Index

A

ACE active (keyword in run.in) active.out (output file)

active.xyz (output file) add_efield (keyword in run.in) add_force (keyword in run.in)

B

basis.in basis_size (keyword in nep.in) batch (keyword in nep.in) BDP

Berendsen barostat Berendsen thermostat Bibliography Bussi-Donadio-Parrinello thermostat

C

Canonical ensemble change_box (keyword in run.in) cohesive.out (output file) compute (keyword in run.in) compute.out (output file) compute_cohesive (keyword in run.in) compute_dos (keyword in run.in) compute_elastic (keyword in run.in) compute_gkma (keyword in run.in) compute_hac (keyword in run.in) compute_hnema (keyword in run.in)

compute_hnemd (keyword in run.in) compute_hnemdec (keyword in run.in) compute_lsqt (keyword in run.in) compute_msd (keyword in run.in) compute_phonon (keyword in run.in) compute_rdf (keyword in run.in) compute_sdc (keyword in run.in) compute_shc (keyword in run.in) compute_viscosity (keyword in run.in) correct_velocity (keyword in run.in) Credits cutoff (keyword in nep.in)

D

D.out (output file) deform (keyword in run.in) dftd3 (keyword in run.in) dipole.out (output file) dipole_test.out (output file) dipole_train.out (output file) DOS dos.out (output file) dump.xyz (output file) dump_beads (keyword in run.in)

dump_dipole (keyword in run.in) dump_exyz (keyword in run.in) dump_force (keyword in run.in) dump_netcdf (keyword in run.in) dump_observer (keyword in run.in) dump_polarizability (keyword in run.in) dump_position (keyword in run.in) dump_restart (keyword in run.in) dump_shock_nemd (keyword in run.in) dump_thermo (keyword in run.in) dump_velocity (keyword in run.in)

E

EAM eigenvector.in electron_stop (keyword in run.in) Embedded atom method EMD

EMD method energy_test.out (output file) energy_train.out (output file) ensemble (keyword in run.in) Ensembles

F

FCP fix (keyword in run.in) Force constant potential force.out (output file)

force_delta (keyword in nep.in) force_test.out (output file) force_train.out (output file) Forces

G

generation (keyword in nep.in) GK GKMA, [1] Glossary GPU gpumd executable gpumd input files Atomic configuration Eigenvectors Simulation model Simulation protocol

gpumd input parameters gpumd output files Green-Kubo method Green-Kubo modal analysis

H

HAC hac.out (output file) Heat current heat current autocorrelation Heat transport heatmode.out (output file)

HNEMA, [1] HNEMD HNEMD method HNEMDEC, [1] Homogeneous non-equilibrium modal analysis Homogeneous non-equilibrium molecular dynamics Homogeneous non-equilibrium molecular dynamics Evans-Cummings algorithm

I

Installation Interaction models

Interatomic potentials Isothermal-isobaric ensemble

K

kappa.out (output file)

kappamode.out (output file) kpoints.in

L

l_max (keyword in nep.in) lambda_1 (keyword in nep.in) lambda_2 (keyword in nep.in) lambda_e (keyword in nep.in) lambda_f (keyword in nep.in) lambda_shear (keyword in nep.in) lambda_v (keyword in nep.in)

Langevin thermostat Lennard-Jones potential LJ loss.txt (output file) LSQT lsqt_dos.out (output file) lsqt_sigma.out (output file) lsqt_velocity.out (output file)

M

MC mc (keyword in run.in) mcmd.out (output file) MD Microcanonical ensemble minimize (keyword in run.in) Modal analysis methods model.xyz model_type (keyword in nep.in)

movie.xyz (output file) MSD msd.out (output file) MSST msst (keyword in run.in) MSST integrator MTTK MTTK integrator mvac.out (output file)

N

n_max (keyword in nep.in) NEMD NEMD method NEP nep executable nep input files nep input parameters NEP loss function nep output files nep.in (input file) nep.restart (output file) nep.txt (output file) NetCDF setup

Neuroevolution potential neuron (keyword in nep.in) NHC NN Non-equilibrium molecular dynamics Nose-Hoover chain thermostat nph_mttk (keyword in run.in) nphug (keyword in run.in) NPHug integrator NPT ensemble npt_mttk (keyword in run.in) NVE ensemble NVT ensemble

O

observer.out (output file) observer.xyz (output file)

omega2.out (output file) onsager.out (output file)

P

PDOS PIMD plumed (keyword in run.in) PLUMED setup polarizability.out (output file)

polarizability_test.out (output file) polarizability_train.out (output file) population (keyword in nep.in) potential (keyword in run.in) prediction (keyword in nep.in) Publications

R

RDF rdf.out (output file) replicate (keyword in run.in) restart.xyz (output file)

RMSE RPMD RTC run (keyword in run.in) run.in

S

SCR SDC sdc.out (output file) SGC SHC shc.out (output file)

SNES Spectral heat current Stochastic cell rescaling barostat Stress tensor stress_test.out (output file) stress_train.out (output file) SVR

T

Tersoff mini-potential Tersoff potential (1988) (1989) test.xyz (input file) Theoretical background thermo.out (output file)

time_step (keyword in run.in) train.xyz (input file) TRPMD Tutorials type (keyword in nep.in) type_weight (keyword in nep.in)

U

use_typewise_cutoff (keyword in nep.in)

use_typewise_cutoff_zbl (keyword in nep.in)

V

VAC VCSGC velocity (keyword in run.in) velocity.out (output file)

version (keyword in nep.in) virial_test.out (output file) virial_train.out (output file) viscosity.out (output file)

Z

ZBL	zbl (keyword in nep.in)