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mlmm pysis — pysisyphus YAML Workflows

Summary: Run pysisyphus YAML workflow files with the mlmm calculator pre-registered. Compatible with v0.1.x YAML-based workflows.

Overview

The mlmm pysis subcommand executes pysisyphus YAML workflow files with the mlmm calculator type automatically registered. This provides backward compatibility with v0.1.x YAML-based workflows where mlmm opt.yaml was the primary interface.

mlmm pysis opt.yaml
mlmm pysis tsopt.yaml
mlmm pysis irc.yaml

YAML Format

pysisyphus YAML files have three main sections: geom, calc, and a workflow section (opt, tsopt, irc, etc.).

Geometry section

geom:
  type: cart          # Coordinate system (cart, redund, dlc)
  fn: complex_layered.pdb

For frozen atoms, use freeze_atoms (1-based indices):

geom:
  type: cart
  fn: complex_layered.pdb
  freeze_atoms: [101, 102, 103, 200, 201]  # 1-based

Calculator section

calc:
  type: mlmm
  input_pdb: complex_layered.pdb
  real_parm7: real.parm7
  model_pdb: ml_region.pdb
  model_charge: 0
  model_mult: 1
  backend: uma
  embedcharge: false

All MLMMCore parameters are accepted as YAML keys. v0.1.x parameter names (real_pdb, etc.) are also accepted with a deprecation warning.

Workflow sections

Optimization

opt:
  type: lbfgs
  max_cycles: 300
  thresh: gau_loose    # gau, gau_tight, gau_vtight, gau_loose, baker
  dump: true

TS optimization

tsopt:
  type: dimer
  max_cycles: 100
  thresh: gau_loose
  dump: true

IRC

irc:
  type: eulerpc
  max_cycles: 75
  step_length: 0.15
  dump: true

Full YAML Examples

Geometry optimization

geom:
  type: cart
  fn: complex_layered.pdb
  freeze_atoms: [101, 102, 200, 201]

calc:
  type: mlmm
  input_pdb: complex_layered.pdb
  real_parm7: real.parm7
  model_pdb: ml_region.pdb
  model_charge: 0
  backend: uma

opt:
  type: lbfgs
  max_cycles: 300
  thresh: gau_loose
  dump: true

Run: mlmm pysis opt.yaml

TS optimization

geom:
  type: cart
  fn: ts_candidate.pdb
  freeze_atoms: [101, 102, 200, 201]

calc:
  type: mlmm
  input_pdb: ts_candidate.pdb
  real_parm7: real.parm7
  model_pdb: ml_region.pdb
  model_charge: 0

tsopt:
  type: dimer
  max_cycles: 100
  thresh: gau_loose
  dump: true

Run: mlmm pysis tsopt.yaml

IRC from TS

geom:
  type: cart
  fn: ts_optimized.pdb

calc:
  type: mlmm
  input_pdb: ts_optimized.pdb
  real_parm7: real.parm7
  model_pdb: ml_region.pdb
  model_charge: 0

irc:
  type: eulerpc
  max_cycles: 75
  step_length: 0.15
  dump: true

Run: mlmm pysis irc.yaml

Migration from v0.1.x

v0.1.x v0.2.x
mlmm opt.yaml mlmm pysis opt.yaml
real_pdb: complex.pdb input_pdb: complex.pdb (or keep real_pdb with warning)
real_rst7: real.rst7 No longer needed (ignored with warning)

Existing v0.1.x YAML files work without modification — deprecated parameter names are accepted with warnings.

See Also