菜单
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.
用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
Use when working in SIMPLE's src/main/nano subsystem, including nanoparticle and molecule data structures, graphene and time-series helpers, and the SINGLE-specific domain logic that supports liquid-cell and nanoparticle workflows.
Use when working on SIMPLE's model_cavgs_rejection application, simple_cavg_quality feature-space selector, class-average quality selection, quality_mode=analyze outputs, cavgs_quality feature/reference tables, chunk vs pool rejection tuning, or microchunk quality-vector integration.
Use when studying, explaining, or modifying SIMPLE's fractional-update and trailing-reconstruction workflow, including update_frac sampling, sampled/updatecnt bookkeeping, matcher reconstruction I/O, partial even/odd reconstruction handoff, rec3D/volassemble ownership, downsampling compatibility, obsfield mirrors, and stage-to-stage previous-reference contracts.
Use when working in SIMPLE's src/main/stream subsystem, including online/mini-stream orchestration, chunk and microchunk processing, staged pipeline steps, watchers, queue/message definitions, and streaming variants of preprocessing and cluster2D workflows.
Use when working on SIMPLE's streaming microchunk class-average rejection, simple_microchunked2D lifecycle sentinels, pass-1/pass-2/refchunk/match generation, skip_pass_2 behavior, simple_cluster2D_rejector criteria, or boundaries with model_cavgs_rejection.
Use when working on SIMPLE's refine3D workflow, including CLI/UI entrypoints, commanders, probabilistic pre-alignment, 3D search and matcher strategies, online partial reconstruction, volassemble, automasking, nonuniform filtering, multi-state behavior, distributed execution, and related abinitio3D refinement code paths.
| 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. |
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.
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.f90If fractional update or probabilistic sampling is involved, also read
doc/policies/importance_sampling_fractional_update_policy.md.
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.prob_align2D chooses the sampled subset, and prob_tab2D plus the matcher
reproduce that subset rather than resampling independently.sampled as the current-round marker and updatecnt as cumulative
update history when 2D workflows share the fractional-update machinery.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.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..github/skills/simple-microchunk-rejection/SKILL.md..github/skills/simple-frac-update-trailing/SKILL.md.cluster2D logic is spread across many simple_strategy2D_* modules.cluster2D code is related but not identical to batch execution.