### Prepare Run

Source: https://opendrift.github.io/autoapi/opendrift/models/openoil/index.html

Performs any necessary setup before starting the simulation run.

```python
prepare_run()
```

--------------------------------

### Download All Examples

Source: https://opendrift.github.io/gallery/index.html

Links to download all gallery examples as Python source code or Jupyter notebooks.

```text
Download all examples in Python source code: gallery_python.zip
```

```text
Download all examples in Jupyter notebooks: gallery_jupyter.zip
```

--------------------------------

### Custom Wave Packet Size Configuration

Source: https://opendrift.github.io/trajan/gallery/example_omb_csv_reader.html

This example demonstrates how to configure custom wave packet sizes and set a start time to ignore older messages. This is useful when firmware has been modified.

```python
# example 2: custom size of wave packets; for users who have changed the firmware to transmit and using a set start time: ignore messages before it more or less spectrum bins
```

--------------------------------

### Download Example Files

Source: https://opendrift.github.io/gallery/example_water_column_stretching.html

Links to download the Jupyter notebook, Python source code, and a zipped archive for the water column stretching example.

```text
Download Jupyter notebook: example_water_column_stretching.ipynb
Download Python source code: example_water_column_stretching.py
Download zipped: example_water_column_stretching.zip
```

--------------------------------

### Install Trajan from Source

Source: https://opendrift.github.io/trajan/_sources/index.rst.txt

Recommended for developers contributing to Trajan. Requires navigating to the source directory and installing.

```console
$ cd trajan  # move to the location of the trajan root, containing the pyproject.toml file
$ pip install .
```

--------------------------------

### Start OpenDrift GUI

Source: https://opendrift.github.io/_sources/gui.rst.txt

Launch the OpenDrift Graphical User Interface. This command assumes OpenDrift is installed or its scripts directory is in the PATH. Alternatively, run 'python opendrift_gui.py' from the scripts folder.

```bash
$ opendrift_gui.py
```

--------------------------------

### Install and Configure Coloredlogs

Source: https://opendrift.github.io/trajan/_downloads/e91a213efe083c695858d56cefa37cd1/example_omb_csv_reader.ipynb

Imports necessary libraries and installs coloredlogs for debugging output. Adjust the log level as needed.

```python
from pathlib import Path
from trajan.readers.omb import read_omb_csv
import coloredlogs
import datetime

# adjust the level of information printed
# coloredlogs.install(level='error')
coloredlogs.install(level='debug')
```

--------------------------------

### Install and configure OpenDrift on WEkEO and EDITO

Source: https://opendrift.github.io/_sources/install.rst.txt

Installs OpenDrift in the JupyterHub workspace and configures Copernicus credentials.

```bash
$ mamba install opendrift
```

```bash
$ export COPERNICUSMARINE_SERVICE_USERNAME=<your CMEMS username>
$ export COPERNICUSMARINE_SERVICE_PASSWORD=<your CMEMS password>
```

```bash
COPERNICUSMARINE_SERVICE_USERNAME=<your CMEMS username>
COPERNICUSMARINE_SERVICE_PASSWORD=<your CMEMS password>
```

--------------------------------

### Logging Setup

Source: https://opendrift.github.io/_sources/autoapi/opendrift/models/eulerdrift/index.rst.txt

Function to set up colorful logging for the application.

```APIDOC
## install_logs(level=logging.DEBUG)

### Description
Set up fanzy, colorful, logging.

### Args
- **level** (logging level) - Optional - Log level.
```

--------------------------------

### Simulation log output

Source: https://opendrift.github.io/gallery/example_oil_thickness.html

Example of the initialization log output from OpenDrift.

```text
08:27:48 INFO    opendrift:568: OpenDriftSimulation initialised (version 1.14.9 / v1.14.9-9-gcde0dcf)
```

--------------------------------

### Get Model Configuration Parameter

Source: https://opendrift.github.io/tutorial.html

Retrieve the current value of a specific configuration parameter. This example gets the 'wind_drift_factor'.

```python
wind_drift_factor = o.get_config('seed:wind_drift_factor')
```

--------------------------------

### Get Git Description

Source: https://opendrift.github.io/_sources/autoapi/opendrift/version/index.rst.txt

Retrieve the git description if the library was installed from a git repository.

```APIDOC
## GET opendrift.version.git_describe

### Description
Returns the git version description if available. This is useful for identifying specific development builds.

### Method
GET

### Endpoint
`opendrift.version.git_describe()`

### Response
#### Success Response (200)
- **git_describe** (string) - The git description string, or an empty string if not available.

#### Response Example
```json
{
  "git_describe": "v1.14.9-5-gabcdef12"
}
```
```

--------------------------------

### Define Seeding Particle Times

Source: https://opendrift.github.io/gallery/example_generic.html

Defines the time instances for seeding particles. This example shows how to set a list of times, including the start time of the atmospheric reader and an offset, or a single start time.

```python
time = [reader_arome.start_time,
        reader_arome.start_time + timedelta(hours=30)]
#time = reader_arome.start_time

```

--------------------------------

### Environment Setup Log

Source: https://opendrift.github.io/gallery/example_openoil_sample_output.html

Log output showing ADIOS database query and fallback environment values.

```text
08:35:12 INFO    opendrift.models.openoil.adios.dirjs:86: Querying ADIOS database for oil: TAU 1999
08:35:12 INFO    opendrift.models.openoil.openoil:1726: Using density 851.002835 and viscosity 0.0012492557043601948 of oiltype TAU 1999
08:35:12 INFO    opendrift.models.basemodel.environment:203: Adding a global landmask from GSHHG
08:35:16 INFO    opendrift.models.basemodel.environment:227: Fallback values will be used for the following variables which have no readers:
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_surface_height: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    upward_sea_water_velocity: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_surface_wave_significant_height: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_surface_wave_stokes_drift_x_velocity: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_surface_wave_stokes_drift_y_velocity: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_surface_wave_period_at_variance_spectral_density_maximum: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_surface_wave_mean_period_from_variance_spectral_density_second_frequency_moment: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_ice_area_fraction: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_ice_x_velocity: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_ice_y_velocity: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_water_temperature: 10.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_water_salinity: 34.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    sea_floor_depth_below_sea_level: 10000.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    horizontal_diffusivity: 0.000000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    ocean_vertical_diffusivity: 0.020000
08:35:16 INFO    opendrift.models.basemodel.environment:230:    ocean_mixed_layer_thickness: 50.000000
```

--------------------------------

### Import necessary libraries for OpenDrift and CMEMS

Source: https://opendrift.github.io/_downloads/ca52802bcb80e8e9a1418baa21d21889/example_long_cmems_currents.ipynb

Imports required modules for data handling, CMEMS integration, and OpenDrift model setup. Ensure these libraries are installed.

```python
from datetime import datetime, timedelta
import cf_xarray
import copernicusmarine
from opendrift.models.oceandrift import OceanDrift
from opendrift.readers.reader_netCDF_CF_generic import Reader
```

--------------------------------

### OpenDrift Initialization Logs

Source: https://opendrift.github.io/gallery/example_LCS_norkyst.html

Example log output showing the initialization of the OpenDrift simulation and reader detection.

```text
08:24:22 INFO    opendrift:568: OpenDriftSimulation initialised (version 1.14.9 / v1.14.9-9-gcde0dcf)
08:24:22 INFO    opendrift.readers:64: Opening file with xr.open_dataset
08:24:22 INFO    opendrift.readers.reader_netCDF_CF_generic:340: Detected dimensions: {'x': 'X', 'y': 'Y', 'z': 'depth', 'time': 'time'}
```

--------------------------------

### Logging Setup Function

Source: https://opendrift.github.io/_modules/opendrift/models/eulerdrift.html

The install_logs function configures colorful and informative logging for the OpenDrift simulation.

```APIDOC
## install_logs

### Description
Set up fanzy, colorful, logging.

### Parameters
#### Arguments
- **level** (int) - Optional - Log level. Defaults to logging.DEBUG.
```

--------------------------------

### Execute a basic simulation

Source: https://opendrift.github.io/tutorial.html

Starts the simulation using default settings.

```python
o.run()
```

--------------------------------

### Get Ocean Current Velocity

Source: https://opendrift.github.io/_modules/opendrift/models/eulerdrift/simulation.html

Retrieves the ocean current velocities (Ux, Uy) at a given time `t` relative to the simulation's start time `t0`. It iterates through registered readers to find velocity data.

```python
def U(self, t):
    """
    Get U (ocean current) for t0 + t
    """
    Ux, Uy = None, None
    t = self.t0 + timedelta(seconds = t)

    for r in self.readers:
        vv = r.variables()
        if 'x_sea_water_velocity' in vv and 'y_sea_water_velocity' in vv:
            Ux, Uy = r.read_grid(self.grid, ['x_sea_water_velocity', 'y_sea_water_velocity'], t)

        if Ux is not None and Uy is not None:
            break

    return Ux, Uy
```

--------------------------------

### Initialize Simulation Environment

Source: https://opendrift.github.io/_downloads/1f273572d35a01780a354710d35e2a1a/example_river_runoff.ipynb

Import necessary libraries and define output file paths for the simulation.

```python
import os
from datetime import datetime, timedelta
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.dates import DateFormatter
import opendrift
from opendrift.models.oceandrift import OceanDrift
from opendrift.readers import reader_oscillating


outfile = 'runoff.nc'  # Raw simulation output
histogram_file = 'runoff_histogram.nc'
```

--------------------------------

### Run Docker Container and Import OpenDrift

Source: https://opendrift.github.io/docker.html

Execute the OpenDrift Docker image to get an interactive shell. The working directory is set to /code, where the repository is cloned. This example also shows importing and checking the OpenDrift version within the container.

```bash
$ docker run -it opendrift/opendrift

Unable to find image 'opendrift/opendrift:latest' locally
latest: Pulling from opendrift/opendrift
cc1a78bfd46b: Already exists
bad124d5894e: Pull complete
ab2b0b173074: Pull complete
018d53043894: Pull complete
4987762b1e47: Pull complete
d58a7f3e3615: Pull complete
86f53a067a28: Pull complete
4c17ec80ca72: Pull complete
aae597ea9e38: Pull complete
Digest: sha256:33807a79ced6ca9c0960bd942e9d12381c7f1066feb75c5c6992ae5b8802f94c
Status: Downloaded newer image for opendrift/opendrift:latest
(base) root@d7ca5fe730b8:/code# python
Python 2.7.15 |Anaconda, Inc.| (default, May  1 2018, 23:32:55)
[GCC 7.2.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import opendrift
>>> opendrift.__version__
'1.0.4'
```

--------------------------------

### Environment Setup Logs

Source: https://opendrift.github.io/gallery/example_checkerboard.html

Log output detailing the environment configuration and fallback values used.

```text
08:23:56 INFO    opendrift.models.basemodel.environment:203: Adding a global landmask from GSHHG
08:24:01 INFO    opendrift.models.basemodel.environment:227: Fallback values will be used for the following variables which have no readers:
08:24:01 INFO    opendrift.models.basemodel.environment:230:    sea_surface_height: 0.000000
08:24:01 INFO    opendrift.models.basemodel.environment:230:    x_wind: 0.000000
08:24:01 INFO    opendrift.models.basemodel.environment:230:    y_wind: 0.000000
08:24:01 INFO    opendrift.models.basemodel.environment:230:    upward_sea_water_velocity: 0.000000
08:24:01 INFO    opendrift.models.basemodel.environment:230:    ocean_vertical_diffusivity: 0.000000
08:24:01 INFO    opendrift.models.basemodel.environment:230:    horizontal_diffusivity: 0.000000
08:24:01 INFO    opendrift.models.basemodel.environment:230:    sea_surface_wave_significant_height: 0.000000
08:24:01 INFO    opendrift.models.basemodel.environment:230:    sea_surface_wave_stokes_drift_x_velocity: 0.000000
08:24:01 INFO    opendrift.models.basemodel.environment:230:    sea_surface_wave_stokes_drift_y_velocity: 0.000000
08:24:01 INFO    opendrift.models.basemodel.environment:230:    ocean_mixed_layer_thickness: 50.000000
08:24:01 INFO    opendrift.models.basemodel.environment:230:    sea_floor_depth_below_sea_level: 10000.000000
```

--------------------------------

### Install Trajan using Pip

Source: https://opendrift.github.io/trajan/_sources/index.rst.txt

Alternative installation method for users using Pip. Installs the package from PyPI.

```console
$ pip install trajan
```

--------------------------------

### Install Logging

Source: https://opendrift.github.io/_sources/autoapi/opendrift/models/eulerdrift/index.rst.txt

Sets up fanzy, colorful logging. Use this to configure the verbosity of OpenDrift's output.

```python
import logging

install_logs(level=logging.DEBUG)
```

--------------------------------

### Initialize environment and imports

Source: https://opendrift.github.io/_downloads/328bb9a2268c424591c715d1fd64b02c/example_wind_measurements.ipynb

Sets up necessary libraries and configures Matplotlib parameters for plotting.

```python
from datetime import datetime, timedelta, date
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.openoil import OceanDrift
from opendrift.readers import reader_timeseries
from opendrift.readers.operators import ops
import opendrift.models.physics_methods as phy
import xarray as xr
import trajan as _
import numpy as np
import pyproj
import matplotlib.pyplot as plt
import matplotlib as mpl

# Preparation of figsize, dpi, fontsize and font style
# Could also be done using mpl style sheet
# https://matplotlib.org/stable/users/explain/customizing.html
mpl.rcParams['figure.figsize'] = (5, 5)
mpl.rcParams['savefig.dpi'] = 300
mpl.rcParams['font.family'] = "sans-serif"
mpl.rcParams['font.sans-serif'] = "DejaVu Sans"
mpl.rcParams['font.size'] = 22
mpl.rcParams['mathtext.fontset'] = "dejavusans"
```

--------------------------------

### Install Trajan using Conda

Source: https://opendrift.github.io/trajan/_sources/index.rst.txt

Recommended installation method for users using Conda. Installs the package from the conda-forge channel.

```console
$ conda install -c conda-forge trajan
```

--------------------------------

### opendrift.readers.basereader.consts.vector_pairs_xy Example

Source: https://opendrift.github.io/autoapi/opendrift/readers/basereader/consts/index.html

An example showing the structure and content of the `vector_pairs_xy` constant.

```APIDOC
## opendrift.readers.basereader.consts.vector_pairs_xy

### Description
This constant defines pairs of x and y components for vector quantities, along with their magnitudes and directions.

### Value Example
```json
[
  ["x_wind", "y_wind", "wind_speed", "wind_to_direction", "wind_from_direction"],
  ...
]
```
```

--------------------------------

### Initialize Simulation with Regular Grid

Source: https://opendrift.github.io/_modules/opendrift/models/eulerdrift/simulation.html

Creates a new simulation instance with a `RegularGrid`. This is the primary way to set up a simulation environment.

```python
import logging
logger = logging.getLogger(__name__)
from .grid import RegularGrid
from . import srs
from .interp import vec_nearest
from abc import abstractmethod
import numpy as np
from datetime import timedelta, datetime




class Simulation:
    r"""
    The simulation.

    It contains the problem to be simulated, means to read necessary input
    variables, and the physics for modeling the convection of the initial
    conditions.

    Convection:

      Convection consists of advection and diffusion.

      Diffusion is given by:

      .. math::

        \frac{\partial U}{\partial t} = D \left( \frac{\partial^2 U}{\partial x^2} + \frac{\partial^2 U}{\partial y^2} \right)


      The convection equation is (`wiki
      <https://en.wikipedia.org/wiki/Convection%E2%80%93diffusion_equation>`_):

      .. math::

        \frac{\partial c}{\partial t} = ...

      with the assumptions that:

        * the diffusion constant `D` is constant for the field,
        * and that the flow `u` is incompressible (i.e. has *no divergence*).

      the equation simplifies to:

      .. math::

        \frac{\partial c}{\partial t} = D \nabla^2 c - \mathbf{v} \cdot \nabla T

      where :math:`\nabla^2 = \triangle` is the Laplacian.
    """

    """The model grid."""
    grid = None

    """Reference time `datetime.Datetime`"""
    t0 = None

    """Current time offset after `t0`"""
    t = 0.

    """
    Diffusivity (:math:`m^2/s`). E.g. between 0.01 and 0.1 for oil on the
    surface of the ocean (`Matsuzakia et. al., 2017
    <https://www.sciencedirect.com/science/article/pii/S0025326X16308426>`_).

    Decreasing diffusivity places stricter stability criteria on time step.
    """
    D = 0.1

    """Porosity, rate of liquid volume to total volume (fraction of flux)"""
    rho = 1.

    """List of readers"""
    readers = None

    def __init__(self, grid):
        self.grid = grid
        self.readers = []
        self.t0 = datetime.now()




    @classmethod
    def new(cls, lon0 = 10., lat0 = 65., res = 10., shape=(100, 100)):
        """
        New simulation on a :class:`.grid.RegularGrid`.

        Args:

            lon0: lower-left corner longitude

            lat0: lower-left corner latitude

            res: resolution (dx and dy)

            shape: shape (size) of grid
        """
        s = cls(grid=RegularGrid.new(lon0, lat0, res, shape))
        logger.info("New %s with Regular Grid" % (cls.__name__))

        return s

```

--------------------------------

### Install OpenDrift via Mamba

Source: https://opendrift.github.io/_sources/install.rst.txt

Installs OpenDrift into a new Python 3 environment.

```bash
$ mamba create -n opendrift python=3 opendrift
$ conda activate opendrift
```

--------------------------------

### Initialize and Run OceanDrift with SCHISM Reader

Source: https://opendrift.github.io/_sources/gallery/example_schism_native.rst.txt

Demonstrates setting up the OceanDrift model, adding a SCHISM native reader with a custom projection, and seeding particles for simulation.

```Python
import numpy as np
from datetime import timedelta, datetime
from opendrift.readers import reader_schism_native
from opendrift.readers import reader_global_landmask
from opendrift.models.oceandrift import OceanDrift

o = OceanDrift(loglevel=20)  # Set loglevel to 0 for debug information


try:
    # NZTM proj4 string found at https://spatialreference.org/ref/epsg/nzgd2000-new-zealand-transverse-mercator-2000/
    proj4str_nztm = '+proj=tmerc +lat_0=0 +lon_0=173 +k=0.9996 +x_0=1600000 +y_0=10000000 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs'
    schism_native = reader_schism_native.Reader(
        filename = 'https://thredds.met.no/thredds/dodsC/metusers/knutfd/thredds/netcdf_unstructured_samples/schism_marl20080101_00z_3D.nc',
        proj4 = proj4str_nztm,
        use_3d = True)
except:
    print('Thredds server not available, cannot run example')
    schism_native = None


if schism_native is not None:
    o.add_reader([schism_native])

    # Seed elements at defined positions, depth and time
    o.seed_elements(lon=174.046669, lat=-40.928116, radius=20, number=100,
                    z=np.linspace(0,-10, 100), time=schism_native.start_time)

    o.seed_elements(lon= 173.8839, lat=-40.9160, radius=20, number=100,
                    z=np.linspace(0,-10, 100), time=schism_native.start_time)

    o.seed_elements(lon=174.2940, lat=-41.0888, radius=20, number=100,
                    z=np.linspace(0,-10, 100), time=schism_native.start_time)

    #%%
    # Running model
    o.run(time_step=900,
```

--------------------------------

### Example Buoy List

Source: https://opendrift.github.io/trajan/gallery/example_indepth_omb_use.html

An example representation of the list of buoys that might be present in the dataset.

```python
list_buoys = [np.str_('drifter_1'), np.str_('drifter_2'), np.str_('drifter_3')]
```

--------------------------------

### POST /run

Source: https://opendrift.github.io/_modules/opendrift/models/basemodel.html

Starts the trajectory simulation loop after initial configuration.

```APIDOC
## POST /run

### Description
Starts a trajectory simulation, performing the main loop to obtain environment data and update particle properties until completion conditions are met.

### Method
POST

### Endpoint
/run

### Parameters
#### Request Body
- **time_step** (float) - Optional - Time step for the simulation.
- **steps** (int) - Optional - Number of steps to run.
- **time_step_output** (float) - Optional - Output interval.
- **duration** (float) - Optional - Total duration of the simulation.
- **end_time** (datetime) - Optional - Specific end time for the simulation.
- **outfile** (string) - Optional - Path to the output file.
- **export_variables** (list) - Optional - List of variables to export.
- **export_buffer_length** (int) - Optional - Buffer length for exports.
- **stop_on_error** (boolean) - Optional - Whether to stop on error.
```

--------------------------------

### Import Required Libraries

Source: https://opendrift.github.io/trajan/_downloads/475e861854270bc30e5e26e6c561a88a/example_drifter_csv.ipynb

Initial setup for data manipulation and visualization.

```python
import pandas as pd
import trajan as ta
import matplotlib.pyplot as plt
```

--------------------------------

### Initialize Sea Lice Model Run

Source: https://opendrift.github.io/_modules/opendrift/models/sealice.html

The prepare_run method initializes model variables by retrieving configuration values and setting up initial population dynamics.

```python
[docs]
    def prepare_run(self):
        logger.info("preparing the run...")
        ### need to find a better way of initialising the variables...
        self.prefix="lice:"
        self.vertical_migration_speed=self.get_config(self.prefix+'vertical_migration_speed') \
                                        *self.time_step.total_seconds()
        self.sensing_distance=2*self.vertical_migration_speed
        self.tau= np.pi+2*np.deg2rad(self.get_config(self.prefix+'twilight')) #width of solar irridation distribution
        self.nu=self.get_config(self.prefix+'nu')
        self.sinking_velocity=self.get_config(self.prefix+'sinking_velocity') \
                                *self.time_step.total_seconds()
        self.freezing_salinity=self.get_config(self.prefix+'freezing_salinity')
        self.avoided_salinity=self.get_config(self.prefix+'avoided_salinity')
        self.k_water=self.get_config(self.prefix+'k_water')
        self.Nauplii_light_trigger=self.get_config(self.prefix+'Nauplii_light_trigger')
        self.Copepodid_light_trigger=self.get_config(self.prefix+'Copepodid_light_trigger')
        self.new_born()
        self.population()
        self.ref_date = datetime(1,1,1,0,0)

        super(SeaLice, self).prepare_run()
```

--------------------------------

### Z Variable Example

Source: https://opendrift.github.io/gallery/example_entrainment_rate_oil_types.html

Example numpy array for 'z', representing the vertical position of trajectories in meters.

```python
array([[  0.        ,  -3.478036  , -25.606453  , ..., -28.828886  ,
         -4.016286  , -10.813123  ],
       [  0.        ,  -3.5911233 ,  -0.3178709 , ..., -10.856451  ,
        -32.934574  ,  -8.29962   ],
       [  0.        , -20.060175  , -19.434288  , ...,  -3.3366625 ,
        -16.211443  ,  -0.17564589],
       ...,
       [  0.        ,  -6.370093  , -11.591485  , ...,  -7.2642117 ,
        -10.766642  ,  -1.8030005 ],
       [  0.        ,  -2.8007238 , -17.953928  , ...,   0.        ,
         -4.529121  , -16.282986  ],
       [  0.        ,  -5.265363  , -20.021646  , ..., -21.785057  ,
        -15.9200115 ,  -3.97356   ]], shape=(1000, 13), dtype=float32)
```

--------------------------------

### Initialize OpenOil simulation parameters

Source: https://opendrift.github.io/_downloads/743ab0cf4d1677920b0ee8cfc13df382/example_oil_thickness.ipynb

Sets up the initial constants and imports required for the OpenOil simulation.

```python
from datetime import datetime, timedelta
import matplotlib.pyplot as plt
import numpy as np
from opendrift.models.openoil import OpenOil


number = 10000
timestep = timedelta(minutes=10)
timestep_output = timedelta(minutes=60)
duration = timedelta(hours=20)
mass_oil = 2000  # mass oil per particle
oil_type = 'GENERIC DIESEL'
#oil_type = 'GENERIC BUNKER C'
```

--------------------------------

### Age Seconds Variable Example

Source: https://opendrift.github.io/gallery/example_entrainment_rate_oil_types.html

Example numpy array for 'age_seconds', representing the age of trajectories in seconds.

```python
array([[    0.,  3600.,  7200., ..., 36000., 39600., 43200.],
       [    0.,  3600.,  7200., ..., 36000., 39600., 43200.],
       [    0.,  3600.,  7200., ..., 36000., 39600., 43200.],
       ...,
       [    0.,  3600.,  7200., ..., 36000., 39600., 43200.],
       [    0.,  3600.,  7200., ..., 36000., 39600., 43200.],
       [    0.,  3600.,  7200., ..., 36000., 39600., 43200.]]],
      shape=(1000, 13), dtype=float32)
```

--------------------------------

### Status Variable Example

Source: https://opendrift.github.io/gallery/example_entrainment_rate_oil_types.html

Example numpy array for the 'status' variable, indicating the active state of trajectories.

```python
array([[0., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.],
       ...,
       [0., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.],
       [0., 0., 0., ..., 0., 0., 0.]], shape=(1000, 13), dtype=float32)
```

--------------------------------

### POST /simulation/new

Source: https://opendrift.github.io/_modules/opendrift/models/eulerdrift/simulation.html

Initializes a new simulation instance on a RegularGrid.

```APIDOC
## POST /simulation/new

### Description
Creates a new simulation instance configured with a RegularGrid based on provided geographic coordinates and resolution.

### Parameters
#### Query Parameters
- **lon0** (float) - Required - Lower-left corner longitude
- **lat0** (float) - Required - Lower-left corner latitude
- **res** (float) - Required - Resolution (dx and dy)
- **shape** (tuple) - Required - Shape (size) of the grid

### Response
#### Success Response (200)
- **simulation** (object) - The initialized simulation instance
```

--------------------------------

### Modify existing installation to editable mode

Source: https://opendrift.github.io/_sources/install.rst.txt

Converts a standard installation to an editable one for source code development.

```bash
$ mamba remove --force opendrift
```

```bash
$ pip install --no-deps -e .
```

--------------------------------

### Initialize OceanDrift and Readers

Source: https://opendrift.github.io/_sources/gallery/example_grid_time.rst.txt

Sets up the simulation environment and loads the necessary NetCDF data and landmask reader.

```Python
from datetime import timedelta
import numpy as np
from opendrift import test_data_folder as tdf
from opendrift.readers import reader_global_landmask
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.oceandrift import OceanDrift

# Seeding at a grid at regular interval
o = OceanDrift(loglevel=20)  # Set loglevel to 0 for debug information

reader_norkyst = reader_netCDF_CF_generic.Reader(tdf +
    '16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
```

```none
08:31:03 INFO    opendrift:568: OpenDriftSimulation initialised (version 1.14.9 / v1.14.9-9-gcde0dcf)
08:31:03 INFO    opendrift.readers:64: Opening file with xr.open_dataset
08:31:03 INFO    opendrift.readers.reader_netCDF_CF_generic:340: Detected dimensions: {'x': 'X', 'y': 'Y', 'z': 'depth', 'time': 'time'}
```

--------------------------------

### Initialize OceanDrift Model

Source: https://opendrift.github.io/_downloads/032bc03d5e69e556134ea47d9f6caed7/example_double_gyre_LCS.ipynb

Sets up the OceanDrift environment and configures the land binary mask.

```python
from datetime import datetime, timedelta
import matplotlib.pyplot as plt

from opendrift.readers import reader_double_gyre
from opendrift.models.oceandrift import OceanDrift

o = OceanDrift(loglevel=20)  # Set loglevel to 0 for debug information

o.set_config('environment:fallback:land_binary_mask', 0)
```

--------------------------------

### Latitude Variable Example

Source: https://opendrift.github.io/gallery/example_entrainment_rate_oil_types.html

Example numpy array for 'lat', representing the latitude coordinates of trajectories in degrees north.

```python
array([[60.0005  , 60.002075, 60.002937, ..., 60.002808, 60.002804,
        60.003265],
       [60.0008  , 60.000973, 60.000946, ..., 60.00001 , 59.998016,
        59.999126],
       [59.999622, 59.999508, 59.997215, ..., 59.998936, 59.998573,
        59.998222],
       ...,
       [60.00014 , 59.9992  , 59.999397, ..., 59.9981  , 59.997295,
        59.997482],
       [59.998974, 59.999462, 59.999477, ..., 59.996986, 59.99567 ,
        59.99584 ],
       [59.998825, 59.9987  , 59.99904 , ..., 60.000134, 59.99921 ,
        59.998894]], shape=(1000, 13), dtype=float32)
```

--------------------------------

### Longitude Variable Example

Source: https://opendrift.github.io/gallery/example_entrainment_rate_oil_types.html

Example numpy array for 'lon', representing the longitude coordinates of trajectories in degrees east.

```python
array([[4.0031614, 4.0010514, 3.9868023, ..., 3.8897908, 3.8765304,
        3.8665862],
       [4.000717 , 3.9920855, 3.9843001, ..., 3.9423246, 3.9285328,
        3.9190435],
       [4.001754 , 3.9898474, 3.9770355, ..., 3.9119923, 3.910552 ,
        3.909527 ],
       ...,
       [4.000169 , 3.9860523, 3.9695342, ..., 3.880206 , 3.8645267,
        3.8530736],
       [3.9979434, 3.9901185, 3.9843402, ..., 3.9321027, 3.948563 ,
        3.93515  ],
       [3.9993582, 3.9876788, 3.9727552, ..., 3.8718767, 3.8583548,
        3.848155 ]], shape=(1000, 13), dtype=float32)
```

--------------------------------

### Initialize PelagicEggDrift model

Source: https://opendrift.github.io/gallery/example_codegg.html

Sets up the simulation environment for pelagic egg drift. Requires the opendrift library and specific model imports.

```python
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.pelagicegg import PelagicEggDrift
from datetime import datetime, timedelta

o = PelagicEggDrift(loglevel=20)  # Set loglevel to 0 for debug information
```

--------------------------------

### Moving Variable Example

Source: https://opendrift.github.io/gallery/example_entrainment_rate_oil_types.html

Example numpy array for the 'moving' variable, indicating whether trajectories are actively moving.

```python
array([[1., 1., 1., ..., 1., 1., 1.],
       [1., 1., 1., ..., 1., 1., 1.],
       [1., 1., 1., ..., 1., 1., 1.],
       ...,
       [1., 1., 1., ..., 1., 1., 1.],
       [1., 1., 1., ..., 1., 1., 1.],
       [1., 1., 1., ..., 1., 1., 1.]], shape=(1000, 13), dtype=float32)
```

--------------------------------

### Prepare Run Initialization

Source: https://opendrift.github.io/_modules/opendrift/models/oceandrift.html

Initializes the run process by calling the superclass's prepare_run method. This is a standard setup step for the simulation.

```python
def prepare_run(self):
        super(OceanDrift, self).prepare_run()
```

--------------------------------

### Log Error for Invalid Transfer Setup

Source: https://opendrift.github.io/_modules/opendrift/models/chemicaldrift.html

Logs an error message if an invalid or unrecognized transfer setup configuration is provided.

```python
logger.error('No valid transfer_setup {}'.format(self.get_config('chemical:transfer_setup')))
```

--------------------------------

### Initialize Reader with different data sources

Source: https://opendrift.github.io/_modules/opendrift/readers/reader_netCDF_CF_generic.html

Demonstrates how to instantiate the Reader class using a single file, a file pattern, an OPeNDAP URL, or an xarray Dataset.

```python
from opendrift.readers.reader_netCDF_CF_generic import Reader
r = Reader("arome_subset_16Nov2015.nc")
```

```python
from opendrift.readers.reader_netCDF_CF_generic import Reader
r = Reader("*.nc")
```

```python
from opendrift.readers.reader_netCDF_CF_generic import Reader
r = Reader('https://thredds.met.no/thredds/dodsC/mepslatest/meps_lagged_6_h_latest_2_5km_latest.nc')
```

```python
from opendrift.readers.reader_netCDF_CF_generic import Reader
r = Reader(ds, zarr_storage_options)
```

--------------------------------

### Shift reader start time

Source: https://opendrift.github.io/_modules/opendrift/readers/basereader.html

Adjusts the temporal coverage of a reader by shifting the start time and updating the associated time list.

```python
    def shift_start_time(self, start_time):
        """Shift the time coverage of reader to match given start_time"""
        if self.start_time is None:
            logger.warning('Reader has no time coverage, cannot shift times')
            return
        shift_time = self.start_time - start_time
        self.start_time = start_time
        self.end_time = self.end_time - shift_time
        self.times = [t - shift_time for t in self.times]
```

--------------------------------

### Initialize Euler Simulation

Source: https://opendrift.github.io/_downloads/3ed80f5391ce56914ddb1ac1bcc4e196/example_eulerdrift_gauss_blob.ipynb

Sets up the simulation environment and adds a constant reader to the grid.

```python
import matplotlib.pyplot as plt
from opendrift.models import eulerdrift

eulerdrift.install_logs() #remove

s = eulerdrift.ExplSimulation.new(shape = (200, 200))
s.readers.append(
    eulerdrift.readers.ConstantReader.new_xy(5, 5))
```

--------------------------------

### Initialize NorKyst Reader and Configuration

Source: https://opendrift.github.io/gallery/example_grid.html

Sets up the NorKyst reader and configures simulation parameters like vertical mixing.

```python
reader_norkyst = reader_netCDF_CF_generic.Reader(tdf + '16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')

o.add_reader(reader_norkyst)
#o.set_config('environment:fallback:land_binary_mask', 0)
o.set_config('drift:vertical_mixing', False)
```

--------------------------------

### Modify Element Properties Example

Source: https://opendrift.github.io/_sources/writing_a_new_model.rst.txt

Example demonstrating direct modification of element properties. Here, element length is set to half the seawater temperature.

```python
self.elements.length = self.environment.sea_water_temperature / 2
```

--------------------------------

### Initialize Species for Custom Transfer Setup

Source: https://opendrift.github.io/_modules/opendrift/models/chemicaldrift.html

Handles the 'custom' transfer setup by doing nothing, implying that species must be set manually by the user.

```python
# Do nothing, species must be set manually
            pass
```

--------------------------------

### Initialize OceanDrift and Run Simulation

Source: https://opendrift.github.io/_downloads/7f4b8d6252a4db6f69a9ca62023651e2/example_convolve_input.ipynb

Sets up the OceanDrift model with a NorKyst reader and runs the initial simulation.

```python
from datetime import datetime, timedelta
import matplotlib.pyplot as plt
from opendrift import test_data_folder as tdf
from opendrift.readers import reader_netCDF_CF_generic
from opendrift.models.oceandrift import OceanDrift


lon = 4.9; lat = 60.0
o = OceanDrift(loglevel=20)

reader_norkyst = reader_netCDF_CF_generic.Reader(tdf + '16Nov2015_NorKyst_z_surface/norkyst800_subset_16Nov2015.nc')
time = reader_norkyst.start_time

o.add_reader([reader_norkyst])
o.seed_elements(lon, lat, radius=1000, number=1000, time=time)
o.run(steps=20)
```

--------------------------------

### Initialize Species for 137Cs_rev Transfer Setup

Source: https://opendrift.github.io/_modules/opendrift/models/chemicaldrift.html

Initializes chemical species configurations for the '137Cs_rev' transfer setup, enabling LMM and particle/sediment reversible states.

```python
self.set_config('chemical:species:LMM',True)
            self.set_config('chemical:species:Particle_reversible', True)
            self.set_config('chemical:species:Sediment_reversible', True)
```

--------------------------------

### Configure and Run OpenDrift Simulation

Source: https://opendrift.github.io/_sources/gallery/example_coastline_options.rst.txt

Sets up the reader, configures coastline actions, seeds elements, and executes the simulation.

```python
o.add_reader([reader_osc])
o.set_config('environment:fallback:y_sea_water_velocity', .2)
o.set_config('general:coastline_action', 'none')
o.seed_elements(lon=12.2, lat=67.7, radius=5000, number=number, time=reader_osc.zero_time)
o.run(duration=duration, time_step=time_step)
print(f'Calculation time: {o.timing["total time"]}')
o.animation()
```