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phase 2 data; evolution is shown as true but was stopped after warmup
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‎.gitignore‎

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.ipynb_checkpoints/
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# Data files
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data/
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.pytest_cache/
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.pytest_cache/
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.DS_Store

‎hpc/run_phase2.sh‎

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#SBATCH --nodes=1
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=32
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#SBATCH --time=04:00:00
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#SBATCH --time=08:00:00
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#SBATCH --mem=16G
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#SBATCH --output=pp_phase2_%j.out
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#SBATCH --error=pp_phase2_%j.err

‎hpc/run_phase3.sh‎

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‎hpc/run_phase4.sh‎

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‎hpc_data/phase2_18684370/experiments.log‎

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2026-01-26 12:12:40,935 [INFO] ============================================================
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2026-01-26 12:12:40,935 [INFO] PREDATOR-PREY HYDRA EFFECT EXPERIMENTS
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2026-01-26 12:12:40,935 [INFO] ============================================================
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2026-01-26 12:12:40,935 [INFO] Phases: [2]
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2026-01-26 12:12:40,935 [INFO] Output: results/phase2_18684370
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2026-01-26 12:12:40,935 [INFO] Cores: 32
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2026-01-26 12:12:40,935 [INFO] Numba: ENABLED
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2026-01-26 12:12:40,935 [INFO]
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2026-01-26 12:12:40,935 [INFO] ============================================================
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2026-01-26 12:12:40,935 [INFO] PHASE 2
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2026-01-26 12:12:40,935 [INFO] ============================================================
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2026-01-26 12:12:40,935 [INFO] Estimated: 800 sims, ~3.5h on 32 cores (~113 core-hours)
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2026-01-26 12:12:40,935 [INFO] Dry run - skipping execution
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2026-01-26 12:12:40,935 [INFO]
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2026-01-26 12:12:40,935 [INFO] ============================================================
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2026-01-26 12:12:40,936 [INFO] EXPERIMENTS COMPLETE
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2026-01-26 12:12:40,936 [INFO] ============================================================
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2026-01-26 12:12:42,118 [INFO] ============================================================
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2026-01-26 12:12:42,119 [INFO] PREDATOR-PREY HYDRA EFFECT EXPERIMENTS
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2026-01-26 12:12:42,119 [INFO] ============================================================
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2026-01-26 12:12:42,119 [INFO] Phases: [2]
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2026-01-26 12:12:42,119 [INFO] Output: results/phase2_18684370
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2026-01-26 12:12:42,119 [INFO] Cores: 32
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2026-01-26 12:12:42,119 [INFO] Numba: ENABLED
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2026-01-26 12:12:42,119 [INFO]
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2026-01-26 12:12:42,119 [INFO] ============================================================
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2026-01-26 12:12:42,119 [INFO] PHASE 2
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2026-01-26 12:12:42,119 [INFO] ============================================================
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2026-01-26 12:12:42,119 [INFO] Estimated: 800 sims, ~3.5h on 32 cores (~113 core-hours)
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2026-01-26 12:12:44,094 [INFO] Phase 2: 400 simulations
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2026-01-26 12:12:44,094 [INFO] prey_birth values: 1
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2026-01-26 12:12:44,094 [INFO] initial prey_death values: 20
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2026-01-26 12:12:44,094 [INFO] Replicates: 20
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2026-01-26 14:31:02,270 [INFO] Phase 2 complete. Results: results/phase2_18684370/phase2_results.jsonl
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2026-01-26 14:31:02,270 [INFO] Phase 2 runtime: 138.3 minutes
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2026-01-26 14:31:02,270 [INFO]
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2026-01-26 14:31:02,270 [INFO] ============================================================
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2026-01-26 14:31:02,270 [INFO] EXPERIMENTS COMPLETE
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2026-01-26 14:31:02,270 [INFO] ============================================================

‎hpc_data/phase2_18684370/phase2_config.json‎

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{
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"grid_size": 1000,
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"densities": [
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0.3,
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0.15
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],
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"grid_sizes": [
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50,
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100,
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250,
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500,
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1000,
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2500
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],
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"prey_birth": 0.2,
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"prey_death": 0.05,
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"predator_birth": 0.8,
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"predator_death": 0.05,
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"critical_prey_birth": 0.22,
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"critical_prey_death": 0.04,
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"prey_birth_range": [
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0.1,
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0.35
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],
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"prey_death_range": [
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0.0,
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0.2
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],
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"n_prey_birth": 1,
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"n_prey_death": 20,
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"predator_birth_values": [
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0.15,
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0.2,
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0.25,
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0.3
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],
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"predator_death_values": [
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],
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"prey_death_offsets": [
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],
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"n_replicates": 20,
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"warmup_steps": 1000,
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"measurement_steps": 5000,
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"with_evolution": true,
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"evolve_sd": 0.01,
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"evolve_min": 0.001,
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"evolve_max": 0.2,
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"sensitivity_sd_values": [
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0.02,
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0.15,
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0.2
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],
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"synchronous": false,
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"directed_hunting": true,
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"directed_hunting_values": [
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false,
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true
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],
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"save_timeseries": false,
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"timeseries_subsample": 10,
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"collect_pcf": false,
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"pcf_sample_rate": 0.2,
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"pcf_max_distance": 20.0,
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"pcf_n_bins": 20,
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"min_density_for_analysis": 0.002,
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"perturbation_magnitude": 0.1,
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"n_jobs": 32
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}

‎hpc_data/phase2_18684370/phase2_metadata.json‎

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{
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"phase": 2,
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"description": "Self-organization toward criticality",
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"n_sims": 400,
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"initial_prey_deaths": [
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0.0,
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0.010526315789473684,
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0.021052631578947368,
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0.031578947368421054,
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0.17894736842105263,
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0.18947368421052632,
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0.2
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],
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"timestamp": "2026-01-26 14:31:02"
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}

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