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Fix: Remove large data files and add to gitignore
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‎.DS_Store‎

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‎.gitignore‎

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hpc_data/phase6_18780164
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hpc_data/**/*.jsonl
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hpc_data/**/*.jsonl

‎docs/HPC_GUIDE.md‎

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@@ -48,7 +48,7 @@ watch -n 10 "ls -1 results_JOBID | wc -l"
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# Fetching the results once the job is done
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scp -r kanagnostopoul@snellius.surf.nl:~/CSS_Project/results/phase6_18824496/ ./results/
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scp -r kanagnostopoul@snellius.surf.nl:~/CSS_Project/results/phase6_18832958/ ./results/
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```
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The jobscript template can be found in ```run_analysis.sh``` (default rome paritition).

‎hpc/run_phase4.sh‎

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#!/bin/bash
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#SBATCH --job-name=pp_phase4
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#SBATCH --partition=rome
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#SBATCH --partition=genoa
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#SBATCH --nodes=1
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#SBATCH --ntasks=1
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#SBATCH --cpus-per-task=64
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#SBATCH --cpus-per-task=128
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#SBATCH --time=08:00:00
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#SBATCH --mem=16G
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#SBATCH --mem=0
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#SBATCH --output=/home/kanagnostopoul/CSS_Project/pp_phase4_%j.out
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#SBATCH --error=/home/kanagnostopoul/CSS_Project/pp_phase4_%j.err
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‎hpc_data/phase1_18831093/experiments.log‎

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2026-01-28 16:37:12,640 [INFO] ============================================================
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2026-01-28 16:37:12,640 [INFO] PREDATOR-PREY HYDRA EFFECT EXPERIMENTS
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2026-01-28 16:37:12,640 [INFO] ============================================================
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2026-01-28 16:37:12,640 [INFO] Phases: [1]
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2026-01-28 16:37:12,640 [INFO] Output: results/phase1_18831093
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2026-01-28 16:37:12,640 [INFO] Cores: 128
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2026-01-28 16:37:12,640 [INFO] Numba: ENABLED
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2026-01-28 16:37:12,640 [INFO]
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2026-01-28 16:37:12,640 [INFO] ============================================================
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2026-01-28 16:37:12,640 [INFO] PHASE 1
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2026-01-28 16:37:12,640 [INFO] ============================================================
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2026-01-28 16:37:12,640 [INFO] Estimated: 9,000 sims, ~3.3h on 128 cores (~423 core-hours)
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2026-01-28 16:37:12,640 [INFO] Dry run - skipping execution
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2026-01-28 16:37:12,640 [INFO]
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2026-01-28 16:37:12,640 [INFO] ============================================================
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2026-01-28 16:37:12,640 [INFO] EXPERIMENTS COMPLETE
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2026-01-28 16:37:12,640 [INFO] ============================================================
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2026-01-28 16:37:13,648 [INFO] ============================================================
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2026-01-28 16:37:13,648 [INFO] PREDATOR-PREY HYDRA EFFECT EXPERIMENTS
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2026-01-28 16:37:13,648 [INFO] ============================================================
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2026-01-28 16:37:13,648 [INFO] Phases: [1]
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2026-01-28 16:37:13,648 [INFO] Output: results/phase1_18831093
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2026-01-28 16:37:13,648 [INFO] Cores: 128
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2026-01-28 16:37:13,648 [INFO] Numba: ENABLED
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2026-01-28 16:37:13,648 [INFO]
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2026-01-28 16:37:13,648 [INFO] ============================================================
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2026-01-28 16:37:13,648 [INFO] PHASE 1
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2026-01-28 16:37:13,648 [INFO] ============================================================
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2026-01-28 16:37:13,648 [INFO] Estimated: 9,000 sims, ~3.3h on 128 cores (~423 core-hours)
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2026-01-28 16:37:14,384 [INFO] Phase 1: 600 simulations
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2026-01-28 16:37:14,384 [INFO] Grid: 20 prey_death values × 30 reps (prey_birth=0.2)
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2026-01-28 16:46:50,474 [INFO] Phase 1 complete. Results: results/phase1_18831093/phase1_results.jsonl
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2026-01-28 16:46:50,523 [INFO] Phase 1 runtime: 9.6 minutes
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2026-01-28 16:46:50,523 [INFO]
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2026-01-28 16:46:50,523 [INFO] ============================================================
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2026-01-28 16:46:50,524 [INFO] EXPERIMENTS COMPLETE
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2026-01-28 16:46:50,524 [INFO] ============================================================

‎hpc_data/phase1_18831093/phase1_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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],
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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": 0.2,
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"critical_prey_death": 0.947,
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"prey_death_range": [
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0.0963,
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0.0973
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],
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"n_prey_birth": 15,
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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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0.05,
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0.1,
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0.15,
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0.2
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],
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"prey_death_offsets": [
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-0.02,
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-0.01,
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0.0,
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0.01,
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0.02
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],
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"n_replicates": 30,
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"warmup_steps": 1000,
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"measurement_steps": 1000,
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"with_evolution": false,
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"evolve_sd": 0.1,
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"evolve_min": 0.0,
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"evolve_max": 0.1,
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"sensitivity_sd_values": [
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0.02,
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0.05,
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0.1,
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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": false,
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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": 128
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}

‎hpc_data/phase1_18831093/phase1_metadata.json‎

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{
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"phase": 1,
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"description": "Parameter sweep for critical point",
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"n_sims": 600,
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"timestamp": "2026-01-28 16:46:50",
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"config": {
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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": 0.2,
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"critical_prey_death": 0.947,
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"prey_death_range": [
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0.0963,
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0.0973
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],
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"n_prey_birth": 15,
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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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0.05,
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0.1,
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0.15,
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0.2
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],
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"prey_death_offsets": [
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-0.02,
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-0.01,
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0.0,
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0.01,
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0.02
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],
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"n_replicates": 30,
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"warmup_steps": 1000,
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"measurement_steps": 1000,
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"with_evolution": false,
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"evolve_sd": 0.1,
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"evolve_min": 0.0,
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"evolve_max": 0.1,
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"sensitivity_sd_values": [
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0.02,
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0.05,
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0.1,
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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": false,
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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": 128
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}
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}

‎hpc_data/phase1_18831093/phase1_results.jsonl‎

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‎hpc_data/phase4.2_18824493/experiments.log‎

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