How zheyuanlai/abf-fisher-rao works
This is a computational research repository evaluating when Fisher–Rao resampling helps Adaptive Biasing Force free-energy estimation across model and molecular systems. The main workflow is to run a benchmark simulation, analyze paired methods and diagnostics, then assemble cross-case findings into the report. The map emphasizes documented study entry points and sampled runtime engines; many other benchmark and analysis modules are visible only in the tree, so their internal wiring is omitted.
Main entry points: build_closure_inventory.py Closure inventory · run_abf_fr_grid.py Metastability runner · run_entropic_bottleneck_study.py Entropic runner · run_wca_production.py WCA production
Components 19
ABF-FR studies
- Metastability runner
scripts/run_abf_fr_grid.py - Entropic runner
scripts/run_entropic_bottleneck_study.py - WCA production
scripts/run_wca_production.py - WCA phase study
scripts/run_wca_phase_diagram.py
System models
- 2D GPU sampler
src/abffr/simulation_torch.py - Entropic core
src/eb_abffr_core.py - WCA ABF-FR core
src/wca_abffr_core.py - Alanine sampler
src/alanine/core2d_ala.py - Alkane distance sampler
src/alkanes/core_dist.py - LTA model
src/lta/core_lta.py - CHA model
src/cha/core_cha.py - ZIF-8 model
src/zif8/core_zif8.py
Analysis
- WCA analysis
scripts/analyze_wca_production.py - Entropy analysis
experiments/entropy_dominant_bottleneck/analyze_entropy_dominant_bottleneck.py - Cross-case analysis
scripts/analyze_convergence_atlas.py - Closure inventory
scripts/build_closure_inventory.py
Reporting
- Report assets
report/scripts/build_report_assets.py - Report checks
report/scripts/check_report_numbers.py
Other components
- Researcher
Connections 16
- Researcher → Metastability runner: starts study
- Researcher → Entropic runner: starts study
- Researcher → WCA production: starts study
- Researcher → WCA phase study: starts study
- Metastability runner → 2D GPU sampler: runs sampler
- Entropic runner → Entropic core: runs core
- WCA production → WCA ABF-FR core: runs core
- WCA phase study → WCA ABF-FR core: runs core
- Researcher → WCA analysis: analyzes runs
- Researcher → Entropy analysis: analyzes sweep
- Researcher → Cross-case analysis: analyzes cases
- Researcher → Closure inventory: builds inventory
- Researcher → Report assets: builds assets
- Researcher → Report checks: checks numbers
- Cross-case analysis → Closure inventory: summarizes evidence
- Closure inventory → Report assets: supplies results