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 startup, 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:
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 propagted from one run
command to the next (Prop.).
Simulation setup¶
Keyword 
Brief description 
Exec. 
Prop. 

Set the initial velocities 
Yes 
N/A 

Set up the interaction model 
Yes 
N/A 

Add the DFTD3 dispersion correction to the NEP model 
Yes 
N/A 

Change the box 
Yes 
N/A 

Deform the simulation box 
No 
No 

Specify the integrator for a MD run 
No 
No 

Fix (freeze) atoms 
No 
No 

Specify the integration time step 
No 
Yes 
Actions¶
Keyword 
Brief description 
Exec. 
Prop. 

Perform an energy minimization 
Yes 
N/A 

Run a number of MD steps 
Yes 
No 

Compute some time and spaceaveraged quantities 
No 
No 

Compute the cohesive energy curve 
Yes 
N/A 

Compute the elastic constants 
Yes 
N/A 

Compute the phonon density of states (PDOS) 
No 
No 

Compute the modal heat current using the GKMA method 
No 
No 

Compute the thermal conductivity using the EMD method 
No 
No 

Compute the modal thermal conductivity using the HNEMA method 
No 
No 

Compute the thermal conductivity using the HNEMD method 
No 
No 

Compute the multicomponent system thermal conductivity using the HNEMDEC method 
No 
No 

Compute the phonon dispersion 
Yes 
N/A 

Compute the selfdiffusion coefficient (SDC) 
No 
No 

Compute the meansquare displacement (MSD) 
No 
No 

Compute the spectral heat current (SHC) 
No 
No 
Output¶
Keyword 
Brief description 
Exec. 
Prop. 

Run onthefly active learning, saving structures that exceeds a set threshold maximum force uncertainty over all specified NEP potentials. 
No 
No 

Write positions and other quantities in extended XYZ format 
No 
No 

Write positions and other quantities for each of the observing NEP potentials, or the average of them, in the extended XYZ format. 
No 
No 

Write the atomic forces 
No 
No 

Write the atomic positions 
No 
No 

Write the atomic positions in netCDF format 
No 
No 

Write a restart file 
No 
No 

Write thermodynamic quantities 
No 
No 

Write the atomic velocities 
No 
No 