# Source code documentation¶

## Model classes¶

The AeoLiS model is based on two main model classes: AeoLiS and AeoLiSRunner. The former is the actual, low-level, BMI-compatible class that implements the basic model functions and numerical schemes. The latter is a convenience class that implements a time loop, netCDF4 output, a progress indicator and a callback function that allows the used to interact with the model during runtime.

The additional WindGenerator class to generate realistic wind time series is available from the same module.

### AeoLiS¶

class model.AeoLiS(configfile)[source]

AeoLiS model class

AeoLiS is a process-based model for simulating supply-limited aeolian sediment transport. This model class is compatible with the Basic Model Interface (BMI) and provides basic model operations, like initialization, time stepping, finalization and data exchange. For higher level operations, like a progress indicator and netCDF4 output is refered to the AeoLiS model runner class, see AeoLiSRunner.

Examples

>>> with AeoLiS(configfile='aeolis.txt') as model:
>>>     while model.get_current_time() <= model.get_end_time():
>>>         model.update()

>>> model = AeoLiS(configfile='aeolis.txt')
>>> model.initialize()
>>> zb = model.get_var('zb')
>>> model.set_var('zb', zb + 1)
>>> for i in range(10):
>>>     model.update(60.) # step 60 seconds forward
>>> model.finalize()

__init__(configfile)[source]

Initialize class

Parameters: configfile (str) – Model configuration file. See read_configfile().
crank_nicolson()[source]

Convenience function for implicit solver based on Crank-Nicolson scheme

static dimensions(var=None)[source]

Static method that returns named dimensions of all spatial grids

Parameters: var (str, optional) – Name of spatial grid Tuple with named dimensions of requested spatial grid or dictionary with all named dimensions of all spatial grids. Returns nothing if requested spatial grid is not defined. tuple or dict
euler_backward()[source]

Convenience function for implicit solver based on Euler backward scheme

euler_forward()[source]

Convenience function for explicit solver based on Euler forward scheme

finalize()[source]

Finalize model

get_count(name)[source]

Get counter value

Parameters: name (str) – Name of counter
get_current_time()[source]
Returns: Current simulation time float
get_end_time()[source]
Returns: Final simulation time float
get_start_time()[source]
Returns: Initial simulation time float
get_var(var)[source]

Returns spatial grid or model configuration parameter

If the given variable name matches with a spatial grid, the spatial grid is returned. If not, the given variable name is matched with a model configuration parameter. If a match is found, the parameter value is returned. Otherwise, nothing is returned.

Parameters: var (str) – Name of spatial grid or model configuration parameter Spatial grid or model configuration parameter np.ndarray or int, float, str or list

Examples

>>> # returns bathymetry grid
... model.get_var('zb')

>>> # returns simulation duration
... model.get_var('tstop')

get_var_count()[source]
Returns: Number of spatial grids int
get_var_name(i)[source]

Returns name of spatial grid by index (in alphabetical order)

Parameters: i (int) – Index of spatial grid Name of spatial grid or -1 in case index exceeds the number of grids str or -1
get_var_rank(var)[source]

Returns rank of spatial grid

Parameters: var (str) – Name of spatial grid Rank of spatial grid or -1 if not found int
get_var_shape(var)[source]

Returns shape of spatial grid

Parameters: var (str) – Name of spatial grid Dimensions of spatial grid or -1 if not found tuple or int
get_var_type(var)[source]

Returns variable type of spatial grid

Parameters: var (str) – Name of spatial grid Variable type of spatial grid or -1 if not found str or int
initialize()[source]

Initialize model

Read model configuration file and initialize parameters and spatial grids dictionary and load bathymetry and bed composition.

set_timestep(dt=-1.0)[source]

Determine optimal time step

If no time step is given the optimal time step is determined. For explicit numerical schemes the time step is based in the Courant-Frierichs-Lewy (CFL) condition. For implicit numerical schemes the time step specified in the model configuration file is used. Alternatively, a preferred time step is given that is maximized by the CFL condition in case of an explicit numerical scheme.

Returns True except when:

1. No time step could be determined, for example when there is no wind and the numerical scheme is explicit. In this case the time step is set arbitrarily to one second.

2. Or when the time step is smaller than -1. In this case the time is updated with the absolute value of the time step, but no model execution is performed. This funcionality can be used to skip fast-forward in time.

Parameters: df (float, optional) – Preferred time step False if determination of time step was unsuccessful, True otherwise bool
set_var(var, val)[source]

Sets spatial grid or model configuration parameter

If the given variable name matches with a spatial grid, the spatial grid is set. If not, the given variable name is matched with a model configuration parameter. If a match is found, the parameter value is set. Otherwise, nothing is set.

Parameters: var (str) – Name of spatial grid or model configuration parameter val (np.ndarray or int, float, str or list) – Spatial grid or model configuration parameter

Examples

>>> # set bathymetry grid
... model.set_var('zb', np.array([[0.,0., ... ,0.]]))

>>> # set simulation duration
... model.set_var('tstop', 3600.)

set_var_index(i, val)[source]

Set spatial grid by index (in alphabetical order)

Parameters: i (int) – Index of spatial grid val (np.ndarray) – Spatial grid
solve(alpha=0.5, beta=1.0)[source]

Implements the explicit Euler forward, implicit Euler backward and semi-implicit Crank-Nicolson numerical schemes

Determines weights of sediment fractions, sediment pickup and instantaneous sediment concentration. Returns a partial spatial grid dictionary that can be used to update the global spatial grid dictionary.

Parameters: alpha (float, optional) – Implicitness coefficient (0.0 for Euler forward, 1.0 for Euler backward or 0.5 for Crank-Nicolson, default=0.5) beta (float, optional) – Centralization coefficient (1.0 for upwind or 0.5 for centralized, default=1.0) Partial spatial grid dictionary dict

Examples

>>> model.s.update(model.solve(alpha=1., beta=1.) # euler backward

>>> model.s.update(model.solve(alpha=.5, beta=1.) # crank-nicolson

update(dt=-1)[source]

Time stepping function

Takes a single step in time. Interpolates wind and hydrodynamic time series to the current time, updates the soil moisture, mixes the bed due to wave action, computes wind velocity threshold and the equilibrium sediment transport concentration. Subsequently runs one of the available numerical schemes to compute the instantaneous sediment concentration and pickup for the next time step and updates the bed accordingly.

For explicit schemes the time step is maximized by the Courant-Friedrichs-Lewy (CFL) condition. See set_timestep().

Parameters: dt (float, optional) – Time step in seconds. The time step specified in the model configuration file is used in case dt is smaller than zero. For explicit numerical schemes the time step is maximized by the CFL confition.

### AeoLiSRunner¶

class model.AeoLiSRunner(configfile='aeolis.txt')[source]

AeoLiS model runner class

This runner class is a convenience class for the BMI-compatible AeoLiS model class (AeoLiS()). It implements a time loop, a progress indicator and netCDF4 output. It also provides the definition of a callback function that can be used to interact with the AeoLiS model during runtime.

The command-line function aeolis is available that uses this class to start an AeoLiS model run.

Examples

>>> # run with default settings
... AeoLiSRunner().run()

>>> AeoLiSRunner(configfile='aeolis.txt').run()

>>> model = AeoLiSRunner(configfile='aeolis.txt')
>>> model.run(callback=lambda model: model.set_var('zb', zb))

>>> model.run(callback='bar.py:add_bar')

__init__(configfile='aeolis.txt')[source]

Initialize class

Reads model configuration file without parsing all referenced files for the progress indicator and netCDF output. If no configuration file is given, the default settings are used.

Parameters: configfile (str, optional) – Model configuration file. See read_configfile().
dump_restartfile()[source]

Dump model state to restart file

get_statistic(var, stat='avg')[source]

Return statistic of spatial grid

Parameters: var (str) – Name of spatial grid stat (str) – Name of statistic (avg, sum, var, min or max) Statistic of spatial grid numpy.ndarray
get_var(var, clear=True)[source]

Returns spatial grid, statistic or model configuration parameter

Overloads the get_var() function and extends it with the functionality to return statistics on spatial grids by adding a postfix to the variable name (e.g. Ct_avg). Supported statistics are avg, sum, var, min and max.

Parameters: var (str) – Name of spatial grid or model configuration parameter. Spatial grid name can be extended with a postfix to request a statistic (_avg, _sum, _var, _min or _max). clear (bool) – Clear output statistics afterwards. Spatial grid, statistic or model configuration parameter np.ndarray or int, float, str or list

Examples

>>> # returns average sediment concentration
... model.get_var('Ct_avg')

>>> # returns variance in wave height
... model.get_var('Hs_var')

initialize()[source]

Initialize model

Overloads the initialize() function, but also initializes output statistics.

load_hotstartfiles()[source]

Load model state from hotstart files

Hotstart files are plain text representations of model state variables that can be used to hotstart the (partial) model state. Hotstart files should have the name of the model state variable it contains and have the extension .hotstart. Hotstart files differ from restart files in that restart files contain entire model states and are pickled Python objects.

load_restartfile(restartfile)[source]

Load model state from restart file

Parameters: restartfile (str) – Path to previously written restartfile.
output_clear()[source]

Clears output statistics dictionary

Creates a matrix for minimum, maximum, variance and summed values for each output variable and sets the time step counter to zero.

output_init()[source]

Initialize netCDF4 output file and output statistics dictionary

output_update()[source]

Updates matrices with minimum, maximum, variance and summed values for each output variable with current spatial grid values and increases time step counter with one.

output_write()[source]

Appends output to netCDF4 output file

If the time since the last output is equal or larger than the set output interval, append current output to the netCDF4 output file. Computes the average and variance values based on available output statistics and clear output statistics dictionary.

parse_callback(callback)[source]

Parses callback definition and returns function

The callback function can be specified in two formats:

• As a native Python function
• As a string refering to a Python script and function, separated by a colon (e.g. example/callback.py:function)
Parameters: callback (str or function) – Callback definition Python callback function function
print_params()[source]

Print model configuration parameters to screen

print_progress(fraction=0.1, min_interval=1.0, max_interval=60.0)[source]

Print progress to screen

Parameters: fraction (float, optional) – Fraction of simulation at which to print progress (default: 10%) min_interval (float, optional) – Minimum time in seconds between subsequent progress prints (default: 1s) max_interval (float, optional) – Maximum time in seconds between subsequent progress prints (default: 60s)
print_stats()[source]

Print model run statistics to screen

run(callback=None, restartfile=None)[source]

Start model time loop

Changes current working directory to the model directory, prints model configuration parameters and progress indicator to the screen, writes netCDF4 output and calls a callback function upon request.

Parameters: callback (str or function) – The callback function is called at the start of every single time step and takes the AeoLiS model object as input. The callback function can be used to interact with the model during simulation (e.g. update the bed with new measurements). See for syntax parse_callback(). restartfile (str) – Path to previously written restartfile. The model state is loaded from this file after initialization of the model.
set_configfile(configfile)[source]

Set model configuration file name

set_params(**kwargs)[source]

Set model configuration parameters

update(dt=-1)[source]

Time stepping function

Overloads the update() function, but also updates output statistics and clears output statistics upon request.

Parameters: dt (float, optional) – Time step in seconds.
write_params()[source]

Write updated model configuration to configuration file

Creates a backup in case the model configration file already exists.

### WindGenerator¶

class model.WindGenerator(mean_speed=9.0, max_speed=30.0, dt=60.0, n_states=30, shape=2.0, scale=2.0)[source]

Wind velocity time series generator

Generates a random wind velocity time series with given mean and maximum wind speed, duration and time resolution. The wind velocity time series is generated using a Markov Chain Monte Carlo (MCMC) approach based on a Weibull distribution. The wind time series can be written to an AeoLiS-compatible wind input file assuming a constant wind direction of zero degrees.

The command-line function aeolis-wind is available that uses this class to generate AeoLiS wind input files.

Examples

>>> wind = WindGenerator(mean_speed=10.).generate(duration=24*3600.)
>>> wind.write_time_series('wind.txt')
>>> wind.plot()
>>> wind.hist()


## Physics modules¶

### Bathymetry and bed composition¶

bed.initialize(s, p)[source]

Initialize bathymetry and bed composition

Initialized bathymetry, computes cell sizes and orientation, bed layer thickness and bed composition.

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict
bed.mixtoplayer(s, p)[source]

Mix grain size distribution in top layer of the bed

Simulates mixing of the top layers of the bed by wave action. The wave action is represented by a local wave height maximized by a maximum wave hieght over depth ratio gamma. The mixing depth is a fraction of the local wave height indicated by facDOD. The mixing depth is used to compute the number of bed layers that should be included in the mixing. The grain size distribution in these layers is then replaced by the average grain size distribution over these layers.

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict
bed.prevent_negative_mass(m, dm, pickup)[source]

Handle situations in which negative mass may occur due to numerics

Negative mass may occur by moving sediment to lower layers down to accomodate deposition of sediments. In particular two cases are important:

1. A net deposition cell has some erosional fractions.

In this case the top layer mass is reduced according to the existing sediment distribution in the layer to accomodate deposition of fresh sediment. If the erosional fraction is subtracted afterwards, negative values may occur. Therefore the erosional fractions are subtracted from the top layer beforehand in this function. An equal mass of deposition fractions is added to the top layer in order to keep the total layer mass constant. Subsequently, the distribution of the sediment to be moved to lower layers is determined and the remaining deposits are accomodated.

2. Deposition is larger than the total mass in a layer.

In this case a non-uniform distribution in the bed may also lead to negative values as the abundant fractions are reduced disproportionally as sediment is moved to lower layers to accomodate the deposits. This function fills the top layers entirely with fresh deposits and moves the existing sediment down such that the remaining deposits have a total mass less than the total bed layer mass. Only the remaining deposits are fed to the routine that moves sediment through the layers.

Parameters: m (np.ndarray) – Sediment mass in bed (nx*ny, nl, nf) dm (np.ndarray) – Total sediment mass exchanged between layers (nx*ny, nf) pickup (np.ndarray) – Sediment pickup (nx*ny, nf) np.ndarray – Sediment mass in bed (nx*ny, nl, nf) np.ndarray – Total sediment mass exchanged between layers (nx*ny, nf) np.ndarray – Sediment pickup (nx*ny, nf)

Note

The situations handled in this function can also be prevented by reducing the time step, increasing the layer mass or increasing the adaptation time scale.

bed.update(s, p)[source]

Update bathymetry and bed composition

Update bed composition by moving sediment fractions between bed layers. The total mass in a single bed layer does not change as sediment removed from a layer is repleted with sediment from underlying layers. Similarly, excess sediment added in a layer is moved to underlying layers in order to keep the layer mass constant. The lowest bed layer exchanges sediment with an infinite sediment source that follows the original grain size distribution as defined in the model configuration file by grain_size and grain_dist. The bathymetry is updated following the cummulative erosion/deposition over the fractions if bedupdate is True.

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict

### Wind velocity and direction¶

wind.get_velocity_at_height(u, z, z0, z1=None)[source]

Compute shear velocity from wind velocity following Prandl-Karman’s Law of the Wall

Parameters: u (numpy.ndarray) – Spatial wind field z (float) – Height above bed where u is measured z0 (float) – Roughness length z1 (float, optional) – Height above bed for which to return wind speeds. Returns wind shear if not given. Array of size u with wind speeds at height z1 numpy.ndarray
wind.initialize(s, p)[source]

Initialize wind model

wind.interpolate(s, p, t)[source]

Interpolate wind velocity and direction to current time step

Interpolates the wind time series for velocity and direction to the current time step. The cosine and sine of the direction angle are interpolated separately to prevent zero-crossing errors. The wind velocity is decomposed in two grid components based on the orientation of each individual grid cell. In case of a one-dimensional model only a single positive component is used.

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters t (float) – Current time Spatial grids dict
class shear.WindShear(x, y, z, dx=1.0, dy=1.0, buffer_width=100.0, buffer_relaxation=None, L=100.0, z0=0.001, l=10.0)[source]

Class for computation of 2DH wind shear perturbations over a topography.

The class implements a 2D FFT solution to the wind shear perturbation on curvilinear grids. As the FFT solution is only defined on an equidistant rectilinear grid with circular boundary conditions that is aligned with the wind direction, a rotating computational grid is automatically defined for the computation. The computational grid is extended in all directions using a logistic sigmoid function as to ensure full coverage of the input grid for all wind directions, circular boundaries and preservation of the alongshore uniformity. An extra buffer distance can be used as to minimize the disturbence from the borders in the input grid. The results are interpolated back to the input grid when necessary.

Frequencies related to wave lengths smaller than a computational grid cell are filtered from the 2D spectrum of the topography using a logistic sigmoid tapering. The filtering aims to minimize the disturbance as a result of discontinuities in the topography that may physically exists, but cannot be solved for in the computational grid used.

Example

>>> w = WindShear(x, y, z)


Notes

To do:

• Actual resulting values are still to be compared with the results
from Kroy et al. (2002)
• Grid interpolation can still be optimized
• Separation bubble is still to be implemented
• Avalanching is still to be implemented
__call__(u0, udir)[source]

Compute wind shear for given wind speed and direction

Parameters: u0 (float) – Free-flow wind speed udir (float) – Wind direction in degrees
add_shear(taux, tauy)[source]

Add wind shear perturbations to a given wind shear field

Parameters: taux (numpy.ndarray) – Wind shear in x-direction tauy (numpy.ndarray) – Wind shear in y-direction taux (numpy.ndarray) – Wind shear including perturbations in x-direction tauy (numpy.ndarray) – Wind shear including perturbations in y-direction
compute_shear(u0, nfilter=(1.0, 2.0))[source]

Compute wind shear perturbation for given free-flow wind speed on computational grid

Parameters: u0 (float) – Free-flow wind speed nfilter (2-tuple) – Wavenumber range used for logistic sigmoid filter. See filter_highfrequencies()
filter_highfrequenies(kx, ky, hs, nfilter=(1, 2), p=0.01)[source]

Filter high frequencies from a 2D spectrum

A logistic sigmoid filter is used to taper higher frequencies from the 2D spectrum. The range over which the sigmoid runs from 0 to 1 with a precision p is given by the 2-tuple nfilter. The range is defined as wavenumbers in terms of gridcells, i.e. a value 1 corresponds to a wave with length dx.

Parameters: kx (numpy.ndarray) – Wavenumbers in x-direction ky (numpy.ndarray) – Wavenumbers in y-direction hs (numpy.ndarray) – 2D spectrum nfilter (2-tuple) – Wavenumber range used for logistic sigmoid filter p (float) – Precision of sigmoid range definition hs – Filtered 2D spectrum numpy.ndarray
static get_borders(x)[source]

Returns borders of a grid as one-dimensional array

static get_exact_grid(xmin, xmax, ymin, ymax, dx, dy)[source]

Returns a grid with given gridsizes approximately within given bounding box

get_shear()[source]

Returns wind shear perturbation field

Returns: dtaux (numpy.ndarray) – Wind shear perturbation in x-direction dtauy (numpy.ndarray) – Wind shear perturbation in y-direction
get_sigmoid(x)[source]

Get sigmoid function value

Get bed level multiplication factor in buffer area based on buffer specificationa and distance to input grid boundary.

Parameters: x (float or numpy.ndarray) – Distance(s) to input grid boundary Bed level multiplication factor (z = factor * z_boundary) float or numpy.ndarray
interpolate(x, y, z, xi, yi)[source]

Interpolate a grid onto another grid

static interpolate_projected_point(a, b, p)[source]

Project point to line segment and return distance and interpolated value

Parameters: a (iterable) – Start vector for line segment b (iterable) – End vector for line segment p (iterable) – Point vector to be projected d (numpy.ndarray) – Distance from point p to projected point q z (float) – Interpolated value at projected point q
plot(ax=None, cmap='Reds', stride=10, computational_grid=False, **kwargs)[source]

Plot wind shear perturbation

Parameters: ax (matplotlib.pyplot.Axes, optional) – Axes to plot onto cmap (matplotlib.cm.Colormap or string, optional) – Colormap for topography (default: Reds) stride (int, optional) – Stride to apply to wind shear vectors (default: 10) computational_grid (bool, optional) – Plot on computational grid rather than input grid (default: False) kwargs (dict) – Additional arguments to matplotlib.pyplot.quiver() ax – Axes used for plotting matplotlib.pyplot.Axes
populate_computational_grid(alpha)[source]

Interpolate input topography to computational grid

Rotates computational grid to current wind direction and interpolates the input topography to the rotated grid. Any grid cells that are not covered by the input grid are filled using a sigmoid function.

Parameters: alpha (float) – Rotation angle in degrees
static rotate(x, y, alpha, origin=(0, 0))[source]

Rotate a matrix over given angle around given origin

set_computational_grid()[source]

Define computational grid

The computational grid is square with dimensions equal to the diagonal of the bounding box of the input grid, plus twice the buffer width.

set_topo(z)[source]

Update topography

Parameters: z (numpy.ndarray) – 2D array with topography of input grid

### Wind velocity threshold¶

threshold.compute(s, p)[source]

Compute wind velocity threshold based on bed surface properties

Computes wind velocity threshold based on grain size fractions, bed slope, soil moisture content, air humidity and the presence of roughness elements. All bed surface properties increase the current wind velocity threshold, except for the grain size fractions. Therefore, the computation is initialized by the grain size fractions and subsequently altered by the other bed surface properties.

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict
threshold.compute_bedslope(s, p)[source]

Modify wind velocity threshold based on bed slopes following Dyer (1986)

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict
threshold.compute_grainsize(s, p)[source]

Compute wind velocity threshold based on grain size fractions following Bagnold (1937)

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict
threshold.compute_humidity(s, p)[source]

Modify wind velocity threshold based on air humidity following Arens (1996)

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict
threshold.compute_moisture(s, p)[source]

Modify wind velocity threshold based on soil moisture content following Belly (1964) or Hotta (1984)

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict
threshold.compute_roughness(s, p)[source]

Modify wind velocity threshold based on the presence of roughness elements following Raupach (1993)

Raupach (1993) presents the following amplification factor for the shear velocity threshold due to the presence of roughness elements.

$R_t = \frac{u_{*,th,s}}{u_{*,th,r}} = \sqrt{\frac{\tau_s''}{\tau}} = \frac{1}{\sqrt{\left( 1 - m \sigma \lambda \right) \left( 1 + m \beta \lambda \right)}}$

$$m$$ is a constant smaller or equal to unity that accounts for the difference between the average stress on the bed surface $$\tau_s$$ and the maximum stress on the bed surface $$\tau_s''$$.

$$\beta$$ is the stress partition coefficient defined as the ratio between the drag coefficient of the roughness element itself $$C_r$$ and the drag coefficient of the bare surface without roughness elements $$C_s$$.

$$\sigma$$ is the shape coefficient defined as the basal area divided by the frontal area: $$\frac{A_b}{A_f}$$. For hemispheres $$\sigma = 2$$, for spheres $$\sigma = 1$$.

$$\lambda$$ is the roughness density defined as the number of elements per surface area $$\frac{n}{S}$$ multiplied by the frontal area of a roughness element $$A_f$$, also known as the frontal area index:

$\lambda = \frac{n b h}{S} = \frac{n A_f}{S}$

If multiplied by $$\sigma$$ the equation simplifies to the mass fraction of non-erodible elements:

$\sigma \lambda = \frac{n A_b}{S} = \sum_{k=n_0}^{n_k} \hat{w}^{\mathrm{bed}}_k$

where $$k$$ is the fraction index, $$n_0$$ is the smallest non-erodible fraction, $$n_k$$ is the largest non-erodible fraction and $$\hat{w}^{\mathrm{bed}}_k$$ is the mass fraction of sediment fraction $$k$$. It is assumed that the fractions are ordered by increasing size.

Substituting the derivation in the Raupach (1993) equation gives the formulation implemented in this function:

$u_{*,th,r} = u_{*,th,s} * \sqrt{\left( 1 - m \sum_{k=n_0}^{n_k} \hat{w}^{\mathrm{bed}}_k \right) \left( 1 + m \frac{\beta}{\sigma} \sum_{k=n_0}^{n_k} \hat{w}^{\mathrm{bed}}_k \right)}$
Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict
threshold.compute_salt(s, p)[source]

Modify wind velocity threshold based on salt content following Nickling and Ecclestone (1981)

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict

### Tides, meteorology and soil moisture content¶

hydro.interpolate(s, p, t)[source]

Interpolate hydrodynamic and meteorological conditions to current time step

Interpolates the hydrodynamic and meteorological time series to the current time step, if available. Meteorological parameters are stored as dictionary rather than a single value.

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters t (float) – Current time Spatial grids dict
hydro.saturation_pressure(T)[source]

Compute saturation pressure based on air temperature

Parameters: T (float) – Air temperature in degrees Celcius Saturation pressure float
hydro.update(s, p, dt)[source]

Update soil moisture content

Updates soil moisture content in all cells. The soil moisure content in flooded cells is set to the porosity. The soil moisture content in non-flooded cells is decreased by simulating infiltration using an exponential decay function with a rate F following:

$M = M \cdot e^{-F \cdot \Delta t}$

Cells are considered flooded if the water depth is larger than eps. Aditionally, is meteorological conditions are provided the soil moisture content is decreased by simulating evaporation following the Penman equation:

$M = M - \frac{m \cdot R + \gamma \cdot 6.43 \cdot (1 + 0.536 \cdot u]) \cdot \delta}{\lambda \cdot (m + \gamma)}$
Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters dt (float) – Current time step Spatial grids dict
hydro.vaporation_pressure_slope(T)[source]

Compute vaporation pressure slope based on air temperature

Parameters: T (float) – Air temperature in degrees Celcius Vaporation pressure slope float

### Sediment transport¶

transport.compute_weights(s, p)[source]

Compute weights for sediment fractions

Multi-fraction sediment transport needs to weigh the transport of each sediment fraction to prevent the sediment transport to increase with an increasing number of sediment fractions. The weighing is not uniform over all sediment fractions, but depends on the sediment availibility in the air and the bed and the bed interaction parameter bi.

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Array with weights for each sediment fraction numpy.ndarray
transport.equilibrium(s, p)[source]

Compute equilibrium sediment concentration following Bagnold (1937)

Parameters: s (dict) – Spatial grids p (dict) – Model configuration parameters Spatial grids dict
transport.renormalize_weights(w, ix)[source]

Renormalizes weights for sediment fractions

Renormalizes weights for sediment fractions such that the sum of all weights is unity. To ensure that the erosion of specific fractions does not exceed the sediment availibility in the bed, the normalization only modifies the weights with index equal or larger than ix.

Parameters: w (numpy.ndarray) – Array with weights for each sediment fraction ix (int) – Minimum index to be modified Array with weights for each sediment fraction numpy.ndarray

## Helper modules¶

### Input/Output¶

inout.backup(fname)[source]

Creates a backup file of the provided file, if it exists

inout.check_configuration(p)[source]

Check model configuration validity

Checks if required parameters are set and if the references files for bathymetry, wind, tide and meteorological input are valid. Throws an error if one or more requirements are not met.

Parameters: p (dict) – Model configuration dictionary with parsed files
inout.get_backupfilename(fname)[source]

Returns a non-existing backup filename

inout.parse_value(val, parse_files=True, force_list=False)[source]

Casts a string to the most appropriate variable type

Parameters: val (str) – String representation of value parse_files (bool) – If True, files referred to by string parameters are parsed by numpy.loadtxt force_list – If True, interpret the value as a list, even if it consists of a single value Casted value misc

Examples

>>> type(parse_value('T'))
bool
>>> type(parse_value('F'))
bool
>>> type(parse_value('123'))
int
>>> type(parse_value('123.2'))
float
>>> type(parse_value('euler_forward'))
str
>>> type(parse_value(''))
NoneType
>>> type(parse_value('zb zs Ct'))
numpy.ndarray
>>> type(parse_value('zb', force_list=True))
numpy.ndarray
>>> type(parse_value('0.1 0.2 0.3')[0])
float
>>> type(parse_value('wind.txt'), parse_files=True)
numpy.ndarray
>>> type(parse_value('wind.txt'), parse_files=False)
str

inout.read_configfile(configfile, parse_files=True, load_defaults=True)[source]

Updates default model configuration based on a model configuration file. The model configuration file should be a text file with one parameter on each line. The parameter name and value are seperated by an equal sign (=). Any lines that start with a percent sign (%) or do not contain an equal sign are omitted.

Parameters are casted into the best matching variable type. If the variable type is str it is optionally interpreted as a filename. If the corresponding file is found it is parsed using the numpy.loadtxt function.

Parameters: configfile (str) – Model configuration file parse_files (bool) – If True, files referred to by string parameters are parsed load_defaults (bool) – If True, default settings are loaded and overwritten by the settings from the configuration file Dictionary with casted and optionally parsed model configuration parameters dict
inout.write_configfile(configfile, p=None)[source]

Write model configuration file

Writes model configuration to file. If no model configuration is given, the default configuration is written to file. Any parameters with a name ending with _file and holding a matrix are treated as separate files. The matrix is then written to an ASCII file using the numpy.savetxt function and the parameter value is replaced by the name of the ASCII file.

Parameters: configfile (str) – Model configuration file p (dict, optional) – Dictionary with model configuration parameters Dictionary with casted and optionally parsed model configuration parameters dict

### netCDF4 output¶

netcdf.append(outputfile, variables)[source]

Append variables to existing netCDF4 output file

Increments the time axis length with one and appends the provided spatial grids along the time axis. The variables dictionary should at least have the time field indicating the current simulation time. The CF time bounds are updated accordingly.

Parameters: outputfile (str) – Name of netCDF4 output file variables (dict) – Dictionary with spatial grids and time

Examples

>>> netcdf.append('aeolis.nc', {'time', 3600.,
...                             'Ct', np.array([[0.,0., ... ,0.]]),
...                             'Cu', np.array([[1.,1., ... ,1.]]))

netcdf.dump(outputfile, dumpfile, var='mass', ix=-1)[source]

Dumps time slice from netCDF4 output file to ASCII file

This function can be used to use a specific time slice from a netCDF4 output file as input file for another AeoLiS model run. For example, the bed composition from a spinup run can be used as initial composition for other runs reducing the spinup time.

Parameters: outputfile (str) – Name of netCDF4 output file dumpfile (str) – Name of ASCII dump file var (str, optional) – Name of spatial grid to be dumped (default: mass) ix (int) – Time slice index to be dumped (default: -1)

Examples

>>> # use bedcomp_file = bedcomp.txt in model configuration file
... netcdf.dump('aeolis.nc', 'bedcomp.txt', var='mass')

netcdf.initialize(outputfile, outputvars, s, p, dimensions)[source]

Create empty CF-compatible netCDF4 output file

Parameters: outputfile (str) – Name of netCDF4 output file outputvars (dictionary) – Spatial grids to be written to netCDF4 output file s (dict) – Spatial grids p (dict) – Model configuration parameters dimensions (dict) – Dictionary that specifies a tuple with the named dimensions for each spatial grid (e.g. (‘ny’, ‘nx’, ‘nfractions’))

Examples

>>> netcdf.initialize('aeolis.nc',
...                   ['Ct', 'Cu', 'zb'],
...                   ['avg', 'max'],
...                   s, p, {'Ct':('ny','nx','nfractions'),
...                          'Cu':('ny','nx','nfractions'),
...                          'zb':('ny','nx')})

netcdf.parse_metadata(outputvars)[source]

Parses the Python comments in constants.py to extract meta data, like units, for the model state variables that can be used as netCDF4 meta data.

Parameters: outputvars (dictionary) – Spatial grids to be written to netCDF4 output file meta – Dictionary with meta data for the output variables dict
netcdf.set_bounds(outputfile)[source]

Sets CF time bounds

Parameters: outputfile (str) – Name of netCDF4 output file

### Plotting¶

plot.profile(outputfile, var, ix=-1, subplots_kw={'figsize': (10, 4)})[source]

Plots profile

Parameters: outputfile (str) – Name of netCDF4 output file var (str) – Name of spatial grid ix (int, optional) – Time slice (default: -1) subplots_kw (dict) – Keyword options to subplots function

### Command-line tools¶

console.aeolis()[source]

aeolis : a process-based model for simulating supply-limited aeolian sediment transport

Usage:
aeolis <config> [options]
Positional arguments:
config configuration file
Options:
 -h, --help show this help message and exit --callback=FUNC reference to callback function (e.g. example/callback.py:callback) --restart=FILE model restart file --verbose=LEVEL logging verbosity [default: 20] --debug write debug logs
console.wind()[source]

aeolis-wind : a wind time series generation tool for the aeolis model

Usage:
aeolis-wind <file> [–mean=MEAN] [–max=MAX] [–duration=DURATION] [–timestep=TIMESTEP]
Positional arguments:
file output file
Options:
 -h, --help show this help message and exit --mean=MEAN mean wind speed [default: 10] --max=MAX maximum wind speed [default: 30] --duration=DURATION duration of time series [default: 3600] --timestep=TIMESTEP timestep of time series [default: 60]

### Miscellaneous¶

utils.apply_mask(arr, mask)[source]

The real part of the complex mask is multiplied with the input array. Subsequently the imaginary part is added and the result returned.

The shape of the mask is assumed to match the first few dimensions of the input array. If the input array is larger than the mask, the mask is repeated for any additional dimensions.

Parameters: arr (numpy.ndarray) – Array or matrix to which the mask needs to be applied mask (numpy.ndarray) – Array or matrix with complex mask values arr – Array or matrix to which the mask is applied numpy.ndarray
utils.format_log(msg, ncolumns=2, **props)[source]

Format log message into columns

Prints log message and additional data into a column format that fits into a 70 character terminal.

Parameters: msg (str) – Main log message ncolumns (int) – Number of columns props (key/value pairs) – Properties to print in column format Formatted log message str

Note

Properties names starting with min, max or nr are respectively replaced by min., max. or #.

utils.interp_array(x, xp, fp, circular=False, **kwargs)[source]

Interpolate multiple time series at once

Parameters: x (array_like) – The x-coordinates of the interpolated values. xp (1-D sequence of floats) – The x-coordinates of the data points, must be increasing. fp (2-D sequence of floats) – The y-coordinates of the data points, same length as xp. circular (bool) – Use the interp_circular() function rather than the numpy.interp() function. kwargs (dict) – Keyword options to the numpy.interp() function The interpolated values, same length as second dimension of fp. ndarray
utils.interp_circular(x, xp, fp, **kwargs)[source]

One-dimensional linear interpolation.

Returns the one-dimensional piecewise linear interpolant to a function with given values at discrete data-points. Values beyond the limits of x are interpolated in circular manner. For example, a value of x > x.max() evaluates as f(x-x.max()) assuming that x.max() - x < x.max().

Parameters: x (array_like) – The x-coordinates of the interpolated values. xp (1-D sequence of floats) – The x-coordinates of the data points, must be increasing. fp (1-D sequence of floats) – The y-coordinates of the data points, same length as xp. kwargs (dict) – Keyword options to the numpy.interp() function y – The interpolated values, same shape as x. {float, ndarray} ValueError – If xp and fp have different length
utils.isarray(x)[source]

Check if variable is an array

utils.isiterable(x)[source]

Check if variable is iterable

utils.makeiterable(x)[source]

Ensure that variable is iterable

utils.normalize(x, ref=None, axis=0, fill=0.0)[source]

Normalize array

Normalizes an array to make it sum to unity over a specific axis. The procedure is safe for dimensions that sum to zero. These dimensions return the fill value instead.

Parameters: x (array_like) – The array to be normalized ref (array_like, optional) – Alternative normalization reference, if not specified, the sum of x is used axis (int, optional) – The normalization axis (default: 0) fill (float, optional) – The return value for all-zero dimensions (default: 0.)
utils.prevent_tiny_negatives(x, max_error=1e-10, replacement=0.0)[source]

Replace tiny negative values in array

Parameters: x (np.ndarray) – Array with potential tiny negative values max_error (float) – Maximum absolute value to be replaced replacement (float) – Replacement value Array with tiny negative values removed np.ndarray
utils.print_value(val, fill='<novalue>')[source]

Construct a string representation from an arbitrary value

Parameters: val (misc) – Value to be represented as string fill (str, optional) – String representation used in case no value is given String representation of value str