Dependencies and installation¶
Before using Planktos, FFmpeg must be installed and accessible via the $PATH environment variable in order to save video files of simulation results.
There are a variety of ways to install FFmpeg, such as the official download links, or using your package manager of choice (e.g. “sudo apt install ffmpeg” on Debian/Ubuntu, “brew install ffmpeg” on OS X, etc.).
Regardless of how FFmpeg is installed, you can check if your environment path is set correctly by running the “ffmpeg” command from the terminal, in which case the version information should appear, as in the following example (truncated for brevity):
$ ffmpeg ffmpeg version 4.3.1 Copyright (c) 2000-2020 the FFmpeg developers built with gcc 10.2.1 (GCC) 20200726
Note: The actual version information displayed here may vary from one system to another; but if a message such as “ffmpeg: command not found” appears instead of the version information, FFmpeg is not properly installed.
Once FFmpeg is installed, Planktos can be installed from source using pip on Python >= 3.7 from the Planktos directory. Navigate to the Planktos directory in a terminal and use the command:
pip install .
Non-optional depdencencies (other than FFmpeg) should automatically be installed.
Planktos is still in active development and updates occur often. You should therefore pull the source repo often and then reinstall using the same command. To avoid needing to reinstall each time you pull the repo, you can instead install Planktos in “editable” mode (requires pip version >= 21.1):
pip install -e .
Planktos can then be imported like any other Python package from any directory. Either approach also allows you to uninstall with the same command (from the Planktos directory):
pip uninstall .
Running Directly From Source (no install)¶
Installing dependencies using Anaconda Python is highly recommended. However, the default package manager, conda, appears unable to handle the Planktos dependencies. The performance of conda has been degrading with time as the number of available Python libraries increases, and this is particularly true in the case of packages listed on the conda-forge channel. As of writing this (July, 2021), it is pretty much broken.
Instead, if you are using Anaconda Python, please first install the package manager mamba and use it in place of conda. The commands are the same (it’s a drop-in replacement for conda) but it is a C++ solver based on libsolv which manages dependencies for RedHat, Debian, etc. Also, it has multi-threaded downloads and doesn’t break when trying to obtain vtk and/or pyvista. Install with the following command:
conda install -c conda-forge mamba
Having done that, the dependencies are as follows:
vtk (if loading vtk data). Use mamba and conda-forge, not conda!! conda seems to break itself trying to install vtk for some reason, and takes an hour to try and solve the dependencies in the process.
mamba install -c conda-forge ffmpeg
pyvista (if saving vtk data). Again, mamba not conda. Same problem as for vtk.
numpy-stl (if loading stl data). Again, get it from conda-forge.
netCDF4 (if loading netCDF data)
pytest (if running tests)
There are several working examples in the examples folder, including a 2D simulation, a 2D simulation demonstrating individual variation, a 3D simulation, a simulation utilizing VTK data obtained from IBAMR (pulled from the tests/IBAMR_test_data folder), and simulations demonstrating subclassing of the get_positions method for user-defined agent behavior. There are also examples demonstrating how to import vertex data (from IB2d and IBAMR), automatically create immersed boundaries out of this data, and then simulate agent movement with these meshes as solid boundaries which the agents respect. More examples will be added as functionality is added. To run any of these examples, change your working directory to the examples directory and then run the desired script.
An important note about immersed boundary meshes: it is assumed that segments of the boundary do not cross except at vertices. This is to keep computational speed up and numerical complexity down. So, especially if you are auto-creating boundaries from vertex data, be sure and check that boundary segments are not intersecting each other away from specified vertices! A quick way to do this is to call environment.plot_envir() after the mesh import is done to zoom in and visually check that the boundary formed correctly and doesn’t cross itself in unexpected ways. There is also a method of the environment class called add_vertices_to_2D_ibmesh which will add vertices at all 2D mesh crossing points, however it’s use is discouraged because it results in complex vertices that attach more than two mesh segments and leftover segments that do not contribute to the dynamics at all. Do not expect meshes resulting from this method to have undergone rigorous testing, and running the method will add significant computational overhead due to the need to search for collisions with each additional line segment. Finally, avoid mesh structures that intersect with a periodic boundary (w.r.t. agents); behavior related to this is not implemented.
Research that utilizes this framework can be seen in:
Ozalp, Miller, Dombrowski, Braye, Dix, Pongracz, Howell, Klotsa, Pasour, Strickland (2020). Experiments and agent based models of zooplankton movement within complex flow environments, Biomimetics, 5(1), 2.
Currently, Planktos has built-in capabilities to load either time-independent or time-dependent 2D or 3D fluid velocity data specified on a regular mesh. ASCII vtk format is supported, as well as ASCII vtu files from COMSOL (single-time vtu data only) and NetCDF. More regular grid formats, especially if part of open-source formats, may be supported in the future; please contact the author (email@example.com) if you have a format you would like to see supported. A few analytical, 1D flow fields are also available and can be generated in either 2D or 3D environments; these include Brinkman flow, two layer channel flow, and canopy flow. Flow fields can also be extended and tiled in simple ways as appropriate. Mesh data must be time-invariant and loaded via IB2d/IBAMR-style vertex data (2D) or via stl file in 3D. Again, more (open source) formats may be considered if requested. Mesh data should never intersect any of the domain boundaries. This will not be checked, but is essential for correct preformance.
For agents, there is support for multiple species (swarms) along with individual variation though a pandas Dataframe property of the swarm class (swarm.props). Individual agents have access to the local flow field through interpolation of the spatial-temporal fluid velocity grid - specifically, Planktos implements a cubic spline in time with linear interpolation in space. In addition to more custom behavior, included in Planktos is an Ito SDE solver (Euler-Maruyama method) for movement specified as an SDE of the type
and an inertial particle behavior for dynamics described by the linearized Maxey-Riley equation 1. These two may be combined, and other, user-supplied ODEs can also be fed into the drift term of the Ito SDE. Finally, agents will treat immersed boundary meshes as solid barriers. Upon encountering an immersed mesh boundary, any remaining movement will be projected onto the mesh. Both concanve and convex mesh joints are supported, and pains have been taken to make the projection algorithm as numerically stable as possible.
Single-time and animation plotting of results is available in 2D and 3D; support for plotting multiple agent species together has not yet been implemented, but is a TODO.
Haller, G. and Sapsis, T. (2008). Where do inertial particles go in fluid flows? Physica D: Nonlinear Phenomena, 237(5), 573-583.