dz_advection):
return_array_at_node(self._grid, dz_advection) # verify that this will work.
self._dz_advection = dz_advection
@property
def rock_id(self):
"""Rock type for deposition.
Parameters
----------
rock_id : value or `(n_nodes, )` shape array, optional
Rock type id for new material if deposited.
This can be changed using the property setter.
Returns
-------
current type of rock being deposited (if deposition occurs)
"""
if self._rock_id is None:
return None
else:
return return_array_at_node(self._grid, self._rock_id)
@rock_id.setter
def rock_id(self, rock_id):
return_array_at_node(self._grid, rock_id) # verify that this will work.
# verify that all rock types are valid
self._rock_id = rock_id
@property
def ids(self):
"""Rock type IDs used by Lithology."""
return list(self._ids)
@property
def tracked_properties(self):
"""Properties tracked by Lithology.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.tracked_properties
['K_sp']
"""
self._properties.sort()
return self._properties
@property
def properties(self):
"""Properties dictionary used by Lithology.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.properties
{'K_sp': {1: 0.001, 2: 0.0001}}
"""
return self._attrs
@property
def thickness(self):
"""Total thickness of the Lithology at each node.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
"""
return self._layers.thickness
@property
def dz(self):
"""Thickness of each layer in the Lithology at each node.
The thickness of each layer in the Lithology as an array of shape
`(number_of_layers, number_of_nodes)`.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
"""
return self._layers.dz
@property
def z_bottom(self):
"""Thickness from the surface to the bottom of each layer in Lithology.
Thickness from the topographic surface to the bottom of each layer as
an array of shape `(number_of_layers, number_of_nodes)`.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.z_bottom
array([[ 8., 8., 8., 8., 8., 8., 8., 8., 8.],
[ 7., 7., 7., 7., 7., 7., 7., 7., 7.],
[ 3., 3., 3., 3., 3., 3., 3., 3., 3.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
"""
thick = np.broadcast_to(self._layers.thickness, self._layers.z.shape)
return thick - self._layers.z + self._layers.dz
@property
def z_top(self):
"""Thickness from the surface to the top of each layer in Lithology.
Thickness from the topographic surface to the top of each layer as
an array of shape `(number_of_layers, number_of_nodes)`.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.z_top
array([[ 7., 7., 7., 7., 7., 7., 7., 7., 7.],
[ 3., 3., 3., 3., 3., 3., 3., 3., 3.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 0., 0., 0., 0., 0., 0., 0., 0., 0.]])
"""
thick = np.broadcast_to(self._layers.thickness, self._layers.z.shape)
return thick - self._layers.z
def _check_property_dictionary(self):
"""Check compatibility of Lithology and property dictionary."""
ids = []
for at in self._properties:
ids.extend(self._attrs[at].keys())
self._ids = frozenset(np.unique(ids))
for at in self._properties:
for i in self._ids:
if i not in self._attrs[at]:
msg = (
"A rock type with ID value " + str(i) + "was "
"specified in Lithology. No value "
"for this ID was provided in property " + at + "."
)
raise ValueError(msg)
def _update_surface_values(self):
"""Update Lithology surface values."""
# Update surface values for each attribute.
self._grid["node"][self._rock_id_name][:] = self._surface_rock_type
for at in self._properties:
self._grid["node"][at][:] = self[at]
def add_layer(self, thickness, rock_id=None):
"""Add a new layer to Lithology.
Parameters
----------
thickness : float or `(n_nodes,)` array
Positive values deposit material on to Lithology while negative
values erode Lithology.
rock_id : single value or `n_nodes` long itterable, optional if only erosion occurs
Rock type ID for new deposits. Can be single value or an number-
of-nodes array.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
We can instantiate Lithology with rock type properties we know we will
use in the future.
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001,
... 3: 0.01}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
Add a layer of thickness 3 and rock type 3.
>>> lith.add_layer(3, rock_id=3)
The value of `K_sp` at node is now updated to the value of rock type 3
>>> mg.at_node['K_sp']
array([ 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01])
A negative value will erode. We can also pass a `(n_nodes,) long array
to erode unevenly. If all parts of the layer erode, then no `rock_id`
needs to be passed.
>>> erosion_amount = [-2., -2., -2., -4., -4., -4., -6., -6., -6.]
>>> lith.add_layer(erosion_amount)
>>> mg.at_node['K_sp']
array([ 0.01 , 0.01 , 0.01 , 0.0001, 0.0001, 0.0001, 0.001 ,
0.001 , 0.001 ])
Now different layers are exposed at the surface and the value of `K_sp`
is spatially variable.
"""
thickness = np.array(thickness)
# verify that Lithology will still have thickness after change
if np.any((self._layers.thickness + thickness) <= 0):
msg = (
"add_layer will result in Lithology having a thickness of "
"zero at at least one node."
)
raise ValueError(msg)
# verify that rock type added exists.
try:
all_ids_present = self._ids.issuperset(rock_id)
new_ids = rock_id
except TypeError:
all_ids_present = self._ids.issuperset([rock_id])
new_ids = [rock_id]
if not all_ids_present:
missing_ids = set(new_ids).difference(self._ids)
if np.any(thickness > 0):
msg = (
"Lithology add_layer was given a rock type id that does "
"not yet exist and will need to deposit. Use a valid "
"rock type or add_rock_type. " + str(missing_ids)
)
raise ValueError(msg)
# add_rock_type
if rock_id is not None:
# add layer
attributes = {self._rock_id_name: rock_id}
self._layers.add(thickness, **attributes)
else:
self._layers.add(thickness)
# update surface rock type
self._surface_rock_type = self._layers.get_surface_values(self._rock_id_name)
# update surface values
self._update_surface_values()
def add_property(self, attrs):
"""Add new property to Lithology.
Parameters
----------
attrs : dict
Rock attribute dictionary for the new property(s).
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.add_property({'D': {1: 0.03,
... 2: 0.004}})
>>> lith.tracked_properties
['D', 'K_sp']
>>> mg.at_node['D']
array([ 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03])
"""
for at in attrs:
if at in self._properties:
msg = (
"add_property is trying to add an existing "
"attribute, this is not permitted. " + str(at)
)
raise ValueError(msg)
new_rids = attrs[at].keys()
for rid in new_rids:
if rid not in self._ids:
msg = (
"add_property has an attribute(" + str(at) + ")"
" for rock type " + str(rid) + " that no other rock "
" type has. This is not permitted."
)
raise ValueError(msg)
for rid in self._ids:
if rid not in new_rids:
msg = (
"add_property needs a value for id " + str(rid) + ""
" and attribute " + str(at) + "."
)
raise ValueError(msg)
for at in attrs:
if at not in self._grid.at_node:
self._grid.add_empty(at, at="node")
self._attrs[at] = attrs[at]
self._properties.append(at)
# update surface values
self._update_surface_values()
def add_rock_type(self, attrs):
"""Add rock type to Lithology.
Parameters
----------
attrs : dict
Rock attribute dictionary for the new rock type(s).
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.add_rock_type({'K_sp': {4: 0.03,
... 6: 0.004}})
>>> lith.ids
[1, 2, 4, 6]
>>> lith.properties
{'K_sp': {1: 0.001, 2: 0.0001, 4: 0.03, 6: 0.004}}
"""
# Check that the new rock type has all existing attributes
for at in self._properties:
if at not in attrs:
msg = "The new rock type is missing attribute " + str(at) + "."
raise ValueError(msg)
# And no new attributes
for at in attrs:
if at not in self._properties:
msg = (
"The new rock type has an attribute (e" + str(at) + ") "
"that no other rock type has. This is not permitted."
)
raise ValueError(msg)
new_ids = []
for at in attrs:
att_dict = attrs[at]
rids = att_dict.keys()
for rid in rids:
if rid in self._layer_ids:
msg = (
"Rock type ID " + str(rid) + " for attribute "
"" + str(at) + " has already been added. This is "
"not allowed"
)
raise ValueError(msg)
else:
new_ids.append(rid)
self._attrs[at][rid] = att_dict[rid]
self._ids = self._ids.union(new_ids)
# update surface values
self._update_surface_values()
def update_rock_properties(self, at, rock_id, value):
"""Update rock type attribute.
Parameters
----------
at : str
Attribute name
rock_id : value
Rock type ID
value : value
New value for rock type attribute
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_zeros("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> mg.at_node['K_sp']
array([ 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001, 0.001,
0.001])
>>> lith.update_rock_properties('K_sp', 1, 0.03)
>>> mg.at_node['K_sp']
array([ 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03, 0.03])
"""
if at not in self._properties:
msg = (
"Lithology cannot update the value of " + str(at) + "as "
"this attribute does not exist."
)
raise ValueError(msg)
if not self._ids.issuperset([rock_id]):
msg = (
"Lithology cannot update the value of rock type "
"" + str(rock_id) + "for attribute " + str(at) + " as "
"this rock type is not yet defined."
)
raise ValueError(msg)
# set the value in the attribute dictionary
self._attrs[at][rock_id] = value
# update surface values
self._update_surface_values()
def _get_surface_values(self, at):
"""Get surface values for attribute."""
return np.array(list(map(self._attrs[at].get, self._surface_rock_type)))
def rock_cube_to_xarray(self, depths):
"""Construct a 3D rock cube of rock type ID as an xarray dataset.
Create an xarray dataset in (x, y, z) that shows the rock type with
depth relative to the current topographic surface.
Here the z dimension is depth relative to the current topographic
surface, NOT depth relative to an absolute datum.
Note also that when this method is called, it will construct the current
values of lithology with depth, NOT the initial values.
Parameters
----------
depths : array
Returns
-------
ds : xarray dataset
"""
depths = np.asarray(depths)
rock_type = self._layers[self._rock_id_name]
rock_cube = np.empty((depths.size, self._grid.shape[0], self._grid.shape[1]))
# at each node point, interpolate between ztop/bottomo correct.y
for sid in range(self._layers.number_of_stacks):
coord = np.unravel_index(sid, (self._grid.shape[0], self._grid.shape[1]))
real_layers = self.dz[:, sid] > 0
f = interp1d(
np.flipud(self.z_top[real_layers, sid]),
np.flipud(rock_type[real_layers, sid]),
kind="previous",
)
vals = f(depths)
rock_cube[:, coord[0], coord[1]] = vals
ds = xr.Dataset(
data_vars={
"rock_type__id": (
("z", "y", "x"),
rock_cube,
{"units": "-", "long_name": "Rock Type ID Code"},
)
},
coords={
"x": (
("x"),
self._grid.x_of_node.reshape(self._grid.shape)[0, :],
{"units": "meters"},
),
"y": (
("y"),
self._grid.y_of_node.reshape(self._grid.shape)[:, 1],
{"units": "meters"},
),
"z": (
("z"),
depths,
{"units": "meters", "long_name": "Depth Below Topographic Surface"},
),
},
)
return ds
def run_one_step(self):
"""Update Lithology.
The ``run_one_step`` method calculates elevation change of the
Lithology surface (taking into account any advection due to external
processes) and then either deposits or erodes based on elevation
change.
Examples
--------
>>> from landlab import RasterModelGrid
>>> from landlab.components import Lithology
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_ones("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs)
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
If we erode the surface, and then update Lithology, the thickness will
change.
>>> z -= 0.5
>>> lith.run_one_step()
>>> lith.thickness
array([ 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5])
The default of Lithology is to use MaterialLayers from the Landlab
layers submodule. This means that when we erode, we will remove a layer
from the layers datastructure if it has no material anywhere.
>>> lith.dz
array([[ 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ],
[ 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. ],
[ 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. ],
[ 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5]])
We can see the value of the rock type at the surface.
>>> mg.at_node['rock_type__id']
array([ 1., 1., 1., 1., 1., 1., 1., 1., 1.])
If you deposit, a valid rock_id must be provided. If the rock type
is the same as the current surface value everywhere, then the layers
will be combined. This rock_id can be provided as part of the init of
Lithology or by setting a property (as shown below).
>>> z += 1.5
>>> lith.rock_id = 1
>>> lith.run_one_step()
>>> lith.thickness
array([ 9., 9., 9., 9., 9., 9., 9., 9., 9.])
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.]])
This contrasts with the behavior of Lithology if we use EventLayers.
Next we repeat this example with EventLayers. Note that no matter which
method you use, the values of the model grid fields will be the same.
These two methods differ only in the details of the data structure they
use to store the layer information.
>>> mg = RasterModelGrid((3, 3))
>>> z = mg.add_ones("topographic__elevation", at="node")
>>> thicknesses = [1, 2, 4, 1]
>>> ids = [1, 2, 1, 2]
>>> attrs = {'K_sp': {1: 0.001,
... 2: 0.0001}}
>>> lith = Lithology(mg, thicknesses, ids, attrs,
... layer_type='EventLayers')
>>> lith.dz
array([[ 1., 1., 1., 1., 1., 1., 1., 1., 1.],
[ 4., 4., 4., 4., 4., 4., 4., 4., 4.],
[ 2., 2., 2., 2., 2., 2., 2., 2., 2.],
[ 1., 1., 1., 1., 1., 1., 1., 1., 1.]])
>>> lith.thickness
array([ 8., 8., 8., 8., 8., 8., 8., 8., 8.])
If we erode the surface, and then update Lithology, the thickness
will change. However, with EventLayers, the ``lith.dz`` structure
will be different. It will have a layer with thickness zero that
represents the event of erosion.
>>> z -= 0.5
>>> lith.run_one_step()
>>> lith.thickness
array([ 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5, 7.5])
>>> lith.dz
array([[ 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ],
[ 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. ],
[ 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. ],
[ 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[ 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ]])
We can see the value of the rock type at the surface. As expected,
it is just the same as if we used MaterialLayers.
>>> mg.at_node['rock_type__id']
array([ 1., 1., 1., 1., 1., 1., 1., 1., 1.])
If you deposit, a valid rock_id must be provided. Unlike
MaterialLayers, these two layers will not be combined, even if they
have the same properties.
>>> z += 1.5
>>> lith.rock_id = 1
>>> lith.run_one_step()
>>> lith.thickness
array([ 9., 9., 9., 9., 9., 9., 9., 9., 9.])
>>> lith.dz
array([[ 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. , 1. ],
[ 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. , 4. ],
[ 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. , 2. ],
[ 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5],
[ 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
[ 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5]])
"""
# calculate amount of erosion
elevation_change = self._grid["node"]["topographic__elevation"] - (
self._last_elevation + self.dz_advection
)
# add layer
self.add_layer(elevation_change, rock_id=self.rock_id)
# update the last elevation.
self._last_elevation = self._grid["node"]["topographic__elevation"][:].copy()
def test_adding_untracked_layer():
layers = MaterialLayers(3)
layers.add(1.0, type=3.0, size="sand")
layers.add([0.0, 0.0, 1.0], type=3.0, size="sand")
with pytest.raises(ValueError):
layers.add([1.0], type=3.0, size="sand", spam="eggs")
def test_adding_untracked_layer():
layers = MaterialLayers(3)
layers.add(1., type=3., size='sand')
layers.add([0., 0., 1.], type=3., size='sand')
with pytest.raises(ValueError):
layers.add([1.], type=3., size='sand', spam='eggs')
def test_adding_untracked_layer():
layers = MaterialLayers(3)
layers.add(1.0, type=3.0, size="sand")
layers.add([0.0, 0.0, 1.0], type=3.0, size="sand")
with pytest.raises(ValueError):
layers.add([1.0], type=3.0, size="sand", spam="eggs")