simple-abinitio2d

name	simple-abinitio2d
description	Use when working on SIMPLE's abinitio2D workflow and its cluster2D stages, including 2D search strategies, probabilistic 2D sampling, class-average restoration, distributed partial class-average assembly, online matcher particle I/O, project updates, and streaming/rejection helpers.

SIMPLE Abinitio2D

Use this skill for the orchestrating abinitio2D workflow and the cluster2D stages it drives. Treat cluster2D as the core stage implementation, not as a separate top-level mental model.

Read First

1. doc/policies/abinitio2D_policy.md
2. src/main/ui/simple/simple_ui_cluster2D.f90
3. src/main/exec/simple_exec_cluster2D.f90
4. src/main/commanders/simple/simple_commanders_cluster2D.f90
5. src/main/strategies/parallelization/simple_cluster2D_strategy.f90
6. src/main/strategies/search/simple_strategy2D_matcher.f90
7. src/main/class/simple_classaverager.f90
8. src/main/class/simple_class_frcs.f90

If fractional update or probabilistic sampling is involved, also read doc/policies/importance_sampling_fractional_update_policy.md.

Ownership Map

• abinitio2D: orchestrating workflow policy and staged cluster2D calls.
• cluster2D: 2D classification stage implementation.
• simple_strategy2D_matcher: online particle alignment, orientation/class updates, and worker partial sums.
• simple_matcher_ptcl_batch: batch image loading and preprocessing.
• class/ and simple_commanders_mkcavgs.f90: class-average products and explicit assembly stages.
• project/ and ori/: particle/class metadata persistence.
• stream/: online and mini-stream 2D variants.

Working Rules

• Keep command/controller code orchestration-focused and matcher code focused on particle-domain alignment and online partial-sum production.
• Preserve the probabilistic sample-once-and-reuse contract: prob_align2D chooses the sampled subset, and prob_tab2D plus the matcher reproduce that subset rather than resampling independently.
• Preserve sampled as the current-round marker and updatecnt as cumulative update history when 2D workflows share the fractional-update machinery.
• Preserve the online single-read particle I/O contract. The 2D matcher should read each particle batch once, keep the already-read raw images for class-average restoration, and restore/update class-average sums from those images after assignment in the same batch.
• Treat explicit offline or terminal class-average assembly commands as separate workflow stages. They may perform their own reads, but that does not relax the matcher worker's online single-read contract.
• For workflows that take a project file, set mkdir=yes before params%new(cline) unless the command is already a child command. Child workflow calls from inside the execution directory should use mkdir=no and the copied local project file.
• Treat previous 2D eo values as input project state. Do not regenerate them with partition_eo in a workflow whose purpose is to consume prior 2D class assignments; validate eo with get_eo() equal to 0 or 1.

Nearby Skills

• For stream microchunk rejection, read .github/skills/simple-microchunk-rejection/SKILL.md.
• For shared fractional-update contracts, read .github/skills/simple-frac-update-trailing/SKILL.md.

Common Traps

• cluster2D logic is spread across many simple_strategy2D_* modules.
• Streaming cluster2D code is related but not identical to batch execution.
• Class averaging, selection, rejection, and project updates often live in different files than the search loop itself.