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:
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 DFT-D3 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 space-averaged 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 self-diffusion coefficient (SDC) |
No |
No |
|
Compute the mean-square displacement (MSD) |
No |
No |
|
Compute the spectral heat current (SHC) |
No |
No |
Output¶
Keyword |
Brief description |
Exec. |
Prop. |
---|---|---|---|
Run on-the-fly 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 |