Simulation protocol (run.in)

The run.in file is used to define the simulation protocol. The code will execute the commands in this file one by one. If the code encounters an invalid command in this file on start-up, it will report an error message and terminate. In this input file, blank lines and lines starting with # are ignored. One can thus write comments after #. All other lines should be of the form:

keyword parameter_1 parameter_2 ...

The overall structure of a run.in file is as follows:

• First, set up the potential model using the potential keyword. * Multiple NEP potentials may be used using the dump_observer keyword. These NEP potentials may either be used to evaluate energy, forces and virials along the trajectory, or averaged together to run the MD on an average PES.

• Then, if needed, use the minimize keyword to minimize the energy of the whole system.

• Then one can use the following keywords to carry out static calculations:

  • Use the compute_cohesive keyword to compute the cohesive energy curve.

  • Use the compute_elastic keyword to compute the elastic constants.

  • Use the compute_phonon keyword to compute the phonon dispersions.

• Then, if one wants to carry out MD simulations, one has to set up the initial velocities using the velocity keyword and carry out a number of MD runs as follows:

  • Specify an integrator using the ensemble keyword and optionally add keywords to further control the evolution and measurement processes.

  • Use the run keyword to run a number of MD steps according to the above settings.

  • The last two steps can be repeated.

The following tables provide an overview of the different keywords. A complete list can also be found here. The last two columns indicate whether the command is executed immediately (Exec.) and whether it is propagated from one run command to the next (Prop.).

Simulation setup

Keyword	Brief description	Exec.	Prop.
replicate	Replicate the simulation model	Yes	N/A
velocity	Set the initial velocities	Yes	N/A
correct_velocity	Remove linear and angular momenta at regular intervals	No	No
potential	Set up the interaction model	Yes	N/A
dftd3	Add the DFT-D3 dispersion correction to the NEP model	Yes	N/A
kspace	Specify the reciprocal-space method used by the interaction model	Yes	N/A
compute_extrapolation	Monitor the NEP extrapolation grade during an MD run	No	No
change_box	Change the box	Yes	N/A
deform	Deform the simulation box	No	No
time_step	Specify the integration time step	No	Yes
ensemble	Specify the integrator for a MD run	No	No
add_force	Add external forces to selected atoms	No	No
add_efield	Apply an electric field to selected atoms	No	No
add_spring	Add spring interactions to selected atom groups	No	No
deposit	Add atoms periodically during a deposition run	No	No
electron_stop	Apply electronic stopping forces to high-energy atoms	No	No
fix	Fix (freeze) atoms	No	No
move	Move selected atoms with a constant velocity	No	No
mc	Carry out Monte Carlo trial steps during an MD run	No	No
plumed	Invoke the PLUMED plugin during an MD run	No	No

Actions

Keyword	Brief description	Exec.	Prop.
minimize	Perform an energy minimization	Yes	N/A
run	Run a number of MD steps	Yes	No
compute	Compute some time and space-averaged quantities	No	No
compute_chunk	Compute time-averaged quantities in dynamic spatial bins	No	No
compute_adf	Compute the angular distribution function (ADF)	No	No
compute_angular_rdf	Compute the angular-dependent radial distribution function (ARDF)	No	No
compute_cohesive	Compute the cohesive energy curve	Yes	N/A
compute_elastic	Compute the elastic constants	Yes	N/A
compute_dos	Compute the phonon density of states (PDOS)	No	No
compute_dpdt	Compute the time derivative of the polarization	No	No
compute_gkma	Compute the modal heat current using the GKMA method	No	No
compute_hac	Compute the thermal conductivity using the EMD method	No	No
compute_ic	Compute the ionic conductivity (IC)	No	No
compute_hnema	Compute the modal thermal conductivity using the HNEMA method	No	No
compute_hnemd	Compute the thermal conductivity using the HNEMD method	No	No
compute_hnemdec	Compute the multicomponent system thermal conductivity using the HNEMDEC method	No	No
compute_orientorder	Compute Steinhardt bond-orientational order parameters	No	No
compute_phonon	Compute the phonon dispersion	Yes	N/A
compute_sdc	Compute the self-diffusion coefficient (SDC)	No	No
compute_msd	Compute the mean-square displacement (MSD)	No	No
compute_rdf	Compute the radial distribution function (RDF)	No	No
compute_shc	Compute the spectral heat current (SHC)	No	No
compute_viscosity	Compute the stress autocorrelation function and viscosity	No	No
compute_lsqt	Compute electronic transport properties using the LSQT method	No	No

Output

Keyword	Brief description	Exec.	Prop.
active	Run on-the-fly active learning, saving structures that exceeds a set threshold maximum force uncertainty over all specified NEP potentials.	No	No
dump_beads	Write bead-resolved positions and optional velocities and forces for PIMD-related runs	No	No
dump_dipole	Write dipoles predicted by a separate tensorial NEP model	No	No
dump_observer	Write positions and other quantities for each of the observing NEP potentials, or the average of them, in the extended XYZ format.	No	No
dump_polarizability	Write polarizabilities predicted by a separate tensorial NEP model	No	No
dump_netcdf	Write the atomic positions in netCDF format	No	No
dump_restart	Write a restart file	No	No
dump_shock_nemd	Write spatial thermodynamic profiles for shock-wave NEMD simulations	No	No
dump_thermo	Write thermodynamic quantities	No	No
dump_xyz	Write positions and other per-atom quantities in extended XYZ format	No	No