Command Manual

This section is the command-by-command manual.

For normal work, you usually need only two commands:

pesmaker validate run.yaml
pesmaker next run.yaml

next runs the local PESMaker steps that are ready. You do not need to run generate, sample-setup, select, scf-setup, collect, train, or train-setup one by one unless you want manual control.

The one thing next does not do is real scheduler submission. When jobs need to be submitted, next writes a dry-run log and prints the exact pesmaker submit ... command to run.

Command List

Command	Use it for
init	Write a starter YAML file.
validate	Check the YAML before doing work.
next	Continue the workflow until a submit, wait, or complete point.
status	Show what next would do without writing files.
generate	Manually generate structures.
sample-setup	Manually prepare GPUMD or LAMMPS-MACE sampling folders.
select	Manually select MD frames.
scf-setup	Manually prepare VASP SCF folders.
submit	Submit prepared submit.sh files.
collect	Build an extxyz dataset from finished VASP outputs.
train	Continue from a training YAML.
train-setup	Prepare model training inputs.
plot	Plot NEP training diagnostics.

How next Thinks

next looks at the YAML sections and the files already on disk.

structures configured + generated/manifest missing -> run generate
sampling configured                                -> prepare sampling
sampling submit not previewed                      -> preview sampling submit
sampling trajectory exists                         -> run select
labeling configured                                -> prepare SCF
SCF submit not previewed                           -> preview SCF submit
OUTCAR exists                                      -> collect train.xyz
training configured                                -> prepare training
training submit not previewed                      -> preview training submit

If the files already exist, next skips that step. If external results are missing, it stops and tells you what it is waiting for.

Manual Commands Are Still Useful

Use manual commands when you want to debug one stage:

pesmaker generate run.yaml
pesmaker scf-setup run.yaml
pesmaker submit run.yaml --dry-run

For production use, start with next. It is less to remember and it gives the next command in the terminal output.