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Analyze Configuration

Source code:

  • bff/workflows/analyze/config.py
  • bff/workflows/analyze/main.py
  • bff/qoi/routines.py

Purpose

bff analyze computes quantities of interest for:

  • the sampled campaigns produced by bff sample
  • the reference trajectories provided by the user

Minimal Example

sample:
  dir: ../03-sample

reference:
  systems:
    - coordinates: ../03-reference/trajectories/system-000/system.gro
      topology: ../03-reference/trajectories/system-000/system.top
      trajectory: ../03-reference/trajectories/system-000/trajectory.xtc
      routines:
        - routine: rdf
          mol_resname: ACE
        - routine: ../inputs/restraint.py:distance_distribution
          atom_pair: [C2, CAL]

run:
  in_memory: true
  gc_collect: false
  maxtasksperchild: 100

output:
  path: ./qoi
  log: ./out.log
  write_raw: true

Top-Level Keys

  • sample Sample slicing and worker settings.
  • reference Reference systems, slicing, and routines.
  • run Runtime settings for multiprocessing and memory handling.
  • output Output prefix and logging settings.

sample Keys

  • dir Sample campaign directory produced by bff sample.
  • start First frame index to analyze.
  • stop Final frame index to analyze.
  • step Frame stride.
  • workers Worker count for sample analysis. -1 means the implementation default.
  • progress_stride Progress update interval for sample processing.

reference Keys

  • start First frame index for reference trajectories.
  • stop Final frame index for reference trajectories.
  • step Frame stride for reference trajectories.
  • systems Non-empty list of reference systems.

reference.systems[] Keys

  • coordinates Coordinate file for the reference system.
  • topology Topology file for the reference system.
  • trajectory Reference trajectory file.
  • routines Non-empty list of QoI routines to evaluate for that system.

Routine Keys

  • routine Either a builtin routine name such as rdf or hb, or a custom routine string in the form path.py:function.
  • any additional keys Passed directly to the routine as keyword arguments.

Builtin routines currently live in:

  • bff/qoi/rdf.py
  • bff/qoi/hbonds.py

Builtin RDF and hydrogen-bond routines analyze the selected trajectory slice directly; they do not perform block averaging internally.

run Keys

  • in_memory Load sample QoI results into memory before reduction.
  • gc_collect Run explicit garbage collection between tasks.
  • maxtasksperchild Worker recycling interval for multiprocessing.

output Keys

  • path Output prefix for the written QoI dataset files.
  • log Log file path.
  • write_raw If true, also write the raw per-block QoI data as JSON.