AMEP example data

In this directory, we provide the simulation data which we have used for all AMEP examples. This data can either be downloaded directly from the repository or with the following download link:

https://download-directory.github.io/?url=https://github.com/amepproject/amep/tree/main/examples/data

For AMEP beginners, we strongly recommend to download this data and run the examples to get familiar with the AMEP workflow.

The data directory

All data is contained in the data directory. It contains the following subdirectories:

• continuum: Raw data of a numerical solution of the Keller-Segel model.
• lammps: Raw data of a LAMMPS simulation of overdamped interacting active Brownian particles.

The file lammps.h5amep has been created by running

import amep
traj = amep.load.traj(
    './data/lammps',
    mode = 'lammps',
    dumps = 'dump*.txt',
    savedir = './data',
    trajfile = 'lammps.h5amep'
)

and the file continuum.h5amep by running

import amep
traj = amep.load.traj(
    './data/continuum',
    mode = 'field',
    dumps = 'field_*.txt',
    timestep = 0.01,
    savedir = './data',
    trajfile = 'continuum.h5amep'
)

which are the corresponding AMEP data files.

Run the continuum simulation

To run the continuum simulation by yourself, you have to install the FiPy Python library, which is a finite-volume solver for partial differential equations, via

pip install fipy

or alternatively via

conda install conda-forge::fipy

Then, you can simply run

python /data/continuum/solver.py

Run the LAMMPS simulation

To run the LAMMPS simulation by yourself, you have to install the latest stable LAMMPS release. Please download the respective version for your operating system from https://www.lammps.org and install it on your machine. The example provided by AMEP requires the BROWNIAN and the DIPOLE packages. To compile it under Linux, you might use the following commands:

cd /path/to/lammps/src
make clean-all
make yes-BROWNIAN
make yes-DIPOLE
make serial

Then, you can run the simulation with the following command:

/path/to/lammps/src/lmp_serial -in abps.run

For further details about LAMMPS, please visit their documentation available at https://docs.lammps.org/Manual.html.

Examples

We provide two basic examples, one for the particle-based simulation data obtained from the LAMMPS simulation (particle-example.py) and one for the continuum data (continuum-data.py). The Jupyter notebook amep-examples.ipynb contains the same examples. These examples serve as a starting point for everyone who uses AMEP for the first time.