Index

Examples often show examples of more than one thing. Below is a list of common operations with a link to the examples that implement each one. Nearly all examples use ConfigSet and OutputSpec. GAP-RSS uses most of Workflow’s functionalities.

Evaluate structures with a calculator

• ORCA: ORCA via python script

• MACE: Parallelize MACE calculator

• EMT:

  • First example

  • Iterative GAP fitting

• XTB:

  • Normal Modes of molecules

  • Molecular Dynamics

  • GAP fit workflow with many wfl use-case examples

• VASP: Functions as independently queued jobs

• FHI-Aims: FHI-Aims Calculator

Generate structures

• Generate Dimer Structures

• Random Structures via buildcell

• From SMILES string:

  • Short example in SMILES to Atoms

  • As part of GAP fit workflow with many wfl use-case examples

• Geometry optimisation: Iterative GAP fitting

• Sample molecular normal modes: Normal Modes (non-periodic)

Run MD

• Sample configs for training:

  • Iterative GAP fitting

  • GAP fit workflow with many wfl use-case examples

• Run ACE MD: MD

Remote execution

• Overview: Functions as independently queued jobs

• ORCA via python script

• Run ACE MD: MD

• GAP fit workflow with many wfl use-case examples

Get descriptors

• Global SOAP:

  • Iterative GAP fitting

  • GAP fit workflow with many wfl use-case examples

Sampling structures

• Furthest point sampling: Sampling of Structures

• CUR: GAP fit workflow with many wfl use-case examples

• With a boolean function: GAP fit workflow with many wfl use-case examples

Fit a potential

• Multistage GAP fit: Iterative GAP fitting

• Simple GAP fit: GAP fit workflow with many wfl use-case examples

Iterative training

• An example of GAP fitting scheme: Iterative GAP fitting

Command line

• Generate structures from SMILES: SMILES to Atoms

Miscellaneous

• Calculate errors:

  • Iterative GAP fitting

  • GAP fit workflow with many wfl use-case examples

• Plot predicted vs reference correlation plots: GAP fit workflow with many wfl use-case examples

• Parallelize your own function: Overview of

• Calculate normal modes of a molecule: Normal Modes(non-periodic)

• Post-process each ORCA calculation on-the-fly: ORCA via python script