User Guide¶
Here we collect a brief introduction to each algorithm, with curated references
for more information along with the configuration settings as implemented
within eOn.
Python client (pyeonclient)¶
For in-process client work (minimization, NEB, Matter objects) use the pip
package pyeonclient — an ASE-shaped API where the path is a
list[Matter], not a working directory:
See also the API reference and the atomistic-cookbook PET-MAD NEB example.
Configuration file (config.ini)¶
Each of the sections and methods may still be included in a configuration file
with the appropriate section header (used by the eonclient binary, the AKMC
server, and optional workdir helpers).
Overview¶
The eOn program can run the following methods or tasks to explore the
configuration space of molecular systems and to accelerate the simulation of
their dynamics over long times. To run eOn, a configuration file must be generated
using the options specified in the documentation. Each section header is denoted
by square brackets, and is followed by the key/value pairs. For example, to set
the job key of the [Main] section to the value process_search, your
configuration file would include the lines:
[Main]
job = process_search
There are specific options for each method, and a set of general options which are shared between methods. Examples of these general options include specification of the interatomic potential and the parameters for doing structural optimizations and comparisons.
Added in version 2.12: Parameters can also be loaded from JSON strings for programmatic usage. See Parameters system for the JSON schema.
eOn is designed to run in serial on one computer or in parallel using a communicator to send jobs from a server to clients and receive the results back. Several parallelization schemes have been implemented, including local communication through files, cluster communication via a queuing system or via mpi.
Methods run in parallel are broken up by the eon server into tasks which are run by client program. The server then compiles the information sent back by the clients in a way that can be used by the sampling or dynamics methods.
Geometry and neighbor lists¶
Pair finding owned by eOn uses vesin. Architecture and ASV measurement surface: Neighbor lists (vesin).
Potentials¶
Some of the potentials require additional installation and setup, which are described in the subsequent sections.
Configuration Sections¶
Potential Energy Surface Traversal
Compound Jobs
Dynamics
Additional configuration
Miscellaneous¶
Some of the potentials require additional installation and setup, which are described in the subsequent sections.