# eOn

> User guide for the eOn algorithms and job types, and the config.ini section schemas.

The pages below are the user guide. Each JSON Schema file is the copy of record
for one config.ini section: keys, defaults, and allowed values.

## User guide

- [User guide](https://eondocs.org/user_guide/index.html): User guide for eOn: algorithms, configuration settings, and job types. Schema: [Main](https://eondocs.org/schema/main.json).
- [pyeonclient](https://eondocs.org/user_guide/pyeonclient.html): pyeonclient Python API: Matter, min-mode (Dimer/Lanczos/Davidson), MinModeSaddleSearch, NEB, Hessian, Prefactor.
- [Neighbor lists (vesin)](https://eondocs.org/user_guide/neighbor_lists.html): Neighbor lists in eOn: vesin as the geometry backend; performance via the ASV eonclient suite.
- [AiiDA (`aiida-eon`)](https://eondocs.org/user_guide/aiida.html): Run eonclient jobs under AiiDA with the aiida-eon plugin.
- [External Potential](https://eondocs.org/user_guide/ext_pot.html): Guide to using the external potential (ext_pot) interface in eOn for wrapping arbitrary calculators via file-based communication. Schema: [Potential](https://eondocs.org/schema/potential.json).
- [LAMMPS Potential](https://eondocs.org/user_guide/lammps_pot.html): Using LAMMPS potentials with eOn via runtime dynamic loading.
- [ASE interface](https://eondocs.org/user_guide/ase_pot.html): Guide to using the Atomic Simulation Environment (ASE) interface in eOn, allowing the use of any ASE calculator as a potential. Schema: [Potential](https://eondocs.org/schema/potential.json).
- [Metatomic interface](https://eondocs.org/user_guide/metatomic_pot.html): Learn how to set up and use the Metatomic interface in eOn for machine learning potentials with metatensor and PyTorch. Schema: [Potential](https://eondocs.org/schema/potential.json), [Metatomic](https://eondocs.org/schema/metatomic.json), [Main](https://eondocs.org/schema/main.json).
- [QUIP with LAMMPS](https://eondocs.org/user_guide/quip.html): Guide on how to use QUIP (QUantum mechanics and Interatomic Potentials) with LAMMPS as a potential within eOn.
- [MPI potential](https://eondocs.org/user_guide/mpi_potential.html): Instructions for using a modified version of VASP with eOn via the MPI Potential interface for parallel calculations.
- [Choosing an algorithm](https://eondocs.org/user_guide/algorithm_selection.html): Guide to selecting the appropriate algorithm in eOn for your simulation task.
- [General simulation parameters](https://eondocs.org/user_guide/main.html): Guide to the general simulation parameters in eOn's main configuration section, covering job types, temperature, and other shared settings. Schema: [Main](https://eondocs.org/schema/main.json).
- [Potential](https://eondocs.org/user_guide/potential.html): A list and description of interatomic potentials supported by eOn, including vendored potentials and interfaces to external codes like VASP, LAMMPS, and ASE. Schema: [Potential](https://eondocs.org/schema/potential.json), [Metatomic](https://eondocs.org/schema/metatomic.json), [XTBPot](https://eondocs.org/schema/xtbpot.json), [ZBLPot](https://eondocs.org/schema/zblpot.json), [SocketNWChemPot](https://eondocs.org/schema/socketnwchempot.json), [ASE_NWCHEM](https://eondocs.org/schema/ase-nwchem.json), [ASE_ORCA](https://eondocs.org/schema/ase-orca.json), [AMS](https://eondocs.org/schema/ams.json), [AMS_IO](https://eondocs.org/schema/ams-io.json), [AMSEnv](https://eondocs.org/schema/amsenv.json).
- [Structure comparison](https://eondocs.org/user_guide/structure_comparison.html): Documentation for the structure comparison settings in eOn, used to configure similarity measures and equivalence cutoffs. Schema: [Structure Comparison](https://eondocs.org/schema/structure-comparison.json).
- [Optimizer](https://eondocs.org/user_guide/optimizer.html): Configuration options for the various geometry optimizers in eOn, including LBFGS, QuickMin, FIRE, CG, SD, and xtsci. Schema: [Optimizer](https://eondocs.org/schema/optimizer.json), [LBFGS](https://eondocs.org/schema/lbfgs.json), [QuickMin](https://eondocs.org/schema/quickmin.json), [FIRE](https://eondocs.org/schema/fire.json), [CG](https://eondocs.org/schema/cg.json), [SD](https://eondocs.org/schema/sd.json), [Xtsci](https://eondocs.org/schema/xtsci.json).
- [Minimization](https://eondocs.org/user_guide/minimization.html): Instructions for running a local energy minimization calculation in eOn to find the nearest stable structure. Schema: [Main](https://eondocs.org/schema/main.json), [Optimizer](https://eondocs.org/schema/optimizer.json), [Xtsci](https://eondocs.org/schema/xtsci.json), [LBFGS](https://eondocs.org/schema/lbfgs.json), [Refine](https://eondocs.org/schema/refine.json).
- [Nudged elastic band](https://eondocs.org/user_guide/neb.html): Guide to the Nudged Elastic Band (NEB) method in eOn for finding saddle points and minimum energy paths between known reactants and products. Schema: [Nudged Elastic Band](https://eondocs.org/schema/nudged-elastic-band.json), [Refine](https://eondocs.org/schema/refine.json).
- [Dimer method](https://eondocs.org/user_guide/dimer.html): Documentation for the Dimer method in eOn, used for finding transition states and lowest eigenmodes using only first derivatives. Schema: [Dimer](https://eondocs.org/schema/dimer.json).
- [Lanczos](https://eondocs.org/user_guide/lanczos.html): Guide to the Lanczos eigenmode method in eOn for saddle point searches. Schema: [Saddle Search](https://eondocs.org/schema/saddle-search.json), [Lanczos](https://eondocs.org/schema/lanczos.json).
- [ARTn (Activation-Relaxation Technique nouveau)](https://eondocs.org/user_guide/artn.html): Guide to the ARTn (Activation-Relaxation Technique nouveau) saddle search method in eOn. Schema: [Saddle Search](https://eondocs.org/schema/saddle-search.json), [ARTn](https://eondocs.org/schema/artn.json).
- [Hessian](https://eondocs.org/user_guide/hessian.html): Guide to Hessian matrix calculation in eOn for vibrational analysis and hTST rate prefactors. Schema: [Main](https://eondocs.org/schema/main.json), [Hessian](https://eondocs.org/schema/hessian.json), [Lanczos](https://eondocs.org/schema/lanczos.json), [Davidson](https://eondocs.org/schema/davidson.json).
- [Prefactor](https://eondocs.org/user_guide/prefactor.html): Guide to harmonic transition state theory (hTST) prefactor calculation in eOn. Schema: [Main](https://eondocs.org/schema/main.json), [Prefactor](https://eondocs.org/schema/prefactor.json).
- [Adaptive kinetic Monte Carlo](https://eondocs.org/user_guide/akmc.html): User guide for the Adaptive Kinetic Monte Carlo (aKMC) method in eOn. Learn how to coarse-grain molecular dynamics for rare event systems. Schema: [AKMC](https://eondocs.org/schema/akmc.json).
- [Saddle search](https://eondocs.org/user_guide/saddle_search.html): Configuration for initiating saddle searches in eOn by displacing atoms from a minimum energy state. Schema: [Saddle Search](https://eondocs.org/schema/saddle-search.json).
- [Basin hopping](https://eondocs.org/user_guide/basin_hopping.html): Guide to the Basin Hopping global optimization method in eOn for exploring potential energy surfaces. Schema: [Basin Hopping](https://eondocs.org/schema/basin-hopping.json).
- [Process search](https://eondocs.org/user_guide/process_search.html): Configuration options for the Process Search job type in eOn, used within the aKMC method to find saddle points and connecting minima. Schema: [Process Search](https://eondocs.org/schema/process-search.json).
- [Recycling](https://eondocs.org/user_guide/recycling.html): Documentation for the saddle point recycling method in eOn, which significantly reduces the computational cost of aKMC simulations. Schema: [Recycling](https://eondocs.org/schema/recycling.json).
- [Coarse graining](https://eondocs.org/user_guide/coarse_graining.html): Guide to coarse-graining methods in eOn, such as MCAMC and AS-KMC, for accelerating simulations with vastly different timescales. Schema: [Coarse Graining](https://eondocs.org/schema/coarse-graining.json).
- [Dynamics](https://eondocs.org/user_guide/dynamics.html): Configuration for running classical molecular dynamics (MD) simulations in eOn based on Newton's equations of motion. Schema: [Main](https://eondocs.org/schema/main.json), [Dynamics](https://eondocs.org/schema/dynamics.json).
- [Parallel replica](https://eondocs.org/user_guide/parallel_replica.html): Guide to Parallel Replica Dynamics (PRD) in eOn, a method to accelerate molecular dynamics simulations by running multiple independent replicas. Schema: [Parallel Replica](https://eondocs.org/schema/parallel-replica.json).
- [Hyperdynamics](https://eondocs.org/user_guide/hyperdynamics.html): Documentation for the Hyperdynamics method in eOn, which uses a bias potential to accelerate the rate of transitions in MD simulations. Schema: [Hyperdynamics](https://eondocs.org/schema/hyperdynamics.json).
- [Communicator](https://eondocs.org/user_guide/communicator.html): Guide to eOn's server-client architecture and communication options for running parallel calculations locally, via MPI, or on a cluster. Schema: [Communicator](https://eondocs.org/schema/communicator.json).
- [Debug](https://eondocs.org/user_guide/debug.html): Information on debug options in eOn for aiding in method development and bug reporting. Schema: [Debug](https://eondocs.org/schema/debug.json).
- [Paths](https://eondocs.org/user_guide/paths.html): Configuration for specifying the directory paths for calculations and output in eOn. Schema: [Paths](https://eondocs.org/schema/paths.json).
- [nvc++ stdpar (NEB image forces)](https://eondocs.org/user_guide/stdpar.html)
- [Kinetic database](https://eondocs.org/user_guide/kdb.html): Guide to using the Kinetic Database (KDB) in eOn to store and reuse information about kinetic processes, speeding up aKMC simulations. Schema: [KDB](https://eondocs.org/schema/kdb.json).
- [rgpot integration (three roles)](https://eondocs.org/user_guide/rgpot_integration.html): How eOn relates to rgpot: in-process engines, RPC serve mode, and optional potserv clients.
- [RgpotPot (direct in-process rgpot)](https://eondocs.org/user_guide/rgpot_pot.html): eOn RGPOT potential: in-process rgpot NWChemPot/CPMDPot via dlopen. Schema: [Main](https://eondocs.org/schema/main.json), [Potential](https://eondocs.org/schema/potential.json), [RgpotPot](https://eondocs.org/schema/rgpotpot.json).
- [Metatomic backends (fat, RGPOT, ASE)](https://eondocs.org/user_guide/rgpot_metatomic.html): Fat Metatomic, RGPOT dlopen engine, and ASE MetatomicCalculator backends in eOn / pyeonclient: same science, different packaging paths. Schema: [Potential](https://eondocs.org/schema/potential.json), [Metatomic](https://eondocs.org/schema/metatomic.json), [RgpotPot](https://eondocs.org/schema/rgpotpot.json).
- [Serve mode](https://eondocs.org/user_guide/serve_mode.html): Guide to using eonclient serve mode to expose any eOn potential over RPC for integration with external tools like ChemGP. Schema: [Metatomic](https://eondocs.org/schema/metatomic.json), [XTBPot](https://eondocs.org/schema/xtbpot.json), [Potential](https://eondocs.org/schema/potential.json), [Serve](https://eondocs.org/schema/serve.json).

## config.ini schema

- [Section index](https://eondocs.org/schema/index.json): one JSON Schema file per config.ini section
- [Main](https://eondocs.org/schema/main.json): MainConfig
- [Potential](https://eondocs.org/schema/potential.json): PotentialConfig
- [Optimizer](https://eondocs.org/schema/optimizer.json): OptimizerConfig
- [Structure Comparison](https://eondocs.org/schema/structure-comparison.json): StructureComparisonConfig
- [Process Search](https://eondocs.org/schema/process-search.json): ProcessSearchConfig
- [Saddle Search](https://eondocs.org/schema/saddle-search.json): SaddleSearchConfig
- [Dimer](https://eondocs.org/schema/dimer.json): DimerConfig
- [Nudged Elastic Band](https://eondocs.org/schema/nudged-elastic-band.json): NudgedElasticBandConfig
- [Lanczos](https://eondocs.org/schema/lanczos.json): LanczosConfig
- [Davidson](https://eondocs.org/schema/davidson.json): DavidsonConfig
- [ARTn](https://eondocs.org/schema/artn.json): ARTnConfig
- [IRA](https://eondocs.org/schema/ira.json): IRAConfig
- [Prefactor](https://eondocs.org/schema/prefactor.json): PrefactorConfig
- [Dynamics](https://eondocs.org/schema/dynamics.json): DynamicsConfig
- [Parallel Replica](https://eondocs.org/schema/parallel-replica.json): ParallelReplicaConfig
- [Hyperdynamics](https://eondocs.org/schema/hyperdynamics.json): HyperdynamicsConfig
- [AKMC](https://eondocs.org/schema/akmc.json): AKMCConfig
- [Basin Hopping](https://eondocs.org/schema/basin-hopping.json): BasinHoppingConfig
- [Communicator](https://eondocs.org/schema/communicator.json): CommunicatorConfig
- [Paths](https://eondocs.org/schema/paths.json): PathsConfig
- [Debug](https://eondocs.org/schema/debug.json): DebugConfig
- [KDB](https://eondocs.org/schema/kdb.json): KDBConfig
- [Recycling](https://eondocs.org/schema/recycling.json): RecyclingConfig
- [Coarse Graining](https://eondocs.org/schema/coarse-graining.json): CoarseGrainingConfig
- [Hessian](https://eondocs.org/schema/hessian.json): HessianConfig
- [Serve](https://eondocs.org/schema/serve.json): ServeConfig
- [Refine](https://eondocs.org/schema/refine.json): RefineConfig
- [Metatomic](https://eondocs.org/schema/metatomic.json): Metatomic
- [XTBPot](https://eondocs.org/schema/xtbpot.json): XTBPot
- [ZBLPot](https://eondocs.org/schema/zblpot.json): ZBLPot
- [SocketNWChemPot](https://eondocs.org/schema/socketnwchempot.json): SocketNWChemPot
- [RgpotPot](https://eondocs.org/schema/rgpotpot.json): RgpotPot
- [ASE_NWCHEM](https://eondocs.org/schema/ase-nwchem.json): ASE_NWCHEM
- [ASE_ORCA](https://eondocs.org/schema/ase-orca.json): ASE_ORCA
- [LBFGS](https://eondocs.org/schema/lbfgs.json): LBFGSConfig
- [CG](https://eondocs.org/schema/cg.json): CGConfig
- [FIRE](https://eondocs.org/schema/fire.json): FIREConfig
- [QuickMin](https://eondocs.org/schema/quickmin.json): QuickMinConfig
- [SD](https://eondocs.org/schema/sd.json): SDConfig
- [Xtsci](https://eondocs.org/schema/xtsci.json): XtsciConfig
- [GPR Dimer](https://eondocs.org/schema/gpr-dimer.json): GPRDimerConfig
- [BGSD](https://eondocs.org/schema/bgsd.json): BGSDConfig
- [Distributed Replica](https://eondocs.org/schema/distributed-replica.json): DistributedReplicaConfig
- [AMS](https://eondocs.org/schema/ams.json): AMSConfig
- [AMS_IO](https://eondocs.org/schema/ams-io.json): AMSIOConfig
- [AMSEnv](https://eondocs.org/schema/amsenv.json): AMSEnvConfig