{
  "model": {
    "own_PDE": "u_t=u_xx+u(1-u)(u-.3), reflect domain length60",
    "pulse": "smooth tanh strip, edge.3; width threshold applies to this family",
    "clocks": "Poisson attempts and constant-speed growing intervals on ring; I supplied, not inferred from PDE noise",
    "spatial_noise": "one finite-grid Gaussian kick, fixed point variance and trace; projected variance is not measured PDE escape probability"
  },
  "thresholds": [
    {
      "h": 0.1,
      "dt": 0.04,
      "length": 60.0,
      "edge_width": 0.3,
      "bracket": [
        2.8842620849609375,
        2.8843765258789062
      ],
      "width_mid": 2.884319305419922
    },
    {
      "h": 0.05,
      "dt": 0.02,
      "length": 60.0,
      "edge_width": 0.3,
      "bracket": [
        2.8842620849609375,
        2.8843765258789062
      ],
      "width_mid": 2.884319305419922
    }
  ],
  "nucleus": {
    "infinite_domain_center": 0.47793654034364647,
    "finite_grid_maximum": 0.4778995352691294,
    "finite_grid_stationary_residual": 1.3540384091736968e-14,
    "top_two_eigenvalues": [
      1.1093115115141404e-12,
      0.18449437420774376
    ],
    "dominant_mode_L2_norm": 1.0,
    "continuum_nucleus_energy": 0.05892943016625889,
    "finite_grid_nucleus_energy": 0.058925929657690085,
    "reflecting_wall_energy_by_symmetry": 0.029464715083129447,
    "spatial_kick_controls": [
      {
        "correlation_length": 0.0,
        "point_variance": 0.0004,
        "trace": 0.24000000000000005,
        "dominant_mode_variance": 3.999999999999997e-05,
        "dominant_mode_sd": 0.006324555320336756
      },
      {
        "correlation_length": 0.1,
        "point_variance": 0.0004,
        "trace": 0.24000000000000005,
        "dominant_mode_variance": 8.652119281917421e-05,
        "dominant_mode_sd": 0.00930167688210971
      },
      {
        "correlation_length": 0.5,
        "point_variance": 0.0004,
        "trace": 0.24000000000000005,
        "dominant_mode_variance": 0.00039684518897666786,
        "dominant_mode_sd": 0.019920973595099912
      },
      {
        "correlation_length": 2.0,
        "point_variance": 0.0004,
        "trace": 0.24000000000000005,
        "dominant_mode_variance": 0.001396551589117235,
        "dominant_mode_sd": 0.037370464127666855
      },
      {
        "correlation_length": 10.0,
        "point_variance": 0.0004,
        "trace": 0.24000000000000005,
        "dominant_mode_variance": 0.003340565448673965,
        "dominant_mode_sd": 0.0577976249397323
      },
      {
        "correlation_length": "inf",
        "point_variance": 0.0004,
        "trace": 0.24000000000000005,
        "dominant_mode_variance": 0.004684834489040836,
        "dominant_mode_sd": 0.06844585078031272
      }
    ]
  },
  "pulse_outcomes": [
    {
      "initial": "subcritical",
      "initial_mass": 2.307455444336058,
      "initial_mean": 0.0384575907389343,
      "time": 180.0,
      "final_mean": 2.9815041494922985e-24,
      "final_max": 3.8719888660880014e-24,
      "fraction_above_half": 0.0
    },
    {
      "initial": "supercritical",
      "initial_mass": 3.461183166503416,
      "initial_mean": 0.05768638610839027,
      "time": 180.0,
      "final_mean": 1.000000000000007,
      "final_max": 1.0000000000000078,
      "fraction_above_half": 1.0
    },
    {
      "initial": "uniform_same_mass",
      "initial_mass": 3.461183166503416,
      "initial_mean": 0.05768638610839027,
      "time": 180.0,
      "final_mean": 2.695273567828813e-25,
      "final_max": 2.6952735678289e-25,
      "fraction_above_half": 0.0
    }
  ],
  "fronts": [
    {
      "h": 0.2,
      "dt": 0.04,
      "measured_speed": 0.28271759999593754,
      "exact_speed": 0.28284271247461906,
      "relative_speed_error": 0.0004423394104338065,
      "maximum_final_profile_error": 0.0017631107850512584
    },
    {
      "h": 0.1,
      "dt": 0.02,
      "measured_speed": 0.2828114576363079,
      "exact_speed": 0.28284271247461906,
      "relative_speed_error": 0.00011050254057361817,
      "maximum_final_profile_error": 0.00044020122847077126
    }
  ],
  "lattice_pinning": [
    {
      "coupling": 0.02,
      "sites": 101,
      "initial_high_sites": 21,
      "time": 300,
      "final_high_sites": 21,
      "min": 1.03385831107594e-49,
      "max": 1.0,
      "drift_residual_max": 1.384309333829492e-15,
      "stationary_max_eigenvalue": -0.14568368601582693
    },
    {
      "coupling": 0.5,
      "sites": 101,
      "initial_high_sites": 21,
      "time": 300,
      "final_high_sites": 101,
      "min": 0.999999999999998,
      "max": 0.999999999999998,
      "drift_residual_max": 1.3988810110276905e-15
    }
  ],
  "poisson_birth_growth": [
    {
      "length": 20.0,
      "attempt_intensity": 0.001,
      "front_speed": 0.28284271247461906,
      "replicates": 1000,
      "first_mean_analytic": 50.0,
      "first_mean_observed": 51.16005898492553,
      "single_nucleus_t90_post_wait": 31.819805153394633,
      "t90_mean": 81.17986863172169,
      "t90_median": 66.69269743367127,
      "t90_95percentile": 182.74947679361316,
      "mean_coarse_fine_t90_difference": 0.015131914703088974,
      "max_coarse_fine_t90_difference": 0.05532985137417512,
      "coverage": [
        {
          "time": 40.0,
          "analytic_mean": 0.3601020761969773,
          "observed_mean": 0.342615234375,
          "replicate_standard_error": 0.01242120023911807
        },
        {
          "time": 80.0,
          "analytic_mean": 0.7124753287568271,
          "observed_mean": 0.7081962890625,
          "replicate_standard_error": 0.013128443462252889
        },
        {
          "time": 120.0,
          "analytic_mean": 0.8708068373121605,
          "observed_mean": 0.8683505859375,
          "replicate_standard_error": 0.009984587672690396
        }
      ]
    },
    {
      "length": 100.0,
      "attempt_intensity": 0.001,
      "front_speed": 0.28284271247461906,
      "replicates": 1000,
      "first_mean_analytic": 10.0,
      "first_mean_observed": 10.40594627022621,
      "single_nucleus_t90_post_wait": 159.09902576697317,
      "t90_mean": 85.63603547997002,
      "t90_median": 82.1949431739989,
      "t90_95percentile": 126.31323925207688,
      "mean_coarse_fine_t90_difference": 0.0648257483670042,
      "max_coarse_fine_t90_difference": 0.30245380895019025,
      "coverage": [
        {
          "time": 40.0,
          "analytic_mean": 0.3639946730435425,
          "observed_mean": 0.359953125,
          "replicate_standard_error": 0.005779620311451115
        },
        {
          "time": 80.0,
          "analytic_mean": 0.836377504275449,
          "observed_mean": 0.829490234375,
          "replicate_standard_error": 0.005530482143884176
        },
        {
          "time": 120.0,
          "analytic_mean": 0.9829726611608761,
          "observed_mean": 0.9794482421875,
          "replicate_standard_error": 0.0020180397140624065
        }
      ]
    },
    {
      "length": 500.0,
      "attempt_intensity": 0.001,
      "front_speed": 0.28284271247461906,
      "replicates": 1000,
      "first_mean_analytic": 2.0,
      "first_mean_observed": 1.9842496184306568,
      "single_nucleus_t90_post_wait": 795.4951288348658,
      "t90_mean": 89.13862382841165,
      "t90_median": 87.72710294686769,
      "t90_95percentile": 110.0892533414708,
      "mean_coarse_fine_t90_difference": 0.21822174783060025,
      "max_coarse_fine_t90_difference": 1.4349167111822965,
      "coverage": [
        {
          "time": 40.0,
          "analytic_mean": 0.3639946730435425,
          "observed_mean": 0.3644296875,
          "replicate_standard_error": 0.0024711976265432653
        },
        {
          "time": 80.0,
          "analytic_mean": 0.836377504275449,
          "observed_mean": 0.8394580078125,
          "replicate_standard_error": 0.0022971798124608637
        },
        {
          "time": 120.0,
          "analytic_mean": 0.9829726611608761,
          "observed_mean": 0.983994140625,
          "replicate_standard_error": 0.0007298080915781256
        }
      ]
    }
  ],
  "author_function_check": {
    "commit": "5e565f2c12306db222bd4b2aab542f4d26f0286a",
    "function": "Hamiltonian",
    "maximum_function_residual": 0.0,
    "states_for_paper_kappa1_field_minus_point5": [
      -0.8546376797184624,
      0.4030317167626847,
      1.4516059629557754
    ],
    "limits": "code Hamiltonian has zero applied field and unweighted spatial sum; defaults L2,kappa.26,D.05 differ from paper Fig6. No original MAM optimization or transition rates rerun."
  }
}