`pesmaker generate`¶

generate builds structure candidates.

Normal users can let next run this stage. Use generate directly when you only want to inspect generated structures.

Use¶

pesmaker generate run.yaml

Minimal YAML¶

project: generate_only

structures:
  - POSCAR

generation:
  output_dir: generated
  supercell: [3, 3, 3]

What It Does¶

For each input structure, PESMaker can apply:

supercell -> surface/vacuum -> defects -> perturbations

Use generation.tasks when one YAML file needs several structure families.

Useful Fields¶

generation:
  output_dir: generated
  tasks:
    - name: surface_331
      supercell: [3, 3, 1]
      surface:
        vacuum: 30.0
        axis: 2
        center: true
      defects:
        mode: random
        seed: 42
        single_vacancies:
          elements: [Te]
          max_count: 4
        line_defects:
          elements: [Pd]
          coordinate_axis: 0
          split_by_axis: 2
          max_count: 5
      perturb:
        include_pristine: true
        pert_num: 10
        format: vasp

For line_defects, coordinate_axis is the fractional coordinate kept fixed when defining the line:

0 -> a axis
1 -> b axis
2 -> c axis

For example, coordinate_axis: 0 builds const_a line defects. In a slab with multiple layers along c, this can remove the same line in every layer. Add split_by_axis: 2 to split candidates by fractional c layer first, so each line-defect variant removes one layer's line instead of all c layers at the same a coordinate. The split tolerance is inferred automatically; set split_tolerance only when the automatic layer grouping is too coarse or too fine.

For a 2D Te-Pd slab where axis: 2 is the vacuum direction, a typical Pd line defect setup is:

generation:
  output_dir: generated
  tasks:
    - name: surface_442
      supercell: [4, 4, 2]
      surface:
        vacuum: 30.0
        axis: 2
        center: true
        defects:
          mode: random
          seed: 12345
          line_defects:
            elements: [Pd]
            coordinate_axis: 0
            split_by_axis: 2
            # optional: split_tolerance: 0.03
            max_count: 5
        perturb:
          pert_num: 3
          cell_pert_fraction: 0.03
          atom_pert_distance: 0.1
          atom_pert_style: normal
          seed: 424
          format: vasp

Outputs¶

generated/
  manifest.jsonl
  generation_summary.txt
  ...

Read generation_summary.txt first. It is the quick human-readable summary. Later stages read manifest.jsonl.

Next Step¶

To prepare VASP folders manually:

pesmaker scf-setup run.yaml

For the normal flow:

pesmaker next run.yaml

pesmaker generate¶