| 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
doc/policies/abinitio2D_policy.mdsrc/main/ui/simple/simple_ui_cluster2D.f90src/main/exec/simple_exec_cluster2D.f90src/main/commanders/simple/simple_commanders_cluster2D.f90src/main/strategies/parallelization/simple_cluster2D_strategy.f90src/main/strategies/search/simple_strategy2D_matcher.f90src/main/class/simple_classaverager.f90src/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.
