Reactive molecular dynamics trajectory analysis.
lionanalysis is short for LAMMPS ion analysis, but it can also be used to analyze trajectories from other programs and be applied to a variety of structures (not just ions).
cd src
# edit Makefile if necessary
make
This should create an executable called lionanalysis.exe. Put this executable somewhere on your PATH.
Check your installation by running
lionanalysis.exe --help
Check the docs/examples/ folder for some self-contained pedagogical examples!
Documentation at lionanalysis.readthedocs.io
- Concentration-Dependent Proton Transfer Mechanisms in Aqueous NaOH Solutions: From Acceptor-Driven to Donor-Driven and Back
- Proton-Transfer Mechanisms at the Water–ZnO Interface: The Role of Presolvation
- Proton-Transfer-Driven Water Exchange Mechanism in the Na+ Solvation Shell
- Structure of aqueous NaOH solutions: insights from neural-network-based molecular dynamics simulations
- Maximally resolved anharmonic OH vibrational spectrum of the water/ZnO(101¯0) interface from a high-dimensional neural network potential
- Nuclear Quantum Effects in Sodium Hydroxide Solutions from Neural Network Molecular Dynamics Simulations
- Structure and Dynamics of the Liquid-Water/Zinc-Oxide Interface from Machine Learning Potential Simulations
- One-dimensional vs. two-dimensional proton transport processes at solid–liquid zinc-oxide–water interfaces
- Temperature effects on the ionic conductivity in concentrated alkaline electrolyte solutions
- Importance of Nuclear Quantum Effects on Aqueous Electrolyte Transport under Confinement in Ti3C2 MXenes
The packages
are included with lionanalysis in the src/include directory.