Configuration Reference¶

Date:

2026-03-14

1 Configuration Reference¶

Complete parameter reference for config.yaml.

2 System Definitions¶

systems:
  my_reaction:
    reactant: /path/to/reactant.con
    product: /path/to/product.con
    use_ira: true  # Enable IRA alignment

Parameter	Type	Required	Description
`reactant`	path	Yes	Reactant structure (.con or .xyz)
`product`	path	Yes	Product structure (.con or .xyz)
`use_ira`	bool	No	Enable IRA alignment (default: true)

3 Model Configuration¶

model:
  name: pet-mad-xs-v1.5.0
  version: v1.5.0
  type: pet-mad-xs

Parameter	Type	Default	Description
`name`	string	`pet-mad-xs-v1.5.0`	Model name
`version`	string	`v1.5.0`	HuggingFace version
`type`	string	`pet-mad-xs`	Model type

3.1 Available Models¶

Model	Size	Accuracy	Use Case
`pet-mad-xs`	Extra small	Good	Quick testing
`pet-mad-s`	Small	Better	Production
`pet-mad`	Medium	Best	High accuracy

4 Compute Settings¶

compute:
  device: cuda  # or cpu, mps

Parameter	Type	Default	Description
`device`	string	`cuda`	Compute device

5 Alignment Parameters¶

alignment:
  kmax: 1.8  # Å⁻¹

Parameter	Type	Default	Description
`kmax`	float	1.8	IRA matching cutoff

5.1 Choosing kmax¶

System Type	kmax Range
Small molecules	1.5-2.0
Medium molecules	2.0-3.0
Difficult mapping	3.0-5.0

6 NEB Parameters¶

6.1 Minimization¶

neb:
  minimization:
    max_iterations: 2000
    converged_force: 0.0514221  # eV/Å
    opt_method: lbfgs
    max_move: 0.1  # Å

Parameter	Type	Default	Description
`max_iterations`	int	2000	Max minimization steps
`converged_force`	float	0.0514	Force tolerance (eV/Å)
`opt_method`	string	`lbfgs`	Optimizer
`max_move`	float	0.1	Max step size (Å)

6.2 Optimization¶

neb:
  optimization:
    images: 18
    max_iterations: 1000
    converged_force: 0.0514221
    opt_method: lbfgs
    max_move: 0.1

    # Energy-weighted springs
    energy_weighted: true
    ew_ksp_min: 0.972  # eV/Å²
    ew_ksp_max: 9.72   # eV/Å²
    ew_trigger: 0.5    # eV

    # Climbing image
    climbing_image_method: true
    ci_after_rel: 0.8

    # MMF refinement
    ci_mmf: true
    ci_mmf_nsteps: 1000

    # IDPP initializer
    sidpp_growth_alpha: 0.33

Parameter	Type	Default	Description
`images`	int	18	Number of NEB images
`max_iterations`	int	1000	Max NEB iterations
`converged_force`	float	0.0514	Force tolerance
`energy_weighted`	bool	true	Energy-weighted springs
`ew_ksp_min`	float	0.972	Min spring constant
`ew_ksp_max`	float	9.72	Max spring constant
`climbing_image_method`	bool	true	Enable CI
`ci_mmf`	bool	true	MMF refinement

6.3 Choosing Number of Images¶

System Complexity	Images
Simple (3-5 atoms)	12-16
Medium (6-15 atoms)	18-24
Complex (16+ atoms)	24-30

7 Plotting Parameters¶

plotting:
  plot_structures: true
  facecolor: white
  title: ""

  figure:
    figsize: [8, 6]
    dpi: 300
    zoom_ratio: 0.3

  fonts:
    base: 12

  ira_kmax: 14  # For 2D RMSD

Parameter	Type	Default	Description
`plot_structures`	bool	true	Show structure insets
`zoom_ratio`	float	0.3	Inset zoom level
`ira_kmax`	float	14	RMSD calculation kmax

8 Path Configuration¶

paths:
  models: results/models
  endpoints: results/endpoints
  neb: results/neb
  idpp: results/idpp
  plots: results/plots
  cache: results/cache

All paths are relative to working directory.